National Library of Energy BETA

Sample records for dynamic simulation tool

  1. Office Of Nuclear Energy Annual Review Meeting Dynamic Simulation Modeling Tool

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Annual Review Meeting Dynamic Simulation Modeling Tool Lou Qualls ORNL September 16-18, 2014 2 Work Package SR-14OR130108 - Modeling Tools for Dynamic Behavior Simulations of SMRs 2 ü FY14 molten salt cooled model deliverable due. n FY15 web application deliverable due. n FY15 model repository establishment due. n FY15 working collaboration with University partners. n Simplified Dynamic Modeling for Advanced SMRs - Numerous dynamic models are needed to simulate plant behavior

  2. FAST Simulation Tool Containing Methods for Predicting the Dynamic Response of Wind Turbines

    Energy Science and Technology Software Center (OSTI)

    2015-08-12

    FAST is a simulation tool (computer software) for modeling tlie dynamic response of horizontal-axis wind turbines. FAST employs a combined modal and multibody structural-dynamics formulation in the time domain.

  3. Advanced beam-dynamics simulation tools for RIA.

    SciTech Connect (OSTI)

    Garnett, R. W.; Wangler, T. P.; Billen, J. H.; Qiang, J.; Ryne, R.; Crandall, K. R.; Ostroumov, P.; York, R.; Zhao, Q.; Physics; LANL; LBNL; Tech Source; Michigan State Univ.

    2005-01-01

    We are developing multi-particle beam-dynamics simulation codes for RIA driver-linac simulations extending from the low-energy beam transport (LEBT) line to the end of the linac. These codes run on the NERSC parallel supercomputing platforms at LBNL, which allow us to run simulations with large numbers of macroparticles. The codes have the physics capabilities needed for RIA, including transport and acceleration of multiple-charge-state beams, beam-line elements such as high-voltage platforms within the linac, interdigital accelerating structures, charge-stripper foils, and capabilities for handling the effects of machine errors and other off-normal conditions. This year will mark the end of our project. In this paper we present the status of the work, describe some recent additions to the codes, and show some preliminary simulation results.

  4. RIAPMTQ/Impact : beam-dynamics simulation tool for RIA.

    SciTech Connect (OSTI)

    Wangler, T. P.; Billen, J. H.; Garnett, R. W.; Qiang, J.; Ryne, R.; Crandall, K. R.; Ostroumov, P.; Aseev, V. N.; Mustapha, B.; York, R. C.; Wu, X.; Zhao, Q.; Gorelov, D.; Doleans, M.; Physics; LANL; Tech Source; Michigan State Univ.

    2006-01-01

    We have developed a pair of multiparticle beam dynamics codes for end-to-end computer simulations of the proposed RIA heavy-ion driver linac. The two codes are: (1) an adaptation of PARMTEQ called RIAPMTQ for the normal-conducting-linac front end, and (2) IMPACT for the superconducting linac. The codes run on a PC as well as on parallel supercomputing platforms such as NERSC at LBNL. The parallel capability allows us to run simulations with large numbers of macroparticles for the computation of beam halo and beam-losses. The codes are being benchmarked for rms beam properties against previously existing codes at ANL and MSU. The work is being performed by a collaboration including LANL, LBNL, ANL, and Michigan State University (MSU). In this paper we present an overview, the status of the work, comparison of simulation results from RIAPMTQ and the ANL code TRACK for the ANL front-end design, and the first RIAPMTQ/IMPACT end-to-end multiprocessor simulation for the MSU design.

  5. Advanced beam-dynamics simulation tools for the RIA driver linac,Part I: Low energy beam transport and radiofrequency quadrupole

    SciTech Connect (OSTI)

    Wangler, Thomas P.; Crandall, Kenneth R.; Garnett, Robert W.; Gorelov, Dmitry; Ostroumov, Petr; Qiang, Ji; Ryne, Robert; York, Richard

    2003-08-26

    Advanced Beam-Dynamics Simulation Tools for the RIA Driver Linac; Low Energy Beam Transport and Radiofrequency Quadrupole.

  6. Regional Transportation Simulation Tool for Emergency Planning

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    rtstep-diag TRACC RESEARCH Computational Fluid Dynamics Computational Structural Mechanics Transportation Systems Modeling Regional Transportation Simulation Tool for Emergency ...

  7. Calibration and Validation of a Spar-Type Floating Offshore Wind Turbine Model using the FAST Dynamic Simulation Tool: Preprint

    SciTech Connect (OSTI)

    Browning, J. R.; Jonkman, J.; Robertson, A.; Goupee, A. J.

    2012-11-01

    In 2007, the FAST wind turbine simulation tool, developed and maintained by the U.S. Department of Energy's (DOE's) National Renewable Energy Laboratory (NREL), was expanded to include capabilities that are suitable for modeling floating offshore wind turbines. In an effort to validate FAST and other offshore wind energy modeling tools, DOE funded the DeepCwind project that tested three prototype floating wind turbines at 1/50th scale in a wave basin, including a semisubmersible, a tension-leg platform, and a spar buoy. This paper describes the use of the results of the spar wave basin tests to calibrate and validate the FAST offshore floating simulation tool, and presents some initial results of simulated dynamic responses of the spar to several combinations of wind and sea states.

  8. Device Simulation Tool - JCAP

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    PAZ0036_v2.jpg Device Simulation Tool Research Why Solar Fuels Goals & Objectives Thrust 1 Thrust 2 Thrust 3 Thrust 4 Publications Research Highlights Videos Innovations User Facilities Expert Team Benchmarking Database Device Simulation Tool XPS Spectral Database Research Introduction Why Solar Fuels? Goals & Objectives Thrusts Thrust 1 Thrust 2 Thrust 3 Thrust 4 Library Publications Research Highlights Videos Resources User Facilities Expert Team Benchmarking Database Device Simulation

  9. Policy Strategies and Paths to promote Sustainable Energy Systems- The dynamic Invert Simulation Tool

    SciTech Connect (OSTI)

    Stadler, Michael; Kranzl, Lukas; Huber, Claus; Haas, Reinhard; Tsioliaridou, Elena

    2006-05-01

    The European Union has established a number of targetsregarding energy efficiency, Renewable Energy Sources (RES) and CO2reductions as the 'GREEN PAPER on Energy Efficiency', the Directive for'promotion of the use of bio-fuels or other renewable fuels fortransport' or 'Directive of the European Parliament of the Council on thepromotion of cogeneration based on a useful heat demand in the internalenergy market'. A lot of the according RES and RUE measures are notattractive for investors from an economic point of view. Thereforegovernmentsall over the world have to spend public money to promotethese technologies/measures to bring them into market. These expenditureshave to be adjusted to budget concerns and should be spent mostefficiently. Therefore, the spent money has to be dedicated totechnologies and efficiency measures with the best yield in CO2 reductionwithout wasting money. The core question: "How can public money - forpromoting sustainable energy systems - be spent most efficiently toreduce GHG-emissions?" has been well investigated by the European projectInvert. In course of this project a simulation tool has been designed toanswer this core question. This paper describes the modelling with theInvert simulation tool and shows the key features necessary forsimulating the energy system. A definition of 'Promotion SchemeEfficiency' is given which allows estimating the most cost effectivetechnologies and/or efficiency measures to reduce CO2 emissions.Investigations performed with the Invert simulation tool deliver anoptimum portfolio mix of technologies and efficiency measures for eachselected region. Within Invert seven European regions were simulated andfor the Austrian case study the detailed portfolio mix is shown andpolitical conclusions are derived.

  10. Calibration and validation of a spar-type floating offshore wind turbine model using the FAST dynamic simulation tool

    DOE PAGES-Beta [OSTI]

    Browning, J. R.; Jonkman, J.; Robertson, A.; Goupee, A. J.

    2014-01-01

    In this study, high-quality computer simulations are required when designing floating wind turbines because of the complex dynamic responses that are inherent with a high number of degrees of freedom and variable metocean conditions. In 2007, the FAST wind turbine simulation tool, developed and maintained by the U.S. Department of Energy's (DOE's) National Renewable Energy Laboratory (NREL), was expanded to include capabilities that are suitable for modeling floating offshore wind turbines. In an effort to validate FAST and other offshore wind energy modeling tools, DOE funded the DeepCwind project that tested three prototype floating wind turbines at 1/50th scale inmore » a wave basin, including a semisubmersible, a tension-leg platform, and a spar buoy. This paper describes the use of the results of the spar wave basin tests to calibrate and validate the FAST offshore floating simulation tool, and presents some initial results of simulated dynamic responses of the spar to several combinations of wind and sea states. Wave basin tests with the spar attached to a scale model of the NREL 5-megawatt reference wind turbine were performed at the Maritime Research Institute Netherlands under the DeepCwind project. This project included free-decay tests, tests with steady or turbulent wind and still water (both periodic and irregular waves with no wind), and combined wind/wave tests. The resulting data from the 1/50th model was scaled using Froude scaling to full size and used to calibrate and validate a full-size simulated model in FAST. Results of the model calibration and validation include successes, subtleties, and limitations of both wave basin testing and FAST modeling capabilities.« less

  11. Calibration and validation of a spar-type floating offshore wind turbine model using the FAST dynamic simulation tool

    SciTech Connect (OSTI)

    Browning, J. R.; Jonkman, J.; Robertson, A.; Goupee, A. J.

    2014-01-01

    In this study, high-quality computer simulations are required when designing floating wind turbines because of the complex dynamic responses that are inherent with a high number of degrees of freedom and variable metocean conditions. In 2007, the FAST wind turbine simulation tool, developed and maintained by the U.S. Department of Energy's (DOE's) National Renewable Energy Laboratory (NREL), was expanded to include capabilities that are suitable for modeling floating offshore wind turbines. In an effort to validate FAST and other offshore wind energy modeling tools, DOE funded the DeepCwind project that tested three prototype floating wind turbines at 1/50th scale in a wave basin, including a semisubmersible, a tension-leg platform, and a spar buoy. This paper describes the use of the results of the spar wave basin tests to calibrate and validate the FAST offshore floating simulation tool, and presents some initial results of simulated dynamic responses of the spar to several combinations of wind and sea states. Wave basin tests with the spar attached to a scale model of the NREL 5-megawatt reference wind turbine were performed at the Maritime Research Institute Netherlands under the DeepCwind project. This project included free-decay tests, tests with steady or turbulent wind and still water (both periodic and irregular waves with no wind), and combined wind/wave tests. The resulting data from the 1/50th model was scaled using Froude scaling to full size and used to calibrate and validate a full-size simulated model in FAST. Results of the model calibration and validation include successes, subtleties, and limitations of both wave basin testing and FAST modeling capabilities.

  12. PV Hourly Simulation Tool

    Energy Science and Technology Software Center (OSTI)

    2010-12-31

    This software requires inputs of simple general building characteristics and usage information to calculate the energy and cost benefits of solar PV. This tool conducts and complex hourly simulation of solar PV based primarily on the area available on the rooftop. It uses a simplified efficiency calculation method and real panel characteristics. It includes a detailed rate structure to account for time-of-use rates, on-peak and off-peak pricing, and multiple rate seasons. This tool includes themore » option for advanced system design inputs if they are known. This tool calculates energy savings, demand reduction, cost savings, incentives and building life cycle costs including: simple payback, discounted payback, net-present value, and savings to investment ratio. In addition this tool also displays the environmental benefits of a project.« less

  13. The Xygra gun simulation tool.

    SciTech Connect (OSTI)

    Garasi, Christopher Joseph; Lamppa, Derek C.; Aubuchon, Matthew S.; Shirley, David Noyes; Robinson, Allen Conrad; Russo, Thomas V.

    2008-12-01

    Inductive electromagnetic launchers, or coilguns, use discrete solenoidal coils to accelerate a coaxial conductive armature. To date, Sandia has been using an internally developed code, SLINGSHOT, as a point-mass lumped circuit element simulation tool for modeling coilgun behavior for design and verification purposes. This code has shortcomings in terms of accurately modeling gun performance under stressful electromagnetic propulsion environments. To correct for these limitations, it was decided to attempt to closely couple two Sandia simulation codes, Xyce and ALEGRA, to develop a more rigorous simulation capability for demanding launch applications. This report summarizes the modifications made to each respective code and the path forward to completing interfacing between them.

  14. Tool - Transportation System Simulation (POLARIS) | Argonne National

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Laboratory Tool - Transportation System Simulation (POLARIS) Tool - Transportation System Simulation (POLARIS) POLARIS is a high-performance, open-source agent-based modeling framework designed for simulating large-scale transportation systems. The suite includes a discrete-event engine, memory management, visualization capabilities, and an extensible repository of common transportation objects which allows the rapid development of simulation software that satisfy individual project needs. A

  15. Look-ahead Dynamic Simulation

    SciTech Connect (OSTI)

    2015-10-20

    Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.

  16. TOPAS Tool for Particle Simulation

    Energy Science and Technology Software Center (OSTI)

    2013-05-30

    TOPAS lets users simulate the passage of subatomic particles moving through any kind of radiation therapy treatment system, can import a patient geometry, can record dose and other quantities, has advanced graphics, and is fully four-dimensional (3D plus time) to handle the most challenging time-dependent aspects of modern cancer treatments.TOPAS unlocks the power of the most accurate particle transport simulation technique, the Monte Carlo (MC) method, while removing the painstaking coding work such methods usedmore » to require. Research physicists can use TOPAS to improve delivery systems towards safer and more effective radiation therapy treatments, easily setting up and running complex simulations that previously used to take months of preparation. Clinical physicists can use TOPAS to increase accuracy while reducing side effects, simulating patient-specific treatment plans at the touch of a button. TOPAS is designed as a “user code” layered on top of the Geant4 Simulation Toolkit. TOPAS includes the standard Geant4 toolkit, plus additional code to make Geant4 easier to control and to extend Geant4 functionality. TOPAS aims to make proton simulation both “reliable” and “repeatable.” “Reliable” means both accurate physics and a high likelihood to simulate precisely what the user intended to simulate, reducing issues of wrong units, wrong materials, wrong scoring locations, etc. “Repeatable” means not just getting the same result from one simulation to another, but being able to easily restore a previously used setup and reducing sources of error when a setup is passed from one user to another. TOPAS control system incorporates key lessons from safety management, proactively removing possible sources of user error such as line-ordering mistakes In control files. TOPAS has been used to model proton therapy treatment examples including the UCSF eye treatment head, the MGH stereotactic alignment in radiosurgery treatment head and the MGH gantry

  17. Cantera Aerosol Dynamics Simulator

    Energy Science and Technology Software Center (OSTI)

    2004-09-01

    The Cantera Aerosol Dynamics Simulator (CADS) package is a general library for aerosol modeling to address aerosol general dynamics, including formation from gas phase reactions, surface chemistry (growth and oxidation), bulk particle chemistry, transport by Brownian diffusion, thermophoresis, and diffusiophoresis with linkage to DSMC studies, and thermal radiative transport. The library is based upon Cantera, a C++ Cal Tech code that handles gas phase species transport, reaction, and thermodynamics. The method uses a discontinuous galerkinmore » formulation for the condensation and coagulation operator that conserves particles, elements, and enthalpy up to round-off error. Both O-D and 1-D time dependent applications have been developed with the library. Multiple species in the solid phase are handled as well. The O-D application, called Tdcads (Time Dependent CADS) is distributed with the library. Tdcads can address both constant volume and constant pressure adiabatic homogeneous problems. An extensive set of sample problems for Tdcads is also provided.« less

  18. DLFM library tools for large scale dynamic applications

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    DLFM library tools for large scale dynamic applications DLFM library tools for large scale dynamic applications Large scale Python and other dynamic applications may spend huge ...

  19. Trace Replay and Network Simulation Tool

    Energy Science and Technology Software Center (OSTI)

    2015-03-23

    TraceR is a trace reply tool built upon the ROSS-based CODES simulation framework. TraceR can be used for predicting network performances and understanding network behavior by simulating messaging in High Performance Computing applications on interconnection networks.

  20. Operational Simulation Tools and Long Term Strategic Planning...

    Energy Savers

    Operational Simulation Tools and Long Term Strategic Planning for High Penetrations of PV in the Southeastern U.S. Operational Simulation Tools and Long Term Strategic Planning for ...

  1. EPICS simulation tools for control system development

    SciTech Connect (OSTI)

    Wright, R.M.; Kerstiens, D.M.; Vaughn, G.D.; Weiss, R.E.

    1994-09-01

    When developing control system software there are many times when the ability to simulate the response of the instrumentation can be very useful. Examples are: (i) when the operator interface is being designed and the users want an idea of what the finished system might took like; (ii) when the interface hardware is not yet available; (iii) when the reaction of the control system to an error condition must be tested, but the actual occurrence of such an error would cause undesirable side effects; (iv) when operators are being trained to use the system; (v) when an improvement or bug fix needs to be tested, but the running system cannot be shut down for long. The Experimental Physics and Industrial Control System (EPICS) provides tools for building simple simulations and interfacing to more complex simulations of accelerator hardware. At the lowest level an individual data channel can be switched to take its input from either a simulated data location or from the actual hardware. At a slightly higher level, sequences can be run on the real-time interface processor so that output to the hardware is intercepted and an appropriate substitute value is provided for the corresponding read-back records. At a still higher level a program can use the Channel Access software bus facility of EPICS to control some global aspect of an accelerator or can interface to an external accelerator simulation instead of the actual accelerator. The goal of testing control system software using simulated hardware is to minimize the changes required in shifting between the simulated system and the real system. The degree of success of the EPICS tools in meeting the minimum change goal will be addressed with suggestions for improvements. The implementation of simulated responses using EPICS tools will be discussed and examples of experience using the EPICS tools to create and interface to simulations will be given.

  2. Methods and Tools to allow molecular flow simulations to be coupled to higher level continuum descriptions of flows in porous/fractured media and aerosol/dust dynamics

    SciTech Connect (OSTI)

    Loyalka, Sudarshan

    2015-04-09

    The purpose of this project was to develop methods and tools that will aid in safety evaluation of nuclear fuels and licensing of nuclear reactors relating to accidents.The objectives were to develop more detailed and faster computations of fission product transport and aerosol evolution as they generally relate to nuclear fuel and/or nuclear reactor accidents. The two tasks in the project related to molecular transport in nuclear fuel and aerosol transport in reactor vessel and containment. For both the tasks, explorations of coupling of Direct Simulation Monte Carlo with Navier-Stokes solvers or the Sectional method were not successful. However, Mesh free methods for the Direct Simulation Monte Carlo method were successfully explored.These explorations permit applications to porous and fractured media, and arbitrary geometries.The computations were carried out in Mathematica and are fully parallelized. The project has resulted in new computational tools (algorithms and programs) that will improve the fidelity of computations to actual physics, chemistry and transport of fission products in the nuclear fuel and aerosol in reactor primary and secondary containments.

  3. Co-Optima Informational Webinar- Simulation Tools

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Simulation Tools Co-Optimizer In cylinder CFD Small volume testing and inputs preparation Summary Simulation workflow includes developing detailed, validated in cylinder CFD from real geometry Necessary inputs to CFD calculations (mechanisms, surrogate composition, initial conditions, liquid fuel properties, model validation...) generated with the aid of small volume test data, idealzied cacluations, synthetic experiements and sensitivity studies Experimental engine 'cloud of points' will be

  4. Dynamic Power Grid Simulation

    Energy Science and Technology Software Center (OSTI)

    2015-09-14

    GridDyn is a part of power grid simulation toolkit. The code is designed using modern object oriented C++ methods utilizing C++11 and recent Boost libraries to ensure compatibility with multiple operating systems and environments.

  5. Dynamic simulation gives 20-20 foresight

    SciTech Connect (OSTI)

    Womack, J.W.

    1986-04-07

    Dynamic simulation is being increasingly recognized as a viable tool for system analysis and design. Its use by Mobil Research and Development Corp. (MRDC) has grown steadily. Applications fall into three major categories: Support of major capital projects, mostly in the form of high-fidelity models capable of answering many of the ''what-if'' questions which arise during the engineering design, construction, and commissioning phases of a project; Simulators for operator training, which have been acquired for an increasing fraction of both new and existing facilities over the past 10 years; Solution of operational problems, evaluate process changes, and in debottlenecking studies of existing facilities. A number of dynamic simulations have been done by contractors or system vendors. MRDC involvement was limited to review and/or acceptance of the work. MRDC did not write any of the training simulator programs, for example, although its inputs often influenced their development.

  6. Dynamic Simulation over Long Time Periods with 100% Solar Generation.

    SciTech Connect (OSTI)

    Concepcion, Ricky James; Elliott, Ryan Thomas

    2015-12-01

    This project aimed to identify the path forward for dynamic simulation tools to accommodate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for potential problems.

  7. Design tools for complex dynamic security systems.

    SciTech Connect (OSTI)

    Byrne, Raymond Harry; Rigdon, James Brian; Rohrer, Brandon Robinson; Laguna, Glenn A.; Robinett, Rush D. III; Groom, Kenneth Neal; Wilson, David Gerald; Bickerstaff, Robert J.; Harrington, John J.

    2007-01-01

    The development of tools for complex dynamic security systems is not a straight forward engineering task but, rather, a scientific task where discovery of new scientific principles and math is necessary. For years, scientists have observed complex behavior but have had difficulty understanding it. Prominent examples include: insect colony organization, the stock market, molecular interactions, fractals, and emergent behavior. Engineering such systems will be an even greater challenge. This report explores four tools for engineered complex dynamic security systems: Partially Observable Markov Decision Process, Percolation Theory, Graph Theory, and Exergy/Entropy Theory. Additionally, enabling hardware technology for next generation security systems are described: a 100 node wireless sensor network, unmanned ground vehicle and unmanned aerial vehicle.

  8. Revamped Simulation Tool to Power Up Wave Energy Development | Department

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    of Energy Revamped Simulation Tool to Power Up Wave Energy Development Revamped Simulation Tool to Power Up Wave Energy Development May 21, 2015 - 2:40pm Addthis Revamped Simulation Tool to Power Up Wave Energy Development Alison LaBonte Marine and Hydrokinetic Technology Manager When engineers want to model new technologies, there's often nothing better than simulation tools. Designing technologies to harness energy from ocean waves is especially complex because engineers have to build them

  9. Dynamic Simulation Nuclear Power Plants

    Energy Science and Technology Software Center (OSTI)

    1992-03-03

    DSNP (Dynamic Simulator for Nuclear Power-Plants) is a system of programs and data files by which a nuclear power plant, or part thereof, can be simulated. The acronym DSNP is used interchangeably for the DSNP language, the DSNP libraries, the DSNP precompiler, and the DSNP document generator. The DSNP language is a special-purpose, block-oriented, digital-simulation language developed to facilitate the preparation of dynamic simulations of a large variety of nuclear power plants. It is amore » user-oriented language that permits the user to prepare simulation programs directly from power plant block diagrams and flow charts by recognizing the symbolic DSNP statements for the appropriate physical components and listing these statements in a logical sequence according to the flow of physical properties in the simulated power plant. Physical components of nuclear power plants are represented by functional blocks, or modules. Many of the more complex components are represented by several modules. The nuclear reactor, for example, has a kinetic module, a power distribution module, a feedback module, a thermodynamic module, a hydraulic module, and a radioactive heat decay module. These modules are stored in DSNP libraries in the form of a DSNP subroutine or function, a block of statements, a macro, or a combination of the above. Basic functional blocks such as integrators, pipes, function generators, connectors, and many auxiliary functions representing properties of materials used in nuclear power plants are also available. The DSNP precompiler analyzes the DSNP simulation program, performs the appropriate translations, inserts the requested modules from the library, links these modules together, searches necessary data files, and produces a simulation program in FORTRAN.« less

  10. Dynamics of Molecular Clouds: Observations, Simulations, and...

    Office of Scientific and Technical Information (OSTI)

    Simulations, and NIF Experiments Citation Details In-Document Search Title: Dynamics of Molecular Clouds: Observations, Simulations, and NIF Experiments You are ...

  11. Tool - Vehicle System Simulation (Autonomie) | Argonne National Laboratory

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Tool - Vehicle System Simulation (Autonomie) Tool - Vehicle System Simulation (Autonomie) Autonomie s a most powerful and robust system simulation tool for vehicle energy consumption and performance analysis. Developed in collaboration with General Motors, Autonomie is a MATLAB©-based software environment and framework for automotive control-system design, simulation, and analysis. Its application covers energy consumption, performance analysis throughout the entire vehicle development process

  12. Analysis of the influence of tool dynamics in diamond turning

    SciTech Connect (OSTI)

    Fawcett, S.C.; Luttrell, D.E.; Keltie, R.F.

    1988-12-01

    This report describes the progress in defining the role of machine and interface dynamics on the surface finish in diamond turning. It contains a review of literature from conventional and diamond machining processes relating tool dynamics, material interactions and tool wear to surface finish. Data from experimental measurements of tool/work piece interface dynamics are presented as well as machine dynamics for the DTM at the Center.

  13. Simulation and sequential dynamical systems

    SciTech Connect (OSTI)

    Mortveit, H.S.; Reidys, C.M.

    1999-06-01

    Computer simulations have a generic structure. Motivated by this the authors present a new class of discrete dynamical systems that captures this structure in a mathematically precise way. This class of systems consists of (1) a loopfree graph {Upsilon} with vertex set {l_brace}1,2,{hor_ellipsis},n{r_brace} where each vertex has a binary state, (2) a vertex labeled set of functions (F{sub i,{Upsilon}}:F{sub 2}{sup n} {yields} F{sub 2}{sup n}){sub i} and (3) a permutation {pi} {element_of} S{sub n}. The function F{sub i,{Upsilon}} updates the state of vertex i as a function of the states of vertex i and its {Upsilon}-neighbors and leaves the states of all other vertices fixed. The permutation {pi} represents the update ordering, i.e., the order in which the functions F{sub i,{Upsilon}} are applied. By composing the functions F{sub i,{Upsilon}} in the order given by {pi} one obtains the dynamical system (equation given in paper), which the authors refer to as a sequential dynamical system, or SDS for short. The authors will present bounds for the number of functionally different systems and for the number of nonisomorphic digraphs {Gamma}[F{sub {Upsilon}},{pi}] that can be obtained by varying the update order and applications of these to specific graphs and graph classes.

  14. Battery Lifetime Analysis and Simulation Tool (BLAST) Documentation

    Office of Scientific and Technical Information (OSTI)

    Battery Lifetime Analysis and Simulation Tool (BLAST) Documentation Neubauer, J. 25 ENERGY STORAGE BATTERY; LITHIUM-ION; STATIONARY ENERGY STORAGE; BLAST; BATTERY DEGRADATION;...

  15. Development of Design and Simulation Tool for Hybrid Geothermal...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    System Development of Design and Simulation Tool for Hybrid Geothermal Heat Pump System This project will expand Expand eQUEST, a building energy analysis software with latest ...

  16. DLFM library tools for large scale dynamic applications

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    DLFM library tools for large scale dynamic applications DLFM library tools for large scale dynamic applications Large scale Python and other dynamic applications may spend huge time at startup. The DLFM library, developed by Mike Davis at Cray, Inc., is a set of functions that can be incorporated into a dynamically-linked application to provide improved performance during the loading of dynamic libraries when running the application at large scale on Edison. To access this library, do module

  17. Tools and Equipment Modeling for Automobile Interactive Assembling Operating Simulation

    SciTech Connect (OSTI)

    Wu Dianliang; Zhu Hongmin

    2010-05-21

    Tools and equipment play an important role in the simulation of virtual assembly, especially in the assembly process simulation and plan. Because of variety in function and complexity in structure and manipulation, the simulation of tools and equipments remains to be a challenge for interactive assembly operation. Based on analysis of details and characteristics of interactive operations for automobile assembly, the functional requirement for tools and equipments of automobile assembly is given. Then, a unified modeling method for information expression and function realization of general tools and equipments is represented, and the handling methods of manual, semi-automatic, automatic tools and equipments are discussed. Finally, the application in assembly simulation of rear suspension and front suspension of Roewe 750 automobile is given. The result shows that the modeling and handling methods are applicable in the interactive simulation of various tools and equipments, and can also be used for supporting assembly process planning in virtual environment.

  18. Development of CFD-Based Simulation Tools for In-Situ Thermal Processing of

    Office of Scientific and Technical Information (OSTI)

    Oil Shale/Sands (Technical Report) | SciTech Connect Development of CFD-Based Simulation Tools for In-Situ Thermal Processing of Oil Shale/Sands Citation Details In-Document Search Title: Development of CFD-Based Simulation Tools for In-Situ Thermal Processing of Oil Shale/Sands In our research, we are taking the novel approach of developing and applying high performance computing, computational fluid dynamics (CFD)-based simulation tools to a modified in-situ process for production of oil

  19. Test Procedures for Building Energy Simulation Tools | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Procedures for Building Energy Simulation Tools Test Procedures for Building Energy Simulation Tools Lead Performer: -- National Renewable Energy Laboratory - Golden, CO -- J. Neymark & Associates - Golden, CO -- Lawrence Berkeley National Laboratory (LBNL) - Berkeley, CA Partners: -- ASHRAE Standing Special Projects Committee 140 -- Residential Energy Services Network (RESNET) -- International Energy Agency (IEA) - Paris, France -- Trane Inc. - Piscataway, NJ -- Carrier Corp. - Alexandria,

  20. Dynamic Simulators | netl.doe.gov

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    NETL AVESTAR Team and Invensys Collaborate to Develop Dynamic Simulators for Supercritical Pulverized Coal and Natural Gas Combined Cycle Power Plants A screen shot of the new ...

  1. Communication: Quantum molecular dynamics simulation of liquid...

    Office of Scientific and Technical Information (OSTI)

    Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach Citation Details In-Document Search Title: Communication:...

  2. Dynamics Simulation in a Wave Environment

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    projects in: Offshore Platforms Wave Energy Converters Wind Power 3 Coupled Dynamics (AEGIR Co-simulation Capability) * Interprocess communication using TCPIP sockets for co- ...

  3. Nonequilibrium molecular dynamics simulations of confined fluids...

    Office of Scientific and Technical Information (OSTI)

    A nonequilibrium molecular dynamics (MD) ... in a single simulation upon compression, whereas fluid molecules in the bulk ... for weak fluid -- wall interactions. ...

  4. simulate the dynamic distribution of lithium in the electrode

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    simulate the dynamic distribution of lithium in the electrode - Sandia Energy Energy ... simulate the dynamic distribution of lithium in the electrode HomeTag:simulate the ...

  5. Parallel Implementation of Power System Dynamic Simulation

    SciTech Connect (OSTI)

    Jin, Shuangshuang; Huang, Zhenyu; Diao, Ruisheng; Wu, Di; Chen, Yousu

    2013-07-21

    Dynamic simulation of power system transient stability is important for planning, monitoring, operation, and control of electrical power systems. However, modeling the system dynamics and network involves the computationally intensive time-domain solution of numerous differential and algebraic equations (DAE). This results in a transient stability implementation that may not maintain the real-time constraints of an online security assessment. This paper presents a parallel implementation of the dynamic simulation on a high-performance computing (HPC) platform using parallel simulation algorithms and computation architectures. It enables the simulation to run even faster than real time, enabling the look-ahead capability of upcoming stability problems in the power grid.

  6. New Automotive Air Conditioning System Simulation Tool Developed in MATLAB/Simulink

    SciTech Connect (OSTI)

    Kiss, T.; Chaney, L.; Meyer, J.

    2013-07-01

    Further improvements in vehicle fuel efficiency require accurate evaluation of the vehicle's transient total power requirement. When operated, the air conditioning (A/C) system is the largest auxiliary load on a vehicle; therefore, accurate evaluation of the load it places on the vehicle's engine and/or energy storage system is especially important. Vehicle simulation software, such as 'Autonomie,' has been used by OEMs to evaluate vehicles' energy performance. A transient A/C simulation tool incorporated into vehicle simulation models would also provide a tool for developing more efficient A/C systems through a thorough consideration of the transient A/C system performance. The dynamic system simulation software Matlab/Simulink was used to develop new and more efficient vehicle energy system controls. The various modeling methods used for the new simulation tool are described in detail. Comparison with measured data is provided to demonstrate the validity of the model.

  7. Operational Simulation Tools and Long Term Strategic Planning for High

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Penetrations of PV in the Southeastern U.S. | Department of Energy Operational Simulation Tools and Long Term Strategic Planning for High Penetrations of PV in the Southeastern U.S. Operational Simulation Tools and Long Term Strategic Planning for High Penetrations of PV in the Southeastern U.S. EPRI logo.jpg In collaboration with the Tennessee Valley Authority Southern Company, the Sacramento Municipal Utility District, the California Independent System Operator, and other partners,

  8. Battery Lifetime Analysis and Simulation Tool (BLAST) Documentation

    Office of Scientific and Technical Information (OSTI)

    (Technical Report) | SciTech Connect Battery Lifetime Analysis and Simulation Tool (BLAST) Documentation Citation Details In-Document Search Title: Battery Lifetime Analysis and Simulation Tool (BLAST) Documentation The deployment and use of lithium-ion (Li-ion) batteries in automotive and stationary energy storage applications must be optimized to justify their high up-front costs. Given that batteries degrade with use and storage, such optimizations must evaluate many years of operation.

  9. WINS. Market Simulation Tool for Facilitating Wind Energy Integration

    SciTech Connect (OSTI)

    Shahidehpour, Mohammad

    2012-10-30

    Integrating 20% or more wind energy into the system and transmitting large sums of wind energy over long distances will require a decision making capability that can handle very large scale power systems with tens of thousands of buses and lines. There is a need to explore innovative analytical and implementation solutions for continuing reliable operations with the most economical integration of additional wind energy in power systems. A number of wind integration solution paths involve the adoption of new operating policies, dynamic scheduling of wind power across interties, pooling integration services, and adopting new transmission scheduling practices. Such practices can be examined by the decision tool developed by this project. This project developed a very efficient decision tool called Wind INtegration Simulator (WINS) and applied WINS to facilitate wind energy integration studies. WINS focused on augmenting the existing power utility capabilities to support collaborative planning, analysis, and wind integration project implementations. WINS also had the capability of simulating energy storage facilities so that feasibility studies of integrated wind energy system applications can be performed for systems with high wind energy penetrations. The development of WINS represents a major expansion of a very efficient decision tool called POwer Market Simulator (POMS), which was developed by IIT and has been used extensively for power system studies for decades. Specifically, WINS provides the following superiorities; (1) An integrated framework is included in WINS for the comprehensive modeling of DC transmission configurations, including mono-pole, bi-pole, tri-pole, back-to-back, and multi-terminal connection, as well as AC/DC converter models including current source converters (CSC) and voltage source converters (VSC); (2) An existing shortcoming of traditional decision tools for wind integration is the limited availability of user interface, i.e., decision

  10. Molecular dynamics simulation studies of electrolytes andelectrolyte...

    Energy.gov (indexed) [DOE]

    Merit Review and Peer Evaluation Meeting, May 18-22, 2009 -- Washington D.C. es40smith.pdf (4 MB) More Documents & Publications Molecular Dynamics Simulation Studies of ...

  11. Sandia Energy - Molecular Dynamics Simulations Predict Fate of...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Molecular Dynamics Simulations Predict Fate of Uranium in Sediments Home Highlights - Energy Research Molecular Dynamics Simulations Predict Fate of Uranium in Sediments Previous...

  12. BESTEST: Test Procedures Building Energy SimulationŽ Tools

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Ron.Judkoff@nrel.gov BESTEST: Test Procedures "Building Energy Simulation" Tools 2014 ... and improving building energy simulation tools and associated documentation. -Increase ...

  13. Beam simulation tools for GEANT4 (and neutrino source applications)

    SciTech Connect (OSTI)

    V.Daniel Elvira, Paul Lebrun and Panagiotis Spentzouris

    2002-12-03

    Geant4 is a tool kit developed by a collaboration of physicists and computer professionals in the High Energy Physics field for simulation of the passage of particles through matter. The motivation for the development of the Beam Tools is to extend the Geant4 applications to accelerator physics. Although there are many computer programs for beam physics simulations, Geant4 is ideal to model a beam going through material or a system with a beam line integrated to a complex detector. There are many examples in the current international High Energy Physics programs, such as studies related to a future Neutrino Factory, a Linear Collider, and a very Large Hadron Collider.

  14. A Dynamic MPI Software Correctness Checking Tool

    Energy Science and Technology Software Center (OSTI)

    2005-10-31

    Umpire is prototype tool developed at LLNL by Bronis R. de Supinski, J. M. May, Martin Schulz and Jeffery Vetter as part of the ASDE TRTS project for detecting programming errors at runtime in message passing applications. Umpire monitors the MPI operations of an application by interposing itself between the application and the MPI runtime system using the MPI profiling layer. Umpire then checks the application’s MPI behavior for specific errors. Umpire detects errors thatmore » are local to individual MPI tasks, including resource errors (e.g., leaks of MPI datatypes and other opaque objects) and overwrites of non-blocking send buffers. It also detects distributed errors, including deadlocks involving any MPI-1 constructs and datatype mismatches between matching communication operations.« less

  15. Simulating the Dynamic Coupling of Market and Physical System Operations

    SciTech Connect (OSTI)

    Widergren, Steven E.; Roop, Joseph M.; Guttromson, Ross T.; Huang, Zhenyu

    2004-06-01

    Abstract-As energy trading products cover shorter time periods and demand response programs move toward real-time pricing, financial market-based activity impacts ever more directly the physical operation of the system. To begin to understand the complex interactions between the market-driven operation signals, the engineered controlled schemes, and the laws of physics, new system modeling and simulation techniques must be explored. This discussion describes requirements for new simulation tools to address such market transaction control interactions and an approach to capture the dynamic coupling between energy markets and the physical operation of the power system appropriate for dispatcher reaction time frames.

  16. Dynamic procedure for filtered gyrokinetic simulations

    SciTech Connect (OSTI)

    Morel, P.; Banon Navarro, A.; Albrecht-Marc, M.; Carati, D.; Merz, F.; Goerler, T.; Jenko, F.

    2012-01-15

    Large eddy simulations (LES) of gyrokinetic plasma turbulence are investigated as interesting candidates to decrease the computational cost. A dynamic procedure is implemented in the gene code, allowing for dynamic optimization of the free parameters of the LES models (setting the amplitudes of dissipative terms). Employing such LES methods, one recovers the free energy and heat flux spectra obtained from highly resolved direct numerical simulations. Systematic comparisons are performed for different values of the temperature gradient and magnetic shear, parameters which are of prime importance in ion temperature gradient driven turbulence. Moreover, the degree of anisotropy of the problem, which can vary with parameters, can be adapted dynamically by the method that shows gyrokinetic large eddy simulation to be a serious candidate to reduce numerical cost of gyrokinetic solvers.

  17. Synergia: a modern tool for accelerator physics simulation

    SciTech Connect (OSTI)

    Spentzouris, P.; Amundson, J.; /Fermilab

    2004-10-01

    High precision modeling of space-charge effects, together with accurate treatment of single-particle dynamics, is essential for designing future accelerators as well as optimizing the performance of existing machines. Synergia is a high-fidelity parallel beam dynamics simulation package with fully three dimensional space-charge capabilities and a higher order optics implementation. We describe the computational techniques, the advanced human interface, and the parallel performance obtained using large numbers of macroparticles.

  18. Dynamic Fracture Simulations of Explosively Loaded Cylinders

    SciTech Connect (OSTI)

    Arthur, Carly W.; Goto, D. M.

    2015-11-30

    This report documents the modeling results of high explosive experiments investigating dynamic fracture of steel (AerMet® 100 alloy) cylinders. The experiments were conducted at Lawrence Livermore National Laboratory (LLNL) during 2007 to 2008 [10]. A principal objective of this study was to gain an understanding of dynamic material failure through the analysis of hydrodynamic computer code simulations. Two-dimensional and three-dimensional computational cylinder models were analyzed using the ALE3D multi-physics computer code.

  19. Design of dynamic load-balancing tools for parallel applications

    SciTech Connect (OSTI)

    Devine, K.D.; Hendrickson, B.A.; Boman, E.G.; St. John, M.; Vaughan, C.T.

    2000-01-03

    The design of general-purpose dynamic load-balancing tools for parallel applications is more challenging than the design of static partitioning tools. Both algorithmic and software engineering issues arise. The authors have addressed many of these issues in the design of the Zoltan dynamic load-balancing library. Zoltan has an object-oriented interface that makes it easy to use and provides separation between the application and the load-balancing algorithms. It contains a suite of dynamic load-balancing algorithms, including both geometric and graph-based algorithms. Its design makes it valuable both as a partitioning tool for a variety of applications and as a research test-bed for new algorithmic development. In this paper, the authors describe Zoltan's design and demonstrate its use in an unstructured-mesh finite element application.

  20. NREL: Dynamic Maps, GIS Data, and Analysis Tools Home Page

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    The Dynamic Maps, Geographic Information System (GIS) Data and Analysis Tools website provides maps, data and tools for renewable energy resources that determine which energy technologies are viable solutions in domestic and international regions. MapSearch - While this site contains detailed information and quality data, if you want to search for the latest and most up-to-date maps created by NREL, please visit our MapSearch: http://www.nrel.gov/gis/mapsearch/ Renewable Energy Technical

  1. Update on Small Modular Reactors Dynamics System Modeling Tool -- Molten Salt Cooled Architecture

    SciTech Connect (OSTI)

    Hale, Richard Edward; Cetiner, Sacit M.; Fugate, David L.; Qualls, A L.; Borum, Robert C.; Chaleff, Ethan S.; Rogerson, Doug W.; Batteh, John J.; Tiller, Michael M.

    2014-08-01

    The Small Modular Reactor (SMR) Dynamic System Modeling Tool project is in the third year of development. The project is designed to support collaborative modeling and study of various advanced SMR (non-light water cooled) concepts, including the use of multiple coupled reactors at a single site. The objective of the project is to provide a common simulation environment and baseline modeling resources to facilitate rapid development of dynamic advanced reactor SMR models, ensure consistency among research products within the Instrumentation, Controls, and Human-Machine Interface (ICHMI) technical area, and leverage cross-cutting capabilities while minimizing duplication of effort. The combined simulation environment and suite of models are identified as the Modular Dynamic SIMulation (MoDSIM) tool. The critical elements of this effort include (1) defining a standardized, common simulation environment that can be applied throughout the program, (2) developing a library of baseline component modules that can be assembled into full plant models using existing geometry and thermal-hydraulic data, (3) defining modeling conventions for interconnecting component models, and (4) establishing user interfaces and support tools to facilitate simulation development (i.e., configuration and parameterization), execution, and results display and capture.

  2. SciDAC advances in beam dynamics simulation: from light sources to colliders

    SciTech Connect (OSTI)

    Qiang, Ji; Qiang, J.; Borland, M.; Kabel, A.; Li, R.; Ryne, R.; Stern, E.; Wang, Y.; Wasserman, H.; Zhang, Y.

    2008-06-16

    In this paper, we report on progress that has been made in beam dynamics simulation, from light sources to colliders, during the first year of SciDAC-II accelerator project,"Community Petascale Project for Accelerator Science and Simulation (ComPASS)." Several parallel computational tools for beam dynamics simulation will be described. A number of applications in current and future accelerator facilities, e.g., LCLS, RHIC, Tevatron, LHC, ELIC, are presented.

  3. RTSTEP regional transportation simulation tool for emergency planning - final report.

    SciTech Connect (OSTI)

    Ley, H.; Sokolov, V.; Hope, M.; Auld, J.; Zhang, K.; Park, Y.; Kang, X.

    2012-01-20

    such materials over a large area, with responders trying to mitigate the immediate danger to the population in a variety of ways that may change over time (e.g., in-place evacuation, staged evacuations, and declarations of growing evacuation zones over time). In addition, available resources will be marshaled in unusual ways, such as the repurposing of transit vehicles to support mass evacuations. Thus, any simulation strategy will need to be able to address highly dynamic effects and will need to be able to handle any mode of ground transportation. Depending on the urgency and timeline of the event, emergency responders may also direct evacuees to leave largely on foot, keeping roadways as clear as possible for emergency responders, logistics, mass transport, and law enforcement. This RTSTEP project developed a regional emergency evacuation modeling tool for the Chicago Metropolitan Area that emergency responders can use to pre-plan evacuation strategies and compare different response strategies on the basis of a rather realistic model of the underlying complex transportation system. This approach is a significant improvement over existing response strategies that are largely based on experience gained from small-scale events, anecdotal evidence, and extrapolation to the scale of the assumed emergency. The new tool will thus add to the toolbox available to emergency response planners to help them design appropriate generalized procedures and strategies that lead to an improved outcome when used during an actual event.

  4. NREL: Energy Storage - Battery Lifetime Analysis and Simulation Tool Suite

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Battery Lifetime Analysis and Simulation Tool Suite Lithium-ion (Li-ion) batteries used in EVs and stationary energy storage applications must be optimized to justify their high upfront costs. Given that batteries degrade with use and storage, strategies for optimization must factor in many years of use with a number of variables, including: Temperature State-of-charge histories Electricity current levels Cycle depth and frequency. These factors can all affect rates of battery degradation,

  5. A Simple Evacuation Modeling and Simulation Tool for First Responders

    SciTech Connect (OSTI)

    Koch, Daniel B; Payne, Patricia W

    2015-01-01

    Although modeling and simulation of mass evacuations during a natural or man-made disaster is an on-going and vigorous area of study, tool adoption by front-line first responders is uneven. Some of the factors that account for this situation include cost and complexity of the software. For several years, Oak Ridge National Laboratory has been actively developing the free Incident Management Preparedness and Coordination Toolkit (IMPACT) to address these issues. One of the components of IMPACT is a multi-agent simulation module for area-based and path-based evacuations. The user interface is designed so that anyone familiar with typical computer drawing tools can quickly author a geospatially-correct evacuation visualization suitable for table-top exercises. Since IMPACT is designed for use in the field where network communications may not be available, quick on-site evacuation alternatives can be evaluated to keep pace with a fluid threat situation. Realism is enhanced by incorporating collision avoidance into the simulation. Statistics are gathered as the simulation unfolds, including most importantly time-to-evacuate, to help first responders choose the best course of action.

  6. Monte Carlo Simulation Tool Installation and Operation Guide

    SciTech Connect (OSTI)

    Aguayo Navarrete, Estanislao; Ankney, Austin S.; Berguson, Timothy J.; Kouzes, Richard T.; Orrell, John L.; Troy, Meredith D.; Wiseman, Clinton G.

    2013-09-02

    This document provides information on software and procedures for Monte Carlo simulations based on the Geant4 toolkit, the ROOT data analysis software and the CRY cosmic ray library. These tools have been chosen for its application to shield design and activation studies as part of the simulation task for the Majorana Collaboration. This document includes instructions for installation, operation and modification of the simulation code in a high cyber-security computing environment, such as the Pacific Northwest National Laboratory network. It is intended as a living document, and will be periodically updated. It is a starting point for information collection by an experimenter, and is not the definitive source. Users should consult with one of the authors for guidance on how to find the most current information for their needs.

  7. Integrated computer simulation on FIR FEL dynamics

    SciTech Connect (OSTI)

    Furukawa, H.; Kuruma, S.; Imasaki, K.

    1995-12-31

    An integrated computer simulation code has been developed to analyze the RF-Linac FEL dynamics. First, the simulation code on the electron beam acceleration and transport processes in RF-Linac: (LUNA) has been developed to analyze the characteristics of the electron beam in RF-Linac and to optimize the parameters of RF-Linac. Second, a space-time dependent 3D FEL simulation code (Shipout) has been developed. The RF-Linac FEL total simulations have been performed by using the electron beam data from LUNA in Shipout. The number of particles using in a RF-Linac FEL total simulation is approximately 1000. The CPU time for the simulation of 1 round trip is about 1.5 minutes. At ILT/ILE, Osaka, a 8.5MeV RF-Linac with a photo-cathode RF-gun is used for FEL oscillation experiments. By using 2 cm wiggler, the FEL oscillation in the wavelength approximately 46 {mu}m are investigated. By the simulations using LUNA with the parameters of an ILT/ILE experiment, the pulse shape and the energy spectra of the electron beam at the end of the linac are estimated. The pulse shape of the electron beam at the end of the linac has sharp rise-up and it slowly decays as a function of time. By the RF-linac FEL total simulations with the parameters of an ILT/ILE experiment, the dependencies of the start up of the FEL oscillations on the pulse shape of the electron beam at the end of the linac are estimated. The coherent spontaneous emission effects and the quick start up of FEL oscillations have been observed by the RF-Linac FEL total simulations.

  8. DynTG: A tool for Interactive, Dynamic Instrumentation

    SciTech Connect (OSTI)

    Schulz, M; May, J; Gyllenhaal, J

    2005-02-16

    With the increasing complexity of today's systems, detailed performance analysis is more important than ever. We have developed DynTG, a tool for interactive, dynamic instrumentation. It uses performance module plugins to reconfigure the data acquisition and provides a source browser that allows users to insert any probe functionality provided by the modules dynamically into the target application. Any instrumentation can be added both before and during the application's execution and the acquired data is presented in realtime within the source viewer. This enables users to monitor their applications' progress and interactively control and adapt the instrumentation based on their observations.

  9. Dynamic simulator for PEFC propulsion plant

    SciTech Connect (OSTI)

    Hiraide, Masataka; Kaneda, Eiichi; Sato, Takao

    1996-12-31

    This report covers part of a joint study on a PEFC propulsion system for surface ships, summarized in a presentation to this Seminar, entitled {open_quote}Study on a Polymer Electrolyte Fuel Cell (PEFC) Propulsion System for Surface Ships{close_quotes}, and which envisages application to a 1,500 DWT cargo vessel. The work presented here focuses on a simulation study on PEFC propulsion plant performance, and particularly on the system response to changes in load. Using a dynamic simulator composed of system components including fuel cell, various simulations were executed, to examine the performance of the system as a whole and of the individual system components under quick and large load changes such as occasioned by maneuvering operations and by racing when the propeller emerges above water in heavy sea.

  10. Microcutting characteristics on the single crystal diamond tool with edge radius using molecular dynamics

    SciTech Connect (OSTI)

    Kim, Jeong-Du; Moon, Chan-Hong

    1995-12-31

    Ultraprecision metal cutting (UPMC) technology which makes possible submicrometer form accuracy and manometer roughness is developed to reach the 1nm nominal (undeformed) thickness of cut. At this thickness level, a few of atom`s layers should be considered. In this paper using the Molecuar Dynamics simulation, the phenomena of microcutting with a subnanometer chip thickness, the cutting mechanism for tool edge configuration to consider the sharp edge and round edge tool, the cut material and cutting speed are evaluated. Cutting mechanism of subnanometer depth of cut is evaluated.

  11. Westinghouse Waste Simulation and Optimization Software Tool - 13493

    SciTech Connect (OSTI)

    Mennicken, Kim [Westinghouse Electric Germany GmbH, Global Waste Management, Dudenstrasse 44, D-68167 Mannheim (Germany)] [Westinghouse Electric Germany GmbH, Global Waste Management, Dudenstrasse 44, D-68167 Mannheim (Germany); Aign, Joerg [Westinghouse Electric Germany GmbH, Global Waste Management, Tarpenring 6, D-22419 Hamburg (Germany)] [Westinghouse Electric Germany GmbH, Global Waste Management, Tarpenring 6, D-22419 Hamburg (Germany)

    2013-07-01

    Radioactive waste is produced during NPP operation and NPP D and D. Different kinds of waste with different volumes and properties have to be treated. Finding a technically and commercially optimized waste treatment concept is a difficult and time consuming process. The Westinghouse waste simulation and optimization software tool is an approach to study the total life cycle cost of any waste management facility. The tool enables the user of the simulation and optimization software to plan processes and storage buildings and to identify bottlenecks in the overall waste management design before starting detailed planning activities. Furthermore, application of the software enables the user to optimize the number of treatment systems, to determine the minimum design capacity for onsite storage facilities, to identify bottlenecks in the overall design and to identify the most cost-effective treatment paths by maintaining optimal waste treatment technologies. In combination with proven waste treatment equipment and integrated waste management solutions, the waste simulation and optimization software provides reliable qualitative results that lead to an effective planning and minimization of the total project planning risk of any waste management activity. (authors)

  12. Computational simulation of dynamic impact problems

    SciTech Connect (OSTI)

    Muenz, T.W.; Rix, K.S.; Willam, K.J.

    1996-12-31

    Recent advances of computing methods make it possible to examine dynamic failure and complicated contact-impact load scenarios in time and space. The response simulation for these extreme load conditions needs to capture dynamic contact between the impactor and the deformable target and progressive failure in the target. Independently from the impact scenario, two basic approaches may be used to describe the failure process in an appropriate manner, namely the Discrete Failure Approach and the Smeared Failure Approach. In the contribution the dynamic impact of a pendulum test and the failure scenario in notched cylindrical specimens (Charpy-type IZOD test) are examined using the explicit dynamic finite element code DYNA3D. The study focuses on the question, whether the smeared crack approach is able to capture the dynamic failure process using von Mises plasticity with a plastic strain-based failure limiter. The computational results indicate that upon consistent mesh refinement the overall energy dissipation approaches the value observed in laboratory experiments.

  13. Summary - System Level Modeling and Simulation Tools for SRS

    Office of Environmental Management (EM)

    Workflo The ob Proces Savann Dispos assess evaluat design evaluat predict to guid * Th so in w es sy * Th is m * Th fle m de fu The pu techni projec Site: S roject: S Report Date: J ited States valuation i Why DOE ow Diagram bjective of the rev ss Simulation To nah River Site (S sition System Pla s whether the too te methods used , construction, p te methods to im ions; and (4) det e actual executio What th he current Syst oftware tools to formation, and aste. These to stimates, but th ystem

  14. Eddy current NDE performance demonstrations using simulation tools

    SciTech Connect (OSTI)

    Maurice, L.; Costan, V.; Guillot, E.; Thomas, P.

    2013-01-25

    To carry out performance demonstrations of the Eddy-Current NDE processes applied on French nuclear power plants, EDF studies the possibility of using simulation tools as an alternative to measurements on steam generator tube mocks-up. This paper focuses on the strategy led by EDF to assess and use code{sub C}armel3D and Civa, on the case of Eddy-Current NDE on wears problem which may appear in the U-shape region of steam generator tubes due to the rubbing of anti-vibration bars.

  15. Battery Lifetime Analysis and Simulation Tool (BLAST) Documentation

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Battery Lifetime Analysis and Simulation Tool (BLAST) Documentation J. Neubauer Technical Report NREL/TP-5400-63246 December 2014 NREL is a national laboratory of the U.S. Department of Energy Office of Energy Efficiency & Renewable Energy Operated by the Alliance for Sustainable Energy, LLC This report is available at no cost from the National Renewable Energy Laboratory (NREL) at www.nrel.gov/publications. Contract No. DE-AC36-08GO28308 National Renewable Energy Laboratory 15013 Denver

  16. Simulating the Effect of Modulated Tool-Path Chip Breaking On Surface Texture and Chip Length

    SciTech Connect (OSTI)

    Smith, K.S.; McFarland, J.T.; Tursky, D. A.; Assaid, T. S.; Barkman, W. E.; Babelay, Jr., E. F.

    2010-04-30

    One method for creating broken chips in turning processes involves oscillating the cutting tool in the feed direction utilizing the CNC machine axes. The University of North Carolina at Charlotte and the Y-12 National Security Complex have developed and are refining a method to reliably control surface finish and chip length based on a particular machine's dynamic performance. Using computer simulations it is possible to combine the motion of the machine axes with the geometry of the cutting tool to predict the surface characteristics and map the surface texture for a wide range of oscillation parameters. These data allow the selection of oscillation parameters to simultaneously ensure broken chips and acceptable surface characteristics. This paper describes the machine dynamic testing and characterization activities as well as the computational method used for evaluating and predicting chip length and surface texture.

  17. CgWind: A high-order accurate simulation tool for wind turbines and wind farms

    SciTech Connect (OSTI)

    Chand, K K; Henshaw, W D; Lundquist, K A; Singer, M A

    2010-02-22

    CgWind is a high-fidelity large eddy simulation (LES) tool designed to meet the modeling needs of wind turbine and wind park engineers. This tool combines several advanced computational technologies in order to model accurately the complex and dynamic nature of wind energy applications. The composite grid approach provides high-quality structured grids for the efficient implementation of high-order accurate discretizations of the incompressible Navier-Stokes equations. Composite grids also provide a natural mechanism for modeling bodies in relative motion and complex geometry. Advanced algorithms such as matrix-free multigrid, compact discretizations and approximate factorization will allow CgWind to perform highly resolved calculations efficiently on a wide class of computing resources. Also in development are nonlinear LES subgrid-scale models required to simulate the many interacting scales present in large wind turbine applications. This paper outlines our approach, the current status of CgWind and future development plans.

  18. Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

    SciTech Connect (OSTI)

    Mereghetti, Paolo; Gabdoulline, Razif; Wade, Rebecca C.

    2010-12-01

    The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solutions of three different proteins with varying concentrations, pH, and ionic strength were performed. The results were compared to experimental data and theoretical values in terms of long-time self-diffusion coefficients, second virial coefficients, and structure factors. The results agree with the experimental trends and, in many cases, experimental values are reproduced quantitatively. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixtures of macromolecules in cell-like crowded environments.

  19. Battery Lifetime Analysis and Simulation Tool (BLAST) Documentation

    SciTech Connect (OSTI)

    Neubauer, J.

    2014-12-01

    The deployment and use of lithium-ion batteries in automotive and stationary energy storage applications must be optimized to justify their high up-front costs. Given that batteries degrade with use and storage, such optimizations must evaluate many years of operation. As the degradation mechanisms are sensitive to temperature, state-of-charge histories, current levels, and cycle depth and frequency, it is important to model both the battery and the application to a high level of detail to ensure battery response is accurately predicted. To address these issues, the National Renewable Energy Laboratory has developed the Battery Lifetime Analysis and Simulation Tool (BLAST) suite of tools. This suite of tools pairs NREL's high-fidelity battery degradation model with a battery electrical and thermal performance model, application-specific electrical and thermal performance models of the larger system (e.g., an electric vehicle), application-specific system use data (e.g., vehicle travel patterns and driving data), and historic climate data from cities across the United States. This provides highly realistic, long-term predictions of battery response and thereby enables quantitative comparisons of varied battery use strategies.

  20. Quantum molecular dynamics simulations of dense matter

    SciTech Connect (OSTI)

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I.

    1997-12-31

    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  1. Extended-Term Dynamic Simulations with High Penetrations of Photovoltaic Generation.

    SciTech Connect (OSTI)

    Concepcion, Ricky James; Elliott, Ryan Thomas; Donnelly, Matt; Sanchez-Gasca, Juan

    2016-01-01

    The uncontrolled intermittent availability of renewable energy sources makes integration of such devices into today's grid a challenge. Thus, it is imperative that dynamic simulation tools used to analyze power system performance are able to support systems with high amounts of photovoltaic (PV) generation. Additionally, simulation durations expanding beyond minutes into hours must be supported. This report aims to identify the path forward for dynamic simulation tools to accom- modate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for po- tential problems. We present a study of fixed time step, explicit numerical integration schemes that may be more suitable for these goals, based on identified requirements for simulating high PV penetration systems. We also present the alternative of variable time step integration. To help determine the characteristics of systems with high PV generation, we performed small signal sta- bility studies and time domain simulations of two representative systems. Along with feedback from stakeholders and vendors, we identify the current gaps in power system modeling including fast and slow dynamics and propose a new simulation framework to improve our ability to model and simulate longer-term dynamics.

  2. On sequential dynamical systems and simulation

    SciTech Connect (OSTI)

    Barrett, C.L.; Mortveit, H.S.; Reidys, C.M.

    1999-06-01

    The generic structure of computer simulations motivates a new class of discrete dynamical systems that captures this structure in a mathematically precise way. This class of systems consists of (1) a loopfree graph {Upsilon} with vertex set {l_brace}1,2,{hor_ellipsis},n{r_brace} where each vertex has a binary state, (2) a vertex labeled set of functions (F{sub i,{Upsilon}}:F{sub 2}{sup n} {r_arrow} F{sub 2}{sup n}){sub i} and (3) a permutation {pi} {element_of} S{sub n}. The function F{sub i,{Upsilon}} updates the state of vertex i as a function of the states of vertex i and its {Upsilon}-neighbors and leaves the states of all other vertices fixed. The permutation {pi} represents the update ordering, i.e., the order in which the functions F{sub i,{Upsilon}} are applied. By composing the functions F{sub i,{Upsilon}} in the order given by {pi} one obtains the dynamical system (equation given in paper) which the authors refer to as a sequential dynamical system, or SDS for short. The authors will present bounds for the number of functionally different systems and for the number of nonisomorphic digraphs {Gamma}[F{sub {Upsilon}},{pi}] that can be obtained by varying the update order and applications of these to specific graphs and graph classes. This will be done using both combinatorial/algebraic techniques and probabilistic techniques. Finally the authors give results on dynamical system properties for some special systems.

  3. DRIVER TO SUPPORT USE OF NUMERICAL SIMULATION TOOLS

    Energy Science and Technology Software Center (OSTI)

    2001-02-13

    UNIPACK is a computer interface that simplifies and enhances the use of numerical simulation tools to design a primary geometry and/or a forming die for a powder compact and/or to design the pressing process used to shape a powder by compaction. More particularly, it is an interface that utilizes predefined generic geometric configurations to simplify the use of finite element method modeling software to simply and more efficiently design: (1) the shape and size amore » powder compact; (2) a forming die to shape a powder compact; and/or (3) the pressing process used to form a powder compact. UNIPACK is a user interface for a predictive model for powder compaction that incorporates unprecedented flexibility to design powder press tooling and powder pressing processes. UNIPACK works with the Sandia National Laboratories (SNL) Engineering Analysis Cide Access System (SEACAS) to generate a finite element (FE) mesh and automatically perform a FE analysis of powder compaction. UNIPACK was developed to allow a non-expert with minimal training to quickly and easily design/construct a variable dimension component or die in real time on a desktop or laptop personal computer.« less

  4. Summary - System Level Modeling and Simulation Tools for SRS

    Office of Environmental Management (EM)

    What th he current Syst oftware tools to formation, and aste. These to stimates, but th ... p here is a need f g tool. f current tools a hampers proces m planning. to increase ...

  5. Nuclear fuel cycle system simulation tool based on high-fidelity component modeling

    SciTech Connect (OSTI)

    Ames, David E.

    2014-02-01

    The DOE is currently directing extensive research into developing fuel cycle technologies that will enable the safe, secure, economic, and sustainable expansion of nuclear energy. The task is formidable considering the numerous fuel cycle options, the large dynamic systems that each represent, and the necessity to accurately predict their behavior. The path to successfully develop and implement an advanced fuel cycle is highly dependent on the modeling capabilities and simulation tools available for performing useful relevant analysis to assist stakeholders in decision making. Therefore a high-fidelity fuel cycle simulation tool that performs system analysis, including uncertainty quantification and optimization was developed. The resulting simulator also includes the capability to calculate environmental impact measures for individual components and the system. An integrated system method and analysis approach that provides consistent and comprehensive evaluations of advanced fuel cycles was developed. A general approach was utilized allowing for the system to be modified in order to provide analysis for other systems with similar attributes. By utilizing this approach, the framework for simulating many different fuel cycle options is provided. Two example fuel cycle configurations were developed to take advantage of used fuel recycling and transmutation capabilities in waste management scenarios leading to minimized waste inventories.

  6. Molecular dynamics simulations of microscale fluid transport

    SciTech Connect (OSTI)

    Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.

    1998-02-01

    Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.

  7. Sandia Energy - Simulations Reveal Ion Dynamics in Polymer Electrolyte

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    and their effects on material properties is important for improved design. Recent molecular-dynamics simulations have revealed new details of ion motion in model ionomers....

  8. Molecular Dynamics Simulations of Gas Selectivity in Amorphous...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Dynamics Simulations of Gas Selectivity in Amorphous Porous Molecular Solids Previous Next List Shan Jiang, Kim E. Jelfs, Daniel Holden, Tom Hasell, Samantha Y. Chong, Maciej...

  9. Dynamic System Simulation of the KRUSTY Experiment (Technical...

    Office of Scientific and Technical Information (OSTI)

    Technical Report: Dynamic System Simulation of the KRUSTY Experiment Citation Details ... Have feedback or suggestions for a way to improve these results? Save Share this ...

  10. Molecular dynamics simulation and ab intio studies of electrolytes...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    More Documents & Publications High Voltage Electrolytes for Li-ion Batteries Molecular Dynamics Simulation Studies of Electrolytes and ElectrolyteElectrode Interfaces

  11. Molecular dynamics simulation and ab intio studies of electrolytes...

    Energy.gov (indexed) [DOE]

    and Vehicle Technologies Program Annual Merit Review and Peer Evaluation es058smith2011o.pdf (854.25 KB) More Documents & Publications Molecular Dynamics Simulation ...

  12. Systems Dynamic ToolBox for Water Resource Planning

    Energy Science and Technology Software Center (OSTI)

    2006-08-01

    The Fully Integrated System Dynamics Tookbox for Water Resources Planning (Toolbox) is a library of generic modules intended to assist in water management planning and decision making in watersheds around the world. The modules - built in a commercially available modeling environment called Powersim Studio Expert, represent the different sub-systems ina watershed, including population, agriculture, economics, climate, reservoirs, stream flows, and fish populations, and provides generic building blocks with which complex models of complex modelsmore » of complex watersheds can be assembled. The resulting models provide a tool for observing how research management decision made in one sector of a basin can affect other sectors. Improved water resource management contributes to improved public health, economic development, ecological sustainability, and overall security and stability.« less

  13. Rotational Brownian Dynamics simulations of clathrin cage formation

    SciTech Connect (OSTI)

    Ilie, Ioana M.; Briels, Wim J.; Otter, Wouter K. den

    2014-08-14

    The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.

  14. Method and apparatus for characterizing and enhancing the dynamic performance of machine tools

    DOE Patents [OSTI]

    Barkman, William E; Babelay, Jr., Edwin F

    2013-12-17

    Disclosed are various systems and methods for assessing and improving the capability of a machine tool. The disclosure applies to machine tools having at least one slide configured to move along a motion axis. Various patterns of dynamic excitation commands are employed to drive the one or more slides, typically involving repetitive short distance displacements. A quantification of a measurable merit of machine tool response to the one or more patterns of dynamic excitation commands is typically derived for the machine tool. Examples of measurable merits of machine tool performance include dynamic one axis positional accuracy of the machine tool, dynamic cross-axis stability of the machine tool, and dynamic multi-axis positional accuracy of the machine tool.

  15. Summary - System Level Modeling and Simulation Tools for Hanford

    Office of Environmental Management (EM)

    What th he current Syst hat are limited t hese tools curr omposition, res ot meeting was ... Departmen n of Sys upport o E-EM Did This reviews was to ulation Tools th RP Life-cycle L ...

  16. Evaluation of System Level Modeling and Simulation Tools in Support of

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Savannah River Site Liquid Waste Process | Department of Energy System Level Modeling and Simulation Tools in Support of Savannah River Site Liquid Waste Process Evaluation of System Level Modeling and Simulation Tools in Support of Savannah River Site Liquid Waste Process Full Document and Summary Versions are available for download Evaluation of System Level Modeling and Simulation Tools in Support of Savannah River Site Liquid Waste Process (1.11 MB) Summary - System Level Modeling and

  17. Expansion techniques for collisionless stellar dynamical simulations

    SciTech Connect (OSTI)

    Meiron, Yohai; Li, Baile; Holley-Bockelmann, Kelly; Spurzem, Rainer

    2014-09-10

    We present graphics processing unit (GPU) implementations of two fast force calculation methods based on series expansions of the Poisson equation. One method is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other method is the multipole expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field methods and optimized for collisionless galactic dynamics, but while SCF is a 'pure' expansion, MEX is an expansion in just the angular part; thus, MEX is capable of capturing radial structure easily, while SCF needs a large number of radial terms. We show that despite the expansion bias, these methods are more accurate than direct techniques for the same number of particles. The performance of our GPU code, which we call ETICS, is profiled and compared to a CPU implementation. On the tested GPU hardware, a full force calculation for one million particles took ∼0.1 s (depending on expansion cutoff), making simulations with as many as 10{sup 8} particles fast for a comparatively small number of nodes.

  18. Kinetic simulations of plasmoid chain dynamics

    SciTech Connect (OSTI)

    Markidis, S. [High Performance Computing and Visualization (HPCViz) Department, KTH Royal Institute of Technology, Stockholm (Sweden)] [High Performance Computing and Visualization (HPCViz) Department, KTH Royal Institute of Technology, Stockholm (Sweden); Henri, P. [Universit de Nice Sophia Antipolis, CNRS, Observatoire de la Cte d'Azur, Nice (France)] [Universit de Nice Sophia Antipolis, CNRS, Observatoire de la Cte d'Azur, Nice (France); Lapenta, G. [Centrum voor Plasma-Astrofysica, Department Wiskunde, Katholieke Universiteit Leuven, Leuven (Belgium)] [Centrum voor Plasma-Astrofysica, Department Wiskunde, Katholieke Universiteit Leuven, Leuven (Belgium); Divin, A. [Swedish Institute of Space Physics, Uppsala (Sweden)] [Swedish Institute of Space Physics, Uppsala (Sweden); Goldman, M.; Newman, D. [Department of Physics and CIPS, University of Colorado, Boulder 80309-0390 (United States)] [Department of Physics and CIPS, University of Colorado, Boulder 80309-0390 (United States); Laure, E. [PDC and High Performance Computing and Visualization (HPCViz) Department, KTH Royal Institute of Technology, Stockholm (Sweden)] [PDC and High Performance Computing and Visualization (HPCViz) Department, KTH Royal Institute of Technology, Stockholm (Sweden)

    2013-08-15

    The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid in the direction of the existing guide field, and bump-on-tail instability, leading to the formation of electron holes, is detected in proximity of the plasmoids.

  19. NREL Developing a Numerical Simulation Tool to Study Hydrokinetic Energy Conversion Devices and Arrays (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-02-01

    New code will help accelerate design improvements by providing a high-fidelity simulation tool to study power performance, structural loading, and the interactions between devices in arrays.

  20. Update on ORNL TRANSFORM Tool: Simulating Multi-Module Advanced Reactor with End-to-End I&C

    SciTech Connect (OSTI)

    Hale, Richard Edward; Fugate, David L.; Cetiner, Sacit M.; Qualls, A. L.

    2015-05-01

    The Small Modular Reactor (SMR) Dynamic System Modeling Tool project is in the fourth year of development. The project is designed to support collaborative modeling and study of various advanced SMR (non-light water cooled reactor) concepts, including the use of multiple coupled reactors at a single site. The focus of this report is the development of a steam generator and drum system model that includes the complex dynamics of typical steam drum systems, the development of instrumentation and controls for the steam generator with drum system model, and the development of multi-reactor module models that reflect the full power reactor innovative small module design concept. The objective of the project is to provide a common simulation environment and baseline modeling resources to facilitate rapid development of dynamic advanced reactor models; ensure consistency among research products within the Instrumentation, Controls, and Human-Machine Interface technical area; and leverage cross-cutting capabilities while minimizing duplication of effort. The combined simulation environment and suite of models are identified as the TRANSFORM tool. The critical elements of this effort include (1) defining a standardized, common simulation environment that can be applied throughout the Advanced Reactors Technology program; (2) developing a library of baseline component modules that can be assembled into full plant models using available geometry, design, and thermal-hydraulic data; (3) defining modeling conventions for interconnecting component models; and (4) establishing user interfaces and support tools to facilitate simulation development (i.e., configuration and parameterization), execution, and results display and capture.

  1. Molecular dynamics simulation and ab intio studies of electrolytes and

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    electrolyte/electrode interfaces | Department of Energy 1 DOE Hydrogen and Fuel Cells Program, and Vehicle Technologies Program Annual Merit Review and Peer Evaluation es058_smith_2011_o.pdf (854.25 KB) More Documents & Publications Molecular Dynamics Simulation Studies of Electrolytes and Electrolyte/Electrode Interfaces Molecular dynamics simulation studies of electrolytes and electrolyte/electrode interfaces

  2. Parallel implementation of three-dimensional molecular dynamic simulation for laser-cluster interaction

    SciTech Connect (OSTI)

    Holkundkar, Amol R.

    2013-11-15

    The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of the experiments reported in the literature. Scaling laws for the computational time is established by varying the number of processor cores and number of macroparticles used. The capabilities of the code are highlighted by implementing various diagnostic tools. To study the dynamics of the laser-cluster interactions, the executable version of the code is available from the author.

  3. NREL: Dynamic Maps, GIS Data, and Analysis Tools - Hydrogen Data

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Biomass Geospatial Toolkits Geothermal Hydrogen International Marine & Hydrokinetic Solar Wind Data Visualization & Geospatial Tools Geospatial Team Publications Contact Us...

  4. NREL: News - Advisor 2002-A Powerful Vehicle Simulation Tool Gets Better

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Advisor 2002-A Powerful Vehicle Simulation Tool Gets Better Golden, Colo., June 11, 2002 A powerful tool for the analysis of advanced and conventional vehicles just got better with the release of ADVISOR 2002. ADVISOR (ADvanced VehIcle SimulatOR) was created by the U.S. Department of Energy's National Renewable Energy Laboratory's (NREL) Center for Transportation Technologies and Systems. It's a flexible modeling tool that rapidly assesses the performance and fuel economy of conventional,

  5. Fast Dynamic Simulation-Based Small Signal Stability Assessment and Control

    SciTech Connect (OSTI)

    Acharya, Naresh; Baone, Chaitanya; Veda, Santosh; Dai, Jing; Chaudhuri, Nilanjan; Leonardi, Bruno; Sanches-Gasca, Juan; Diao, Ruisheng; Wu, Di; Huang, Zhenyu; Zhang, Yu; Jin, Shuangshuang; Zheng, Bin; Chen, Yousu

    2014-12-31

    Power grid planning and operation decisions are made based on simulation of the dynamic behavior of the system. Enabling substantial energy savings while increasing the reliability of the aging North American power grid through improved utilization of existing transmission assets hinges on the adoption of wide-area measurement systems (WAMS) for power system stabilization. However, adoption of WAMS alone will not suffice if the power system is to reach its full entitlement in stability and reliability. It is necessary to enhance predictability with "faster than real-time" dynamic simulations that will enable the dynamic stability margins, proactive real-time control, and improve grid resiliency to fast time-scale phenomena such as cascading network failures. Present-day dynamic simulations are performed only during offline planning studies, considering only worst case conditions such as summer peak, winter peak days, etc. With widespread deployment of renewable generation, controllable loads, energy storage devices and plug-in hybrid electric vehicles expected in the near future and greater integration of cyber infrastructure (communications, computation and control), monitoring and controlling the dynamic performance of the grid in real-time would become increasingly important. The state-of-the-art dynamic simulation tools have limited computational speed and are not suitable for real-time applications, given the large set of contingency conditions to be evaluated. These tools are optimized for best performance of single-processor computers, but the simulation is still several times slower than real-time due to its computational complexity. With recent significant advances in numerical methods and computational hardware, the expectations have been rising towards more efficient and faster techniques to be implemented in power system simulators. This is a natural expectation, given that the core solution algorithms of most commercial simulators were developed

  6. SciDAC Advances in Beam Dynamics Simulation: From Light Sources to Colliders

    SciTech Connect (OSTI)

    Qiang, J.; Borland, M.; Kabel, A.; Li, R.; Ryne, R.; Stern, E.; Wang, Y.; Wasserman, H.; Zhang, Y.; /SLAC

    2011-11-14

    In this paper, we report on progress that has been made in beam dynamics simulation, from light sources to colliders, during the first year of the SciDAC-2 accelerator project 'Community Petascale Project for Accelerator Science and Simulation (ComPASS).' Several parallel computational tools for beam dynamics simulation are described. Also presented are number of applications in current and future accelerator facilities (e.g., LCLS, RHIC, Tevatron, LHC, and ELIC). Particle accelerators are some of most important tools of scientific discovery. They are widely used in high-energy physics, nuclear physics, and other basic and applied sciences to study the interaction of elementary particles, to probe the internal structure of matter, and to generate high-brightness radiation for research in materials science, chemistry, biology, and other fields. Modern accelerators are complex and expensive devices that may be several kilometers long and may consist of thousands of beamline elements. An accelerator may transport trillions of charged particles that interact electromagnetically among themselves, that interact with fields produced by the accelerator components, and that interact with beam-induced fields. Large-scale beam dynamics simulations on massively parallel computers can help provide understanding of these complex physical phenomena, help minimize design cost, and help optimize machine operation. In this paper, we report on beam dynamics simulations in a variety of accelerators ranging from next generation light sources to high-energy ring colliders that have been studied during the first year of the SciDAC-2 accelerator project.

  7. First-principles molecular dynamics simulations of condensed...

    Office of Scientific and Technical Information (OSTI)

    phase V-type nerve agent reaction pathways and energy barriers Citation Details In-Document Search Title: First-principles molecular dynamics simulations of condensed phase V-type ...

  8. Molecular Dynamics Simulation Studies of Electrolytes andElectrolyte...

    Energy.gov (indexed) [DOE]

    Review and Peer Evaluation Meeting, June 7-11, 2010 -- Washington D.C. PDF icon es058smith2010p.pdf More Documents & Publications Molecular dynamics simulation and ab intio ...

  9. Towards Molecular Dynamics Simulations of InGaN Nanostructures.

    Office of Scientific and Technical Information (OSTI)

    (Conference) | SciTech Connect Towards Molecular Dynamics Simulations of InGaN Nanostructures. Citation Details In-Document Search Title: Towards Molecular Dynamics Simulations of InGaN Nanostructures. Abstract not provided. Authors: Zhou, Xiaowang ; Jones, Reese E. Publication Date: 2015-05-01 OSTI Identifier: 1258140 Report Number(s): SAND2015-4035C 584006 DOE Contract Number: AC04-94AL85000 Resource Type: Conference Resource Relation: Conference: Proposed for presentation at the 2015

  10. Towards Molecular Dynamics Simulations of InGaN Nanostructures.

    Office of Scientific and Technical Information (OSTI)

    (Conference) | SciTech Connect Towards Molecular Dynamics Simulations of InGaN Nanostructures. Citation Details In-Document Search Title: Towards Molecular Dynamics Simulations of InGaN Nanostructures. Abstract not provided. Authors: Zhou, Xiaowang ; Jones, Reese E. Publication Date: 2015-05-01 OSTI Identifier: 1258265 Report Number(s): SAND2015-4035C 584006 DOE Contract Number: AC04-94AL85000 Resource Type: Conference Resource Relation: Conference: Proposed for presentation at the 2015

  11. A Perspective of Molecular Dynamics (MD) Simulations. (Conference) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect A Perspective of Molecular Dynamics (MD) Simulations. Citation Details In-Document Search Title: A Perspective of Molecular Dynamics (MD) Simulations. Abstract not provided. Authors: Zhou, Xiaowang Publication Date: 2015-03-01 OSTI Identifier: 1246841 Report Number(s): SAND2015-1657PE 579717 DOE Contract Number: AC04-94AL85000 Resource Type: Conference Resource Relation: Conference: Proposed for presentation at the Collaboration opportunities with universities held March

  12. Dynamic System Simulation of the KRUSTY Experiment (Technical Report) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Technical Report: Dynamic System Simulation of the KRUSTY Experiment Citation Details In-Document Search Title: Dynamic System Simulation of the KRUSTY Experiment The proposed KRUSTY experiment is a demonstration of a reactor operating at power. The planned experimental configuration includes a highly enriched uranium (HEU) reflected core, cooled by multiple heat pipes leading to Stirling engines for primary heat rejection. Operating power is expected to be approximately four

  13. NREL: Dynamic Maps, GIS Data, and Analysis Tools - Federal Energy...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    The Federal Energy Management Program (FEMP) teamed with Geospatial Analysis staff at NREL ... Data Resources Data Visualization & Geospatial Tools Geospatial Data Science Team ...

  14. Sandia Energy - Computational Fluid Dynamics Simulations Provide...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    from a VWiS large-eddy simulation. One of the primary roles of Sandia's Scaled Wind Farm Technology (SWiFT) facility will be to conduct detailed experiments on turbine wakes and...

  15. Computational Fluid Dynamics Simulation of Fluidized Bed Polymerization Reactors

    SciTech Connect (OSTI)

    Rong Fan

    2006-08-09

    Fluidized beds (FB) reactors are widely used in the polymerization industry due to their superior heat- and mass-transfer characteristics. Nevertheless, problems associated with local overheating of polymer particles and excessive agglomeration leading to FB reactors defluidization still persist and limit the range of operating temperatures that can be safely achieved in plant-scale reactors. Many people have been worked on the modeling of FB polymerization reactors, and quite a few models are available in the open literature, such as the well-mixed model developed by McAuley, Talbot, and Harris (1994), the constant bubble size model (Choi and Ray, 1985) and the heterogeneous three phase model (Fernandes and Lona, 2002). Most these research works focus on the kinetic aspects, but from industrial viewpoint, the behavior of FB reactors should be modeled by considering the particle and fluid dynamics in the reactor. Computational fluid dynamics (CFD) is a powerful tool for understanding the effect of fluid dynamics on chemical reactor performance. For single-phase flows, CFD models for turbulent reacting flows are now well understood and routinely applied to investigate complex flows with detailed chemistry. For multiphase flows, the state-of-the-art in CFD models is changing rapidly and it is now possible to predict reasonably well the flow characteristics of gas-solid FB reactors with mono-dispersed, non-cohesive solids. This thesis is organized into seven chapters. In Chapter 2, an overview of fluidized bed polymerization reactors is given, and a simplified two-site kinetic mechanism are discussed. Some basic theories used in our work are given in detail in Chapter 3. First, the governing equations and other constitutive equations for the multi-fluid model are summarized, and the kinetic theory for describing the solid stress tensor is discussed. The detailed derivation of DQMOM for the population balance equation is given as the second section. In this section

  16. Dynamic extension of the Simulation Problem Analysis Kernel (SPANK)

    SciTech Connect (OSTI)

    Sowell, E.F. . Dept. of Computer Science); Buhl, W.F. )

    1988-07-15

    The Simulation Problem Analysis Kernel (SPANK) is an object-oriented simulation environment for general simulation purposes. Among its unique features is use of the directed graph as the primary data structure, rather than the matrix. This allows straightforward use of graph algorithms for matching variables and equations, and reducing the problem graph for efficient numerical solution. The original prototype implementation demonstrated the principles for systems of algebraic equations, allowing simulation of steady-state, nonlinear systems (Sowell 1986). This paper describes how the same principles can be extended to include dynamic objects, allowing simulation of general dynamic systems. The theory is developed and an implementation is described. An example is taken from the field of building energy system simulation. 2 refs., 9 figs.

  17. Development of simulation tools for virus shell assembly. Final report

    SciTech Connect (OSTI)

    Berger, Bonnie

    2001-01-05

    Prof. Berger's major areas of research have been in applying computational and mathematical techniques to problems in biology, and more specifically to problems in protein folding and genomics. Significant progress has been made in the following areas relating to virus shell assembly: development has been progressing on a second-generation self-assembly simulator which provides a more versatile and physically realistic model of assembly; simulations are being developed and applied to a variety of problems in virus assembly; and collaborative efforts have continued with experimental biologists to verify and inspire the local rules theory and the simulator. The group has also worked on applications of the techniques developed here to other self-assembling structures in the material and biological sciences. Some of this work has been conducted in conjunction with Dr. Sorin Istrail when he was at Sandia National Labs.

  18. NREL: Dynamic Maps, GIS Data, and Analysis Tools - Geothermal Prospector

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Geothermal Prospector Start exploring U.S. geothermal resources with an easy-to-use map by selecting data layers that are NGDS compatible. Bookmark and Share Geothermal Prospector The Geothermal Prospector mapping tool provides an excellent data resource for visual exploration of geothermal resources using the tools and datasets required to produce and disseminate both exploration gap analysis and Enhanced Geothermal System (EGS) planning and analysis. In 2010, NREL developed Geothermal

  19. Nonequilibrium candidate Monte Carlo: A new tool for efficient equilibrium simulation

    SciTech Connect (OSTI)

    Nilmeier, Jerome P.; Crooks, Gavin E.; Minh, David D. L.; Chodera, John D.

    2011-11-08

    Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also rapidly sample uncorrelated configurations. Here, we introduce a new class of moves based on nonequilibrium dynamics: candidate configurations are generated through a finite-time process in which a system is actively driven out of equilibrium, and accepted with criteria that preserve the equilibrium distribution. The acceptance rule is similar to the Metropolis acceptance probability, but related to the nonequilibrium work rather than the instantaneous energy difference. Our method is applicable to sampling from both a single thermodynamic state or a mixture of thermodynamic states, and allows both coordinates and thermodynamic parameters to be driven in nonequilibrium proposals. While generating finite-time switching trajectories incurs an additional cost, driving some degrees of freedom while allowing others to evolve naturally can lead to large enhancements in acceptance probabilities, greatly reducing structural correlation times. Using nonequilibrium driven processes vastly expands the repertoire of useful Monte Carlo proposals in simulations of dense solvated systems.

  20. Development of CFD-Based Simulation Tools for In-Situ Thermal...

    Office of Scientific and Technical Information (OSTI)

    CFD-Based Simulation Tools for In-Situ Thermal Processing of Oil ShaleSands None 04 OIL SHALES AND TAR SANDS In our research, we are taking the novel approach of developing and...

  1. Development of a dynamic simulator for a natural gas combined cycle (NGCC) power plant with post-combustion carbon capture

    SciTech Connect (OSTI)

    Liese, E.; Zitney, S.

    2012-01-01

    The AVESTAR Center located at the U.S. Department of Energy’s National Energy Technology Laboratory and West Virginia University is a world-class research and training environment dedicated to using dynamic process simulation as a tool for advancing the safe, efficient and reliable operation of clean energy plants with CO{sub 2} capture. The AVESTAR Center was launched with a high-fidelity dynamic simulator for an Integrated Gasification Combined Cycle (IGCC) power plant with pre-combustion carbon capture. The IGCC dynamic simulator offers full-scope Operator Training Simulator (OTS) Human Machine Interface (HMI) graphics for realistic, real-time control room operation and is integrated with a 3D virtual Immersive Training Simulator (ITS), thus allowing joint control room and field operator training. The IGCC OTS/ITS solution combines a “gasification with CO{sub 2} capture” process simulator with a “combined cycle” power simulator into a single high-performance dynamic simulation framework. This presentation will describe progress on the development of a natural gas combined cycle (NGCC) dynamic simulator based on the syngas-fired combined cycle portion of AVESTAR’s IGCC dynamic simulator. The 574 MW gross NGCC power plant design consisting of two advanced F-class gas turbines, two heat recovery steam generators (HRSGs), and a steam turbine in a multi-shaft 2x2x1 configuration will be reviewed. Plans for integrating a post-combustion carbon capture system will also be discussed.

  2. Summary - System Level Modeling and Simulation Tools for Hanford

    Office of Environmental Management (EM)

    The ob curren plannin Dispos yield re to mod plannin to imp (4) det actual * Th th Th co no in pl * In fo op sy as di re de co an * Th en m ha ev sc The pu techni projec Site: H roject: H Report Date: S ited States valuation in Su Why DOE bjective of the r nt Process Simu ng basis for OR sition System P easonable esti del facilities cur ng or operation rove the rate o termine if addit execution of in What th he current Syst hat are limited t hese tools curr omposition, res ot meeting was itial

  3. Creating Interoperable Meshing and Discretization Software: The Terascale Simulation Tools and Technology Center

    SciTech Connect (OSTI)

    Brown, D.; Freitag, L.; Glimm, J.

    2002-03-28

    We present an overview of the technical objectives of the Terascale Simulation Tools and Technologies center. The primary goal of this multi-institution collaboration is to develop technologies that enable application scientists to easily use multiple mesh and discretization strategies within a single simulation on terascale computers. The discussion focuses on our efforts to create interoperable mesh generation tools, high-order discretization techniques, and adaptive meshing strategies.

  4. CREATING INTEROPERABLE MESHING AND DISCRETIZATION SOFTWARE: THE TERASCALE SIMULATION TOOLS AND TECHNOLOGY CENTER.

    SciTech Connect (OSTI)

    BROWN,D.; FREITAG,L.; GLIMM,J.

    2002-06-02

    We present an overview of the technical objectives of the Terascale Simulation Tools and Technologies center. The primary goal of this multi-institution collaboration is to develop technologies that enable application scientists to easily use multiple mesh and discretization strategies within a single simulation on terascale computers. The discussion focuses on our efforts to create interoperable mesh generation tools, high-order discretization techniques, and adaptive meshing strategies.

  5. Numerical simulation of undersea cable dynamics

    SciTech Connect (OSTI)

    Ablow, C.M.; Schechter, S.

    1983-01-01

    A fully three-dimensional code has been written to compute the motion of a towed cable. The code is based on a robust and stable finite difference approximation to the differential equations derived from basic dynamics. A 3500-ft cable pulled at 18.5 knots (hr/sup -1/) through a circular turn of 700 yd radius has been computed in about half of the real time of the maneuver. The computed displacements are close to the measured ones; the changes in depth are within 2%.

  6. Use dynamic simulation to model HPU reactor depressuring

    SciTech Connect (OSTI)

    Ernest, J.B.; Depew, C.A. )

    1995-01-01

    Dynamic simulation is the best available method for the analysis of hydroprocessing unit (HPU) depressuring. Depressuring is crucial for the safe operation of hydrocracking and other HPUs with catalysts that have hydrocracking activity. Effective design for depressuring is valuable for all types of HPUs, both grass-roots and revamps. Reactor loop depressuring can set design temperatures and pressures for the reactor effluent cooling train and other equipment and piping in an HPU. Unfortunately, usual methods for determining equipment and piping design conditions during depressuring leave much room for improvement because they poorly account for time-dependent temperature and pressure changes. Dynamic simulation makes it practical to more accurately estimate these transient conditions. The paper discusses depressuring design, including the nature of depressuring, the impact of depressuring on design, and depressuring calculation methods. The author then describes modeling of hydroprocessing unit depressuring by discussing the general and particular correspondence of simulation modules to physical equipment using the base case of total electrical power failure. The special data that is required for dynamic simulation is described and typical simulation results are given. Lastly, the advantages of dynamic simulation are summarized.

  7. Dynamic stall simulation including turbulence modeling

    SciTech Connect (OSTI)

    Allet, A.; Halle, S.; Paraschivoiu, I.

    1995-09-01

    The objective of this study is to investigate the two-dimensional unsteady flow around an airfoil undergoing a Darrieus motion in dynamic stall conditions. For this purpose, a numerical solver based on the solution of the Reynolds-averaged Navier-Stokes equations expressed in a streamfunction-vorticity formulation in a non-inertial frame of reference was developed. The governing equations are solved by the streamline upwind Petrov-Galerkin finite element method (FEM). Temporal discretization is achieved by second-order-accurate finite differences. The resulting global matrix system is linearized by the Newton method and solved by the generalized minimum residual method (GMRES) with an incomplete triangular factorization preconditioning (ILU). Turbulence effects are introduced in the solver by an eddy viscosity model. The investigation centers on an evaluation of the possibilities of several turbulence models, including the algebraic Cebeci-Smith model (CSM) and the nonequilibrium Johnson-King model (JKM). In an effort to predict dynamic stall features on rotating airfoils, first the authors present some testing results concerning the performance of both turbulence models for the flat plate case. Then, computed flow structure together with aerodynamic coefficients for a NACA 0015 airfoil in Darrieus motion under stall conditions are presented.

  8. Modeling ramp compression experiments using large-scale molecular dynamics simulation.

    SciTech Connect (OSTI)

    Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I.; Winey, J. Michael; Gupta, Yogendra Mohan; Lane, J. Matthew D.; Ditmire, Todd; Quevedo, Hernan J.

    2011-10-01

    Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

  9. Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.

    SciTech Connect (OSTI)

    Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael; Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl

    2011-09-01

    Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.

  10. Modeling and simulation of consumer response to dynamic pricing.

    SciTech Connect (OSTI)

    Valenzuela, J.; Thimmapuram, P.; Kim, J

    2012-08-01

    Assessing the impacts of dynamic-pricing under the smart grid concept is becoming extremely important for deciding its full deployment. In this paper, we develop a model that represents the response of consumers to dynamic pricing. In the model, consumers use forecasted day-ahead prices to shift daily energy consumption from hours when the price is expected to be high to hours when the price is expected to be low while maintaining the total energy consumption as unchanged. We integrate the consumer response model into the Electricity Market Complex Adaptive System (EMCAS). EMCAS is an agent-based model that simulates restructured electricity markets. We explore the impacts of dynamic-pricing on price spikes, peak demand, consumer energy bills, power supplier profits, and congestion costs. A simulation of an 11-node test network that includes eight generation companies and five aggregated consumers is performed for a period of 1 month. In addition, we simulate the Korean power system.

  11. Lessons Learned From Dynamic Simulations of Advanced Fuel Cycles

    SciTech Connect (OSTI)

    Steven J. Piet; Brent W. Dixon; Jacob J. Jacobson; Gretchen E. Matthern; David E. Shropshire

    2009-04-01

    Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe “lessons learned” from dynamic simulations but attempt to answer the “so what” question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.

  12. A SOFTWARE TOOL TO COMPARE MEASURED AND SIMULATED BUILDING ENERGY PERFORMANCE DATA

    SciTech Connect (OSTI)

    Maile, Tobias; Bazjanac, Vladimir; O'Donnell, James; Garr, Matthew

    2011-11-01

    Building energy performance is often inadequate when compared to design goals. To link design goals to actual operation one can compare measured with simulated energy performance data. Our previously developed comparison approach is the Energy Performance Comparison Methodology (EPCM), which enables the identification of performance problems based on a comparison of measured and simulated performance data. In context of this method, we developed a software tool that provides graphing and data processing capabilities of the two performance data sets. The software tool called SEE IT (Stanford Energy Efficiency Information Tool) eliminates the need for manual generation of data plots and data reformatting. SEE IT makes the generation of time series, scatter and carpet plots independent of the source of data (measured or simulated) and provides a valuable tool for comparing measurements with simulation results. SEE IT also allows assigning data points on a predefined building object hierarchy and supports different versions of simulated performance data. This paper briefly introduces the EPCM, describes the SEE IT tool and illustrates its use in the context of a building case study.

  13. Molecular dynamics simulation and ab intio studies of electrolytes and

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    electrolyte/electrode interfaces | Department of Energy 2 DOE Hydrogen and Fuel Cells Program and Vehicle Technologies Program Annual Merit Review and Peer Evaluation Meeting es058_bedrov_2012_p.pdf (3.66 MB) More Documents & Publications High Voltage Electrolytes for Li-ion Batteries Molecular Dynamics Simulation Studies of Electrolytes and Electrolyte/Electrode Interfaces

  14. Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

    SciTech Connect (OSTI)

    Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter

    2015-12-07

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  15. Generic solar photovoltaic system dynamic simulation model specification.

    SciTech Connect (OSTI)

    Ellis, Abraham; Behnke, Michael Robert; Elliott, Ryan Thomas

    2013-10-01

    This document is intended to serve as a specification for generic solar photovoltaic (PV) system positive-sequence dynamic models to be implemented by software developers and approved by the WECC MVWG for use in bulk system dynamic simulations in accordance with NERC MOD standards. Two specific dynamic models are included in the scope of this document. The first, a Central Station PV System model, is intended to capture the most important dynamic characteristics of large scale (> 10 MW) PV systems with a central Point of Interconnection (POI) at the transmission level. The second, a Distributed PV System model, is intended to represent an aggregation of smaller, distribution-connected systems that comprise a portion of a composite load that might be modeled at a transmission load bus.

  16. Rensselaer Component of the Terascale Simulation Tools and Technologies - Final Report

    SciTech Connect (OSTI)

    Mark S. Shephard

    2009-08-03

    The Terascale Simulation Tools and Technologies (TSTT) SciDAC center focused on the development and application on SciDAC applications of advanced technologies to support unstructured grid simulations. As part of the TSTT team the RPI group focused on developing automated adaptive mesh control tools and working with SciDAC accelerator and fusion applications on the use of these technologies to execute their simulations. The remainder of this report provides a brief summary of the efforts carried out by the RPI team to support SciDAC applications (Section 2) and to develop the TSTT technologies needed for those automated adaptive simulations (Section 3). More complete information on the technical developments can be found in the cited references and previous progress reports.

  17. Beam Dynamics Design and Simulation in Ion Linear Accelerators (

    Energy Science and Technology Software Center (OSTI)

    2006-08-01

    Orginally, the ray tracing code TRACK has been developed to fulfill the many special requirements for the Rare Isotope Accelerator Facility known as RIA. Since no available beam-dynamics code met all the necessary requirements, modifications to the code TRACK were introduced to allow end-to-end (from the ion souce to the production target) simulations of the RIA machine, TRACK is a general beam-dynamics code and can be applied for the design, commissioning and operation of modernmore » ion linear accelerators and beam transport systems.« less

  18. Simulating vehicle dynamics: The importance of a valid forcing function

    SciTech Connect (OSTI)

    Ferguson, G.L.

    1988-01-01

    The recent evolution of vehicle systems has required they be structurally sound with minimum weight. Historically, a trial and error approach to marketing a vehicle was used. The 1970s saw mainframe computers speed the vehicle design process. In the early 1980s simulating vehicle dynamics became the accepted design procedure. The forcing function used in this technique is also its major drawback. This paper summarizes the results of one sled vehicle used in a detailed study done at the U. S. Air Force's High Speed Test Track. The study concluded that results from simulation studies are valid only if an accurate forcing function is used. 6 refs., 14 figs.

  19. Dislocation dynamics simulations of plasticity at small scales

    SciTech Connect (OSTI)

    Zhou, Caizhi

    2010-12-15

    As metallic structures and devices are being created on a dimension comparable to the length scales of the underlying dislocation microstructures, the mechanical properties of them change drastically. Since such small structures are increasingly common in modern technologies, there is an emergent need to understand the critical roles of elasticity, plasticity, and fracture in small structures. Dislocation dynamics (DD) simulations, in which the dislocations are the simulated entities, offer a way to extend length scales beyond those of atomistic simulations and the results from DD simulations can be directly compared with the micromechanical tests. The primary objective of this research is to use 3-D DD simulations to study the plastic deformation of nano- and micro-scale materials and understand the correlation between dislocation motion, interactions and the mechanical response. Specifically, to identify what critical events (i.e., dislocation multiplication, cross-slip, storage, nucleation, junction and dipole formation, pinning etc.) determine the deformation response and how these change from bulk behavior as the system decreases in size and correlate and improve our current knowledge of bulk plasticity with the knowledge gained from the direct observations of small-scale plasticity. Our simulation results on single crystal micropillars and polycrystalline thin films can march the experiment results well and capture the essential features in small-scale plasticity. Furthermore, several simple and accurate models have been developed following our simulation results and can reasonably predict the plastic behavior of small scale materials.

  20. Molecular dynamics simulation of radiation damage cascades in diamond

    SciTech Connect (OSTI)

    Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.

    2015-06-28

    Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

  1. Molecular dynamics simulations of Si etching in Cl- and Br-based...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Molecular dynamics simulations of Si etching in ... thickness, surface stoichiometry, and depth profile of surface products simulated for ...

  2. Molecular dynamics simulation of mechanical deformation of ultra-thin metal and ceramic films

    SciTech Connect (OSTI)

    Belak, J.; Glosli, J.N.; Boercker, D.B.; Stowers, I.F.

    1995-04-01

    We present an overview of the molecular dynamics computer simulation method as employed in the study of the mechanical properties of surfaces at the manometer scale. The embedded atom method is used to model a clean metal surface and the bond-order model is used to model ceramic surfaces. The computer experiment consists of the indentation and scraping of a hard diamond-like tool into and across the surface. Results are presented for the (111) surface of copper and silver and for the (100) surface of silicon. We explicitly demonstrate in our point indentation simulations that nanoscale plasticity in metals takes place by nondislocation mechanisms, a result suggested by recent nanoindentation experiments. We also observe the surface to accommodate nearly the entire volume of the tip and the annealing out of plastic work as the tip is removed. In our orthogonal cutting simulation, we observe an interesting phenomenon: the system dynamically reorients the gain in front of the tool tip to minimize the work performed on the shear plane (i.e. the shear plane becomes an easy slip plane). Silicon transforms into an amorphous state which then flows plastically.

  3. ParaDiS-FEM dislocation dynamics simulation code primer (Technical...

    Office of Scientific and Technical Information (OSTI)

    ParaDiS-FEM dislocation dynamics simulation code primer Citation Details In-Document Search Title: ParaDiS-FEM dislocation dynamics simulation code primer You are accessing a ...

  4. Dynamic simulation of kinematic Stirling engines: Coupled and decoupled analysis

    SciTech Connect (OSTI)

    Fischer, K.; Lemrani, H.; Stouffs, P.

    1995-12-31

    A coupled analysis modelling method of Stirling engines is presented. The main feature of this modelling method is the use of a software package combining the capabilities of a pre-/post-processor with a differential algebraic equations solver. As a result, modelling is merely a matter of linking appropriate objects from a model library and the outcoming tool is very flexible and powerful. Some simulation results are presented and compared with those obtained from a decoupled analysis. It clearly appears that the main imperfection of the model does not come from the modelling process itself but from their incomplete knowledge of the physics behind the Stirling engine operation.

  5. Molecular dynamics simulations of hydrogen diffusion in aluminum

    DOE PAGES-Beta [OSTI]

    Zhou, X. W.; El Gabaly, F.; Stavila, V.; Allendorf, M. D.

    2016-03-23

    In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear howmore » they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.« less

  6. Molecular Dynamics Simulations from SNL's Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Plimpton, Steve; Thompson, Aidan; Crozier, Paul

    LAMMPS (http://lammps.sandia.gov/index.html) stands for Large-scale Atomic/Molecular Massively Parallel Simulator and is a code that can be used to model atoms or, as the LAMMPS website says, as a parallel particle simulator at the atomic, meso, or continuum scale. This Sandia-based website provides a long list of animations from large simulations. These were created using different visualization packages to read LAMMPS output, and each one provides the name of the PI and a brief description of the work done or visualization package used. See also the static images produced from simulations at http://lammps.sandia.gov/pictures.html The foundation paper for LAMMPS is: S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995), but the website also lists other papers describing contributions to LAMMPS over the years.

  7. Simulation tool for optical design of PET detector modules including scintillator material and sensor array

    SciTech Connect (OSTI)

    Jatekos, B.; Erdei, G.; Lorincz, E.

    2011-07-01

    The appearance of single photon avalanche diodes (SPADs) in the field of PET detector modules made it necessary to apply more complex optical design methods to refine the performance of such assemblies. We developed a combined simulation tool that is capable to model complex detector structures including scintillation material, light guide, light collection optics and sensor, correctly taking into account the statistical behavior of emission of scintillation light and its absorbance in SPADs. As a validation we compared simulation results obtained by our software and another optical design program. Calculations were performed for a simple PET detector arrangement used for testing purposes. According to the results, deviation of center of gravity coordinates between the two simulations is 0.0195 mm, the average ratio of total counts 1.0052. We investigated the error resulting from finite sampling in wavelength space and we found that 20 nm pitch is sufficient for the simulation in case of the given spectral dependencies. (authors)

  8. Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

    SciTech Connect (OSTI)

    Mullick, Shanta; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, SummerHill, Shimla - 171005 (India); Pathania, Y. [Chitkara University, Atal Shiksha Kunj, Atal Nagar, Barotiwala, Dist Solan, Himachal Pradesh - 174103 (India)

    2011-12-12

    This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12{sigma}, 14{sigma} and 16{sigma} and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.

  9. Parareal in Time for Dynamic Simulations of Power Systems

    SciTech Connect (OSTI)

    Gurrala, Gurunath; Dimitrovski, Aleksandar D; Pannala, Sreekanth; Simunovic, Srdjan; Starke, Michael R

    2015-01-01

    In recent years, there have been significant developments in parallel algorithms and high performance parallel computing platforms. Parareal in time algorithm has become popular for long transient simulations (e.g., molecular dynamics, fusion, reacting flows). Parareal is a parallel algorithm which divides the time interval into sub-intervals and solves them concurrently. This paper investigates the applicability of the parareal algorithm to power system dynamic simulations. Preliminary results on the application of parareal for multi-machine power systems are reported in this paper. Two widely used test systems, WECC 3-generator 9-bus system, New England 10-generator 39- bus system, is used to explore the effectiveness of the parareal. Severe 3 phase bus faults are simulated using both the classical and detailed models of multi-machine power systems. Actual Speedup of 5-7 times is observed assuming ideal parallelization. It has been observed that the speedup factors of the order of 20 can be achieved by using fast coarse approximations of power system models. Dependency of parareal convergence on fault duration and location has been observed.

  10. Clustering effects in ionic polymers: Molecular dynamics simulations

    SciTech Connect (OSTI)

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.

  11. Clustering effects in ionic polymers: Molecular dynamics simulations

    DOE PAGES-Beta [OSTI]

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing themore » electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.« less

  12. SolOPT: PV and Solar Hot Water Hourly Simulation Software Tool - Energy

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Innovation Portal Solar Photovoltaic Solar Photovoltaic Building Energy Efficiency Building Energy Efficiency Find More Like This Return to Search SolOPT: PV and Solar Hot Water Hourly Simulation Software Tool National Renewable Energy Laboratory Contact NREL About This Technology Publications: PDF Document Publication Using SolOPT (835 KB) Technology Marketing Summary In order to increase the speed and scale of Renewable Energy (RE) solar project deployment on buildings, energy savings

  13. Molecular dynamics simulations of field emission from a planar nanodiode

    SciTech Connect (OSTI)

    Torfason, Kristinn; Valfells, Agust; Manolescu, Andrei

    2015-03-15

    High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space-charge and emitter radius are examined and compared to previous results concerning transition from Fowler-Nordheim to Child-Langmuir current [Y. Y. Lau, Y. Liu, and R. K. Parker, Phys. Plasmas 1, 2082 (1994) and Y. Feng and J. P. Verboncoeur, Phys. Plasmas 13, 073105 (2006)]. The Fowler-Nordheim law is used to determine the current density injected into the system and the Metropolis-Hastings algorithm to find a favourable point of emission on the emitter surface. A simple fluid like model is also developed and its results are in qualitative agreement with the simulations.

  14. Dynamic simulation of the in-tank precipitation process

    SciTech Connect (OSTI)

    Hang, T.; Shanahan, K.L.; Gregory, M.V.; Walker, D.D.

    1993-12-31

    As part of the High-Level Waste Tank Farm at the Savannah River Site (SRS), the In-Tank Precipitation (ITP) facility was designed to decontaminate the radioactive waste supernate by removing cesium as precipitated cesium tetraphenylborate. A dynamic computer model of the ITP process was developed using SPEEDUP{sup TM} software to provide guidance in the areas of operation and production forecast, production scheduling, safety, air emission, and process improvements. The model performs material balance calculations in all phase (solid, liquid, and gas) for 50 key chemical constituents to account for inventory accumulation, depletion, and dilution. Calculations include precipitation, benzene radiolytic reactions, evaporation, dissolution, adsorption, filtration, and stripping. To control the ITP batch operation a customized FORTRAN program was generated and linked to SPEEDUP{sup TM} simulation This paper summarizes the model development and initial results of the simulation study.

  15. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

    SciTech Connect (OSTI)

    Mugnai, Mauro L.; Elber, Ron

    2015-01-07

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.

  16. Modifying the Soil and Water Assessment Tool to Simulate Cropland Carbon Flux: Model Development and Initial Evaluation

    SciTech Connect (OSTI)

    Zhang, Xuesong; Izaurralde, Roberto C.; Arnold, Jeffrey; Williams, Jimmy R.; Srinivasan, Raghavan

    2013-10-01

    Climate change is one of the most compelling modern issues and has important implications for almost every aspect of natural and human systems. The Soil and Water Assessment Tool (SWAT) model has been applied worldwide to support sustainable land and water management in a changing climate. However, the inadequacies of the existing carbon algorithm in SWAT limit its application in assessing impacts of human activities on CO2 emission, one important source of greenhouse gases (GHGs) that traps heat in the earth system and results in global warming. In this research, we incorporate a revised version of the CENTURY carbon model into SWAT to describe dynamics of soil organic matter (SOM)- residue and simulate land-atmosphere carbon exchange.

  17. Description of waste pretreatment and interfacing systems dynamic simulation model

    SciTech Connect (OSTI)

    Garbrick, D.J.; Zimmerman, B.D.

    1995-05-01

    The Waste Pretreatment and Interfacing Systems Dynamic Simulation Model was created to investigate the required pretreatment facility processing rates for both high level and low level waste so that the vitrification of tank waste can be completed according to the milestones defined in the Tri-Party Agreement (TPA). In order to achieve this objective, the processes upstream and downstream of the pretreatment facilities must also be included. The simulation model starts with retrieval of tank waste and ends with vitrification for both low level and high level wastes. This report describes the results of three simulation cases: one based on suggested average facility processing rates, one with facility rates determined so that approximately 6 new DSTs are required, and one with facility rates determined so that approximately no new DSTs are required. It appears, based on the simulation results, that reasonable facility processing rates can be selected so that no new DSTs are required by the TWRS program. However, this conclusion must be viewed with respect to the modeling assumptions, described in detail in the report. Also included in the report, in an appendix, are results of two sensitivity cases: one with glass plant water recycle steams recycled versus not recycled, and one employing the TPA SST retrieval schedule versus a more uniform SST retrieval schedule. Both recycling and retrieval schedule appear to have a significant impact on overall tank usage.

  18. A low dose simulation tool for CT systems with energy integrating detectors

    SciTech Connect (OSTI)

    Zabic, Stanislav; Morton, Thomas; Brown, Kevin M.; Wang Qiu

    2013-03-15

    Purpose: This paper introduces a new strategy for simulating low-dose computed tomography (CT) scans using real scans of a higher dose as an input. The tool is verified against simulations and real scans and compared to other approaches found in the literature. Methods: The conditional variance identity is used to properly account for the variance of the input high-dose data, and a formula is derived for generating a new Poisson noise realization which has the same mean and variance as the true low-dose data. The authors also derive a formula for the inclusion of real samples of detector noise, properly scaled according to the level of the simulated x-ray signals. Results: The proposed method is shown to match real scans in number of experiments. Noise standard deviation measurements in simulated low-dose reconstructions of a 35 cm water phantom match real scans in a range from 500 to 10 mA with less than 5% error. Mean and variance of individual detector channels are shown to match closely across the detector array. Finally, the visual appearance of noise and streak artifacts is shown to match in real scans even under conditions of photon-starvation (with tube currents as low as 10 and 80 mA). Additionally, the proposed method is shown to be more accurate than previous approaches (1) in achieving the correct mean and variance in reconstructed images from pure-Poisson noise simulations (with no detector noise) under photon-starvation conditions, and (2) in simulating the correct noise level and detector noise artifacts in real low-dose scans. Conclusions: The proposed method can accurately simulate low-dose CT data starting from high-dose data, including effects from photon starvation and detector noise. This is potentially a very useful tool in helping to determine minimum dose requirements for a wide range of clinical protocols and advanced reconstruction algorithms.

  19. Extensions to Dynamic System Simulation of Fissile Solution Systems

    SciTech Connect (OSTI)

    Klein, Steven Karl; Bernardin, John David; Kimpland, Robert Herbert; Spernjak, Dusan

    2015-08-24

    Previous reports have documented the results of applying dynamic system simulation (DSS) techniques to model a variety of fissile solution systems. The SUPO (Super Power) aqueous homogeneous reactor (AHR) was chosen as the benchmark for comparison of model results to experimental data for steadystate operation.1 Subsequently, DSS was applied to additional AHR to verify results obtained for SUPO and extend modeling to prompt critical excursions, ramp reactivity insertions of various magnitudes and rate, and boiling operations in SILENE and KEWB (Kinetic Experiment Water Boiler).2 Additional models for pressurized cores (HRE: Homogeneous Reactor Experiment), annular core geometries, and accelerator-driven subcritical systems (ADAHR) were developed and results reported.3 The focus of each of these models is core dynamics; neutron kinetics, thermal hydraulics, radiolytic gas generation and transport are coupled to examine the time-based evolution of these systems from start-up through transition to steady-state. A common characteristic of these models is the assumption that (a) core cooling system inlet temperature and flow and (b) plenum gas inlet pressure and flow are held constant; no external (to core) component operations that may result in dynamic change to these parameters are considered. This report discusses extension of models to include explicit reference to cooling structures and radiolytic gas handling. The accelerator-driven subcritical generic system model described in References 3 and 4 is used as a basis for this extension.

  20. Dynamic simulation models and performance of an OTEC power plant

    SciTech Connect (OSTI)

    Wormley, D.N.; Carmichael, D.A.; Umans, S.

    1983-08-01

    In this study, the aspects of plant performance which influence the potential for integration of an OTEC plant into a utility grid are considered. A set of simulation models have been developed for the evaluation of OTEC dynamic plant performance. A detailed nonlinear dynamic model has been forumlated which is useful for the assessment of component performance including heat exchangers, turbines, pumps and control systems. A reduced order linear model has been developed which is useful for studies of plant stability, control system development and transient performance of the plant connected to a utility grid. This model is particularly suitable for transient dynamic studies of an OTEC plant as a unit in a utility grid. A quasi-steady power availability model has also been developed which is useful to determine plant ouput power as a function of ocean thermal gradients so that the influence of daily and seasonal temperature variations may be easily computed. The study has found no fundamental technical barriers which would prohibit the interconnection of an OTEC plant into a utility grid. It has also shown that detailed consideration of turbine nozzle angle control is merited and such a control has the potential to provide superior performance in comparison to turbine bypass valve control.

  1. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    SciTech Connect (OSTI)

    Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki

    2015-08-17

    The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

  2. New Structural-Dynamics Module for Offshore Multimember Substructures within the Wind Turbine Computer-Aided Engineering Tool FAST: Preprint

    SciTech Connect (OSTI)

    Song, H.; Damiani, R.; Robertson, A.; Jonkman, J.

    2013-08-01

    FAST, developed by the National Renewable Energy Laboratory (NREL), is a computer-aided engineering (CAE) tool for aero-hydro-servo-elastic analysis of land-based and offshore wind turbines. This paper discusses recent upgrades made to FAST to enable loads simulations of offshore wind turbines with fixed-bottom, multimember support structures (e.g., jackets and tripods, which are commonly used in transitional-depth waters). The main theory and strategies for the implementation of the multimember substructure dynamics module (SubDyn) within the new FAST modularization framework are introduced. SubDyn relies on two main engineering schematizations: 1) a linear frame finite-element beam (LFEB) model and 2) a dynamics system reduction via Craig-Bampton's method. A jacket support structure and an offshore system consisting of a turbine atop a jacket substructure were simulated to test the SubDyn module and to preliminarily assess results against results from a commercial finite-element code.

  3. APEX - a Petri net process modeling tool built on a discrete-event simulation system

    SciTech Connect (OSTI)

    Gish, J.W.

    1996-12-31

    APEX, the Animated Process Experimentation tool, provides a capability for defining, simulating and animating process models. Primarily constructed for the modeling and analysis of software process models, we have found that APEX is much more broadly applicable and is suitable for process modeling tasks outside the domain of software processes. APEX has been constructed as a library of simulation blocks that implement timed hierarchical colored Petri Nets. These Petri Net blocks operate in conjunction with EXTEND, a general purpose continuous and discrete-event simulation tool. EXTEND provides a flexible, powerful and extensible environment with features particularly suitable for the modeling of complex processes. APEX`s Petri Net block additions to EXTEND provide an inexpensive capability with well-defined and easily understood semantics that is a powerful, easy to use, flexible means to engage in process modeling and evaluation. The vast majority of software process research has focused on the enactment of software processes. Little has been said about the actual creation and evaluation of software process models necessary to support enactment. APEX has been built by the Software Engineering Process Technology Project at GTE Laboratories which has been focusing on this neglected area of process model definition and analysis. We have constructed high-level software lifecycle models, a set of models that demonstrate differences between four levels of the SEI Capability Maturity Model (CMM), customer care process models, as well as models involving more traditional synchronization and coordination problems such as producer-consumer and 2-phase commit. APEX offers a unique blend of technology from two different disciplines: discrete-event simulation and Petri Net modeling. Petri Nets provide a well-defined and rich semantics in a simple, easy to understand notation. The simulation framework allows for execution, animation, and measurement of the resultant models.

  4. Assessment of Tools and Data for System-Level Dynamic Analyses

    SciTech Connect (OSTI)

    Steven J. Piet; Nick R. Soelberg

    2011-06-01

    The only fuel cycle for which dynamic analyses and assessments are not needed is the null fuel cycle - no nuclear power. For every other concept, dynamic analyses are needed and can influence relative desirability of options. Dynamic analyses show how a fuel cycle might work during transitions from today's partial fuel cycle to something more complete, impact of technology deployments, location of choke points, the key time lags, when benefits can manifest, and how well parts of fuel cycles work together. This report summarizes the readiness of existing Fuel Cycle Technology (FCT) tools and data for conducting dynamic analyses on the range of options. VISION is the primary dynamic analysis tool. Not only does it model mass flows, as do other dynamic system analysis models, but it allows users to explore various potential constraints. The only fuel cycle for which constraints are not important are those in concept advocates PowerPoint presentations; in contrast, comparative analyses of fuel cycles must address what constraints exist and how they could impact performance. The most immediate tool need is extending VISION to the thorium/U233 fuel cycle. Depending on further clarification of waste management strategies in general and for specific fuel cycle candidates, waste management sub-models in VISION may need enhancement, e.g., more on 'co-flows' of non-fuel materials, constraints in waste streams, or automatic classification of waste streams on the basis of user-specified rules. VISION originally had an economic sub-model. The economic calculations were deemed unnecessary in later versions so it was retired. Eventually, the program will need to restore and improve the economics sub-model of VISION to at least the cash flow stage and possibly to incorporating cost constraints and feedbacks. There are multiple sources of data that dynamic analyses can draw on. In this report, 'data' means experimental data, data from more detailed theoretical or empirical

  5. A Distributed Electrochemistry Modeling Tool for Simulating SOFC Performance and Degradation

    SciTech Connect (OSTI)

    Recknagle, Kurtis P.; Ryan, Emily M.; Khaleel, Mohammad A.

    2011-10-13

    This report presents a distributed electrochemistry (DEC) model capable of investigating the electrochemistry and local conditions with the SOFC MEA based on the local microstructure and multi-physics. The DEC model can calculate the global current-voltage (I-V) performance of the cell as determined by the spatially varying local conditions through the thickness of the electrodes and electrolyte. The simulation tool is able to investigate the electrochemical performance based on characteristics of the electrode microstructure, such as particle size, pore size, electrolyte and electrode phase volume fractions, and triple-phase-boundary length. It can also investigate performance as affected by fuel and oxidant gas flow distributions and other environmental/experimental conditions such as temperature and fuel gas composition. The long-term objective for the DEC modeling tool is to investigate factors that cause electrode degradation and the decay of SOFC performance which decrease longevity.

  6. Dynamic simulation of a direct carbonate fuel cell power plant

    SciTech Connect (OSTI)

    Ernest, J.B.; Ghezel-Ayagh, H.; Kush, A.K.

    1996-12-31

    Fuel Cell Engineering Corporation (FCE) is commercializing a 2.85 MW Direct carbonate Fuel Cell (DFC) power plant. The commercialization sequence has already progressed through construction and operation of the first commercial-scale DFC power plant on a U.S. electric utility, the 2 MW Santa Clara Demonstration Project (SCDP), and the completion of the early phases of a Commercial Plant design. A 400 kW fuel cell stack Test Facility is being built at Energy Research Corporation (ERC), FCE`s parent company, which will be capable of testing commercial-sized fuel cell stacks in an integrated plant configuration. Fluor Daniel, Inc. provided engineering, procurement, and construction services for SCDP and has jointly developed the Commercial Plant design with FCE, focusing on the balance-of-plant (BOP) equipment outside of the fuel cell modules. This paper provides a brief orientation to the dynamic simulation of a fuel cell power plant and the benefits offered.

  7. Beam dynamics simulations of the NML photoinjector at Fermilab

    SciTech Connect (OSTI)

    Piot, P.; Sun, Y.-E.; Church, M.; /Fermilab

    2010-08-01

    Fermilab is currently constructing a superconducting RF (SRF) test linear accelerator at the New Muon Lab (NML). Besides testing SRF accelerating modules for ILC and Project-X, NML will also eventually support a variety of advanced accelerator R&D experiments. The NML incorporates a 40 MeV photoinjector capable of providing electron bunches with variable parameters. The photoinjector is based on the 1+1/2 cell DESY-type gun followed by two superconducting cavities. It also includes a magnetic bunch compressor, a round-to-flat beam transformer and a low-energy experimental area for beam physics experiments and beam diagnostics R&D. In this paper, we explore, via beam dynamics simulations, the performance of the photoinjector for different operating scenarios.

  8. Relationship between nanocrystalline and amorphous microstructures by molecular dynamics simulation

    SciTech Connect (OSTI)

    Keblinski, P.; Phillpot, S.R.; Wolf, D.; Gleiter, H.

    1996-08-01

    A recent molecular dynamics simulation method for growth of fully dense nanocrystalline materials crystallized from melt was used with the Stillinger-Weber three-body potential to synthesize nanocrystalline Si with a grain size up to 75{Angstrom}. Structures of the highly constrained grain boundaries (GBs), triple lines, and point grain junctions were found to be highly disordered and similar to the structure of amorphous Si. These and earlier results for fcc metals suggest that a nanocrystalline microstructure may be viewed as a two-phase system, namely an ordered crystalline phase in the grain interiors connected by an amorphous, intergranular, glue-like phase. Analysis of the structures of bicrystalline GBs in the same materials reveals the presence of an amorphous intergranular equilibrium phase only in the high-energy but not the low-energy GBs, suggesting that only high-energy boundaries are present in nanocrystalline microstructures.

  9. Molecular dynamics simulation of annealed ZnO surfaces

    SciTech Connect (OSTI)

    Min, Tjun Kit; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    The effect of thermally annealing a slab of wurtzite ZnO, terminated by two surfaces, (0001) (which is oxygen-terminated) and (0001{sup ¯}) (which is Zn-terminated), is investigated via molecular dynamics simulation by using reactive force field (ReaxFF). We found that upon heating beyond a threshold temperature of ∼700 K, surface oxygen atoms begin to sublimate from the (0001) surface. The ratio of oxygen leaving the surface at a given temperature increases as the heating temperature increases. A range of phenomena occurring at the atomic level on the (0001) surface has also been explored, such as formation of oxygen dimers on the surface and evolution of partial charge distribution in the slab during the annealing process. It was found that the partial charge distribution as a function of the depth from the surface undergoes a qualitative change when the annealing temperature is above the threshold temperature.

  10. Molecular dynamics computer simulation of permeation in solids

    SciTech Connect (OSTI)

    Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M.

    1997-12-31

    In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.

  11. Molecular dynamics simulations of methane hydrate using polarizable force fields

    SciTech Connect (OSTI)

    Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

    2007-03-01

    Molecular dynamics simulations of methane hydrate have been carried out using the AMOEBA and COS/G2 polarizable force fields. Properties examined include the temperature dependence of the lattice constant, the OC and OO radial distribution functions and the vibrational spectra. Both the AMOEBA and COS/G2 models are found to successfully account for the available experimental data, with overall slightly better agreement with experiment being found for the AMOEBA model. Several properties calculated using the AMOEBA and COS/G2 models differ appreciable from the corresponding results obtained previously using the polarizable TIP4P-FQ model. This appears to be due to the inadequacy of the treatment of polarization, especially, the restriction of polarization to in-plane only, in the TIP4P-FQ model.

  12. Simulator for Wind Farm Applications

    Energy Science and Technology Software Center (OSTI)

    2012-01-06

    A modular tool for simulating wind plant aerodynamics with computational fluid dynamics and turbine structural and control response to the incoming flow.

  13. Enhanced molecular dynamics for simulating porous interphase layers in batteries.

    SciTech Connect (OSTI)

    Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan

    2009-10-01

    Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.

  14. Molecular Dynamics Simulation of Thermodynamic Properties in Uranium Dioxide

    SciTech Connect (OSTI)

    Wang, Xiangyu; Wu, Bin; Gao, Fei; Li, Xin; Sun, Xin; Khaleel, Mohammad A.; Akinlalu, Ademola V.; Liu, L.

    2014-03-01

    In the present study, we investigated the thermodynamic properties of uranium dioxide (UO2) by molecular dynamics (MD) simulations. As for solid UO2, the lattice parameter, density, and enthalpy obtained by MD simulations were in good agreement with existing experimental data and previous theoretical predictions. The calculated thermal conductivities matched the experiment results at the midtemperature range but were underestimated at very low and very high temperatures. The calculation results of mean square displacement represented the stability of uranium at all temperatures and the high mobility of oxygen toward 3000 K. By fitting the diffusivity constant of oxygen with the Vogel-Fulcher-Tamman law, we noticed a secondary phase transition near 2006.4 K, which can be identified as a strong to fragile supercooled liquid or glass phase transition in UO2. By fitting the oxygen diffusion constant with the Arrhenius equation, activation energies of 2.0 and 2.7 eV that we obtained were fairly close to the recommended values of 2.3 to 2.6 eV. Xiangyu Wang, Bin Wu, Fei Gao, Xin Li, Xin Sun, Mohammed A. Khaleel, Ademola V. Akinlalu and Li Liu

  15. Technical Highlight: NREL Evaluates the Thermal Performance of Uninsulated Walls to Improve the Accuracy of Building Energy Simulation Tools

    SciTech Connect (OSTI)

    Ridouane, E.H.

    2012-01-01

    This technical highlight describes NREL research to develop models of uninsulated wall assemblies that help to improve the accuracy of building energy simulation tools when modeling potential energy savings in older homes.

  16. Nucleation Rate Analysis of Methane Hydrate from Molecular Dynamics Simulations

    DOE PAGES-Beta [OSTI]

    Yuhara, Daisuke; Barnes, Brian C.; Suh, Donguk; Knott, Brandon C.; Beckham, Gregg T.; Yasuoka, Kenji; Wu, David T.; Amadeu K. Sum

    2015-01-06

    Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Moreover, various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP)more » methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates were calculated by MFPT and SP methods and are within 5%; the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.« less

  17. Direct Dynamics Simulation of Dissociation of the [CH3--I--OH...

    Office of Scientific and Technical Information (OSTI)

    Ion-Molecule Complex Citation Details In-Document Search Title: Direct Dynamics Simulation of Dissociation of the CH3--I--OH- Ion-Molecule Complex Direct dynamics ...

  18. Development of an object-oriented dynamics simulator for a LFR DEMO

    SciTech Connect (OSTI)

    Ponciroli, R.; Bortot, S.; Lorenzi, S.; Cammi, A.

    2012-07-01

    A control-oriented dynamics simulator for a Generation IV Lead-cooled Fast Reactor (LFR) demonstrator (DEMO) has been developed aimed at providing a flexible, simple and fast-running tool allowing to perform design-basis transient and stability analyses, and to lay the foundations for the study of the system control strategy. For such purposes, a model representing a compromise between accuracy and straightforwardness has been necessarily sought, and in this view an object-oriented approach based on the Modelica language has been adopted. The reactor primary and secondary systems have been implemented by assembling both component models already available in a specific thermal-hydraulic library, and ad hoc developed nuclear component models suitably modified according to the specific DEMO configuration. The resulting overall plant simulator, incorporating also the balance of plant, consists in the following essential parts: core, integrated steam generator/primary pump block, cold and hot legs, primary coolant cold pool, turbine, heat sink, secondary coolant pump. Afterwards, the reactor response to typical transient initiators has been investigated: feedwater mass flow rate and temperature enhancement, turbine admission valve coefficient variation, increase of primary coolant mass flow rate, and transient of overpower have been simulated; results have been compared with the outcomes of analogous analyses performed by employing a lumped-parameter DEMO plant model. (authors)

  19. The ArcSDE GIS Dynamic Population Model Tool for Savannah River Site Emergency Response

    SciTech Connect (OSTI)

    MCLANE, TRACY; JONES, DWIGHT

    2005-10-03

    The Savannah River Site (SRS) is a 310-square-mile Department of Energy site located near Aiken, South Carolina. With a workforce of over 10,000 employees and subcontractors, SRS emergency personnel must be able to respond to an emergency event in a timely and effective manner, in order to ensure the safety and security of the Site. Geographic Information Systems (GIS) provides the technology needed to give managers and emergency personnel the information they need to make quick and effective decisions. In the event of a site evacuation, knowing the number of on-site personnel to evacuate from a given area is an essential piece of information for emergency staff. SRS has developed a GIS Dynamic Population Model Tool to quickly communicate real-time information that summarizes employee populations by facility area and building and then generates dynamic maps that illustrate output statistics.

  20. Reservoir Modeling by Data Integration via Intermediate Spaces and Artificial Intelligence Tools in MPS Simulation Frameworks

    SciTech Connect (OSTI)

    Ahmadi, Rouhollah; Khamehchi, Ehsan

    2013-12-15

    Conditioning stochastic simulations are very important in many geostatistical applications that call for the introduction of nonlinear and multiple-point data in reservoir modeling. Here, a new methodology is proposed for the incorporation of different data types into multiple-point statistics (MPS) simulation frameworks. Unlike the previous techniques that call for an approximate forward model (filter) for integration of secondary data into geologically constructed models, the proposed approach develops an intermediate space where all the primary and secondary data are easily mapped onto. Definition of the intermediate space, as may be achieved via application of artificial intelligence tools like neural networks and fuzzy inference systems, eliminates the need for using filters as in previous techniques. The applicability of the proposed approach in conditioning MPS simulations to static and geologic data is verified by modeling a real example of discrete fracture networks using conventional well-log data. The training patterns are well reproduced in the realizations, while the model is also consistent with the map of secondary data.

  1. Learning environment simulator: a tool for local decision makers and first responders

    SciTech Connect (OSTI)

    Leclaire, Rene J; Hirsch, Gary B

    2009-01-01

    The National Infrastructure Simulation and Analysis Center (NISAC) has developed a prototype learning environment simulator (LES) based on the Critical Infrastructure Protection Decision Support System (CIPDSS) infrastructure and scenario models. The LES is designed to engage decision makers at the grass-roots level (local/city/state) to deepen their understanding of an evolving crisis, enhance their intuition and allow them to test their own strategies for events before they occur. An initial version is being developed, centered on a pandemic influenza outbreak and has been successfully tested with a group of hospital administrators and first responders. LES is not a predictive tool but rather a simulated environment allowing the user to experience the complexities of a crisis before it happens. Users can contrast various approaches to the crisis, competing with alternative strategies of their own or other participants. LES is designed to assist decision makers in making informed choices by functionally representing relevant scenarios before they occur, including impacts to critical infrastructures with their interdependencies, and estimating human health & safety and economic impacts. In this paper a brief overview of the underlying models are given followed by a description of the LES, its interface and usage and an overview of the experience testing LES with a group of hospital administrators and first responders. The paper concludes with a brief discussion of the work remaining to make LES operational.

  2. Large-Scale Condensed Matter and Fluid Dynamics Simulations in...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Simulations in Three Diverse Areas: Whole Brain Blood Flow Simulations PI Name: Peter ... blood flow behavior in the neighborhood of bifurcations and aneurysms within the brain. ...

  3. On theoretical issues of computer simulations sequential dynamical systems

    SciTech Connect (OSTI)

    Barrett, C.L.; Mortveit, H.S.; Reidys, C.M.

    1998-12-01

    The authors study a class of discrete dynamical systems that is motivated by the generic structure of simulations. The systems consist of the following data: (a) a finite graph Y with vertex set {l_brace}1,...,n{r_brace} where each vertex has a binary state, (b) functions F{sub i}:F{sub 2}{sup n} {r_arrow} F{sub 2}{sup n} and (c) an update ordering {pi}. The functions F{sub i} update the binary state of vertex i as a function of the state of vertex i and its Y-neighbors and leave the states of all other vertices fixed. The update ordering is a permutation of the Y-vertices. They derive a decomposition result, characterize invertible SDS and study fixed points. In particular they analyze how many different SDS that can be obtained by reordering a given multiset of update functions and give a criterion for when one can derive concentration results on this number. Finally, some specific SDS are investigated.

  4. HyPro: A Financial Tool for Simulating Hydrogen Infrastructure Development, Final Report

    SciTech Connect (OSTI)

    Brian D. James, Peter O. Schmidt, Julie Perez

    2008-12-01

    This report summarizes a multi-year Directed Technologies Inc. (DTI) project to study the build-out of hydrogen production facilities during the transition from gasoline internal combustion engine vehicle to hydrogen fuel cell vehicles. The primary objectives of the project are to develop an enhanced understanding of hydrogen production issues during the transition period (out to 2050) and to develop recommendations for the DOE on areas of further study. These objectives are achieved by conducting economic and scenario analysis to predict how industry would provide the hydrogen production, delivery and dispensing capabilities necessary to satisfy increased hydrogen demand. The primary tool used for the analysis is a custom created MatLab simulation tool entitled HyPro (short for Hydrogen Production). This report describes the calculation methodology used in HyPro, the baseline assumptions, the results of the baseline analysis and several corollary studies. The appendices of this report included a complete listing of model assumptions (capital costs, efficiencies, feedstock prices, delivery distances, etc.) and a step-by-step manual on the specific operation of the HyPro program. This study was made possible with funding from the U.S. Department of Energy (DOE).

  5. Development of a Groundwater Transport Simulation Tool for Remedial Process Optimization

    SciTech Connect (OSTI)

    Ivarson, Kristine A.; Hanson, James P.; Tonkin, M.; Miller, Charles W.; Baker, S.

    2015-01-14

    The groundwater remedy for hexavalent chromium at the Hanford Site includes operation of five large pump-and-treat systems along the Columbia River. The systems at the 100-HR-3 and 100-KR-4 groundwater operable units treat a total of about 9,840 liters per minute (2,600 gallons per minute) of groundwater to remove hexavalent chromium, and cover an area of nearly 26 square kilometers (10 square miles). The pump-and-treat systems result in large scale manipulation of groundwater flow direction, velocities, and most importantly, the contaminant plumes. Tracking of the plumes and predicting needed system modifications is part of the remedial process optimization, and is a continual process with the goal of reducing costs and shortening the timeframe to achieve the cleanup goals. While most of the initial system evaluations are conducted by assessing performance (e.g., reduction in contaminant concentration in groundwater and changes in inferred plume size), changes to the well field are often recommended. To determine the placement for new wells, well realignments, and modifications to pumping rates, it is important to be able to predict resultant plume changes. In smaller systems, it may be effective to make small scale changes periodically and adjust modifications based on groundwater monitoring results. Due to the expansive nature of the remediation systems at Hanford, however, additional tools were needed to predict the plume reactions to system changes. A computer simulation tool was developed to support pumping rate recommendations for optimization of large pump-and-treat groundwater remedy systems. This tool, called the Pumping Optimization Model, or POM, is based on a 1-layer derivation of a multi-layer contaminant transport model using MODFLOW and MT3D.

  6. Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments

    SciTech Connect (OSTI)

    Jin, Shuangshuang; Chen, Yousu; Wu, Di; Diao, Ruisheng; Huang, Zhenyu

    2015-12-09

    Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Message Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.

  7. The Quick Energy Simulation Tool (eQUEST) | Open Energy Information

    Open Energy Information (Open El) [EERE & EIA]

    search Tool Summary LAUNCH TOOL Name: eQUEST AgencyCompany Organization: James J. Hirsh & Associates Partner: Lawrence Berkeley National Laboratory (LBNL) Sector: Energy...

  8. Dynamic simulation of kinematic Stirling engines: Coupled and...

    Office of Scientific and Technical Information (OSTI)

    Subject: 42 ENGINEERING NOT INCLUDED IN OTHER CATEGORIES; STIRLING ENGINES; MATHEMATICAL MODELS; COMPUTERIZED SIMULATION; CALCULATION METHODS; COMPARATIVE EVALUATIONS; PRESSURE ...

  9. The Terascale Simulation Tools and Technologies Center Annual Report August 15, 2001-September 30, 2002

    SciTech Connect (OSTI)

    Glimm, J; Brown, D L; Freitag, L

    2002-09-30

    The overall goal of the TSTT Center is to enable the scientific community to more easily use modern high-order, adaptive, parallel mesh and discretization tools. To achieve this goal, we are following three distinct but related paths. The first is to work directly with a number of lead application teams (for the most part SciDAC-funded) to use such technologies in their application domains. The second is to create new technology that eases the use of such tools, not only for our designated application partners, but across a broad range of application areas that require mesh and discretization tools for scientific simulation. The main technology thrust is not to create new tools (although some of this will occur), but to create new capabilities that will allow the use of these tools interoperably. This very profound step can be compared to the shift from hand craftmanship to manufactured products with interchangable components which revolutionized the world economy one to two centuries ago. The third component of our efforts is to embed this work in a larger framework of related activities, each seeking a similar, and profound, change in the practice of computational science. To ensure the relevance of our work to the SciDAC program goals, we originally selected six application areas, and in each, one or more application projects and teams with which to work directly. One application collaboration which targeted the development of an adaptive mesh refinement capability for the oceanographic code POP was postponed and may be dropped due to unanticipated technical obstacles in the specific goal selected. One new application involving jet breakup for spray combustion was added. The initial job of establishing good working relations, agreement on a plan of action, and obtaining initial results was accomplished in all cases. In general, our work with the applications has been more difficult than anticipated, in spite of the experience of the TSTT team members in similar

  10. Experimental characterization of energetic material dynamics for multiphase blast simulation.

    SciTech Connect (OSTI)

    Beresh, Steven Jay; Wagner, Justin L.; Kearney, Sean Patrick; Wright, Elton K.; Baer, Melvin R.; Pruett, Brian Owen Matthew

    2011-09-01

    Currently there is a substantial lack of data for interactions of shock waves with particle fields having volume fractions residing between the dilute and granular regimes, which creates one of the largest sources of uncertainty in the simulation of energetic material detonation. To close this gap, a novel Multiphase Shock Tube has been constructed to drive a planar shock wave into a dense gas-solid field of particles. A nearly spatially isotropic field of particles is generated in the test section by a gravity-fed method that results in a spanwise curtain of spherical 100-micron particles having a volume fraction of about 19%. Interactions with incident shock Mach numbers of 1.66, 1.92, and 2.02 were achieved. High-speed schlieren imaging simultaneous with high-frequency wall pressure measurements are used to reveal the complex wave structure associated with the interaction. Following incident shock impingement, transmitted and reflected shocks are observed, which lead to differences in particle drag across the streamwise dimension of the curtain. Shortly thereafter, the particle field begins to propagate downstream and spread. For all three Mach numbers tested, the energy and momentum fluxes in the induced flow far downstream are reduced about 30-40% by the presence of the particle field. X-Ray diagnostics have been developed to penetrate the opacity of the flow, revealing the concentrations throughout the particle field as it expands and spreads downstream with time. Furthermore, an X-Ray particle tracking velocimetry diagnostic has been demonstrated to be feasible for this flow, which can be used to follow the trajectory of tracer particles seeded into the curtain. Additional experiments on single spherical particles accelerated behind an incident shock wave have shown that elevated particle drag coefficients can be attributed to increased compressibility rather than flow unsteadiness, clarifying confusing results from the historical database of shock tube

  11. Development of generalized mapping tools to improve implementation of data driven computer simulations (04-ERD-083)

    SciTech Connect (OSTI)

    Ramirez, A; Pasyanos, M; Franz, G A

    2004-09-17

    The Stochastic Engine (SE) is a data driven computer simulation tool for predicting the characteristics of complex systems. The SE integrates accurate simulators with the Monte Carlo Markov Chain (MCMC) approach (a stochastic inverse technique) to identify alternative models that are consistent with available data and ranks these alternatives according to their probabilities. Implementation of the SE is currently cumbersome owing to the need to customize the pre-processing and processing steps that are required for a specific application. This project widens the applicability of the Stochastic Engine by generalizing some aspects of the method (i.e. model-to-data transformation types, configuration, model representation). We have generalized several of the transformations that are necessary to match the observations to proposed models. These transformations are sufficiently general not to pertain to any single application. This approach provides a framework that increases the efficiency of the SE implementation. The overall goal is to reduce response time and make the approach as ''plug-and-play'' as possible, and will result in the rapid accumulation of new data types for a host of both earth science and non-earth science problems. When adapting the SE approach to a specific application, there are various pre-processing and processing steps that are typically needed to run a specific problem. Many of these steps are common to a wide variety of specific applications. Here we list and describe several data transformations that are common to a variety of subsurface inverse problems. A subset of these steps have been developed in a generalized form such that they could be used with little or no modifications in a wide variety of specific applications. This work was funded by the LDRD Program (tracking number 04-ERD-083).

  12. First Principals and Classical Molecular Dynamics Simulations of Solvated Benzene

    SciTech Connect (OSTI)

    Allesch, M; Lightstone, F; Schwegler, E; Galli, G

    2007-09-11

    We have performed extensive ab initio and classical MD simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that non-polarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.

  13. ParaDiS-FEM dislocation dynamics simulation code primer (Technical...

    Office of Scientific and Technical Information (OSTI)

    When we try to perform discrete dislocation dynamics simulations for finite systems such as thin films or cylinders, the ParaDiS code must be extended. First, dislocations need to ...

  14. Quantify Water Extraction by TBP/Dodecane via Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    Khomami, Bamin; Cui, Shengting; de Almeida, Valmor F.; Felker, Kevin

    2013-05-16

    The purpose of this project is to quantify the interfacial transport of water into the most prevalent nuclear reprocessing solvent extractant mixture, namely tri-butyl- phosphate (TBP) and dodecane, via massively parallel molecular dynamics simulations on the most powerful machines available for open research. Specifically, we will accomplish this objective by evolving the water/TBP/dodecane system up to 1 ms elapsed time, and validate the simulation results by direct comparison with experimentally measured water solubility in the organic phase. The significance of this effort is to demonstrate for the first time that the combination of emerging simulation tools and state-of-the-art supercomputers can provide quantitative information on par to experimental measurements for solvent extraction systems of relevance to the nuclear fuel cycle. Results: Initially, the isolated single component, and single phase systems were studied followed by the two-phase, multicomponent counterpart. Specifically, the systems we studied were: pure TBP; pure n-dodecane; TBP/n-dodecane mixture; and the complete extraction system: water-TBP/n-dodecane two phase system to gain deep insight into the water extraction process. We have completely achieved our goal of simulating the molecular extraction of water molecules into the TBP/n-dodecane mixture up to the saturation point, and obtained favorable comparison with experimental data. Many insights into fundamental molecular level processes and physics were obtained from the process. Most importantly, we found that the dipole moment of the extracting agent is crucially important in affecting the interface roughness and the extraction rate of water molecules into the organic phase. In addition, we have identified shortcomings in the existing OPLS-AA force field potential for long-chain alkanes. The significance of this force field is that it is supposed to be optimized for molecular liquid simulations. We found that it failed for dodecane and

  15. Dynamic simulation of the Hanford tank waste remediation system

    SciTech Connect (OSTI)

    Harmsen, R.W., Westinghouse Hanford

    1996-05-03

    Cleaning up and disposing of approximately 50 years of nuclear waste is the main mission at the U.S. Department of Energy`s Hanford Nuclear Reservation, located in the southeastern part of the state of Washington. A major element of the total cleanup effort involves retrieving, processing, and disposing of radioactive and hazardous waste stored in 177 underground storage tanks. This effort, referred to as the Tank Waste Remediation System (TWRS), is expected to cost billions of dollars and take approximately 25 years to complete. Several computer simulations of this project are being created, focusing on both programmatic and detailed engineering issues. This paper describes one such simulation activity, using the ithink(TM)computer simulation software. The ithink(TM) simulation includes a representation of the complete TWRS cleanup system, from retrieval of waste through intermediate processing and final vitrification of waste for disposal. Major issues addressed to date by the simulation effort include the need for new underground storage tanks to support TWRS activities, and the estimated design capacities for various processing facilities that are required to support legally mandated program commitment dates. This paper discusses how the simulation was used to investigate these questions.

  16. AMIP Simulation with the CAM4 Spectral Element Dynamical Core

    SciTech Connect (OSTI)

    Evans, Katherine J; Lauritzen, Peter; Mishra, Saroj; Neale, Rich; Taylor, Mark; Tribbia, Joe

    2013-01-01

    We evaluate the climate produced by the Community Earth System Model, version 1, running with the new spectral-element atmospheric dynamical core option. The spectral-element method is congured to use a cubed-sphere grid, providing quasi-uniform resolution over the sphere, increased parallel scalability and removing the need for polar filters. It uses a fourth order accurate spatial discretization which locally conserves mass and moist total energy. Using the Atmosphere Model Intercomparison Project protocol, we compare the results from the spectral-element dy- namical core with those produced by the default nite-volume dynamical core and with observations.

  17. Carbon atom, dimer and trimer chemistry on diamond surfaces from molecular dynamics simulations

    SciTech Connect (OSTI)

    Valone, S.M.

    1995-07-01

    Spectroscopic studies of various atmospheres appearing in diamond film synthesis suggest evidence for carbon atoms, dimers, or trimers. Molecular dynamics simulations with the Brenner hydrocarbon potential are being used to investigate the elementary reactions of these species on a hydrogen-terminated diamond (111) surface. In principle these types of simulations can be extended to simulations of growth morphologies, in the 1-2 monolayer regime presently.

  18. Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture

    SciTech Connect (OSTI)

    Feng, Wei; Xu, Luting; Li, Xin-Qi; Fang, Weihai; Yan, YiJing

    2014-07-15

    Mixed-quantum-classical molecular dynamics simulation implies an effective quantum measurement on the electronic states by the classical motion of atoms. Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.

  19. Development of Design and Simulation Tool for Hybrid Geothermal Heat Pump System

    Energy.gov [DOE]

    This project will expand Expand eQUEST, a building energy analysis software with latest implementation of DOE-2, for simulations of HGSHP systems and improve its existing simulation capabilities for ordinary GSHP systems.

  20. Dynamic simulation of a solar-driven carbon dioxide transcritical power system for small scale combined heat and power production

    SciTech Connect (OSTI)

    Chen, Y.; Lundqvist, Per; Pridasawas, Wimolsiri

    2010-07-15

    Carbon dioxide is an environmental benign natural working fluid and has been proposed as a working media for a solar-driven power system. In the current work, the dynamic performance of a small scale solar-driven carbon dioxide power system is analyzed by dynamic simulation tool TRNSYS 16 and Engineering Equation Solver (EES) using co-solving technique. Both daily performance and yearly performance of the proposed system have been simulated. Different system operating parameters, which will influence the system performance, have been discussed. Under the Swedish climatic condition, the maximum daily power production is about 12 kW h and the maximum monthly power production is about 215 kW h with the proposed system working conditions. Besides the power being produced, the system can also produce about 10 times much thermal energy, which can be used for space heating, domestic hot water supply or driving absorption chillers. The simulation results show that the proposed system is a promising and environmental benign alternative for conventional low-grade heat source utilization system. (author)

  1. Growth of bi- and tri-layered graphene on silicon carbide substrate via molecular dynamics simulation

    SciTech Connect (OSTI)

    Min, Tjun Kit; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    Molecular dynamics (MD) simulation with simulated annealing method is used to study the growth process of bi- and tri-layered graphene on a 6H-SiC (0001) substrate via molecular dynamics simulation. Tersoff-Albe-Erhart (TEA) potential is used to describe the inter-atomic interactions among the atoms in the system. The formation temperature, averaged carbon-carbon bond length, pair correlation function, binding energy and the distance between the graphene formed and the SiC substrate are quantified. The growth mechanism, graphitization of graphene on the SiC substrate and characteristics of the surface morphology of the graphene sheet obtained in our MD simulation compare well to that observed in epitaxially grown graphene experiments and other simulation works.

  2. A comparison of simulation models for predicting soil water dynamics in bare and vegetated lysimeters

    SciTech Connect (OSTI)

    Link, S.O.; Kickert, R.N.; Fayer, M.J.; Gee, G.W.

    1993-06-01

    This report describes the results of simulation models used to predict soil water storage dynamics at the Field Lysimeter Test Facility (FLTF) weighing lysimeters. The objectives of this research is to develop the capability to predict soil water storage dynamics with plants in support of water infiltration control studies for the Hanford Permanent Isolation Barrier Development Program. It is important to gain confidence in one`s ability to simulate soil water dynamics over long time periods to assess the barrier`s ability to prevent drainage. Two models were compared for their ability to simulate soil water storage dynamics with and without plants in weighing lysimeters, the soil water infiltration and movement (SWIM) and the simulation of production and utilization of rangelands (SPUR-91) models. These models adequately simulated soil water storage dynamics for the weighing lysimeters. The range of root mean square error values for the two models was 7.0 to 19.8. This compares well with the range reported by Fayer et al. (1992) for the bare soil data sets of 8.1 to 22.1. Future research will test the predictive capability of these models for longer term lysimeter data sets and for historical data sets collected in various plant community types.

  3. Hybrid Electro-Mechanical Simulation Tool for Wind Turbine Generators: Preprint

    SciTech Connect (OSTI)

    Singh, M.; Muljadi, E.; Jonkman, J.

    2013-05-01

    This paper describes the use of MATLAB/Simulink to simulate the electrical and grid-related aspects of a WTG and the FAST aero-elastic wind turbine code to simulate the aerodynamic and mechanical aspects of the WTG. The combination of the two enables studies involving both electrical and mechanical aspects of the WTG.

  4. NREL: Dynamic Maps, GIS Data, and Analysis Tools - Data Visualization &

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Geospatial Tools MapSearch Searching for maps has never been easier. A screen capture of the MapSearch Map view option Bookmark and Share Data Visualization & Geospatial Tools NREL's Geospatial Data Science Team has developed tools that allow users to apply these data. These tools help determine things such as how much electricity can be produced from solar systems on a house or what renewable resources are available in a specific areas. Please visit http://maps.nrel.gov/ for the most

  5. Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

    SciTech Connect (OSTI)

    Cawkwell, M. J. Niklasson, Anders M. N.; Dattelbaum, Dana M.

    2015-02-14

    The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

  6. Low Wind Speed Technology Phase II: Offshore Floating Wind Turbine Concepts: Fully Coupled Dynamic Response Simulations; Massachusetts Institute of Technology

    SciTech Connect (OSTI)

    Not Available

    2006-03-01

    This fact sheet describes a subcontract with Massachusetts Institute of Technology to study dynamic response simulations to evaluate floating platform concepts for offshore wind turbines.

  7. Simulation of injector dynamics during steady inductive helicity injection current drive in the HIT-SI experiment

    SciTech Connect (OSTI)

    Hansen, C.; Marklin, G.; Victor, B.; Akcay, C.; Jarboe, T.

    2015-04-15

    We present simulations of inductive helicity injection in the Helicity Injected Torus with Steady Inductive helicity injection (HIT-SI) device that treats the entire plasma volume in a single dynamic MHD model. A new fully 3D numerical tool, the PSI-center TETrahedral mesh code, was developed that provides the geometric flexibility required for this investigation. Implementation of a zero-? Hall MHD model using PSI-TET will be presented including formulation of a new self-consistent magnetic boundary condition for the wall of the HIT-SI device. Results from simulations of HIT-SI are presented focusing on injector dynamics that are investigated numerically for the first time. Asymmetries in the plasma loading between the two helicity injectors and progression of field reversal in each injector are observed. Analysis indicates cross-coupling between injectors through confinement volume structures. Injector impedance is found to scale with toroidal current at fixed density, consistent with experimental observation. Comparison to experimental data with an injector drive frequency of 14.5 kHz shows good agreement with magnetic diagnostics. Global mode structures from Bi-Orthogonal decomposition agree well with experimental data for the first four modes.

  8. Molecular dynamics simulations of soliton-like structures in a dusty plasma medium

    SciTech Connect (OSTI)

    Tiwari, Sanat Kumar Das, Amita; Sen, Abhijit; Kaw, Predhiman

    2015-03-15

    The existence and evolution of soliton-like structures in a dusty plasma medium are investigated in a first principles approach using molecular dynamic (MD) simulations of particles interacting via a Yukawa potential. These localized structures are found to exist in both weakly and strongly coupled regimes with their structures becoming sharper as the correlation effects between the dust particles get stronger. A surprising result, compared to fluid simulations, is the existence of rarefactive soliton-like structures in our non-dissipative system, a feature that arises from the charge conjugation symmetry property of the Yukawa fluid. Our simulation findings closely resemble many diverse experimental results reported in the past.

  9. NREL: Dynamic Maps, GIS Data, and Analysis Tools - MapSearch

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Bookmark and Share MapSearch MapSearch Logo is a computer monitor with a magnifying glass suspended in the air before it. Use our MapSearch tool to easily search our collection of maps created by the Geospatial Data Science Team. Please use the search box and the filters on the left of the screen to limit results. The tool is designed to work with NREL's OpenEI so users will have one site to search and view NREL created maps. If you have any feedback or comments on this tool, contact the

  10. Femtosecond photoelectron spectroscopy: a new tool for the study of anion dynamics

    SciTech Connect (OSTI)

    Greenblatt, B.J.

    1999-02-01

    A new experimental technique for the time-resolved study of anion reactions is presented. Using femtosecond laser pulses, which provide extremely fast ({approx} 100 fs) time resolution, in conjunction with photoelectron spectroscopy, which reveals differences between anion and neutral potential energy surfaces, a complex anion reaction can be followed from its inception through the formation of asymptotic products. Experimental data can be modeled quantitatively using established theoretical approaches, allowing for the refinement of potential energy surfaces as well as dynamical models. After a brief overview, a detailed account of the construction of the experimental apparatus is presented. Documentation of the data acquisition program is contained in the Appendix. The first experimental demonstration of the technique is then presented for I{sub 2}{sup -} photodissociation, modeled using a simulation program which is also detailed in the Appendix. The investigation of I{sub 2}{sup -} photodissociation in several size-selected I{sub 2}{sup -}(Ar){sub n} (n = 6-20) and I{sub 2}{sup -}(CO{sub 2}){sub n} (n = 4-16) clusters forms the heart of the dissertation. In a series of chapters, the numerous effects of solvation on this fundamental bond-breaking reaction are explored, the most notable of which is the recombination of I{sub 2}{sup -} on the ground {tilde X}({sup 2}{Sigma}{sub u}{sup +}) state in sufficiently large clusters. Recombination and trapping of I{sub 2}{sup -} on the excited {tilde A}({sup 2}{Pi}{sub 3/2,g}) state is also observed in both types of clusters. The studies have revealed electronic state transitions, the first step in recombination, on a {approx}500 fs to {approx}10 ps timescale. Accompanying the changes in electronic state is solvent reorganization, which occurs on a similar timescale. Over longer periods ({approx}1 ps to >200 ps), energy is transferred from vibrationally excite d I{sub 2}{sup -} to modes of the solvent, which in turn leads

  11. Impact of Resolution on Simulation of Closed Mesoscale Cellular Convection Identified by Dynamically Guided Watershed Segmentation

    SciTech Connect (OSTI)

    Martini, Matus; Gustafson, William I.; Yang, Qing; Xiao, Heng

    2014-11-27

    Organized mesoscale cellular convection (MCC) is a common feature of marine stratocumulus that forms in response to a balance between mesoscale dynamics and smaller scale processes such as cloud radiative cooling and microphysics. We use the Weather Research and Forecasting model with chemistry (WRF-Chem) and fully coupled cloud-aerosol interactions to simulate marine low clouds during the VOCALS-REx campaign over the southeast Pacific. A suite of experiments with 3- and 9-km grid spacing indicates resolution-dependent behavior. The simulations with finer grid spacing have smaller liquid water paths and cloud fractions, while cloud tops are higher. The observed diurnal cycle is reasonably well simulated. To isolate organized MCC characteristics we develop a new automated method, which uses a variation of the watershed segmentation technique that combines the detection of cloud boundaries with a test for coincident vertical velocity characteristics. This ensures that the detected cloud fields are dynamically consistent for closed MCC, the most common MCC type over the VOCALS-REx region. We demonstrate that the 3-km simulation is able to reproduce the scaling between horizontal cell size and boundary layer height seen in satellite observations. However, the 9-km simulation is unable to resolve smaller circulations corresponding to shallower boundary layers, instead producing invariant MCC horizontal scale for all simulated boundary layers depths. The results imply that climate models with grid spacing of roughly 3 km or smaller may be needed to properly simulate the MCC structure in the marine stratocumulus regions.

  12. Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

    DOE PAGES-Beta [OSTI]

    Gordiz, Kiarash; Singh, David J.; Henry, Asegun

    2015-01-29

    In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such asmore » first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.« less

  13. Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report ?? Phase I

    SciTech Connect (OSTI)

    Mark S. Schmalz

    2011-07-24

    Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G} for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient

  14. Recovery act. Development of design and simulation tool for hybrid geothermal heat pump system

    SciTech Connect (OSTI)

    Wang, Shaojie; Ellis, Dan

    2014-05-29

    The ground source heat pump (GSHP) system is one of the most energy efficient HVAC technologies in the current market. However, the heat imbalance may degrade the ability of the ground loop heat exchanger (GLHX) to absorb or reject heat. The hybrid GSHP system, which combines a geothermal well field with a supplemental boiler or cooling tower, can balance the loads imposed on the ground loop heat exchangers to minimize its size while retaining superior energy efficiency. This paper presents a recent simulation-based study with an intention to compare multiple common control strategies used in hybrid GSHP systems, including fixed setpoint, outside air reset, load reset, and wetbulb reset. A small office in Oklahoma City conditioned by a hybrid GSHP system was simulated with the latest version of eQUEST 3.7[1]. The simulation results reveal that the hybrid GSHP system has the excellent capability to meet the cooling and heating setpoints during the occupied hours, balance thermal loads on the ground loop, as well as improve the thermal comfort of the occupants with the undersized well field.

  15. Interplay between the structure and dynamics in liquid and undercooled boron: An ab initio molecular dynamics simulation study

    SciTech Connect (OSTI)

    Jakse, N.; Pasturel, A.

    2014-12-21

    In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.

  16. Atomistic Simulation of Nafion Membrane: 2. Dynamics of Water Molecules and Hydronium Ions

    SciTech Connect (OSTI)

    Devanathan, Ram; Venkatnathan, Arun; Dupuis, Michel

    2007-10-20

    We have performed a detailed and comprehensive analysis of the dynamics of water molecules and hydronium ions in hydrated Nafion using classical molecular dynamics simulations with the DREIDING force field. In addition to calculating diffusion coefficients as a function of hydration level, we have also determined mean residence time of H2O molecules and H3O+ ions in the first solvation shell of SO3- groups. The diffusion coefficient of H2O molecules increases with increasing hydration level and is in good agreement with experiment. The mean residence time of H2O molecules decreases with increasing membrane hydration from 1 ns at a low hydration level to 75 ps at the highest hydration level studied. These dynamical changes are related to the changes in membrane nanostructure reported in the first part of this work. Our results provide insights into slow proton dynamics observed in neutron scattering experiments and are consistent with the Gebel model of Nafion structure.

  17. A dynamic process model of a natural gas combined cycle -- Model development with startup and shutdown simulations

    SciTech Connect (OSTI)

    Liese, Eric; Zitney, Stephen E.

    2013-01-01

    Research in dynamic process simulation for integrated gasification combined cycles (IGCC) with carbon capture has been ongoing at the National Energy Technology Laboratory (NETL), culminating in a full operator training simulator (OTS) and immersive training simulator (ITS) for use in both operator training and research. A derivative work of the IGCC dynamic simulator has been a modification of the combined cycle section to more closely represent a typical natural gas fired combined cycle (NGCC). This paper describes the NGCC dynamic process model and highlights some of the simulator’s current capabilities through a particular startup and shutdown scenario.

  18. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

    SciTech Connect (OSTI)

    Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

    2014-12-01

    X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-?s MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that proteinsolvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

  19. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

    DOE PAGES-Beta [OSTI]

    Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

    2014-12-01

    X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less

  20. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

    SciTech Connect (OSTI)

    Zen, Andrea; Luo, Ye Mazzola, Guglielmo Sorella, Sandro; Guidoni, Leonardo

    2015-04-14

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

  1. A Micro-Grid Simulator Tool (SGridSim) using Effective Node-to-Node Complex Impedance (EN2NCI) Models

    SciTech Connect (OSTI)

    Udhay Ravishankar; Milos manic

    2013-08-01

    This paper presents a micro-grid simulator tool useful for implementing and testing multi-agent controllers (SGridSim). As a common engineering practice it is important to have a tool that simplifies the modeling of the salient features of a desired system. In electric micro-grids, these salient features are the voltage and power distributions within the micro-grid. Current simplified electric power grid simulator tools such as PowerWorld, PowerSim, Gridlab, etc, model only the power distribution features of a desired micro-grid. Other power grid simulators such as Simulink, Modelica, etc, use detailed modeling to accommodate the voltage distribution features. This paper presents a SGridSim micro-grid simulator tool that simplifies the modeling of both the voltage and power distribution features in a desired micro-grid. The SGridSim tool accomplishes this simplified modeling by using Effective Node-to-Node Complex Impedance (EN2NCI) models of components that typically make-up a micro-grid. The term EN2NCI models means that the impedance based components of a micro-grid are modeled as single impedances tied between their respective voltage nodes on the micro-grid. Hence the benefit of the presented SGridSim tool are 1) simulation of a micro-grid is performed strictly in the complex-domain; 2) faster simulation of a micro-grid by avoiding the simulation of detailed transients. An example micro-grid model was built using the SGridSim tool and tested to simulate both the voltage and power distribution features with a total absolute relative error of less than 6%.

  2. Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

    SciTech Connect (OSTI)

    Fogarty, Aoife C. Potestio, Raffaello Kremer, Kurt

    2015-05-21

    A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

  3. MHD SIMULATIONS OF ACTIVE GALACTIC NUCLEUS JETS IN A DYNAMIC GALAXY CLUSTER MEDIUM

    SciTech Connect (OSTI)

    Mendygral, P. J.; Jones, T. W.; Dolag, K.

    2012-05-10

    We present a pair of three-dimensional magnetohydrodynamical simulations of intermittent jets from a central active galactic nucleus (AGN) in a galaxy cluster extracted from a high-resolution cosmological simulation. The selected cluster was chosen as an apparently relatively relaxed system, not having undergone a major merger in almost 7 Gyr. Despite this characterization and history, the intracluster medium (ICM) contains quite active 'weather'. We explore the effects of this ICM weather on the morphological evolution of the AGN jets and lobes. The orientation of the jets is different in the two simulations so that they probe different aspects of the ICM structure and dynamics. We find that even for this cluster, which can be characterized as relaxed by an observational standard, the large-scale, bulk ICM motions can significantly distort the jets and lobes. Synthetic X-ray observations of the simulations show that the jets produce complex cavity systems, while synthetic radio observations reveal bending of the jets and lobes similar to wide-angle tail radio sources. The jets are cycled on and off with a 26 Myr period using a 50% duty cycle. This leads to morphological features similar to those in 'double-double' radio galaxies. While the jet and ICM magnetic fields are generally too weak in the simulations to play a major role in the dynamics, Maxwell stresses can still become locally significant.

  4. Evaporative cooling of microscopic water droplets in vacuo: Molecular dynamics simulations and kinetic gas theory

    DOE PAGES-Beta [OSTI]

    Schlesinger, Daniel; Sellberg, Jonas A.; Nilsson, Anders; Pettersson, Lars G. M.

    2016-03-22

    In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Lastly, our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics.

  5. Dielectric relaxation of ethylene carbonate and propylene carbonate from molecular dynamics simulations

    DOE PAGES-Beta [OSTI]

    Chaudhari, Mangesh I.; You, Xinli; Pratt, Lawrence R.; Rempe, Susan B.

    2015-11-24

    Ethylene carbonate (EC) and propylene carbonate (PC) are widely used solvents in lithium (Li)-ion batteries and supercapacitors. Ion dissolution and diffusion in those media are correlated with solvent dielectric responses. Here, we use all-atom molecular dynamics simulations of the pure solvents to calculate dielectric constants and relaxation times, and molecular mobilities. The computed results are compared with limited available experiments to assist more exhaustive studies of these important characteristics. As a result, the observed agreement is encouraging and provides guidance for further validation of force-field simulation models for EC and PC solvents.

  6. RAVEN as a tool for dynamic probabilistic risk assessment: Software overview

    SciTech Connect (OSTI)

    Alfonsi, A.; Rabiti, C.; Mandelli, D.; Cogliati, J. J.; Kinoshita, R. A.

    2013-07-01

    RAVEN is a software tool under development at the Idaho National Laboratory (INL) that acts as the control logic driver and post-processing tool for the newly developed Thermal-Hydraulic code RELAP-7. The scope of this paper is to show the software structure of RAVEN and its utilization in connection with RELAP-7. A short overview of the mathematical framework behind the code is presented along with its main capabilities such as on-line controlling/ monitoring and Monte-Carlo sampling. A demo of a Station Black Out PRA analysis of a simplified Pressurized Water Reactor (PWR) model is shown in order to demonstrate the Monte-Carlo and clustering capabilities. (authors)

  7. RAVEN AS A TOOL FOR DYNAMIC PROBABILISTIC RISK ASSESSMENT: SOFTWARE OVERVIEW

    SciTech Connect (OSTI)

    Alfonsi Andrea; Mandelli Diego; Rabiti Cristian; Joshua Cogliati; Robert Kinoshita

    2013-05-01

    RAVEN is a software tool under development at the Idaho National Laboratory (INL) that acts as the control logic driver and post-processing tool for the newly developed Thermo-Hydraylic code RELAP- 7. The scope of this paper is to show the software structure of RAVEN and its utilization in connection with RELAP-7. A short overview of the mathematical framework behind the code is presented along with its main capabilities such as on-line controlling/monitoring and Monte-Carlo sampling. A demo of a Station Black Out PRA analysis of a simplified Pressurized Water Reactor (PWR) model is shown in order to demonstrate the Monte-Carlo and clustering capabilities.

  8. Validation and verification of MCNP6 as a new simulation tool useful for medical applications

    SciTech Connect (OSTI)

    Mashnik, Stepan G

    2011-01-06

    MCNP6, the latest and most advanced LANL transport code, representing a merger of MCNP5 and MCNPX has been Validated and Verified (V&V) against different experimental data and results by other codes relevant to medical applications. In the present work, we V&V MCNP6 using mainly the latest modifications of the Cascade-Exciton Model (CEM) and of the Los Alamos version of the Quark-Gluon String Model (LAQGSM) event generators CEM03.02 and LAQGSM03.03. We found that MCNP6 describes well data of interest for medical applications measured on both thin and thick targets and agrees very well with similar results obtained with other codes; MCNP6 may be a very useful tool for medical applications We plan to make MCNP6 available to the public via RSICC at Oak Ridge in the middle of 2011 but we are allowed to provide it to friendly US Beta-users outside LANL already now.

  9. Dynamical consequences of a constraint on the Langevin thermostat in molecular cluster simulation

    SciTech Connect (OSTI)

    Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

    2014-11-17

    We investigate some unusual behaviour observed while performing molecular dynamics simulations with the DL_POLY_4.03 code. Under the standard Langevin thermostat, atoms appear to be thermalised to different temperatures, depending on their mass and on the total number of particles in the system. We find that an imposed constraint whereby no thermal noise acts on the centre of mass of the system is the cause of the unexpected behaviour. This is demonstrated by solving the stochastic dynamics for the constrained thermostat and comparing the results with simulation data. The effect of the constraint can be considerable for small systems with disparate masses. By removing the constraint the Langevin thermostat may be restored to its intended behaviour and this has been implemented as an option in DL_POLY_4.05. SMK was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

  10. Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

    SciTech Connect (OSTI)

    Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; Huang, Patrick; Lightstone, Felice C.

    2015-10-22

    Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholine catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.

  11. Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

    DOE PAGES-Beta [OSTI]

    Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; Huang, Patrick; Lightstone, Felice C.

    2015-10-22

    Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholinemore » catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.« less

  12. Dynamical properties of fractal networks: Scaling, numerical simulations, and physical realizations

    SciTech Connect (OSTI)

    Nakayama, T.; Yakubo, K. ); Orbach, R.L. )

    1994-04-01

    This article describes the advances that have been made over the past ten years on the problem of fracton excitations in fractal structures. The relevant systems to this subject are so numerous that focus is limited to a specific structure, the percolating network. Recent progress has followed three directions: scaling, numerical simulations, and experiment. In a happy coincidence, large-scale computations, especially those involving array processors, have become possible in recent years. Experimental techniques such as light- and neutron-scattering experiments have also been developed. Together, they form the basis for a review article useful as a guide to understanding these developments and for charting future research directions. In addition, new numerical simulation results for the dynamical properties of diluted antiferromagnets are presented and interpreted in terms of scaling arguments. The authors hope this article will bring the major advances and future issues facing this field into clearer focus, and will stimulate further research on the dynamical properties of random systems.

  13. A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor

    DOE PAGES-Beta [OSTI]

    Yang, L. H.; Brooks III, E. D.; Belak, J.

    1992-01-01

    A molecular dynamics algorithm for performing large-scale simulations using the Parallel C Preprocessor (PCP) programming paradigm on the BBN TC2000, a massively parallel computer, is discussed. The algorithm uses a linked-cell data structure to obtain the near neighbors of each atom as time evoles. Each processor is assigned to a geometric domain containing many subcells and the storage for that domain is private to the processor. Within this scheme, the interdomain (i.e., interprocessor) communication is minimized.

  14. Anion pairs in room temperature ionic liquids predicted by molecular dynamics simulation, verified by spectroscopic characterization

    SciTech Connect (OSTI)

    Schwenzer, Birgit; Kerisit, Sebastien N.; Vijayakumar, M.

    2014-01-01

    Molecular-level spectroscopic analyses of an aprotic and a protic room-temperature ionic liquid, BMIM OTf and BMIM HSO4, respectively, have been carried out with the aim of verifying molecular dynamics simulations that predict anion pair formation in these fluid structures. Fourier-transform infrared spectroscopy, Raman spectroscopy and nuclear magnetic resonance spectroscopy of various nuclei support the theoretically-determined average molecular arrangements.

  15. Dispersion curves from short-time molecular dynamics simulation. 1. Diatomic chain results

    SciTech Connect (OSTI)

    Noid, D.W.; Broocks, B.T.; Gray, S.K.; Marple, S.L.

    1988-06-16

    The multiple signal classification method (MUSIC) for frequency estimation is used to compute the frequency dispersion curves of a diatomic chain from the time-dependent structure factor. In this paper, the authors demonstrate that MUSIC can accurately determine the frequencies from very short time trajectories. MUSIC is also used to show how the frequencies can vary in time, i.e., along a trajectory. The method is ideally suited for analyzing molecular dynamics simulations of large systems.

  16. Insights into photodissociation dynamics of acetaldehyde from ab initio calculations and molecular dynamics simulations

    SciTech Connect (OSTI)

    Chen Shilu; Fang Weihai

    2009-08-07

    In the present paper we report a theoretical study on mechanistic photodissociation of acetaldehyde (CH{sub 3}CHO). Stationary structures for H{sub 2} and CO eliminations in the ground state (S{sub 0}) have been optimized with density functional theory method, which is followed by the intrinsic reaction coordinate and ab initio molecular dynamics calculations to confirm the elimination mechanism. Equilibrium geometries, transition states, and intersection structures for the C-C and C-H dissociations in excited states were determined by the complete-active-space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations were refined by performing the single-point calculations using the multireference configuration interaction method. Upon the low-energy irradiation of CH{sub 3}CHO (265 nm<{lambda}<318 nm), the T{sub 1} C-C bond fission following intersystem crossing from the S{sub 1} state is the predominant channel and the minor channel, the ground-state elimination to CH{sub 4}+CO after internal conversion (IC) from S{sub 1} to S{sub 0}, could not be excluded. With the photon energy increasing, another pathway of IC, achieved via an S{sub 1}/S{sub 0} intersection point resulting from the S{sub 1} C-C bond fission, becomes accessible and increases the yield of CH{sub 4}+CO.

  17. Benchmark of numerical tools simulating beam propagation and secondary particles in ITER NBI

    SciTech Connect (OSTI)

    Sartori, E. Veltri, P.; Serianni, G.; Dlougach, E.; Hemsworth, R.; Singh, M.

    2015-04-08

    Injection of high energy beams of neutral particles is a method for plasma heating in fusion devices. The ITER injector, and its prototype MITICA (Megavolt ITER Injector and Concept Advancement), are large extrapolations from existing devices: therefore numerical modeling is needed to set thermo-mechanical requirements for all beam-facing components. As the power and charge deposition originates from several sources (primary beam, co-accelerated electrons, and secondary production by beam-gas, beam-surface, and electron-surface interaction), the beam propagation along the beam line is simulated by comprehensive 3D models. This paper presents a comparative study between two codes: BTR has been used for several years in the design of the ITER HNB/DNB components; SAMANTHA code was independently developed and includes additional phenomena, such as secondary particles generated by collision of beam particles with the background gas. The code comparison is valuable in the perspective of the upcoming experimental operations, in order to prepare a reliable numerical support to the interpretation of experimental measurements in the beam test facilities. The power density map calculated on the Electrostatic Residual Ion Dump (ERID) is the chosen benchmark, as it depends on the electric and magnetic fields as well as on the evolution of the beam species via interaction with the gas. Finally the paper shows additional results provided by SAMANTHA, like the secondary electrons produced by volume processes accelerated by the ERID fringe-field towards the Cryopumps.

  18. Spin Dynamics Simulations of Multiple Echo Spacing Pulse Sequences in Grossly Inhomogeneous Fields

    SciTech Connect (OSTI)

    Heidler, R.; Bachman, H. N.; Johansen, Y.

    2008-12-05

    Pulse sequences with multiple lengths of echo spacings are used in oilfield NMR logging for diffusion-based NMR applications such as rock and fluid characterization. One specific implementation is the so-called diffusion editing sequence comprising two long echo spacings followed by a standard CPMG at a shorter echo spacing. The echoes in the CPMG portion contain signal from both the direct and stimulated echoes.Modern oilfield NMR logging tools are designed for continuous depth logging of earth formations by projecting both the static (B{sub 0}) and dynamic (B{sub 1}) fields into the formation. Both B{sub 0} and B{sub 1} profiles are grossly inhomogeneous which results in non-steady-state behavior in the early echoes. The spin dynamics effects present a challenge for processing the echo amplitudes to measure porosity (amplitude extrapolated to zero time) and attenuations for fluid or pore size characterization.In this work we describe a calculation of the spin dynamics of the diffusion editing sequence with two long echo spacings. The calculation takes into account full B{sub 1} and B{sub 0} field maps, and comparisons will be made for sensors and parameters typical of oilfield logging tools and environments.

  19. Dissipative particle dynamics simulation of dilute polymer solutions—Inertial effects and hydrodynamic interactions

    SciTech Connect (OSTI)

    Zhao, Tongyang; Wang, Xiaogong; Jiang, Lei; Larson, Ronald G.

    2014-07-01

    We examine the accuracy of dissipative particle dynamics (DPD) simulations of polymers in dilute solutions with hydrodynamic interaction (HI), at the theta point, modeled by setting the DPD conservative interaction between beads to zero. We compare the first normal-mode relaxation time extracted from the DPD simulations with theoretical predictions from a normal-mode analysis for theta chains. We characterize the influence of bead inertia within the coil by a ratio L{sub m}/R{sub g}, where L{sub m} is the ballistic distance over which bead inertia is lost, and R{sub g} is the radius of gyration of the polymer coil, while the HI strength per bead h* is determined by the ratio of bead hydrodynamic radius (r{sub H}) to the equilibrium spring length. We show how to adjust h* through the spring length and monomer mass, and how to optimize the accuracy of DPD for fixed h* by increasing the friction coefficient (γ ≥ 9) and by incorporating a nonlinear distance dependence into the frictional interaction. Even with this optimization, DPD simulations exhibit deviations of over 20% from the theoretical normal-mode predictions for high HI strength with h* ≥ 0.20, for chains with as many as 100 beads, which is a larger deviation than is found for Stochastic rotation dynamics simulations for similar chains lengths and values of h*.

  20. Spectral solver for multi-scale plasma physics simulations with dynamically adaptive number of moments

    SciTech Connect (OSTI)

    Vencels, Juris; Delzanno, Gian Luca; Johnson, Alec; Peng, Ivy Bo; Laure, Erwin; Markidis, Stefano

    2015-06-01

    A spectral method for kinetic plasma simulations based on the expansion of the velocity distribution function in a variable number of Hermite polynomials is presented. The method is based on a set of non-linear equations that is solved to determine the coefficients of the Hermite expansion satisfying the Vlasov and Poisson equations. In this paper, we first show that this technique combines the fluid and kinetic approaches into one framework. Second, we present an adaptive strategy to increase and decrease the number of Hermite functions dynamically during the simulation. The technique is applied to the Landau damping and two-stream instability test problems. Performance results show 21% and 47% saving of total simulation time in the Landau and two-stream instability test cases, respectively.

  1. Spectral solver for multi-scale plasma physics simulations with dynamically adaptive number of moments

    DOE PAGES-Beta [OSTI]

    Vencels, Juris; Delzanno, Gian Luca; Johnson, Alec; Peng, Ivy Bo; Laure, Erwin; Markidis, Stefano

    2015-06-01

    A spectral method for kinetic plasma simulations based on the expansion of the velocity distribution function in a variable number of Hermite polynomials is presented. The method is based on a set of non-linear equations that is solved to determine the coefficients of the Hermite expansion satisfying the Vlasov and Poisson equations. In this paper, we first show that this technique combines the fluid and kinetic approaches into one framework. Second, we present an adaptive strategy to increase and decrease the number of Hermite functions dynamically during the simulation. The technique is applied to the Landau damping and two-stream instabilitymore » test problems. Performance results show 21% and 47% saving of total simulation time in the Landau and two-stream instability test cases, respectively.« less

  2. Phantom-based experimental validation of computational fluid dynamics simulations on cerebral aneurysms

    SciTech Connect (OSTI)

    Sun Qi; Groth, Alexandra; Bertram, Matthias; Waechter, Irina; Bruijns, Tom; Hermans, Roel; Aach, Til

    2010-09-15

    Purpose: Recently, image-based computational fluid dynamics (CFD) simulation has been applied to investigate the hemodynamics inside human cerebral aneurysms. The knowledge of the computed three-dimensional flow fields is used for clinical risk assessment and treatment decision making. However, the reliability of the application specific CFD results has not been thoroughly validated yet. Methods: In this work, by exploiting a phantom aneurysm model, the authors therefore aim to prove the reliability of the CFD results obtained from simulations with sufficiently accurate input boundary conditions. To confirm the correlation between the CFD results and the reality, virtual angiograms are generated by the simulation pipeline and are quantitatively compared to the experimentally acquired angiograms. In addition, a parametric study has been carried out to systematically investigate the influence of the input parameters associated with the current measuring techniques on the flow patterns. Results: Qualitative and quantitative evaluations demonstrate good agreement between the simulated and the real flow dynamics. Discrepancies of less than 15% are found for the relative root mean square errors of time intensity curve comparisons from each selected characteristic position. The investigated input parameters show different influences on the simulation results, indicating the desired accuracy in the measurements. Conclusions: This study provides a comprehensive validation method of CFD simulation for reproducing the real flow field in the cerebral aneurysm phantom under well controlled conditions. The reliability of the CFD is well confirmed. Through the parametric study, it is possible to assess the degree of validity of the associated CFD model based on the parameter values and their estimated accuracy range.

  3. Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

    SciTech Connect (OSTI)

    Xie, Binbin; Liu, Lihong; Cui, Ganglong; Fang, Wei-Hai; Cao, Jun; Feng, Wei; Li, Xin-qi

    2015-11-21

    In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as the final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.

  4. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    Pan, Jianjun [University of South Florida, Tampa (USF)] [University of South Florida, Tampa (USF); Cheng, Xiaolin [ORNL] [ORNL; Monticelli, Luca [Institut National de la Sant et de la Recherche Mdicale (INSERM) and INTS, France] [Institut National de la Sant et de la Recherche Mdicale (INSERM) and INTS, France; Heberle, Frederick A [ORNL] [ORNL; Kucerka, Norbert [Atomic Energy of Canada Limited (AECL), Canadian Neutron Beam Centre (CNBC) and Comenius University,] [Atomic Energy of Canada Limited (AECL), Canadian Neutron Beam Centre (CNBC) and Comenius University,; Tieleman, D. Peter [University of Calgary, ALberta, Canada] [University of Calgary, ALberta, Canada; Katsaras, John [ORNL] [ORNL

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  5. SU-E-T-100: Designing a QA Tool for Enhance Dynamic Wedges Based On Dynalog Files

    SciTech Connect (OSTI)

    Yousuf, A; Hussain, A

    2014-06-01

    Purpose: A robust quality assurance (QA) program for computer controlled enhanced dynamic wedge (EDW) has been designed and tested. Calculations to perform such QA test is based upon the EDW dynamic log files generated during dose delivery. Methods: Varian record and verify system generates dynamic log (dynalog) files during dynamic dose delivery. The system generated dynalog files contain information such as date and time of treatment, energy, monitor units, wedge orientation, and type of treatment. It also contains the expected calculated segmented treatment tables (STT) and the actual delivered STT for the treatment delivery as a verification record. These files can be used to assess the integrity and precision of the treatment plan delivery. The plans were delivered with a 6 MV beam from a Varian linear accelerator. For available EDW angles (10°, 15°, 20°, 25°, 30°, 45°, and 60°) Varian STT values were used to manually calculate monitor units for each segment. It can also be used to calculate the EDW factors. Independent verification of fractional MUs per segment was performed against those generated from dynalog files. The EDW factors used to calculate MUs in TPS were dosimetrically verified in solid water phantom with semiflex chamber on central axis. Results: EDW factors were generated from the STT provided by Varian and verified against practical measurements. The measurements were in agreement of the order of 1 % to the calculated EDW data. Variation between the MUs per segment obtained from dynalog files and those manually calculated was found to be less than 2%. Conclusion: An efficient and easy tool to perform routine QA procedure of EDW is suggested. The method can be easily implemented in any institution without a need for expensive QA equipment. An error of the order of ≥2% can be easily detected.

  6. 1D GAS-DYNAMIC SIMULATION OF SHOCK-WAVE PROCESSES VIA INTERNET

    SciTech Connect (OSTI)

    Khishchenko, K. V.; Levashov, P. R.; Povarnitsyn, M. E.; Zakharenkov, A. S.

    2009-12-28

    We present a Web-interface for 1D simulation of different shock-wave experiments. The choosing of initial parameters, the modeling itself and output data treatment can be made directly via the Internet. The interface is based upon the expert system on shock-wave data and equations of state and contains both the Eulerian and Lagrangian Godunov hydrocodes. The availability of equations of state for a broad set of substances makes this system a useful tool for planning and interpretation of shock-wave experiments. As an example of simulation with the system, results of modeling of multistep shock loading of potassium between polytetrafluoroethylene and stainless steel plates are presented in comparison with experimental data from Shakhray et al.(2005).

  7. Dynamics Modeling and Loads Analysis of an Offshore Floating Wind Turbine

    SciTech Connect (OSTI)

    Jonkman, J. M.

    2007-12-01

    This report describes the development, verification, and application of a comprehensive simulation tool for modeling coupled dynamic responses of offshore floating wind turbines.

  8. Molecular dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

    SciTech Connect (OSTI)

    Tringe, J. W.; Ileri, N.; Levie, H. W.; Stroeve, P.; Ustach, V.; Faller, R.; Renaud, P.

    2015-08-01

    We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.

  9. Molecular dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

    DOE PAGES-Beta [OSTI]

    Tringe, J. W.; Ileri, N.; Levie, H. W.; Stroeve, P.; Ustach, V.; Faller, R.; Renaud, P.

    2015-08-01

    We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage.more » Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.« less

  10. Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

    SciTech Connect (OSTI)

    Varanasi, S. R. E-mail: guskova@ipfdd.de; John, A.; Guskova, O. A. E-mail: guskova@ipfdd.de; Sommer, J.-U.

    2015-06-14

    Fullerene C{sub 60} sub-colloidal particle with diameter ?1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C{sub 60} fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientational correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent moleculeswater retardationin the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the dangling OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some dry regions of C{sub 60} are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.

  11. Advanced time integration algorithms for dislocation dynamics simulations of work hardening

    DOE PAGES-Beta [OSTI]

    Sills, Ryan B.; Aghaei, Amin; Cai, Wei

    2016-04-25

    Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relativemore » to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.« less

  12. Integrated atomistic chemical imaging and reactive force field molecular dynamic simulations on silicon oxidation

    SciTech Connect (OSTI)

    Dumpala, Santoshrupa; Broderick, Scott R.; Rajan, Krishna; Khalilov, Umedjon; Neyts, Erik C.; Duin, Adri C. T. van; Provine, J; Howe, Roger T.

    2015-01-05

    In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO{sub 2} and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature.

  13. Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations

    SciTech Connect (OSTI)

    Mester, Zoltan; Panagiotopoulos, Athanassios Z.

    2015-01-28

    The mean ionic activity coefficients of aqueous NaCl solutions of varying concentrations at 298.15 K and 1 bar have been obtained from molecular dynamics simulations by gradually turning on the interactions of an ion pair inserted into the solution. Several common non-polarizable water and ion models have been used in the simulations. Gibbs-Duhem equation calculations of the thermodynamic activity of water are used to confirm the thermodynamic consistency of the mean ionic activity coefficients. While the majority of model combinations predict the correct trends in mean ionic activity coefficients, they overestimate their values at high salt concentrations. The solubility predictions also suffer from inaccuracies, with all models underpredicting the experimental values, some by large factors. These results point to the need for further ion and water model development.

  14. Translational diffusion of water inside hydrophobic carbon micropores studied by neutron spectroscopy and molecular dynamics simulation

    DOE PAGES-Beta [OSTI]

    Diallo, S. O.; Vlcek, L.; Mamontov, E.; Keum, J. K.; Chen, Jihua; Hayes, J. S.; Chialvo, A. A.

    2015-02-17

    When water molecules are confined to nanoscale spacings, such as in the nanometer-size pores of activated carbon fiber (ACF), their freezing point gets suppressed down to very low temperatures (~150 K), leading to a metastable liquid state with remarkable physical properties. Here we have investigated the ambient pressure diffusive dynamics of water in microporous Kynol ACF-10 (average pore size ~11.6 Å, with primarily slit-like pores) from temperature T = 280 K in its stable liquid state down to T = 230 K into the metastable supercooled phase. The observed characteristic relaxation times and diffusion coefficients are found to be, respectively, higher and lower than those in bulk water, indicating a slowing down of the water mobility with decreasing temperature. The observed temperature-dependent average relaxation time (more » $${{\\tau}}$$) when compared to previous findings indicate that it is the width of the slit pores-not their curvature-that primarily affects the dynamics of water for pore sizes larger than 10 Å. The experimental observations are compared to complementary molecular dynamics simulations of a model system, in which we studied the diffusion of water within the 11.6 Å gap of two parallel graphene sheets. We find generally a reasonable agreement between the observed and calculated relaxation times at the low momentum transfer Q (Q ≤ 0.9 Å-1). At high Q, however, where localized dynamics becomes relevant, this ideal system does not satisfactorily reproduce the measurements. Consequently, the simulations are compared to the experiments at low Q, where the two can be best reconciled. The best agreement is obtained for the diffusion parameter D associated with the hydrogen-site when a representative stretched exponential function, rather than the standard bimodal exponential model, is used to parametrize the self-correlation function I (Q,t).« less

  15. Molecular dynamics simulations of organic SIMS with Cu{sub n} (n=1-3) clusters

    SciTech Connect (OSTI)

    Townes, J. A.; White, A. K.; Krantzman, K. D.; Garrison, B. J.

    1999-06-10

    Molecular dynamics simulations have been performed to study the effect of cluster size on the emission yield and damage cross section in organic SIMS. A model system composed of a monolayer of biphenyl molecules on a Cu(001) substrate was bombarded with Cu{sub n} (n=1-3) projectiles at kinetic energies of 0.100 keV per atom. The yield increases with cluster size, but a nonlinear enhancement in yield is not observed. The yield-to-damage ratio, on the other hand, increases with the use of clusters, indicating that clusters have the potential to improve the sensitivity of SIMS.

  16. Use of Aria to simulate laser weld pool dynamics for neutron generator production.

    SciTech Connect (OSTI)

    Noble, David R.; Notz, Patrick K.; Martinez, Mario J.; Kraynik, Andrew Michael

    2007-09-01

    This report documents the results for the FY07 ASC Integrated Codes Level 2 Milestone number 2354. The description for this milestone is, 'Demonstrate level set free surface tracking capabilities in ARIA to simulate the dynamics of the formation and time evolution of a weld pool in laser welding applications for neutron generator production'. The specialized boundary conditions and material properties for the laser welding application were implemented and verified by comparison with existing, two-dimensional applications. Analyses of stationary spot welds and traveling line welds were performed and the accuracy of the three-dimensional (3D) level set algorithm is assessed by comparison with 3D moving mesh calculations.

  17. Molecular dynamics simulations of grain boundaries in thin nanocrystalline silicon films

    SciTech Connect (OSTI)

    Berman, G.P.; Doolen, G.D.; Mainieri, R.; Campbell, D.K.; Luchnikov, V.A. |

    1997-10-01

    Using molecular dynamics simulations, the grain boundaries in thin polycrystalline silicon films (considered as promising material for future nanoelectronic devices) are investigated. It is shown that in polysilicon film with randomly oriented grains the majority of grain boundaries are disordered. However, some grains with small mutual orientation differences can form extended crystalline patterns. The structure of the grain boundaries satisfies the thermodynamical criterion. The majority of atoms in the grain boundaries are tetrahedrally coordinated with the nearest neighbors, even though the grain boundaries are disordered. The grain boundary matter is characterized as an amorphous phase with a characteristic tetragonality value.

  18. Simulations of fluorescence solvatochromism in substituted PPV oligomers from excited state molecular dynamics with implicit solvent

    SciTech Connect (OSTI)

    Bjorgaard, J. A.; Nelson, T.; Kalinin, K.; Kuzmenko, V.; Velizhanin, K. A.; Tretiak, S.

    2015-04-28

    In this study, an efficient method of treating solvent effects in excited state molecular dynamics (ESMD) is implemented and tested by exploring the solvatochromic effects in substituted p-phenylene vinylene oligomers. A continuum solvent model is used which has very little computational overhead. This allows simulations of ESMD with solvent effects on the scale of hundreds of picoseconds for systems of up to hundreds of atoms. At these time scales, solvatochromic shifts in fluoresence spectra can be described. Solvatochromic shifts in absorption and fluorescence spectra from ESMD are compared with time-dependent density functional theory calculations and experiments.

  19. A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

    SciTech Connect (OSTI)

    Shimojo, Fuyuki; Hattori, Shinnosuke; Department of Physics, Kumamoto University, Kumamoto 860-8555 ; Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya; Kunaseth, Manaschai; National Nanotechnology Center, Pathumthani 12120 ; Ohmura, Satoshi; Department of Physics, Kumamoto University, Kumamoto 860-8555; Department of Physics, Kyoto University, Kyoto 606-8502 ; Shimamura, Kohei; Department of Physics, Kumamoto University, Kumamoto 860-8555; Department of Applied Quantum Physics and Nuclear Engineering, Kyushu University, Fukuoka 819-0395

    2014-05-14

    We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of

  20. Molecular Dynamics Simulations of Displacement Cascades in Single and Polycrystalline Zirconia

    SciTech Connect (OSTI)

    Du Jincheng

    2009-03-10

    Displacement cascades in zirconia have been studied using classical molecular dynamics simulations. Polycrystalline zirconia with nano-meter grains were created using Voronoi polyhedra construction and studied in comparison with single crystalline zirconia. The results show that displacement cascades with similar kinetic energy generated larger number of displaced atoms in polycrystalline than in the single crystal structure. The fraction of atoms with coordination number change was also higher in polycrystalline zirconia that was explained to be due to the diffusion of oxygen and relaxation at grain boundaries.

  1. Integrated Simulation Development and Decision Support Tool-Set for Utility Market and Distributed Solar Power Generation Electricore, Inc.

    SciTech Connect (OSTI)

    Daye, Tony

    2013-09-30

    This project will enable utilities to develop long-term strategic plans that integrate high levels of renewable energy generation, and to better plan power system operations under high renewable penetration. The program developed forecast data streams for decision support and effective integration of centralized and distributed solar power generation in utility operations. This toolset focused on real time simulation of distributed power generation within utility grids with the emphasis on potential applications in day ahead (market) and real time (reliability) utility operations. The project team developed and demonstrated methodologies for quantifying the impact of distributed solar generation on core utility operations, identified protocols for internal data communication requirements, and worked with utility personnel to adapt the new distributed generation (DG) forecasts seamlessly within existing Load and Generation procedures through a sophisticated DMS. This project supported the objectives of the SunShot Initiative and SUNRISE by enabling core utility operations to enhance their simulation capability to analyze and prepare for the impacts of high penetrations of solar on the power grid. The impact of high penetration solar PV on utility operations is not only limited to control centers, but across many core operations. Benefits of an enhanced DMS using state-of-the-art solar forecast data were demonstrated within this project and have had an immediate direct operational cost savings for Energy Marketing for Day Ahead generation commitments, Real Time Operations, Load Forecasting (at an aggregate system level for Day Ahead), Demand Response, Long term Planning (asset management), Distribution Operations, and core ancillary services as required for balancing and reliability. This provided power system operators with the necessary tools and processes to operate the grid in a reliable manner under high renewable penetration.

  2. Inter-cage dynamics in structure I, II, and H fluoromethane hydrates as studied by NMR and molecular dynamics simulations

    SciTech Connect (OSTI)

    Trueba, Alondra Torres; Kroon, Maaike C.; Peters, Cor J.; Moudrakovski, Igor L.; Ratcliffe, Christopher I.; Ripmeester, John A.; Alavi, Saman

    2014-06-07

    Prospective industrial applications of clathrate hydrates as materials for gas separation require further knowledge of cavity distortion, cavity selectivity, and defects induction by guest-host interactions. The results presented in this contribution show that under certain temperature conditions the guest combination of CH{sub 3}F and a large polar molecule induces defects on the clathrate hydrate framework that allow intercage guest dynamics. {sup 13}C NMR chemical shifts of a CH{sub 3}F/CH{sub 4}/TBME sH hydrate and a temperature analysis of the {sup 2}H NMR powder lineshapes of a CD{sub 3}F/THF sII and CD{sub 3}F/TBME sH hydrate, displayed evidence that the populations of CH{sub 4} and CH{sub 3}F in the D and D{sup ?} cages were in a state of rapid exchange. A hydrogen bonding analysis using molecular dynamics simulations on the TBME/CH{sub 3}F and TBME/CH{sub 4} sH hydrates showed that the presence of CH{sub 3}F enhances the hydrogen bonding probability of the TBME molecule with the water molecules of the cavity. Similar results were obtained for THF/CH{sub 3}F and THF/CH{sub 4} sII hydrates. The enhanced hydrogen bond formation leads to the formation of defects in the water hydrogen bonding lattice and this can enhance the migration of CH{sub 3}F molecules between adjacent small cages.

  3. Simulation and dynamics of entropy-driven, molecular self-assembly processes

    SciTech Connect (OSTI)

    Mayer, B.; Kohler, G.,; Rasmussen, S.,

    1997-04-01

    Molecular self-assembly is frequently found to generate higher-order functional structures in biochemical systems. One such example is the self-assembly of lipids in aqueous solution forming membranes, micelles, and vesicles; another is the dynamic formation and rearrangement of the cytoskeleton. These processes are often driven by local, short-range forces and therefore the dynamics is solely based on local interactions. In this paper, we introduce a cellular automata based simulation, the lattice molecular automaton, in which data structures, representing different molecular entities such as water and hydrophilic and hydrophobic monomers, share locally propagated force information on a hexagonal, two-dimensional lattice. The purpose of this level of description is the simulation of entropic and enthalpic flows in a microcanonical, molecular ensemble to gain insight about entropy-driven processes in molecular many-particle systems. Three applications are shown, i.e., modeling structural features of a polar solvent, cluster formation of hydrophobic monomers in a polar environment, and the self-assembly of polymers. Processes leading to phase separation on a molecular level are discussed. A thorough discussion of the computational details, advantages, and limitations of the lattice molecular automaton approach is given elsewhere [B. Mayer and S. Rasmussen (unpublished)]. {copyright} {ital 1997} {ital The American Physical Society}

  4. Study on the thermal resistance in secondary particles chain of silica aerogel by molecular dynamics simulation

    SciTech Connect (OSTI)

    Liu, M. [Institute of Engineering Thermophysics, Chinese Academy of Sciences, Beijing100190 (China); Department of Physics, University of Chinese Academy of Sciences, Beijing 100049 (China); Qiu, L., E-mail: qiulin111@sina.com, E-mail: jzzhengxinghua@163.com; Zheng, X. H., E-mail: qiulin111@sina.com, E-mail: jzzhengxinghua@163.com; Zhu, J.; Tang, D. W. [Institute of Engineering Thermophysics, Chinese Academy of Sciences, Beijing100190 (China)

    2014-09-07

    In this article, molecular dynamics simulation was performed to study the heat transport in secondary particles chain of silica aerogel. The two adjacent particles as the basic heat transport unit were modelled to characterize the heat transfer through the calculation of thermal resistance and vibrational density of states (VDOS). The total thermal resistance of two contact particles was predicted by non-equilibrium molecular dynamics simulations (NEMD). The defects were formed by deleting atoms in the system randomly first and performing heating and quenching process afterwards to achieve the DLCA (diffusive limited cluster-cluster aggregation) process. This kind of treatment showed a very reasonable prediction of thermal conductivity for the silica aerogels compared with the experimental values. The heat transport was great suppressed as the contact length increased or defect concentration increased. The constrain effect of heat transport was much significant when contact length fraction was in the small range (<0.5) or the defect concentration is in the high range (>0.5). Also, as the contact length increased, the role of joint thermal resistance played in the constraint of heat transport was increasing. However, the defect concentration did not affect the share of joint thermal resistance as the contact length did. VDOS of the system was calculated by numerical method to characterize the heat transport from atomic vibration view. The smaller contact length and greater defect concentration primarily affected the longitudinal acoustic modes, which ultimately influenced the heat transport between the adjacent particles.

  5. A model of lipid-free Apolipoprotein A-I revealed by iterative molecular dynamics simulation

    SciTech Connect (OSTI)

    Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli

    2015-03-20

    Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore, by integrating various experimental results, we proposed a new structural model for lipidfree apo A-I, which contains a bundled four-helix N-terminal domain (1–192) that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193–243). This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.

  6. A model of lipid-free Apolipoprotein A-I revealed by iterative molecular dynamics simulation

    DOE PAGES-Beta [OSTI]

    Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli

    2015-03-20

    Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore,more » by integrating various experimental results, we proposed a new structural model for lipidfree apo A-I, which contains a bundled four-helix N-terminal domain (1–192) that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193–243). This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.« less

  7. Molecular simulation study of dynamical properties of room temperature ionic liquids with carbon pieces

    DOE PAGES-Beta [OSTI]

    Feng, Guang; Zhao, Wei; Cummings, Peter T.; Li, Song

    2016-03-29

    Room temperature ionic liquids (RTILs) with dispersed carbon pieces exhibit distinctive physiochemical properties. In order to explore the molecular mechanism, RTILs/carbon pieces mixture we investigated it by molecular dynamics (MD) simulation in this work. Rigid and flexible carbon pieces in the form of graphene with different thicknesses and carbon nanotubes in different sizes were dispersed in a representative RTIL 1-butyl-3-methyl-imidazolium dicyanamide ([Bmim][DCA]). Our study demonstrated that the diffusion coefficients of RTILs in the presence of flexible carbons are similar to those of bulk RTILs at varying temperatures, which is in contrast to the decreased diffusion of RTILs in the presencemore » of rigid carbons. In addition, interfacial ion number density at rigid carbon surfaces was higher than that at flexible ones, which is correlated with the accessible external surface area of carbon pieces. The life time of cation-anion pair in the presence of carbon pieces also exhibited a dependence on carbon flexibility. RTILs with dispersed rigid carbon pieces showed longer ion pair life time than those with flexible ones, in consistence with the observation in diffusion coefficients. Furthermore, this work highlights the necessity of including the carbon flexibility when performing MD simulation of RTILs in the presence of dispersed carbon pieces in order to obtain the reliable dynamical and interfacial structural properties.« less

  8. High Resolution Simulation of Beam Dynamics in Electron Linacs for Free Electron Lasers

    SciTech Connect (OSTI)

    Ryne, R.D.; Venturini, M.; Zholents, A.A.; Qiang, J.

    2009-01-05

    In this paper we report on large scale multi-physics simulation of beam dynamics in electron linacs for next generation free electron lasers (FELs). We describe key features of a parallel macroparticle simulation code including three-dimensional (3D) space-charge effects, short-range structure wake fields, longitudinal coherent synchrotron radiation (CSR) wake fields, and treatment of radiofrequency (RF) accelerating cavities using maps obtained from axial field profiles. A macroparticle up-sampling scheme is described that reduces the shot noise from an initial distribution with a smaller number of macroparticles while maintaining the global properties of the original distribution. We present a study of the microbunching instability which is a critical issue for future FELs due to its impact on beam quality at the end of the linac. Using parameters of a planned FEL linac at Lawrence Berkeley National Laboratory (LBNL), we show that a large number of macroparticles (beyond 100 million) is needed to control numerical shot noise that drives the microbunching instability. We also explore the effect of the longitudinal grid on simulation results. We show that acceptable results are obtained with around 2048 longitudinal grid points, and we discuss this in view of the spectral growth rate predicted from linear theory. As an application, we present results from simulations using one billion macroparticles of the FEL linac under design at LBNL. We show that the final uncorrelated energy spread of the beam depends not only on the initial uncorrelated energy spread but also depends strongly on the shape of the initial current profile. By using a parabolic initial current profile, 5 keV initial uncorrelated energy spread at 40 MeV injection energy, and improved linac design, those simulations demonstrate that a reasonable beam quality can be achieved at the end of the linac, with the final distribution having about 100 keV energy spread, 2.4 GeV energy, and 1.2 kA peak

  9. Modified Baryonic Dynamics: two-component cosmological simulations with light sterile neutrinos

    SciTech Connect (OSTI)

    Angus, G.W.; Gentile, G.; Diaferio, A.; Famaey, B.; Heyden, K.J. van der E-mail: diaferio@ph.unito.it E-mail: gianfranco.gentile@ugent.be

    2014-10-01

    In this article we continue to test cosmological models centred on Modified Newtonian Dynamics (MOND) with light sterile neutrinos, which could in principle be a way to solve the fine-tuning problems of the standard model on galaxy scales while preserving successful predictions on larger scales. Due to previous failures of the simple MOND cosmological model, here we test a speculative model where the modified gravitational field is produced only by the baryons and the sterile neutrinos produce a purely Newtonian field (hence Modified Baryonic Dynamics). We use two-component cosmological simulations to separate the baryonic N-body particles from the sterile neutrino ones. The premise is to attenuate the over-production of massive galaxy cluster halos which were prevalent in the original MOND plus light sterile neutrinos scenario. Theoretical issues with such a formulation notwithstanding, the Modified Baryonic Dynamics model fails to produce the correct amplitude for the galaxy cluster mass function for any reasonable value of the primordial power spectrum normalisation.

  10. Modifications to WRFs dynamical core to improve the treatment of moisture for large-eddy simulations

    SciTech Connect (OSTI)

    Xiao, Heng; Endo, Satoshi; Wong, May; Skamarock, William C.; Klemp, Joseph B.; Fast, Jerome D.; Gustafson, Jr., William I.; Vogelmann, Andrew; Wang, Hailong; Liu, Yangang; Lin, Wuyin

    2015-10-29

    Yamaguchi and Feingold (2012) note that the cloud fields in their large-eddy simulations (LESs) of marine stratocumulus using the Weather Research and Forecasting (WRF) model exhibit a strong sensitivity to time stepping choices. In this study, we reproduce and analyze this sensitivity issue using two stratocumulus cases, one marine and one continental. Results show that (1) the sensitivity is associated with spurious motions near the moisture jump between the boundary layer and the free atmosphere, and (2) these spurious motions appear to arise from neglecting small variations in water vapor mixing ratio (qv) in the pressure gradient calculation in the acoustic sub-stepping portion of the integration procedure. We show that this issue is remedied in the WRF dynamical core by replacing the prognostic equation for the potential temperature θ with one for the moist potential temperature θm=θ(1+1.61qv), which allows consistent treatment of moisture in the calculation of pressure during the acoustic sub-steps. With this modification, the spurious motions and the sensitivity to the time stepping settings (i.e., the dynamic time step length and number of acoustic sub-steps) are eliminated in both of the example stratocumulus cases. In conclusion, this modification improves the applicability of WRF for LES applications, and possibly other models using similar dynamical core formulations, and also permits the use of longer time steps than in the original code.

  11. Modifications to WRFs dynamical core to improve the treatment of moisture for large-eddy simulations

    DOE PAGES-Beta [OSTI]

    Xiao, Heng; Endo, Satoshi; Wong, May; Skamarock, William C.; Klemp, Joseph B.; Fast, Jerome D.; Gustafson, Jr., William I.; Vogelmann, Andrew; Wang, Hailong; Liu, Yangang; et al

    2015-10-29

    Yamaguchi and Feingold (2012) note that the cloud fields in their large-eddy simulations (LESs) of marine stratocumulus using the Weather Research and Forecasting (WRF) model exhibit a strong sensitivity to time stepping choices. In this study, we reproduce and analyze this sensitivity issue using two stratocumulus cases, one marine and one continental. Results show that (1) the sensitivity is associated with spurious motions near the moisture jump between the boundary layer and the free atmosphere, and (2) these spurious motions appear to arise from neglecting small variations in water vapor mixing ratio (qv) in the pressure gradient calculation in themore » acoustic sub-stepping portion of the integration procedure. We show that this issue is remedied in the WRF dynamical core by replacing the prognostic equation for the potential temperature θ with one for the moist potential temperature θm=θ(1+1.61qv), which allows consistent treatment of moisture in the calculation of pressure during the acoustic sub-steps. With this modification, the spurious motions and the sensitivity to the time stepping settings (i.e., the dynamic time step length and number of acoustic sub-steps) are eliminated in both of the example stratocumulus cases. In conclusion, this modification improves the applicability of WRF for LES applications, and possibly other models using similar dynamical core formulations, and also permits the use of longer time steps than in the original code.« less

  12. Molecular Dynamics Simulation and Analysis of Interfacial Water at Selected Sulfide Mineral Surfaces under Anaerobic Conditions

    SciTech Connect (OSTI)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.

    2014-04-10

    In this paper, we report on a molecular dynamics simulation (MDS) study of the behavior of interfacial water at selected sulfide mineral surfaces under anaerobic conditions. The study revealed the interfacial water structure and wetting characteristics of the pyrite (100) surface, galena (100) surface, chalcopyrite (012) surface, sphalerite (110) surface, and molybdenite surfaces (i.e., the face, armchair-edge, and zigzag-edge surfaces), including simulated contact angles, relative number density profiles, water dipole orientations, hydrogen-bonding, and residence times. For force fields of the metal and sulfur atoms in selected sulfide minerals used in the MDS, we used the universal force field (UFF) and another set of force fields optimized by quantum chemical calculations for interactions with interfacial water molecules at selected sulfide mineral surfaces. Simulation results for the structural and dynamic properties of interfacial water molecules indicate the natural hydrophobic character for the selected sulfide mineral surfaces under anaerobic conditions as well as the relatively weak hydrophobicity for the sphalerite (110) surface and two molybdenite edge surfaces. Part of the financial support for this study was provided by the U.S. Department of Energy (DOE) under Basic Science Grant No. DE-FG-03-93ER14315. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE, funded work performed by Liem X. Dang. Battelle operates Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES. The authors are grateful to Professor Tsun-Mei Chang for valuable discussions.

  13. High-rate Plastic Deformation of Nanocrystalline Tantalum to Large Strains: Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Rudd, R E

    2009-02-05

    Recent advances in the ability to generate extremes of pressure and temperature in dynamic experiments and to probe the response of materials has motivated the need for special materials optimized for those conditions as well as a need for a much deeper understanding of the behavior of materials subjected to high pressure and/or temperature. Of particular importance is the understanding of rate effects at the extremely high rates encountered in those experiments, especially with the next generation of laser drives such as at the National Ignition Facility. Here we use large-scale molecular dynamics (MD) simulations of the high-rate deformation of nanocrystalline tantalum to investigate the processes associated with plastic deformation for strains up to 100%. We use initial atomic configurations that were produced through simulations of solidification in the work of Streitz et al [Phys. Rev. Lett. 96, (2006) 225701]. These 3D polycrystalline systems have typical grain sizes of 10-20 nm. We also study a rapidly quenched liquid (amorphous solid) tantalum. We apply a constant volume (isochoric), constant temperature (isothermal) shear deformation over a range of strain rates, and compute the resulting stress-strain curves to large strains for both uniaxial and biaxial compression. We study the rate dependence and identify plastic deformation mechanisms. The identification of the mechanisms is facilitated through a novel technique that computes the local grain orientation, returning it as a quaternion for each atom. This analysis technique is robust and fast, and has been used to compute the orientations on the fly during our parallel MD simulations on supercomputers. We find both dislocation and twinning processes are important, and they interact in the weak strain hardening in these extremely fine-grained microstructures.

  14. Simulation of spray drying in superheated steam using computational fluid dynamics

    SciTech Connect (OSTI)

    Frydman, A.; Vasseur, J.; Ducept, F.; Sionneau, M.; Moureh, J.

    1999-09-01

    This paper presents a numerical simulation and experimental validation of a spray dryer using superheated steam instead of air as drying medium, modeled with a computational fluid dynamics (CFD) code. The model describes momentum, heat and mass transfer between two phases--a discrete phase of droplets, and a continuous gas phase--through a finite volume method. For the simulation, droplet size distribution is represented by 6 discrete classes of diameter, fitting to the experimental distribution injected from the nozzle orifice, taking into account their peculiar shrinkage during drying. This model is able to predict the most important features of the dryer: fields of gas temperature and gas velocity inside the chamber, droplets trajectories and eventual deposits on to the wall. The results of simulation are compared to a pilot scale dryer, using water. In the absence of risk of power ignition in steam, the authors have tested rather high steam inlet temperature (973K), thus obtaining a high volumic efficiency. The model is validated by comparison between experimental and predicted values of temperature inside the chamber, verifying the coupling between the 3 different types of transfer without adjustment. This type of model can be used for chamber design, or scale up. Using superheated steam instead of air in a spray dryer can allow a high volumic evaporation rate (20 k.h.m{sup 3}), high energy recovery and better environment control.

  15. Dynamic simulations of geologic materials using combined FEM/DEM/SPH analysis

    SciTech Connect (OSTI)

    Morris, J P; Johnson, S M

    2008-03-26

    An overview of the Lawrence Discrete Element Code (LDEC) is presented, and results from a study investigating the effect of explosive and impact loading on geologic materials using the Livermore Distinct Element Code (LDEC) are detailed. LDEC was initially developed to simulate tunnels and other structures in jointed rock masses using large numbers of polyhedral blocks. Many geophysical applications, such as projectile penetration into rock, concrete targets, and boulder fields, require a combination of continuum and discrete methods in order to predict the formation and interaction of the fragments produced. In an effort to model this class of problems, LDEC now includes implementations of Cosserat point theory and cohesive elements. This approach directly simulates the transition from continuum to discontinuum behavior, thereby allowing for dynamic fracture within a combined finite element/discrete element framework. In addition, there are many application involving geologic materials where fluid-structure interaction is important. To facilitate solution of this class of problems a Smooth Particle Hydrodynamics (SPH) capability has been incorporated into LDEC to simulate fully coupled systems involving geologic materials and a saturating fluid. We will present results from a study of a broad range of geomechanical problems that exercise the various components of LDEC in isolation and in tandem.

  16. Molecular dynamics simulations of 30 and 2 keV Ga in Si

    SciTech Connect (OSTI)

    Giannuzzi, Lucille A.; Garrison, Barbara J.

    2007-09-15

    Focused Ga{sup +} ion beams are routinely used at high incident angles for specimen preparation. Molecular dynamics simulations of 2 and 30 keV Ga bombardment of Si(011) at a grazing angle of 88 deg. were conducted to assess sputtering characteristics and damage depth. The bombardment of atomically flat surfaces and surfaces with vacancies shows little energy transfer yielding ion reflection. The bombardment of surfaces with adatoms allows for the coupling of the energy of motion parallel to the surface into the substrate resulting in sputtering. The adatom and one other Si atom eject, and motion in the substrate occurs down to a depth of 13 A. Experimental evidence shows that sputtering is a reality, suggesting that an atomically flat surface is never achieved.

  17. Melting behaviour of gold-platinum nanoalloy clusters by molecular dynamics simulations

    SciTech Connect (OSTI)

    Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    The melting behavior of bimetallic gold-platinum nanoclusters is studied by applying Brownian-type isothermal molecular dynamics (MD) simulation, a program modified from the cubic coupling scheme (CCS). The process begins with the ground-state structures obtained from global minimum search algorithm and proceeds with the investigation of the effect of temperature on the thermal properties of gold-platinum nanoalloy clusters. N-body Gupta potential has been employed in order to account for the interactions between gold and platinum atoms. The ground states of the nanoalloy clusters, which are core-shell segregated, are heated until they become thermally segregated. The detailed melting mechanism of the nanoalloy clusters is studied via this approach to provide insight into the thermal stability of the nanoalloy clusters.

  18. Dynamically consistent method for mixed quantum-classical simulations: A semiclassical approach

    SciTech Connect (OSTI)

    Antipov, Sergey V.; Ye, Ziyu; Ananth, Nandini

    2015-05-14

    We introduce a new semiclassical (SC) framework, the Mixed Quantum-Classical Initial Value Representation (MQC-IVR), that can be tuned to reproduce existing quantum-limit and classical-limit SC approximations to quantum real-time correlation functions. Applying a modified Filinov transformation to a quantum-limit SC formulation leads to the association of a Filinov parameter with each degree of freedom in the system; varying this parameter from zero to infinity controls the extent of quantization of the corresponding mode. The resulting MQC-IVR expression provides a consistent dynamic framework for mixed quantum-classical simulations and we demonstrate its numerical accuracy in the calculation of real-time correlation functions for a model 1D system and a model 2D system over the full range of quantum- to classical-limit behaviors.

  19. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    SciTech Connect (OSTI)

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

  20. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    SciTech Connect (OSTI)

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-28

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  1. Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-08-01

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

  2. Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-06-01

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

  3. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    DOE PAGES-Beta [OSTI]

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; et al

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobicmore » environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.« less

  4. Plant-wide dynamic simulation of an IGCC plant with CO2 capture

    SciTech Connect (OSTI)

    Bhattacharyya, D.; Turton, R.; Zitney, S.

    2009-01-01

    To eliminate the harmful effects of greenhouse gases, especially that of CO2, future coalfired power plants need to consider the option for CO2 capture. The loss in efficiency for CO2 capture is less in an Integrated Gasification Combined Cycle (IGCC) plant compared to other conventional coal combustion processes. However, no IGCC plant with CO2 capture currently exists in the world. Therefore, it is important to consider the operability and controllability issues of such a plant before it is commercially built. With this objective in mind, a detailed plant-wide dynamic simulation of an IGCC plant with CO2 capture has been developed. The plant considers a General Electric Energy (GEE)-type downflow radiant-only gasifier followed by a quench section. A two-stage water gas shift (WGS) reaction is considered for conversion of about 96 mol% of CO to CO2. A two-stage acid gas removal (AGR) process based on a physical solvent is simulated for selective capture of H2S and CO2. The clean syngas is sent to a gas turbine (GT) followed by a heat recovery steam generator (HRSG). The steady state results are validated with data from a commercial gasifier. A 5 % ramp increase in the flowrate of coal is introduced to study the system dynamics. To control the conversion of CO at a desired level in the WGS reactors, the steam/CO ratio is manipulated. This strategy is found to be efficient for this operating condition. In the absence of an efficient control strategy in the AGR process, the environmental emissions exceeded the limits by a great extent.

  5. Dynamics of a globular protein and its hydration water studied by neutron scattering and MD simulations

    DOE PAGES-Beta [OSTI]

    Chen, Sow-Hsin; Lagi, Marco; Chu, Xiang-qiang; Zhang, Yang; Kim, Chansoo; Faraone, Antonio; Fratini, Emiliano; Baglioni, Piero

    2010-01-01

    This review article describes our neutron scattering experiments made in the past four years for the understanding of the single-particle (hydrogen atom) dynamics of a protein and its hydration water and the strong coupling between them. We found that the key to this strong coupling is the existence of a fragile-to-strong dynamic crossover (FSC) phenomenon occurring at around T L = 225±5 K in the hydration water. On lowering of the temperature toward FSC, the structure of hydration water makes a transition from predominantly the high density form (HDL), a more fluid state, to predominantly the low density formmore » (LDL), a less fluid state, derived from the existence of a liquid–liquid critical point at an elevated pressure. We show experimentally that this sudden switch in the mobility of hydration water on Lysozyme, B-DNA and RNA triggers the dynamic transition, at a temperature T D = 220 K, for these biopolymers. In the glassy state, below T D , the biopolymers lose their vital conformational flexibility resulting in a substantial diminishing of their biological functions. We also performed molecular dynamics (MD) simulations on a realistic model of hydrated lysozyme powder, which confirms the existence of the FSC and the hydration level dependence of the FSC temperature. Furthermore, we show a striking feature in the short time relaxation ( β -relaxation) of protein dynamics, which is the logarithmic decay spanning 3 decades (from ps to ns). The long time α -relaxation shows instead a diffusive behavior, which supports the liquid-like motions of protein constituents. We then discuss our recent high-resolution X-ray inelastic scattering studies of globular proteins, Lysozyme and Bovine Serum Albumin. We were able to measure the dispersion relations of collective, intra-protein phonon-like excitations in these proteins for the first time. We found that the phonon energies show a marked softening and at the same time their population increases

  6. Theoretical studies of zirconium and carbon clusters with molecular dynamics simulations

    SciTech Connect (OSTI)

    Zhang, B.

    1993-08-01

    In this dissertation, we will present a systematic study of structures of fullerenes ranging from C{sub 20} to C{sub 100} by introducing a novel scheme. Using our new scheme, we not only reproduce all known fullerene structures but also successfully predicted several other fullerene structures which were confirmed by experiments. By utilizing the tight-binding molecular-dynamic (TBMD) simulation, we also studied the dynamical behavior of fullerenes: Vibrations, thermal disintegration of individual clusters as well as collisions between fullerenes. If the beauty of carbon fullerene is not enough, people found that carbon can also form tubules and even speculated that they can form three-dimensional graphite-like networks. By extending our fullerene structure searching scheme, we performed a search for the ground-state structure of three dimensional carbon network. We found the most stable structure people ever proposed for simple cubic based networks. From the difference of this new form of carbon and graphite in the electronic and vibrational properties, we propose an experimental probe to identify these novel three-dimensional carbon networks.

  7. Dynamic Simulation of Shipping Package Subjected to Torque Load and Sequential Impacts

    SciTech Connect (OSTI)

    Wu, T

    2006-04-17

    A numerical technique has been developed to simulate the structural responses of radioactive material packaging components requiring closure-tightening torque to the scenarios of the hypothetical accident conditions (HAC) defined in the Code of Federal Regulations Title 10 part 71 (10CFR 71). A rigorous solution to this type of problem poses a considerable mathematical challenge. Conventional methods for evaluating the residue stresses due to the torque load are either inaccurate or not applicable to dynamic analyses. In addition, the HAC events occur sequentially and the cumulative damage to the package needs to be evaluated. Commonly, individual HAC events are analyzed separately and the cumulative damage is not addressed. As a result, strict compliance of the package with the requirements specified in 10CFR 71 is usually demonstrated by physical testing. The proposed technique utilizes the combination of kinematic constraints, rigid-body motions and structural deformations to overcome some of the difficulties encountered in modeling the effect of cumulative damage in numerical solutions. The analyses demonstrating use of this technique were performed to determine the cumulative damage of torque preload, a 30-foot drop, a 30-foot dynamic crush and a 40-inch free fall onto a mild steel pipe.

  8. Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

    DOE PAGES-Beta [OSTI]

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.

    2015-01-31

    In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimentalmore » observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less

  9. Inelastic neutron scattering and molecular simulation of the dynamics of interlayer water in smectite clay minerals

    DOE PAGES-Beta [OSTI]

    Cygan, Randall T.; Daemen, Luke L.; Ilgen, Anastasia G.; Krumhansl, James L.; Nenoff, Tina M.

    2015-11-16

    The study of mineral–water interfaces is of great importance to a variety of applications including oil and gas extraction, gas subsurface storage, environmental contaminant treatment, and nuclear waste repositories. Understanding the fundamentals of that interface is key to the success of those applications. Confinement of water in the interlayer of smectite clay minerals provides a unique environment to examine the interactions among water molecules, interlayer cations, and clay mineral surfaces. Smectite minerals are characterized by a relatively low layer charge that allows the clay to swell with increasing water content. Montmorillonite and beidellite varieties of smectite were investigated to comparemore » the impact of the location of layer charge on the interlayer structure and dynamics. Inelastic neutron scattering of hydrated and dehydrated cation-exchanged smectites was used to probe the dynamics of the interlayer water (200–900 cm–1 spectral region) and identify the shift in the librational edge as a function of the interlayer cation. Molecular dynamics simulations of equivalent phases and power spectra, derived from the resulting molecular trajectories, indicate a general shift in the librational behavior with interlayer cation that is generally consistent with the neutron scattering results for the monolayer hydrates. Both neutron scattering and power spectra exhibit librational structures affected by the location of layer charge and by the charge of the interlayer cation. Furthermore, divalent cations (Ba2+ and Mg2+) characterized by large hydration enthalpies typically exhibit multiple broad librational peaks compared to monovalent cations (Cs+ and Na+), which have relatively small hydration enthalpies.« less

  10. Inelastic neutron scattering and molecular simulation of the dynamics of interlayer water in smectite clay minerals

    SciTech Connect (OSTI)

    Cygan, Randall T.; Daemen, Luke L.; Ilgen, Anastasia G.; Krumhansl, James L.; Nenoff, Tina M.

    2015-11-16

    The study of mineral–water interfaces is of great importance to a variety of applications including oil and gas extraction, gas subsurface storage, environmental contaminant treatment, and nuclear waste repositories. Understanding the fundamentals of that interface is key to the success of those applications. Confinement of water in the interlayer of smectite clay minerals provides a unique environment to examine the interactions among water molecules, interlayer cations, and clay mineral surfaces. Smectite minerals are characterized by a relatively low layer charge that allows the clay to swell with increasing water content. Montmorillonite and beidellite varieties of smectite were investigated to compare the impact of the location of layer charge on the interlayer structure and dynamics. Inelastic neutron scattering of hydrated and dehydrated cation-exchanged smectites was used to probe the dynamics of the interlayer water (200–900 cm–1 spectral region) and identify the shift in the librational edge as a function of the interlayer cation. Molecular dynamics simulations of equivalent phases and power spectra, derived from the resulting molecular trajectories, indicate a general shift in the librational behavior with interlayer cation that is generally consistent with the neutron scattering results for the monolayer hydrates. Both neutron scattering and power spectra exhibit librational structures affected by the location of layer charge and by the charge of the interlayer cation. Furthermore, divalent cations (Ba2+ and Mg2+) characterized by large hydration enthalpies typically exhibit multiple broad librational peaks compared to monovalent cations (Cs+ and Na+), which have relatively small hydration enthalpies.

  11. Ab initio molecular dynamics simulation of pressure-induced phase transformation of BeO

    SciTech Connect (OSTI)

    Xiao, H. Y.; Duan, G.; Zu, X. T.; Weber, W. J.

    2011-05-05

    Ab initio molecular dynamics (MD) method has been used to study high pressure-induced phase transformation in BeO based on the local density approximation (LDA) and the generalized gradient approximation (GGA). Both methods show that the wurtzite (WZ) and zinc blende (ZB) BeO transforms to the rocksalt (RS) structure smoothly at high pressure. The transition pressures obtained from the LDA method are about 40 GPa larger than the GGA result for both WZ ? RS and ZB ? RS phase transformations, and the phase transformation mechanisms revealed by the LDA and GGA methods are different. For WZ ? RS phase transformations both mechanisms obtained from the LDA and GGA methods are not comparable to the previous ab initio MD simulations of WZ BeO at 700 GPa based on the GGA method. It is suggested that the phase transformation mechanisms of BeO revealed by the ab initio MD simulations are affected remarkably by the exchangecorrelation functional employed and the way of applying pressure.

  12. Molecular dynamics simulations of shock waves in hydroxyl-terminated polybutadiene melts: Mechanical and structural responses

    SciTech Connect (OSTI)

    Frhlich, Markus G. E-mail: ThompsonDon@missouri.edu; Sewell, Thomas D. Thompson, Donald L. E-mail: ThompsonDon@missouri.edu

    2014-01-14

    The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup ?1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ?0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.

  13. Tractionseparation relationships for hydrogen induced grain boundary embrittlement in nickel via molecular dynamics simulations

    SciTech Connect (OSTI)

    Barrows, Wesley; Dingreville, Rmi; Spearot, Douglas

    2015-10-19

    A statistical approach combined with molecular dynamics simulations is used to study the influence of hydrogen on intergranular decohesion. This methodology is applied to a Ni ?3(112)[110] symmetric tilt grain boundary. Hydrogenated grain boundaries with different H concentrations are constructed using an energy minimization technique with initial H atom positions guided by Monte Carlo simulation results. Decohesion behavior is assessed through extraction of a tractionseparation relationship during steady-state crack propagation in a statistically meaningful approach, building upon prior work employing atomistic cohesive zone volume elements (CZVEs). A sensitivity analysis is performed on the numerical approach used to extract the tractionseparation relationships, clarifying the role of CZVE size, threshold parameters necessary to differentiate elastic and decohesion responses, and the numerical averaging technique. Results show that increasing H coverage at the Ni ?3(112)[110] grain boundary asymmetrically influences the crack tip velocity during propagation, leads to a general decrease in the work of separation required for crack propagation, and provides a reduction in the peak stress in the extracted tractionseparation relationship. Furthermore the present framework offers a meaningful vehicle to pass atomistically derived interfacial behavior to higher length scale formulations for intergranular fracture.

  14. Testing thermal gradient driving force for grain boundary migration using molecular dynamics simulations

    SciTech Connect (OSTI)

    Bai, Xian-Ming; Zhang, Yongfeng; Tonks, Michael R.

    2015-02-01

    Strong thermal gradients in low-thermal-conductivity ceramics may drive extended defects, such as grain boundaries and voids, to migrate in preferential directions. In this work, molecular dynamics simulations are conducted to study thermal gradient driven grain boundary migration and to verify a previously proposed thermal gradient driving force equation, using uranium dioxide as a model system. It is found that a thermal gradient drives grain boundaries to migrate up the gradient and the migration velocity increases under a constant gradient owing to the increase in mobility with temperature. Different grain boundaries migrate at very different rates due to their different intrinsic mobilities. The extracted mobilities from the thermal gradient driven simulations are compared with those calculated from two other well-established methods and good agreement between the three different methods is found, demonstrating that the theoretical equation of the thermal gradient driving force is valid, although a correction of one input parameter should be made. The discrepancy in the grain boundary mobilities between modeling and experiments is also discussed.

  15. Energy dynamics and current sheet structure in fluid and kinetic simulations of decaying magnetohydrodynamic turbulence

    SciTech Connect (OSTI)

    Makwana, K. D. Cattaneo, F.; Zhdankin, V.; Li, H.; Daughton, W.

    2015-04-15

    Simulations of decaying magnetohydrodynamic (MHD) turbulence are performed with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfvén waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k{sub ⊥}{sup −1.3}. The kinetic code shows a spectral slope of k{sub ⊥}{sup −1.5} for smaller simulation domain, and k{sub ⊥}{sup −1.3} for larger domain. We estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the driving scale of the turbulence. In the fluid code, their thickness is determined by the grid resolution as there is no explicit diffusivity. In the kinetic code, their thickness is very close to the skin-depth, irrespective of the grid resolution. This work shows that kinetic codes can reproduce the MHD inertial range dynamics at large scales, while at the same time capturing important kinetic physics at small scales.

  16. Molecular dynamics simulation of diffusion and electrical conductivity in montmorillonite interlayers

    DOE PAGES-Beta [OSTI]

    Greathouse, Jeffery A.; Cygan, Randall T.; Fredrich, Joanne T.; Jerauld, Gary R.

    2016-01-20

    In this study, the diffusion of water and ions in the interlayer region of smectite clay minerals represents a direct probe of the type and strength of clay–fluid interactions. Interlayer diffusion also represents an important link between molecular simulation and macroscopic experiments. Here we use molecular dynamics simulation to investigate trends in cation and water diffusion in montmorillonite interlayers, looking specifically at the effects of layer charge, interlayer cation and cation charge (sodium or calcium), water content, and temperature. For Na-montmorillonite, the largest increase in ion and water diffusion coefficients occurs between the one-layer and two-layer hydrates, corresponding to themore » transition from inner-sphere to outer-sphere surface complexes. Calculated activation energies for ion and water diffusion in Na-montmorillonite are similar to each other and to the water hydrogen bond energy, suggesting the breaking of water–water and water–clay hydrogen bonds as a likely mechanism for interlayer diffusion. A comparison of interlayer diffusion with that of bulk electrolyte solutions reveals a clear trend of decreasing diffusion coefficient with increasing electrolyte concentration, and in most cases the interlayer diffusion results are nearly coincident with the corresponding bulk solutions. Trends in electrical conductivities computed from the ion diffusion coefficients are also compared.« less

  17. Traction–separation relationships for hydrogen induced grain boundary embrittlement in nickel via molecular dynamics simulations

    DOE PAGES-Beta [OSTI]

    Barrows, Wesley; Dingreville, Rémi; Spearot, Douglas

    2015-10-19

    A statistical approach combined with molecular dynamics simulations is used to study the influence of hydrogen on intergranular decohesion. This methodology is applied to a Ni Σ3(112)[11¯0] symmetric tilt grain boundary. Hydrogenated grain boundaries with different H concentrations are constructed using an energy minimization technique with initial H atom positions guided by Monte Carlo simulation results. Decohesion behavior is assessed through extraction of a traction–separation relationship during steady-state crack propagation in a statistically meaningful approach, building upon prior work employing atomistic cohesive zone volume elements (CZVEs). A sensitivity analysis is performed on the numerical approach used to extract the traction–separationmore » relationships, clarifying the role of CZVE size, threshold parameters necessary to differentiate elastic and decohesion responses, and the numerical averaging technique. Results show that increasing H coverage at the Ni Σ3(112)[11¯0] grain boundary asymmetrically influences the crack tip velocity during propagation, leads to a general decrease in the work of separation required for crack propagation, and provides a reduction in the peak stress in the extracted traction–separation relationship. Furthermore the present framework offers a meaningful vehicle to pass atomistically derived interfacial behavior to higher length scale formulations for intergranular fracture.« less

  18. Numerical simulation of the compressor coil of the plasma dynamic accelerator

    SciTech Connect (OSTI)

    Thomas, P.

    1997-01-01

    The plasma dynamic accelerator accelerates a plasma to very high velocities in a coaxial accelerator and then compresses it in a compressor coil, achieving high densities. The axial component of the current distribution, extending from the tip of the coaxial accelerator`s center electrode to the coil turns, causes compressing forces, the radial component yields accelerating forces. The rapid change of the coil current induces azimuthal eddy currents in the plasma that interact with the coil`s magnetic field, again yielding Lorentz forces. Aerodynamic compression may also be an important effect. A new two-dimensional magnetohydrodynamics code is used to investigate which of these effects are really important for the compression. The code allows one to simulate all effects mentioned separately and in combination. In a first step only aerodynamic compression is considered. Then each electromagnetic effect is imposed on the system. Finally, a complete simulation of the compressor coil is performed. The analysis of the results provides new insights in the way the coil operates. This paper presents important aspects of the mathematical model and of the numerical implementation and reports results.

  19. Development of EEM based siliconwater and silicawater wall potentials for non-reactive molecular dynamics simulations

    SciTech Connect (OSTI)

    Kim, Junghan; Iype, Eldhose; Frijns, Arjan J.H.; Nedea, Silvia V.; Steenhoven, Anton A. van

    2014-07-01

    Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluidsolid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate watersilicon and watersilica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a siliconwater contact angle of 129, a quartzwater contact angle of 0, and a cristobalitewater contact angle of 40, which are in reasonable agreement with experimental values.

  20. Driving Down HB-LED Costs. Implementation of Process Simulation Tools and Temperature Control Methods of High Yield MOCVD Growth

    SciTech Connect (OSTI)

    Quinn, William

    2012-04-30

    The overall objective of this multi-faceted program is to develop epitaxial growth systems that meet a goal of 75% (4X) cost reduction in the epitaxy phase of HB-LED manufacture. A 75% reduction in yielded epitaxy cost is necessary in order to achieve the cost goals for widespread penetration of HB-LED's into back-lighting units (BLU) for LCD panels and ultimately for solid-state lighting (SSL). To do this, the program will address significant improvements in overall equipment Cost of Ownership, or CoO. CoO is a model that includes all costs associated with the epitaxy portion of production. These aspects include cost of yield, capital cost, operational costs, and maintenance costs. We divide the program into three phases where later phases will incorporate the gains of prior phases. Phase one activities are enabling technologies. In collaboration with Sandia National Laboratories we develop a Fluent-compatible chemistry predictive model and a set of mid-infrared and near-ultraviolet pyrometer monitoring tools. Where previously the modeling of the reactor dynamics were studied within FLUENT alone, here, FLUENT and Chemkin are integrated into a comprehensive model of fluid dynamics and the most advanced transport equations developed for Chemkin. Specifically, the Chemkin model offered the key reaction terms for gas-phase nucleation, a key consideration in the optimization of the MOCVD process. This new predictive model is used to design new MOCVD reactors with optimized growth conditions and the newly developed pyrometers are used monitor and control the MOCVD process temperature to within 0.5°C run-to-run and within each wafer. This portion of the grant is in collaboration with partners at Sandia National Laboratories. Phase two activities are continuous improvement projects which extend the current reactor platform along the lines of improved operational efficiency, improved systems control for throughput, and carrier modifications for increased yield

  1. Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

    SciTech Connect (OSTI)

    Wu, Xiaokun; Han, Min; Ming, Dengming

    2015-10-07

    Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

  2. NREL Evaluates Thermal Performance of Uninsulated Walls to Improve Accuracy of Building Energy Simulation Tools (Fact Sheet), NREL Highlights, Research & Development, NREL (National Renewable Energy Laboratory)

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    researchers discover ways to increase accuracy in building energy simulations tools to improve predictions of potential energy savings in homes. Uninsulated walls are typical in older U.S. homes where the wall cavities were not insulated during construction or where the insulating material has settled. Researchers at the National Renewable Energy Laboratory (NREL) are investigating ways to more accurately calculate heat transfer through building enclosures to verify the benefit of energy

  3. Technology Transfer Webinar on November 12: High-Performance Hybrid Simulation/Measurement-Based Tools for Proactive Operator Decision-Support

    Energy.gov [DOE]

    DOE/OE and EPRI will host a technology transfer webinar on Wednesday, November 12, 2014 from noon to 2 p.m. (ET). The purpose of this open webinar is to disseminate results and outcomes of the recently completed project “High-Performance Hybrid Simulation/Measurement-Based Tools for Proactive Operator Decision-Support,” which is one of the awarded projects of the DOE Advanced Modeling Grid Research Program.

  4. Consequences of Urban Stability Conditions for Computational Fluid Dynamics Simulations of Urban Dispersion

    SciTech Connect (OSTI)

    Lundquist, J K; Chan, S T

    2005-11-30

    The validity of omitting stability considerations when simulating transport and dispersion in the urban environment is explored using observations from the Joint URBAN 2003 field experiment and computational fluid dynamics simulations of that experiment. Four releases of sulfur hexafluoride, during two daytime and two nighttime intensive observing periods, are simulated using the building-resolving computational fluid dynamics model, FEM3MP to solve the Reynolds Averaged Navier-Stokes equations with two options of turbulence parameterizations. One option omits stability effects but has a superior turbulence parameterization using a non-linear eddy viscosity (NEV) approach, while the other considers buoyancy effects with a simple linear eddy viscosity (LEV) approach for turbulence parameterization. Model performance metrics are calculated by comparison with observed winds and tracer data in the downtown area, and with observed winds and turbulence kinetic energy (TKE) profiles at a location immediately downwind of the central business district (CBD) in the area we label as the urban shadow. Model predictions of winds, concentrations, profiles of wind speed, wind direction, and friction velocity are generally consistent with and compare reasonably well with the field observations. Simulations using the NEV turbulence parameterization generally exhibit better agreement with observations. To further explore this assumption of a neutrally-stable atmosphere within the urban area, TKE budget profiles slightly downwind of the urban wake region in the 'urban shadow' are examined. Dissipation and shear production are the largest terms which may be calculated directly. The advection of TKE is calculated as a residual; as would be expected downwind of an urban area, the advection of TKE produced within the urban area is a very large term. Buoyancy effects may be neglected in favor of advection, shear production, and dissipation. For three of the IOPs, buoyancy production may

  5. Load Model Data Tool

    SciTech Connect (OSTI)

    David Chassin, Pavel Etingov

    2013-04-30

    The LMDT software automates the process of the load composite model data preparation in the format supported by the major power system software vendors (GE and Siemens). Proper representation of the load composite model in power system dynamic analysis is very important. Software tools for power system simulation like GE PSLF and Siemens PSSE already include algorithms for the load composite modeling. However, these tools require that the input information on composite load to be provided in custom formats. Preparation of this data is time consuming and requires multiple manual operations. The LMDT software enables to automate this process. Software is designed to generate composite load model data. It uses the default load composition data, motor information, and bus information as an input. Software processes the input information and produces load composition model. Generated model can be stored in .dyd format supported by GE PSLF package or .dyr format supported by Siemens PSSE package.

  6. Load Model Data Tool

    Energy Science and Technology Software Center (OSTI)

    2013-04-30

    The LMDT software automates the process of the load composite model data preparation in the format supported by the major power system software vendors (GE and Siemens). Proper representation of the load composite model in power system dynamic analysis is very important. Software tools for power system simulation like GE PSLF and Siemens PSSE already include algorithms for the load composite modeling. However, these tools require that the input information on composite load to bemore » provided in custom formats. Preparation of this data is time consuming and requires multiple manual operations. The LMDT software enables to automate this process. Software is designed to generate composite load model data. It uses the default load composition data, motor information, and bus information as an input. Software processes the input information and produces load composition model. Generated model can be stored in .dyd format supported by GE PSLF package or .dyr format supported by Siemens PSSE package.« less

  7. Simulation of micro-magnet stray-field dynamics for spin qubit manipulation

    SciTech Connect (OSTI)

    Neumann, R.; Schreiber, L. R.

    2015-05-21

    High-fidelity control and unprecedented long dephasing times in silicon-based single spin qubits have recently confirmed the prospects of solid-state quantum computation. We investigate the feasibility of using a micro-magnet stray field for all-electrical, addressable spin qubit control in a Si/SiGe double quantum dot. For a micro-magnet geometry optimized for high Rabi-frequency, addressability, and robustness to fabrication misalignment as previously demonstrated by Yoneda et al. [Phys. Rev. Lett. 113, 267601 (2014)], we simulate the qubit decoherence due to magnetic stray-field fluctuations, which may dominate in nuclear spin-free systems, e.g., quantum dots in Si/SiGe, Si-MOS structures and (bilayer) graphene. With calculated Rabi-frequencies of 15 MHz, a qubit addressability error below 10{sup −3} is achievable. Magnetic fluctuations from a micro-magnet limits the spin relaxation time to T{sub 1} ≳ 3 s, while pure spin dephasing is negligible. Our results show that micro-magnets are a promising tool for spin qubit computation in nuclear spin-free systems.

  8. Energy dynamics and current sheet structure in fluid and kinetic simulations of decaying magnetohydrodynamic turbulence

    SciTech Connect (OSTI)

    Makwana, K. D.; Zhdankin, V.; Li, H.; Daughton, W.; Cattaneo, F.

    2015-04-10

    We performed simulations of decaying magnetohydrodynamic (MHD) turbulence with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfvén waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k-1.3⊥k⊥-1.3. The kinetic code shows a spectral slope of k-1.5⊥k⊥-1.5 for smaller simulation domain, and k-1.3⊥k⊥-1.3 for larger domain. We then estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the driving scale of the turbulence. In the fluid code, their thickness is determined by the grid resolution as there is no explicit diffusivity. In the kinetic code, their thickness is very close to the skin-depth, irrespective of the grid resolution. Finally, this work shows that kinetic codes can reproduce the MHD inertial range dynamics at large scales, while at the same time capturing important kinetic physics at small scales.

  9. Energy dynamics and current sheet structure in fluid and kinetic simulations of decaying magnetohydrodynamic turbulence

    DOE PAGES-Beta [OSTI]

    Makwana, K. D.; Zhdankin, V.; Li, H.; Daughton, W.; Cattaneo, F.

    2015-04-10

    We performed simulations of decaying magnetohydrodynamic (MHD) turbulence with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfvén waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k-1.3⊥k⊥-1.3. The kinetic code shows a spectral slope of k-1.5⊥k⊥-1.5 for smallermore » simulation domain, and k-1.3⊥k⊥-1.3 for larger domain. We then estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the driving scale of the turbulence. In the fluid code, their thickness is determined by the grid resolution as there is no explicit diffusivity. In the kinetic code, their thickness is very close to the skin-depth, irrespective of the grid resolution. Finally, this work shows that kinetic codes can reproduce the MHD inertial range dynamics at large scales, while at the same time capturing important kinetic physics at small scales.« less

  10. Manipulative Virtual Tools for Tool Mark Characterization | The...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Manipulative Virtual Tools for Tool Mark Characterization DESCRIPTION: The goal of this project is to develop a methodology whereby a three-dimensional (3-D) computer simulation of...

  11. The use of finite elements to model soil/track interactions in coupled multi-body dynamic simulations: Is real time simulation feasible?

    SciTech Connect (OSTI)

    Canfield, T.R.; Murray, M.J.

    1992-05-01

    Finite element methods (FEM) employing the arbitrary Lagrangian-Eulerian (ALE) formulation may be used to model soil in contact with the wheels or the tracks of vehicles in off-road mobility simulations. Coupling ALE finite element methods with recursive multi-body dynamics may allow real-time simulation of vehicles off-road provided sufficient computational resources are available. The requirements of these approach will be discussed with emphasis on parallel implementation. Estimates of expected performance are calculated based on the current trend in the development of advanced computer architectures. Factors important in estimating the feasibility of using finite element methodology in real time will be considered. Among these factors are the element size, the number of elements and the rate of computation, as well as the physical requirements of the simulations.

  12. The use of finite elements to model soil/track interactions in coupled multi-body dynamic simulations: Is real time simulation feasible

    SciTech Connect (OSTI)

    Canfield, T.R. ); Murray, M.J. )

    1992-05-01

    Finite element methods (FEM) employing the arbitrary Lagrangian-Eulerian (ALE) formulation may be used to model soil in contact with the wheels or the tracks of vehicles in off-road mobility simulations. Coupling ALE finite element methods with recursive multi-body dynamics may allow real-time simulation of vehicles off-road provided sufficient computational resources are available. The requirements of these approach will be discussed with emphasis on parallel implementation. Estimates of expected performance are calculated based on the current trend in the development of advanced computer architectures. Factors important in estimating the feasibility of using finite element methodology in real time will be considered. Among these factors are the element size, the number of elements and the rate of computation, as well as the physical requirements of the simulations.

  13. Final technical report [ACCELERATED MOLECULAR DYNAMICS SIMULATIONS OF REACTIVE HYDROCARBON SYSTEMS

    SciTech Connect (OSTI)

    Stuart, Steven J.

    2014-02-25

    The research activities in this project consisted of four different sub-projects. Three different accelerated dynamics techniques (parallel replica dynamics, hyperdynamics, and temperature-accelerated dynamics) were applied to the modeling of pyrolysis of hydrocarbons. In addition, parallel replica dynamics was applied to modeling of polymerization.

  14. Lubricant characterization by molecular simulation

    SciTech Connect (OSTI)

    Moore, J.D.; Cui, S.T.; Cummings, P.T.; Cochran, H.D.

    1997-12-01

    The authors have reported the calculation of the kinematic viscosity index of squalane from nonequilibrium molecular dynamics simulations. This represents the first accurate quantitative prediction of this measure of lubricant performance by molecular simulation. Using the same general alkane potential model, this computational approach offers the possibility of predicting the performance of potential lubricants prior to synthesis. Consequently, molecular simulation is poised to become an important tool for future lubricant development.

  15. A surface ice module for wind turbine dynamic response simulation using FAST

    DOE PAGES-Beta [OSTI]

    Yu, Bingbin; Karr, Dale G.; Song, Huimin; Sirnivas, Senu

    2016-06-03

    It is a fact that developing offshore wind energy has become more and more serious worldwide in recent years. Many of the promising offshore wind farm locations are in cold regions that may have ice cover during wintertime. The challenge of possible ice loads on offshore wind turbines raises the demand of modeling capacity of dynamic wind turbine response under the joint action of ice, wind, wave, and current. The simulation software FAST is an open source computer-aided engineering (CAE) package maintained by the National Renewable Energy Laboratory. In this paper, a new module of FAST for assessing the dynamicmore » response of offshore wind turbines subjected to ice forcing is presented. In the ice module, several models are presented which involve both prescribed forcing and coupled response. For conditions in which the ice forcing is essentially decoupled from the structural response, ice forces are established from existing models for brittle and ductile ice failure. For conditions in which the ice failure and the structural response are coupled, such as lock-in conditions, a rate-dependent ice model is described, which is developed in conjunction with a new modularization framework for FAST. In this paper, analytical ice mechanics models are presented that incorporate ice floe forcing, deformation, and failure. For lower speeds, forces slowly build until the ice strength is reached and ice fails resulting in a quasi-static condition. For intermediate speeds, the ice failure can be coupled with the structural response and resulting in coinciding periods of the ice failure and the structural response. A third regime occurs at high speeds of encounter in which brittle fracturing of the ice feature occurs in a random pattern, which results in a random vibration excitation of the structure. An example wind turbine response is simulated under ice loading of each of the presented models. This module adds to FAST the capabilities for analyzing the response of wind

  16. Molecular dynamics simulations of uranyl adsorption and structure on the basal surface of muscovite

    SciTech Connect (OSTI)

    Teich-McGoldrick, Stephanie L.; Greathouse, Jeffery A.; Cygan, Randall T.

    2014-02-05

    Anthropogenic activities have led to an increased concentration of uranium on the Earth’s surface and potentially in the subsurface with the development of nuclear waste repositories. Uranium is soluble in groundwater, and its mobility is strongly affected by the presence of clay minerals in soils and in subsurface sediments. We use molecular dynamics simulations to probe the adsorption of aqueous uranyl (UO22+) ions onto the basal surface of muscovite, a suitable proxy for typically ultrafine-grained clay phases. Model systems include the competitive adsorption between potassium counterions and aqueous ions (0.1 M and 1.0 M UO2Cl2 , 0.1 M NaCl). We find that for systems with potassium and uranyl ions present, potassium ions dominate the adsorption phenomenon. Potassium ions adsorb entirely as inner-sphere complexes associated with the ditrigonal cavity of the basal surface. Uranyl ions adsorb in two configurations when it is the only ion species present, and in a single configuration in the presence of potassium. Finally, the majority of adsorbed uranyl ions are tilted less than 45° relative to the muscovite surface, and are associated with the Si4Al2 rings near aluminum substitution sites.

  17. Effect of point defects on the thermal conductivity of UO2: molecular dynamics simulations

    SciTech Connect (OSTI)

    Liu, Xiang-Yang; Stanek, Christopher Richard; Andersson, Anders David Ragnar

    2015-07-21

    The thermal conductivity of uranium dioxide (UO2) fuel is an important materials property that affects fuel performance since it is a key parameter determining the temperature distribution in the fuel, thus governing, e.g., dimensional changes due to thermal expansion, fission gas release rates, etc. [1] The thermal conductivity of UO2 nuclear fuel is also affected by fission gas, fission products, defects, and microstructural features such as grain boundaries. Here, molecular dynamics (MD) simulations are carried out to determine quantitatively, the effect of irradiation induced point defects on the thermal conductivity of UO2, as a function of defect concentrations, for a range of temperatures, 300 – 1500 K. The results will be used to develop enhanced continuum thermal conductivity models for MARMOT and BISON by INL. These models express the thermal conductivity as a function of microstructure state-variables, thus enabling thermal conductivity models with closer connection to the physical state of the fuel [2].

  18. Molecular dynamics simulations of uranyl adsorption and structure on the basal surface of muscovite

    DOE PAGES-Beta [OSTI]

    Teich-McGoldrick, Stephanie L.; Greathouse, Jeffery A.; Cygan, Randall T.

    2014-02-05

    Anthropogenic activities have led to an increased concentration of uranium on the Earth’s surface and potentially in the subsurface with the development of nuclear waste repositories. Uranium is soluble in groundwater, and its mobility is strongly affected by the presence of clay minerals in soils and in subsurface sediments. We use molecular dynamics simulations to probe the adsorption of aqueous uranyl (UO22+) ions onto the basal surface of muscovite, a suitable proxy for typically ultrafine-grained clay phases. Model systems include the competitive adsorption between potassium counterions and aqueous ions (0.1 M and 1.0 M UO2Cl2 , 0.1 M NaCl). Wemore » find that for systems with potassium and uranyl ions present, potassium ions dominate the adsorption phenomenon. Potassium ions adsorb entirely as inner-sphere complexes associated with the ditrigonal cavity of the basal surface. Uranyl ions adsorb in two configurations when it is the only ion species present, and in a single configuration in the presence of potassium. Finally, the majority of adsorbed uranyl ions are tilted less than 45° relative to the muscovite surface, and are associated with the Si4Al2 rings near aluminum substitution sites.« less

  19. Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations

    SciTech Connect (OSTI)

    Wang, Jing-Fang; Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235; Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130 ; Chou, Kuo-Chen

    2009-12-18

    Rab5a is currently a most interesting target because it is responsible for regulating the early endosome fusion in endocytosis and possibly the budding process. We utilized longtime-scale molecular dynamics simulations to investigate the internal motion of the wild-type Rab5a and its A30P mutant. It was observed that, after binding with GTP, the global flexibility of the two proteins is increasing, while the local flexibility in their sensitive sites (P-loop, switch I and II regions) is decreasing. Also, the mutation of Ala30 to Pro30 can cause notable flexibility variations in the sensitive sites. However, this kind of variations is dramatically reduced after binding with GTP. Such a remarkable feature is mainly caused by the water network rearrangements in the sensitive sites. These findings might be of use for revealing the profound mechanism of the displacements of Rab5a switch regions, as well as the mechanism of the GDP dissociation and GTP association.

  20. Molecular dynamics simulations of the melting curve of NiAl alloy under pressure

    SciTech Connect (OSTI)

    Zhang, Wenjin; Peng, Yufeng; Liu, Zhongli

    2014-05-15

    The melting curve of B2-NiAl alloy under pressure has been investigated using molecular dynamics technique and the embedded atom method (EAM) potential. The melting temperatures were determined with two approaches, the one-phase and the two-phase methods. The first one simulates a homogeneous melting, while the second one involves a heterogeneous melting of materials. Both approaches reduce the superheating effectively and their results are close to each other at the applied pressures. By fitting the well-known Simon equation to our melting data, we yielded the melting curves for NiAl: 1783(1 + P/9.801){sup 0.298} (one-phase approach), 1850(1 + P/12.806){sup 0.357} (two-phase approach). The good agreement of the resulting equation of states and the zero-pressure melting point (calc., 1850 25 K, exp., 1911 K) with experiment proved the correctness of these results. These melting data complemented the absence of experimental high-pressure melting of NiAl. To check the transferability of this EAM potential, we have also predicted the melting curves of pure nickel and pure aluminum. Results show the calculated melting point of Nickel agrees well with experiment at zero pressure, while the melting point of aluminum is slightly higher than experiment.

  1. Molecular dynamics simulations of H{sub 2} adsorption in tetramethyl ammonium lithium phthalocyanine crystalline structures.

    SciTech Connect (OSTI)

    Lamonte, K.; Gomez Gualdron, D.; Scanlon, L. G.; Sandi, G.; Feld, W.; Balbuena, P. B.; Chemical Sciences and Engineering Division; Texas A&M Univ.; Wright-Patterson Air Force Base; Wright State Univ.

    2008-11-01

    Tetramethyl ammonium lithium phthalocyanine is explored as a potential material for storage of molecular hydrogen. Density functional theory calculations are used to investigate the molecular structure and the dimer conformation. Additional scans performed to determine the interactions of a H{sub 2} molecule located at various distances from the molecular sites are used to generate a simple force field including dipole-induced-dipole interactions. This force field is employed in molecular dynamics simulations to calculate adsorption isotherms at various pressures. The regions of strongest adsorption are quantified as functions of temperature, pressure, and separation between molecules in the adsorbent phase, and compared to the regions of strongest binding energy as given by the proposed force field. It is found that the total adsorption could not be predicted only from the spatial distribution of the strongest binding energies; the available volume is the other contributing factor even if the volume includes regions of much lower binding energy. The results suggest that the complex anion is primarily involved in the adsorption process with molecular hydrogen, whereas the cation serves to provide access for hydrogen adsorption in both sides of the anion molecular plane, and spacing between the planes.

  2. Molecular dynamics simulation for arrangement of nickel atoms filled in carbon nanotubes

    SciTech Connect (OSTI)

    Bai, Liu Zhenyu, Zhao; Lirui, Liu

    2014-08-28

    Carbon Nanotubes (CNTs) filled with metals can be used in capacitors, sensors, rechargeable batteries, and so on. Atomic arrangement of the metals has an important role in the function of the composites. The tips of CNTs were opened, and then nickel was filled by means of hydrothermal oxidation/ultrasonic vibration method. The tests of TEM, HREM, and EDX (energy-dispersive X-ray spectroscopy) analysis showed that Ni was filled in CNTs successfully. The atomic arrangement of nickel filled into single wall carbon nanotubes was investigated by molecular dynamics simulation. The radial distribution function and bond orientation order were established to analyze the atomic arrangement of nickel filled in carbon nanotubes during the cooling process. The results show that nickel atoms became in order gradually and preferably crystallized on the inner wall of carbon nanotubes when the temperature decreased from 1600?K. After it cooled to 100?K, the arrangement of nickel atoms in outermost circle was regular and dense, but there were many defects far from the wall of CNTs. According to the calculation of bond orientation order parameters Q{sub 6} and its visualization, the structure of nickel is Face-centered cube (f.c.c). (1,1,1){sub Ni} was close on the inner surface of carbon nanotubes. Radial direction of CNTs was [1,1,1] crystal orientation. Axial direction of CNTs, namely, filling direction, was [1{sup }, 1{sup },2] crystal orientation.

  3. An 8-node tetrahedral finite element suitable for explicit transient dynamic simulations

    SciTech Connect (OSTI)

    Key, S.W.; Heinstein, M.W.; Stone, C.M.

    1997-12-31

    Considerable effort has been expended in perfecting the algorithmic properties of 8-node hexahedral finite elements. Today the element is well understood and performs exceptionally well when used in modeling three-dimensional explicit transient dynamic events. However, the automatic generation of all-hexahedral meshes remains an elusive achievement. The alternative of automatic generation for all-tetrahedral finite element is a notoriously poor performer, and the 10-node quadratic tetrahedral finite element while a better performer numerically is computationally expensive. To use the all-tetrahedral mesh generation extant today, the authors have explored the creation of a quality 8-node tetrahedral finite element (a four-node tetrahedral finite element enriched with four midface nodal points). The derivation of the element`s gradient operator, studies in obtaining a suitable mass lumping and the element`s performance in applications are presented. In particular, they examine the 80node tetrahedral finite element`s behavior in longitudinal plane wave propagation, in transverse cylindrical wave propagation, and in simulating Taylor bar impacts. The element only samples constant strain states and, therefore, has 12 hourglass modes. In this regard, it bears similarities to the 8-node, mean-quadrature hexahedral finite element. Given automatic all-tetrahedral meshing, the 8-node, constant-strain tetrahedral finite element is a suitable replacement for the 8-node hexahedral finite element and handbuilt meshes.

  4. Structure of rigid polymers confined to nanoparticles: Molecular dynamics simulations insight

    DOE PAGES-Beta [OSTI]

    Maskey, Sabina; Lane, J. Matthew D.; Perahia, Dvora; Grest, Gary S.

    2016-02-04

    Nanoparticles (NPs) grafted with organic layers form hybrids able to retain their unique properties through integration into the mesoscopic scale. The organic layer structure and response often determine the functionality of the hybrids on the mesoscopic length scale. Using molecular dynamics (MD) simulations, we probe the conformation of luminescent rigid polymers, dialkyl poly(p-phenylene ethynylene)s (PPE), end-grafted onto a silica nanoparticle in different solvents as the molecular weights and polymer coverages are varied. We find that, in contrast to NP-grafted flexible polymers, the chains are fully extended independent of the solvent. In toluene and decane, which are good solvents, the graftedmore » PPEs chains assume a similar conformation to that observed in dilute solutions. In water, which is a poor solvent for the PPEs, the polymer chains form one large cluster but remain extended. The radial distribution of the chains around the core of the nanoparticle is homogeneous in good solvents, whereas in poor solvents clusters are formed independent of molecular weights and coverages. As a result, the clustering is distinctively different from the response of grafted flexible and semiflexible polymers.« less

  5. Reactor physics simulations with coupled Monte Carlo calculation and computational fluid dynamics.

    SciTech Connect (OSTI)

    Seker, V.; Thomas, J. W.; Downar, T. J.; Purdue Univ.

    2007-01-01

    A computational code system based on coupling the Monte Carlo code MCNP5 and the Computational Fluid Dynamics (CFD) code STAR-CD was developed as an audit tool for lower order nuclear reactor calculations. This paper presents the methodology of the developed computer program 'McSTAR'. McSTAR is written in FORTRAN90 programming language and couples MCNP5 and the commercial CFD code STAR-CD. MCNP uses a continuous energy cross section library produced by the NJOY code system from the raw ENDF/B data. A major part of the work was to develop and implement methods to update the cross section library with the temperature distribution calculated by STARCD for every region. Three different methods were investigated and implemented in McSTAR. The user subroutines in STAR-CD are modified to read the power density data and assign them to the appropriate variables in the program and to write an output data file containing the temperature, density and indexing information to perform the mapping between MCNP and STAR-CD cells. Preliminary testing of the code was performed using a 3x3 PWR pin-cell problem. The preliminary results are compared with those obtained from a STAR-CD coupled calculation with the deterministic transport code DeCART. Good agreement in the k{sub eff} and the power profile was observed. Increased computational capabilities and improvements in computational methods have accelerated interest in high fidelity modeling of nuclear reactor cores during the last several years. High-fidelity has been achieved by utilizing full core neutron transport solutions for the neutronics calculation and computational fluid dynamics solutions for the thermal-hydraulics calculation. Previous researchers have reported the coupling of 3D deterministic neutron transport method to CFD and their application to practical reactor analysis problems. One of the principal motivations of the work here was to utilize Monte Carlo methods to validate the coupled deterministic neutron

  6. Enhanced dynamics of hydrated tRNA on nanodiamond surfaces: A combined neutron scattering and MD simulation study

    DOE PAGES-Beta [OSTI]

    Dhindsa, Gurpreet K.; Bhowmik, Debsindhu; Goswami, Monojoy; O’Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G.; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang -qiang

    2016-09-01

    Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on NDmore » surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. As a result, our new findings may provide new design principles for safer, improved drug delivery platforms.« less

  7. Use of a dynamic simulation model to understand nitrogen cycling in the middle Rio Grande, NM.

    SciTech Connect (OSTI)

    Meixner, Tom; Tidwell, Vincent Carroll; Oelsner, Gretchen; Brooks, Paul; Roach, Jesse D.

    2008-08-01

    Water quality often limits the potential uses of scarce water resources in semiarid and arid regions. To best manage water quality one must understand the sources and sinks of both solutes and water to the river system. Nutrient concentration patterns can identify source and sink locations, but cannot always determine biotic processes that affect nutrient concentrations. Modeling tools can provide insight into these large-scale processes. To address questions about large-scale nitrogen removal in the Middle Rio Grande, NM, we created a system dynamics nitrate model using an existing integrated surface water--groundwater model of the region to evaluate our conceptual models of uptake and denitrification as potential nitrate removal mechanisms. We modeled denitrification in groundwater as a first-order process dependent only on concentration and used a 5% denitrification rate. Uptake was assumed to be proportional to transpiration and was modeled as a percentage of the evapotranspiration calculated within the model multiplied by the nitrate concentration in the water being transpired. We modeled riparian uptake as 90% and agricultural uptake as 50% of the respective evapotranspiration rates. Using these removal rates, our model results suggest that riparian uptake, agricultural uptake and denitrification in groundwater are all needed to produce the observed nitrate concentrations in the groundwater, conveyance channels, and river as well as the seasonal concentration patterns. The model results indicate that a total of 497 metric tons of nitrate-N are removed from the Middle Rio Grande annually. Where river nitrate concentrations are low and there are no large nitrate sources, nitrate behaves nearly conservatively and riparian and agricultural uptake are the most important removal mechanisms. Downstream of a large wastewater nitrate source, denitrification and agricultural uptake were responsible for approximately 90% of the nitrogen removal.

  8. Architectural Improvements and New Processing Tools for the Open XAL Online Model

    SciTech Connect (OSTI)

    Allen, Christopher K; Pelaia II, Tom; Freed, Jonathan M

    2015-01-01

    The online model is the component of Open XAL providing accelerator modeling, simulation, and dynamic synchronization to live hardware. Significant architectural changes and feature additions have been recently made in two separate areas: 1) the managing and processing of simulation data, and 2) the modeling of RF cavities. Simulation data and data processing have been completely decoupled. A single class manages all simulation data while standard tools were developed for processing the simulation results. RF accelerating cavities are now modeled as composite structures where parameter and dynamics computations are distributed. The beam and hardware models both maintain their relative phase information, which allows for dynamic phase slip and elapsed time computation.

  9. Lenard-Balescu calculations and classical molecular dynamics simulations of electrical and thermal conductivities of hydrogen plasmas

    DOE PAGES-Beta [OSTI]

    Whitley, Heather D.; Scullard, Christian R.; Benedict, Lorin X.; Castor, John I.; Randles, Amanda; Glosli, James N.; Richards, David F.; Desjarlais, Michael P.; Graziani, Frank R.

    2015-12-04

    Here, we present a discussion of kinetic theory treatments of linear electrical and thermal transport in hydrogen plasmas, for a regime of interest to inertial confinement fusion applications. In order to assess the accuracy of one of the more involved of these approaches, classical Lenard-Balescu theory, we perform classical molecular dynamics simulations of hydrogen plasmas using 2-body quantum statistical potentials and compute both electrical and thermal conductivity from out particle trajectories using the Kubo approach. Our classical Lenard-Balescu results employing the identical statistical potentials agree well with the simulations.

  10. Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach

    SciTech Connect (OSTI)

    Hyeon-Deuk, Kim; Ando, Koji

    2014-05-07

    Liquid para-hydrogen (p-H{sub 2}) is a typical quantum liquid which exhibits strong nuclear quantum effects (NQEs) and thus anomalous static and dynamic properties. We propose a real-time simulation method of wave packet (WP) molecular dynamics (MD) based on non-empirical intra- and inter-molecular interactions of non-spherical hydrogen molecules, and apply it to condensed-phase p-H{sub 2}. The NQEs, such as WP delocalization and zero-point energy, are taken into account without perturbative expansion of prepared model potential functions but with explicit interactions between nuclear and electron WPs. The developed MD simulation for 100 ps with 1200 hydrogen molecules is realized at feasible computational cost, by which basic experimental properties of p-H{sub 2} liquid such as radial distribution functions, self-diffusion coefficients, and shear viscosities are all well reproduced.

  11. New tools for modeling fracture networks and simulating gas flow in low-permeability sand and shale reservoirs

    SciTech Connect (OSTI)

    McKoy, M.L.; Sams, W.N.

    1996-09-01

    The U.S. Department of Energy, Morgantown Energy Technology Center, has an on-going project to model and simulate gas flow in low-permeability sands and shales that contain irregular, sometimes discontinuous, fracture networks (i.e., the types of networks not adequately represented by existing models/simulators). A FORTRAN code and methodology for modeling and simulating flow in these fracture networks has been developed. The goal was to convert the locations and orientations of fractures, as observed along a horizontal well bore, into two-dimensional, geometrically and hydraulically equivalent networks, which can be used to study variability in yield and drainage pattern. The fracture network generator implements four models of increasing complexity through a Monte Carlo process of selecting fracture network attributes from fitted statistical distributions. A process of shifting fracture end-point locations along the axes of fractures provides a partial control of fracture intersection/termination frequencies. Output consists of fracture end-points and apertures. The flow simulator divides each fracture-bounded matrix block into subregions that drain to the midpoint of the adjacent fracture segment in accordance with a one-dimensional, unsteady idealization. The idealization approximates both the volume and the mean flow path length of each subregion. Volumetric flow rate in the fractures is modeled as a linear function of the pressure difference between the recharge points and the fracture intersections. The requirement of material balance between all intersections couples the individual recharge models together, and the resulting equations are solved by a Newton-Raphson technique.

  12. Development Plan for the Fuel Cycle Simulator

    SciTech Connect (OSTI)

    Brent Dixon

    2011-09-01

    The Fuel Cycle Simulator (FCS) project was initiated late in FY-10 as the activity to develop a next generation fuel cycle dynamic analysis tool for achieving the Systems Analysis Campaign 'Grand Challenge.' This challenge, as documented in the Campaign Implementation Plan, is to: 'Develop a fuel cycle simulator as part of a suite of tools to support decision-making, communication, and education, that synthesizes and visually explains the multiple attributes of potential fuel cycles.'

  13. Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

    DOE PAGES-Beta [OSTI]

    Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

    2015-10-30

    An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease statesmore » in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.« less

  14. Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

    SciTech Connect (OSTI)

    Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

    2015-10-30

    An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease states in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.

  15. User Guide for PV Dynamic Model Simulation Written on PSCAD Platform

    SciTech Connect (OSTI)

    Muljadi, E.; Singh, M.; Gevorgian, V.

    2014-11-01

    This document describes the dynamic photovoltaic model developed by the National Renewable Energy Laboratory and is intended as a guide for users of these models.

  16. Molecular dynamics simulation of Coulomb explosion, melting and shock wave creation in silicon after an ionization pulse

    SciTech Connect (OSTI)

    Li, Zhongyu; Shao, Lin; Chen, Di; Wang, Jing

    2014-04-14

    Strong electronic stopping power of swift ions in a semiconducting or insulating substrate can lead to localized electron stripping. The subsequent repulsive interactions among charged target atoms can cause Coulomb explosion. Using molecular dynamics simulation, we simulate Coulomb explosion in silicon by introducing an ionization pulse lasting for different periods, and at different substrate temperatures. We find that the longer the pulse period, the larger the melting radius. The observation can be explained by a critical energy density model assuming that melting required thermal energy density is a constant value and the total thermal energy gained from Coulomb explosion is linearly proportional to the ionization period. Our studies also show that melting radius is larger at higher substrate temperatures. The temperature effect is explained due to a longer structural relaxation above the melting temperature at original ionization boundary due to lower heat dissipation rates. Furthermore, simulations show the formation of shock waves, created due to the compression from the melting core.

  17. Molecular dynamics simulations of D{sub 2}O ice photodesorption

    SciTech Connect (OSTI)

    Arasa, C.; Andersson, S.; Cuppen, H. M.; Dishoeck, E. F. van; Kroes, G. J.

    2011-04-28

    Molecular dynamics (MD) calculations have been performed to study the ultraviolet (UV) photodissociation of D{sub 2}O in an amorphous D{sub 2}O ice surface at 10, 20, 60, and 90 K, in order to investigate the influence of isotope effects on the photodesorption processes. As for H{sub 2}O, the main processes after UV photodissociation are trapping and desorption of either fragments or D{sub 2}O molecules. Trapping mainly takes place in the deeper monolayers of the ice, whereas desorption occurs in the uppermost layers. There are three desorption processes: D atom, OD radical, and D{sub 2}O molecule photodesorption. D{sub 2}O desorption takes places either by direct desorption of a recombined D{sub 2}O molecule, or when an energetic D atom produced by photodissociation kicks a surrounding D{sub 2}O molecule out of the surface by transferring part of its momentum. Desorption probabilities are calculated for photoexcitation of D{sub 2}O in the top four monolayers and are compared quantitatively with those for H{sub 2}O obtained from previous MD simulations of UV photodissociation of amorphous water ice at different ice temperatures [Arasa et al., J. Chem. Phys. 132, 184510 (2010)]. The main conclusions are the same, but the average D atom photodesorption probability is smaller than that of the H atom (by about a factor of 0.9) because D has lower kinetic energy than H, whereas the average OD radical photodesorption probability is larger than that of OH (by about a factor of 2.5-2.9 depending on ice temperature) because OD has higher translational energy than OH for every ice temperature studied. The average D{sub 2}O photodesorption probability is larger than that of H{sub 2}O (by about a factor of 1.4-2.3 depending on ice temperature), and this is entirely due to a larger contribution of the D{sub 2}O kick-out mechanism. This is an isotope effect: the kick-out mechanism is more efficient for D{sub 2}O ice, because the D atom formed after D{sub 2}O photodissociation

  18. Anharmonic lattice dynamics of Ag2O studied by inelastic neutron scattering and first-principles molecular dynamics simulations

    SciTech Connect (OSTI)

    Lan, Tian; Li, Chen; Niedziela, Jennifer L; Smith, Hillary; Abernathy, Douglas L; Rossman, George; Fultz, B.

    2014-01-01

    Inelastic neutron scattering measurements on silver oxide (Ag2O) with the cuprite structure were performed at temperatures from 40 to 400 K, and Fourier transform far-infrared spectra were measured from 100 to 300 K. The measured phonon densities of states and the infrared spectra showed unusually large energy shifts with temperature, and large linewidth broadenings. First principles molecular dynamics (MD) calculations were performed at various temperatures, successfully accounting for the negative thermal expansion (NTE) and local dynamics. Using the Fourier-transformed velocity autocorrelation method, the MD calculations reproduced the large anharmonic effects of Ag2O, and were in excellent agreement with the neutron scattering data. The quasiharmonic approximation (QHA) was less successful in accounting for much of the phonon behavior. The QHA could account for some of the NTE below 250 K, although not at higher temperatures. Strong anharmonic effects were found for both phonons and for the NTE. The lifetime broadenings of Ag2O were explained by anharmonic perturbation theory, which showed rich interactions between the Ag-dominated modes and the O-dominated modes in both up- and down-conversion processes.

  19. Challenges in Simulation of Aerodynamics, Hydrodynamics, and Mooring-Line Dynamics of Floating Offshore Wind Turbines

    SciTech Connect (OSTI)

    Matha, D.; Schlipf, M.; Cordle, A.; Pereira, R.; Jonkman, J.

    2011-10-01

    This paper presents the current major modeling challenges for floating offshore wind turbine design tools and describes aerodynamic and hydrodynamic effects due to rotor and platform motions and usage of non-slender support structures.

  20. SU-E-T-349: Verification of a Monte Carlo Simulation Tool as a Second Check for TomoTherapy Treatment Planning

    SciTech Connect (OSTI)

    Yuan, J; Zheng, Y; Sohn, J; Wessels, B; Chen, Q

    2014-06-01

    Purpose: To verify a virtual source model used in Monte Carlo (MC) TomoTherapy simulations and to provide a tool for the dose distribution second check for TomoTherapy treatment planning. Methods: Published studies adopted the full MC model to simulate helical TomoTherapy which use phase space files (PSFs) at different scoring planes to facilitate patient dose calculations. We have developed a simple virtual source model (VSM) based on the commissioning data of helical TomoTherapy unit which can be exported from the treatment planning station (TPS). To calculate the patient dose distribution, TPS-generated sinograms are extracted from archived patient XML files and fluence maps are created by incorporating the openclose leaf time with leaf filter, jaw penumbra, and leaf latency. The VSM has been validated for various geometrical set-ups including open fields, heterogeneous media and clinical DQA cases. Results: Good agreement was obtained between our VSM and a published full MC model for the test case of heterogeneous media. For the complex clinical head and neck (HN) case, the MC simulation of the DQA plan agreed with the film measurement with 98% of planar dose pixels passing the 2%/2 mm gamma value test. For the patient treatment plan itself, the MC simulation showed comparable DVHs for the planning target volumes (PTVs) and organs-at-risk (OARs). Deviations observed were consistent with literature. Conclusion: The proposed VSM can be used in the MC method to accurately simulate the patient dose distributions for helical TomoTherapy.

  1. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    SciTech Connect (OSTI)

    Lee, Mal Soon; McGrail, B. Peter; Rousseau, Roger J.; Glezakou, Vassiliki Alexandra

    2015-10-12

    The interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivity and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T=323 K and P=90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences, Geosciences and Biosciences

  2. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    DOE PAGES-Beta [OSTI]

    Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki -Alexandra

    2015-10-12

    Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivitymore » and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences

  3. Does fluoride disrupt hydrogen bond network in cationic lipid bilayer? Time-dependent fluorescence shift of Laurdan and molecular dynamics simulations

    SciTech Connect (OSTI)

    Pokorna, Sarka; Jurkiewicz, Piotr; Hof, Martin; Vazdar, Mario; Cwiklik, Lukasz; Jungwirth, Pavel

    2014-12-14

    Time-dependent fluorescence shift (TDFS) of Laurdan embedded in phospholipid bilayers reports on hydration and mobility of the phospholipid acylgroups. Exchange of H{sub 2}O with D{sub 2}O prolongs the lifetime of lipid-water and lipid-water-lipid interactions, which is reflected in a significantly slower TDFS kinetics. Combining TDFS measurements in H{sub 2}O and D{sub 2}O hydrated bilayers with atomistic molecular dynamics (MD) simulations provides a unique tool for characterization of the hydrogen bonding at the acylgroup level of lipid bilayers. In this work, we use this approach to study the influence of fluoride anions on the properties of cationic bilayers composed of trimethylammonium-propane (DOTAP). The results obtained for DOTAP are confronted with those for neutral phosphatidylcholine (DOPC) bilayers. Both in DOTAP and DOPC H{sub 2}O/D{sub 2}O exchange prolongs hydrogen-bonding lifetime and does not disturb bilayer structure. These results are confirmed by MD simulations. TDFS experiments show, however, that for DOTAP this effect is cancelled in the presence of fluoride ions. We interpret these results as evidence that strongly hydrated fluoride is able to steal water molecules that bridge lipid carbonyls. Consequently, when attracted to DOTAP bilayer, fluoride disrupts the local hydrogen-bonding network, and the differences in TDFS kinetics between H{sub 2}O and D{sub 2}O hydrated bilayers are no longer observed. A distinct behavior of fluoride is also evidenced by MD simulations, which show different lipid-ion binding for Cl{sup −} and F{sup −}.

  4. Effect of surface roughness and size of beam on squeeze-film damping—Molecular dynamics simulation study

    SciTech Connect (OSTI)

    Kim, Hojin; Strachan, Alejandro

    2015-11-28

    We use large-scale molecular dynamics (MD) to characterize fluid damping between a substrate and an approaching beam. We focus on the near contact regime where squeeze film (where fluid gap is comparable to the mean free path of the gas molecules) and many-body effects in the fluid become dominant. The MD simulations provide explicit description of many-body and non-equilibrium processes in the fluid as well as the surface topography. We study how surface roughness and beam width increases the damping coefficient due to their effect on fluid mobility. We find that the explicit simulations are in good agreement with prior direct simulation Monte Carlo results except at near-contact conditions where many-body effects in the compressed fluid lead the increased damping and weaker dependence on beam width. We also show that velocity distributions near the beam edges and for short gaps deviate from the Boltzmann distribution indicating a degree of local non-equilibrium. These results will be useful to parameterize compact models used for microsystem device-level simulations and provide insight into mesoscale simulations of near-contact damping.

  5. Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

    SciTech Connect (OSTI)

    Jakobtorweihen, S. Ingram, T.; Gerlach, T.; Smirnova, I.; Zuniga, A. Chaides; Keil, F. J.

    2014-07-28

    Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations.

  6. Dynamic Simulation Studies of the Frequency Response of the Three U.S. Interconnections with Increased Wind Generation

    SciTech Connect (OSTI)

    Mackin, Peter; Daschmans, R.; Williams, B.; Haney, B.; Hung, R.; Ellis, J.

    2010-12-20

    Utility Systems Efficiencies, Inc. was tasked by Lawrence Berkeley National Laboratory (LBNL) to conduct dynamic simulation studies of the three U.S. interconnections (Eastern, Western, and Texas). The simulations were prepared in support of LBNL's project for the Federal Energy Regulatory Commission to study frequency-response-related issues that must be addressed to operate the power system reliably with large amounts of variable renewable generation. The objective of the simulation studies of each interconnection was to assess the effects of different amounts of wind generation on frequency behavior of each interconnection following a sudden loss of generation. The scenarios created to study these effects considered an operating circumstance in which system load is at or close to its minimum. The event studied was the sudden loss of the largest amount of generation recorded within each interconnection. The simulations calculated the impact of this event on interconnection frequency for three levels of wind generation. In addition to varying the amount of wind generation, the simulations varied the amount of operating reserves between a high level representative of current operating practices and a low level representative of the minimum required by present operating rules.

  7. Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

    DOE PAGES-Beta [OSTI]

    Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; Opper, Kathleen L.; Wagener, Kenneth B.; Stevens, Mark J.; Frischknecht, Amalie Lucile; Winey, Karen I.

    2015-02-09

    Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the

  8. A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon

    SciTech Connect (OSTI)

    D`Azevedo, E.F.; Romine, C.H.

    1994-12-01

    This report describes the use of shared memory emulation with DOLIB (Distributed Object Library) to simplify parallel programming on the Intel Paragon. A molecular dynamics application is used as an example to illustrate the use of the DOLIB shared memory library. SOTON-PAR, a parallel molecular dynamics code with explicit message-passing using a Lennard-Jones 6-12 potential, is rewritten using DOLIB primitives. The resulting code has no explicit message primitives and resembles a serial code. The new code can perform dynamic load balancing and achieves better performance than the original parallel code with explicit message-passing.

  9. Effect of Cu2+ Activation on Interfacial Water Structure at the Sphalerite Surface as Studied by Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.

    2015-12-10

    In the first part of this paper, an experimental contact angle study of the fresh and Cu2+ activated sphalerite-ZnS surface as well as the covellite-CuS (001) surface is reported describing the increased hydrophobic character of the surface during Cu2+ activation. In addition to these experimental results, the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite- CuS2 (100), and covellite-CuS (001) surfaces were examined using Molecular Dynamics Simulation (MDS). Our MDS results on the behavior of interfacial water at the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite-CuS2 (100), and covellite-CuS (001) surfaces include simulated contact angles, water number density distribution, water dipole orientation, water residence time, and hydrogen-bonding considerations. The copper content at the Cu2+ activated sphalerite surface seems to account for the increased hydrophobicity as revealed by both experimental and MD simulated contact angle measurements. The relatively greater hydrophobic character developed at the Cu2+ activated sphalerite surface and at the copper-zinc sulfide surface has been described by MDS, based on the structure of interfacial water and its dynamic properties. L.X.D. acknowledges funding from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

  10. Nonlinear Theoretical Tools for Fusion-related Microturbulence: Historical Evolution, and Recent Applications to Stochastic Magnetic Fields, Zonal-flow Dynamics, and Intermittency

    SciTech Connect (OSTI)

    J.A. Krommes

    2009-05-19

    Fusion physics poses an extremely challenging, practically complex problem that does not yield readily to simple paradigms. Nevertheless, various of the theoretical tools and conceptual advances emphasized at the KaufmanFest 2007 have motivated and/or found application to the development of fusion-related plasma turbulence theory. A brief historical commentary is given on some aspects of that specialty, with emphasis on the role (and limitations) of Hamiltonian/symplectic approaches, variational methods, oscillation-center theory, and nonlinear dynamics. It is shown how to extract a renormalized ponderomotive force from the statistical equations of plasma turbulence, and the possibility of a renormalized K-χ theorem is discussed. An unusual application of quasilinear theory to the problem of plasma equilibria in the presence of stochastic magnetic fields is described. The modern problem of zonal-flow dynamics illustrates a confluence of several techniques, including (i) the application of nonlinear-dynamics methods, especially center-manifold theory, to the problem of the transition to plasma turbulence in the face of self-generated zonal flows; and (ii) the use of Hamiltonian formalism to determine the appropriate (Casimir) invariant to be used in a novel wave-kinetic analysis of systems of interacting zonal flows and drift waves. Recent progress in the theory of intermittent chaotic statistics and the generation of coherent structures from turbulence is mentioned, and an appeal is made for some new tools to cope with these interesting and difficult problems in nonlinear plasma physics. Finally, the important influence of the intellectually stimulating research environment fostered by Prof. Allan Kaufman on the author's thinking and teaching methodology is described.

  11. Three-dimensional ordering of cold ion beams in a storage ring: A molecular-dynamics simulation study

    SciTech Connect (OSTI)

    Yuri, Yosuke

    2015-06-29

    Three-dimensional (3D) ordering of a charged-particle beams circulating in a storage ring is systematically studied with a molecular-dynamics simulation code. An ion beam can exhibit a 3D ordered configuration at ultralow temperature as a result of powerful 3D laser cooling. Various unique characteristics of the ordered beams, different from those of crystalline beams, are revealed in detail, such as the single-particle motion in the transverse and longitudinal directions, and the dependence of the tune depression and the Coulomb coupling constant on the operating points.

  12. Radiation damage in cubic ZrO2 and yttria-stabilized zirconia from molecular dynamics simulations

    DOE PAGES-Beta [OSTI]

    Aidhy, Dilpuneet S.; Zhang, Yanwen; Weber, William J.

    2014-11-20

    Here, we perform molecular dynamics simulation on cubic ZrO2 and yttria-stabilized zirconia (YSZ) to elucidate defect cluster formation resulting from radiation damage, and evaluate the impact of Y-dopants. Interstitial clusters composed of split-interstitial building blocks, i.e., Zr-Zr or Y-Zr are formed. Moreover, oxygen vacancies control cation defect migration; in their presence, Zr interstitials aggregate to form split-interstitials whereas in their absence Zr interstitials remain immobile, as isolated single-interstitials. Y-doping prevents interstitial cluster formation due to sequestration of oxygen vacancies.

  13. Radiation damage in cubic-ZrO2 and yttria-stabilized zirconia from molecular dynamics simulations

    SciTech Connect (OSTI)

    Aidhy, Dilpuneet S; Zhang, Yanwen; Weber, William J

    2015-01-01

    We perform molecular dynamics simulation on cubic ZrO2 and yttria-stabilized zirconia (YSZ) to elucidate defect cluster formation resulting from radiation damage, and evaluate the impact of Y-dopants. Interstitial clusters composed of split-interstitial building blocks, i.e., Zr-Zr or Y-Zr are formed. Oxygen vacancies control cation defect migration; in their presence, Zr interstitials aggregate to form split-interstitials whereas in their absence Zr interstitials remain immobile, as isolated single-interstitials. Y-doping prevents interstitial cluster formation due to sequestration of oxygen vacancies.

  14. Adapting SAFT-? perturbation theory to site-based molecular dynamics simulation. I. Homogeneous fluids

    SciTech Connect (OSTI)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2013-12-21

    In this work, we aim to develop a version of the Statistical Associating Fluid Theory (SAFT)-? equation of state (EOS) that is compatible with united-atom force fields, rather than experimental data. We rely on the accuracy of the force fields to provide the relation to experimental data. Although, our objective is a transferable theory of interfacial properties for soft and fused heteronuclear chains, we first clarify the details of the SAFT-? approach in terms of site-based simulations for homogeneous fluids. We show that a direct comparison of Helmholtz free energy to molecular simulation, in the framework of a third order Weeks-Chandler-Andersen perturbation theory, leads to an EOS that takes force field parameters as input and reproduces simulation results for Vapor-Liquid Equilibria (VLE) calculations. For example, saturated liquid density and vapor pressure of n-alkanes ranging from methane to dodecane deviate from those of the Transferable Potential for Phase Equilibria (TraPPE) force field by about 0.8% and 4%, respectively. Similar agreement between simulation and theory is obtained for critical properties and second virial coefficient. The EOS also reproduces simulation data of mixtures with about 5% deviation in bubble point pressure. Extension to inhomogeneous systems and united-atom site types beyond those used in description of n-alkanes will be addressed in succeeding papers.

  15. Fully 3D Multiple Beam Dynamics Processes Simulation for the Fermilab Tevatron

    SciTech Connect (OSTI)

    Stern, E.; Amundson, J.; Spentzouris, P; Valishev, A.; /Fermilab

    2010-06-01

    The Fermilab Tevatron has been, until 2010, the premier high-energy physics collider in the world. The data collected over the last decade by high-energy physics experiments running at the Tevatron have been analyzed to make important measurements in fundamental areas such as B meson masses and flavor oscillation, searches for the Higgs boson, and supersymmetry. Collecting these data at the limits of detectability has required the Tevatron to operate reliably at high beam intensities to maximize the number of collisions to analyze. This impressive achievement has been assisted by the use of HPC resources and software provided through the SciDAC program. This paper describes the enhancements to the BeamBeam3d code to realistically simulate the Tevatron, the validation of these simulations, and the improvement in equipment reliability and personal safety achieved with the aid of simulations.

  16. Molecular dynamics simulations of the effects of salts on the aggregation properties of benzene in water.

    SciTech Connect (OSTI)

    Smith, P. E.

    2003-07-16

    The specific aims of the project were: to provide an atomic level description of the interactions between benzene, water and ions in solutions. To determine the degree of association between two benzene molecules in aqueous and salt solutions. To investigate the structure and dynamics of the interface between benzene and water or salt solution.

  17. Molecular dynamic simulation of Ar-Kr mixture across a rough walled nanochannel: Velocity and temperature profiles

    SciTech Connect (OSTI)

    Pooja, Ahluwalia, P. K.; Pathania, Y.

    2015-05-15

    This paper presents the results from a molecular dynamics simulation of mixture of argon and krypton in the Poiseuille flow across a rough walled nanochannel. The roughness effect on liquid nanoflows has recently drawn attention The computational software used for carrying out the molecular dynamics simulations is LAMMPS. The fluid flow takes place between two parallel plates and is bounded by horizontal rough walls in one direction and periodic boundary conditions are imposed in the other two directions. Each fluid atom interacts with other fluid atoms and wall atoms through Leenard-Jones (LJ) potential with a cut off distance of 5.0. To derive the flow a constant force is applied whose value is varied from 0.1 to 0.3 and velocity profiles and temperature profiles are noted for these values of forces. The velocity profile and temperature profiles are also looked at different channel widths of nanochannel and at different densities of mixture. The velocity profile and temperature profile of rough walled nanochannel are compared with that of smooth walled nanochannel and it is concluded that mean velocity increases with increase in channel width, force applied and decrease in density also with introduction of roughness in the walls of nanochannel mean velocity again increases and results also agree with the analytical solution of a Poiseuille flow.

  18. Particle simulation of collision dynamics for ion beam injection into a rarefied gas

    SciTech Connect (OSTI)

    Giuliano, Paul N.; Boyd, Iain D.

    2013-03-15

    This study details a comparison of ion beam simulations with experimental data from a simplified plasma test cell in order to study and validate numerical models and environments representative of electric propulsion devices and their plumes. The simulations employ a combination of the direct simulation Monte Carlo and particle-in-cell methods representing xenon ions and atoms as macroparticles. An anisotropic collision model is implemented for momentum exchange and charge exchange interactions between atoms and ions in order to validate the post-collision scattering behaviors of dominant collision mechanisms. Cases are simulated in which the environment is either collisionless or non-electrostatic in order to prove that the collision models are the dominant source of low- and high-angle particle scattering and current collection within this environment. Additionally, isotropic cases are run in order to show the importance of anisotropy in these collision models. An analysis of beam divergence leads to better characterization of the ion beam, a parameter that requires careful analysis. Finally, suggestions based on numerical results are made to help guide the experimental design in order to better characterize the ion environment.

  19. Effect of Surface Oxidation on Interfacial Water Structure at a Pyrite (100) Surface as Studied by Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.

    2015-06-01

    In the first part of this paper, a Scanning Electron Microscopy and contact angle study of a pyrite surface (100) is reported describing the relationship between surface oxidation and the hydrophilic surface state. In addition to these experimental results, the following simulated surface states were examined using Molecular Dynamics Simulation (MDS): fresh unoxidized (100) surface; polysulfide at the (100) surface; elemental sulfur at the (100) surface. Crystal structures for the polysulfide and elemental sulfur at the (100) surface were simulated using Density Functional Theory (DFT) quantum chemical calculations. The well known oxidation mechanism which involves formation of a metal deficient layer was also described with DFT. Our MDS results of the behavior of interfacial water at the fresh and oxidized pyrite (100) surfaces without/with the presence of ferric hydroxide include simulated contact angles, number density distribution for water, water dipole orientation, water residence time, and hydrogen-bonding considerations. The significance of the formation of ferric hydroxide islands in accounting for the corresponding hydrophilic surface state is revealed not only from experimental contact angle measurements but also from simulated contact angle measurements using MDS. The hydrophilic surface state developed at oxidized pyrite surfaces has been described by MDS, on which basis the surface state is explained based on interfacial water structure. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE funded work performed by Liem X. Dang. Battelle operates the Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.

  20. Computational Tools to Accelerate Commercial Development

    SciTech Connect (OSTI)

    Miller, David C

    2013-01-01

    The goals of the work reported are: to develop new computational tools and models to enable industry to more rapidly develop and deploy new advanced energy technologies; to demonstrate the capabilities of the CCSI Toolset on non-proprietary case studies; and to deploy the CCSI Toolset to industry. Challenges of simulating carbon capture (and other) processes include: dealing with multiple scales (particle, device, and whole process scales); integration across scales; verification, validation, and uncertainty; and decision support. The tools cover: risk analysis and decision making; validated, high-fidelity CFD; high-resolution filtered sub-models; process design and optimization tools; advanced process control and dynamics; process models; basic data sub-models; and cross-cutting integration tools.

  1. Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

    SciTech Connect (OSTI)

    Lisal, Martin; Izak, Pavel

    2013-07-07

    Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf{sub 2}N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 {mu}mol/m{sup 2} at 300 K. For [bmim][Tf{sub 2}N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are {+-}0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf{sub 2}N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

  2. Mass transport properties of Pu/DT mixtures from orbital free molecular dynamics simulations

    SciTech Connect (OSTI)

    Kress, Joel David; Ticknor, Christopher; Collins, Lee A.

    2015-09-16

    Mass transport properties (shear viscosity and diffusion coefficients) for Pu/DT mixtures were calculated with Orbital Free Molecular Dynamics (OFMD). The results were fitted to simple functions of mass density (for ρ=10.4 to 62.4 g/cm3) and temperature (for T=100 up to 3,000 eV) for Pu/DT mixtures consisting of 100/0, 25/75, 50/50, and 75/25 by number.

  3. Predictive Simulation and Design of Materials by Quasicontinuum and Accelerated Dynamics Methods

    SciTech Connect (OSTI)

    Luskin, Mitchell; James, Richard; Tadmor, Ellad

    2014-03-30

    This project developed the hyper-QC multiscale method to make possible the computation of previously inaccessible space and time scales for materials with thermally activated defects. The hyper-QC method combines the spatial coarse-graining feature of a finite temperature extension of the quasicontinuum (QC) method (aka “hot-QC”) with the accelerated dynamics feature of hyperdynamics. The hyper-QC method was developed, optimized, and tested from a rigorous mathematical foundation.

  4. An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water

    SciTech Connect (OSTI)

    Fanourgakis, Georgios S.; Tipparaju, Vinod; Nieplocha, Jarek; Xantheas, Sotiris S.

    2007-01-01

    An efficient parallelization scheme for classical Molecular Dynamics simulations with flexible polarizable empirical potentials is presented. It is based on the standard Ewald summation technique to handle the long-range electrostatic and induction interactions. The algorithm for this parallelization scheme is designed for systems containing several thousands of polarizable sites in the simulation box. Its performance is evaluated during Molecular Dynamics simulations under periodic boundary conditions with unit cell sizes ranging from 128-512 water molecules employing two exible, polarizable water models [POL1(F) and TTM2-F] containing 1 and 3 polarizable sites respectively. The efficiency of the algorithm, is evaluated against a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient calculations of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed in several cases. To the best of our knowledge, this is the first attempt for a parallel implementation of a polarizable potential under periodic boundary conditions. Guidelines for adapting the algorithm for larger systems are also discussed. This research was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences laboratory, a national scientific user facility sponsored by the U.S. Department of Energys Office of Biological and Environmental Research located at the Pacific Northwest National Laboratory. The Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy under contract DE-AC05-76RL01830.

  5. Numerical simulation of dynamic stall around an airfoil in Darrieus motion

    SciTech Connect (OSTI)

    Allet, A.; Halle, S.; Paraschivoiu, I.

    1999-02-01

    The objective of this study is to investigate the two-dimensional unsteady flow around an airfoil undergoing a Darrieus motion in dynamic stall conditions. For this purpose, a numerical solver based on the solution of the Reynolds-averaged Navier-Stokes equations expressed in a streamfunction-vorticity formulation in a non-inertial frame of reference was developed. The governing equations are solved by the streamline upwind Petrov-Galerkin finite element method (FEM). Temporal discretization is achieved by second-order-accurate finite differences. The resulting global matrix system is linearized by the Newton method and solved by the generalized minimum residual method (GMRES) with an incomplete triangular factorization preconditioning (ILU). Turbulence effects are introduced in the solver by an eddy viscosity model. The investigation centers on an evaluation of the algebraic Cebeci-Smith model (CSM) and the nonequilibrium Johnson-King model (JKM). In an effort to predict dynamic stall features on rotating airfoils, first the authors present some testing results concerning the performance of both turbulence models for the flat plate case. Then, computed flow structure together with aerodynamic coefficients for a NACA 0015 airfoil in Darrieus motion under dynamic stall conditions are presented.

  6. Computational fluid dynamics simulation of the air/suppressant flow in an uncluttered F18 engine nacelle

    SciTech Connect (OSTI)

    Lopez, A.R.; Gritzo, L.A.; Hassan, B.

    1997-06-01

    For the purposes of designing improved Halon-alternative fire suppression strategies for aircraft applications, Computational Fluid Dynamics (CFD) simulations of the air flow, suppressant transport, and air-suppressant mixing within an uncluttered F18 engine nacelle were performed. The release of inert gases from a Solid Propellant Gas Generator (SPGG) was analyzed at two different injection locations in order to understand the effect of injection position on the flow patterns and the mixing of air and suppression agent. An uncluttered engine nacelle was simulated to provide insight into the global flow features as well as to promote comparisons with previous nacelle fire tests and recent water tunnel tests which included little or no clutter. Oxygen concentration levels, fuel/air residence times that would exist if a small fuel leak were present, velocity contours, and streamline patterns are presented inside the engine nacelle. The numerical results show the influence of the gent release location on regions of potential flame extinction due to oxygen inerting and high flame strain. The occurrence of inflow through the exhaust ducts on the aft end of the nacelle is also predicted. As expected, the predicted oxygen concentration levels were consistently higher than the measured levels since a fire was not modeled in this analysis. Despite differences in the conditions of these simulations and the experiments, good agreement was obtained between the CFD predictions and the experimental measurements.

  7. Numerical simulation of gas dynamics and heat exchange tasks in fuel assemblies of the nuclear reactors

    SciTech Connect (OSTI)

    Zhuchenko, S. V.

    2014-11-12

    This report presents a PC-based program for solution gas dynamics and heat exchange mathematical tasks in fuel assemblies of the fast-neutron nuclear reactors. A fuel assembly consisting of bulk heat-generating elements, which are integrated together by the system of supply and pressure manifolds, is examined. Spherical heat-generating microelements, which contain nuclear fuel, are pulled into the heat-generating elements. Gaseous coolant proceed from supply manifolds to heat-generating elements, where it withdraws the nuclear reaction heat and assembles in pressure manifolds.

  8. Simulation and Field Evaluation Support for ESTCP Dynamic Windows: Cooperative Research and Development Final Report, CRADA Number CRD-12-492

    SciTech Connect (OSTI)

    Guglielmetti, R.

    2015-02-01

    We will leverage new building performance and daylighting simulation tools to characterize the performance of a new electrochromic (EC) glazing as well as perform a field evaluation of the same product installed in a DoD facility. The in situ data will be used to validate and calibrate the simulation model, which will then be used to extrapolate the performance of the product across all US climate zones. The property as part of this agreement will be installed at MCAS Miramar, California.

  9. Simulative research on the anode plasma dynamics in the high-power electron beam diode

    SciTech Connect (OSTI)

    Cai, Dan; Liu, Lie; Ju, Jin-Chuan; Zhang, Tian-Yang; Zhao, Xue-Long; Zhou, Hong-Yu

    2015-07-15

    Anode plasma generated by electron beams could limit the electrical pulse-length, modify the impedance and stability of diode, and affect the generator to diode power coupling. In this paper, a particle-in-cell code is used to study the dynamics of anode plasma in the high-power electron beam diode. The effect of gas type, dynamic characteristic of ions on the diode operation with bipolar flow model are presented. With anode plasma appearing, the amplitude of diode current is increased due to charge neutralizations of electron flow. The lever of neutralization can be expressed using saturation factor. At same pressure of the anode gas layer, the saturation factor of CO{sub 2} is bigger than the H{sub 2}O vapor, namely, the generation rate of C{sup +} ions is larger than the H{sup +} ions at the same pressure. The transition time of ions in the anode-cathode gap could be used to estimate the time of diode current maximum.

  10. Simulation study of dynamic aperture with head-on beam-beam compensation in the RHIC

    SciTech Connect (OSTI)

    Luo, Y.; Fischer, W.

    2010-08-01

    In this note we summarize the calculated 10{sup 6} turn dynamic apertures with the proposed head-on beam-beam compensation in the Relativistic Heavy Ion Collider (RHIC). To compensate the head-on beam-beam effect in the RHIC 250 GeV polarized proton run, we are planning to introduce a DC electron beam with the same transverse profile as the proton beam to collide with the proton beam. Such a device to provide the electron beam is called an electron lens (e-lens). In this note we first present the optics and beam parameters and the tracking setup. Then we compare the calculated dynamic apertures without and with head-on beam-beam compensation. The effects of adjusted phase advances between IP8 and the center of e-lens and second order chromaticity correction are checked. In the end we will scan the proton and electron beam parameters with head-on beam-beam compensation.

  11. Using a dynamic point-source percolation model to simulate bubble growth.

    SciTech Connect (OSTI)

    Zimmerman, Jonathan A.; Zeigler, David A.; Cowgill, Donald F.

    2004-05-01

    Accurate modeling of nucleation, growth and clustering of helium bubbles within metal tritide alloys is of high scientific and technological importance. Of interest is the ability to predict both the distribution of these bubbles and the manner in which these bubbles interact at a critical concentration of helium-to-metal atoms to produce an accelerated release of helium gas. One technique that has been used in the past to model these materials, and again revisited in this research, is percolation theory. Previous efforts have used classical percolation theory to qualitatively and quantitatively model the behavior of interstitial helium atoms in a metal tritide lattice; however, higher fidelity models are needed to predict the distribution of helium bubbles and include features that capture the underlying physical mechanisms present in these materials. In this work, we enhance classical percolation theory by developing the dynamic point-source percolation model. This model alters the traditionally binary character of site occupation probabilities by enabling them to vary depending on proximity to existing occupied sites, i.e. nucleated bubbles. This revised model produces characteristics for one and two dimensional systems that are extremely comparable with measurements from three dimensional physical samples. Future directions for continued development of the dynamic model are also outlined.

  12. Variability in the sensitivity among model simulations of permafrost and carbon dynamics in the permafrost region between 1960 and 2009

    DOE PAGES-Beta [OSTI]

    McGuire, A. David; Koven, Charles; Lawrence, David M.; Clein, Joy S.; Xia, Jiangyang; Beer, Christian; Burke, Eleanor; Chen, Guangsheng; Chen, Xiaodong; Delire, Christine; et al

    2016-07-08

    A significant portion of the large amount of carbon (C) currently stored in soils of the permafrost region in the Northern Hemisphere has the potential to be emitted as the greenhouse gases CO2 and CH4 under a warmer climate. In this study we evaluated the variability in the sensitivity of permafrost and C in recent decades among land surface model simulations over the permafrost region between 1960 and 2009. The 15 model simulations all predict a loss of near-surface permafrost (within 3 m) area over the region, but there are large differences in the magnitude of the simulated rates ofmore » loss among the models (0.2 to 58.8 × 103 km2 yr–1). Sensitivity simulations indicated that changes in air temperature largely explained changes in permafrost area, although interactions among changes in other environmental variables also played a role. All of the models indicate that both vegetation and soil C storage together have increased by 156 to 954 Tg C yr–1 between 1960 and 2009 over the permafrost region even though model analyses indicate that warming alone would decrease soil C storage. Increases in gross primary production (GPP) largely explain the simulated increases in vegetation and soil C. The sensitivity of GPP to increases in atmospheric CO2 was the dominant cause of increases in GPP across the models, but comparison of simulated GPP trends across the 1982–2009 period with that of a global GPP data set indicates that all of the models overestimate the trend in GPP. Disturbance also appears to be an important factor affecting C storage, as models that consider disturbance had lower increases in C storage than models that did not consider disturbance. Furthermore, to improve the modeling of C in the permafrost region, there is the need for the modeling community to standardize structural representation of permafrost and carbon dynamics among models that are used to evaluate the permafrost C feedback and for the modeling and observational communities to

  13. Numerical simulation of cathode plasma dynamics in magnetically insulated vacuum transmission lines

    SciTech Connect (OSTI)

    Thoma, C.; Genoni, T. C.; Welch, D. R.; Rose, D. V.; Clark, R. E.; Miller, C. L.; Stygar, W. A.; Kiefer, M. L.

    2015-03-15

    A novel algorithm for the simulation of cathode plasmas in particle-in-cell codes is described and applied to investigate cathode plasma evolution in magnetically insulated transmission lines (MITLs). The MITL electron sheath is modeled by a fully kinetic electron species. Electron and ion macroparticles, both modeled as fluid species, form a dense plasma which is initially localized at the cathode surface. Energetic plasma electron particles can be converted to kinetic electrons to resupply the electron flux at the plasma edge (the “effective” cathode). Using this model, we compare results for the time evolution of the cathode plasma and MITL electron flow with a simplified (isothermal) diffusion model. Simulations in 1D show a slow diffusive expansion of the plasma from the cathode surface. But in multiple dimensions, the plasma can expand much more rapidly due to anomalous diffusion caused by an instability due to the strong coupling of a transverse magnetic mode in the electron sheath with the expanding resistive plasma layer.

  14. Dynamic

    Office of Legacy Management (LM)

    Dynamic , and Static , Res.ponse of the Government Oil Shale Mine at ' , . , Rifle, Colorado, to the Rulison Event. , . ; . . DISCLAIMER Portions of this document may be illegible in electronic image products. Images are produced from the best available original document. p ( y c - - a 2-1 0 -4- REPORT AT (29-2) 914 USBM 1 0 0 1 UNITED STATES DEPARTMENT O F THE I NTERIOR BUREAU OF MINES e s.09 P. L. R U S S E L L RESEARCH D l RECTOR Februory 2, lB7O DYNAMIC AND STATIC RESPONSE 'OF THE GOVERNMENT

  15. Atomistic Time-Domain Simulations of Light-Harvesting and Charge-Transfer Dynamics in Novel Nanoscale Materials for Solar Hydrogen Production.

    SciTech Connect (OSTI)

    Prezhdo, Oleg V.

    2012-03-22

    provided a unified atomistic picture of the nature and dynamics of photoexcited states in semiconductor QDs. We also summarized our recent findings about the photoinduced electron dynamics at the chromophore-semiconductor interfaces from a time-domain ab initio perspective. The interface provides the foundation for a new, promising type of solar cell and presents a fundamentally important case study for several fields, including photo-, electro- and analytical chemistries, molecular electronics, and photography. Further, the interface offers a classic example of an interaction between an organic molecular species and an inorganic bulk material. Scientists employ different concepts and terminologies to describe molecular and solid states of matter, and these differences make it difficult to describe the interface with a single model. At the basic atomistic level of description, however, this challenge can be largely overcome. Recent advances in non-adiabatic molecular dynamics and time-domain density functional theory have created a unique opportunity for simulating the ultrafast, photoinduced processes on a computer very similar to the way that they occur in nature. These state-of-the-art theoretical tools offered a comprehensive picture of a variety of electron transfer processes that occur at the interface, including electron injection from the chromophore to the semiconductor, electron relaxation and delocalization inside the semiconductor, back-transfer of the electron to the chromophore and to the electrolyte, and regeneration of the neutral chromophore by the electrolyte. The ab initio time-domain modeling is particularly valuable for understanding these dynamic features of the ultrafast electron transfer processes, which cannot be represented by a simple rate description. We demonstrated using symmetry adapted cluster theory with configuration interaction (SAC-CI) that charging of small PbSe nanocrystals (NCs) greatly modifies their electronic states and optical

  16. Results of a Neutronic Simulation of HTR-Proteus Core 4.2 using PEBBED and other INL Reactor Physics Tools: FY-09 Report

    SciTech Connect (OSTI)

    Hans D. Gougar

    2009-08-01

    The Idaho National Laboratorys deterministic neutronics analysis codes and methods were applied to the computation of the core multiplication factor of the HTR-Proteus pebble bed reactor critical facility. A combination of unit cell calculations (COMBINE-PEBDAN), 1-D discrete ordinates transport (SCAMP), and nodal diffusion calculations (PEBBED) were employed to yield keff and flux profiles. Preliminary results indicate that these tools, as currently configured and used, do not yield satisfactory estimates of keff. If control rods are not modeled, these methods can deliver much better agreement with experimental core eigenvalues which suggests that development efforts should focus on modeling control rod and other absorber regions. Under some assumptions and in 1D subcore analyses, diffusion theory agrees well with transport. This suggests that developments in specific areas can produce a viable core simulation approach. Some corrections have been identified and can be further developed, specifically: treatment of the upper void region, treatment of inter-pebble streaming, and explicit (multiscale) transport modeling of TRISO fuel particles as a first step in cross section generation. Until corrections are made that yield better agreement with experiment, conclusions from core design and burnup analyses should be regarded as qualitative and not benchmark quality.

  17. Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations

    SciTech Connect (OSTI)

    Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro

    2015-12-31

    Ab initio molecular dynamics simulations have been used to inspect the adsorption of O{sub 2} to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O{sub 2} and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O{sub 2} adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.

  18. Dislocation Dynamics Simulations of Junctions in Hexagonal Close-Packed Crystals

    SciTech Connect (OSTI)

    Wu, C; Aubry, S; Chung, P; Arsenlis, A

    2011-12-05

    The formation and strength of dislocations in the hexagonal closed packed material beryllium are studied through dislocation junctions and the critical stress required to break them. Dislocation dynamics calculations (using the code ParaDiS) of junction maps are compared to an analytical line tension approximation in order to validate our model. Results show that the two models agree very well. Also the critical shear stress necessary to break 30{sup o} - 30{sup o} and 30{sup o} - 90{sup o} dislocation junctions is computed numerically. Yield surfaces are mapped out for these junctions to describe their stability regions as function of resolved shear stresses on the glide planes. The example of two non-coplanar binary dislocation junctions with slip planes [2-1-10] (01-10) and [-12-10] (0001) corresponding to a prismatic and basal slip respectively is chosen to verify and validate our implementation.

  19. HALL EFFECT CONTROLLED GAS DYNAMICS IN PROTOPLANETARY DISKS. II. FULL 3D SIMULATIONS TOWARD THE OUTER DISK

    SciTech Connect (OSTI)

    Bai, Xue-Ning

    2015-01-10

    We perform three-dimensional stratified shearing-box magnetohydrodynamic (MHD) simulations on the gas dynamics of protoplanetary disks with a net vertical magnetic flux of B {sub z0}. All three nonideal MHD effects, Ohmic resistivity, the Hall effect, and ambipolar diffusion, are included in a self-consistent manner based on equilibrium chemistry. We focus on regions toward outer disk radii, from 5 to 60 AU, where Ohmic resistivity tends to become negligible, ambipolar diffusion dominates over an extended region across the disk height, and the Hall effect largely controls the dynamics near the disk midplane. We find that at around R = 5 AU the system launches a laminar or weakly turbulent magnetocentrifugal wind when the net vertical field B {sub z0} is not too weak. Moreover, the wind is able to achieve and maintain a configuration with reflection symmetry at the disk midplane. The case with anti-aligned field polarity (Ω⋅B{sub z0}<0) is more susceptible to the magnetorotational instability (MRI) when B {sub z0} decreases, leading to an outflow oscillating in radial directions and very inefficient angular momentum transport. At the outer disk around and beyond R = 30 AU, the system shows vigorous MRI turbulence in the surface layer due to far-UV ionization, which efficiently drives disk accretion. The Hall effect affects the stability of the midplane region to the MRI, leading to strong/weak Maxwell stress for aligned/anti-aligned field polarities. Nevertheless, the midplane region is only very weakly turbulent in both cases. Overall, the basic picture is analogous to the conventional layered accretion scenario applied to the outer disk. In addition, we find that the vertical magnetic flux is strongly concentrated into thin, azimuthally extended shells in most of our simulations beyond 15 AU, leading to enhanced radial density variations know as zonal flows. Theoretical implications and observational consequences are briefly discussed.

  20. Test Cases for Wind Power Plant Dynamic Models on Real-Time Digital Simulator: Preprint

    SciTech Connect (OSTI)

    Singh, M.; Muljadi, E.; Gevorgian, V.

    2012-06-01

    The objective of this paper is to present test cases for wind turbine generator and wind power plant models commonly used during commissioning of wind power plants to ensure grid integration compatibility. In this paper, different types of wind power plant models based on the Western Electricity Coordinating Council Wind Generator Modeling Group's standardization efforts are implemented on a real-time digital simulator, and different test cases are used to gauge their grid integration capability. The low-voltage ride through and reactive power support capability and limitations of wind turbine generators under different grid conditions are explored. Several types of transient events (e.g., symmetrical and unsymmetrical faults, frequency dips) are included in the test cases. The differences in responses from different types of wind turbine are discussed in detail.

  1. On computing stress in polymer systems involving multi-body potentials from molecular dynamics simulation

    SciTech Connect (OSTI)

    Fu, Yao E-mail: jhsong@cec.sc.edu; Song, Jeong-Hoon E-mail: jhsong@cec.sc.edu

    2014-08-07

    Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.

  2. A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-01

    Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N3) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix, based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.

  3. A model for plasticity kinetics and its role in simulating the dynamic behavior of Fe at high strain rates

    SciTech Connect (OSTI)

    Colvin, J D; Minich, R W; Kalantar, D H

    2007-03-29

    The recent diagnostic capability of the Omega laser to study solid-solid phase transitions at pressures greater than 10 GPa and at strain rates exceeding 10{sup 7} s{sup -1} has also provided valuable information on the dynamic elastic-plastic behavior of materials. We have found, for example, that plasticity kinetics modifies the effective loading and thermodynamic paths of the material. In this paper we derive a kinetics equation for the time-dependent plastic response of the material to dynamic loading, and describe the model's implementation in a radiation-hydrodynamics computer code. This model for plasticity kinetics incorporates the Gilman model for dislocation multiplication and saturation. We discuss the application of this model to the simulation of experimental velocity interferometry data for experiments on Omega in which Fe was shock compressed to pressures beyond the {alpha}-to-{var_epsilon} phase transition pressure. The kinetics model is shown to fit the data reasonably well in this high strain rate regime and further allows quantification of the relative contributions of dislocation multiplication and drag. The sensitivity of the observed signatures to the kinetics model parameters is presented.

  4. The liquid surface of chiral ionic liquids as seen from molecular dynamics simulations combined with intrinsic analysis

    SciTech Connect (OSTI)

    Lísal, Martin

    2013-12-07

    We present molecular-level insight into the liquid/gas interface of two chiral room-temperature ionic liquids (RTILs) derived from 1-n-butyl-3-methylimidazolium bromide ([bmim][Br]); namely, (R)-1-butyl-3-(3-hydroxy-2-methylpropyl)imidazolium bromide (hydroxypropyl) and 1-butyl-3-[(1R)-nopyl]imidazolium bromide (nopyl). We use our currently developed force field which was validated against the experimental bulk density, heat of vaporization, and surface tension of [bmim][Br]. The force field for the RTILs adopts the Chemistry at Harvard Molecular Mechanics (CHARMM) parameters for the intramolecular and repulsion-dispersion interactions along with the reduced partial atomic charges based on ab initio calculations. The net charges of the ions are around ±0.8e, which mimic the anion to cation charge transfer and many-body effects. Molecular dynamics simulations in the slab geometry combined with the intrinsic interface analysis are employed to provide a detailed description of the RTIL/gas interface in terms of the structural and dynamic properties of the interfacial, sub-interfacial, and central layers at a temperature of 300 K. The focus is on the comparison of the liquid/gas interface for the chiral RTILs with the interface for parent [bmim][Br]. The structure of the interface is elucidated by evaluating the surface roughness, intrinsic atomic density profiles, and orientation ordering of the cations. The dynamics of the ions at the interfacial region is characterized by computing the survival probability, and normal and lateral self-diffusion coefficients in the layers.

  5. Distance Restraints from Crosslinking Mass Spectrometry: Mining a Molecular Dynamics Simulation Database to Evaluate Lysine-Lysine Distances

    SciTech Connect (OSTI)

    Merkley, Eric D.; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P.; Daggett, Valerie; Adkins, Joshua N.

    2014-03-18

    Integrative structural biology models the structures of protein complexes that are intractable by classical structural methods (because of extreme size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such method is chemical cross-linking mass spectrometry (XL-MS), in which cross-linked peptides, derived from a covalently cross-linked protein complex and identified by liquid chromatography-mass spectrometry, pinpoint protein residues close in three-dimensional space. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS3) have a linker arm that is 11.4 Å long when fully extended. However, XL-MS studies on proteins of known structure frequently report cross-links that exceed this distance. Typically, a tolerance of ~3 Å is added to the theoretical maximum to account for this observation, with little justification for the value chosen. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of all protein folds, to investigate the change in lysine-lysine distances resulting from native-state dynamics on the time-scale of tens of nanoseconds. We conclude that observed cross-links are consistent with a protein structure if the distance between cross-linked lysine Nζ atoms is less than the cross-linker length plus 11.3 Å. For DSS or BS3, this corresponds to a Cα to Cα distance of 30.4 Å. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures, and indicates the appropriate values of an XLMS derived distance constraint to use in structural modeling.

  6. Best practices for system dynamics model design and construction with powersim studio.

    SciTech Connect (OSTI)

    Malczynski, Leonard A.

    2011-06-01

    This guide addresses software quality in the construction of Powersim{reg_sign} Studio 8 system dynamics simulation models. It is the result of almost ten years of experience with the Powersim suite of system dynamics modeling tools (Constructor and earlier Studio versions). It is a guide that proposes a common look and feel for the construction of Powersim Studio system dynamics models.

  7. Molecular Dynamics Simulations of Tri-n-butyl-phosphate/n-Dodecane Mixture: Thermophysical Properties and Molecular Structure

    SciTech Connect (OSTI)

    de Almeida, Valmor F; Cui, Shengting; Khomami, Bamin

    2014-01-01

    Molecular dynamics simulations of tri-n-butyl-phosphate (TBP)/n-dodecane mixture in the liquid phase have been carried out using two recently developed TBP force field models (J. Phys. Chem. B 2012, 116, 305) in combination with the all-atom optimized potentials for liquid simulations (OPLS-AA) force field model for n-dodecane. Specifically, the electric dipole moment of TBP, mass density of the mixture, and the excess volume of mixing were computed with TBP mole fraction ranging from 0 to 1. It is found that the aforementioned force field models accurately predict the mass density of the mixture in the entire mole fraction range. Commensurate with experimental measurements, the electric dipole moment of the TBP was found to slightly increase with the mole fraction of TBP in the mixture. Also, in accord with experimental data, the excess volume of mixing is positive in the entire mole fraction range, peaking at TBP mole fraction range 0.3 0.5. Finally, a close examination of the spatial pair correlation functions between TBP molecules, and between TBP and n-dodecane molecules, revealed formation of TBP dimers through self-association at close distance, a phenomenon with ample experimental evidence.

  8. Effect of bound state of water on hydronium ion mobility in hydrated Nafion using molecular dynamics simulations

    SciTech Connect (OSTI)

    Mabuchi, Takuya; Tokumasu, Takashi

    2014-09-14

    We have performed a detailed analysis of the structural properties of the sulfonate groups in terms of isolated and overlapped solvation shells in the nanostructure of hydrated Nafion membrane using classical molecular dynamics simulations. Our simulations have demonstrated the correlation between the two different areas in bound water region, i.e., the first solvation shell, and the vehicular transport of hydronium ions at different water contents. We have employed a model of the Nafion membrane using the improved force field, which is newly modified and validated by comparing the density and water diffusivity with those obtained experimentally. The first solvation shells were classified into the two types, the isolated area and the overlapped area. The mean residence times of solvent molecules explicitly showed the different behaviors in each of those areas in terms of the vehicular transport of protons: the diffusivity of classical hydronium ions in the overlapped area dominates their total diffusion at lower water contents while that in the isolated area dominates for their diffusion at higher water contents. The results provided insights into the importance role of those areas in the solvation shells for the diffusivity of vehicular transport of hydronium ions in hydrated Nafion membrane.

  9. A Dynamic Simulation of the Indirect Land Use Implications of Recent Biofuel Production and Use in the United States.

    SciTech Connect (OSTI)

    Oladosu, Gbadebo A; Kline, Keith L

    2013-01-01

    The global indirect land use change (ILUC) implications of biofuel use in the United States of America (USA) from 2001 to 2010 are evaluated with a dynamic general equilibrium model. The effects of biofuels production on agricultural land area vary by year; from a net expansion of 0.17 ha per 1000 gallons produced (2002) to a net contraction of 0.13 ha per 1000 gallons (2018) in Case 1 of our simulation. In accordance with the general narrative about the implications of biofuel policy, agricultural land area increased in many regions of the world. However, oil-export dependent economies experienced agricultural land contraction because of reductions in their revenues. Reducing crude oil imports is a major goal of biofuel policy, but the land use change implications have received little attention in the literature. Simulations evaluating the effects of doubling supply elasticities for land and fossil resources show that these parameters can significantly influence the land use change estimates. Therefore, research that provides empirically-based and spatially-detailed agricultural land-supply curves and capability to project future fossil energy prices is critical for improving estimates of the effects of biofuel policy on land use.

  10. Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

    SciTech Connect (OSTI)

    Parkes, Marie V.; Demir, Hakan; Teich-McGoldrick, Stephanie L.; Sholl, David S.; Greathouse, Jeffery A.; Allendorf, Mark D.

    2014-03-28

    Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of framework force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.

  11. Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

    DOE PAGES-Beta [OSTI]

    Parkes, Marie V.; Demir, Hakan; Teich-McGoldrick, Stephanie L.; Sholl, David S.; Greathouse, Jeffery A.; Allendorf, Mark D.

    2014-03-28

    Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of frameworkmore » force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.« less

  12. 369 TFlop/s molecular dynamics simulations on the Roadrunner general-purpose heterogeneous supercomputer

    SciTech Connect (OSTI)

    Swaminarayan, Sriram; Germann, Timothy C; Kadau, Kai; Fossum, Gordon C

    2008-01-01

    The authors present timing and performance numbers for a short-range parallel molecular dynamics (MD) code, SPaSM, that has been rewritten for the heterogeneous Roadrunner supercomputer. Each Roadrunner compute node consists of two AMD Opteron dual-core microprocessors and four PowerXCell 8i enhanced Cell microprocessors, so that there are four MPI ranks per node, each with one Opteron and one Cell. The interatomic forces are computed on the Cells (each with one PPU and eight SPU cores), while the Opterons are used to direct inter-rank communication and perform I/O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard-Jones pair potential benchmark reached a peak of 369 Tflop/s double-precision floating-point performance on the full Roadrunner system (27.7% of peak), corresponding to 124 MFlop/Watt/s at a price of approximately 3.69 MFlops/dollar. They demonstrate an initial target application, the jetting and ejection of material from a shocked surface.

  13. Reframing Accelerator Simulations

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Simulations Mori-1.png Key Challenges: Use advanced simulation tools to study the feasibility of plasma-based linear colliders and to optimize conceptual designs. Much of the...

  14. Fluid dynamic studies for a simulated Melton Valley Storage Tank slurry

    SciTech Connect (OSTI)

    Hylton, T.D.; Youngblood, E.L.; Cummins, R.L.

    1994-07-01

    The Melton Valley Storage Tanks (MVSTs), are used for the collection and storage of remote-handled radioactive liquid wastes. These wastes, which were typically acidic when generated, were neutralized with the addition of sodium hydroxide to protect the storage tanks from corrosion, but this caused the transuranic and heavy metals to precipitate. These wastes will eventually need to be removed from the tanks for ultimate disposal. The objective of the research activities discussed in this report is to support the design of a pipeline transport system between the MVSTs and a treatment facility. Since the wastes in the MVSTs are highly radioactive, a surrogate slurry was developed for this study. Rheological properties of the simulated slurry were determined in a test loop in which the slurry was circulated through three pipeline viscometers of different diameters. Pressure drop data at varying flow rates were used to obtain shear stress and shear rate data. The data were analyzed, and the slurry rheological properties were analyzed by the Power Law model and the Bingham plastic model. The plastic viscosity and yield stress data obtained from the rheological tests were used as inputs for a piping design software package, and the pressure drops predicted by the software compared well with the pressure drop data obtained from the test loop. The minimum transport velocity was determine for the slurry by adding known nominal sizes of glass spheres to the slurry. However, it was shown that the surrogate slurry exhibited hindered settling, which may substantially decrease the minimum transport velocity. Therefore, it may be desired to perform additional tests with a surrogate with a lower concentration of suspended solids to determine the minimum transport velocity.

  15. Development Tools

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    More Python Tools Python is an interpreted, general-purpose high-level programming language that is usually accompanied by a variety of useful tools for scientific programming...

  16. Software Tools

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Software Tools Software Tools Copyright materials are released under different mechanisms: Open Source Software and Portfolio Software. CONTACT thumbnail of Kathleen McDonald Head ...

  17. Models & Tools

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Models & Tools - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us ... Multimedia & Software Videos Images Models & Tools Partnerships Tribal Energy Program ...

  18. A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations

    SciTech Connect (OSTI)

    Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean -Luc; Emigh, Aiyana; Lightstone, Felice C.; Salsbury , Jr, Freddie

    2015-04-13

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.

  19. A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations

    DOE PAGES-Beta [OSTI]

    Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean -Luc; Emigh, Aiyana; Lightstone, Felice C.; Salsbury , Jr, Freddie

    2015-04-13

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone andmore » sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.« less

  20. Molecular dynamics simulation of diffusion coefficients and structural properties of some alkylbenzenes in supercritical carbon dioxide at infinite dilution

    SciTech Connect (OSTI)

    Wang, Jinyang; Zhong, Haimin; Qiu, Wenda; Chen, Liuping; Feng, Huajie

    2014-03-14

    The binary infinite dilute diffusion coefficients, D{sub 12}{sup ?}, of some alkylbenzenes (Ph-C{sub n}, from Ph-H to Ph-C{sub 12}) from 313 K to 333 K at 15 MPa in supercritical carbon dioxide (scCO{sub 2}) have been studied by molecular dynamics (MD) simulation. The MD values agree well with the experimental ones, which indicate MD simulation technique is a powerful way to predict and obtain diffusion coefficients of solutes in supercritical fluids. Besides, the local structures of Ph-C{sub n}/CO{sub 2} fluids are further investigated by calculating radial distribution functions and coordination numbers. It qualitatively convinces that the first solvation shell of Ph-C{sub n} in scCO{sub 2} is significantly influenced by the structure of Ph-C{sub n} solute. Meanwhile, the mean end-to-end distance, the mean radius of gyration and dihedral angle distribution are calculated to gain an insight into the structural properties of Ph-C{sub n} in scCO{sub 2}. The abnormal trends of radial distribution functions and coordination numbers can be reasonably explained in term of molecular flexibility. Moreover, the computed results of dihedral angle clarify that flexibility of long-chain Ph-C{sub n} is the result of internal rotation of C-C single bond (?{sub c-c}) in alkyl chain. It is interesting that compared with n-alkane, because of the existence of benzene ring, the flexibility of alkyl chain in Ph-C{sub n} with same carbon atom number is significantly reduced, as a result, the carbon chain dependence of diffusion behaviors for long-chain n-alkane (n ? 5) and long-chain Ph-C{sub n} (n ? 4) in scCO{sub 2} are different.

  1. Neutron Scattering of Residual Hydrogen in 1,4-Dioxane-D8 Liquid. Understanding Measurements with Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    de Almeida, Valmor F.; Liu, Hongjun; Herwig, Kenneth W.; Kidder, Michelle

    2016-01-01

    That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to inter-molecular scattering and that uncertainty in the extent of deuteration account for discrepancies between simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen-deuterium pair, and complementary interference from the deuterium-deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298K and at 343K) protiated mole fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. Although we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids and similar systematic experimental/computational studies can be performed to either

  2. Neutron scattering of residual hydrogen in 1,4-dioxane d8 liquid: Understanding measurements with molecular dynamics simulations

    DOE PAGES-Beta [OSTI]

    Liu, Hongjun; Herwig, Kenneth W.; Kidder, Michelle K.; de Almeida, Valmor F.

    2016-06-08

    That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well-known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to intermolecular scattering and that uncertainty in the extent of deuteration account for discrepancies betweenmore » simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen–deuterium pair, and complementary interference from the deuterium–deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298 K and at 343 K) protiated molar fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here, we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. As a result, we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids, and similar systematic experimental/computational studies can be

  3. Conceptual design of the HTTR-IS hydrogen production system - dynamic simulation code development for advanced process heat exchanger in the HTTR-IS system

    SciTech Connect (OSTI)

    Sato, Hiroyuki; Kubo, Shinji; Sakaba, Nariaki; Ohashi, Hirofumi; Sano, Naoki; Nishihara, Tetsuo; Kunitomi, Kazuhiko

    2007-07-01

    The objective of this study is to confirm the availability of proposed mitigation methodology against thermal load increase events initiated by the thermochemical water splitting IS process hydrogen production system (IS process) coupling with the High temperature Engineering Test Reactor (HTTR). Japan Atomic Energy Agency (JAEA) has been performing the development of dynamic simulation code which can evaluate complex phenomena in the HTTR-IS system all at one once to achieve the requirement. The notable feature of the developed code is the Advanced Process Heat Exchanger (APHX) module which enables to estimate the IS process thermal load variation considering phase change and chemical reaction behavior assumed in the APHX. In this paper, two cases of dynamic calculation for the thermal load increase events were performed using the newly developed APHX module. The results of the analytical studies clearly show the availability of the developed model for dynamic simulation of the HTTR-IS system and the thermal load increase mitigation methodology. (authors)

  4. Enrollment Tools

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Careers, Jobs » Employee, Retiree Resources » New Hire » Benefits » Enrollment Tools Enrollment Tools A comprehensive benefits package with plan options for health care and retirement to take care of our employees today and tomorrow. Contacts Benefits Office (505) 667-1806 Email Enrollment Tools New Hire Benefits Checklist (pdf) New Hire Enrollment Tool (xls

  5. Pair dynamics and the intermolecular nuclear Overhauser effect (NOE) in liquids analysed by simulation and model theories: Application to an ionic liquid

    SciTech Connect (OSTI)

    Gabl, Sonja; Schröder, Christian; Braun, Daniel; Steinhauser, Othmar; Weingärtner, Hermann

    2014-05-14

    Combining simulation and model theories, this paper analyses the impact of pair dynamics on the intermolecular nuclear Overhauser effect (NOE) in liquids. For the first time, we give a distance resolved NOE. When applied to the ionic liquid 1-ethyl-3-methyl-imidazolium tetrafluoroborate the NOE turns out to be of long-range nature. This behaviour translates to the experimentally measured cross- and longitudinal relaxation rates. We were able to calculate the heteronuclear NOE from simulation data, despite the high computational effort. Model theories are computationally less demanding and cover the complete frequency range of the respective spectral density function, they are usually based on a very simple pair distribution function and the solution of the diffusion equation. In order to model the simulated data sufficiently, these simplifications in structure and dynamics have to be generalised considerably.

  6. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    SciTech Connect (OSTI)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  7. Large scale test simulations using the Virtual Environment for Test Optimization (VETO)

    SciTech Connect (OSTI)

    Klenke, S.E.; Heffelfinger, S.R.; Bell, H.J.; Shierling, C.L.

    1997-10-01

    The Virtual Environment for Test Optimization (VETO) is a set of simulation tools under development at Sandia to enable test engineers to do computer simulations of tests. The tool set utilizes analysis codes and test information to optimize design parameters and to provide an accurate model of the test environment which aides in the maximization of test performance, training, and safety. Previous VETO effort has included the development of two structural dynamics simulation modules that provide design and optimization tools for modal and vibration testing. These modules have allowed test engineers to model and simulate complex laboratory testing, to evaluate dynamic response behavior, and to investigate system testability. Further development of the VETO tool set will address the accurate modeling of large scale field test environments at Sandia. These field test environments provide weapon system certification capabilities and have different simulation requirements than those of laboratory testing.

  8. The Adaptive Multi-scale Simulation Infrastructure

    SciTech Connect (OSTI)

    Tobin, William R.

    2015-09-01

    The Adaptive Multi-scale Simulation Infrastructure (AMSI) is a set of libraries and tools developed to support the development, implementation, and execution of general multimodel simulations. Using a minimal set of simulation meta-data AMSI allows for minimally intrusive work to adapt existent single-scale simulations for use in multi-scale simulations. Support for dynamic runtime operations such as single- and multi-scale adaptive properties is a key focus of AMSI. Particular focus has been spent on the development on scale-sensitive load balancing operations to allow single-scale simulations incorporated into a multi-scale simulation using AMSI to use standard load-balancing operations without affecting the integrity of the overall multi-scale simulation.

  9. Effect of surface free energies on the heterogeneous nucleation of water droplet: A molecular dynamics simulation approach

    SciTech Connect (OSTI)

    Xu, W.; Lan, Z.; Peng, B. L.; Wen, R. F.; Ma, X. H.

    2015-02-07

    Heterogeneous nucleation of water droplet on surfaces with different solid-liquid interaction intensities is investigated by molecular dynamics simulation. The interaction potentials between surface atoms and vapor molecules are adjusted to obtain various surface free energies, and the nucleation process and wetting state of nuclei on surfaces are investigated. The results indicate that near-constant contact angles are already established for nano-scale nuclei on various surfaces, with the contact angle decreasing with solid-liquid interaction intensities linearly. Meanwhile, noticeable fluctuation of vapor-liquid interfaces can be observed for the nuclei that deposited on surfaces, which is caused by the asymmetric forces from vapor molecules. The formation and growth rate of nuclei are increasing with the solid-liquid interaction intensities. For low energy surface, the attraction of surface atoms to water molecules is comparably weak, and the pre-existing clusters can depart from the surface and enter into the bulk vapor phase. The distribution of clusters within the bulk vapor phase becomes competitive as compared with that absorbed on surface. For moderate energy surfaces, heterogeneous nucleation predominates and the formation of clusters within bulk vapor phase is suppressed. The effect of high energy particles that embedded in low energy surface is also discussed under the same simulation system. The nucleation preferably initiates on the high energy particles, and the clusters that formed on the heterogeneous particles are trapped around their original positions instead of migrating around as that observed on smooth surfaces. This feature makes it possible for the heterogeneous particles to act as fixed nucleation sites, and simulation results also suggest that the number of nuclei increases monotonously with the number of high energy particles. The growth of nuclei on high energy particles can be divided into three sub-stages, beginning with the formation

  10. Molecular dynamical simulation of the behavior of early precipitated stage in aging process in dilute Cu-Cr alloy

    SciTech Connect (OSTI)

    Feng, J.; Liu, L.; Chen, J.; Du, Y.; Zhou, R.; Xiao, B.

    2010-06-15

    The aging behaviors of Cu-Cr alloys in the early stage at different temperatures are investigated by molecular dynamics simulations. First principles potentials are used for the interactions between Cu and Cr atoms. The initial behavior of precipitation is characterized by transmission electron microscope and electron energy disperse spectroscopy. The results showed that Cu-Cr supersaturated solid solution is thermodynamically unstable. The mean-square displacements of the atoms are used to describe the diffusivity. At room temperature, the atoms only show harmonic vibrations near the equilibrium positions. The mutual diffusion at 873 K is different from the unidirectional diffusion in low temperatures. The calculation shows that aging process is accelerated with increasing temperature, which is not only due to the lower diffusion activation energy of Cr at higher temperature, but also because Cu atoms are also participated in the aging process. When ''aging'' at 1073 K, the precipitation of Cr element is dissolved again into Cu matrix, which is an ''over-aging'' state of Cu-Cr alloy at high temperature.

  11. Homogeneous hydride formation path in α-Zr: Molecular dynamics simulations with the charge-optimized many-body potential

    DOE PAGES-Beta [OSTI]

    Zhang, Yongfeng; Bai, Xian-Ming; Yu, Jianguo; Tonks, Michael R.; Noordhoek, Mark J.; Phillpot, Simon R.

    2016-06-01

    A formation path for homogeneous γ hydride formation in hcp α-Zr, from solid solution to the ζ and then the γ hydride, was demonstrated using molecular static calculations and molecular dynamic simulations with the charge-optimized many-body (COMB) potential. Hydrogen has limited solubility in α-Zr. Once the solubility limit is exceeded, the stability of solid solution gives way to that of coherent hydride phases such as the ζ hydride by planar precipitation of hydrogen. At finite temperatures, the ζ hydride goes through a partial hcp-fcc transformation via 1/3 <1¯100> slip on the basal plane, and transforms into a mixture of γmore » hydride and α-Zr. In the ζ hydride, slip on the basal plane is favored thermodynamically with negligible barrier, and is therefore feasible at finite temperatures without mechanical loading. The transformation process involves slips of three equivalent shear partials, in contrast to that proposed in the literature where only a single shear partial was involved. The adoption of multiple slip partials minimizes the macroscopic shape change of embedded hydride clusters and the shear strain accumulation in the matrix, and thus reduces the overall barrier needed for homogeneous γ hydride formation. In conclusion, this formation path requires finite temperatures for hydrogen diffusion without mechanical loading. Therefore, it should be effective at the cladding operating conditions.« less

  12. Anisotropy of the solid–liquid interface properties of the Ni–Zr B33 phase from molecular dynamics simulation

    DOE PAGES-Beta [OSTI]

    Wilson, S. R.; Mendelev, M. I.

    2015-01-08

    Solid–liquid interface (SLI) properties of the Ni–Zr B33 phase were determined from molecular dynamics simulations. In order to perform these measurements, a new semi-empirical potential for Ni–Zr alloy was developed that well reproduces the material properties required to model SLIs in the Ni50.0Zr50.0 alloy. In particular, the developed potential is shown to provide that the solid phase emerging from the liquid Ni50.0Zr50.0alloy is B33 (apart from a small fraction of point defects), in agreement with the experimental phase diagram. The SLI properties obtained using the developed potential exhibit an extraordinary degree of anisotropy. It is observed that anisotropies in bothmore » the interfacial free energy and mobility are an order of magnitude larger than those measured to date in any other metallic compound. Moreover, the [0 1 0] interface is shown to play a significant role in the observed anisotropy. Our data suggest that the [0 1 0] interface simultaneously corresponds to the lowest mobility, the lowest free energy and the highest stiffness of all inclinations in B33 Ni–Zr. This finding can be understood by taking into account a rather complicated crystal structure in this crystallographic direction.« less

  13. The role of twinning deformation on the hardening response of polycrystalline magnesium from discrete dislocation dynamics simulations

    DOE PAGES-Beta [OSTI]

    Fan, Haidong; Aubry, Sylvie; Arsenlis, Athanasios; El-Awady, Jaafar A.

    2015-04-13

    The mechanical response of micro-twinned polycrystalline magnesium was studied through three-dimensional discrete dislocation dynamics (DDD). A systematic interaction model between dislocations and (1012) tension twin boundaries (TBs) was proposed and introduced into the DDD framework. In addition, a nominal grain boundary (GB) model agreeing with experimental results was also introduced to mimic the GB’s barrier effect. The current simulation results show that TBs act as a strong obstacle to gliding dislocations, which contributes significantly to the hardening behavior of magnesium. On the other hand, the deformation accommodated by twinning plays a softening role. Therefore, the concave shape of the Mgmore » stress-strain curve results from the competition between dislocation-TB induced hardening and twinning deformation induced softening. At low strain levels, twinning deformation induced softening dominates and a decreasing hardening rate is observed in Stage-I. In Stage-II, both the hardening and softening effects decline, but twinning deformation induced softening declines faster, which leads to an increasing hardening rate.« less

  14. Molecular dynamics simulation of self-rotation effects on ultra-precision polishing of single-crystal copper

    SciTech Connect (OSTI)

    Yang, Yihan; Zhao, Hongwei; Zhang, Lin; Shao, Mingkun; Liu, Hongda; Huang, Hu

    2013-10-15

    Understanding the behaviors of the material removal mechanism of ultra-precision polishing process has been a critical issue of generating well-formed surface. In order to make clear the abrasive self-rotation effects on material removal at the atomic level, a three-dimensional molecular dynamics (MD) model is conducted to study the mechanics of ultra-precision polishing on single-crystal copper with a diamond abrasive and the effects of abrasive self-rotation velocity and direction. Morse potential energy function and EAM potential energy function are applied to model the copper/diamond and copper/copper interactions, respectively. The simulation results show that the deformation mechanism of single-crystal copper is due to the formation and movement of dislocations in the specimen. In addition, with the increasing of abrasive self-rotation velocity, the deformation mechanism falls from cutting to plowing regimes. The abrasive self-rotation velocity and direction have effects on the morphology and quality of the specimen surface, distribution and evolution of defects under the surface of the specimen. Also, the interatomic force between abrasive and specimen is studied to account for the effects of different polishing conditions.

  15. Preparation, temperature dependent structural, molecular dynamics simulations studies and electrochemical properties of LiFePO{sub 4}

    SciTech Connect (OSTI)

    Rao, R. Prasada; Reddy, M.V.; Adams, S.; Chowdari, B.V.R.

    2015-06-15

    Highlights: • LiFePO{sub 4} compound was prepared by carbothermal reduction method. • In-situ XRD studies were carried out on LiFePO{sub 4} at various temperatures. • Dedicated imperial potentials used to explain the variation of lattice constants. • It exhibited reversible capacity of 140 (±5) mAh g{sup −1}, stable up to 400 cycles. - Abstract: LiFePO{sub 4} was prepared using carbothermal reduction method. In-situ temperature dependent structural studies were carried using X-ray diffraction. Molecular dynamics simulations were conducted for the LiFePO{sub 4} using empirical potentials developed using bond valence approach to investigate the structural variations. Electrochemical behaviour of LiFePO{sub 4} was evaluated using cyclic voltammetry and galvanostatic cycling studies at room temperature. Charge–discharge cycling studies showed a reversible capacities 140 (±5) mAh g{sup −1} at the end of 50th cycle and these capacity values were stable up to 400 cycles and almost nil capacity fade between 50 and 400 cycles, showing excellent capacity retention, low capacity fading. The cyclic voltammetry studies showed a main cathodic and anodic redox peaks at 3.34 and 3.5 V vs. Li, respectively.

  16. Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

    DOE PAGES-Beta [OSTI]

    Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.; Valdez, Carlos A.

    2016-02-04

    Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

  17. Coordination and Hydrolysis of Plutonium Ions in Aqueous Solution using Car-Parrinello Molecular Dynamics Free Energy Simulations

    SciTech Connect (OSTI)

    Odoh, Samuel O.; Bylaska, Eric J.; De Jong, Wibe A.

    2013-11-27

    Car-Parrinello molecular dynamics (CPMD) simulations have been used to examine the hydration structures, coordination energetics and the first hydrolysis constants of Pu3+, Pu4+, PuO2+ and PuO22+ ions in aqueous solution at 300 K. The coordination numbers and structural properties of the first shell of these ions are in good agreement with available experimental estimates. The hexavalent PuO22+ species is coordinated to 5 aquo ligands while the pentavalent PuO2+ complex is coordinated to 4 aquo ligands. The Pu3+ and Pu4+ ions are both coordinated to 8 water molecules. The first hydrolysis constants obtained for Pu3+ and PuO22+ are 6.65 and 5.70 respectively, all within 0.3 pH units of the experimental values (6.90 and 5.50 respectively). The hydrolysis constant of Pu4+, 0.17, disagrees with the value of -0.60 in the most recent update of the Nuclear Energy Agency Thermochemical Database (NEA-TDB) but supports recent experimental findings. The hydrolysis constant of PuO2+, 9.51, supports the experimental results of Bennett et al. (Radiochim. Act. 1992, 56, 15). A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found.

  18. Time Ordered Astrophysics Scalable Tools

    Energy Science and Technology Software Center (OSTI)

    2011-12-14

    This software package provides tools for astrophysical experiments which record data in the form of individual time streams from discrete detectors. TOAST provides tools from meta-data manipulation and job set up, I/O operation, telescope pointing reconstruction, and map-making. It also provides tools for constructing simulated observations.

  19. AIRMaster+ LogTool | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    LogTool AIRMaster+ LogTool The AIRMaster+ LogTool is a companion tool to AIRMaster+ that helps industrial users determine the operating dynamics of a compressed system. Use the LogTool first to gather critical data in preparation for AIRMaster+. Then, input that data into AIRMaster+ to model existing and future compressed air system upgrades. LogTool V2 Install.zip (19.13 MB) More Documents & Publications AIRMaster+ Tool Introduction AIRMaster+ AIRMaster+ Fact Sheet

  20. Energy Choice Simulator | Open Energy Information

    Open Energy Information (Open El) [EERE & EIA]

    Choice Simulator Jump to: navigation, search Tool Summary LAUNCH TOOL Name: Energy Choice Simulator AgencyCompany Organization: Great Plains Institute Sector: Energy Focus Area:...

  1. Dynamical simulation of energy dissipation in asymmetric heavy-ion induced fission of {sup 200}Pb, {sup 213}Fr, and {sup 251}Es

    SciTech Connect (OSTI)

    Mirfathi, S. M.; Pahlavani, M. R.

    2008-12-15

    The dynamical model based on the asymmetric mass division has been applied to calculate pre-scission neutron multiplicity from heavy-ion induced fusion-fission reactions. Links between the pre-scission neutron multiplicity, excitation energy, and asymmetric mass distribution are clarified based on the Monte Carlo simulation and Langevin dynamics. The pre-scission neutron multiplicity is calculated and compared with the respective experimental data over a wide range of excitation energy and nonconstant viscosity. The analysis indicates a different effect for the application of asymmetric mass division in different energy regions of such processes.

  2. Manipulative Virtual Tools for Tool Mark Characterization | The Ames

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Laboratory Manipulative Virtual Tools for Tool Mark Characterization FWP/Project Description: The goal of this project is to develop a methodology whereby a three-dimensional (3-D) computer simulation of a tool tip is generated. Quantitative 3-D data from the suspected tool and evidence toolmark will be acquired and a virtual reality program developed that takes this data and reconstructs a "virtual tool" for computer manipulation to create "virtual tool marks." Duplicate

  3. Percussion tool

    DOE Patents [OSTI]

    Reed, Teddy R.

    2006-11-28

    A percussion tool is described and which includes a housing mounting a tool bit; a reciprocally moveable hammer borne by the housing and which is operable to repeatedly strike the tool bit; and a reciprocally moveable piston enclosed within the hammer and which imparts reciprocal movement to the reciprocally moveable hammer.

  4. Impact of Dynamic Specimen Shape Evolution on the Atom Probe Tomography Results of Doped Epitaxial Oxide Multilayers: Comparison of Experiment and Simulation

    SciTech Connect (OSTI)

    Madaan, Nitesh; Bao, Jie; Nandasiri, Manjula I.; Xu, Zhijie; Thevuthasan, Suntharampillai; Devaraj, Arun

    2015-08-31

    The experimental atom probe tomography results from two different specimen orientations (top-down and side-ways) of a high oxygen ion conducting Samaria-doped-ceria/Scandia-stabilized-zirconia multilayer thin film solid oxide fuel cell electrolyte was correlated with level-set method based field evaporation simulations for the same specimen orientations. This experiment-theory correlation explains the dynamic specimen shape evolution and ion trajectory aberrations that can induce density artifacts in final reconstruction leading to inaccurate estimation of interfacial intermixing. This study highlights the need and importance of correlating experimental results with field evaporation simulations when using atom probe tomography for studying oxide heterostructure interfaces.

  5. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    SciTech Connect (OSTI)

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

    2015-12-31

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.

  6. THREE-DIMENSIONAL GAS DYNAMIC SIMULATION OF THE INTERACTION BETWEEN THE EXOPLANET WASP-12b AND ITS HOST STAR

    SciTech Connect (OSTI)

    Bisikalo, D.; Kaygorodov, P.; Ionov, D.; Shematovich, V.; Lammer, H.; Fossati, L.

    2013-02-10

    Hubble Space Telescope transit observations in the near-UV performed in 2009 made WASP-12b one of the most 'mysterious' exoplanets; the system presents an early ingress, which can be explained by the presence of optically thick matter located ahead of the planet at a distance of {approx}4-5 planet radii. This work follows previous attempts to explain this asymmetry with an exospheric outflow or a bow shock, induced by a planetary magnetic field, and provides a numerical solution of the early ingress, though we did not perform any radiative transfer calculation. We performed pure 3D gas dynamic simulations of the plasma interaction between WASP-12b and its host star and describe the flow pattern in the system. In particular, we show that the overfilling of the planet's Roche lobe leads to a noticeable outflow from the upper atmosphere in the direction of the L{sub 1} and L{sub 2} points. Due to the conservation of the angular momentum, the flow to the L{sub 1} point is deflected in the direction of the planet's orbital motion, while the flow toward L{sub 2} is deflected in the opposite direction, resulting in a non-axisymmetric envelope, surrounding the planet. The supersonic motion of the planet inside the stellar wind leads to the formation of a bow shock with a complex shape. The existence of the bow shock slows down the outflow through the L{sub 1} and L{sub 2} points, allowing us to consider a long-living flow structure that is in the steady state.

  7. Intel_tools.pptx

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    ! Cray QBR, Apr 8, 2015 Intel Tools for optimizations HBM tools are available on Edison * The memkind library is a user extensible heap manager. It can be used to test/simulate the benefit of high hand width memory (HBM or HBW) on the dual socket Edison compute nodes today. - Use the QPI bus to simulate slow memory - This is not an accurate model of the bandwidth and latency characteristics of the KNL on package memory, but is a reasonable way to determine which data structures rely critically

  8. Planning Tool for Strategic Evaluation of Facility Plans - 13570

    SciTech Connect (OSTI)

    Magoulas, Virginia; Cercy, Michael; Hall, Irin

    2013-07-01

    Savannah River National Laboratory (SRNL) has developed a strategic planning tool for the evaluation of the utilization of its unique resources for processing and research and development of nuclear materials. The Planning Tool is a strategic level tool for assessing multiple missions that could be conducted utilizing the SRNL facilities and showcasing the plan. Traditional approaches using standard scheduling tools and laying out a strategy on paper tended to be labor intensive and offered either a limited or cluttered view for visualizing and communicating results. A tool that can assess the process throughput, duration, and utilization of the facility was needed. SRNL teamed with Newport News Shipbuilding (NNS), a division of Huntington Ingalls Industries, to create the next generation Planning Tool. The goal of this collaboration was to create a simulation based tool that allows for quick evaluation of strategies with respect to new or changing missions, and clearly communicates results to the decision makers. This tool has been built upon a mature modeling and simulation software previously developed by NNS. The Planning Tool provides a forum for capturing dependencies, constraints, activity flows, and variable factors. It is also a platform for quickly evaluating multiple mission scenarios, dynamically adding/updating scenarios, generating multiple views for evaluating/communicating results, and understanding where there are areas of risks and opportunities with respect to capacity. The Planning Tool that has been developed is useful in that it presents a clear visual plan for the missions at the Savannah River Site (SRS). It not only assists in communicating the plans to SRS corporate management, but also allows the area stakeholders a visual look at the future plans for SRS. The design of this tool makes it easily deployable to other facility and mission planning endeavors. (authors)

  9. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    SciTech Connect (OSTI)

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  10. Comparison of the Dynamic Wake Meandering Model, Large-Eddy Simulation, and Field Data at the Egmond aan Zee Offshore Wind Plant: Preprint

    SciTech Connect (OSTI)

    Churchfield, M. J.; Moriarty, P. J.; Hao, Y.; Lackner, M. A.; Barthelmie, R.; Lundquist, J.; Oxley, G. S.

    2014-12-01

    The focus of this work is the comparison of the dynamic wake meandering model and large-eddy simulation with field data from the Egmond aan Zee offshore wind plant composed of 36 3-MW turbines. The field data includes meteorological mast measurements, SCADA information from all turbines, and strain-gauge data from two turbines. The dynamic wake meandering model and large-eddy simulation are means of computing unsteady wind plant aerodynamics, including the important unsteady meandering of wakes as they convect downstream and interact with other turbines and wakes. Both of these models are coupled to a turbine model such that power and mechanical loads of each turbine in the wind plant are computed. We are interested in how accurately different types of waking (e.g., direct versus partial waking), can be modeled, and how background turbulence level affects these loads. We show that both the dynamic wake meandering model and large-eddy simulation appear to underpredict power and overpredict fatigue loads because of wake effects, but it is unclear that they are really in error. This discrepancy may be caused by wind-direction uncertainty in the field data, which tends to make wake effects appear less pronounced.

  11. Computational Tools for Accelerating Carbon Capture Process Development

    SciTech Connect (OSTI)

    Miller, David

    2013-01-01

    The goals of the work reported are: to develop new computational tools and models to enable industry to more rapidly develop and deploy new advanced energy technologies; to demonstrate the capabilities of the CCSI Toolset on non-proprietary case studies; and to deploy the CCSI Toolset to industry. Challenges of simulating carbon capture (and other) processes include: dealing with multiple scales (particle, device, and whole process scales); integration across scales; verification, validation, and uncertainty; and decision support. The tools cover: risk analysis and decision making; validated, high-fidelity CFD; high-resolution filtered sub-models; process design and optimization tools; advanced process control and dynamics; process models; basic data sub-models; and cross-cutting integration tools.

  12. SOWFA Super-Controller: A High-Fidelity Tool for Evaluating Wind Plant Control Approaches

    SciTech Connect (OSTI)

    Fleming, P.; Gebraad, P.; van Wingerden, J. W.; Lee, S.; Churchfield, M.; Scholbrock, A.; Michalakes, J.; Johnson, K.; Moriarty, P.

    2013-01-01

    This paper presents a new tool for testing wind plant controllers in the Simulator for Offshore Wind Farm Applications (SOWFA). SOWFA is a high-fidelity simulator for the interaction between wind turbine dynamics and the fluid flow in a wind plant. The new super-controller testing environment in SOWFA allows for the implementation of the majority of the wind plant control strategies proposed in the literature.

  13. The Development of Dynamic Human Reliability Analysis Simulations for Inclusion in Risk Informed Safety Margin Characterization Frameworks

    SciTech Connect (OSTI)

    Jeffrey C. Joe; Diego Mandelli; Ronald L. Boring; Curtis L. Smith; Rachel B. Shirley

    2015-07-01

    The United States Department of Energy is sponsoring the Light Water Reactor Sustainability program, which has the overall objective of supporting the near-term and the extended operation of commercial nuclear power plants. One key research and development (R&D) area in this program is the Risk-Informed Safety Margin Characterization pathway, which combines probabilistic risk simulation with thermohydraulic simulation codes to define and manage safety margins. The R&D efforts to date, however, have not included robust simulations of human operators, and how the reliability of human performance or lack thereof (i.e., human errors) can affect risk-margins and plant performance. This paper describes current and planned research efforts to address the absence of robust human reliability simulations and thereby increase the fidelity of simulated accident scenarios.

  14. Omics Tools

    SciTech Connect (OSTI)

    Schaumberg, Andrew

    2012-12-21

    The Omics Tools package provides several small trivial tools for work in genomics. This single portable package, the “omics.jar” file, is a toolbox that works in any Java-based environment, including PCs, Macs, and supercomputers. The number of tools is expected to grow. One tool (called cmsearch.hadoop or cmsearch.local), calls the external cmsearch program to predict non-coding RNA in a genome. The cmsearch program is part of the third-party Infernal package. Omics Tools does not contain Infernal. Infernal may be installed separately. The cmsearch.hadoop subtool requires Apache Hadoop and runs on a supercomputer, though cmsearch.local does not and runs on a server. Omics Tools does not contain Hadoop. Hadoop mat be installed separartely The other tools (cmgbk, cmgff, fastats, pal, randgrp, randgrpr, randsub) do not interface with third-party tools. Omics Tools is written in Java and Scala programming languages. Invoking the “help” command shows currently available tools, as shown below: schaumbe@gpint06:~/proj/omics$ java -jar omics.jar help Known commands are: cmgbk : compare cmsearch and GenBank Infernal hits cmgff : compare hits among two GFF (version 3) files cmsearch.hadoop : find Infernal hits in a genome, on your supercomputer cmsearch.local : find Infernal hits in a genome, on your workstation fastats : FASTA stats, e.g. # bases, GC content pal : stem-loop motif detection by palindromic sequence search (code stub) randgrp : random subsample without replacement, of groups randgrpr : random subsample with replacement, of groups (fast) randsub : random subsample without replacement, of file lines For more help regarding a particular command, use: java -jar omics.jar command help Usage: java -jar omics.jar command args

  15. Omics Tools

    Energy Science and Technology Software Center (OSTI)

    2012-12-21

    The Omics Tools package provides several small trivial tools for work in genomics. This single portable package, the “omics.jar” file, is a toolbox that works in any Java-based environment, including PCs, Macs, and supercomputers. The number of tools is expected to grow. One tool (called cmsearch.hadoop or cmsearch.local), calls the external cmsearch program to predict non-coding RNA in a genome. The cmsearch program is part of the third-party Infernal package. Omics Tools does not containmore » Infernal. Infernal may be installed separately. The cmsearch.hadoop subtool requires Apache Hadoop and runs on a supercomputer, though cmsearch.local does not and runs on a server. Omics Tools does not contain Hadoop. Hadoop mat be installed separartely The other tools (cmgbk, cmgff, fastats, pal, randgrp, randgrpr, randsub) do not interface with third-party tools. Omics Tools is written in Java and Scala programming languages. Invoking the “help” command shows currently available tools, as shown below: schaumbe@gpint06:~/proj/omics$ java -jar omics.jar help Known commands are: cmgbk : compare cmsearch and GenBank Infernal hits cmgff : compare hits among two GFF (version 3) files cmsearch.hadoop : find Infernal hits in a genome, on your supercomputer cmsearch.local : find Infernal hits in a genome, on your workstation fastats : FASTA stats, e.g. # bases, GC content pal : stem-loop motif detection by palindromic sequence search (code stub) randgrp : random subsample without replacement, of groups randgrpr : random subsample with replacement, of groups (fast) randsub : random subsample without replacement, of file lines For more help regarding a particular command, use: java -jar omics.jar command help Usage: java -jar omics.jar command args« less

  16. Simulations of the quart (101-bar1)/water interface: A comparison of classical force fields, ab initi molecular dynamics, and x-ray reflectivity experiments.

    SciTech Connect (OSTI)

    Skelton, Adam; Fenter, Paul; Kubicki, James D.; Wesolowski, David J; Cummings, Peter T

    2011-01-01

    Classical molecular dynamics (CMD) simulations of the (1011) surface of quartz interacting with bulk liquid water are performed using three different classical force fields, Lopes et al., ClayFF, and CHARMM water contact angle (CWCA), and compared to ab initio molecular dynamics (AIMD) and X-ray reflectivity (XR) results. The axial densities of the water and surface atoms normal to the surface are calculated and compared to previous XR experiments. Favorable agreement is shown for all the force fields with respect to the position of the water atoms. Analyses such as the radial distribution functions between water and hydroxyl atoms and the average cosine of the angle between the water dipole vector and the normal of the surface are also calculated for each force field. Significant differences are found between the different force fields from such analyses, indicating differing descriptions of the structured water in the near vicinity of the surface. AIMD simulations are also performed to obtain the water and hydroxyl structure for comparison among the predictions of the three classical force fields to better understand which force field is most accurate. It is shown that ClayFF exhibits the best agreement with the AIMD simulations for water hydroxyl radial distribution functions, suggesting that ClayFF treats the hydrogen bonding more accurately.

  17. Prioritization Tool

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    * Performance improvement * Cost * Market * Lifetime Analysis * Stock and flow dynamics * ... (with a critical eye) * Conduct sensitivity analyses ("what if" scenarios) to ...

  18. Dynamic response of CSM composite plates - simulation using material No. 58 in LS-DYNA3D

    SciTech Connect (OSTI)

    Bilkhu, S.S.; Founas, M.; Fong, W.; Agaram, V.

    1997-12-31

    The paper deals with finite element simulations of transverse impact response of plates made from continuous strand mat(CSM) glass/acrylic composite which is a potential candidate for making light weight automotive body panels. Two impact tests on the plates which result in two very different kinds of response, a drop tower test and a dart test, have been simulated using anisotropic material damage model No. 58 in LS-DYNA3D. In view of the results obtained in this study, the authors discuss the suitability of material model No. 58 for simulations of impact response in a bending environment.

  19. Demand Response Quick Assessment Tool

    Energy Science and Technology Software Center (OSTI)

    2008-12-01

    DRQAT (Demand Response Quick Assessment Tool) is the tool for assessing demand response saving potentials for large commercial buildings. This tool is based on EnergyPlus simulations of prototypical buildings and HVAC equipment. The opportunities for demand reduction and cost savings with building demand responsive controls vary tremendously with building type and location. The assessment tools will predict the energy and demand savings, the economic savings, and the thermal comfor impact for various demand responsive strategies.more » Users of the tools will be asked to enter the basic building information such as types, square footage, building envelope, orientation, utility schedule, etc. The assessment tools will then use the prototypical simulation models to calculate the energy and demand reduction potential under certain demand responsive strategies, such as precooling, zonal temperature set up, and chilled water loop and air loop set points adjustment.« less

  20. Regulatory Tools

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Regulatory Tools Home CRA - 2004 Final Recertification Decision CRA Comments & Responses CCA - 1996 CRA CARDs & TSDs CCA CARDs & TSDs Regulatory Tools Title 40 CFR Part 191 Environmental Radiation Protection Standards for Management and Disposal of Spent Nuclear Fuel, High-Level and Transuranic Radioactive Wastes. Title 40 CFR Part 194 Criteria for the Certification and Re-Certification of the Waste Isolation Pilot Plant's Compliance With the 40 CFR Part 191 Disposal Regulations.

  1. Software Tools

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Software Tools Software Tools Copyright materials are released under different mechanisms: Open Source Software and Portfolio Software. CONTACT thumbnail of Kathleen McDonald Head of Intellectual Property, Business Development Executive Kathleen McDonald Richard P. Feynman Center for Innovation (505) 665-9090 Email The Richard P. Feynman Center for Innovation (FCI) releases copyright materials from Los Alamos under different mechanisms. Open Source Software GitHub Explore all open source

  2. New Modeling Tool Analyzes Floating Platform Concepts for Offshore Wind Turbines (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2011-02-01

    Researchers at the National Renewable Energy Laboratory (NREL) developed a new complex modeling and analysis tool capable of analyzing floating platform concepts for offshore wind turbines. The new modeling tool combines the computational methodologies used to analyze land-based wind turbines with the comprehensive hydrodynamic computer programs developed for offshore oil and gas industries. This new coupled dynamic simulation tool will enable the development of cost-effective offshore technologies capable of harvesting the rich offshore wind resources at water depths that cannot be reached using the current technology.

  3. Hybrid Quantum Mechanics/Molecular Mechanics-Based Molecular Dynamics Simulation of Acid-Catalyzed Dehydration of Polyols in Liquid Water

    SciTech Connect (OSTI)

    Caratzoulas, Stavros; Courtney, Timothy; Vlachos, Dionisios G.

    2011-01-01

    We use the conversion of protonated glycerol to acrolein for a case study of the mechanism of acid-catalyzed dehydration of polyols in aqueous environments. We employ hybrid Quamtum Mechanics/Molecular Mechanics Molecular Dynamics (QM/MM MD) simulations with biased sampling and perform free energy calculations for the elementary steps of the reaction. We investigate the effects of solvent dynamics and in particular the role of quantum mechanical water in the dehydration mechanism. We present results supporting a mechanism that proceeds via water-mediated proton transfers and thus through an enol intermediate. We find that the first dehydration may take place by two, low-energy pathways requiring, respectively, 20.9 and 18.8 kcal/mol of activation free energy. The second dehydration requires 19.9 kcal/mol of activation free energy while for the overall reaction we compute a free energy change of -8 kcal/mol.

  4. NREL: Energy Analysis - Models and Tools Archive

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Models and Tools Archive Through the years, NREL has developed and supported several models and tools to assess, analyze, and optimize renewable energy and energy efficiency technologies. Some of these have been transferred to the private market. This page lists tools we have supported, but that are no longer active. See current models and tools here. ADVISOR (ADvanced VehIcle SimulatOR) Simulate and analyze conventional, advanced, light, and heavy vehicles, including hybrid electric and fuel

  5. Wind Data and Tools | Wind | NREL

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Wind Data and Tools Learn more about wind energy through these NREL data and tools. A photo of two men silhouetted against a computer-generated simulation with white and blue rows illustrating wind plant aerodynamics. NWTC Information Portal This open-source library houses NREL's wind and water power simulation and modeling software and data, including computer-aided engineering tools and integrated system design and analysis tools. All software is available for download. Wind-Wildlife Impacts

  6. Application of computational fluid dynamics for the simulation of cryogenic molecular sieve bed absorber of hydrogen isotopes recovery system for Indian LLCB-TBM

    SciTech Connect (OSTI)

    Gayathri Devi, V.; Sircar, A.; Sarkar, B.

    2015-03-15

    One of the most challenging tasks in the design of the fuel cycle system lies in the effective design of Tritium Extraction System (TES) which involves proper extraction and purification of tritium in the fuel cycle of the fusion reactor. Indian Lead Lithium cooled Ceramic Breeder Test Blanket Module (LLCB-TBM) would extract hydrogen isotopes through Cryogenic Molecular Sieve Bed (CMSB) adsorber system. A prototype Hydrogen Isotopes Recovery System (HIRS) is being developed to validate the concepts for tritium extraction by adsorption mass transfer mechanism. In this study, a design model has been developed and analyzed to simulate the adsorption mass transfer kinetics in a fixed bed adsorption column. The simulation leads primarily to effective design of HIRS, which is a state-of-the-art technology. The paper describes the process simulation approach and the results of Computational Fluid Dynamics (CFD) analysis. The effects of different operating conditions are studied to investigate their influence on the hydrogen isotopes adsorption capacity. The results of the present simulation study would be used to understand the best optimized transport phenomenon before realizing the TES as a system for LLCB-TBM. (authors)

  7. Numerical simulations of epitaxial growth process in MOVPE reactor as a tool for design of modern semiconductors for high power electronics

    SciTech Connect (OSTI)

    Skibinski, Jakub; Wejrzanowski, Tomasz; Caban, Piotr; Kurzydlowski, Krzysztof J.

    2014-10-06

    In the present study numerical simulations of epitaxial growth of gallium nitride in Metal Organic Vapor Phase Epitaxy reactor AIX-200/4RF-S is addressed. Epitaxial growth means crystal growth that progresses while inheriting the laminar structure and the orientation of substrate crystals. One of the technological problems is to obtain homogeneous growth rate over the main deposit area. Since there are many agents influencing reaction on crystal area such as temperature, pressure, gas flow or reactor geometry, it is difficult to design optimal process. According to the fact that it's impossible to determine experimentally the exact distribution of heat and mass transfer inside the reactor during crystal growth, modeling is the only solution to understand the process precisely. Numerical simulations allow to understand the epitaxial process by calculation of heat and mass transfer distribution during growth of gallium nitride. Including chemical reactions in numerical model allows to calculate the growth rate of the substrate and estimate the optimal process conditions for obtaining the most homogeneous product.

  8. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    SciTech Connect (OSTI)

    Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki -Alexandra

    2015-10-12

    Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivity and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of

  9. Application of a New Ensemble Conserving Quantum Dynamics Simulation Algorithm to Liquid para-Hydrogen and ortho-Deuterium

    DOE PAGES-Beta [OSTI]

    Smith, Kyle K.G.; Poulsen, Jens Aage; Nyman, Gunnar; Cunsolo, Alessandro; Rossky, Peter J.

    2015-06-30

    Here, we apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm-3) and (T = 23.0 K, n = 24.61 nm-3), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. Moreover, this shows that FK-QCWmore » provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

  10. The Agricultural Policy/Environmental Extender (Apex) Model: An Emerging Tool for Landscape and Watershed Environmental Analyses

    SciTech Connect (OSTI)

    Gassman, Philip W.; Williams, Jimmy R.; Wang, Xiuying; Saleh, Ali; Osei, Edward; Hauck, Larry; Izaurralde, Roberto C.; Flowers, Joan

    2010-06-01

    The Agricultural Policy Environmental eXtender (APEX) model was developed by the Blacklands Research and Extension Center in Temple, Texas. APEX is a flexible and dynamic tool that is capable of simulating a wide array of management practices, cropping systems, and other land uses across a broad range of agricultural landscapes, including whole farms and small watersheds.

  11. Accelerating population balance-Monte Carlo simulation for coagulation dynamics from the Markov jump model, stochastic algorithm and GPU parallel computing

    SciTech Connect (OSTI)

    Xu, Zuwei; Zhao, Haibo Zheng, Chuguang

    2015-01-15

    This paper proposes a comprehensive framework for accelerating population balance-Monte Carlo (PBMC) simulation of particle coagulation dynamics. By combining Markov jump model, weighted majorant kernel and GPU (graphics processing unit) parallel computing, a significant gain in computational efficiency is achieved. The Markov jump model constructs a coagulation-rule matrix of differentially-weighted simulation particles, so as to capture the time evolution of particle size distribution with low statistical noise over the full size range and as far as possible to reduce the number of time loopings. Here three coagulation rules are highlighted and it is found that constructing appropriate coagulation rule provides a route to attain the compromise between accuracy and cost of PBMC methods. Further, in order to avoid double looping over all simulation particles when considering the two-particle events (typically, particle coagulation), the weighted majorant kernel is introduced to estimate the maximum coagulation rates being used for acceptance–rejection processes by single-looping over all particles, and meanwhile the mean time-step of coagulation event is estimated by summing the coagulation kernels of rejected and accepted particle pairs. The computational load of these fast differentially-weighted PBMC simulations (based on the Markov jump model) is reduced greatly to be proportional to the number of simulation particles in a zero-dimensional system (single cell). Finally, for a spatially inhomogeneous multi-dimensional (multi-cell) simulation, the proposed fast PBMC is performed in each cell, and multiple cells are parallel processed by multi-cores on a GPU that can implement the massively threaded data-parallel tasks to obtain remarkable speedup ratio (comparing with CPU computation, the speedup ratio of GPU parallel computing is as high as 200 in a case of 100 cells with 10 000 simulation particles per cell). These accelerating approaches of PBMC are

  12. The Open Source Stochastic Building Simulation Tool SLBM and Its Capabilities to Capture Uncertainty of Policymaking in the U.S. Building Sector

    SciTech Connect (OSTI)

    Stadler, Michael; Marnay, Chris; Azevedo, Ines Lima; Komiyama, Ryoichi; Lai, Judy

    2009-05-14

    The increasing concern about climate change as well as the expected direct environmental economic impacts of global warming will put considerable constraints on the US building sector, which consumes roughly 48percent of the total primary energy, making it the biggest single source of CO2 emissions. It is obvious that the battle against climate change can only be won by considering innovative building approaches and consumer behaviors and bringing new, effective low carbon technologies to the building / consumer market. However, the limited time given to mitigate climate change is unforgiving to misled research and / or policy. This is the reason why Lawrence Berkeley National Lab is working on an open source long range Stochastic Lite Building Module (SLBM) to estimate the impact of different policies and consumer behavior on the market penetration of low carbon building technologies. SLBM is designed to be a fast running, user-friendly model that analysts can readily run and modify in its entirety through a visual interface. The tool is fundamentally an engineering-economic model with technology adoption decisions based on cost and energy performance characteristics of competing technologies. It also incorporates consumer preferences and passive building systems as well as interactions between technologies (such as internal heat gains). Furthermore, everything is based on service demand, e.g. a certain temperature or luminous intensity, instead of energy intensities. The core objectives of this paper are to demonstrate the practical approach used, to start a discussion process between relevant stakeholders and to build collaborations.

  13. Java Vertexing Tools

    SciTech Connect (OSTI)

    Strube, Jan; Graf, Norman; /SLAC

    2006-03-03

    This document describes the implementation of the topological vertex finding algorithm ZVTOP within the org.lcsim reconstruction and analysis framework. At the present date, Java vertexing tools allow users to perform topological vertexing on tracks that have been obtained from a Fast MC simulation. An implementation that will be able to handle fully reconstructed events is being designed from the ground up for longevity and maintainability.

  14. Vehicle Technologies Office: Transportation System Analytical Tools |

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Department of Energy Modeling, Testing, Data & Results » Vehicle Technologies Office: Transportation System Analytical Tools Vehicle Technologies Office: Transportation System Analytical Tools The Vehicle Technologies Office (VTO) has supported the development of a number of software packages and online tools to model individual vehicles and the overall transportation system. Most of these tools are available for free or a nominal charge. Modeling tools that simulate entire vehicles and

  15. Household Response To Dynamic Pricing Of Electricity: A Survey...

    Open Energy Information (Open El) [EERE & EIA]

    Household Response To Dynamic Pricing Of Electricity: A Survey Of The Experimental Evidence Jump to: navigation, search Tool Summary LAUNCH TOOL Name: Household Response To Dynamic...

  16. Thermal transport in UO2 with defects and fission products by molecular dynamics simulations

    SciTech Connect (OSTI)

    Liu, Xiang-Yang; Cooper, Michael William Donald; Mcclellan, Kenneth James; Lashley, Jason Charles; Byler, Darrin David; Stanek, Christopher Richard; Andersson, Anders David Ragnar

    2015-10-14

    The importance of the thermal transport in nuclear fuel has motivated a wide range of experimental and modelling studies. In this report, the reduction of thermal transport in UO2 due to defects and fission products has been investigated using non-equilibrium MD simulations, with two sets of empirical potentials for studying the degregation of UO2 thermal conductivity including a Buckingham type interatomic potential and a recently developed EAM type interatomic potential. Additional parameters for U5+ and Zr4+ in UO2 have been developed for the EAM potential. The thermal conductivity results from MD simulations are then corrected for the spin-phonon scattering through Callaway model formulations. To validate the modelling results, comparison was made with experimental measurements on single crystal hyper-stoichiometric UO2+x samples.

  17. Molecular dynamics simulations and thermochemistry of reactive ion etching of silicon by chlorine, chlorine dimer, bromine, and bromine dimer cations

    SciTech Connect (OSTI)

    Valone, S.M.; Hanson, D.E.; Kress, J.D.

    1998-05-08

    Simulations of Cl plasma etch of Si surfaces with MD techniques agree reasonably well with the available experimental information on yields and surface morphologies. This information has been supplied to a Monte Carlo etch profile resulting in substantial agreement with comparable inputs provided through controlled experiments. To the extent that more recent measurements of etch rates are more reliable than older ones, preliminary MD simulations using bond-order corrections to the atomic interactions between neighboring Si atoms on the surface improves agreement with experiment through an increase in etch rate and improved agreement with XPS measurements of surface stoichiometry. Thermochemical and geometric analysis of small Si-Br molecules is consistent with the current notions of the effects of including brominated species in etchant gases.

  18. Dynamics of positive probes in underdense, strongly magnetized, E×B drifting plasma: Particle-in-cell simulations

    SciTech Connect (OSTI)

    Heinrich, Jonathon R.; Cooke, David L.

    2013-09-15

    Electron trapping, electron heating, space-charge wings, wake eddies, and current collection by a positive probe in E×B drifting plasma were studied in three-dimensional electromagnetic particle-in-cell simulations. In these simulations, electrons and ions were magnetized with respect to the probe and the plasma was underdense (ω{sub pe}<ω{sub ce}). A large drift velocity (Mach 4.5 with respect to the ion acoustic speed) between the plasma and probe was created with background electric and magnetic fields. Four distinct regions developed in the presences of the positive probe: a quasi-trapped electron region, an electron-depletion wing, an ion-rich wing, and a wake region. We report on the observations of strong electron heating mechanisms, space-charge wings, ion cyclotron charge-density eddies in the wake, electron acceleration due to a magnetic presheath, and the current-voltage relationship.

  19. Using EnergyPlus to Simulate the Dynamic Response of a Residential Building to Advanced Cooling Strategies: Preprint

    SciTech Connect (OSTI)

    Booten, C.; Tabares-Velasco, P. C.

    2012-08-01

    This study demonstrates the ability of EnergyPlus to accurately model complex cooling strategies in a real home with a goal of shifting energy use off peak and realizing energy savings. The house was retrofitted through the Sacramento Municipal Utility District's (SMUD) deep energy retrofit demonstration program; field tests were operated by the National Renewable Energy Laboratory (NREL). The experimental data were collected as part of a larger study and are used here to validate simulation predictions.

  20. Chaos in plasma simulation and experiment

    SciTech Connect (OSTI)

    Watts, C.; Newman, D.E.; Sprott, J.C.

    1993-09-01

    We investigate the possibility that chaos and simple determinism are governing the dynamics of reversed field pinch (RFP) plasmas using data from both numerical simulations and experiment. A large repertoire of nonlinear analysis techniques is used to identify low dimensional chaos. These tools include phase portraits and Poincard sections, correlation dimension, the spectrum of Lyapunov exponents and short term predictability. In addition, nonlinear noise reduction techniques are applied to the experimental data in an attempt to extract any underlying deterministic dynamics. Two model systems are used to simulate the plasma dynamics. These are -the DEBS code, which models global RFP dynamics, and the dissipative trapped electron mode (DTEM) model, which models drift wave turbulence. Data from both simulations show strong indications of low,dimensional chaos and simple determinism. Experimental data were obtained from the Madison Symmetric Torus RFP and consist of a wide array of both global and local diagnostic signals. None of the signals shows any indication of low dimensional chaos or other simple determinism. Moreover, most of the analysis tools indicate the experimental system is very high dimensional with properties similar to noise. Nonlinear noise reduction is unsuccessful at extracting an underlying deterministic system.

  1. LHC RF System Time-Domain Simulation

    SciTech Connect (OSTI)

    Mastorides, T.; Rivetta, C.

    2010-09-14

    Non-linear time-domain simulations have been developed for the Positron-Electron Project (PEP-II) and the Large Hadron Collider (LHC). These simulations capture the dynamic behavior of the RF station-beam interaction and are structured to reproduce the technical characteristics of the system (noise contributions, non-linear elements, and more). As such, they provide useful results and insight for the development and design of future LLRF feedback systems. They are also a valuable tool for the study of diverse longitudinal beam dynamics effects such as coupled-bunch impedance driven instabilities and single bunch longitudinal emittance growth. Results from these studies and related measurements from PEP-II and LHC have been presented in multiple places. This report presents an example of the time-domain simulation implementation for the LHC.

  2. Downhole tool

    DOE Patents [OSTI]

    Hall, David R.; Muradov, Andrei; Pixton, David S.; Dahlgren, Scott Steven; Briscoe, Michael A.

    2007-03-20

    A double shouldered downhole tool connection comprises box and pin connections having mating threads intermediate mating primary and secondary shoulders. The connection further comprises a secondary shoulder component retained in the box connection intermediate a floating component and the primary shoulders. The secondary shoulder component and the pin connection cooperate to transfer a portion of makeup load to the box connection. The downhole tool may be selected from the group consisting of drill pipe, drill collars, production pipe, and reamers. The floating component may be selected from the group consisting of electronics modules, generators, gyroscopes, power sources, and stators. The secondary shoulder component may comprises an interface to the box connection selected from the group consisting of radial grooves, axial grooves, tapered grooves, radial protrusions, axial protrusions, tapered protrusions, shoulders, and threads.

  3. Adapting SAFT-? perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

    SciTech Connect (OSTI)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-07-14

    In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-? WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-? refers to the particular form of statistical associating fluid theory that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A new chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH{sub 2} and CH{sub 3} and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ?2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ?1% from simulation data while the theory reproduces

  4. Numerical simulation of effective mechanical properties of stochastic composites with consideration for structural evolution under intensive dynamic loading

    SciTech Connect (OSTI)

    Karakulov, Valerii V.; Smolin, Igor Yu. E-mail: skrp@ftf.tsu.ru; Skripnyak, Vladimir A. E-mail: skrp@ftf.tsu.ru

    2014-11-14

    Mechanical behavior of stochastic metal-ceramic composites with the aluminum matrix under high-rate deformation at shock-wave loading is numerically simulated with consideration for structural evolution. Effective values of mechanical parameters of metal-ceramic composites AlB{sub 4}C, AlSiC, and AlAl{sub 2}O{sub 3} are evaluated depending on different concentration of ceramic inclusions.

  5. Simulating coarse-scale vegetation dynamics using the Columbia River Basin succession model-crbsum. Forest Service general technical report

    SciTech Connect (OSTI)

    Keane, R.E.; Long, D.G.; Menakis, J.P.; Hann, W.J.; Bevins, C.D.

    1996-10-01

    The paper details the landscape succession model developed for the coarse-scale assessment called CRBSUM (Columbia River Basin SUccession Model) and presents some general results of the application of this model to the entire basin. CRBSUM was used to predict future landscape characteristics to evaluate management alternatives for both mid-and coarse-scale efforts. A test and sensitivity analysis of CRBSUM is also presented. This paper was written as a users guide for those who wish to run the model and interprete results, and its was also written as documentation for some results of the Interior Columbia River Basin simulation effort.

  6. Ootw Tool Requirements in Relation to JWARS

    SciTech Connect (OSTI)

    Hartley III, D.S.; Packard, S.L.

    1998-01-01

    This document reports the results of the CMke of the Secretary of Defense/Program Analysis & Evaluation (OSD/PA&E) sponsored project to identify how Operations Other Than War (OOTW) tool requirements relate to the Joint Warfare Simulation (JWARS) and, more generally, to joint analytical modeling and simulation (M&S) requirements. It includes recommendations about which OOTW tools (and functionality within tools) should be included in JWARS, which should be managed as joint analytical modeling and simulation (M&S) tools, and which should be left for independent development.

  7. Molecular dynamics simulation of radiation damage in CaCd{sub 6} quasicrystal cubic approximant up to 10 keV

    SciTech Connect (OSTI)

    Chen, P. H.; Avchachov, K.; Nordlund, K.; Pussi, K.

    2013-06-21

    Due to the peculiar nature of the atomic order in quasicrystals, examining phase transitions in this class of materials is of particular interest. Energetic particle irradiation can provide a way to modify the structure locally in a quasicrystal. To examine irradiation-induced phase transitions in quasicrystals on the atomic scale, we have carried out molecular dynamics simulations of collision cascades in CaCd{sub 6} quasicrystal cubic approximant with energies up to 10 keV at 0 and 300 K. The results show that the threshold energies depend surprisingly strongly on the local coordination environments. The energy dependence of stable defect formation exhibits a power-law dependence on cascade energy, and surviving defects are dominated by Cd interstitials and vacancies. Only a modest effect of temperature is observed on defect survival, while irradiation temperature increases lead to a slight increase in the average size of both vacancy clusters and interstitial clusters.

  8. Spectral shapes of Ar-broadened HCl lines in the fundamental band by classical molecular dynamics simulations and comparison with experiments

    SciTech Connect (OSTI)

    Tran, H.; Domenech, J.-L.

    2014-08-14

    Spectral shapes of isolated lines of HCl perturbed by Ar are investigated for the first time using classical molecular dynamics simulations (CMDS). Using reliable intermolecular potentials taken from the literature, these CMDS provide the time evolution of the auto-correlation function of the dipole moment, whose Fourier-Laplace transform leads to the absorption spectrum. In order to test these calculations, room temperature spectra of various lines in the fundamental band of HCl diluted in Ar are measured, in a large pressure range, with a difference-frequency laser spectrometer. Comparisons between measured and calculated spectra show that the CMDS are able to predict the large Dicke narrowing effect on the shape of HCl lines and to satisfactorily reproduce the shapes of HCl spectra at different pressures and for various rotational quantum numbers.

  9. Terascale High-Fidelity Simulations of Turbulent Combustion with Detailed Chemistry: Spray Simulations

    SciTech Connect (OSTI)

    Rutland, Christopher J.

    2009-04-26

    The Terascale High-Fidelity Simulations of Turbulent Combustion (TSTC) project is a multi-university collaborative effort to develop a high-fidelity turbulent reacting flow simulation capability utilizing terascale, massively parallel computer technology. The main paradigm of the approach is direct numerical simulation (DNS) featuring the highest temporal and spatial accuracy, allowing quantitative observations of the fine-scale physics found in turbulent reacting flows as well as providing a useful tool for development of sub-models needed in device-level simulations. Under this component of the TSTC program the simulation code named S3D, developed and shared with coworkers at Sandia National Laboratories, has been enhanced with new numerical algorithms and physical models to provide predictive capabilities for turbulent liquid fuel spray dynamics. Major accomplishments include improved fundamental understanding of mixing and auto-ignition in multi-phase turbulent reactant mixtures and turbulent fuel injection spray jets.

  10. Geochemical Reaction Mechanism Discovery from Molecular Simulation

    SciTech Connect (OSTI)

    Stack, Andrew G.; Kent, Paul R. C.

    2014-11-10

    Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineral surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.

  11. Geochemical Reaction Mechanism Discovery from Molecular Simulation

    DOE PAGES-Beta [OSTI]

    Stack, Andrew G.; Kent, Paul R. C.

    2014-11-10

    Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less

  12. Nanoparticle generation and transport resulting from femtosecond laser ablation of ultrathin metal films: Time-resolved measurements and molecular dynamics simulations

    SciTech Connect (OSTI)

    Rouleau, C. M. Puretzky, A. A.; Geohegan, D. B.; Shih, C.-Y.; Wu, C.; Zhigilei, L. V.

    2014-05-12

    The synthesis of metal nanoparticles by ultrafast laser ablation of nanometers-thick metal films has been studied experimentally and computationally. Near-threshold backside laser ablation of 2–20 nm-thick Pt films deposited on fused silica substrates was found to produce nanoparticles with size distributions that were bimodal for the thicker films, but collapsed into a single mode distribution for the thinnest film. Time-resolved imaging of blackbody emission from the Pt nanoparticles was used to reveal the nanoparticle propagation dynamics and estimate their temperatures. The observed nanoparticle plume was compact and highly forward-directed with a well-defined collective velocity that permitted multiple rebounds with substrates to be revealed. Large-scale molecular dynamics simulations were used to understand the evolution of compressive and tensile stresses in the thicker melted liquid films that lead to their breakup and ejection of two groups of nanoparticles with different velocity and size distributions. Ultrafast laser irradiation of ultrathin (few nm) metal films avoids the splitting of the film and appears to be a method well-suited to cleanly synthesize and deposit nanoparticles from semitransparent thin film targets in highly directed beams.

  13. Two dimensional numerical simulations of carrier dynamics during time-resolved photoluminescence decays in two-photon microscopy measurements in semiconductors

    SciTech Connect (OSTI)

    Kanevce, Ana; Kuciauskas, Darius; Levi, Dean H.; Johnston, Steven W.; Allende Motz, Alyssa M.

    2015-07-28

    We use two-dimensional numerical simulations to analyze high spatial resolution time-resolved spectroscopy data. This analysis is applied to two-photon excitation time-resolved photoluminescence (2PE-TRPL) but is broadly applicable to all microscopic time-resolved techniques. By solving time-dependent drift-diffusion equations, we gain insight into carrier dynamics and transport characteristics. Accurate understanding of measurement results establishes the limits and potential of the measurement and enhances its value as a characterization method. Diffusion of carriers outside of the collection volume can have a significant impact on the measured decay but can also provide an estimate of carrier mobility as well as lifetime. In addition to material parameters, the experimental conditions, such as spot size and injection level, can impact the measurement results. Although small spot size provides better resolution, it also increases the impact of diffusion on the decay; if the spot size is much smaller than the diffusion length, it impacts the entire decay. By reproducing experimental 2PE-TRPL decays, the simulations determine the bulk carrier lifetime from the data. The analysis is applied to single-crystal and heteroepitaxial CdTe, material important for solar cells, but it is also applicable to other semiconductors where carrier diffusion from the excitation volume could affect experimental measurements.

  14. Algal functional annotation tool

    SciTech Connect (OSTI)

    Lopez, D.; Casero, D.; Cokus, S. J.; Merchant, S. S.; Pellegrini, M.

    2012-07-01

    The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion.

  15. BEAM SIMULATIONS USING VIRTUAL DIAGNOSTICS FOR THE DRIVER LINAC

    SciTech Connect (OSTI)

    R. C. York; X. Wu; Q. Zhao

    2011-12-21

    End-to-end beam simulations for the driver linac have shown that the design meets the necessary performance requirements including having adequate transverse and longitudinal acceptances. However, to achieve reliable operational performance, the development of appropriate beam diagnostic systems and control room procedures are crucial. With limited R&D funding, beam simulations provide a cost effective tool to evaluate candidate beam diagnostic systems and to provide a critical basis for developing early commissioning and later operational activities. We propose to perform beam dynamic studies and engineering analyses to define the requisite diagnostic systems of the driver linac and through simulation to develop and test commissioning and operational procedures.

  16. Prototype simplified daylighting design tool

    SciTech Connect (OSTI)

    Treado, S.J.; Goodin, P.J.

    1992-07-01

    The report describes a prototype simplified design tool which has been developed to provide information for developing effective building fenestration systems. A computer software system was developed to search through and select the best available fenestration designs from a large database of previously simulated buildings. Fenestration designs can be selected based on energy usage, energy cost or peak loads. The determination of fenestration energy costs is discussed. The design tool is primarily intended for commercial, industrial or institutional buildings of any type.

  17. A reduced-order modeling approach to represent subgrid-scale hydrological dynamics for land-surface simulations: application in a polygonal tundra landscape

    DOE PAGES-Beta [OSTI]

    Pau, G. S. H.; Bisht, G.; Riley, W. J.

    2014-09-17

    Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO2, CH4) exchanges with the atmosphere range from the molecular scale (pore-scale O2 consumption) to tens of kilometers (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a reduced-order modeling (ROM) technique known as "proper orthogonal decomposition mapping method" that reconstructs temporally resolvedmore » fine-resolution solutions based on coarse-resolution solutions. We developed four different methods and applied them to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface–subsurface isothermal simulations were performed for summer months (June–September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998–2000) to build ROMs of the 4-D soil moisture field for the study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 103) with very small relative approximation error (< 0.1%) for 2 validation years not used in training the ROM. We also demonstrate that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training data set with relatively good accuracy (< 1.7% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. By coupling the ROMs constructed at different scales together hierarchically, this method has the potential to efficiently increase the resolution of land models for coupled

  18. A reduced order modeling approach to represent subgrid-scale hydrological dynamics for regional- and climate-scale land-surface simulations: application in a polygonal tundra landscape

    DOE PAGES-Beta [OSTI]

    Pau, G. S. H.; Bisht, G.; Riley, W. J.

    2014-04-04

    Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO2, CH4) exchanges with the atmosphere range from molecular scale (pore-scale O2 consumption) to tens of kilometer scale (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a particular reduced-order modeling (ROM) technique known as "Proper Orthogonal Decomposition mapping method" that reconstructs temporally-resolvedmore » fine-resolution solutions based on coarse-resolution solutions. We applied this technique to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface-subsurface isothermal simulations were performed for summer months (June–September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998–2000) to build ROMs of the 4-D soil moisture field for the four study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 103) with very small relative approximation error (< 0.1%) for two validation years not used in training the ROM. We also demonstrated that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training dataset with relatively good accuracy (< 1.5% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. This method has the potential to efficiently increase the resolution of land models for coupled climate simulations, allowing LSMs to be used at spatial scales consistent with

  19. Dynamic simulation and load-following control of an integrated gasification combined cycle (IGCC) power plant with CO{sub 2} capture

    SciTech Connect (OSTI)

    Bhattacharyya, D,; Turton, R.; Zitney, S.

    2012-01-01

    Load-following control of future integrated gasification combined cycle (IGCC) plants with pre-combustion CO{sub 2} capture is expected to be far more challenging as electricity produced by renewable energy is connected to the grid and strict environmental limits become mandatory requirements. To study control performance during load following, a plant-wide dynamic simulation of a coal-fed IGCC plant with CO{sub 2} capture has been developed. The slurry-fed gasifier is a single-stage, downward-fired, oxygen-blown, entrained-flow type with a radiant syngas cooler (RSC). The syngas from the outlet of the RSC goes to a scrubber followed by a two-stage sour shift process with inter-stage cooling. The acid gas removal (AGR) process is a dual-stage physical solvent-based process for selective removal of H{sub 2}S in the first stage and CO{sub 2} in the second stage. Sulfur is recovered using a Claus unit with tail gas recycle to the AGR. The recovered CO{sub 2} is compressed by a split-shaft multistage compressor and sent for sequestration after being treated in an absorber with triethylene glycol for dehydration. The clean syngas is sent to two advanced “F”-class gas turbines (GTs) partially integrated with an elevated-pressure air separation unit. A subcritical steam cycle is used for heat recovery steam generation. A treatment unit for the sour water strips off the acid gases for utilization in the Claus unit. The steady-state model developed in Aspen Plus® is converted to an Aspen Plus Dynamics® simulation and integrated with MATLAB® for control studies. The results from the plant-wide dynamic model are compared qualitatively with the data from a commercial plant having different configuration, operating condition, and feed quality than what has been considered in this work. For load-following control, the GT-lead with gasifier-follow control strategy is considered. A modified proportional–integral–derivative (PID) control is considered for the syngas

  20. Logistics Process Analysis ToolProcess Analysis Tool

    Energy Science and Technology Software Center (OSTI)

    2008-03-31

    LPAT is the resulting integrated system between ANL-developed Enhanced Logistics Intra Theater Support Tool (ELIST) sponsored by SDDC-TEA and the Fort Future Virtual Installation Tool (sponsored by CERL). The Fort Future Simulation Engine was an application written in the ANL Repast Simphony framework and used as the basis for the process Anlysis Tool (PAT) which evolved into a stand=-along tool for detailed process analysis at a location. Combined with ELIST, an inter-installation logistics component wasmore » added to enable users to define large logistical agent-based models without having to program. PAT is the evolution of an ANL-developed software system called Fort Future Virtual Installation Tool (sponsored by CERL). The Fort Future Simulation Engine was an application written in the ANL Repast Simphony framework and used as the basis for the Process Analysis Tool(PAT) which evolved into a stand-alone tool for detailed process analysis at a location (sponsored by the SDDC-TEA).« less

  1. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

    SciTech Connect (OSTI)

    MacDermaid, Christopher M. Klein, Michael L.; Fiorin, Giacomo; Kashyap, Hemant K.; DeVane, Russell H.; Shinoda, Wataru; Klauda, Jeffery B.

    2015-12-28

    The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.

  2. A direct numerical simulation-based investigation and modeling of pressure Hessian effects on compressible velocity gradient dynamics

    SciTech Connect (OSTI)

    Danish, Mohammad Suman, Sawan Srinivasan, Balaji

    2014-12-15

    The pressure Hessian tensor plays a key role in shaping the behavior of the velocity gradient tensor, and in turn, that of many incumbent non-linear processes in a turbulent flow field. In compressible flows, the role of pressure Hessian is even more important because it represents the level of fluid-thermodynamic coupling existing in the flow field. In this work, we first perform a direct numerical simulation-based study to clearly identify, isolate, and understand various important inviscid mechanisms that govern the evolution of the pressure Hessian tensor in compressible turbulence. The ensuing understanding is then employed to introduce major improvements to the existing Lagrangian model of the pressure Hessian tensor (the enhanced Homogenized Euler equation or EHEE) in terms of (i) non-symmetric, non-isentropic effects and (ii) improved representation of the anisotropic portion of the pressure Hessian tensor. Finally, we evaluate the new model extensively by comparing the new model results against known turbulence behavior over a range of Reynolds and Mach numbers. Indeed, the new model shows much improved performance as compared to the EHEE model.

  3. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

    SciTech Connect (OSTI)

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-03-07

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeperthe binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnOit has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.

  4. Nonlinear coupling network to simulate the development of the r mode instability in neutron stars. II. Dynamics

    SciTech Connect (OSTI)

    Brink, Jeandrew; Teukolsky, Saul A; Wasserman, Ira

    2005-03-15

    Two mechanisms for nonlinear mode saturation of the r mode in neutron stars have been suggested: the parametric instability mechanism involving a small number of modes and the formation of a nearly continuous Kolmogorov-type cascade. Using a network of oscillators constructed from the eigenmodes of a perfect fluid incompressible star, we investigate the transition between the two regimes numerically. Our network includes the 4995 inertial modes up to n{<=}30 with 146 998 direct couplings to the r mode and 1 306 999 couplings with detuning <0.002 (out of a total of approximately 10{sup 9} possible couplings). The lowest parametric instability thresholds for a range of temperatures are calculated and it is found that the r mode becomes unstable to modes with 13dynamics. The behavior of the r mode is complicated, but its amplitude is still no larger than about 10{sup -4} on average. For high temperature, weakly damped models the r mode feeds energy into a sea of oscillators that achieve approximate equipartition. In this case the r-mode amplitude settles to a value for which the rate to achieve equipartition is approximately the linear instability growth rate.

  5. Tool Basics | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Commercial Buildings » Analysis Tools » Energy Asset Score » Tool Basics Tool Basics Asset Score Scale The Asset Score uses a 10-point scale to evaluate the energy efficiency of a building's physical characteristics and major energy-related systems. The point value is assigned based on a building's predicted source energy use intensity (EUI) according to the energy simulation results. Scores are rounded to the nearest half-point increment (i.e., "6", "6.5", "7",

  6. Terascale Simulation Tools and Technologies (Technical Report...

    Office of Scientific and Technical Information (OSTI)

    Close Cite: Bibtex Format Close 0 pages in this document matching the terms "" Search For Terms: Enter terms in the toolbar above to search the full text of this document for ...

  7. Autonomie Automotive Simulation Tool | Open Energy Information

    Open Energy Information (Open El) [EERE & EIA]

    industrial, aerospace, and automotive applications. It provides an efficient methodology that includes four key elements in the development process: modeling a plant (from...

  8. Electrical Circuit Simulation Code

    Energy Science and Technology Software Center (OSTI)

    2001-08-09

    Massively-Parallel Electrical Circuit Simulation Code. CHILESPICE is a massively-arallel distributed-memory electrical circuit simulation tool that contains many enhanced radiation, time-based, and thermal features and models. Large scale electronic circuit simulation. Shared memory, parallel processing, enhance convergence. Sandia specific device models.

  9. Magnetic resonance imaging and computational fluid dynamics (CFD) simulations of rabbit nasal airflows for the development of hybrid CFD/PBPK models

    SciTech Connect (OSTI)

    Corley, Richard A.; Minard, Kevin R.; Kabilan, Senthil; Einstein, Daniel R.; Kuprat, Andrew P.; harkema, J. R.; Kimbell, Julia; Gargas, M. L.; Kinzell, John H.

    2009-06-01

    The percentages of total air?ows over the nasal respiratory and olfactory epithelium of female rabbits were cal-culated from computational ?uid dynamics (CFD) simulations of steady-state inhalation. These air?ow calcula-tions, along with nasal airway geometry determinations, are critical parameters for hybrid CFD/physiologically based pharmacokinetic models that describe the nasal dosimetry of water-soluble or reactive gases and vapors in rabbits. CFD simulations were based upon three-dimensional computational meshes derived from magnetic resonance images of three adult female New Zealand White (NZW) rabbits. In the anterior portion of the nose, the maxillary turbinates of rabbits are considerably more complex than comparable regions in rats, mice, mon-keys, or humans. This leads to a greater surface area to volume ratio in this region and thus the potential for increased extraction of water soluble or reactive gases and vapors in the anterior portion of the nose compared to many other species. Although there was considerable interanimal variability in the ?ne structures of the nasal turbinates and air?ows in the anterior portions of the nose, there was remarkable consistency between rabbits in the percentage of total inspired air?ows that reached the ethmoid turbinate region (~50%) that is presumably lined with olfactory epithelium. These latter results (air?ows reaching the ethmoid turbinate region) were higher than previous published estimates for the male F344 rat (19%) and human (7%). These di?erences in regional air?ows can have signi?cant implications in interspecies extrapolations of nasal dosimetry.

  10. Interactive Activity Detection Tools

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Activity Detection Tools Interactive Activity Detection Tools Tools for detecting specified activities in video data provide a key intelligence capability. High numbers of false ...

  11. Tools for Public Information

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Tools for Public Information Tools for Public Information A list of resources for the public, including Intellus, an online tool that provides transparency and accessibility to the ...

  12. Overview of New Tools to Perform Safety Analysis: BWR Station Black Out Test Case

    SciTech Connect (OSTI)

    D. Mandelli; C. Smith; T. Riley; J. Nielsen; J. Schroeder; C. Rabiti; A. Alfonsi; Cogliati; R. Kinoshita; V. Pasucci; B. Wang; D. Maljovec

    2014-06-01

    Dynamic Probabilistic Risk Assessment (DPRA) methodologies couple system simulator codes (e.g., RELAP, MELCOR) with simulation controller codes (e.g., RAVEN, ADAPT). While system simulator codes accurately model system dynamics deterministically, simulation controller codes introduce both deterministic (e.g., system control logic, operating procedures) and stochastic (e.g., component failures, parameter uncertainties) elements into the simulation. Typically, a DPRA is performed by: 1) sampling values of a set of parameters from the uncertainty space of interest (using the simulation controller codes), and 2) simulating the system behavior for that specific set of parameter values (using the system simulator codes). For complex systems, one of the major challenges in using DPRA methodologies is to analyze the large amount of information (i.e., large number of scenarios ) generated, where clustering techniques are typically employed to allow users to better organize and interpret the data. In this paper, we focus on the analysis of a nuclear simulation dataset that is part of the Risk Informed Safety Margin Characterization (RISMC) Boiling Water Reactor (BWR) station blackout (SBO) case study. We apply a software tool that provides the domain experts with an interactive analysis and visualization environment for understanding the structures of such high-dimensional nuclear simulation datasets. Our tool encodes traditional and topology-based clustering techniques, where the latter partitions the data points into clusters based on their uniform gradient flow behavior. We demonstrate through our case study that both types of clustering techniques complement each other in bringing enhanced structural understanding of the data.

  13. High Performance Tools And Technologies

    SciTech Connect (OSTI)

    Collette, M R; Corey, I R; Johnson, J R

    2005-01-24

    This goal of this project was to evaluate the capability and limits of current scientific simulation development tools and technologies with specific focus on their suitability for use with the next generation of scientific parallel applications and High Performance Computing (HPC) platforms. The opinions expressed in this document are those of the authors, and reflect the authors' current understanding and functionality of the many tools investigated. As a deliverable for this effort, we are presenting this report describing our findings along with an associated spreadsheet outlining current capabilities and characteristics of leading and emerging tools in the high performance computing arena. This first chapter summarizes our findings (which are detailed in the other chapters) and presents our conclusions, remarks, and anticipations for the future. In the second chapter, we detail how various teams in our local high performance community utilize HPC tools and technologies, and mention some common concerns they have about them. In the third chapter, we review the platforms currently or potentially available to utilize these tools and technologies on to help in software development. Subsequent chapters attempt to provide an exhaustive overview of the available parallel software development tools and technologies, including their strong and weak points and future concerns. We categorize them as debuggers, memory checkers, performance analysis tools, communication libraries, data visualization programs, and other parallel development aides. The last chapter contains our closing information. Included with this paper at the end is a table of the discussed development tools and their operational environment.

  14. Quantitative in-situ scanning electron microscope pull-out experiments and molecular dynamics simulations of carbon nanotubes embedded in palladium

    SciTech Connect (OSTI)

    Hartmann, S., E-mail: steffen.hartmann@etit.tu-chemnitz.de; Blaudeck, T.; Hermann, S.; Wunderle, B. [Technische Universitt Chemnitz, Reichenhainer Str. 70, 09126 Chemnitz (Germany); Hlck, O. [Technische Universitt Chemnitz, Reichenhainer Str. 70, 09126 Chemnitz (Germany); Fraunhofer IZM Berlin, Gustav-Meyer-Allee 25, 13355 Berlin (Germany); Schulz, S. E.; Gessner, T. [Technische Universitt Chemnitz, Reichenhainer Str. 70, 09126 Chemnitz (Germany); Fraunhofer ENAS Chemnitz, Technologie-Campus 3, 09126 Chemnitz (Germany)

    2014-04-14

    In this paper, we present our results of experimental and numerical pull-out tests on carbon nanotubes (CNTs) embedded in palladium. We prepared simple specimens by employing standard silicon wafers, physical vapor deposition of palladium and deposition of CNTs with a simple drop coating technique. An AFM cantilever with known stiffness connected to a nanomanipulation system was utilized inside a scanning electron microscope (SEM) as a force sensor to determine forces acting on a CNT during the pull-out process. SEM-images of the cantilever attached to a CNT have been evaluated for subsequent displacement steps with greyscale correlation to determine the cantilever deflection. We compare the experimentally obtained pull-out forces with values of numerical investigations by means of molecular dynamics and give interpretations for deviations according to material impurities or defects and their influence on the pull-out data. We find a very good agreement of force data from simulation and experiment, which is 17 nN and in the range of 1061 nN, respectively. Our findings contribute to the ongoing research of the mechanical characterization of CNT-metal interfaces. This is of significant interest for the design of future mechanical sensors utilizing the intrinsic piezoresistive effect of CNTs or other future devices incorporating CNT-metal interfaces.

  15. The thermal conductivity of mixed fuel UxPu1-xO2: molecular dynamics simulations

    SciTech Connect (OSTI)

    Liu, Xiang-Yang; Cooper, Michael William Donald; Stanek, Christopher Richard; Andersson, Anders David Ragnar

    2015-10-16

    Mixed oxides (MOX), in the context of nuclear fuels, are a mixture of the oxides of heavy actinide elements such as uranium, plutonium and thorium. The interest in the UO2-PuO2 system arises from the fact that these oxides are used both in fast breeder reactors (FBRs) as well as in pressurized water reactors (PWRs). The thermal conductivity of UO2 fuel is an important material property that affects fuel performance since it is the key parameter determining the temperature distribution in the fuel, thus governing, e.g., dimensional changes due to thermal expansion, fission gas release rates, etc. For this reason it is important to understand the thermal conductivity of MOX fuel and how it differs from UO2. Here, molecular dynamics (MD) simulations are carried out to determine quantitatively, the effect of mixing on the thermal conductivity of UxPu1-xO2, as a function of PuO2 concentrations, for a range of temperatures, 300 – 1500 K. The results will be used to develop enhanced continuum thermal conductivity models for MARMOT and BISON by INL. These models express the thermal conductivity as a function of microstructure state-variables, thus enabling thermal conductivity models with closer connection to the physical state of the fuel.

  16. Ab initio molecular dynamics simulations of short-range order in Zr50Cu45Al5 and Cu50Zr45Al5 metallic glasses

    DOE PAGES-Beta [OSTI]

    Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

    2016-02-01

    Comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0 > is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2 > and < 0,2,8,1 >, are prominent. And the < 0,2,8,2 > polyhedra in Cu50Zr45Al5more » MG mainly originate from Al-centered clusters, while the < 0,0,12,0 > in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. Lastly, the relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.« less

  17. Ab initio molecular dynamics simulations of short-range order in Zr50Cu45Al5 and Cu50Zr45Al5 metallic glasses

    DOE PAGES-Beta [OSTI]

    Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

    2016-02-01

    In this study, comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons <0,0,12,0> is dominant, and in the Cu-rich one the distorted icosahedral orders, especially <0,2,8,2> and <0,2,8,1>, are prominent. And the <0,2,8,2> polyhedra in Cu50Zr45Al5 MG mainly originate from Al-centeredmore » clusters, while the <0,0,12,0> in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. The relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.« less

  18. CO{sub 2} isolated line shapes by classical molecular dynamics simulations: Influence of the intermolecular potential and comparison with new measurements

    SciTech Connect (OSTI)

    Larcher, G.; Tran, H. Schwell, M.; Chelin, P.; Landsheere, X.; Hartmann, J.-M.; Hu, S.-M.

    2014-02-28

    Room temperature absorption spectra of various transitions of pure CO{sub 2} have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 μm and 0.8 μm regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO{sub 2} lines, in terms of both the Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO{sub 2} transitions are almost independent of the rotational quantum number of the considered lines.

  19. Understanding misfit strain releasing mechanisms via molecular dynamics simulations of CdTe growth on {112}zinc-blende CdS

    DOE PAGES-Beta [OSTI]

    Zhou, Xiaowang; Chavez, Jose J.; Almeida, Sergio F.; Zubia, David

    2016-07-25

    Molecular dynamics simulations have been used to analyse microstructures of CdTe films grown on {112} surfaces of zinc-blende CdS. Interestingly, CdTe films grow in <331> orientations as opposed to <112> epitaxial orientations. At the CdTe-{331}/CdS-{112} interface, however, there exists an axis that is parallel to the <110> orientation of both CdS and CdTe. It is the direction orthogonal to this <110> that becomes different, being <116> for CdTe and <111> for CdS, respectively. Missing CdTe-{110} planes are found along the <110> axis, suggesting that the misfit strain is released by the conventional misfit dislocation mechanism along this axis. In themore » orthogonal axis, the misfit strain is found to be more effectively released by the new grain orientation mechanism. Our finding is supported by literature experimental observations of the change of growth direction when Cd0.96Zn0.04Te films are deposited on GaAs. Lastly the analyses of energetics clearly demonstrate the cause for the formation of the new orientation, and the insights gained from our studies can help understand the grain structures experimentally observed in lattice mismatched systems.« less

  20. Power Plant Modeling and Simulation

    ScienceCinema (OSTI)

    None

    2016-07-12

    The National Energy Technology Laboratory's Office of Research and Development provides open source tools and expetise for modeling and simulating power plants and carbon sequestration technologies.