National Library of Energy BETA

Sample records for dynamic simulation tool

  1. Dynamic wind turbine models in power system simulation tool

    E-Print Network [OSTI]

    Dynamic wind turbine models in power system simulation tool DIgSILENT Anca D. Hansen, Florin Iov Iov, Poul Sørensen, Nicolaos Cutululis, Clemens Jauch, Frede Blaabjerg Title: Dynamic wind turbine system simulation tool PowerFactory DIgSILENT for different wind turbine concepts. It is the second

  2. Tools for dynamic model development

    E-Print Network [OSTI]

    Schaber, Spencer Daniel

    2014-01-01

    For this thesis, several tools for dynamic model development were developed and analyzed. Dynamic models can be used to simulate and optimize the behavior of a great number of natural and engineered systems, from the ...

  3. Automating Dynamic Decoupling in Object-Oriented Modelling and Simulation Tools

    E-Print Network [OSTI]

    Como, Giacomo

    a Modelica transla- tor. Simulation tests demonstrate the technique, and the re- alised implementation than of simulation theory. In this work we refer as "EOO Modelling Tool" to a Modelica translator, to allow exemplifying the (more general) presented ideas. For a Modelica translator, the EOO modelling

  4. Developing an integrated building design tool by coupling building energy simulation and computational fluid dynamics programs

    E-Print Network [OSTI]

    Zhai, Zhiqiang, 1971-

    2003-01-01

    Building energy simulation (ES) and computational fluid dynamics (CFD) can play important roles in building design by providing essential information to help design energy-efficient, thermally comfortable and healthy ...

  5. 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.

  6. Theoretical tools for simulations of cluster dynamics in strong laser pulses

    E-Print Network [OSTI]

    Palade, Dragos I

    2015-01-01

    The main theoretical tools used in the physics of cluster-laser interaction are discussed starting from the basic principles of Quantum Mechanics and ending with purely classical methods. The schematic overview of the theory is complemented by direct links with various types of phenomena, regimes of interaction and quantities to be studied. Finally, the theory is reflected in a wide range of numerical simulations in order to prove their validity and the work done in the fi?eld by the author.

  7. 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.

  8. Molecular dynamics simulation: a tool for exploration and discovery using simple models

    E-Print Network [OSTI]

    D. C. Rapaport

    2014-11-13

    Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome is not always a foregone conclusion. The present survey focuses on several simple model systems that exhibit surprisingly rich emergent behavior, all studied by MD simulation. The examples are taken from the disparate fields of fluid dynamics, granular matter and supramolecular self-assembly. In studies of fluids modeled at the detailed microscopic level using discrete particles, the simulations demonstrate that complex hydrodynamic phenomena in rotating and convecting fluids, the Taylor-Couette and Rayleigh-B\\'enard instabilities, can not only be observed within the limited length and time scales accessible to MD, but even quantitative agreement can be achieved. Simulation of highly counterintuitive segregation phenomena in granular mixtures, again using MD methods, but now augmented by forces producing damping and friction, leads to results that resemble experimentally observed axial and radial segregation in the case of a rotating cylinder, and to a novel form of horizontal segregation in a vertically vibrated layer. Finally, when modeling self-assembly processes analogous to the formation of the polyhedral shells that package spherical viruses, simulation of suitably shaped particles reveals the ability to produce complete, error-free assembly, and leads to the important general observation that reversible growth steps contribute to the high yield. While there are limitations to the MD approach, both computational and conceptual, the results offer a tantalizing hint of the kinds of phenomena that can be explored, and what might be discovered when sufficient resources are brought to bear on a problem.

  9. Using designer confidence and a dynamic Monte Carlo simulation tool to evaluate uncertainty in system models

    E-Print Network [OSTI]

    Lyons, Jeffrey M. (Jeffrey Michael), 1973-

    2000-01-01

    As the use of distributed engineering models becomes more prevalent, engineers need tools to evaluate the quality of these models and understand how subsystem uncertainty affects predictions of system behavior. This thesis ...

  10. Incorporating LCA tools in integrated simulation environments

    E-Print Network [OSTI]

    Pal, Vineeta; Papamichael, Konstantinos; Bourassa, Norman; Loffeld, John J.

    2001-01-01

    and Meil, J. K. , "ATHENA™: An LCA Decision Support Tool -in the Proceedings. INCORPORATING LCA TOOLS IN INTEGRATEDof Energy. INCORPORATING LCA TOOLS IN INTEGRATED SIMULATION

  11. 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.

  12. Next generation computational tools for extreme-scale simulation of dynamic fracture and fragmentation in three dimensions

    E-Print Network [OSTI]

    Seagraves, Andrew Nathan

    2013-01-01

    The accurate modeling of dynamic fracture and fragmentation remains one of the most difficult challenges in computational mechanics research. As part of this thesis, a scalable algorithm for modeling dynamic fracture and ...

  13. Intelligent Simulation Tools for Mining Large Scienti c Data Sets 1 Intelligent Simulation Tools for Mining

    E-Print Network [OSTI]

    Bailey-Kellogg, Chris

    Intelligent Simulation Tools for Mining Large Scienti#12;c Data Sets 1 Intelligent Simulation Tools for Mining Large Scienti#12;c Data Sets Feng ZHAO Xerox Palo Alto Research Center 3333 Coyote Hill Road, Palo. Keywords Intelligent simulation, Scienti#12;c data mining, Qualitative reasoning, Reasoning about physical

  14. Revamped Simulation Tool to Power Up Wave Energy Development...

    Energy Savers [EERE]

    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...

  15. DLFM library tools for large scale dynamic applications.

    Broader source: All U.S. Department of Energy (DOE) Office 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...

  16. Dynamic Positioning Simulator Dynamic Positioning Simulator

    E-Print Network [OSTI]

    Vuik, Kees

    to the ocean floor, without using anchors accomplished by two or more propulsive devices controlled by inputs Dynamic Positioning: No tugboats needed; Offshore set-up is quick; Power saving; Precision situations more on Ship: Wind Force Fw = 1 2 air V 2 rw CXw (rw )AT 1 2 air V 2 rw CYw (rw )AL Mw = 1 2 air V 2 rw CMw (rw

  17. Smart House Simulation Tool Cyryl Krzyska

    E-Print Network [OSTI]

    Smart House Simulation Tool Cyryl Krzyska Kongens Lyngby 2006 #12;2 Technical University of Denmark Informatics and Mathematical Modelling Building 321, DK+2800 Kongens Lyngby, Denmark Phone +45 45253351, fax;5 Abstract Smart house installations are becoming more and more popular all over the world. They help

  18. 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.

  19. Simulations with dynamical HISQ quarks

    E-Print Network [OSTI]

    A. Bazavov; C. Bernard; C. DeTar; W. Freeman; Steven Gottlieb; U. M. Heller; J. E. Hetrick; J. Laiho; L. Levkova; M. Oktay; J. Osborn; R. L. Sugar; D. Toussaint; R. S. Van de Water

    2010-12-06

    We report on the status of a program of generating and using configurations with four flavors of dynamical quarks, using the HISQ action. We study the lattice spacing dependence of physical quantities in these simulations, using runs at several lattice spacings, but with the light quark mass held fixed at two tenths of the strange quark mass. We find that the lattice artifacts in the HISQ simulations are much smaller than those in the asqtad simulations at the same lattice spacings and quark masses. We also discuss methods for setting the scale, or assigning a lattice spacing to ensembles run at unphysical parameters.

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

    Open Energy Info (EERE)

    Development of Design and Simulation Tool for Hybrid Geothermal Heat Pump System Geothermal Project Jump to: navigation, search Last modified on July 22, 2011. Project Title...

  1. 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;...

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

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    studies of electrolytes and electrolyteelectrode interfaces Molecular dynamics simulation studies of electrolytes and electrolyteelectrode interfaces 2009 DOE Hydrogen Program...

  3. 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.

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

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Molecular Dynamics Simulation Studies of Electrolytes and ElectrolyteElectrode Interfaces Molecular dynamics simulation studies of electrolytes and electrolyteelectrode...

  5. 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.

  6. Large-Scale Hybrid Dynamic Simulation Employing Field Measurements

    SciTech Connect (OSTI)

    Huang, Zhenyu; Guttromson, Ross T.; Hauer, John F.

    2004-06-30

    Simulation and measurements are two primary ways for power engineers to gain understanding of system behaviors and thus accomplish tasks in system planning and operation. Many well-developed simulation tools are available in today's market. On the other hand, large amount of measured data can be obtained from traditional SCADA systems and currently fast growing phasor networks. However, simulation and measurement are still two separate worlds. There is a need to combine the advantages of simulation and measurements. In view of this, this paper proposes the concept of hybrid dynamic simulation which opens up traditional simulation by providing entries for measurements. A method is presented to implement hybrid simulation with PSLF/PSDS. Test studies show the validity of the proposed hybrid simulation method. Applications of such hybrid simulation include system event playback, model validation, and software validation.

  7. A design tool for reusing integration knowledge in simulation models

    E-Print Network [OSTI]

    Han, Sangmok

    2006-01-01

    In the academic field of computer-aided product development, the role of the design tool is to support engineering designers to develop and integrate simulation models. Used to save time and costs in product development ...

  8. 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.

  9. Co-Simulation Tools for Networked Control Systems

    E-Print Network [OSTI]

    Branicky, Michael S.

    , unmanned vehicles, home robotics, distributed virtual environments, power distribution, and building-simulation. The first two tools are extensions to ns-2 called Agent/Plant and NSCSPlant; the third tool integrates and control of the physical world. (right) A networked control system with one controlled system (a.k.a. plant

  10. 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 results are often text-based demonstrations. WINS includes a powerful visualization tool and user interface capability for transmission analyses, planning, and assessment, which will be of great interest to power market participants, power system planners and operators, and state and federal regulatory entities; and (3) WINS can handle extended transmission models for wind integration studies. WINS models include limitations on transmission flow as well as bus voltage for analyzing power system states. The existing decision tools often consider transmission flow constraints (dc power flow) alone which could result in the over-utilization of existing resources when analyzing wind integration. WINS can be used to assist power market participants including transmission companies, independent system operators, power system operators in vertically integrated utilities, wind energy developers, and regulatory agencies to analyze economics, security, and reliability of various options for wind integration including transmission upgrades and the planning of new transmission facilities. WINS can also be used by industry for the offline training of reliability and operation personnel when analyzing wind integration uncertainties, identifying critical spots in power system operation, analyzing power system vulnerabilities, and providing credible decisions for examining operation and planning options for wind integration. Researches in this project on wind integration included (1) Development of WINS; (2) Transmission Congestion Analysis in the Eastern Interconnection; (3) Analysis of 2030 Large-Scale Wind Energy Integration in the Eastern Interconnection; (4) Large-scale Analysis of 2018 Wind Energy Integration in the Eastern U.S. Interconnection. The research resulted in 33 papers, 9 presentations, 9 PhD degrees, 4 MS degrees, and 7 awards. The education activities in this project on wind energy included (1) Wind Energy Training Facility Development; (2) Wind Energy Course Development.

  11. 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:...

  12. GILK: A dynamic instrumentation tool for the Linux Kernel

    E-Print Network [OSTI]

    Pearce, David J.

    GILK: A dynamic instrumentation tool for the Linux Kernel David J. Pearce, Paul H.J. Kelly, Tony Abstract. This paper describes a dynamic instrumentation tool for the Linux Kernel which allows a stock Linux kernel to be modi#12;ed while in ex- ecution, with instruments implemented as kernel modules

  13. 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.

  14. GILK: A dynamic instrumentation tool for the Linux Kernel

    E-Print Network [OSTI]

    Pearce, David J.

    GILK: A dynamic instrumentation tool for the Linux Kernel A. Nonymous, B. Nonymous, C.Nonymous No Institute Given Abstract. This document describes a novel instrumentation tool for the Linux Kernel function, and insert user-speci#12;ed instrumentation before or after any basic block. The instruments

  15. Pin: Building Customized Program Analysis Tools with Dynamic Instrumentation

    E-Print Network [OSTI]

    Hazelwood, Kim

    Pin: Building Customized Program Analysis Tools with Dynamic Instrumentation Chi-Keung Luk Robert.project@intel.com Abstract Robust and powerful software instrumentation tools are essential for program analysis tasks instrumentation system called Pin. Our goals are to pro- vide easy-to-use, portable, transparent, and efficient

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

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Dynamics Simulation Studies of Electrolytes and ElectrolyteElectrode Interfaces Molecular Dynamics Simulation Studies of Electrolytes and ElectrolyteElectrode Interfaces 2010 DOE...

  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. 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.

  19. Efficient dynamic synchronous machine simulation with harmonics

    SciTech Connect (OSTI)

    Haskew, T.A.; Stern, H.P.; Chen, Z. [Univ. of Alabama, Tuscaloosa, AL (United States). Dept. of Electrical Engineering] [Univ. of Alabama, Tuscaloosa, AL (United States). Dept. of Electrical Engineering

    1996-06-01

    Within this paper, an efficient procedure for the dynamic simulation of faulted synchronous machines operating in the presence of harmonics is presented. The algorithm employs steady-state frequency domain techniques for simulation of the transmission system sequence networks and time domain methods for the synchronous machines represented in the odq frame of reference. The procedure affords greater accuracy than conventional fault analysis techniques based strictly on steady-state methods, yet requires far less computational time than full system dynamic simulations such as those using the EMTP.

  20. Distributed parameter model simulation tool for PEM fuel cells

    E-Print Network [OSTI]

    Batlle, Carles

    for proton exchange membrane fuel cells (PEMFC) has been developed, based on a distributed parameter model and durability of PEMFC. Keywords: PEMFC, distributed parameter modeling, dynamic simulation 1. Introduction The proton exchange membrane fuel cells (PEMFC) technology has been incorporated to a wide range of portable

  1. 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.

  2. 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

    Large-scale evacuations from major cities during no-notice events - such as chemical or radiological attacks, hazardous material spills, or earthquakes - have an obvious impact on large regions rather than on just the directly affected area. The scope of impact includes the accommodation of emergency evacuation traffic throughout a very large area; the planning of resources to respond appropriately to the needs of the affected population; the placement of medical supplies and decontamination equipment; and the assessment and determination of primary escape routes, as well as routes for incoming emergency responders. Compared to events with advance notice, such as evacuations based on hurricanes approaching an affected area, the response to no-notice events relies exclusively on pre-planning and general regional emergency preparedness. Another unique issue is the lack of a full and immediate understanding of the underlying threats to the population, making it even more essential to gain extensive knowledge of the available resources, the chain of command, and established procedures. Given the size of the area affected, an advanced understanding of the regional transportation systems is essential to help with the planning for such events. The objectives of the work described here (carried out by Argonne National Laboratory) is the development of a multi-modal regional transportation model that allows for the analysis of different evacuation scenarios and emergency response strategies to build a wealth of knowledge that can be used to develop appropriate regional emergency response plans. The focus of this work is on the effects of no-notice evacuations on the regional transportation network, as well as the response of the transportation network to the sudden and unusual demand. The effects are dynamic in nature, with scenarios changing potentially from minute to minute. The response to a radiological or chemical hazard will be based on the time-delayed dispersion of 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.

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

    SciTech Connect (OSTI)

    Koch, Daniel B [ORNL; Payne, Patricia W [ORNL

    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.

  4. 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.

  5. 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.

  6. Application of Various HVAC Simulation Programs and Visual Tools to Commissioning 

    E-Print Network [OSTI]

    Zheng, M.; Pan, S.

    2007-01-01

    Various existing HVAC system simulation programs and visualization tools are considered to be potentially powerful tools for commissioning. Although not originally developed as commissioning tools, these programs facilitate the confirmation...

  7. 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.

  8. 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)

  9. Feed drive modelling for the simulation of tool path tracking in multi-axis High Speed Machining

    E-Print Network [OSTI]

    Prévost, David; Lartigue, Claire; Dumur, Didier

    2011-01-01

    Within the context of High Speed Machining, it is essential to manage the trajectory generation to achieve both high surface quality and high productivity. As feed drives are one part of the set Machine tool - Numerical Controller, it is necessary to improve their performances to optimize feed drive dynamics during trajectory follow up. Hence, this paper deals with the modelling of the feed drive in the case of multi axis machining. This model can be used for the simulation of axis dynamics and tool-path tracking to tune parameters and optimize new frameworks of command strategies. A procedure of identification based on modern NC capabilities is presented and applied to industrial HSM centres. Efficiency of this modelling is assessed by experimental verifications on various representative trajectories. After implementing a Generalized Predictive Control, reliable simulations are performed thanks to the model. These simulations can then be used to tune parameters of this new framework according to the tool-pat...

  10. Eddy current NDE performance demonstrations using simulation tools

    SciTech Connect (OSTI)

    Maurice, L. [EDF - CEIDRE, 2 rue Ampere, 93206 Saint-Denis Cedex 1 (France); Costan, V.; Guillot, E.; Thomas, P. [EDF - R and D, THEMIS, 1, avenue du General de Gaulle, 92141 Clamart (France)

    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.

  11. Physics results from dynamical overlap fermion simulations

    E-Print Network [OSTI]

    Shoji Hashimoto

    2008-11-08

    I summarize the physics results obtained from large-scale dynamical overlap fermion simulations by the JLQCD and TWQCD collaborations. The numerical simulations are performed at a fixed global topological sector; the physics results in the theta-vacuum is reconstructed by correcting the finite volume effect, for which the measurement of the topological susceptibility is crucial. Physics applications we studied so far include a calculation of chiral condensate, pion mass, decay constant, form factors, as well as (vector and axial-vector) vacuum polarization functions and nucleon sigma term.

  12. Perturbation centrality: a novel centrality measure obtained by the general network dynamics tool, Turbine

    E-Print Network [OSTI]

    Szalay, Kristof Z

    2013-01-01

    Analysis of network dynamics became increasingly important to understand the mechanisms and consequences of changes in biological systems from macromolecules to cells and organisms. Currently available network dynamics tools are mostly tailored for specific tasks such as calculation of molecular or neural dynamics. Our Turbine software offers a generic framework enabling the simulation of any algorithmically definable dynamics of any network. Turbine is also optimized for handling very large networks in the range of millions of nodes and edges. Using a perturbation transmission model inspired by communicating vessels, here we introduce a novel centrality measure termed as perturbation centrality. Perturbation centrality is the reciprocal of the time needed to dissipate a starting perturbation in the network. Hubs and inter-modular nodes proved to be highly efficient in perturbation propagation. High perturbation centrality nodes of the Met-tRNA synthetase protein structure network were identified as amino aci...

  13. 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.

  14. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    SciTech Connect (OSTI)

    Steven R Prescott; Curtis Smith

    2011-07-01

    Through continued advancement in computational resources, development that was previously done by trial and error production is now performed through computer simulation. These virtual physical representations have the potential to provide accurate and valid modeling results and are being used in many different technical fields. Risk assessment now has the opportunity to use 3D simulation to improve analysis results and insights, especially for external event analysis. By using simulations, the modeler only has to determine the likelihood of an event without having to also predict the results of that event. The 3D simulation automatically determines not only the outcome of the event, but when those failures occur. How can we effectively incorporate 3D simulation into traditional PRA? Most PRA plant modeling is made up of components with different failure modes, probabilities, and rates. Typically, these components are grouped into various systems and then are modeled together (in different combinations) as a “system” with logic structures to form fault trees. Applicable fault trees are combined through scenarios, typically represented by event tree models. Though this method gives us failure results for a given model, it has limitations when it comes to time-based dependencies or dependencies that are coupled to physical processes which may themselves be space- or time-dependent. Since, failures from a 3D simulation are naturally time related, they should be used in that manner. In our simulation approach, traditional static models are converted into an equivalent state diagram representation with start states, probabilistic driven movements between states and terminal states. As the state model is run repeatedly, it converges to the same results as the PRA model in cases where time-related factors are not important. In cases where timing considerations are important (e.g., when events are dependent upon each other), then the simulation approach will typically provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.

  15. Exploiting an Object-Oriented Simulation Tool to Model a PCS Network

    E-Print Network [OSTI]

    Malloy, Brian

    III[14], together with the development of simulation tools such as Extend[5] and ProModel[1Exploiting an Object-Oriented Simulation Tool to Model a PCS Network Brian A. Malloy and Bin Chen In this paper, we describe the design and implementation of a simulator for a personal communica- tion service

  16. A Simulation Tool for Real-time Systems using Environmental Energy Harvesting Maryline CHETTO

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    A Simulation Tool for Real-time Systems using Environmental Energy Harvesting Maryline CHETTO, we present a simulation tool for real-time systems using environmental energy harvesting. Energy. The simulator enables to construct an optimal schedule for any task set, battery capacity and energy source

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

    E-Print Network [OSTI]

    LBNL-6184E A SOFTWARE TOOL TO COMPARE MEASURED AND SIMULATED BUILDING ENERGY PERFORMANCE DATA of California. #12;A SOFTWARE TOOL TO COMPARE MEASURED AND SIMULATED BUILDING ENERGY PERFORMANCE DATA Tobias goals. To link design goals to actual operation one can compare measured with simulated energy

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

    Office of Environmental Management (EM)

    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 batches. T anning tool tha ncomplete sync or...

  1. 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.

  2. A PRODUCTION SIMULATION TOOL FOR SYSTEMS WITH INTEGRATED WIND ENERGY RESOURCES

    E-Print Network [OSTI]

    Gross, George

    A PRODUCTION SIMULATION TOOL FOR SYSTEMS WITH INTEGRATED WIND ENERGY RESOURCES BY NICOLAS BENOIT of renewable energy sources in order to reduce CO2 emissions. In fact, several jurisdictions around the world production simulation tool with the capability to quantify the variable effects of systems with varying wind

  3. 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.

  4. Plasticity of metal wires in torsion: molecular dynamics and dislocation dynamics simulations

    E-Print Network [OSTI]

    Cai, Wei

    Plasticity of metal wires in torsion: molecular dynamics and dislocation dynamics simulations-4040 Abstract The orientation dependent plasticity in metal nanowires is investigated using molecular dynamics metal wires controls the mechanisms of plastic deformation. For wires oriented along 110 , dislocations

  5. A Quasi-Dynamic HVAC and Building Simulation Methodology 

    E-Print Network [OSTI]

    Davis, Clinton Paul

    2012-07-16

    This thesis introduces a quasi-dynamic building simulation methodology which complements existing building simulators by allowing transient models of HVAC (heating, ventilating and air-conditioning) systems to be created in an analogous way...

  6. The structural simulation toolkit :a tool for exploring parallel...

    Office of Scientific and Technical Information (OSTI)

    States Language: English Subject: 99 GENERAL AND MISCELLANEOUSMATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; COMPUTERIZED SIMULATION; COMPUTER ARCHITECTURE; COMPUTER CODES...

  7. Paper O.1.4.2 -1 -A SIMPLE TOOL FOR SIMULATION OF GROUND SOURCE HEAT

    E-Print Network [OSTI]

    Paper O.1.4.2 - 1 - A SIMPLE TOOL FOR SIMULATION OF GROUND SOURCE HEAT PUMP SYSTEMS Jeffrey D developed a number of ground heat exchanger models for use in simulation of ground source heat pump systems. Nevertheless, there are many situations where an easy to use hourly simulation of a ground source heat pump

  8. 3. Computing Observables Computer simulation methods are by now an established tool in many

    E-Print Network [OSTI]

    Heermann, Dieter W.

    3. Computing Observables Computer simulation methods are by now an established tool in many branches of science. The motivations for computer simulations of physical systems are manifold. One-type approximation. With a computer simulation we have the ability to study systems not yet tractable with analytical

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

    Office of Environmental Management (EM)

    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 planning he capability of...

  10. Dynamic Simulation of Electric Machines on FPGA Boards

    E-Print Network [OSTI]

    Zambreno, Joseph A.

    Dynamic Simulation of Electric Machines on FPGA Boards Hao Chen, Song Sun, Dionysios C. Aliprantis, and Joseph Zambreno Department of Electrical and Computer Engineering Iowa State University, Ames, IA 50011 USA Abstract--This paper presents the implementation of an induc- tion machine dynamic simulation

  11. Integrated Dynamic Simulation for Process Optimization and Control

    E-Print Network [OSTI]

    Rubloff, Gary W.

    Integrated Dynamic Simulation for Process Optimization and Control G. Brian Lu, Laura L. Tedder ­ Film Deposition · Applications in Process Optimization for Manufacturing and the Environment ­ Process efficient processes, equipment, sensor, and control systems #12;Dynamic Simulators for Sensor-Based Process

  12. Dynamic Simulation Model of a Consumer Foods Production Process !

    E-Print Network [OSTI]

    Sun, Yu

    schedule based on product list The SIMUL8 Component 1. Over 200 lines of simula0on code 2. ReadsDynamic Simulation Model of a Consumer Foods Production Process ! Goals · Create a dynamic simula0 Created par0ally automated Excel files to go handin hand with simula0on o Contains all SKUs and meat

  13. Chapter 7 Molecular Dynamics Simulations of Fluoro Polymers

    E-Print Network [OSTI]

    Goddard III, William A.

    131 Chapter 7 Molecular Dynamics Simulations of Fluoro Polymers: Prediction of Glass Transition for molecular dynamics simulation of the uoro polymers: Polytetra uoroethylene PTFE, Polyvinylidene uoride PVDF using a Build-Anneal-Quench procedure. For PTFE, PVDF, and ETFE uoro polymers, these results predict

  14. Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy

    E-Print Network [OSTI]

    Fayer, Michael D.

    Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level

  15. 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 decades ago, when High Performance Computing (HPC) resources were not commonly available.

  16. Fast Thermal Simulation for Architecture Level Dynamic Thermal Management

    E-Print Network [OSTI]

    Tan, Sheldon X.-D.

    Fast Thermal Simulation for Architecture Level Dynamic Thermal Management Pu Liu, Zhenyu Qi, Hang temperature by dynamic thermal managements becomes necessary. This paper proposes a novel approach to the thermal analysis at chip architecture level for efficient dynamic thermal management. Our new approach

  17. Simulation of chemical reaction dynamics on an NMR quantum computer

    E-Print Network [OSTI]

    Dawei Lu; Nanyang Xu; Ruixue Xu; Hongwei Chen; Jiangbin Gong; Xinhua Peng; Jiangfeng Du

    2011-05-21

    Quantum simulation can beat current classical computers with minimally a few tens of qubits and will likely become the first practical use of a quantum computer. One promising application of quantum simulation is to attack challenging quantum chemistry problems. Here we report an experimental demonstration that a small nuclear-magnetic-resonance (NMR) quantum computer is already able to simulate the dynamics of a prototype chemical reaction. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future.

  18. Annual Report 1999 Environmental Dynamics and Simulation

    SciTech Connect (OSTI)

    NS Foster-Mills

    2000-06-28

    This annual report describes selected 1999 research accomplishments for the Environmental Dynamics and Simulation (ED and S) directorate, one of six research organizations in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). These accomplishments are representative of the different lines of research underway in the ED and S directorate. EMSL is one of US Department of Energy's (DOE) national scientific user facilities and is the centerpiece of DOE's commitment to providing world-class experimental, theoretical, and computational capabilities for solving the nation's environmental problems. Capabilities in the EMSL include over 100 major instrument systems for use by the resident research staff, their collaborators, and users of the EMSL. These capabilities are used to address the fundamental science that will be the basis for finding solutions to national environmental issues such as cleaning up contamianted areas at DOE sites across the country and developing green technologies that will reduce or eliminate future pollution production. The capabilities are also used to further the understanding of global climate change and environmental issues relevant to energy production and use and health effects resulting from exposure to contaminated environments.

  19. 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. [Université de Nice Sophia Antipolis, CNRS, Observatoire de la Côte d'Azur, Nice (France)] [Université de Nice Sophia Antipolis, CNRS, Observatoire de la Côte 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.

  20. Learning Curve: A Simulation-based Approach to Dynamic Pricing

    E-Print Network [OSTI]

    Greenwald, Amy

    , a market simulator designed for analyzing agent pricing strategies in markets under finite time horizons algorithms using a market simulator that is capable of simulating many different market scenarios, the market environment, and the seller's supply at the moment of the transaction. As dynamic pricing becomes

  1. A Forest Fire Simulation Tool for Economic Planning in Fire Suppression Management

    E-Print Network [OSTI]

    Standiford, Richard B.

    A Forest Fire Simulation Tool for Economic Planning in Fire Suppression Management Models fire spread behavior of forest fires provides important information for decision-making. Specific resource positioning to control and extinguish forest fire, decisions can be validated before

  2. 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...

  3. 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.

  4. 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.

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

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious Rank EERE:Financing Tool Fits theCommittee Charter Operating Experience202-05-03 | Department

  6. HYBRID GROUND SOURCE HEAT PUMP SYSTEM SIMULATION USING VISUAL MODELING TOOL FOR HVACSIM+

    E-Print Network [OSTI]

    HYBRID GROUND SOURCE HEAT PUMP SYSTEM SIMULATION USING VISUAL MODELING TOOL FOR HVACSIM+ M.H. Khan, 74078, USA ABSTRACT This paper presents a simulation of a hybrid ground source heat pump system, performed using a new graphical user interface for HVACSIM+. Hybrid ground source heat pump systems

  7. Numerical simulation of high-speed penetration-perforation dynamics in layered armor shields

    E-Print Network [OSTI]

    Ayzenberg-Stepanenko, Mark

    2012-01-01

    Penetration models and calculating algorithms are presented, describing the dynamics and fracture of composite armor shields penetrated by high-speed small arms. A shield considered consists of hard (metal or ceramic) facing and multilayered fabric backing. A simple formula is proved for the projectile residual velocity after perforation of a thin facing. A new plastic-flow jet model is proposed for calculating penetration dynamics in the case of a thick facing of ceramic or metal-ceramic FGM materials. By bringing together the developed models into a calculating algorithm, a computer tool is designed enabling simulations of penetration processes in the above-mentioned shields and analysis of optimization problems. Some results of computer simulation are presented. It is revealed in particular that strength proof of pliable backing can be better as compared with more rigid backing. Comparison of calculations and test data shows sufficient applicability of the models and the tool.

  8. Numerical simulation of high-speed penetration-perforation dynamics in layered armor shields

    E-Print Network [OSTI]

    Mark Ayzenberg-Stepanenko; Grigory Osharovich

    2012-03-07

    Penetration models and calculating algorithms are presented, describing the dynamics and fracture of composite armor shields penetrated by high-speed small arms. A shield considered consists of hard (metal or ceramic) facing and multilayered fabric backing. A simple formula is proved for the projectile residual velocity after perforation of a thin facing. A new plastic-flow jet model is proposed for calculating penetration dynamics in the case of a thick facing of ceramic or metal-ceramic FGM materials. By bringing together the developed models into a calculating algorithm, a computer tool is designed enabling simulations of penetration processes in the above-mentioned shields and analysis of optimization problems. Some results of computer simulation are presented. It is revealed in particular that strength proof of pliable backing can be better as compared with more rigid backing. Comparison of calculations and test data shows sufficient applicability of the models and the tool.

  9. 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.

  10. Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films 

    E-Print Network [OSTI]

    Kim, Bo Hung

    2010-07-14

    Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal interactions at the wall-fluid interface...

  11. Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene

    E-Print Network [OSTI]

    Yi, Peng

    Using a realistic united-atom force field, molecular dynamics simulations were performed to study homogeneous nucleation of the crystal phase at about 30% supercooling from the melts of n-pentacontahectane (C150) and a ...

  12. Simulation Algorithms in Vehicle System Dynamics MARTIN ARNOLD

    E-Print Network [OSTI]

    be considered as integration platform for simulation in vehicle system dynamics. In the present report we report the analysis of distributed physical phenomena like the elastic deformation of car components

  13. Physics issues in simulations with dynamical overlap fermions

    E-Print Network [OSTI]

    Thomas DeGrand; Stefan Schaefer

    2004-12-01

    We discuss the impact of various improvements on simulations of dynamical overlap fermions using the Hybrid Monte Carlo algorithm. We focus on the usage of fat links and multiple pseudo-fermion fields.

  14. Brittle and ductile fracture of semiconductor nanowires --molecular dynamics simulations

    E-Print Network [OSTI]

    Cai, Wei

    Brittle and ductile fracture of semiconductor nanowires -- molecular dynamics simulations Keonwook November 9, 2006 Abstract Fracture of silicon and germanium nanowires in tension at room temperature potentials predict brittle fracture initiated by crack nucleation from the surface, most potentials predict

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

    Office of Scientific and Technical Information (OSTI)

    simulations, density, velocity, and orientational profiles of the confined film were accumulated along the Z (perpendicular to the walls) and Y (parallel to the walls...

  16. An Analysis Tool for Flight Dynamics Monte Carlo Simulations 

    E-Print Network [OSTI]

    Restrepo, Carolina 1982-

    2011-05-20

    for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, John Hurtado Committee Members, John Junkins Raktim Bhattacharya Ricardo Gutierrez-Osuna Head of Department, Dimitris Lagoudas August 2011 Major Subject: Aerospace Engineering iii... full day with me working out math and discussing new possible solutions. I would also like to thank my committee members, Dr. John Junkins, Dr. Raktim Bhattacharya, and Dr. Ricardo Gutierrez-Osuna, for all that I have learned from them through...

  17. Modelling and Dynamic Simulation for Process Control

    E-Print Network [OSTI]

    Skogestad, Sigurd

    principles for model development are outlined, and these principles are applied to a simple ash tank (which. In this paper we consider dynamic process models obtained using fundamental principles (eg. based reactor, a simple trend analysis using temperature measurements may be suÆcient. Dynamic models

  18. Modeling and Simulation of the Longitudinal Beam Dynamics - RF Station Interaction in the LHC Rings

    SciTech Connect (OSTI)

    Mastorides, T; Rivetta, C.; Fox, J.D.; Winkle, D.Van; /SLAC; Baudrenghien, P.; Tuckmantel, J.; /CERN

    2008-07-07

    A non-linear time-domain simulation has been developed to study the interaction between longitudinal beam dynamics and RF stations in the LHC rings. The motivation for this tool is to determine optimal LLRF configurations, to study system sensitivity on various parameters, and to define the operational and technology limits. It will be also used to study the effect of RF station noise, impedance, and perturbations on the beam life time and longitudinal emittance. It allows the study of alternative LLRF implementations and control algorithms. The insight and experience gained from our PEP-II simulation is important for this work. In this paper we discuss properties of the simulation tool that will be helpful in analyzing the LHC RF system and its initial results. Partial verification of the model with data taken during the LHC RF station commissioning is presented.

  19. Reweighting QCD simulations with dynamical overlap fermions

    E-Print Network [OSTI]

    Thomas DeGrand

    2008-10-03

    I apply a recently developed algorithm for reweighting simulations of lattice QCD from one quark mass to another to simulations performed with overlap fermions in the epsilon regime. I test it by computing the condensate from distributions of the low lying eigenvalues of the Dirac operator. Results seem favorable.

  20. Dynamic Spherical Volumetric Simplex Splines with Applications in Biomedical Simulation

    E-Print Network [OSTI]

    Hua, Jing

    Dynamic Spherical Volumetric Simplex Splines with Applications in Biomedical Simulation Yunhao Tan computational framework based on dy- namic spherical volumetric simplex splines for simulation of genus- zero to reconstruct the high-fidelity digi- tal model of a real-world object with spherical volumetric simplex splines

  1. A new tool in nuclear physics: Nuclear lattice simulations

    E-Print Network [OSTI]

    Ulf-G. Meißner

    2015-05-26

    In the last years, chiral effective field theory has been successfully developed for and applied to systems with few nucleons. Here, I present a new approach for ab initio calculations of nuclei that combines these precise and systematic forces with Monte Carlo simulation techniques that allow for exact solutions of the nuclear A-body problem. A short introduction of this method is given and a few assorted results concerning the spectrum and structure of 12C and 16O are presented. The framework further allows one to study the properties of nuclei in worlds that have fundamental parameters different from the ones in Nature. This allows for a physics test of the anthropic principle by addressing the question how strongly the generation of the life-relevant elements depends on the light quark masses and the electromagnetic fine structure constant.

  2. Simulation Methodologies for Satellite Solar Array Dynamics 

    E-Print Network [OSTI]

    Mohsenizadeh, Navid

    2010-07-16

    The purpose of the present thesis is to furnish diverse studies on the dynamic response of satellite solar arrays. The term flexible structure or, briefly, structure has different interpretations and definitions, depending ...

  3. Plasticity of metallic nanostructures : molecular dynamics simulations 

    E-Print Network [OSTI]

    Healy, Con

    2014-11-27

    During high speed cutting processes, metals are subject to high strains and strain rates. The dynamic nature of the deformation during high speed cutting makes it difficult to detect atomic scale deformation mechanisms ...

  4. 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.

  5. Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations

    E-Print Network [OSTI]

    Cai, Wei

    Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations t The orientation dependent plasticity in metal nanowires is investigated using molecular dynamics and dislocation wires controls the mechanisms of plastic deformation. For wires oriented along /1 1 0S, dislocations

  6. Field Test Best Practices: A Dynamic Web Tool for Practical Guidance

    Energy Savers [EERE]

    b y t he A lliance f or S ustainable E nergy, L LC. Field Test Best Practices A dynamic web tool for practical guidance BA Webinar Lieko Earle & Bethany Sparn March 18, 2015...

  7. Using Product Specific Simulation Models in a Tool for Manual Commissioning of Air Handling Units 

    E-Print Network [OSTI]

    Eriksson, J.

    2003-01-01

    . Cetetherm IQHeat. Cetetherm. Ronneby. Sweden. 3. Portland Energy Conservation Inc. Methods for automated and continuous commissioning of build- ings. Air-Conditioning and refrigeraration technol- ogy institute, Arlington, Virginia. 4. T. Haasl, D... SPECIFIC SIMULATION MODELS IN A TOOL FOR MANUAL COMMISSIONING OF AIR HANDLING UNITS JÖRGEN ERIKSSON ÅF-INSTALLATION AB GOTHENBURG, SWEDEN ABSTRACT This short paper describes an outline of a tool for manual commissioning of air handling units...

  8. A Simulation Environment for the Dynamic Evaluation of Disaster Preparedness Policies

    E-Print Network [OSTI]

    Swarup, Samarth

    capturing dynamics. We have developed a data-centric simulation environment for applying a systems approach

  9. A Taxonomy of Buffer Overflows for Evaluating Static and Dynamic Software Testing Tools*

    E-Print Network [OSTI]

    A Taxonomy of Buffer Overflows for Evaluating Static and Dynamic Software Testing Tools* Kendra Phone: 7819812711 Email: LIPPMANN@LL.MIT.EDU ABSTRACT A taxonomy that uses 22 attributes detection tools. Attributes in the taxonomy include the buffer location (e.g. stack, heap, data

  10. Undulator radiation simulation tools in view of proton beam diagnostics in LHC

    E-Print Network [OSTI]

    Ponce, L; CERN. Geneva. SPS and LHC Division

    2001-01-01

    As a superconducting undulator is planned to be used for beam diagnostics in LHC, it appeared to be necessary to adapt the simulation tools. Hence, a new procedure UNDULATOR has been implemented in the ray-tracing code Zgoubi and is assessed in this paper. After a brief recall of the numerical methods of concern, some simulations with UNDULATOR are compared, first with classical analytical models and then with field map based methods using the procedure TOSCA.

  11. SimSect Hybrid Dynamical Simulation Environment

    E-Print Network [OSTI]

    Saranlý, Uluç

    ) runner and a compliant hexapod. The former example illustrates the basic elements of programming models. It was mainly built to simulate a hexapod robot with compliant legs. It can. however, be used to define with the Spring­Loaded Inverted Pendulum(SLIP) and the Compliant Hexapod Model definitions. 1.3 Overview Sim

  12. SimSect Hybrid Dynamical Simulation Environment

    E-Print Network [OSTI]

    Saranlý, Uluç

    ) runner and a compliant hexapod. The former example illustrates the basic elements of programming models. It was mainly built to simulate a hexapod robot with compliant legs. It can. however, be used to define with the Spring-Loaded Inverted Pendulum(SLIP) and the Compliant Hexapod Model definitions. 1.3 Overview Sim

  13. Use dynamic simulation to model HPU reactor depressuring

    SciTech Connect (OSTI)

    Ernest, J.B.; Depew, C.A. (Fluor Daniel, Inc., Irvine, CA (United States))

    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.

  14. Tools of the Trade Tracking the dynamics of the social brain: ERP

    E-Print Network [OSTI]

    Tools of the Trade Tracking the dynamics of the social brain: ERP approaches for social cognitive-related potential (ERP) approaches to social cognitive and affective neuroscience (SCAN) are not as widely used temporal resolution of ERP measures of neural activity make them ideally suited for studying the dynamic

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

    SciTech Connect (OSTI)

    Valenzuela, J.; Thimmapuram, P.; Kim, J (Decision and Information Sciences); (Auburn Univ.)

    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.

  16. A new report delivers MSHP performance data for use in whole-building simulation tools.

    E-Print Network [OSTI]

    cost effectiveness and performance in U.S. homes, National Renewable Energy Laboratory (NREL that performance across a range of temperature, humidity, and equipment speed could be evaluated. Key ResultA new report delivers MSHP performance data for use in whole-building simulation tools. Mini

  17. NREL researchers discover ways to increase accuracy in building energy simulations tools to improve predictions of

    E-Print Network [OSTI]

    NREL researchers discover ways to increase accuracy in building energy simulations tools to improve calculate heat transfer through building enclosures to verify the benefit of energy efficiency upgrades) analysis to calculate the energy loss/gain through building walls and visualize different heat transfer

  18. Dynamical QCD+QED simulation with staggered quarks

    E-Print Network [OSTI]

    Ran Zhou; Steven Gottlieb

    2014-11-15

    Electromagnetic effects play an important role in many phenomena such as isospin-symmetry breaking in the hadron spectrum and the hadronic contributions to g-2. We have generalized the MILC QCD code to include the electromagnetic field. In this work, we focus on simulations including charged sea quarks using the RHMC algorithm. We show details of the dynamical QCD+QED simulation algorithm with compact QED. We analyze the code performance and results for hadron-spectrum observables.

  19. 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%.

  20. Mesoscale simulations of polymer dynamics in microchannel flows

    E-Print Network [OSTI]

    L. Cannavacciuolo; R. G. Winkler; G. Gompper

    2007-09-24

    The non-equilibrium structural and dynamical properties of flexible polymers confined in a square microchannel and exposed to a Poiseuille flow are investigated by mesoscale simulations. The chain length and the flow strength are systematically varied. Two transport regimes are identified, corresponding to weak and strong confinement. For strong confinement, the transport properties are independent of polymer length. The analysis of the long-time tumbling dynamics of short polymers yields non-periodic motion with a sublinear dependence on the flow strength. We find distinct differences for conformational as well as dynamical properties from results obtained for simple shear flow.

  1. Analytical Rescaling of Polymer Dynamics from Mesoscale Simulations

    E-Print Network [OSTI]

    I. Y. Lyubimov; J. McCarty; A. Clark; M. G. Guenza

    2011-03-10

    We present a theoretical approach to scale the artificially fast dynamics of simulated coarse-grained polymer liquids down to its realistic value. As coarse-graining affects entropy and dissipation, two factors enter the rescaling: inclusion of intramolecular vibrational degrees of freedom, and rescaling of the friction coefficient. Because our approach is analytical, it is general and transferable. Translational and rotational diffusion of unentangled and entangled polyethylene melts, predicted from mesoscale simulations of coarse-grained polymer melts using our rescaling procedure, are in quantitative agreement with united atom simulations and with experiments.

  2. DLFM library tools for large scale dynamic applications

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB Packet Hanford Advisory Board6/23/2014DLFM library tools for large

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJessework usesof EnergyY-12 NationalNO FEARIntegratedAGeospatial Tools

  4. Reaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties of chemically reacting mixtures

    E-Print Network [OSTI]

    Lisal, Martin

    diffusion) as well as reaction equilibria for chemically reacting mixtures. DOI: 10.1103/PhysRevE.70.) on chemical reaction equilibria is critical in many fields of science including mixture separationReaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties

  5. Investigating Wear Mechanisms of Alkylsilane Monolayers through Molecular Dynamics Simulation

    E-Print Network [OSTI]

    represent the substrates used in laboratory studies of self-assembled monolayers, as a resultInvestigating Wear Mechanisms of Alkylsilane Monolayers through Molecular Dynamics Simulation detachment of chains based on bond distances · Investigate the influence of chain length on free

  6. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

    E-Print Network [OSTI]

    Rapaport, Dennis C.

    Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine D 2009; published 30 April 2009 A nanoscale-sized Stirling engine with an atomistic working fluid has s : 02.70.Ns, 05.70.Ln, 47.61. k The Stirling engine, an external combustion engine in- vented almost two

  7. NUMERICAL SIMULATION OF AIR POLLUTION DYNAMICS DUE TO

    E-Print Network [OSTI]

    Olszewski Jr., Edward A.

    spots. ­ Global weather patterns effected. ­ CO2 and other pollutant emissions contributing to globalNUMERICAL SIMULATION OF AIR POLLUTION DYNAMICS DUE TO POINT SOURCE EMISSIONS FROM AN INDUSTRIAL, and ultimately effects the global climate balance. · About 60% of emissions from point sources · Major pollutants

  8. Dynamic Simulation of DFIG Wind Turbines on FPGA Boards

    E-Print Network [OSTI]

    Zambreno, Joseph A.

    Dynamic Simulation of DFIG Wind Turbines on FPGA Boards Hao Chen, Student Member, IEEE, Song Sun is a friction coefficient. The wind turbine model is based on the relation between the upstream wind speed V w + 1 where p is the air density; Rw is the wind turbine radius; cp (A, (3) is the performance

  9. Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation

    E-Print Network [OSTI]

    Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation S.J.V. Frankland *, D hydrogen in individual single-shell carbon nanotubes and nanotube ropes using a semiclassical model. The calculations predict that isolated hydrogen molecules inside of nanotubes have a Raman frequency that increases

  10. SIMULATING MARKET TRANSFORMATION DYNAMICS USING A HYBRID ENERGY ECONOMY MODEL

    E-Print Network [OSTI]

    ii SIMULATING MARKET TRANSFORMATION DYNAMICS USING A HYBRID ENERGY ECONOMY MODEL: A LOOK the likely effects of alternative policies, potential adoption rates of clean technologies, and costs to society in the long run. My goal was to use a "hybrid" energy economy model (CIMS), which combines

  11. Dynamically Adaptive Partition-based Interest Management in Distributed Simulation

    E-Print Network [OSTI]

    Kumova, Bora

    Dynamically Adaptive Partition-based Interest Management in Distributed Simulation Bora . Kumova on the effectiveness of the employed interest management (IM) schema that aims at reducing the overall computational the processing load from overloaded areas of the shared data to less loaded hosts, the partition-based technique

  12. DYNAMIC IMAGE SIMULATIONS FOR ADAPTIVE SENSOR PERFORMANCE PREDICTIONS

    E-Print Network [OSTI]

    Kerekes, John

    devices such as MEMS-based micromirrors can be modeled, but the desired overall sensor application oftenDYNAMIC IMAGE SIMULATIONS FOR ADAPTIVE SENSOR PERFORMANCE PREDICTIONS Michael D. Presnara,b , John is necessary for predicting real-life performance of adaptive sensor models. Physics-based modeling

  13. A Molecular Dynamics Simulation of Hydrogen Storage with SWNTs

    E-Print Network [OSTI]

    Maruyama, Shigeo

    A Molecular Dynamics Simulation of Hydrogen Storage with SWNTs S. Maruyama and T. Kimura, Bunkyo-ku, Tokyo 113-8656, Japan The mechanism of efficient hydrogen storage (1) with SWNTs (2, and the storage amount became about 5 wt % regardless of the tube radius. The number of absorbed hydrogen

  14. Bottom baryons from a dynamical lattice QCD simulation

    E-Print Network [OSTI]

    Randy Lewis; R. M. Woloshyn

    2009-01-12

    Bottom baryon masses are calculated based on a 2+1 flavor dynamical lattice QCD simulation. The gauge field configurations were computed by the CP-PACS and JLQCD collaborations using an improved clover action. The bottom quark is described using lattice NRQCD. Results are presented for single and double-b baryons at one lattice spacing. Comparison with experimental values is discussed.

  15. The stressstrain behavior of polymernanotube composites from molecular dynamics simulation

    E-Print Network [OSTI]

    Brenner, Donald W.

    -3538(03)00059-9 Composites Science and Technology 63 (2003) 1655­1661 www.elsevier.com/locate/compscitech * CorrespondingThe stress­strain behavior of polymer­nanotube composites from molecular dynamics simulation S, Hampton, VA 23681, USA c Department of Materials Science and Engineering, North Carolina State University

  16. Simple dynamics as a tool In this chapter, the progression of the course from simple to complicated dynamics

    E-Print Network [OSTI]

    Katok, Anatole

    uses. Accordingly, the main theme of this chapter is to present case studies of using the Contraction theory of differential equations. In this chapter we maintain the same standard of proof as in the course development, and are standard tools in dynamics. This chapter does not present nearly all such applications

  17. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    E-Print Network [OSTI]

    Radek Erban

    2015-08-12

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  18. Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics with reaction

    E-Print Network [OSTI]

    Lisal, Martin

    Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics. R. Smith, J. Chem. Phys. 125, 16490 2006 , a mesoscale simulation technique for studying polymer

  19. 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.

  20. 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.

  1. An investigation of soil-tool interaction theories as they apply to a Lunar soil simulant 

    E-Print Network [OSTI]

    Willman, Brian Michael

    1992-01-01

    be met given certain groundrules, guidelines and assumptions. Even so, there has been a wide variety of excavation systems proposed, each having their important design criterion. Proposed excavating systems have varied from a 60 lb-mass dragline bucket.... This was originally done using a lunar simulant and the testing of a microrobot and dragline bucket (Bernold 1989). In this research, a presentation of some soil-tool interaction theories (Sohne 1956) (Balovnev 1983) was made, but they were not used to predict...

  2. 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.

  3. 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.

  4. Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics with reaction ensemble Monte Carlo.

    E-Print Network [OSTI]

    Lisal, Martin

    Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics a mesoscale simulation technique, called the reaction ensemble dissipative particle dynamics RxDPD method. Coarse-grained, particle- based mesoscale models that retain only the most essential features

  5. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

    E-Print Network [OSTI]

    Rapaport, D C

    2009-01-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

  6. Reweighted ensemble dynamics simulations: theory, improvement, and application

    E-Print Network [OSTI]

    Linchen Gong; Xin Zhou; Zhong-Can Ou-Yang

    2015-02-22

    Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provides schemes on selection of basis functions, determination of free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enable to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems.

  7. Large-Scale Molecular Dynamics Simulations for Highly Parallel Infrastructures

    E-Print Network [OSTI]

    Pazúriková, Jana

    2014-01-01

    Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body problem of atoms$-$it computes movements of atoms according to Newtonian physics and empirical descriptions of atomic electrostatic interactions. These simulations require high performance computing resources, as evaluations within each step are computationally demanding and billions of steps are needed to reach interesting timescales. Current methods decompose the spatial domain of the problem and calculate on parallel/distributed infrastructures. Even the methods with the highest strong scaling hit the limit at half a million cores: they are not able to cut the time to result if provided with more processors. At the dawn of exascale computing with massively parallel computational resources, we want to increase the level of parallelism by incorporating parallel-in-time comput...

  8. 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.

  9. Virtual Reality Simulation of Fire Fighting Robot Dynamic and Motion

    E-Print Network [OSTI]

    Setiawan, Joga D; Budiyono, Agus

    2008-01-01

    This paper presents one approach in designing a Fire Fighting Robot which has been contested annually in a robotic student competition in many countries following the rules initiated at the Trinity College. The approach makes use of computer simulation and animation in a virtual reality environment. In the simulation, the amount of time, starting from home until the flame is destroyed, can be confirmed. The efficacy of algorithms and parameter values employed can be easily evaluated. Rather than spending time building the real robot in a trial and error fashion, now students can explore more variation of algorithm, parameter and sensor-actuator configuration in the early stage of design. Besides providing additional excitement during learning process and enhancing students understanding to the engineering aspects of the design, this approach could become a useful tool to increase the chance of winning the contest.

  10. 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.

  11. Recovering position-dependent diffusion from biased molecular dynamics simulations

    SciTech Connect (OSTI)

    Ljubeti?, Ajasja; Urban?i?, Iztok; Štrancar, Janez, E-mail: janez.strancar@ijs.si [Laboratory of Biophysics, Condensed Matter Physics Department, “Jožef Stefan” Institute, 1000 Ljubljana (Slovenia)] [Laboratory of Biophysics, Condensed Matter Physics Department, “Jožef Stefan” Institute, 1000 Ljubljana (Slovenia)

    2014-02-28

    All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.

  12. 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.

  13. 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.

  14. Kinetic distance and kinetic maps from molecular dynamics simulation

    E-Print Network [OSTI]

    Noe, Frank

    2015-01-01

    Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine...

  15. Molecular Dynamics Simulations of Solutions at Constant Chemical Potential

    E-Print Network [OSTI]

    Perego, Claudio; Parrinello, Michele

    2015-01-01

    Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, that range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, that influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the C$\\mu$MD method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$\\mu$MD method to the paradigmatic case of urea crystall...

  16. Investigations of Solar Prominence Dynamics Using Laboratory Simulations

    SciTech Connect (OSTI)

    Paul M Bellan

    2008-05-28

    Laboratory experiments simulating many of the dynamical features of solar coronal loops have been carried out. These experiments manifest collimation, kinking, jet flows, and S-shapes. Diagnostics include high-speed photography and x-ray detectors. Two loops having opposite or the same magnetic helicity polarities have been merged and it is found that counter-helicity merging provides much greater x-ray emission. A non-MHD particle orbit instability has been discovered whereby ions going in the opposite direction of the current flow direction can be ejected from a magnetic flux tube.

  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. 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 calculations on technology performance, and assumptions such as the earliest date a technology can be deployed. The only fuel cycles for which we currently have adequate data are those we are sure we will never build, e.g., a PUREX plant in the U.S. For actual candidates, even for once through LWRs, there remain missing data such as how the fuel cycle would be completed with a geologic repository. The most immediate data needs are probably basic reactor physics data for new concepts and data associated with waste management for anything other than current technology. The readiness of tools and data is fluid and depends on what purposes are envisioned to drive upcoming analyses and further definition of the waste-related characteristics of fuel cycle candidates. Tools and data sets evolve as needs evolve. Thus, much of the document explains that if the FCT program wants a certain type of analysis, then the tools and data needs are as indicated. For example, functions can be treated as either commodities or facilities. Reactors, separation, fuel fabrication, repository are treated as facility types. Other functions such as uranium mining, conversion, enrichment, and waste packaging and non-repository disposal are treated as commodities and therefore not modeled as extensively. In summary, the tools are functional and can answer many fuel cycle questions but some analyses will require that the tools be modified to support those analyses.

  19. Molecular Dynamics Simulations of Shock-Induced Thermite Reaction Vikas Tomar1,a

    E-Print Network [OSTI]

    Tomar, Vikas

    Molecular Dynamics Simulations of Shock-Induced Thermite Reaction Vikas Tomar1,a and Min Zhou1,b 1 Dynamics, Thermite Mixture Abstract. A computational framework for molecular dynamics (MD) simulations of shock-induced reactions in thermite mixtures is developed. The system under study is an Fe2O3+Al

  20. Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes Shigeo MARUYAMA1,2

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes * Shigeo-8656 The hydrogen storage mechanism of SWNTs was studied through molecular dynamics simulations. Assuming the simple : Molecular Dynamics Method, Hydrogen Storage, Single Walled Carbon Nanotubes, Lennard-Jones, Adsorption

  1. Modeling dilute sediment suspension using large-eddy simulation with a dynamic mixed model

    E-Print Network [OSTI]

    Fringer, Oliver B.

    Modeling dilute sediment suspension using large-eddy simulation with a dynamic mixed model Yi Transport of suspended sediment in high Reynolds number channel flows Re=O 600 000 is simulated using large-eddy simulation along with a dynamic-mixed model DMM . Because the modeled sediment concentration is low

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

    SciTech Connect (OSTI)

    Leclaire, Rene J [Los Alamos National Laboratory; Hirsch, Gary B [CLE, INCORPORATED

    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.

  3. 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.

  4. Current status of MCNP6 as a simulation tool useful for space and accelerator applications

    SciTech Connect (OSTI)

    Mashnik, Stepan G [Los Alamos National Laboratory; Bull, Jeffrey S [Los Alamos National Laboratory; Hughes, H. Grady [Los Alamos National Laboratory; Prael, Richard E [Los Alamos National Laboratory; Sierk, Arnold J [Los Alamos National Laboratory

    2012-07-20

    For the past several years, a major effort has been undertaken at Los Alamos National Laboratory (LANL) to develop the transport code MCNP6, the latest LANL Monte-Carlo transport code representing a merger and improvement of MCNP5 and MCNPX. We emphasize a description of the latest developments of MCNP6 at higher energies to improve its reliability in calculating rare-isotope production, high-energy cumulative particle production, and a gamut of reactions important for space-radiation shielding, cosmic-ray propagation, and accelerator applications. We present several examples of validation and verification of MCNP6 compared to a wide variety of intermediate- and high-energy experimental data on reactions induced by photons, mesons, nucleons, and nuclei at energies from tens of MeV to about 1 TeV/nucleon, and compare to results from other modern simulation tools.

  5. 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).

  6. Strategies for coupling energy simulation and computational fluid dynamics programs

    E-Print Network [OSTI]

    Zhai, Zhiqiang; Chen, Qingyan; Klems, Joseph H.; Haves, Philip

    2001-01-01

    2000. “EnergyPlus: Energy Simulation Program” . ASHRAEA Coupled Airflow-and-Energy Simulation Program for IndoorSTRATEGIES FOR COUPLING ENERGY SIMULATION AND COMPUTATIONAL

  7. NUMERICAL SIMULATION OF ELECTROMECHANICAL DYNAMICS IN PACED CARDIAC TISSUE Xiaopeng Zhao

    E-Print Network [OSTI]

    Zhao, Xiaopeng

    NUMERICAL SIMULATION OF ELECTROMECHANICAL DYNAMICS IN PACED CARDIAC TISSUE Henian Xia Xiaopeng Zhao of Tennessee Knoxville, TN 37996 kwong@utk.edu ABSTRACT We study electromechanical dynamics in paced cardiac physics fields are integrated, including electrophysiology, electromechanics, and mechanoelectrical

  8. How trehalose protects DNA in the dry state: a molecular dynamics simulation 

    E-Print Network [OSTI]

    Fu, Xuebing

    2008-10-10

    Molecular dynamics simulations were conducted on a system consisting of a decamer DNA solvated by trehalose and water (molecular ratio= 1:2), to mimic a relatively dry state for the DNA molecule. Simulations were performed ...

  9. Sediment Dynamics Simulation via Cellular Automata Artificial Intelligence -SYNOPSIS 1.0 Dr. Juan M. Restrepo

    E-Print Network [OSTI]

    Fatkullin, Ibrahim

    Sediment Dynamics Simulation via Cellular Automata Artificial Intelligence - SYNOPSIS 1.0 Dr. Juan dynamics and artificial intelligence. Sediment Dynamics Sediment dynamics is the physics of sedimentary's work, and proved to be quite a task indeed. Artificial Intelligence Because this research project

  10. Exploring the Reactivity of Carbene Cycloadditions with Electronic Structure Theory Calculations and Molecular Dynamics Simulations

    E-Print Network [OSTI]

    Sader, Charles Avery

    2015-01-01

    Electronic Structure Theory Calculations and Molecular DynamicsElectronic Structure Theory Calculations and Molecular Dynamicsdynamics simulation requires identification of an electronic structure calculation

  11. Physics and Algorithm Enhancements for a Validated MCNP/X Monte Carlo Simulation Tool, Phase VII

    SciTech Connect (OSTI)

    McKinney, Gregg W [Los Alamos National Laboratory

    2012-07-17

    Currently the US lacks an end-to-end (i.e., source-to-detector) radiation transport simulation code with predictive capability for the broad range of DHS nuclear material detection applications. For example, gaps in the physics, along with inadequate analysis algorithms, make it difficult for Monte Carlo simulations to provide a comprehensive evaluation, design, and optimization of proposed interrogation systems. With the development and implementation of several key physics and algorithm enhancements, along with needed improvements in evaluated data and benchmark measurements, the MCNP/X Monte Carlo codes will provide designers, operators, and systems analysts with a validated tool for developing state-of-the-art active and passive detection systems. This project is currently in its seventh year (Phase VII). This presentation will review thirty enhancements that have been implemented in MCNPX over the last 3 years and were included in the 2011 release of version 2.7.0. These improvements include 12 physics enhancements, 4 source enhancements, 8 tally enhancements, and 6 other enhancements. Examples and results will be provided for each of these features. The presentation will also discuss the eight enhancements that will be migrated into MCNP6 over the upcoming year.

  12. 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.

  13. Discontinuous Shear Thickening in Brownian Suspensions By Dynamic Simulation

    E-Print Network [OSTI]

    Mari, Romain; Morris, Jeffrey F; Denn, Morton M

    2015-01-01

    Dynamic particle-scale numerical simulations are used to show that the shear thickening observed in dense colloidal, or Brownian, suspensions is of a similar nature to that observed in non-colloidal suspensions, i.e., a stress-induced transition from a flow of lubricated near-contacting particles to a flow of a frictionally contacting network of particles. Abrupt (or discontinuous) shear thickening is found to be a geometric rather than hydrodynamic phenomenon; it stems from the strong sensitivity of the jamming volume fraction to the nature of contact forces between suspended particles. The thickening obtained in a colloidal suspension of purely hard frictional spheres is qualitatively similar to experimental observations. However the agreement cannot be made quantitative with only hydrodynamics, frictional contacts and Brownian forces. Therefore the role of a short-range repulsive potential mimicking the stabilization of actual suspensions on the thickening is studied. The effects of Brownian and repulsive ...

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

    E-Print Network [OSTI]

    Maile, Tobias

    2014-01-01

    and simulated building energy performance data. Ph.D.AND SIMULATED BUILDING ENERGY PERFORMANCE DATA Author(s),AND SIMULATED BUILDING ENERGY PERFORMANCE DATA Tobias Maile

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

    E-Print Network [OSTI]

    Maile, Tobias

    2014-01-01

    on calibration of building energy simulation programs: Uses,resulting from energy simulations. A detailed analysis ofmore Building Energy Performance Simulation (BEPS) models.

  16. 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)

  17. 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.

  18. Photoionization analysis of chemo-dynamical dwarf galaxies simulations

    E-Print Network [OSTI]

    Melekh, B; Hensler, G; Buhajenko, O

    2015-01-01

    Photoionization modelling allows to follow the transport, the emergence, and the absorption of photons taking into account all important processes in nebular plasmas. Such modelling needs the spatial distribution of density, chemical abundances and temperature, that can be provided by chemo-dynamical simulations (ChDS) of dwarf galaxies. We perform multicomponent photoionization modelling (MPhM) of the ionized gas using 2-D ChDSs of dwarf galaxies. We calculate emissivity maps for important nebular emission lines. Their intensities are used to derive the chemical abundance of oxygen by the so-called Te- and R23-methods. Some disagreements are found between oxygen abundances calculated with these methods and the ones coming from the ChDSs. We investigate the fraction of ionizing radiation emitted in the star-forming region which is able to leak out the galaxy. The time- and direction-averaged escape fraction in our simulation is 0.35-0.4. Finally, we have calculated the total Halpha lumi- nosity of our model g...

  19. RECENT PROGRESS IN DYNAMIC PROCESS SIMULATION OF CRYOGENIC REFRIGERATORS

    SciTech Connect (OSTI)

    Kuendig, A. [Linde Kryotechnik AG, Dattlikonerstrasse 5, CH-8422 Pfungen (Switzerland)

    2008-03-16

    At the CEC 2005 a paper with the title 'Helium refrigerator design for pulsed heat load in Tokamaks' was presented. That paper highlighted the control requirements for cryogenic refrigerators to cope with the expected load variations of future nuclear fusion reactors. First dynamic computer simulations have been presented.In the mean time, the computer program is enhanced and a new series of process simulations are available. The new program considers not only the heat flows and the temperature variations within the heat exchangers, but also the variation of mass flows and pressure drops. The heat transfer numbers now are calculated in dependence of the flow speed and the gas properties. PI-controllers calculate the necessary position of specific valves for maintaining pressures, temperatures and the rotation speed of turbines.Still unsatisfactory is the fact, that changes in the process arrangement usually are attended by adjustments in the program code. It is the main objective of the next step of development a more flexible code which enables that any user defined process arrangements can be assembled by input data.

  20. Discontinuous Shear Thickening in Brownian Suspensions By Dynamic Simulation

    E-Print Network [OSTI]

    Romain Mari; Ryohei Seto; Jeffrey F. Morris; Morton M. Denn

    2015-08-05

    Dynamic particle-scale numerical simulations are used to show that the shear thickening observed in dense colloidal, or Brownian, suspensions is of a similar nature to that observed in non-colloidal suspensions, i.e., a stress-induced transition from a flow of lubricated near-contacting particles to a flow of a frictionally contacting network of particles. Abrupt (or discontinuous) shear thickening is found to be a geometric rather than hydrodynamic phenomenon; it stems from the strong sensitivity of the jamming volume fraction to the nature of contact forces between suspended particles. The thickening obtained in a colloidal suspension of purely hard frictional spheres is qualitatively similar to experimental observations. However the agreement cannot be made quantitative with only hydrodynamics, frictional contacts and Brownian forces. Therefore the role of a short-range repulsive potential mimicking the stabilization of actual suspensions on the thickening is studied. The effects of Brownian and repulsive forces on the onset stress can be combined in an additive manner. The simulations including Brownian and stabilizing forces show excellent agreement with experimental data for the viscosity $\\eta$ and the second normal stress difference $N_2$.

  1. 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.

  2. SIMULATION OF HENs This chapter describes how dynamic simulations of HENs can be carried out. The type and

    E-Print Network [OSTI]

    Skogestad, Sigurd

    be carried out. The type and complexity of the model of each heat exchanger significantly affect the efforts required for HEN simulation, and focus is on the development of a general heat exchanger model countercurrent heat exchangers are briefly described, and the chapter closes by explaining how dynamic simulation

  3. Microscopic Mechanisms and Dynamics Simulations of S3/2) Reacting with Methane

    E-Print Network [OSTI]

    1 Microscopic Mechanisms and Dynamics Simulations of O+ (4 S3/2) Reacting with Methane Lipeng Sun: The reaction O+ (4 S3/2) + methane is studied as a benchmark for developing the theory of polymer erosion by O;2 Microscopic Mechanisms and Dynamics Simulations of O+ (4 S3/2) Reacting with Methane spacecraft,3 surprisingly

  4. Molecular dynamics simulations of a chemical reaction; conditions for local equilibrium in a temperature gradient

    E-Print Network [OSTI]

    Kjelstrup, Signe

    Molecular dynamics simulations of a chemical reaction; conditions for local equilibrium have examined a simple chemical reaction in a temperature gradient; 2F $ F2. A mechanical model molecular dynamics simulations showed that the chemical reaction is in local thermodynamic as well

  5. A Molecular Dynamics Simulation of Hydrogen Storage by SWNTs Tatsuto Kimuraa

    E-Print Network [OSTI]

    Maruyama, Shigeo

    A Molecular Dynamics Simulation of Hydrogen Storage by SWNTs Tatsuto Kimuraa and Shigeo Maruyamab of efficient hydrogen storage [1] with SWNTs [2,3] was studied through classical molecular dynamics simulations adsorbed hydrogen molecules was almost proportional to the number of carbon atoms, and the storage amount

  6. Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes Shigeo MARUYAMA #12;The hydrogen storage mechanism of SWNTs was studied through molecular dynamics simulations,12) Fig. 6 Hydrogen storage inside each SWNT #12;Table 1 Potential parameters between SWNTs Tube d0 [Å

  7. Virtual interactive simulation and inspection tool (VISIT) Modeling sensor networks in a virtual city

    SciTech Connect (OSTI)

    Moore, D. M. (David M.)

    2004-01-01

    The U.S. government is currently investigating the deployment of radiation sensor systems to protect cities against nuclear and radiological threats. Due to the high cost of installing such systems, there is a need to analyze the effectiveness of a variety of sensor configurations in detecting such threats before installing such systems in the field. The Virtual Interactive Simulation and Inspection Tool (VISIT) is a computer program developed for various virtual-reality applications in national security programs, and is presently being adapted to test the efficacy of a variety of sensor configurations in a virtual urban environment. The value of a particular sensor configuration will be assessed by running virtual exercises in which a threat team will choose a radiological device and route to a target and a detection team will specify the locations and types of sensors to be placed in the city to attempt detection of the threat prior to it reaching its target. This paper will discuss the VISIT package, its proposed application, and lessons learned from modeling done to date.

  8. The Momentum Cloud Method for Dynamic Simulation of Rigid Body Systems

    E-Print Network [OSTI]

    Sweetman, Bert

    is presented for a 6-body floating wind turbine system. CE Database subject headings: Simulation, Structural dynamics, Rigid-body dynamics, Wind power, Floating structures 1. Introduction and Background A multibody. Featherstone (Featherstone, 2008) investigates the dynamics formulation of a floating-base rigid-body system

  9. 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.

  10. Instabilities in Molecular Dynamics Integrators used in Hybrid Monte Carlo Simulations

    E-Print Network [OSTI]

    B. Joo; UKQCD Collaboration

    2001-10-11

    We discuss an instability in the leapfrog integration algorithm, widely used in current Hybrid Monte Carlo (HMC) simulations of lattice QCD. We demonstrate the instability in the simple harmonic oscillator (SHO) system where it is manifest. We demonstrate the instability in HMC simulations of lattic QCD with dynamical Wilson-Clover fermions and discuss implications for future simulations of lattice QCD.

  11. Dynamics of pebbles in the vicinity of a growing planetary embryo: hydro-dynamical simulations

    E-Print Network [OSTI]

    Morbidelli, Alessandro

    2012-01-01

    Understanding the growth of the cores of giant planets is a difficult problem. Recently, Lambrechts and Johansen (2012; LJ12) proposed a new model in which the cores grow by the accretion of pebble-size objects, as the latter drift towards the star due to gas drag. Here, we investigate the dynamics of pebble-size objects in the vicinity of planetary embryos of 1 and 5 Earth masses and the resulting accretion rates. We use hydrodynamical simulations, in which the embryo influences the dynamics of the gas and the pebbles suffer gas drag according to the local gas density and velocities. The pebble dynamics in the vicinity of the planetary embryo is non-trivial, and it changes significantly with the pebble size. Nevertheless, the accretion rate of the embryo that we measure is within an order of magnitude of the rate estimated in LJ12 and tends to their value with increasing pebble-size. We conclude that the model by LJ12 has the potential to explain the rapid growth of giant planet cores. The actual accretion r...

  12. Diffusive Dynamics of Water inside Hydrophobic Carbon Micropores Studied by Neutron Spectroscopy and Molecular Dynamics Simulation

    E-Print Network [OSTI]

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

    2014-12-15

    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 ($\\sim$ 150 K), leading to a metastable liquid state with remarkable physical properties. We have investigated the ambient pressure diffusive dynamics of water in microporous Kynol\\texttrademark ACF-10 (average pore size $\\sim$11.6 {\\AA}, 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 $$ when compared to previous findings indicate that it is the size of the confining pores - not their shape - that primarily affects the dynamics of water for pore sizes larger than 10 {\\AA}. 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 {\\AA} gap of two parallel graphene sheets. We find generally a reasonable agreement between the observed and calculated relaxation times at the low momentum transfer $Q$ ($Q\\le 0.9$ \\AA${^{-1}}$). At high $Q$ however, where localized dynamics becomes relevant, this ideal system does not satisfactorily reproduce the measurements. 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 bi-modal exponential model, is used to parameterize the self-correlation function $I(Q,t)$.

  13. A Domain Specific Language for Spatial Simulation Scenarios(DSL3S): Introduction and Tool Support

    E-Print Network [OSTI]

    da Silva, Alberto Rodrigues

    and may require a long learning process. In con- trast, Model-level tools, such as LANDIS [9] or TELSA [8

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

    Broader source: 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.

  15. 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/or longer chains for this particular solvent extraction application. We have proposed a simple way to circumvent the artificial crystallization of the chains at ambient temperature.

  16. Finite Element Modelling and Molecular Dynamic Simulations of Carbon nanotubes/ Polymer Composites 

    E-Print Network [OSTI]

    Gaddamanugu, Dhatri

    2010-07-14

    Modeling of single-walled carbon nanotubes, multi-walled nanotubes and nanotube reinforced polymer composites using both the Finite Element method and the Molecular Dynamic simulation technique is presented. Nanotubes subjected to mechanical loading...

  17. Graphitization of small diamond cluster --Molecular dynamics simulation A. Brdka a,, T.W. Zerda b

    E-Print Network [OSTI]

    Powles, Rebecca

    Elsevier B.V. All rights reserved. Keywords: Nanodiamond; Graphitization; Molecular dynamics simulation 1 of nanodiamond clus- ters (nD-c) [2] is the method that can provide carbon onions with uniform size in a large

  18. Plastic Deformation of Semicrystalline Polyethylene under Extension, Compression, and Shear Using Molecular Dynamics Simulation

    E-Print Network [OSTI]

    Kim, Jun Mo

    Plastic deformation of the stack of alternating crystal and amorphous layers typical of semicrystalline polyethylene is studied by molecular dynamics simulation. A previous investigation of the semicrystalline layered stack ...

  19. A model simulation of white-winged dove population dynamics in the Tamaulipan Biotic Province 

    E-Print Network [OSTI]

    Martinez, Cristina Ann

    2002-01-01

    I present the development, evaluation, and sensitivity analysis of a simulation model representing two components of population dynamics-natality and mortality-for the white-winged dove (Zenaida asiatica asiatica; WWDO). I also discuss the role...

  20. A Finite Element-Multibody Dynamics Co-simulation Methodology Applied to FAST 

    E-Print Network [OSTI]

    Suryakumar, Vishvas Samuel

    2013-05-02

    A co-simulation methodology is explored whereby a finite element code and a multi-body dynamics code featuring flexible cantilevered beams can be coupled and interactively executed. The floating frame of reference formulation is used to develop...

  1. Dynamical Simulation of Fluidized Beds --- Hydrodynamically Interacting Granular Particles

    E-Print Network [OSTI]

    Kengo Ichiki; Hisao Hayakawa

    1995-03-01

    A numerical simulation of a gas-fluidized bed is performed without introduction of any empirical parameters. Realistic bubbles and slugs are observed in our simulation. It is found that the convective motion of particles is important for the bubbling phase and there is no convection in the slugging phase. From the simulation results, non-Gaussian distributions are found in the particle velocities and the relation between the deviation from Gaussian and the local density of particles is suggested. It is also shown that the power spectra of particle velocities obey power laws. A brief explanation on the relationship between the simulation results and the Kolmogorov scaling argument is discussed.

  2. AN APPROACH TO EVALUATING COMPUTER NETWORK SIMULATION TOOL SUPPORT FOR VERIFICATION AND VALIDATION

    E-Print Network [OSTI]

    capture the observed characteristics of the selected tools. After assigning a quantitative or qualitative by Jonathan Douglas Gibbs A Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master

  3. Simulation of an atomistic dynamic field theory for monatomic liquids: Freezing and glass formation

    E-Print Network [OSTI]

    Grant, Martin

    Simulation of an atomistic dynamic field theory for monatomic liquids: Freezing and glass formation regime. The thermodynamics and dynamics of freezing and glass formation in this model system are studied.70.P , 64.70.D , 61.43. j, 81.05.Kf When a simple liquid is supercooled below its freezing temperature

  4. A continuum-atomistic method for incorporating Joule heating into classical molecular dynamics simulations

    E-Print Network [OSTI]

    Brenner, Donald W.

    binding electronic structure calculations, pertur- bation models, and quantum-classical Hamiltonians [6 depends on the degree of approximation used in solving the electronic structure problem, which can add-scale molecular dynamics (MD) simulation is not to model electron dynamics, but rather to numerically solve

  5. CFD Simulation of Dynamic Thrust and Radial Forces on a Vertical Axis Wind Turbine Blade

    E-Print Network [OSTI]

    Tullis, Stephen

    CFD Simulation of Dynamic Thrust and Radial Forces on a Vertical Axis Wind Turbine Blade K. Mc vibration source of a small scale vertical axis wind turbine. The dynamic loading on the blades of the turbine, as they rotate about the central shaft and travel through a range of relative angles of attack

  6. The `neighbor effect': Simulating dynamics in consumer preferences for new vehicle technologies

    E-Print Network [OSTI]

    to capture dynamics in consumer preferences. We estimate Canadians' preferences for new vehicle technologiesANALYSIS The `neighbor effect': Simulating dynamics in consumer preferences for new vehicle technologies Paulus Maua,1 , Jimena Eyzaguirrea,1 , Mark Jaccarda,, Colleen Collins-Doddb,2 , Kenneth

  7. Coarse-grained Molecular Dynamics Simulation Approach for Polymer Nano-Composites Rubber

    E-Print Network [OSTI]

    Katsumoto, Shingo

    -composite materials are widely used in our daily life. Improvements by nano science and technology are required in orCoarse-grained Molecular Dynamics Simulation Approach for Polymer Nano-Composites Rubber Katsumi dynamics of entangled long- polymer melts and filled polymer rubber by us- ing coarse-grained model. We

  8. Molecular dynamics simulations of atomic-level brittle fracture mechanisms in amorphous silica

    E-Print Network [OSTI]

    Deymier, Pierre

    Molecular dynamics simulations of atomic-level brittle fracture mechanisms in amorphous silica Abstract We have examined the atomic dynamics of the brittle fracture process in amorphous silica using the change in local coordina- tion of atoms. Introduction The brittle fracture process has been a subject

  9. Climate Dynamics Diagnosis of the Marine Low Cloud Simulation in the NCAR Community Earth System

    E-Print Network [OSTI]

    Bretherton, Chris

    -of-the-art coupled atmosphere-ocean models: the NCAR Community Earth System Model (CESM) and the NCEP Global of the Marine Low Cloud Simulation in the NCAR1 Community Earth System Model (CESM) and the NCEP Global2Climate Dynamics Diagnosis of the Marine Low Cloud Simulation in the NCAR Community Earth System

  10. On the modeling and simulation of reaction-transfer dynamics in semiconductor-electrolyte solar cells

    E-Print Network [OSTI]

    Ren, Kui

    On the modeling and simulation of reaction-transfer dynamics in semiconductor-electrolyte solar-performance semiconductor-liquid junction solar cells. We propose in this work a macroscopic mathematical model, a sys- tem-liquid junction, solar cell simulation, naso-scale device modeling. 1 Introduction The mathematical modeling

  11. Large-Scale First-Principles Molecular Dynamics simulations on the BlueGene/L Platform

    E-Print Network [OSTI]

    Franchetti, Franz

    . Keywords Electronic structure. Molecular Dynamics. Ab initio simulations. First-principles simulations of the electronic properties of the system. The electronic structure calculation is the most time-consuming part the past three decades to the development of efficient implementations of the electronic structure

  12. Section 1526 Real-time, Non-linear, Dynamic Simulation in Teaching Structures

    E-Print Network [OSTI]

    Martini, Kirk

    Section 1526 Real-time, Non-linear, Dynamic Simulation in Teaching Structures: Elementary simulation in topics ranging from introductory statics to advanced steel design and earthquake engineering, and plastic collapse mechanisms. The program performs computations in real time, so that models respond

  13. Microelectronics Journal 39 (2008) 190201 Prototyping bio-nanorobots using molecular dynamics simulation and

    E-Print Network [OSTI]

    Mavroidis, Constantinos

    2008-01-01

    Abstract This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled-nano environments in VR, the operator can design and characterize through physical simulation and 3D visualization) in their native environment. Their use as elementary bio-nanorobotic components are also simulated and the results

  14. Molecular dynamics simulation of formation process of single-walled carbon nanotubes by CCVD method

    E-Print Network [OSTI]

    Maruyama, Shigeo

    chemical vapor deposition (CCVD) method [4-7] has been contrived for a scalable, large-scale production of SWNTs, with various carbon-source molecules tested such as carbon monoxide [4, 7], methane [5 simulations [10, 11] with the Brenner potential [12] or tight-binding molecular dynamics (TBMD) simulation [13

  15. Simulating Perforation of Thin Plates Using Molecular Dynamics Approach Anton M. Krivtsov

    E-Print Network [OSTI]

    Krivtsov, Anton M.

    1 Simulating Perforation of Thin Plates Using Molecular Dynamics Approach Anton M. Krivtsov or molecules, but as elements of the mesoscale level, such as material grains [4,5]. Fig.1: Oblique perforation of plate by ogive-nose projectile. This approach is used in the current work to simulate perforation

  16. 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)

  17. 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.

  18. Office Of Nuclear Energy Annual Review Meeting Dynamic Simulation...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Simulations of SMRs 2 FY14 molten salt cooled model deliverable due. n FY15 web application deliverable due. n FY15 model repository establishment due. n FY15...

  19. Abstract--This paper describes a web-based electric power market simulation tool called POWERWEB. It can be used as an

    E-Print Network [OSTI]

    1 Abstract--This paper describes a web-based electric power market simulation tool called POWERWEB markets and physical system characteristics. It is an Internet based platform, with a web browser

  20. Paper submitted for EWEC'04, London, 2004 IPSYS A simulation tool for performance assessment and

    E-Print Network [OSTI]

    A key factor in hybrid systems performance assessment is the ability to model the power system for easy exchange of controllers. The modelling concept and verification is presented. System performance this a new tool has been developed, IPSYS. This includes explicit modelling of the power system using a multi

  1. V CONGRESO NACIONAL DE PILAS DE COMBUSTIBLE DISTRIBUTED PARAMETER MODEL SIMULATION TOOL

    E-Print Network [OSTI]

    Batlle, Carles

    cells (PEMFC) has been developed, based on a distributed parameter model. The tool is designed others that have significant effects on the performance and durability of PEMFC. Palabras clave: PEMFC, modelado de parámetros distribuidos, simulación dinámica Keywords: PEMFC, distributed parameter modeling

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

    SciTech Connect (OSTI)

    Liese, Eric [U.S. DOE; Zitney, Stephen E. [U.S. DOE

    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.

  3. Dynamic Particle Coupling for GPU-based Fluid Simulation

    E-Print Network [OSTI]

    Blanz, Volker

    -vi ¯j 2 W( Pi -Pj ,h). Here pj = k( ¯j - 0) is the pressure with gas constant k and rest density 0 for modeling dynamic particle coupling solely based on individual particle contributions. This technique does and µ is the fluid viscosity constant. To model the surface tension, M¨uller et.al. [MCG03] use the so

  4. Flight Dynamics and Simulation of Laser Propelled Christopher G. Ballard

    E-Print Network [OSTI]

    Anderson, Kurt S.

    Propulsion Laboratory, Pasadena, California 91109 Kurt S. Anderson Leik Myrabo Department of Mechanical of lift, drag, and aerodynamic pitching moment were derived from Fluent computational fluid dynamics. e-mail:Christopher.G.Ballard@jpl.nasa.gov Corresponding author: Department of Mechanical, Aerospace

  5. Dynamic Simulations of Elastic Rods for Medical Applications 

    E-Print Network [OSTI]

    Nuti, Sravani

    2014-12-05

    This study deals with a detailed development of a computational model based on the Cosserat rod theory to describe the motion of elastic filaments such as threads and hair. The need for a simulation software for the act of suturing has motivated...

  6. Darlington tritium removal facility and station upgrading plant dynamic process simulation

    SciTech Connect (OSTI)

    Busigin, A. [NITEK USA, Inc., 6405 NW 77 PL, Parkland, FL 33067 (United States); Williams, G. I. D.; Wong, T. C. W.; Kulczynski, D.; Reid, A. [Ontario Power Generation Nuclear, Box 4000, Bowmanville, ON L1C 3Z8 (Canada)

    2008-07-15

    Ontario Power Generation Nuclear (OPGN) has a 4 x 880 MWe CANDU nuclear station at its Darlington Nuclear Div. located in Bowmanville. The station has been operating a Tritium Removal Facility (TRF) and a D{sub 2}O station Upgrading Plant (SUP) since 1989. Both facilities were designed with a Distributed Control System (DCS) and programmable logic controllers (PLC) for process control. This control system was replaced with a DCS only, in 1998. A dynamic plant simulator was developed for the Darlington TRF (DTRF) and the SUP, as part of the computer control system replacement. The simulator was used to test the new software, required to eliminate the PLCs. The simulator is now used for operator training and testing of process control software changes prior to field installation. Dynamic simulation will be essential for the ITER isotope separation system, where the process is more dynamic than the relatively steady-state DTRF process. This paper describes the development and application of the DTRF and SUP dynamic simulator, its benefits, architecture, and the operational experience with the simulator. (authors)

  7. Adaptive tool selection strategies for drilling in flexible manufacturing systems 

    E-Print Network [OSTI]

    Chander, Karthik Balachandran

    2004-09-30

    ) layout. The system designed serves as back end intelligence to drilling machines (INTELLIDRILL) in a Flexible Manufacturing System for making dynamic and real time decisions. INTELLIDRILL uses mathematical and adaptive tool reliability models to simulate...

  8. Spherically Symmetric N-body Simulations with General Relativistic Dynamics

    E-Print Network [OSTI]

    Adamek, Julian; Hotchkiss, Shaun

    2015-01-01

    Within a cosmological context, we study the behaviour of collisionless particles in the weak field approximation to General Relativity, allowing for large gradients of the fields and relativistic velocities for the particles. We consider a spherically symmetric setup such that high resolution simulations are possible with minimal computational resources. We test our formalism by comparing it to two exact solutions: the Schwarzschild solution and the Lema\\^itre-Tolman-Bondi model. In order to make the comparison we consider redshifts and lensing angles of photons passing through the simulation. These are both observable quantities and hence are gauge independent. We demonstrate that our scheme is more accurate than a Newtonian scheme, correctly reproducing the leading-order post-Newtonian correction. In addition, our setup is able to handle shell-crossings, which is not possible within a fluid model. Furthermore, by introducing angular momentum, we find configurations corresponding to bound objects which may p...

  9. Molecular dynamics simulation of chains mobility in polyethylene crystal

    E-Print Network [OSTI]

    V. I. Sultanov; V. V. Atrazhev; D. V. Dmitriev; S. F. Burlatsky

    2014-01-17

    The mobility of polymer chains in perfect polyethylene (PE) crystal was calculated as a function of temperature and chain length through Molecular dynamics (MD) in united atom approximation. The results demonstrate that the chain mobility drastically increases in the vicinity of the phase transition from the orthorhombic to quasi-hexagonal phase. In the quasi-hexagonal phase, the chain mobility is almost independent on temperature and inversely proportional to the chain length.

  10. Towards Better Integrators for Dissipative Particle Dynamics Simulations

    E-Print Network [OSTI]

    Gerhard Besold; Ilpo Vattulainen; Mikko Karttunen; James M. Polson

    2000-10-16

    Coarse-grained models that preserve hydrodynamics provide a natural approach to study collective properties of soft-matter systems. Here, we demonstrate that commonly used integration schemes in dissipative particle dynamics give rise to pronounced artifacts in physical quantities such as the compressibility and the diffusion coefficient. We assess the quality of these integration schemes, including variants based on a recently suggested self-consistent approach, and examine their relative performance. Implications of integrator-induced effects are discussed.

  11. Project REED (Residential Energy Efficiency Design) is a Web-based building performance simulation tool

    E-Print Network [OSTI]

    ABSTRACT Project REED (Residential Energy Efficiency Design) is a Web-based building performance or kilowatts of elec- tricity. Their bottom line is money. REED is an easy-to-use, ratepayer-friendly web system. The simulation engine behind this new web site is SO- LAR-5, one of the nations most widely used

  12. Helmet Streamers with Triple Structures: Simulations of resistive dynamics

    E-Print Network [OSTI]

    T. Wiegelmann; K. Schindler; T. Neukirch

    2008-01-21

    Recent observations of the solar corona with the LASCO coronagraph on board of the SOHO spacecraft have revealed the occurrence of triple helmet streamers even during solar minimum, which occasionally go unstable and give rise to large coronal mass ejections. There are also indications that the slow solar wind is either a combination of a quasi-stationary flow and a highly fluctuating component or may even be caused completely by many small eruptions or instabilities. As a first step we recently presented an analytical method to calculate simple two-dimensional stationary models of triple helmet streamer configurations. In the present contribution we use the equations of time- dependent resistive magnetohydrodynamics to investigate the stability and the dynamical behaviour of these configurations. We particularly focus on the possible differences between the dynamics of single isolated streamers and triple streamers and on the way in which magnetic reconnection initiates both small scale and large scale dynamical behaviour of the streamers. Our results indicate that small eruptions at the helmet streamer cusp may incessantly accelerate small amounts of plasma without significant changes of the equilibrium configuration and might thus contribute to the non-stationary slow solar wind. On larger time and length scales, large coronal eruptions can occur as a consequence of large scale magnetic reconnection events inside the streamer configuration. Our results also show that triple streamers are usually more stable than a single streamer.

  13. 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%.

  14. Criteria for the accuracy of small polaron quantum master equation in simulating excitation energy transfer dynamics

    SciTech Connect (OSTI)

    Chang, Hung-Tzu; Cheng, Yuan-Chung [Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan (China)] [Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan (China); Zhang, Pan-Pan [Department of Physics and Institute of Modern Physics, Ningbo University, Ningbo 315211 (China)] [Department of Physics and Institute of Modern Physics, Ningbo University, Ningbo 315211 (China)

    2013-12-14

    The small polaron quantum master equation (SPQME) proposed by Jang et al. [J. Chem. Phys. 129, 101104 (2008)] is a promising approach to describe coherent excitation energy transfer dynamics in complex molecular systems. To determine the applicable regime of the SPQME approach, we perform a comprehensive investigation of its accuracy by comparing its simulated population dynamics with numerically exact quasi-adiabatic path integral calculations. We demonstrate that the SPQME method yields accurate dynamics in a wide parameter range. Furthermore, our results show that the accuracy of polaron theory depends strongly upon the degree of exciton delocalization and timescale of polaron formation. Finally, we propose a simple criterion to assess the applicability of the SPQME theory that ensures the reliability of practical simulations of energy transfer dynamics with SPQME in light-harvesting systems.

  15. P2VSIM: A SIMULATION AND VISUALIZATION TOOL FOR THE P2V COMPILER 

    E-Print Network [OSTI]

    Almeida, Oscar

    2010-07-14

    of the Monitored Signals ..................... 17 3.3. Static Parsing of Embedded PSL Assertions into Time Intervals ........ 23 3.3.1. Generating Elements from PSL Assertions........................... 24 3.3.2. The ?element_handler? Method... ............................................ 25 3.3.3. The ?next_e_handler? and ?next_a_handler? Methods ........... 26 3.3.4. The ?and_handler? and ?or_handler? Methods....................... 33 3.4. PSL Property Checking and Simulating PSL Assertions .................... 34...

  16. 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.

  17. Virtual control system environment: A modeling and simulation tool for process control systems

    SciTech Connect (OSTI)

    Lee, E.; Michalski, J.; Sholander, P.; Van Leeuwen, B. [Sandia National Laboratories, Albuquerque, NM 87111 (United States)

    2006-07-01

    The development of tools and techniques for security testing and performance testing of Process Control Systems (PCS) is needed since those systems are vulnerable to the same classes of threats as other networked computer systems. In practice, security testing is difficult to perform on operational PCS because it introduces an unacceptable risk of disruption to the critical systems (e.g., power grids) that they control. In addition, the hardware used in PCS is often expensive, making full-scale mockup systems for live experiments impractical. A more flexible approach to these problems can be provided through test beds that provide the proper mix of real, emulated, and virtual elements to model large, complex systems such as critical infrastructures. This paper describes a 'Virtual Control System Environment' that addresses these issues. (authors)

  18. Simulations of beam envelope dynamics in circular accelerators

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Chao, Hung-Chun; Lee, S.?Y.

    2015-02-01

    The envelope instability of high intensity beams in circular accelerators is studied via multiparticle simulations. The space charge kicks are derived from a Gaussian potential model for an efficient tracking. The evolution of the envelope phase space coordinates are derived from the bunch distribution. We found that the envelope stop band played an important role in emittance growth. Correction schemes of the envelope stop bands are studied. Because the space charge force pushes the envelope tunes downward, harmonics less than twice the betatron tunes are also important on emittance growth. Our code is efficient and fast, it can be usedmore »to study the effect of space charge force on high power accelerators.« less

  19. 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.

  20. 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 to solvent evaporation. These effects become more important as cluster size increases. In addition, differences in timescale and mechanism are observed between clusters of Ar, which binds to I{sup -} and I{sub 2}{sup -} rather weakly, and CO{sub 2}, whose large quadruple moment allows substantially stronger binding to these anions.

  1. DYNAMIC SIMULATION OF MONO-TUBE CAVITY RECEIVERS FOR DIRECT STEAM GENERATION

    E-Print Network [OSTI]

    for intended deployment in large arrays of dishes, with steam directed to a central large steam turbine powerDYNAMIC SIMULATION OF MONO-TUBE CAVITY RECEIVERS FOR DIRECT STEAM GENERATION José Zapata 1 , John dish has been in operation since 2010 with a mono-tube steam cavity receiver, the SG4 system

  2. PHYSICAL REVIEW B 85, 184301 (2012) Spin-lattice-electron dynamics simulations of magnetic materials

    E-Print Network [OSTI]

    2012-01-01

    of experiments on laser-induced demagnetization of iron thin films, and estimate the rates of heat transfer of a magnetic material. They evaluated the total free energies and heat capacities of Fe, Co, and Ni usingPHYSICAL REVIEW B 85, 184301 (2012) Spin-lattice-electron dynamics simulations of magnetic

  3. Non-linear and Non-planar Free Thermal Vibration of SWNT in Molecular Dynamic Simulation

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Non-linear and Non-planar Free Thermal Vibration of SWNT in Molecular Dynamic Simulation Heeyuen Koh, James Cannon, Shohei Chiashi, Junichiro Shiomi and Shigeo Maruyama Department of Mechanical-mail: maruyama@photon.t.u-tokyo.ac.jp 1. Introduction Vibration of suspended and cantilevered nanotubes

  4. Molecular dynamics simulations of the elastic properties of polymer/carbon nanotube composites

    E-Print Network [OSTI]

    Elliott, James

    Molecular dynamics simulations of the elastic properties of polymer/carbon nanotube composites Yue of polymer/CNT composites was initially reported by Ajayan et al. [3]. In their research, multi-wall carbon 20 June 2006 Abstract Carbon nanotubes (CNTs) are promising additives to polymeric materials due

  5. Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide into a

    E-Print Network [OSTI]

    Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide- residue Ebola virus fusion peptide into a membrane bilayer. We applied a multi-resolution computational viruses, the filoviruses contain a highly compact genome, consisting of only seven encoded proteins

  6. Biochemical Engineering Journal 36 (2007) 239249 Dynamic simulation of benzene vapor treatment by

    E-Print Network [OSTI]

    Daugulis, Andrew J.

    2007-01-01

    Biochemical Engineering Journal 36 (2007) 239­249 Dynamic simulation of benzene vapor treatment microorganisms. The system being considered involves the treatment of benzene vapors by Achro- mobacter biotechnology developed to treat waste gases that has shown promise for removing toxic VOCs, such as benzene

  7. Biochemical Engineering Journal 36 (2007) 250261 Dynamic simulation of benzene vapor treatment by a

    E-Print Network [OSTI]

    Daugulis, Andrew J.

    2007-01-01

    Biochemical Engineering Journal 36 (2007) 250­261 Dynamic simulation of benzene vapor treatment for the treatment of benzene waste gases by Achromobacter xylosoxidans Y234 with n-hexadecane as an immiscible, organic phase. Model calibration was performed to account for observed enhancements of benzene

  8. Simulating and Animating Social Dynamics: Embedding Small Pedestrian Groups in Crowds

    E-Print Network [OSTI]

    Cao, Yong

    Abstract We present a crowd model derives from Common Ground theory to accommodate high-level socially, crowd simu- lation, common ground theory 1 Introduction Incorporating the sense of social intelligenceSimulating and Animating Social Dynamics: Embedding Small Pedestrian Groups in Crowds paper id: 37

  9. Mechanical properties of connected carbon nanorings via molecular dynamics simulation Nan Chen and Mark T. Lusk*

    E-Print Network [OSTI]

    van Duin, Adri

    over carbon reinforced resins currently used in industry.5­7 Other approaches for mechanical design as elementary construction components, but other carbon nanostructures may offer additional choices in designingMechanical properties of connected carbon nanorings via molecular dynamics simulation Nan Chen

  10. Non-Fourier heat conduction in a single-walled carbon nanotube: Classical molecular dynamics simulations

    E-Print Network [OSTI]

    Maruyama, Shigeo

    of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Non-stationary heat conduction in a single-picoseconds. The investigation was based on classical molecular dynamics simulations, where the heat pulse was generated. In a typical macroscopic description, a well-known model of heat wave propagation was formulated by Cattaneo

  11. Assessing possible dynamical effects of condensate in high resolution climate simulations

    E-Print Network [OSTI]

    Dai, Aiguo

    Assessing possible dynamical effects of condensate in high resolution climate simulations J. T, condensed water species can add significant mass to an atmospheric column. This mass can create positive the pressure induced by condensates. A simple parameterization of this condensate loading as a function

  12. Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Hydrogen Combustion

    E-Print Network [OSTI]

    Goddard III, William A.

    Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Hydrogen Combustion concept (BB), which we validate here for describing hydrogen combustion. The bond order, undercoordination determined the detailed sequence of reactions for hydrogen combustion with and without the BB. We validate

  13. Observations, Simulations, and Dynamics of Jet Stream Variability and Annular Modes JOSEPH KIDSTON

    E-Print Network [OSTI]

    Kidston, Joseph

    Observations, Simulations, and Dynamics of Jet Stream Variability and Annular Modes JOSEPH KIDSTON jet stream. It is shown that the strength of the thermally indirect circulation that gives rise- lation of the equivalent barotropic eddy-driven jet streams and embedded storm tracks (Kidson 1988; Mo

  14. Simulation of exhaust gas pollution within an eventdriven multimodal dynamic traffic model

    E-Print Network [OSTI]

    Toint, Philippe

    . The second is the temporal evolution of the pollution level, both globally and at the scale of specific city1 Simulation of exhaust gas pollution within an event­driven multimodal dynamic traffic model E development of the last decade, and the quality of life in cities is part of these emerging and widely spread

  15. Molecular dynamics simulation of atomic layer etching of silicon Satish D. Athavale and Demetre J. Economoua)

    E-Print Network [OSTI]

    Economou, Demetre J.

    one layer at a time. Much attention has been paid to deposition, but etching with atomic layerMolecular dynamics simulation of atomic layer etching of silicon Satish D. Athavale and Demetre J atomic layer etching ALET of Si. The total reaction yield Si atoms removed per ion was 0.172; 84

  16. Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes YASUSHI SHIBUTA, SHIGEO MARUYAMA Nucleation process of single-walled carbon nanotubes by the catalytic chemical with randomly distributed carbon-source molecules and a nickel cluster to investigate the metal-catalyzed growth

  17. A next-generation modeling capability assesses wind turbine array fluid dynamics and aeroelastic simulations

    E-Print Network [OSTI]

    A next-generation modeling capability assesses wind turbine array fluid dynamics and aeroelastic simulations Characterizing and optimizing overall performance of wind plants composed of large numbers at the National Renewable Energy Laboratory (NREL) are coupling physical models of the atmosphere and wind

  18. Local and chain dynamics in miscible polymer blends: A Monte Carlo simulation study

    E-Print Network [OSTI]

    Luettmer-Strathmann, Jutta

    44325-4001 Received 7 November 2005; accepted 1 March 2006; published online 5 May 2006 Local chain of the chains. These are combined with a local mobility determined from the acceptance rate and the effectiveLocal and chain dynamics in miscible polymer blends: A Monte Carlo simulation study Jutta Luettmer

  19. Exploring the Dynamic Costs of Process-aware Information Systems through Simulation

    E-Print Network [OSTI]

    Ulm, Universität

    Exploring the Dynamic Costs of Process-aware Information Systems through Simulation Bela Mutschler systems, case handling systems) is associated with high costs. Though cost evaluation has received utilizes si- mulation models for investigating costs related to PAIS engineering projects. We motivate

  20. Molecular Dynamics Simulation of Thin Films with Rough and Asymmetric Interfaces

    E-Print Network [OSTI]

    Walker, D. Greg

    Molecular Dynamics Simulation of Thin Films with Rough and Asymmetric Interfaces N.A. Roberts with the use of interfaces and shows that pristine, imperfect and asymmetric interfaces in thin films can interface whose features are of the order of the phonon wavelength. At a constant temperature difference

  1. Long-time protein folding dynamics from short-time molecular dynamics simulations

    E-Print Network [OSTI]

    Chodera, J D; Swope, W C; Pitera, J W; Dill, Ken A

    2006-01-01

    On the simulation of protein folding by short time scaleand W. A. Eaton, The protein folding “speed limit,” Curr.and T. Head-Gordon, Protein folding by distributed computing

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

    E-Print Network [OSTI]

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

    2006-01-01

    strategies, DSM, RES-E, RES-CHP, district heating, bio-and heat production (RES-CHP) and for bio-fuel production.schemes for RUE, RES-E, RES-CHP, and bio-fuels as well as

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

    E-Print Network [OSTI]

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

    2006-01-01

    which considers a rebound in energy consumption due torebound effect which leads to a partly compensation of energy

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

    E-Print Network [OSTI]

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

    2006-01-01

    DSM, RES-E, RES-CHP, district heating, bio- fuels, solarcorresponding E.g. missing district heating grid, in urbanHeating plus DHW) dh district heating connection is in

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

    E-Print Network [OSTI]

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

    2006-01-01

    the past two decades. Gas and district heating are stronglypromotion of biomass and district heating which constituteschemes are biomass and district heating related schemes.

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

    E-Print Network [OSTI]

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

    2006-01-01

    of the building sector in the RES-E/CHP and bio-fuel part noCHP 11 District heating Bio-fuels CO 2 tax Invest- ment subsidy Soft Loan Feed in tariff Building

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

    E-Print Network [OSTI]

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

    2006-01-01

    heating connection of one floor heating system; ss singlecovering one floor respectively central heating; additionalsystems and heating systems covering one floor. • Subsidy

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

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankADVANCED MANUFACTURINGEnergy Bills and ReduceNovemberDOE's PrioritiesOctober 2013 Pradeep Ramuhalli,

  9. Ultrafast reaction dynamics in cluster ions: Simulation of the transient photoelectron spectrum of I2 Arn photodissociation

    E-Print Network [OSTI]

    Faeder, Jim

    Hamiltonian model of electronic structure with nonadiabatic molecular dynamics simulations, we calculate of the electronic structure of a manifold of states strongly coupled to the many solvent degrees of freedomUltrafast reaction dynamics in cluster ions: Simulation of the transient photoelectron spectrum

  10. Particle dynamics in two-dimensional random energy landscapes - experiments and simulations

    E-Print Network [OSTI]

    Florian Evers; Christoph Zunke; Richard D. L. Hanes; Joerg Bewerunge; Imad Ladadwa; Andreas Heuer; Stefan U. Egelhaaf

    2013-06-13

    The dynamics of individual colloidal particles in random potential energy landscapes were investigated experimentally and by Monte Carlo simulations. The value of the potential at each point in the two-dimensional energy landscape follows a Gaussian distribution. The width of the distribution, and hence the degree of roughness of the energy landscape, was varied and its effect on the particle dynamics studied. This situation represents an example of Brownian dynamics in the presence of disorder. In the experiments, the energy landscapes were generated optically using a holographic set-up with a spatial light modulator, and the particle trajectories were followed by video microscopy. The dynamics are characterized using, e.g., the time-dependent diffusion coefficient, the mean squared displacement, the van Hove function and the non-Gaussian parameter. In both, experiments and simulations, the dynamics are initially diffusive, show an extended sub-diffusive regime at intermediate times before diffusive motion is recovered at very long times. The dependence of the long-time diffusion coefficient on the width of the Gaussian distribution agrees with theoretical predictions. Compared to the dynamics in a one-dimensional potential energy landscape, the localization at intermediate times is weaker and the diffusive regime at long times reached earlier, which is due to the possibility to avoid local maxima in two-dimensional energy landscapes.

  11. Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report â?? 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 parallel computation of particle and fluid dynamics simulations. These problems occur throughout DOE, military and commercial sectors: the potential payoff is high. We plan to license or sell the solution to contractors for military and domestic applications such as disaster simulation (aerodynamic and hydrodynamic), Government agencies (hydrological and environmental simulations), and medical applications (e.g., in tomographic image reconstruction). Keywords - High-performance Computing, Graphic Processing Unit, Fluid/Particle Simulation. Summary for Members of Congress - Department of Energy has many simulation codes that must compute faster, to be effective. The Phase I research parallelized particle/fluid simulations for rocket combustion, for high-performance computing systems.

  12. Coupled Dynamic Analysis of Multiple Unit Floating Offshore Wind Turbine 

    E-Print Network [OSTI]

    Bae, Yoon Hyeok

    2013-04-23

    In the present study, a numerical simulation tool has been developed for the rotor-floater-tether coupled dynamic analysis of Multiple Unit Floating Offshore Wind Turbine (MUFOWT) in the time domain including aero-blade-tower dynamics and control...

  13. Development and application of chemical tools for investigating dynamic processes in cell migration

    E-Print Network [OSTI]

    Goguen, Brenda Nicole

    2011-01-01

    Cell migration is a dynamic process essential for many fundamental physiological functions, including wound repair and the immune response. Migration relies on precisely orchestrated events that are regulated in a spatially ...

  14. Exploration of High Dynamic Range Photography As a Useful Tool for Lighting Design

    E-Print Network [OSTI]

    Saifan, Mariam

    2014-12-31

    This thesis introduces a camera-aided imaging method, better known as high dynamic range (HDR) photography, and how this method could potentially help improve the quality of lighting design analysis. The imaging method captures 18 million luminance...

  15. 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.

  16. Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo

    E-Print Network [OSTI]

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

    2015-04-21

    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.

  17. Quantum simulations of dissipative dynamics: time-dependence instead of size

    E-Print Network [OSTI]

    Benjamin Dive; Florian Mintert; Daniel Burgarth

    2015-05-08

    The simulation of quantum systems has been a key aim of quantum technologies for decades, and the generalisation to open systems is necessary to include physically realistic systems. We introduce an approach for quantum simulations of open system dynamics in terms of an environment of minimal size and a time-dependent Hamiltonian. This enables the implementation of a continuous-time simulation with a finite environment, whereas state of the art methods require an infinite environment or only match the simulation at discrete times. We find necessary and sufficient conditions for this Hamiltonian to be well behaved and, when these are not met, we show that there exists an approximate Hamiltonian that is, and look into its applications.

  18. Interactions between Ether Phospholipids and Cholesterol as Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    Pan, Jianjun [ORNL; Cheng, Xiaolin [ORNL; Heberle, Frederick A [ORNL; Mostofian, Barmak [ORNL; Kucerka, Norbert [Canadian Neutron Beam Centre and Comelius University (Slovakia); Drazba, Paul [ORNL; Katsaras, John [ORNL

    2012-01-01

    Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol s molecular interactions with ether lipids as determined using a combination of small-angle neutron and Xray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.

  19. 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.

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

    SciTech Connect (OSTI)

    Wall, Michael E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Van Benschoten, Andrew H. [Univ. of California, San Francisco, CA (United States); Sauter, Nicholas K. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Adams, Paul D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Fraser, James S. [Univ. of California, San Francisco, CA (United States); Terwilliger, Thomas C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    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 protein–solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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 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

  2. 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.

  3. 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)

  4. Water harvesting using a conducting polymer: A study by molecular dynamics simulation

    SciTech Connect (OSTI)

    Ostwal, Mayur M.; Sahimi, Muhammad; Tsotsis, Theodore T. [Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211 (United States)

    2009-06-15

    The results of extensive molecular simulations of adsorption and diffusion of water vapor in polyaniline, made conducting by doping it with HCl or HBr over a broad range of temperatures, are reported. The atomistic model of the polymers was generated using energy minimization, equilibrium molecular dynamics simulations, and two different force fields. The computed sorption isotherms are in excellent agreement with the experimental data. The computed activation energies for the diffusion of water molecules in the polymers also compare well with what has been reported in the literature. The results demonstrate the potential of conducting polyaniline for water harvesting from air.

  5. Coherent structures in Dissipative Particle Dynamics simulations of the transition to turbulence in compressible shear flows

    E-Print Network [OSTI]

    van de Meent, Jan-Willem; Somfai, Ellak; Sultan, Eric; van Saarloos, Wim

    2008-01-01

    We present simulations of coherent structures in compressible flows near the transition to turbulence using the Dissipative Particle Dynamics (DPD) method. The structures we find are remarkably consistent with experimental observations and DNS simulations of incompressible flows, despite a difference in Mach number of several orders of magnitude. The bifurcation from the laminar flow is bistable and shifts to higher Reynolds numbers when the fluid becomes more compressible. This work underlines the robustness of coherent structures in the transition to turbulence and illustrates the ability of particle-based methods to reproduce complex non-linear instabilities.

  6. Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated with the Chappuis band of ozone

    SciTech Connect (OSTI)

    Batista, V.S.; Miller, W.H. [Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)] [Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    1998-01-01

    In this paper we investigate the nonadiabatic ultrafast dynamics of interconversion between the two lower lying excited states of {sup 1}A{sup {double_prime}} symmetry (1 {sup 1}A{sup {double_prime}} and 2 {sup 1}A{sup {double_prime}}) of ozone following photoexcitation of the molecule in the gas phase with visible light. Our algorithm involves a semiclassical initial value representation method which is able to describe electronically nonadiabatic processes within the time dependent picture through the quantization of the classical electron{endash}nuclear model Hamiltonian of Meyer and Miller [J. Chem. Phys. {bold 70}, 7 (1979)]. We explore the capabilities of these techniques as applied to studying the dynamics of a realistic reaction of photodissociation on full {ital ab initio} electronic potential energy surfaces. Our semiclassical results provide an intuitive understanding of the most fundamental dynamical features involved in the process of predissociation, such as decay and recurrence events, as well as an interpretation of experimental studies of the Chappuis band of ozone in the frequency domain. {copyright} {ital 1998 American Institute of Physics.}

  7. High Performance Molecular Dynamic Simulation on Single and Multi-GPU Systems

    SciTech Connect (OSTI)

    Villa, Oreste; Chen, Long; Krishnamoorthy, Sriram

    2010-05-30

    The programming techniques supported and employed on these GPUs and Multi-GPUs systems are not sufficient to address problems exhibiting irregular, and unbalanced workload such as Molecular Dynamic (MD) simulations of systems with non-uniform densities. In this paper, we propose a task-based dynamic load-balancing solution to employ on MD simulations for single- and multi-GPU systems. The solution allows load balancing at a finer granularity than what is supported in existing APIs such as NVIDIA’s CUDA. Experimental results with a single-GPU configuration show that our fine-grained task solution can utilize the hardware more efficiently than the CUDA scheduler. On multi-GPU systems, our solution achieves near-linear speedup, load balance, and significant performance improvement over techniques based on standard CUDA APIs.

  8. A Molecular Dynamics Simulation of the Turbulent Couette Minimal Flow Unit

    E-Print Network [OSTI]

    Smith, E R

    2015-01-01

    A molecular dynamics (MD) simulation of planar Couette flow is presented for the minimal channel in which turbulence structures can be sustained. Evolution over a single breakdown and regeneration cycle is compared to computational fluid dynamics (CFD) simulations. Qualitative similar structures are observed and turbulent statistics show excellent quantitative agreement. The molecular scale law of the wall is presented in which stick-slip molecular wall-fluid interactions replace the no-slip conditions. The impact of grid resolution is explored and the observed structures are seen to be dependant on averaging time and length scales. The kinetic energy spectra show a range of scales are present in the molecular system and that spectral content is dependent on the grid resolution employed. The subgrid velocity of the molecules is compared to spatial averaged velocity using joint probability density functions. Molecular trajectories, diffusions and Lagrangian statistics are presented. The importance of sub-grid ...

  9. A framework for simulating and estimating the state and functional topology of complex dynamic geometric networks

    E-Print Network [OSTI]

    Marius Buibas; Gabriel A. Silva

    2010-06-22

    We present a framework for simulating signal propagation in geometric networks (i.e. networks that can be mapped to geometric graphs in some space) and for developing algorithms that estimate (i.e. map) the state and functional topology of complex dynamic geometric net- works. Within the framework we define the key features typically present in such networks and of particular relevance to biological cellular neural networks: Dynamics, signaling, observation, and control. The framework is particularly well-suited for estimating functional connectivity in cellular neural networks from experimentally observable data, and has been implemented using graphics processing unit (GPU) high performance computing. Computationally, the framework can simulate cellular network signaling close to or faster than real time. We further propose a standard test set of networks to measure performance and compare different mapping algorithms.

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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.

  11. 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.

  12. 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.

  13. Ab initio molecular dynamics simulation of proton hopping in a model polymer membrane

    SciTech Connect (OSTI)

    Devanathan, Ramaswami; Idupulapati, Nagesh B.; Baer, Marcel D.; Mundy, Christopher J.; Dupuis, Michel

    2013-12-10

    We report the results of ab initio molecular dynamics simulations of a model NafionTM polymer membrane initially equilibrated using classical molecular dynamics simulations. We studied three hydration levels (?) of 3, 9, and 15 H2O/SO3- corresponding to dry, hydrated and saturated fuel cell membrane, respectively. The barrier for proton transfer from the SO3-–H3O+ contact ion pair to a solvent-separated ion pair decreased from 2.3 kcal/mol for ? = 3 to 0.8 kcal/mol for ? = 15. The barrier for proton transfer between two water molecules was in the range from 0.7 to 0.8 kcal/mol for the ? values studied. The number of proton shuttling events between a pair of water molecules is an order of magnitude more than the number of proton hops across three distinct water molecules. The proton diffusion coefficient at ? = 15 is about 0.9x10-5 cm2/s, which is in good agreement with experiment and our previous quantum hopping molecular dynamics simulations.

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJessework usesof EnergyY-12 NationalNO FEARIntegratedAGeospatial Tools

  15. Hydrostatic Simulation of Earth's Atmospheric Gas Using Multi-particle Collision Dynamics

    E-Print Network [OSTI]

    Pattisahusiwa, Asis; Virid, Sparisoma

    2015-01-01

    Multi-particle collision dynamics (MPCD) is a mesoscopic simulation method to simulate fluid particle-like flows. MPCD has been widely used to simulate various problems in condensed matter. In this study, hydrostatic behavior of gas in the Earth's atmospheric layer is simulated by using MPCD method. The simulation is carried out by assuming the system under ideal state and is affected only by gravitational force. Gas particles are homogeneous and placed in 2D box. Interaction of the particles with the box is applied through implementation of boundary conditions (BC). Periodic BC is applied on the left and the right side, specular reflection on the top side, while bounce-back on the bottom side. Simulation program is executed in Arch Linux and running in notebook with processor Intel i5 @2700 MHz with 10 GB DDR3 RAM. The results show behaviors of the particles obey kinetic theory for ideal gas when gravitational acceleration value is proportional to the particle mass. Density distribution as a function of alti...

  16. FORCE FIELDS FOR PROTEIN SIMULATIONS By JAY W. PONDER* AND DAVID A. CASE

    E-Print Network [OSTI]

    Ponder, Jay

    by means of quantum chemistry electronic structure calculations, so most practical simulations use a set, are by now widely used as tools to investigate their structure and dynamics under a wide variety Solvent Models.......................................................... 64 C. Molecular Dynamics

  17. Computer simulation study of surface wave dynamics at the crystal--melt interface

    E-Print Network [OSTI]

    Jorge Benet; Luis G. MacDowell; Eduardo Sanz

    2014-10-01

    We study, by means of computer simulations, the crystal-melt interface of three different systems: hard-spheres, Lennard Jones and the TIP4P/2005 water model. In particular, we focus on the dynamics of surface waves. We observe that the processes involved in the relaxation of surface waves are characterized by distinct time scales: a slow one related to the continuous recrystallization and melting, that is governed by capillary forces; and a fast one which we suggest to be due to a combination of processes that quickly cause small perturbations to the shape of the interface (like e. g. Rayleigh waves, subdiffusion, or attachment/detachment of particles to/from the crystal). The relaxation of surface waves becomes dominated by the slow process as the wavelength increases. Moreover, we see that the slow relaxation is not influenced by the details of the microscopic dynamics. In a time scale characteristic for the diffusion of the liquid phase, the relaxation dynamics of the crystal-melt interface of water is around one order of magnitude slower than that of Lennard Jones or hard spheres, which we ascribe to the presence of orientational degrees of freedom in the water molecule. Finally, we estimate the rate of crystal growth from our analysis of the capillary wave dynamics and compare it with previous simulation studies and with experiments for the case of water.

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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

  19. Adhesion between elastic solids with randomly rough surfaces: comparison of analytical theory with molecular dynamics simulations

    E-Print Network [OSTI]

    N. Mulakaluri; B. N. J. Persson

    2011-12-22

    The adhesive contact between elastic solids with randomly rough, self affine fractal surfaces is studied by molecular dynamics (MD) simulations. The interfacial binding energy obtained from the simulations of nominally flat and curved surfaces is compared with the predictions of the contact mechanics theory by Persson. Theoretical and simulation results agree rather well, and most of the differences observed can be attributed to finite size effects and to the long-range nature of the interaction between the atoms in the block and the substrate in the MD model, as compared to the analytical theory which is for an infinite system with interfacial contact interaction. For curved surfaces (JKR-type of problem) the effective interfacial energy exhibit a weak hysteresis which may be due to the influence of local irreversible detachment processes in the vicinity of the opening crack tip during pull-off.

  20. Integrated two-dimensional simulations of dynamic hohlraum driven inertial fusion capsule implosions

    SciTech Connect (OSTI)

    Slutz, S. A.; Peterson, K. J.; Vesey, R. A.; Lemke, R. W.; Bailey, J. E.; Varnum, W.; Ruiz, C. L.; Cooper, G. W.; Chandler, G. A.; Rochau, G. A.; Mehlhorn, T. A. [Sandia National Laboratories, Albuquerque, New Mexico 87185-1186 (United States)

    2006-10-15

    Simulations have been useful for improving the design of dynamic hohlraums for the purpose of imploding inertial fusion capsules [S. A. Slutz, J. E. Bailey, G. A. Chandler et al., Phys. Plasmas 10, 1875 (2003)]. These design changes, which have resulted in capsule implosions with hot dense cores [J. E. Bailey, G. A. Chandler, S. A. Slutz et al., Phys. Rev. Lett. 92, 085002 (2004)] and the production of thermonuclear neutrons [C. L. Ruiz, G. Cooper, S. A. Slutz et al., Phys. Rev. Lett. 93, 015001 (2005)], were based primarily on a series of one-dimensional numerical simulations, which treated the dynamic hohlraum and the capsule implosion separately. In this paper we present simulations which are fully integrated to include the implosion of wire arrays onto foam convertors, the implosion of the capsule imbedded in the foam, and the absorption of radiation into the electrodes. These simulations yield predictions that are in remarkably good agreement with measured values considering the complexity of the problem, which spans more than 100 ns of wire implosion with the subsequent capsule implosion on a few ns timescale. For example, the predicted neutron yields are less than a factor of 2 higher than the measured values, while the predicted shock velocity is about 30% higher than the measured value. The spectroscopically inferred imploded capsule gas core temperatures are somewhat lower than predicted by the simulations, while the gas densities are about a factor of 2 higher. Simulations indicate that a more slowly rising radiation drive temperature yields higher core densities and lower temperatures and thus better agreement with experimental measurements. Possible reasons for a more slowly rising radiation drive are discussed.

  1. Exponential Demand Simulation Tool

    E-Print Network [OSTI]

    Reed, Derek D.

    2015-05-15

    Operant behavioral economics investigates the relation between environmental constraint and reinforcer consumption. The standard approach to quantifying this relation is through the use of behavioral economic demand curves. ...

  2. Mixed Mode Simulation Tools

    E-Print Network [OSTI]

    Gandhi, Priya; Brager, Gail; Dutton, Spencer

    2014-01-01

    M. (2006). Multizone airflow model in Modelica. In Proc.of the 5-th International Modelica Conference (Vol. 2, pp.releases/v1.1_build1/bie/modelica/Buildings/Resour ces/

  3. 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).

  4. Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

    E-Print Network [OSTI]

    Im, Wonpil; Roux, Benoî t

    2001-01-01

    A general method has been developed to include the electrostatic reaction field in Brownian dynamics (BD) simulations of ions diffusing through complex molecular channels of arbitrary geometry. Assuming that the solvent ...

  5. Simulation of polar stratospheric clouds in the specified dynamics version of the whole atmosphere community climate model

    E-Print Network [OSTI]

    Wegner, T.

    We evaluate the simulation of polar stratospheric clouds (PSCs) in the Specified Dynamics version of the Whole Atmosphere Community Climate Model for the Antarctic winter 2005. In this model, PSCs are assumed to form ...

  6. Molecular dynamics simulation of complex molecules at interfaces: dendritic surfactants in clay and amyloid peptides near lipid bilayers 

    E-Print Network [OSTI]

    Han, Kunwoo

    2009-06-02

    We apply a molecular dynamics (MD) simulation technique to complex molecules at interfaces. Partitioning of dendritic surfactants into clay gallery and Ab protein behavior near hydrated lipids are chosen for the purpose. ...

  7. The role of sex in parasite dynamics: Model simulations on transmission of Heligmosomoides polygyrus in populations of

    E-Print Network [OSTI]

    Pugliese, Andrea

    The role of sex in parasite dynamics: Model simulations on transmission of Heligmosomoides Abstract We investigated possible mechanisms that could cause sex-biased parasite transmission. Two, not mutually exclusive, hypotheses were examined: that sex-bi- ased parasite transmission

  8. 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 Santé et de la Recherche Médicale (INSERM) and INTS, France] [Institut National de la Santé et de la Recherche Médicale (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.

  9. Development of a Pilot Study Simulation to Investigate the Impact of Target Costing on Team Dynamics and Design Aesthetics 

    E-Print Network [OSTI]

    Gottipati, Udaya Naidu

    2011-10-21

    OF A PILOT STUDY SIMULATION TO INVESTIGATE THE IMPACT OF TARGET COSTING ON TEAM DYNAMICS AND DESIGN AESTHETICS A Thesis by UDAYA NAIDU GOTTIPATI Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment... of the requirements for the degree of MASTER OF SCIENCE August 2010 Major Subject: Construction Management Development of a Pilot Study Simulation to Investigate the Impact of Target Costing on Team Dynamics...

  10. Local and chain dynamics in miscible polymer blends: A Monte Carlo simulation study

    E-Print Network [OSTI]

    Jutta Luettmer-Strathmann; Manjeera Mantina

    2005-11-07

    Local chain structure and local environment play an important role in the dynamics of polymer chains in miscible blends. In general, the friction coefficients that describe the segmental dynamics of the two components in a blend differ from each other and from those of the pure melts. In this work, we investigate polymer blend dynamics with Monte Carlo simulations of a generalized bond-fluctuation model, where differences in the interaction energies between non-bonded nearest neighbors distinguish the two components of a blend. Simulations employing only local moves and respecting a non-bond crossing condition were carried out for blends with a range of compositions, densities, and chain lengths. The blends investigated here have long-chain dynamics in the crossover region between Rouse and entangled behavior. In order to investigate the scaling of the self-diffusion coefficients, characteristic chain lengths $N_\\mathrm{c}$ are calculated from the packing length of the chains. These are combined with a local mobility $\\mu$ determined from the acceptance rate and the effective bond length to yield characteristic self-diffusion coefficients $D_\\mathrm{c}=\\mu/N_\\mathrm{c}$. We find that the data for both melts and blends collapse onto a common line in a graph of reduced diffusion coefficients $D/D_\\mathrm{c}$ as a function of reduced chain length $N/N_\\mathrm{c}$. The composition dependence of dynamic properties is investigated in detail for melts and blends with chains of length twenty at three different densities. For these blends, we calculate friction coefficients from the local mobilities and consider their composition and pressure dependence. The friction coefficients determined in this way show many of the characteristics observed in experiments on miscible blends.

  11. Sandia Energy - Scattering Dynamics

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Scattering Dynamics Home Transportation Energy Predictive Simulation of Engines Combustion Chemistry Chemical Dynamics Scattering Dynamics Scattering DynamicsAshley...

  12. Development of a dynamic network monitoring tool – Interactive map based on LLDP and SNMP

    E-Print Network [OSTI]

    Haen, Christophe; Mesnard, E

    2010-01-01

    The European Organization for Nuclear Research (French: Organisation Européenne pour la Recherche Nucléaire), known as CERN is the world’s largest particle physics laboratory, established in 1954 near Geneva. CERN’s main function is to provide the particle accelerators and other infrastructure needed for high-energy physics research. The LHCb (standing for “Large Hadron Collider beauty”) experiment is one of six particle physics detector experiments built on the Large Hadron Collider, the world’s largest and highest-energy particle accelerator. This experiment produces a large amount of data which needs to be treated. This task is processed by some 2000 computing servers and 400 control servers. The LHCb Online team is responsible of the data, from their creation in the detector, till the storage. The purpose of my internship was to develop a software from scratch able to dynamically discover the network, draw a map of it, gather information of the network equipments, and implement basic monitorin...

  13. Flow of colloidal solids and fluids through constrictions: dynamical density functional theory versus simulation

    E-Print Network [OSTI]

    Urs Zimmermann; Frank Smallenburg; Hartmut Löwen

    2015-12-02

    Using both dynamical density functional theory and particle-resolved Brownian dynamics simulations, we explore the flow of two-dimensional colloidal solids and fluids driven through a linear channel with a geometric constriction. The flow is generated by a constant external force acting on all colloids. The initial configuration is equilibrated in the absence of flow and then the external force is switched on instantaneously. Upon starting the flow, we observe four different scenarios: a complete blockade, a monotonic decay to a constant particle flux (typical for a fluid), a damped oscillatory behaviour in the particle flux, and a long-lived stop-and-go behaviour in the flow (typical for a solid). The dynamical density functional theory describes all four situations but predicts infinitely long undamped oscillations in the flow which are always damped in the simulations. We attribute the mechanisms of the underlying stop-and-go flow to symmetry conditions on the flowing solid. Our predictions are verifiable in real-space experiments on magnetic colloidal monolayers which are driven through structured microchannels and can be exploited to steer the flow throughput in microfluidics.

  14. Interfacial water on crystalline silica: A comparative molecular dynamics simulation study

    SciTech Connect (OSTI)

    Ho, Tuan A. [University of Oklahoma, Norman; Argyris, D. [University of Oklahoma, Norman; Cole, David [Ohio State University; Striolo, Alberto [Oklahoma University

    2011-01-01

    All-atom molecular dynamics simulations were conducted to study the dynamics of aqueous electrolyte solutions confined in slit-shaped silica nanopores of various degrees of protonation. Five degrees of protonation were prepared by randomly removing surface hydrogen atoms from fully protonated crystalline silica surfaces. Aqueous electrolyte solutions containing NaCl or CsCl salt were simulated at ambient conditions. In all cases, the ionic concentration was 1 M. The results were quantified in terms of atomic density distributions within the pores, and the self-diffusion coefficient along the direction parallel to the pore surface. We found evidence for ion-specific properties that depend on ion surface, water ion, and only in some cases ion ion correlations. The degree of protonation strongly affects the structure, distribution, and the dynamic behavior of confined water and electrolytes. Cl ions adsorb on the surface at large degrees of protonation, and their behavior does not depend significantly on the cation type (either Na+ or Cs+ ions are present in the systems considered). The cations show significant ion-specific behavior. Na+ ions occupy different positions within the pore as the degree of protonation changes, while Cs+ ions mainly remain near the pore center at all conditions considered. For a given degree of protonation, the planar self-diffusion coefficient of Cs+ is always greater than that of Na+ ions. The results are useful for better understanding transport under confinement, including brine behavior in the subsurface, with important applications such as environmental remediation.

  15. Modeling, simulation, and testing of the mechanical dynamics of and RF MEMS switch.

    SciTech Connect (OSTI)

    Sumali, Hartono; Epp, David S.; Massad, Jordan Elias; Dyck, Christopher William; Starr, Michael James

    2005-07-01

    Mechanical dynamics can be a determining factor for the switching speed of radio-frequency microelectromechanical systems (RF MEMS) switches. This paper presents the simulation of the mechanical motion of a microswitch under actuation. The switch has a plate suspended by springs. When an electrostatic actuation is applied, the plate moves toward the substrate and closes the switch. Simulations are calculated via a high-fidelity finite element model that couples solid dynamics with electrostatic actuation. It incorporates non-linear coupled dynamics and accommodates fabrication variations. Experimental modal analysis gives results in the frequency domain that verifies the natural frequencies and mode shapes predicted by the model. An effective 1D model is created and used to calculate an actuation voltage waveform that minimizes switch velocity at closure. In the experiment, the switch is actuated with this actuation voltage, and the displacements of the switch at various points are measured using a laser Doppler velocimeter through a microscope. The experiments are repeated on several switches from different batches. The experimental results verify the model.

  16. Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer: an application to polymer lubrication

    E-Print Network [OSTI]

    Shugo Yasuda; Ryoichi Yamamoto

    2014-07-16

    The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid elements to calculate the local stresses and temperatures and are synchronized at certain time intervals to satisfy the macroscopic heat- and momentum- transport equations. This method is applied to the lubrication of a polymeric liquid composed of short chains with ten beads between parallel plates. The rheological properties and conformation of polymer chains coupled with the local viscous heating are investigated with a non-dimensional parameter, i.e., the Nahme-Griffith number, which is defined by the ratio of the viscous heating to the thermal conduction at the characteristic temperature required to sufficiently change the viscosity. The present simulation demonstrates that strong shear thinning and transitional behavior of the conformation of the polymer chains occur with a rapid temperature rise when the Nahme-Griffith number exceeds unity. The results also clarify that the reentrant transition of the linear stress-optical relation occurs for large shear stresses due to the coupling of the conformation of polymer chains and heat generation under shear flows.

  17. Dark-ages Reionization & Galaxy Formation Simulation I: The dynamical lives of high redshift galaxies

    E-Print Network [OSTI]

    Poole, Gregory B; Mutch, Simon J; Power, Chris; Duffy, Alan R; Geil, Paul M; Mesinger, Andrei; Wyithe, Stuart B

    2015-01-01

    We present the Dark-ages Reionization and Galaxy-formation Observables from Numerical Simulations (DRAGONS) program and Tiamat, the collisionless N-body simulation program upon which DRAGONS is built. The primary trait distinguishing Tiamat from other large simulation programs is its density of outputs at high redshift (100 from z=35 to z=5; roughly one every 10 Myr) enabling the construction of very accurate merger trees at an epoch when galaxy formation is rapid and mergers extremely frequent. We find that the friends-of-friends halo mass function agrees well with the prediction of Watson et al. at high masses, but deviates at low masses, perhaps due to our use of a different halo finder or perhaps indicating a break from "universal" behaviour. We then analyse the dynamical evolution of galaxies during the Epoch of Reionization finding that only a small fraction (~20%) of galactic halos are relaxed. We illustrate this using standard relaxation metrics to establish two dynamical recovery time-scales: i) halo...

  18. Dynamics of the terrestrial planets from a large number of N-body simulations"! Rebecca A. Fischer1,

    E-Print Network [OSTI]

    ! 1 Dynamics of the terrestrial planets from a large number of N-body simulations"! #! Rebecca A and planetesimals was the final stage of""! terrestrial planet formation. This process is modeled using N of planetary#&! accretion as particular accretion pathways may be representative of a given dynamic#'! scenario

  19. On the modeling and simulation of of reaction-transfer dynamics in semiconductor-electrolyte solar cells

    E-Print Network [OSTI]

    On the modeling and simulation of of reaction-transfer dynamics in semiconductor-electrolyte solar-performance semiconductor-liquid junction solar cells. We propose in this work a macroscopic mathematical model, a sys- tem-liquid junction, solar cell simulation, naso-scale device modeling. 1 Introduction The mathematical modeling

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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

  1. Diffusion of a Janus nanoparticle in an explicit solvent: A molecular dynamics simulation study

    E-Print Network [OSTI]

    Ali Kharazmi; Nikolai V. Priezjev

    2015-05-14

    Molecular dynamics simulations are carried out to study the translational and rotational diffusion of a single Janus particle immersed in a dense Lennard-Jones fluid. We consider a spherical particle with two hemispheres of different wettability. The analysis of the particle dynamics is based on the time-dependent orientation tensor, particle displacement, as well as the translational and angular velocity autocorrelation functions. It was found that both translational and rotational diffusion coefficients increase with decreasing surface energy at the nonwetting hemisphere, provided that the wettability of the other hemisphere remains unchanged. We also observed that in contrast to homogeneous particles, the nonwetting hemisphere of the Janus particle tends to rotate in the direction of the displacement vector during the rotational relaxation time.

  2. Calculation technique for simulation of wave and fracture dynamics in a reinforced sheet

    E-Print Network [OSTI]

    M. Ayzenberg-Stepanenko; Z. Yanovitsky; G. Osharovich

    2012-03-08

    Mathematical models and computer algorithms are developed to calculate dynamic stress concentration and fracture wave propagation in a reinforced composite sheet. The composite consists of a regular system alternating extensible fibers and pliable adhesive layers. In computer simulations, we derive difference algorithms preventing or minimizing the parasite distortions caused by the mesh dispersion and obtain precise numerical solutions in the plane fracture problem of a pre-stretched sheet along the fibers. Interactive effects of microscale dynamic deformation and multiple damage in fibers and adhesive are studied. Two engineering models of the composite are considered: the first assumes that adhesive can be represented by inertionless bonds of constant stiffness, while in the second one an adhesive is described by inertial medium perceived shear stresses. Comparison of results allows the evaluation of facilities of models in wave and fracture patterns analysis.

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

    Broader source: All U.S. Department of Energy (DOE) Office 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...

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

    SciTech Connect (OSTI)

    Shimojo, Fuyuki; Hattori, Shinnosuke [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States) [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States)] [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Kunaseth, Manaschai [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States) [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); National Nanotechnology Center, Pathumthani 12120 (Thailand); Ohmura, Satoshi [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States) [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Department of Physics, Kyoto University, Kyoto 606-8502 (Japan); Shimamura, Kohei [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States) [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Department of Applied Quantum Physics and Nuclear Engineering, Kyushu University, Fukuoka 819-0395 (Japan)

    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 techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.

  5. Simulation of the relativistic electron dynamics and acceleration in a linearly-chirped laser pulse

    E-Print Network [OSTI]

    Jisrawi, Najeh M; Salamin, Yousef I

    2014-01-01

    Theoretical investigations are presented, and their results are discussed, of the laser acceleration of a single electron by a chirped pulse. Fields of the pulse are modeled by simple plane-wave oscillations and a $\\cos^2$ envelope. The dynamics emerge from analytic and numerical solutions to the relativistic Lorentz-Newton equations of motion of the electron in the fields of the pulse. All simulations have been carried out by independent Mathematica and Python codes, with identical results. Configurations of acceleration from a position of rest as well as from injection, axially and sideways, at initial relativistic speeds are studied.

  6. Entropic measure to prevent energy over-minimization in molecular dynamics simulations

    E-Print Network [OSTI]

    Rydzewski, Jakub; Nowak, Wieslaw

    2015-01-01

    Geometry optimization via energy minimization is one of the most common steps in computer modelling of biological structures. Nowadays computer power encourage numerous researches to use conjugated gradient minimizations exceeding 1000 steps. However, our research reveals that such over-minimization may lead to thermodynamically unstable conformations. We show that these conformations are not optimum starting points for equilibrium molecular dynamics simulations. We propose a measure based on the Pareto front of total entropy for quality assessment of minimized protein which warrants a proper selection of minimization steps.

  7. 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.

  8. 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.

  9. Mesoscale simulation of semiflexible chains. I. Endpoint distribution and chain dynamics

    E-Print Network [OSTI]

    Robert D. Groot

    2013-06-06

    The endpoint distribution and dynamics of semiflexible fibers is studied by numerical simulation. A brief overview is given over the analytical theory of flexible and semiflexible polymers. In particular, a closed expression is given for the relaxation spectrum of wormlike chains, which determines polymer diffusion and rheology. Next a simulation model for wormlike chains with full hydrodynamic interaction is described, and relations for the bending and torsion modulus are given. Two methods are introduced to include torsion stiffness into the model. The model is validated by simulating single chains in a heat bath, and comparing the endpoint distribution of the chains with established Monte Carlo results. It is concluded that torsion stiffness leads to a slightly shorter effective persistence length for a given bending stiffness. To further validate the simulation model, polymer diffusion is studied for fixed persistence length and varying polymer length N. The diffusion constant shows crossover from Rouse to reptation behaviour. The terminal relaxation time obtained from the monomer displacement is consistent with the theory of wormlike chains. The probability for chain crossing has also been studied. This probability is so low that it does not influence the present results.

  10. Leveraging on Easy Java Simulation tool and open source computer simulation library to create interactive digital media for mass customization of high school physics curriculum

    E-Print Network [OSTI]

    Wee, Loo Kang

    2012-01-01

    This paper highlights the diverse possibilities in the rich community of educators from the Conceptual Learning of Science (CoLoS) and Open Source Physics (OSP) movement to engage, enable and empower educators and students, to create interactive digital media through computer modeling. This concept revolves around a paradigmatic shift towards participatory learning through immersive computer modeling, as opposed to using technology for information transmission. We aim to engage high school educators to professionally develop themselves by creating and customizing simulations possible through Easy Java Simulation (Ejs) and its learning community. Ejs allows educators to be designers of learning environments through modifying source codes of the simulation. Educators can conduct lessons with students' using these interactive digital simulations and rapidly enhance the simulation through changing the source codes personally. Ejs toolkit, its library of simulations and growing community contributed simulation cod...

  11. Elements of naturality in dynamical simulation frameworks for Hamiltonian, thermostatic, and Lindbladian flows on classical and quantum state-spaces

    E-Print Network [OSTI]

    John A. Sidles; Joseph L. Garbini; Jonathan P. Jacky; Rico A. R. Picone; Scott A. Harsila

    2010-07-12

    The practical focus of this work is the dynamical simulation of polarization transport processes in quantum spin microscopy and spectroscopy. The simulation framework is built-up progressively, beginning with state-spaces (configuration manifolds) that are geometrically natural, introducing coordinates that are algebraically natural; and finally specifying dynamical potentials that are physically natural; in each respect explicit criteria are given for "naturality." The resulting framework encompasses Hamiltonian flow (both classical and quantum), quantum Lindbladian processes, and classical thermostatic processes. Constructive validation and verification criteria are given for metric and symplectic flows on classical, quantum, and hybrid state-spaces, with particular emphasis to tensor network state-spaces. Both classical and quantum examples are presented, including dynamic nuclear polarization (DNP). A broad span of applications and challenges is discussed, ranging from the design and simulation of quantum spin microscopes to the design and simulation of quantum oracles.

  12. 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.

  13. 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}

  14. 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.

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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

  16. The answer is blowing in the wind: Simulating the interaction of jets with dynamic cluster atmospheres

    E-Print Network [OSTI]

    S. Heinz; M. Brueggen; A. Young; E. Levesque

    2006-06-28

    We present numerical simulations investigating the interaction of AGN jets with galaxy clusters, for the first time taking into account the dynamic nature of the cluster gas and detailed cluster physics. The simulations successfully reproduce the observed morphologies of radio sources in clusters. We find that cluster inhomogeneities and large scale flows have significant impact on the morphology of the radio source and cannot be ignored a-priori when investigating radio source dynamics. Morphological comparison suggests that the gas in the centres of clusters like Virgo and Abell 4059 shows significant shear and/or rotation. We find that shear and rotation in the intra-cluster medium move large amounts of cold material back into the path of the jet, ensuring that subsequent jet outbursts encounter a sufficient column density of gas to couple with the inner cluster gas, thus alleviating the problem of evacuated channels discussed in the recent literature. The same effects redistribute the excess energy Delta_E deposited by the jets, making the distribution of Delta_E at late times consistent with being isotropic.

  17. 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.

  18. 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 current.

  19. Benchmarking of measurement and simulation of transverse rms...

    Office of Scientific and Technical Information (OSTI)

    beams at the GSI UNILAC. In order to define measures to reduce this growth appropriated tools to simulate the beam dynamics are indispensable. This paper is about the benchmarking...

  20. 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.

  1. Architectural Improvements and New Processing Tools for the Open XAL Online Model

    SciTech Connect (OSTI)

    Allen, Christopher K [ORNL; Pelaia II, Tom [ORNL; Freed, Jonathan M [ORNL

    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.

  2. 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.

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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 ? with one for the moist potential temperature ?m=?(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

  4. A new algorithm for contact angle estimation in molecular dynamics simulations

    E-Print Network [OSTI]

    Sumith YD; Shalabh C. Maroo

    2015-05-22

    It is important to study contact angle of a liquid on a solid surface to understand its wetting properties, capillarity and surface interaction energy. While performing transient molecular dynamics (MD) simulations it requires calculating the time evolution of contact angle. This is a tedious effort to do manually or with image processing algorithms. In this work we propose a new algorithm to estimate contact angle from MD simulations directly and in a computationally efficient way. This algorithm segregates the droplet molecules from the vapor molecules using Mahalanobis distance (MND) technique. Then the density is smeared onto a 2D grid using 4th order B-spline interpolation function. The vapor liquid interface data is estimated from the grid using density filtering. With the interface data a circle is fitted using Landau method. The equation of this circle is solved for obtaining the contact angle. This procedure is repeated by rotating the droplet about the vertical axis. We have applied this algorithm to a number of studies (different potentials and thermostat methods) which involves the MD simulation of water.

  5. 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.

  6. 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.

  7. Elements of naturality in dynamical simulation frameworks for Hamiltonian, thermostatic, and Lindbladian flows on classical and quantum state-spaces

    E-Print Network [OSTI]

    Sidles, John A; Jacky, Jonathan P; Picone, Rico A R; Harsila, Scott A

    2010-01-01

    The practical focus of this work is the dynamical simulation of polarization transport processes in quantum spin microscopy and spectroscopy. The simulation framework is built-up progressively, beginning with state-spaces (configuration manifolds) that are geometrically natural, introducing coordinates that are algebraically natural; and finally specifying dynamical potentials that are physically natural; in each respect explicit criteria are given for "naturality." The resulting framework encompasses Hamiltonian flow (both classical and quantum), quantum Lindbladian processes, and classical thermostatic processes. Constructive validation and verification criteria are given for metric and symplectic flows on classical, quantum, and hybrid state-spaces, with particular emphasis to tensor network state-spaces. Both classical and quantum examples are presented, including dynamic nuclear polarization (DNP). A broad span of applications and challenges is discussed, ranging from the design and simulation of quantum...

  8. Is the Calcite-Water Interface Understood? Direct Comparisons of Molecular Dynamics Simulations with Specular X-ray Reflectivity Data

    SciTech Connect (OSTI)

    Fenter, Paul; Kerisit, Sebastien N.; Raiteri, Paolo; Gale, Julian D.

    2013-04-01

    New insights into the structure of the calcite-water interface are obtained through direct model-independent comparison of multiple classical molecular dynamics (MD) simulations with high-resolution specular X-ray reflectivity (XR) data. This set of comparisons, with four different state-of-the-art force fields (including two non-polarizable, one polarizable, and one reactive force field), reveal new insights into the absolute accuracy of the simulated structures and the uniqueness of the XR-derived structural results. These four simulations, while qualitatively similar, have visibly distinct interfacial structure, and are distinguished through a quantitative comparison of the XR signals calculated from these simulations with experimental XR data. The results demonstrate that the simulated calcite-water interface structures, as a whole, are not consistent with the XR data (i.e., within their precision and accuracy). This disagreement is largely due to the simulation of the calcite lattice. The simulated interfacial water profiles show substantially different levels of agreement with the XR data. Of these, the rigid-ion model (RIM) simulations show the best consistency with the experimental XR data. Further model-dependent comparisons of the structural parameters that describe the interfacial structure (derived from both the MD simulations and the XR data) provide further insight into the sources of differences between these two approaches. Using the new insights from the RIM simulations, new structures of the calcite-water interface consistent with both the experimental data and the simulation are identified and compared to recent results.

  9. A comparison of crystalline and molten structures of zirconolite (CaZrTi?O?), a potential plutonium wasteform medium, by molecular dynamics simulation and topological analysis

    E-Print Network [OSTI]

    Rich, Sarah Celeste

    2008-01-01

    Molecular dynamics simulations of the ceramic compound zirconolite (CaZrTi?O?), a potential crystalline wasteform host for plutonium, were carried out for ideal and experimental crystalline forms and a simulated molten ...

  10. Development of EEM based silicon–water and silica–water 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 fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica 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 silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.

  11. Power Parks System Simulation Sandia National Laboratories

    E-Print Network [OSTI]

    , a simulation tool will be very useful in evaluating the systems, and optimizing their performance with respect to efficiency and cost. 1 Proceedings of the 2002 U.S. DOE Hydrogen Program Review NREL/CP-610-32405 #12. Simulink performs dynamic simulation by integrating the system in time using a collection of ordinary

  12. Molecular dynamics simulations of grain boundary thermal resistance in UO2

    SciTech Connect (OSTI)

    Tianyi Chen; Di Chen; Bulent H. Sencer; Lin Shao

    2014-09-01

    By means of molecular dynamics (MD) simulations, we have calculated Kaptiza resistance of UO2 with or without radiation damage. For coincident site lattice boundaries of different configurations, the boundary thermal resistance of unirradiated UO2 can be well described by a parameter-reduced formula by using boundary energies as variables. We extended the study to defect-loaded UO2 by introducing damage cascades in close vicinity to the boundaries. Following cascade annealing and defect migrations towards grain boundaries, the boundary energy increases and so does Kaptiza resistance. The correlations between these two still follow the same formula extracted from the unirradiated UO2. The finding will benefit multi-scale modeling of UO2 thermal properties under extreme radiation conditions by combining effects from boundary configurations and damage levels.

  13. Synchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates

    E-Print Network [OSTI]

    Yasuda, Shugo

    2015-01-01

    The Synchronized Molecular-Dynamics simulation which was recently proposed by authors [Phys. Rev. X {\\bf 4}, 041011 (2014)] is applied to the analysis of polymer lubrication between parallel plates. The rheological properties, conformational change of polymer chains, and temperature rise due to the viscous heating are investigated with changing the values of thermal conductivity of the polymeric liquid. It is found that at a small applied shear stress on the plate, the temperature of polymeric liquid only slightly increases in inverse proportion to the thermal conductivity and the apparent viscosity of polymeric liquid is not much affected by changing the thermal conductivity. However, at a large shear stress, the transitional behaviors of the polymeric liquid occur due to the interplay of the shear deformation and viscous heating by changing the thermal conductivity. This transition is characterized by the Nahme-Griffith number $Na$ which is defined as the ratio of the viscous heating to the thermal conducti...

  14. 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.

  15. 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.

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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

  17. Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers

    SciTech Connect (OSTI)

    Guallar, V.; Batista, V.S.; Miller, W.H. [Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)] [Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    1999-05-01

    An {ital ab initio} excited state potential energy surface is constructed for describing excited state double proton transfer in the tautomerization reaction of photo-excited 7-azaindole dimers, and the ultrafast dynamics is simulated using the semiclassical (SC) initial value representation (IVR). The potential energy surface, determined in a reduced dimensionality, is obtained at the CIS level of quantum chemistry, and an approximate version of the SC-IVR approach is introduced which scales {ital linearly} with the number of degrees of freedom of the molecular system. The accuracy of this approximate SC-IVR approach is verified by comparing our semiclassical results with full quantum mechanical calculations. We find that proton transfer usually occurs during the first intermonomer symmetric-stretch vibration, about 100 fs after photoexcitation of the system, and produces an initial 15 percent population decay of the reactant base-pair, which is significantly reduced by isotopic substitution. {copyright} {ital 1999 American Institute of Physics.} thinsp

  18. 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.

  19. 3.021J / 1.021J / 10.333J / 18.361J / 22.00J Introduction to Modeling and Simulation, Spring 2011

    E-Print Network [OSTI]

    Buehler, Markus

    This subject provides an introduction to modeling and simulation (IM/S), covering continuum methods, atomistic and molecular simulation (e.g. molecular dynamics) as well as quantum mechanics. These tools play an increasingly ...

  20. Polymer segregation under confinement: Free energy calculations and segregation dynamics simulations

    E-Print Network [OSTI]

    James M. Polson; Logan G. Montgomery

    2014-10-09

    Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance between the centers of mass of the polymers, lambda, and examine the effects on the free energy functions of varying the channel diameter D and length L, as well as the polymer length N and bending rigidity, kappa. For infinitely long cylinders, F is a maximum at lambda=0, and decreases with lambda until the polymers are no longer in contact. For flexible chains, the polymers overlap along the cylinder for low lambda, while above some critical value of lambda they are longitudinally compressed and non-overlapping while still in contact. We find that the free energy barrier height, scales as Delta F/k_BT~ND^{-1.93+/-0.01}. In addition, the overlap free energy scales as F/k_BT=Nf(lambda/N;D), where f is a function parameterized by D. For channels of finite L, the free energy barrier height increases with increasing confinement aspect ratio L/D at fixed volume fraction phi, and it decreases with increasing phi at fixed L/D. Increasing the polymer bending rigidity kappa monotonically reduces the overlap free energy. For strongly confined systems, F varies linearly with lambda with a slope that scales as F'(lambda)~-k_BT D^{-beta} P^{-alpha}, where beta approx 2 and alpha approx 0.37 for N=200 chains. These exponent values deviate slightly from those predicted using a simple model, possibly due to insufficiently satisfying the conditions defining the Odijk regime. Finally, we use Monte Carlo dynamics simulations to examine polymer segregation dynamics for fully flexible chains and observe segregation rates that decrease with decreasing entropic force magnitude. The polymers are not conformationally relaxed at later times during segregation.

  1. 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.

  2. Modelling Large Pathways: A Hybrid Agent-Based Discrete Event Simulation Tool for Emergency Medical Services Improvement

    E-Print Network [OSTI]

    Oakley, Jeremy

    -Based Ambulance Service model on Geographical Information System. 3. To develop a Discrete Event Simulation model services. The incorporation of geographical information systems (GIS) can provide precise data Services Improvement Anastasia Anagnostou and Simon Taylor School of Information Systems, Computing

  3. Simulation as a Tool to Develop Guidelines of Envelope Design of a Typical Office Building in Egypt 

    E-Print Network [OSTI]

    Samaan, M.M.; Ahmed, A.N.; Farag, O.M.A.; El-Sayed Khalil, M.

    2011-01-01

    This paper describes the use of building performance simulation software in order to develop guidelines for designing energy-efficient office building. In Egypt energy codes for all building types are being under development. On the other hand...

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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 aroundTL= 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 form (LDL), a less fluidmore »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 temperatureTD= 220 K, for these biopolymers. In the glassy state, belowTD, 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 (?-relaxation) of protein dynamics, which is the logarithmic decay spanning 3 decades (from ps to ns). The long time?-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 substantially in a certain wave vector range when temperature crosses over theTD. Thus the increase of biological activities aboveTDhas positive correlation with activation of slower and large amplitude collective motions of a protein.« less

  5. 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 exchange–correlation functional employed and the way of applying pressure.

  6. 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.

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

    SciTech Connect (OSTI)

    Fröhlich, 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.

  8. Binding kinetics of membrane-anchored receptors and ligands: molecular dynamics simulations and theory

    E-Print Network [OSTI]

    Jinglei Hu; Guang-Kui Xu; Reinhard Lipowsky; Thomas R. Weikl

    2015-11-24

    The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring of the proteins. In this article, we (i) present detailed data for the binding of membrane-anchored proteins from coarse-grained molecular dynamics simulations, and (ii) provide a theory that describes how the binding kinetics depends on the average separation and thermal roughness of the adhering membranes, and on the anchoring, lengths, and length variations of the proteins. An important element of our theory is the tilt of bound receptor-ligand complexes and transition-state complexes relative to the membrane normals. This tilt results from an interplay of the anchoring energy and rotational entropy of the complexes and facilitates the formation of receptor-ligand bonds at membrane separations smaller than the preferred separation for binding. In our simulations, we have considered both lipid-anchored and transmembrane receptor and ligand proteins. We find that the binding equilibrium constant and binding on-rate constant of lipid-anchored proteins are considerably smaller than the binding constant and on-rate constant of rigid transmembrane proteins with identical binding domains.

  9. Homogeneous SPC/E water nucleation in large molecular dynamics simulations

    E-Print Network [OSTI]

    Angelil, R; Tanaka, K; Tanaka, H

    2015-01-01

    We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to $\\sim 4\\cdot 10^6$ molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to $\\sim 10^{19}\\,\\textrm{cm}^{-3}\\textrm{s}^{-1}$, helping close the gap between experimentally measured rates $\\sim 10^{17}\\,\\textrm{cm}^{-3}\\textrm{s}^{-1}$. We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst, a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run avera...

  10. Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding

    E-Print Network [OSTI]

    Guido Tiana; Carlo Camilloni

    2012-07-05

    The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations that build out the transition state is particularly cumbersome, mainly because of the large computational cost of generating a statistically-sound set of folding trajectories. Here we show that a biasing algorithm, based on the physics of the ratchet-and-pawl, can be used to identify efficiently the transition state. The basic idea is that the algorithmic ratchet exerts a force on the protein when it is climbing the free-energy barrier, while it is inactive when it is descending. The transition state can be identified as the point of the trajectory where the ratchet changes regime. Besides discussing this strategy in general terms, we test it within a protein model whose transition state can be studied independently by plain molecular dynamics simulations. Finally, we show its power in explicit-solvent simulations, obtaining and characterizing a set of transition--state conformations for ACBP and CI2.

  11. Self-siphon simulation using molecular dynamics method: a preliminary study

    E-Print Network [OSTI]

    Viridi, Sparisoma; Khotimah, Siti Nurul; Novitrian,; Masterika, Fannia

    2011-01-01

    A self activated siphon, which is also known as self-siphon or self-priming siphon, is simulated using molecular dynamics (MD) method in order to study its behavior, especially why it has a critical height that prevents fluid from flowing through it. The trajectory of the fluid interface with air in front of the flow or the head is also fitted the trajectory modeled by parametric equations s, which is derived from geometry construction of the self-siphon. Numerical equations solved using MD method is derived from equations of motion of the head which is obtained by introducing all considered forces influencing the movement of it. Time duration needed for fluid to pass the entire tube of the self-siphon, {\\tau}, obtained from the simulation is compared quantitatively to the observation data from the previous work and it shows inverse behavior. Length of the three vertical segments are varied independently using a parameter for each segment, which are N5, N3, and N1. Room parameters of N5, N3, and N1 are constr...

  12. Abstract --The simulation of Proton Exchange Membrane Fuel Cells (PEMFC) may work as a powerful tool in the

    E-Print Network [OSTI]

    Simões, Marcelo Godoy

    be included in the fuel cell model. However, the current high costs of the FC stacks make both development tool in the development and widespread testing of alternative energy sources. In order to obtain hydropower), the Fuel Cell (FC) stacks have received heightened attention in the last few years

  13. Molecular-dynamics simulations of thin polyisoprene films confined between amorphous silica substrates

    SciTech Connect (OSTI)

    Guseva, D. V., E-mail: d.v.guseva@tue.nl [Theory of Polymers and Soft Matter, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB, Eindhoven (Netherlands); Physics Department, Chair of Polymer and Crystal Physics, M. V. Lomonosov Moscow State University, 119991 Moscow (Russian Federation); Komarov, P. V. [Department of Theoretical Physics, Tver State University, Sadovyj per. 35, 170002 Tver, Russia and Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova st. 28, 119991 Moscow (Russian Federation)] [Department of Theoretical Physics, Tver State University, Sadovyj per. 35, 170002 Tver, Russia and Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova st. 28, 119991 Moscow (Russian Federation); Lyulin, Alexey V. [Theory of Polymers and Soft Matter, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB, Eindhoven (Netherlands)] [Theory of Polymers and Soft Matter, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB, Eindhoven (Netherlands)

    2014-03-21

    Constant temperature–constant pressure (NpT) molecular-dynamics computer simulations have been carried out for the united-atom model of a non-crosslinked (1,4) cis-polyisoprene (PI) melt confined between two amorphous, fully coordinated silica surfaces. The Lennard-Jones 12-6 potential was implemented to describe the polymer–silica interactions. The thickness H of the produced PI–silica film has been varied in a wide range, 1 < H/R{sub g} < 8, where R{sub g} is the individual PI chain radius of gyration measured under the imposed confinement. After a thorough equilibration, the PI film stratified structure and polymer segmental dynamics have been studied. The chain structure in the middle of the films resembles that in a corresponding bulk, but the polymer-density profile shows a pronounced ordering of the polymer segments in the vicinity of silica surfaces; this ordering disappears toward the film middles. Tremendous slowing down of the polymer segmental dynamics has been observed in the film surface layers, with the segmental relaxation more than 150 times slower as compared to that in a PI bulk. This effect increases with decreasing the polymer-film thickness. The segmental relaxation in the PI film middles shows additional relaxation process which is absent in a PI bulk. Even though there are fast relaxation processes in the film middle, its overall relaxation is slower as compared to that in a bulk sample. The interpretation of the results in terms of polymer glassy bridges has been discussed.

  14. 15.872 System Dynamics II, Fall 2010

    E-Print Network [OSTI]

    Sterman, John

    15.872 is a continuation of 15.871 Introduction to System Dynamics. It emphasizes tools and methods needed to apply systems thinking and simulation modeling successfully in complex real-world settings. The course uses ...

  15. 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 be neglected entirely, and for one IOP, buoyancy production contributes approximately 25% of the total TKE at this location. For both nighttime releases, the contribution of buoyancy to the total TKE budget is always negligible though positive. Results from the simulations provide estimates of the average TKE values in the upwind, downtown, downtown shadow, and urban wake zones of the computational domain. These values suggest that building-induced turbulence can cause the average turbulence intensity in the urban area to increase by as much as much as seven times average 'upwind' values, explaining the minimal role of buoyant forcing in the downtown region. The downtown shadow exhibits an exponential decay in average TKE, while the distant downwind wake region approaches the average upwind values. For long-duration releases in downtown and downtown shadow areas, the assumption of neutral stability is valid because building-induced turbulence dominates the budget. However, further downwind in the urban wake region, which we find to be approximately 1500 m beyond the perimeter of downtown Oklahoma City, the levels of building-induced turbulence greatly subside, and therefore the assumption of neutral stability is less valid.

  16. Dynamic fluid kinetic (DyFK) simulation of auroral ion transport: Synergistic effects of parallel potentials, transverse ion heating, and

    E-Print Network [OSTI]

    Lotko, William

    by the soft electron precipitation to topside altitudes, where the wave-driven transverse ion heating pumps transport, wave heating, hybrid simulation Citation: Wu, X.-Y., J. L. Horwitz, and J.-N. Tu, Dynamic fluid potentials, transverse ion heating, and soft electron precipitation X.-Y. Wu, J. L. Horwitz, and J.-N. Tu

  17. ENS'05 Paris, France, 14-16 December 2005 PROTOTYPING BIO-NANOROBOTS USING MOLECULAR DYNAMIC SIMULATION

    E-Print Network [OSTI]

    Mavroidis, Constantinos

    @coe.neu.edu ABSTRACT This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled the operator can design, characterize and prototype the behavior of bio-nanorobotic components and structures) in their native environment. Their use as elementary bio-nanorobotic components are also simulated and the results

  18. Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

    E-Print Network [OSTI]

    Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations The heat capacity has played a major role in relating microscopic and macroscopic properties of proteins, and configurational averaging. To better understand these factors on calculating a protein heat capacity, we provide

  19. Hypermolecular dynamics simulations of monovacancy X.M. Duan *, D.Y. Sun, X.G. Gong

    E-Print Network [OSTI]

    Gong, Xingao

    Hypermolecular dynamics simulations of monovacancy diusion X.M. Duan *, D.Y. Sun, X.G. Gong@theory.issp.ac.cn (X.M. Duan), dysun@theory.issp.ac.cn (D.Y. Sun), gong@theory.issp.ac.cn (X.G. Gong). 0927 of moving at- oms, which prohibits application to large systems. Very recently, Gong and Wilkins [17

  20. An Energy-Aware Simulation Model and Transaction Protocol for Dynamic Workload Distribution in Mobile Ad Hoc Networks1

    E-Print Network [OSTI]

    Pedram, Massoud

    An Energy-Aware Simulation Model and Transaction Protocol for Dynamic Workload Distribution an undesirable occurrence. Uneven distribution of energy resources and computational workloads is especially for detailed evaluation of the performance of different energy management policies in a MANET. Next it presents

  1. THE JOURNAL OF CHEMICAL PHYSICS 138, 244310 (2013) Molecular dynamics simulations for CO2 spectra. IV. Collisional line-mixing

    E-Print Network [OSTI]

    Boyer, Edmond

    2013-01-01

    atmosphere of Venus (about 96.5% of CO2) where the pressure is high (up to 90 bar). Similarly, narrow involving CO2 with a few for the pure gas in the infrared at high pressure12­17 and Raman Q branches.4THE JOURNAL OF CHEMICAL PHYSICS 138, 244310 (2013) Molecular dynamics simulations for CO2 spectra

  2. A molecular dynamics simulation of the melting points and glass transition temperatures of myo-and neo-inositol

    E-Print Network [OSTI]

    de Gispert, Adrià

    A molecular dynamics simulation of the melting points and glass transition temperatures of myo transition temperature are calculated for myo- and neo-inositol, using the condensed-phase optimized temperatures for myo- and neo-inositol also compare very well to the experimentally obtained data. The glass

  3. Molecular Dynamics Simulation of Heat Transfer Issues of Nanotubes. > Yasuhiro Igarashi, Yuki Taniguchi, Yasushi Shibuta and Shigeo Maruyama

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Molecular Dynamics Simulation of Heat Transfer Issues of Nanotubes. ·> Yasuhiro Igarashi, Yuki 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Heat transfer between single-walled carbon nanotubes, which was 0.105 µm. In other words, when the length of SWNT is 0.105 µm, the radial heat transfer

  4. Development of a Simplified Simulation Tool for High Performance K-5 Schools in Hot and Humid Climates 

    E-Print Network [OSTI]

    Im, P.; Haberl, J. S.

    2008-01-01

    hourly building energy usage: The great energy predictor shootout-overview and discussion of results. ASHRAE Transactions 100(2):1104-1118. Perkins, B. 2001. Building type basics for elementary and secondary schools, John Wiley & Sons, INC. New York... are developed, this tool is intended to be used to estimate building energy consumption with limited information about the school building. This paper reports on the classification scheme and automatic building shape generator, as well as preliminary results...

  5. Development and simulation of a cylindrical cusped-field thruster and a diagnostics tool for plasma-materials interactions

    E-Print Network [OSTI]

    Pang, Anthony

    2013-01-01

    A low power, Hall-effect type plasma thruster known as the MIT-Cylindrical Cusped- Field Thruster (MIT-CCFT) has been developed and simulated using a fully-kinetic plasma model, the Plasma Thruster particle-in-cell (PTpic) ...

  6. To create a Virtual Design Environment, leveraging tools from musculoskeletal analysis, optimization, simulation-based design, that

    E-Print Network [OSTI]

    Krovi, Venkat

    Systems. How to evaluate the effects of ergonomics & regimen for a rehabilitation program? How to refine, optimization, simulation-based design, that will permit a therapist to systematically and rapidly evaluate of such functional interactions are geometric placementgeometric placement of useruser-- device (ergonomics

  7. STRUCTURAL VALIDATION OF SYSTEM DYNAMICS AND AGENT-BASED SIMULATION MODELS

    E-Print Network [OSTI]

    Tesfatsion, Leigh

    , population dynamics, energy systems, and urban planning. The usefulness of these models is predicated including global warming, population dynamics, energy systems, and urban planning simply defy a face

  8. 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.

  9. Synchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates

    E-Print Network [OSTI]

    Shugo Yasuda; Ryoichi Yamamoto

    2015-03-25

    The Synchronized Molecular-Dynamics simulation which was recently proposed by authors [Phys. Rev. X {\\bf 4}, 041011 (2014)] is applied to the analysis of polymer lubrication between parallel plates. The rheological properties, conformational change of polymer chains, and temperature rise due to the viscous heating are investigated with changing the values of thermal conductivity of the polymeric liquid. It is found that at a small applied shear stress on the plate, the temperature of polymeric liquid only slightly increases in inverse proportion to the thermal conductivity and the apparent viscosity of polymeric liquid is not much affected by changing the thermal conductivity. However, at a large shear stress, the transitional behaviors of the polymeric liquid occur due to the interplay of the shear deformation and viscous heating by changing the thermal conductivity. This transition is characterized by the Nahme-Griffith number $Na$ which is defined as the ratio of the viscous heating to the thermal conduction at a characteristic temperature. When the Nahme-Griffith number exceeds the unity, the temperature of polymeric liquid increases rapidly and the apparent viscosity also exponentially decreases as the thermal conductivity decreases. The conformation of polymer chains is stretched and aligned by the shear flow for $Na1$.

  10. 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.

  11. Segregated structure of ring polymer melts near the surface: Molecular dynamics simulation study

    E-Print Network [OSTI]

    Eunsang Lee; YounJoon Jung

    2015-10-20

    We study structural properties of a ring polymeric melt confined in a film in comparison to a linear counterpart using molecular dynamics simulations. Local structure orderings of ring and linear polymers in the vicinity of the surface are similar to each other because the length scale of surface-monomer excluded volume interaction is smaller than the size of an ideal blob of the ring. In a long length scale, while the Silberberg hypothesis can be used to provide a physical origin of confined linear polymer results, it no longer holds for a ring polymer case. We also present different structural properties of ring and linear polymers in a melt, including the size of polymers, an adsorbed amount, and the coordination number of a polymer. Our observation reveals that a confined ring in a melt adopts highly segregated conformation due to a topological excluded volume repulsion, which may provide a new perspective to understand the nature of biological processes, such as territorial segregation of chromosomes in eukaryotic nuclei.

  12. Use of a dynamic simulation model to understand nitrogen cycling in the middle Rio Grande, NM.

    SciTech Connect (OSTI)

    Meixner, Tom (University of Arizona, Tucson, AZ); Tidwell, Vincent Carroll; Oelsner, Gretchen (University of Arizona, Tucson, AZ); Brooks, Paul (University of Arizona, Tucson, AZ); 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.

  13. 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.

  14. Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach

    SciTech Connect (OSTI)

    Hyeon-Deuk, Kim; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 ; 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.

  15. A Study of UO2 Grain Boundary Structure and Thermal Resistance Change under Irradiation using Molecular Dynamics Simulations 

    E-Print Network [OSTI]

    Chen, Tianyi

    2013-08-02

    OF UO2 GRAIN BOUNDARY STUCTURE AND THERMAL RESISTANCE CHANGE UNDER IRRADIATION USING MOLECULAR DYNAMICS SIMULATIONS A Thesis by TIANYI CHEN Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment...] As the fuel expands to reach the cladding, the fuel cladding interaction begins to draw attention. The first thing is the fuel/cladding mechanical interaction. This phenomenon is very serious in early designed reactors since they do not have enough spaces...

  16. Simulation of hydrology and population dynamics of Anopheles mosquitoes around the Koka Reservoir in Ethiopia

    E-Print Network [OSTI]

    Endo, Noriko S.M. Massachusetts Institute of Technology

    2014-01-01

    This thesis applies the HYDRology, Entomology and MAlaria Transmission Simulator (HYDREMATS) to the environment around a water resources reservoir in Ethiopia. HYDREMATS was modified to simulate the local hydrology and the ...

  17. A Robust Four-Fluid Transient Flow Simulator as an Analysis and Decision Making Tool for Dynamic Kill Operation 

    E-Print Network [OSTI]

    Haghshenas, Arash

    2013-04-24

    The worst scenario of drilling operation is blowout which is uncontrolled flow of formation fluid into the wellbore. Blowouts result in environmental damage with potential risk of injuries and fatalities. Although not all blowouts result in disaster...

  18. 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 ?}.

  19. Design and Simulation for Architectural Geometry Figure 1: Daytime and nighttime scenes of designed roof by using the developed computational tools

    E-Print Network [OSTI]

    roof by using the developed computational tools 031.PDF Keywords: Architectural Geometry, Procedural an innovative computational design tool used to edit architectural geometry interactively and demonstrates the process of designing geometry using the developed tool. The background, related work, implementation

  20. A comparison of neutron scattering studies and computer simulations of polymer melts

    E-Print Network [OSTI]

    Utah, University of

    A comparison of neutron scattering studies and computer simulations of polymer melts G.D. Smith a; in ®nal form 22 May 2000 Abstract Neutron scattering and computer simulations are powerful tools in particular. When neutron scattering studies and quan- titative atomistic molecular dynamics simulations

  1. Matching Law Visualization Tool

    E-Print Network [OSTI]

    Reed, Derek D.

    2015-05-15

    , the matching law remains an elusive principle to students of behavior analysis lacking requisite training in quantitative analyses. This simulation tool is intended to visually describe how manipulations of the parameters of the quantitative models modulate...

  2. DEVELOPMENT OF A QUANTITATIVE MEASURE OF THE FUNCTIONALITY OF FRAME WALLS ENHANCED WITH PHASE CHANGE MATERIALS USING A DYNAMIC WALL SIMULATOR

    E-Print Network [OSTI]

    Evers, Angela C.

    2008-07-25

    Frame walls enhanced with phase change materials (paraffin-based, hydrated salt-based, and eutectic) mixed in cellulose insulation were developed and tested. The frame walls were heated and allowed to cool in a dynamic wall simulator that replicated...

  3. 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.

  4. 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.

  5. Fire dynamics during the 20th century simulated by the Community Land Model

    E-Print Network [OSTI]

    2010-01-01

    contemporary fire car- bon emissions to satellite-basedon the simulated fire car- bon emissions to explain thedeforestation) fire car- bon emissions were between 2.0 and

  6. Dynamics in a supercooled molecular liquid: Theory and simulations Adele Rinaldi, Francesco Sciortino, and Piero Tartaglia

    E-Print Network [OSTI]

    Sciortino, Francesco

    , computer simulations are starting to provide a detailed pic- ture of the structure of the potential energy; published 22 May 2001 We report extensive simulations of liquid supercooled states for a simple three precisely in a large q-vector range self-correlation and collective correlation functions, providing a clean

  7. Software interoperability for energy simulation

    E-Print Network [OSTI]

    Hitchcock, Robert J.

    2002-01-01

    Tools,” in Building Energy Simulation User News, Vol. 22,Interoperability for Energy Simulation Robert J. Hitchcock,Interoperability for Energy Simulation Robert J. Hitchcock,

  8. Anharmonic lattice dynamics of Ag2O studied by inelastic neutron scattering and first-principles molecular dynamics simulations

    SciTech Connect (OSTI)

    Lan, Tian [California Institute of Technology, Pasadena] [California Institute of Technology, Pasadena; Li, Chen [ORNL] [ORNL; Niedziela, Jennifer L [ORNL] [ORNL; Smith, Hillary [California Institute of Technology, Pasadena] [California Institute of Technology, Pasadena; Abernathy, Douglas L [ORNL] [ORNL; Rossman, George [California Institute of Technology, Pasadena] [California Institute of Technology, Pasadena; Fultz, B. [California Institute of Technology, Pasadena] [California Institute of Technology, Pasadena

    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.

  9. 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.

  10. Femtosecond photoelectron spectroscopy of the I{sub 2}{sup {minus}} anion: A semiclassical molecular dynamics simulation method

    SciTech Connect (OSTI)

    Batista, V.S.; Zanni, M.T.; Greenblatt, B.J.; Neumark, D.M.; Miller, W.H. [Department of Chemistry, University of California, Berkeley, California 94720 (United States)] [Department of Chemistry, University of California, Berkeley, California 94720 (United States); [Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    1999-02-01

    In this paper we describe a new semiclassical method for simulating femtosecond pump{endash}probe photoelectron spectroscopy, and its implementation to study the excited state photodissociation dynamics of the I{sub 2}{sup {minus}} anion. Our algorithm involves a forward{endash}backward (FB) semiclassical (SC) initial value representation (IVR) method for calculating the time dependent photodetachment spectrum P({epsilon},{Delta}t) as a function of the kinetic energy {epsilon} of the photodetached electron and the delay time {Delta}t between the pump and probe pulses. We describe the radiation-chromophore interaction perturbatively to first order in both pulse fields, assuming the Condon approximation for the electronic transition dipole moments. Our computed spectra are in excellent agreement with full quantum mechanical simulations. {copyright} {ital 1999 American Institute of Physics.}

  11. Study of iron structure stability in high temperature molten lead-bismuth eutectic with oxygen injection using molecular dynamics simulation

    SciTech Connect (OSTI)

    Arkundato, Artoto [Physics Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Su'ud, Zaki [Physics Department, Faculty of Mathematical and Natural Sciences, Bandung Institute of Technology, Jl. Ganesha 10, Bandung (Indonesia); Sudarko [Chemistry Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Shafii, Mohammad Ali [Physics Department, Faculty of Mathematical and Natural Sciences, Andalas University, Padang (Indonesia); Celino, Massimo [ENEA, CR Casaccia, Via Anguillarese 301, Rome (Italy)

    2014-09-30

    Corrosion of structural materials in high temperature molten lead-bismuth eutectic is a major problem for design of PbBi cooled reactor. One technique to inhibit corrosion process is to inject oxygen into coolant. In this paper we study and focus on a way of inhibiting the corrosion of iron using molecular dynamics method. For the simulation results we concluded that effective corrosion inhibition of iron may be achieved by injection 0.0532 wt% to 0.1156 wt% oxygen into liquid lead-bismuth. At this oxygen concentration the structure of iron material will be maintained at about 70% in bcc crystal structure during interaction with liquid metal.

  12. 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.

  13. Stokesian dynamic simulations and analyses of interfacial and bulk colloidal fluids 

    E-Print Network [OSTI]

    Anekal, Samartha Guha

    2006-10-30

    , and hydrodynamic forces to model dynamics of colloidal dispersions. In addition, we develop theoretical expressions for quantifying self-diffusion in colloids interacting via different particle-particle and particle-wall potentials. Specifically, we have used...

  14. An innovative dynamic bus lane system and its simulation-based performance investigation

    E-Print Network [OSTI]

    Yang, Hong

    The strategy of exempting bus from other traffic through exclusive bus lanes (XBL) is prevalent. Rather than just deploying the XBL system, in this study, a new innovative dynamic bus lane (DBL) operation system which is ...

  15. FAST STATIC AND DYNAMIC GRID LEVEL THERMAL SIMULATION CONSIDERING TEMPERATURE DEPENDENT THERMAL CONDUCTIVITY OF SILICON

    E-Print Network [OSTI]

    Ziabari, Amirkoushyar

    2012-01-01

    Power Blurring: Fast Chip-Level Static and Transient ThermalOF CALIFORNIA SANTA CRUZ FAST STATIC AND DYNAMIC GRID LEVEL3.3.3 A Static Case Study………………………………………………. 3.3.4 Transient

  16. Development of dynamic models of reactive distillation columns for simulation and determination of control 

    E-Print Network [OSTI]

    Chakrabarty, Arnab

    2005-02-17

    variables were simulated. The data generated by the step responses was used for fitting transfer functions between the manipulated and the controlled variables. RGA analysis was performed to find the optimal pairing for controller design. Feedback...

  17. Development of a Robotic Simulation Platform for Spacecraft Proximity Operations and Contact Dynamics Experiments 

    E-Print Network [OSTI]

    Probe, Austin Breien

    2013-12-03

    launch opportunities for verification and validation. A ground facility with the capability for six degree-of-freedom robotic spacecraft emulation that enables laboratory-based hardware-in-the-loop experiments is desired, to allow for the simulation...

  18. NuFact'11 Aug. 4, 2011 1 Simulation of Dynamic Interaction of

    E-Print Network [OSTI]

    McDonald, Kirk

    : Modeling of cavitation bubbles during disruption of the Hg Jet/Pool LS-Dyna simulations: #12;NuFact'11 Aug described numerically (user input into LS-DYNA) Incorporate all effects (hydrodynamic, beam, solenoid field

  19. NuFact'11 Aug. 3, 2011 1 Simulation of Dynamic Interaction of

    E-Print Network [OSTI]

    McDonald, Kirk

    Challenge: Modeling of cavitation bubbles during disruption of the Hg Jet/Pool LS-Dyna simulations: #12;Nu described numerically (user input into LS-DYNA) Incorporate all effects (hydrodynamic, beam, solenoid field

  20. Transport properties of CO2-expanded acetonitrile from molecular dynamics simulations

    E-Print Network [OSTI]

    Houndonougbo, Yao; Laird, Brian Bostian; Kuczera, Krzysztof

    2007-02-21

    Carbon-dioxide-expanded liquids, which are mixtures of organic liquids and compressed CO2, are novel media used in chemical processing. The authors present a molecular simulation study of the transport properties of liquid mixtures formed...

  1. Dynamic simulation of heart mitral valve with transversely isotropic material model

    E-Print Network [OSTI]

    Weinberg, Eli, 1979-

    2005-01-01

    This thesis develops two methods for simulating, in the finite element setting, the material behavior of heart mitral valve leaflet tissue. First, a mixed pressure-displacement formulation is used to implement the constitutive ...

  2. Collision dynamics of two barchan dunes simulated by a simple model

    E-Print Network [OSTI]

    Atsunari Katsuki; Hiraku Nishimori; Noritaka Endo; Keisuke Taniguchi

    2004-12-24

    The collision processes of two crescentic dunes called barchans are systematically studied using a simple computer simulation model. The simulated processes, coalescence, ejection and reorganization, qualitatively correspond to those observed in a water tank experiment. Moreover we found the realized types of collision depend both on the mass ratio and on the lateral distance between barchans under initial conditions. A simple set of differential equations to describe the collision of one-dimensional (1D) dunes is introduced.

  3. 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.

  4. 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.

  5. Real time dynamics and proposal for feasible experiments of lattice gauge-Higgs model simulated by cold atoms

    E-Print Network [OSTI]

    Yoshihito Kuno; Kenichi Kasamatsu; Yoshiro Takahashi; Ikuo Ichinose; Tetsuo Matsui

    2015-06-05

    Lattice gauge theory has provided a crucial non-perturbative method in studying canonical models in high-energy physics such as quantum chromodynamics. Among other models of lattice gauge theory, the lattice gauge-Higgs model is a quite important one because it describes wide variety of phenomena/models related to the Anderson-Higgs mechanism such as superconductivity, the standard model of particle physics, and inflation process of the early universe. In this paper, we first show that atomic description of the lattice gauge model allows us to explore real time dynamics of the gauge variables by using the Gross-Pitaevskii equations. Numerical simulations of the time development of an electric flux reveal some interesting characteristics of dynamical aspect of the model and determine its phase diagram. Next, to realize a quantum simulator of the U(1) lattice gauge-Higgs model on an optical lattice filled by cold atoms, we propose two feasible methods: (i) Wannier states in the excited bands and (ii) dipolar atoms in a multilayer optical lattice. We pay attentions to respect the constraint of Gauss's law and avoid nonlocal gauge interactions.

  6. 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.

  7. ECE 432/532 Dynamics of Electromechanical Energy Conversion Catalog Description: Generalized machine theory. Techniques for dynamic analysis of

    E-Print Network [OSTI]

    drives Transfer functions and basic control theory Electric machine and drives simulation Measurable of electrical machines (ABET Outcomes A, c, E, K) 6. Use high level simulation tools for machine analysis (ABET machine theory. Techniques for dynamic analysis of electromechanical machines: dq representations

  8. Supplemental Simulation Case Studies of Dynamic Evaporator Modeling Paradigms with Variable Fluid Phases 

    E-Print Network [OSTI]

    Rodriguez, E.; Rasmussen, B.

    2015-01-01

    at Texas A&M University, College Station, TX 77843-3123, USA 2Associate Professor in the Department of Mechanical Engineering at Texas A&M University, College Station, TX 77843- 3123, USA June 1, 2015 DRAFT ESL-TR-15-06-01 2TABLE I: Operating Conditions... Simulation time (s) 400 Simulation step size (s) 0.01 Solver Fourth Order Runge-Kutta June 1, 2015 DRAFT ESL-TR-15-06-01 3A. Length Threshold Analysis Fig. 1: Comparison of minimum normalized threshold length, leps, for enthalpy based SMB model - Case 1a June...

  9. July 26 NuFACT Target Meeting 1 Simulation of Dynamic Interaction of the Neutrino Factory

    E-Print Network [OSTI]

    McDonald, Kirk

    pulses will be arriving, interacting with Hg jet and Hg pool (+ Jet interacting with pool How does the Hg phase diagram and introduce it to codes such as LS-DYNA Energy Deposition introduction into Hg jet/pool Dynamics and Hg Jet/Pool #12;July 26 NuFACT Target Meeting 13 Local pressure outside formed bubble can

  10. 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.

  11. Dynamic Simulation of Splashing Fluids James F. O'Brien and Jessica K. Hodgins

    E-Print Network [OSTI]

    O'Brien, James F.

    with natural phenomena that are remarkable in their form and movements: a tree blow- ing in the wind, lightning us- ing dynamic models of the fluid and the impacting object. imaginary physical laws of the animated of the computational cost increases with the cube of the model's resolutio

  12. PHYSICAL REVIEW E 91, 062304 (2015) Glassy dynamics of athermal self-propelled particles: Computer simulations

    E-Print Network [OSTI]

    Berthier, Ludovic

    2015-01-01

    motivation stems from the nonequilibrium nature of active systems that are driven by internal, nonthermal-propulsion is increased, the local structure becomes more pronounced, whereas the long-time dynamics first accelerates]. Recently, the collective behavior of systems consisting of interacting self-propelled particles attracted

  13. Rate constants from the reaction path Hamiltonian. I. Reactive flux simulations for dynamically correct rates

    E-Print Network [OSTI]

    Bell, Alexis T.

    As ab initio electronic structure calculations become more accurate, inherent sources of error, facilitate reactive flux calculations. As an example we compute the dynamically corrected rate constant on which the reaction occurs. A large number of electronic structure theo- ries are available

  14. Molecular Dynamics Simulations of Supported Pt Nanoclusters with Sutton-Chen Potentials

    E-Print Network [OSTI]

    Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group

    -time ab-initio calculations may provide fundamental insight into the dynamical electronic and physical structure of catalytic nanoparticles, yet these calculations can prove to be extremely computationally structural disorder, negative thermal expan- sion, and thermally induced changes in electronic struc- ture.3

  15. Computational fluid dynamic simulations of chemical looping fuel reactors utilizing gaseous fuels

    SciTech Connect (OSTI)

    Mahalatkar, K.; Kuhlman, J.; Huckaby, E.D.; O'Brien, T.

    2011-01-01

    A computational fluid dynamic(CFD) model for the fuel reactor of chemical looping combustion technology has been developed,withspecialfocusonaccuratelyrepresentingtheheterogeneous chemicalreactions.Acontinuumtwo-fluidmodelwasusedtodescribeboththegasandsolidphases. Detailedsub-modelstoaccountforfluid–particleandparticle–particleinteractionforceswerealso incorporated.Twoexperimentalcaseswereanalyzedinthisstudy(Son andKim,2006; Mattisonetal., 2001). SimulationswerecarriedouttotestthecapabilityoftheCFDmodeltocapturechangesinoutletgas concentrationswithchangesinnumberofparameterssuchassuperficialvelocity,metaloxide concentration,reactortemperature,etc.Fortheexperimentsof Mattissonetal.(2001), detailedtime varyingoutletconcentrationvalueswerecompared,anditwasfoundthatCFDsimulationsprovideda reasonablematchwiththisdata.

  16. A non-stationary model for simulating the dynamics of ocular aberrations

    E-Print Network [OSTI]

    Dainty, Chris

    Signal Processing and Signal Modeling (Wiley Series in Telecommunications and Signal Processing, 2001). 2 of aberration components in the human eye," In IEEE Signal Process. Workshop Statist. pages 241-244 (2001). 12 and retinal image quality due to tear film dynamics," Opt. Express 14, 12552-12559 (2006). 18. L. Rankine, N

  17. 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.

  18. Dynamic Simulation and Analysis of Heating Energy Consumption in a Residential Building 

    E-Print Network [OSTI]

    Liu, J.; Yang, M.; Zhao, X.; Zhu, N.

    2006-01-01

    In winter, much of the building energy is used for heating in the north region of China. In this study, the heating energy consumption of a residential building in Tianjin during a heating period was simulated by using the EnergyPlus energy...

  19. Fire dynamics during the 20th century simulated by the Community Land Model

    E-Print Network [OSTI]

    Kloster, S.; Mahowald, N. M.; Randerson, J. T.; Thornton, P. E.; Hoffman, F. M.; Levis, Samuel; Lawrence, Peter J.; Feddema, Johannes J.; Oleson, Keith W.; Lawrence, David M.

    2010-01-01

    on the work by Arora and Boer (2005). We obtained substantial improvement when we explicitly considered human caused ignition and fire suppression as a function of population density. Simulated fire carbon emissions ranged between 2.0 and 2.4 Pg C...

  20. Computational Fluid Dynamics Simulation of Green Water Around a Two-dimensional Platform 

    E-Print Network [OSTI]

    Zhao, Yucheng

    2010-07-14

    An interface-preserving level set method is incorporated into the Reynolds-Averaged Navier-Stokes (RANS) numerical method to simulate the application of the green water phenomena around a platform and the breaking wave above the deck. In the present...

  1. Brownian dynamics simulations of reversible reactions in one dimension Arieh L. Edelstein and Noam Agmon

    E-Print Network [OSTI]

    Agmon, Noam

    concentration-independent power is predicted only with a modified preexponent. Random-walk simulations in one decays as a power law, Atma, with time.22 The power a is d/2, where d is the spatial dimensionality dimension'3'6 have produced a of approximately 0.5. In contrast, experimental results of Huppert and co

  2. Integrating Models and Simulations of Continuous Dynamics into SysML

    E-Print Network [OSTI]

    In this paper, we combine modeling constructs from SysML and Modelica to improve the support for Model, structures, functions, and behaviors. Complementing these SysML constructs, the Modelica language has emerged and the corresponding Modelica models; and the integration of simulation experiments with other SysML constructs

  3. 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.

  4. Charge conductivity in peptides: Dynamic simulations of a bifunctional model supporting experimental data

    E-Print Network [OSTI]

    Sheu, Sheh-Yi

    simulations of transport, a model of extreme transduction efficiency. It ex- plains the high efficiency- bution peaked at about 140 fs, in close agreement with our direct femtosecond measurements. In logic gate language this is a strongly conducting ON state resulting from small firing energies, the system otherwise

  5. Energy dynamics in a simulation of LAPD turbulence B. Friedman,1,a)

    E-Print Network [OSTI]

    Carter, Troy

    in a 3D fluid simulation of drift wave turbulence in the linear Large Plasma Device [W. Gekelman et al of magnetically confined plasmas that neglect stable branches of the linear dispersion relation often miss details, USA 3 Department of Physics, University of York, Heslington, York YO10 5DD, United Kingdom (Received 5

  6. Effects of macroH2A and H2A.Z on nucleosome structure and dynamics as elucidated by molecular dynamics simulations

    E-Print Network [OSTI]

    Bowerman, Samuel

    2015-01-01

    Eukaryotes tune the transcriptional activity of their genome by altering the nucleosome core particle through multiple chemical processes. In particular, replacement of the canonical H2A histone with the variants macroH2A and H2A.Z has been shown to affect DNA accessibility and nucleosome stability; however, the processes by which this occurs remain poorly understood. Here, we elucidate the molecular mechanisms of these variants with an extensive molecular dynamics study of the canonical nucleosome along with three variant-containing structures: H2A.Z, macroH2A, and an H2A mutant with macroH2A-like L1 loops. Simulation results show that variant L1 loops play a pivotal role in stabilizing DNA binding to the octamer through direct interactions, core structural rearrangements, and altered allosteric networks in the nucleosome. All variants influence dynamics; however, macroH2A-like systems have the largest effect on energetics. In addition, we provide a comprehensive analysis of allosteric networks in the nucleo...

  7. 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

    Funded by the DOE grant (i) we continued to study and analyze the atomistic detail of the electron transfer (ET) across the chromophore-TiO2 interface in Gratzel cell systems for solar hydrogen production. (ii) We extensively investigated the nature of photoexcited states and excited state dynamics in semiconductor quantum dots (QD) designed for photovoltaic applications. (iii) We continued a newly initiated research direction focusing on excited state properties and electron-phonon interactions in nanoscale carbon materials. Over the past year, the results of the DOE funded research were summarized in 3 review articles. 12 original manuscripts were written. The research results were reported in 28 invited talks at conferences and university seminars. 20 invitations were accepted for talks in the near future. 2 symposia at national and international meetings have being organized this year on topics closely related to the DOE funded project, and 2 more symposia have been planned for the near future. We summarized the insights into photoinduced dynamics of semiconductor QDs, obtained from our time-domain ab initio studies. QDs exhibit both molecular and bulk properties. Unlike either bulk or molecular materials, QD properties can be modified continuously by changing QD shape and size. However, the chemical and physical properties of molecular and bulk materials often contradict each other, which can lead to differing viewpoints about the behavior of QDs. For example, the molecular view suggests strong electron-hole and charge-phonon interactions, as well as slow energy relaxation due to mismatch between electronic energy gaps and phonon frequencies. In contrast, the bulk view advocates that the kinetic energy of quantum confinement is greater than electron-hole interactions, that charge-phonon coupling is weak, and that the relaxation through quasi-continuous bands is rapid. By synthesizing the bulk and molecular viewpoints, we clarified the controversies and 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 excitations. Conduction and valence band transitions that are not available in neutral NCs dominate

  8. Simulation of Particle Size Effect on Dynamic Properties and Fracture of PTFE-W-Al Composites

    E-Print Network [OSTI]

    E. B. Herbold; J. Cai; D. J. Benson; V. F. Nesterenko

    2007-08-09

    Recent investigations of the dynamic compressive strength of cold isostatically pressed composites of polytetrafluoroethylene (PTFE), tungsten (W) and aluminum (Al) powders show significant differences depending on the size of metallic particles. The addition of W increases the density and overall strength of the sample. To investigate relatively large deformations multi-material Eulerian and arbitrary Lagrangian-Eulerian methods, which have the ability to efficiently handle the formation of free surfaces, were used. The calculations indicate that the increased strength of the sample with fine metallic particles is due to the formation of force chains under dynamic loading. This phenomenon occurs even at larger porosity of the PTFE matrix in comparison with samples with larger particle size of W and higher density of the PTFE matrix.

  9. Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code

    SciTech Connect (OSTI)

    Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

    1980-04-01

    This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability.

  10. 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.

  11. 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)

  12. Structural, vibrational, and elastic properties of a calcium aluminosilicate glass from molecular dynamics simulations: The role of the potential

    SciTech Connect (OSTI)

    Bauchy, M., E-mail: bauchy@mit.edu [Concrete Sustainability Hub, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA and Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095 (United States)

    2014-07-14

    We study a calcium aluminosilicate glass of composition (SiO{sub 2}){sub 0.60}(Al{sub 2}O{sub 3}){sub 0.10}(CaO){sub 0.30} by means of molecular dynamics. To this end, we conduct parallel simulations, following a consistent methodology, but using three different potentials. Structural and elastic properties are analyzed and compared to available experimental data. This allows assessing the respective abilities of the potentials to produce a realistic glass. We report that, although all these potentials offer a reasonable glass structure, featuring tricluster oxygen atoms, their respective vibrational and elastic predictions differ. This allows us to draw some general conclusions about the crucial role, or otherwise, of the interaction potential in silicate systems.

  13. Experiments and finite element simulations on micro-milling of Ti6Al4V alloy with uncoated and cBN coated micro-tools

    E-Print Network [OSTI]

    Ozel, Tugrul

    BN coated micro-tools T. O¨ zel (2)a, *, T. Thepsonthi a , D. Ulutan a , B. Kaftanoglu (1)b a Manufacturing. In these micro-tools, sharp cutting edges cannot be fabricated due to the limited edge strength; hence often of titanium alloys [8] and particularly advantages of cubic boron nitrite (cBN) coatings in cutting of Ti­6Al

  14. Fire dynamics during the 20th century simulated by the Community Land Model

    SciTech Connect (OSTI)

    Kloster, Silvia [Cornell University; Mahowald, Natalie [Cornell University; Randerson, Jim [University of California, Irvine; Thornton, Peter E [ORNL; Hoffman, Forrest M [ORNL; Levis, Sam [National Center for Atmospheric Research (NCAR); Lawrence, Peter J. [National Center for Atmospheric Research (NCAR); Feddema, Johan J. [University of Kansas; Oleson, Keith [National Center for Atmospheric Research (NCAR); Lawrence, David M. [National Center for Atmospheric Research (NCAR)

    2011-01-01

    Fire is an integral Earth System process that interacts with climate in multiple ways. Here we assessed the parametrization of fires in the Community Land Model (CLM-CN) and improved the ability of the model to reproduce contemporary global patterns of burned areas and fire emissions. In addition to wildfires we extended CLM-CN to account for fires related to deforestation. We compared contemporary fire carbon emissions predicted by the model to satellite-based estimates in terms of magnitude and spatial extent as well as interannual and seasonal variability. Long-term trends during the 20th century were compared with historical estimates. Overall we found the best agreement between simulation and observations for the fire parametrization based on the work by Arora and Boer (2005). We obtained substantial improvement when we explicitly considered human caused ignition and fire suppression as a function of population density. Simulated fire carbon emissions ranged between 2.0 and 2.4 Pg C/year for the period 1997 2004. Regionally the simulations had a low bias over Africa and a high bias over South America when compared to satellite-based products. The net terrestrial carbon source due to land use change for the 1990s was 1.2 Pg C/year with 11% stemming from deforestation fires. During 2000 2004 this flux decreased to 0.85 Pg C/year with a similar relative contribution from deforestation fires. Between 1900 and 1960 we predicted a slight downward trend in global fire emissions caused by reduced fuels as a consequence of wood harvesting and also by increases in fire suppression. The model predicted an upward trend during the last three decades of the 20th century as a result of climate variations and large burning events associated with ENSO-induced drought conditions.

  15. 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.

  16. Superstatistical velocity distributions of cold trapped ions in molecular dynamics simulations

    E-Print Network [OSTI]

    Rouse, I

    2015-01-01

    We present a realistic molecular-dynamics treatment of laser-cooled ions in radiofrequency ion traps which avoids previously made simplifications such as modeling laser cooling as a friction force and combining individual heating mechanisms into a single effective heating force. Based on this implementation, we show that infrequent energetic collisions of single ions with background gas molecules lead to pronounced heating of the entire ion ensemble and a time-varying secular ensemble temperature which manifests itself in a superstatistical time-averaged velocity distribution of the ions. The effect of this finding on the experimental determination of ion temperatures and rate constants for cold chemical reactions is discussed.

  17. 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.

  18. Molecular dynamics simulations of water confined between matched pairs of hydrophobic and hydrophilic self-assembled monolayers.

    SciTech Connect (OSTI)

    Chandross, Michael Evan; Grest, Gary Stephen; Lane, J. Matthew D.; Lorenz, Christian Douglas (King's College London, London, UK); Stevens, Mark Jackson

    2008-12-01

    We have conducted a molecular dynamics (MD) simulation study of water confined between methyl-terminated and carboxyl-terminated alkylsilane self-assembled monolayers (SAMs) on amorphous silica substrates. In doing so, we have investigated the dynamic and structural behavior of the water molecules when compressed to loads ranging from 20 to 950 MPa for two different amounts of water (27 and 58 water molecules/nm{sup 2}). Within the studied range of loads, we observe that no water molecules penetrate the hydrophobic region of the carboxyl-terminated SAMs. However, we observe that at loads larger than 150 MPa water molecules penetrate the methyl-terminated SAMs and form hydrogen-bonded chains that connect to the bulk water. The diffusion coefficient of the water molecules decreases as the water film becomes thinner and pressure increases. When compared to bulk diffusion coefficients of water molecules at the various loads, we found that the diffusion coefficients for the systems with 27 water molecules/nm{sup 2} are reduced by a factor of 20 at low loads and by a factor of 40 at high loads, while the diffusion coefficients for the systems with 58 water molecules/nm{sup 2} are reduced by a factor of 25 at all loads.

  19. 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.

  20. Effect of bound state of water on hydronium ion mobility in hydrated Nafion using molecular dynamics simulations

    SciTech Connect (OSTI)

    Mabuchi, Takuya, E-mail: mabuchi@nanoint.ifs.tohoku.ac.jp [Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8577 (Japan); Tokumasu, Takashi [Institute of Fluid Science, Tohoku University, Sendai, Miyagi 980-8577 (Japan)

    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.

  1. Lithium Ion Transport Mechanism in Ternary Polymer Electrolyte-Ionic Liquid Mixtures - A Molecular Dynamics Simulation Study

    E-Print Network [OSTI]

    Diddo Diddens; Andreas Heuer

    2013-02-20

    The lithium transport mechanism in ternary polymer electrolytes, consisting of PEO/LiTFSI and various fractions of the ionic liquid N-methyl-N-propylpyrrolidinium bis(trifluoromethane)sulfonimide, are investigated by means of MD simulations. This is motivated by recent experimental findings [Passerini et al., Electrochim. Acta 2012, 86, 330-338], which demonstrated that these materials display an enhanced lithium mobility relative to their binary counterpart PEO/LiTFSI. In order to grasp the underlying microscopic scenario giving rise to these observations, we employ an analytical, Rouse-based cation transport model [Maitra at al., PRL 2007, 98, 227802], which has originally been devised for conventional polymer electrolytes. This model describes the cation transport via three different mechanisms, each characterized by an individual time scale. It turns out that also in the ternary electrolytes essentially all lithium ions are coordinated by PEO chains, thus ruling out a transport mechanism enhanced by the presence of ionic-liquid molecules. Rather, the plasticizing effect of the ionic liquid contributes to the increased lithium mobility by enhancing the dynamics of the PEO chains and consequently also the motion of the attached ions. Additional focus is laid on the prediction of lithium diffusion coefficients from the simulation data for various chain lengths and the comparison with experimental data, thus demonstrating the broad applicability of our approach.

  2. A phenomenological electronic stopping power model for molecular dynamics and Monte Carlo simulation of ion implantation into silicon

    E-Print Network [OSTI]

    Cai, D; Snell, C M; Beardmore, K M; Cai, David; Gronbech-Jensen, Niels; Snell, Charles M.; Beardmore, Keith M.

    1996-01-01

    It is crucial to have a good phenomenological model of electronic stopping power for modeling the physics of ion implantation into crystalline silicon. In the spirit of the Brandt-Kitagawa effective charge theory, we develop a model for electronic stopping power for an ion, which can be factorized into (i) a globally averaged effective charge taking into account effects of close and distant collisions by target electrons with the ion, and (ii) a local charge density dependent electronic stopping power for a proton. This phenomenological model is implemented into both molecular dynamics and Monte Carlo simulations. There is only one free parameter in the model, namely, the one electron radius rs0 for unbound electrons. By fine tuning this parameter, it is shown that the model can work successfully for both boron and arsenic implants. We report that the results of the dopant profile simulation for both species are in excellent agreement with the experimental profiles measured by secondary-ion mass spectrometry(...

  3. 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.

  4. 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.

  5. Simulation of Quantum Spin Dynamics by Phase Space Sampling of BBGKY Trajectories

    E-Print Network [OSTI]

    Lorenzo Pucci; Analabha Roy; Michael Kastner

    2015-12-10

    A numerical method, suitable for the simulation of the time evolution of quantum spin models of arbitrary lattice dimension, is presented. The method combines sampling of the Wigner function with evolution equations obtained from the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) hierarchy. Going to higher orders of the BBGKY hierarchy allows for a systematic refinement of the method. Quantum correlations are treated through both, the Wigner function sampling and the BBGKY evolution, bringing about highly accurate estimates of correlation functions. The method is particularly suitable for long-range interacting systems, and we demonstrate its power by comparing with exact results as well as other numerical methods. As an application we compute spin squeezing in a two-dimensional lattice with power-law interactions and a transverse field, which should be accessible in future ion trap experiments.

  6. Quantum path integral molecular dynamics simulations on transport properties of dense liquid helium

    E-Print Network [OSTI]

    Kang, Dongdong; Sun, Huayang; Yuan, Jianmin

    2015-01-01

    Transport properties of dense liquid helium under the conditions of planet's core and cool atmosphere of white dwarfs have been investigated by using the improved centroid path-integral simulations combined with density functional theory. The self-diffusion is largely higher and the shear viscosity is notably lower predicted with the quantum mechanical description of the nuclear motion compared with the description by Newton equation. The results show that nuclear quantum effects (NQEs), which depends on the temperature and density of the matter via the thermal de Broglie wavelength and the ionization of electrons, are essential for the transport properties of dense liquid helium at certain astrophysical conditions. The Stokes-Einstein relation between diffusion and viscosity in strongly coupled regime is also examined to display the influences of NQEs.

  7. Non-contacting transfer of elastic energy into explosive simulants for dynamic property estimation

    SciTech Connect (OSTI)

    Greeney, Nathan S.; Strovink, Kurt M.; Scales, John A. [Physics Department, Colorado School of Mines, Golden, Colorado 80401 (United States); Jessop, Andrew M.; Stuart Bolton, J. [Ray W. Herrick Laboratories, Purdue University, West Lafayette, Indiana 47907-2099 (United States); Watson, Christopher C.; Adams, Douglas E. [Purdue Center for Systems Integrity, Purdue University, Lafayette, Indiana 47905 (United States)

    2014-05-21

    Non-contacting acoustical methods can be used to extract various material properties of liquid or solid samples without disturbing the sample. These methods are useful even in the lab since they do not involve coupling anything to the sample, which might change its properties. A forteriori, when dealing with potentially dangerous materials, non-contacting methods may be the only safe solutions to mechanical characterization. Here, we show examples of using laser ultrasound to remotely insonify and monitor the elastic properties of several granular explosive simulants. The relatively short near-infrared laser pulse length (a few hundred nanoseconds) provides a broad-band thermoelastic source of ultrasound; we intentionally stay in the thermoelastic regime to avoid damaging the material. Then, we use a scanning laser Doppler vibrometer to measure the ultrasonic response of the sample. LDV technology is well established and very sensitive at ultrasonic frequencies; atomic level motions can be measured with modest averaging. The resulting impulse response of the explosive simulant can be analyzed to determine decay rates and wave speeds, with stiffer samples showing faster wave speeds and lower decay rates. On the other hand, at the low-frequency end of the acoustic spectrum, we use an electronically phased array to couple into a freely suspended sample's normal modes. This allows us to gently heat up the sample (3?°C in just under 5 min, as shown with a thermal IR camera). In addition to the practical interest in making the sample more chemically visible through heat, these two measurements (low-frequency resonant excitation vs high-frequency wave propagation) bracket the frequency range of acoustic non-destructive evaluation methods available.

  8. 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.

  9. 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.

  10. Molecular dynamics simulations of low-energy ,,25200 eV... argon ion interactions with silicon surfaces: Sputter yields and product

    E-Print Network [OSTI]

    Economou, Demetre J.

    Molecular dynamics simulations of low-energy ,,25­200 eV... argon ion interactions with silicon surfaces: Sputter yields and product formation pathways Nawoyuki A. Kubota and Demetre J. Economoua) Plasma energy ( 200 eV ion interactions with surfaces. In particular, atomic layer etching requires etching

  11. Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

    E-Print Network [OSTI]

    Walter, Nils G.

    Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H+ Forms. Biochemical and structural data have implicated guanine 8 (G8) and adenine 38 (A38) as catalytic participants of the protonation states of G8 and A38, and the inactivating A-1(2-methoxy) substitution employed in crystallography

  12. The 1st International Symposium on Micro & Nano Technology, 14-17 March, 2004, Honolulu, Hawaii, USA MOLECULAR DYNAMICS SIMULATIONS OF HEAT TRANSFER ISSUES

    E-Print Network [OSTI]

    Maruyama, Shigeo

    , USA MOLECULAR DYNAMICS SIMULATIONS OF HEAT TRANSFER ISSUES IN CARBON NANOTUBES S. Maruyama, Y-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, JAPAN ABSTRACT Several heat transfer problems related to single, and thermal boundary resistance in a junction of nanotubes are reviewed. Then, the heat transfer from an SWNT

  13. 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.

  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. Mesoscale simulation of semiflexible chains. II. Evolution dynamics and stability of fiber bundle networks

    E-Print Network [OSTI]

    Robert D. Groot

    2013-06-06

    Network formation of associative semiflexible fibers and mixtures of fibers and colloidal particles is simulated for the Johnson-Kendall-Roberts (JKR) model of elastic contacts, and a phase diagram in terms of particle elasticity and surface energy is presented. When fibers self-assemble they form a network for sufficiently large fiber-solvent surface energy. If the surface energy is above the value where single particles crystallize the adhesion forces drive diffusion-limited aggregation. Two mechanisms contribute to coarsening: non-associated chains joining existing bundles, and fiber bundles merging. Coarsening stops when the length of the network connections is roughly the persistence length, independent of surface energy. If the surface energy is below the value where single particles crystallize, a network can still be formed but at a much slower (reaction limited) rate. Loose (liquid-like) assemblies between chains form when they happen to run more-or-less parallel. These assemblies grow by diffusion and aggregation and form a loose network, which sets in micro-phase separation, i.e. syneresis. Only when the clusters crystallize, the coarsening process stops. In this case the length of the network connections is larger than the persistence length of a single chain, and depends on the value of the surface energy. All networks of semiflexible homopolymers in this study show syneresis. Mixtures of fibers and colloid particles also form fiber bundle networks, but by choosing the colloid volume fraction sufficiently low, swelling gels are obtained. Applications of this model are in biological systems where fibers self-assemble into cell walls and bone tissue.

  16. Dynamic Simulation Studies of the Frequency Response of the Three U.S. Interconnections with Increased Wind Generation

    E-Print Network [OSTI]

    Mackin, Peter

    2011-01-01

    2009. “North America Dynamic Wind Generator Modeling Update,work performed by the WECC Wind Generator Modeling Group andIEEE Dynamic Performance of Wind Power Generation Working

  17. A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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

  18. 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.

  19. Nonstandard Tools for Nonsmooth Analysis

    E-Print Network [OSTI]

    S. S. Kutateladze

    2012-06-11

    This is an overview of the basic tools of nonsmooth analysis which are grounded on nonstandard models of set theory. By way of illustration we give a criterion for an infinitesimally optimal path of a general discrete dynamic system.

  20. 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.

  1. Force and heat current formulas for many-body potentials in molecular dynamics simulation with applications to thermal conductivity calculations

    E-Print Network [OSTI]

    Fan, Zheyong; Wang, Hui-Qiong; Zheng, Jin-Cheng; Donadio, Davide; Harju, Ari

    2015-01-01

    We derive expressions of interatomic force and heat current for many-body potentials such as the Tersoff, the Brenner, and the Stillinger-Weber potential used extensively in molecular dynamics simulations of covalently bonded materials. Although these potentials have a many-body nature, a pairwise force expression that follows Newton's third law can be found without referring to any partition of the potential. Based on this force formula, a stress applicable for periodic systems can be unambiguously defined. The force formula can then be used to derive the heat current formulas using a natural potential partitioning. Our heat current formulation is found to be equivalent to most of the seemingly different heat current formulas used in the literature, but to deviate from the stress-based formula derived from two-body potential. We validate our formulation numerically on various systems descried by the Tersoff potential, namely three-dimensional silicon and diamond, two-dimensional graphene, and quasi-one-dimen...

  2. Dynamics of the Photogenerated Hole at the Rutile TiO2(110)/Water Interface: A Nonadiabatic Simulation Study

    E-Print Network [OSTI]

    Simulation Study Georgios A. Tritsaris, Dmitry Vinichenko, Grigory Kolesov, Cynthia M. Friend, and Efthimios

  3. Dynamic analysis of the parallel-plate EMP (Electromagnetic Pulse) simulator using a wire-mesh approximation and the numerical electromagnetics code. Final report

    SciTech Connect (OSTI)

    Gedney, S.D.

    1987-09-01

    The electromagnetic pulse (EMP) produced by a high-altitude nuclear blast presents a severe threat to electronic systems due to its extreme characteristics. To test the vulnerability of large systems, such as airplanes, missiles, or satellites, they must be subjected to a simulated EMP environment. One type of simulator that has been used to approximate the EMP environment is the Large Parallel-Plate Bounded-Wave Simulator. It is a guided-wave simulator which has properties of a transmission line and supports a single TEM model at sufficiently low frequencies. This type of simulator consists of finite-width parallel-plate waveguides, which are excited by a wave launcher and terminated by a wave receptor. This study addresses the field distribution within a finite-width parallel-plate waveguide that is matched to a conical tapered waveguide at either end. Characteristics of a parallel-plate bounded-wave EMP simulator were developed using scattering theory, thin-wire mesh approximation of the conducting surfaces, and the Numerical Electronics Code (NEC). Background is provided for readers to use the NEC as a tool in solving thin-wire scattering problems.

  4. Automated energy monitoring of machine tools

    E-Print Network [OSTI]

    Vijayaraghavan, Athulan; Dornfeld, David

    2010-01-01

    in a 3- axis precision milling machine. The simulated pro?lea Mori Seiki NV1500 DCG milling machine by the Machine Tool

  5. Dynamical simulation of heavy-ion collisions in the energy range from a few tens MeV/A to a few hundreds MeV/A

    E-Print Network [OSTI]

    M. V. Garzelli

    2008-10-13

    The overlapping stage of heavy-ion reactions can be simulated by dynamical microscopical models, such as those built on the basis of the Molecular Dynamics (MD) approaches, allowing to study the fragment formation process. The present performances of the Quantum MD (QMD) code developed at the University of Milano are discussed, showing results concerning fragment and particle production at bombarding energies up to $\\lsim$ 700 MeV/A, as well as a preliminary analysis on the isoscaling behaviour of isotopic yield ratios for reactions with isospin composition N/Z in the (1 - 1.2) range, at a 45 MeV/A bombarding energy.

  6. Software-based tool path evaluation for environmental sustainability

    E-Print Network [OSTI]

    KONG, DAEYOUNG; Seungchoun Choi; Yusuke Yasui; Sushrut Pavanaskar; Dornfeld, David; Wright, Paul

    2011-01-01

    press as: Kong D, et al. Software-based tool path evaluationArchitecture of the simulation software. Besides the studiesanalysis of machining. Software-based simulation tools have

  7. Developing a risk management "flight simulator" for manned space programs : a user interface to a system dynamic simulation of system safety at NASA

    E-Print Network [OSTI]

    Friedenthal, Stephen R. (Stephen Roger)

    2006-01-01

    Simulators are a staple of any engineering project and manned space flight in particular. From pilot and crew training to maintenance and emergency repairs, very little is done without it first being thoroughly practiced ...

  8. A benchmark study of 2D and 3D finite element calculations simulating dynamic pulse buckling tests of cylindrical shells under axial impact

    SciTech Connect (OSTI)

    Hoffman, E.L.; Ammerman, D.J.

    1993-08-01

    A series of tests investigating dynamic pulse buckling of a cylindrical shell under axial impact is compared to several finite element simulations of the event. The purpose of the study is to compare the performance of the various analysis codes and element types with respect to a problem which is applicable to radioactive material transport packages, and ultimately to develop a benchmark problem to qualify finite element analysis codes for the transport package design industry.

  9. Dynamic Simulation of Unsteady Flow of Water in Unsaturated Soils and its Application to Subirrigation System Design 

    E-Print Network [OSTI]

    Hiler, E. A.; Bhuiyan, S. I.

    1971-01-01

    Two computer programs were developed. One simulated vertical unsteady infiltration through the surface into a homogeneous unsaturated soil. Simulation results were obtained for three different soils--Yolo light clay, ...

  10. Slip behavior in liquid films on surfaces of patterned wettability: Comparison between continuum and molecular dynamics simulations

    E-Print Network [OSTI]

    Nikolai V. Priezjev; Anton A. Darhuber; Sandra M. Troian

    2005-05-10

    We investigate the behavior of the slip length in Newtonian liquids subject to planar shear bounded by substrates with mixed boundary conditions. The upper wall, consisting of a homogenous surface of finite or vanishing slip, moves at a constant speed parallel to a lower stationary wall, whose surface is patterned with an array of stripes representing alternating regions of no-shear and finite or no-slip. Velocity fields and effective slip lengths are computed both from molecular dynamics (MD) simulations and solution of the Stokes equation for flow configurations either parallel or perpendicular to the stripes. Excellent agreement between the hydrodynamic and MD results is obtained when the normalized width of the slip regions, $a/\\sigma \\gtrsim {\\cal O}(10)$, where $\\sigma$ is the (fluid) molecular diameter characterizing the Lennard-Jones interaction. In this regime, the effective slip length increases monotonically with $a/\\sigma$ to a saturation value. For $a/\\sigma \\lesssim {\\cal O}(10)$ and transverse flow configurations, the non-uniform interaction potential at the lower wall constitutes a rough surface whose molecular scale corrugations strongly reduce the effective slip length below the hydrodynamic results. The translational symmetry for longitudinal flow eliminates the influence of molecular scale roughness; however, the reduced molecular ordering above the wetting regions of finite slip for small values of $a/\\sigma$ increases the value of the effective slip length far above the hydrodynamic predictions. The strong inverse correlation between the effective slip length and the liquid structure factor representative of the first fluid layer near the patterned wall illustrates the influence of molecular ordering effects on slip in non-inertial flows.

  11. Queer Tools

    E-Print Network [OSTI]

    Hacker, Randi; Tsutsui, William

    2007-11-19

    Broadcast Transcript: Chindogu. Did someone say "Bless you?" No need. This is a Japanese word that means "queer tools" and it was coined to describe the Japanese penchant for unusual inventions. From toilet paper rolls that attach to the head...

  12. Workflow Tools

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    at NERSC go here. Galaxy - Galaxy is a web based workflow tool that is use by the genomics community. It allows you to define job dependencies via a web based workflow engine....

  13. 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.

  14. Java Vertexing Tools

    SciTech Connect (OSTI)

    Strube, Jan; /Oregon U.; 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.

  15. 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.

  16. 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.

  17. Dynamic Simulation Studies of the Frequency Response of the Three U.S. Interconnections with Increased Wind Generation

    E-Print Network [OSTI]

    Mackin, Peter

    2011-01-01

    IEEE Dynamic Performance of Wind Power Generation Workingof the impacts of wind generation on power system frequencywith Increased Wind Generation 9. Siemens Power Technologies

  18. Scattering Density Profile Model of POPG Bilayers as Determined by Molecular Dynamics Simulations and Small-Angle Neutron and X-ray Scattering Experiments

    SciTech Connect (OSTI)

    Kucerka, Norbert [Canadian Neutron Beam Centre and Comelius University (Slovakia); Holland, B [University of Guelph; Gray, C.G [University of Guelph; Tomberli, B [Brandon University; Katsaras, John [ORNL

    2012-01-01

    We combine molecular dynamics (MD) simulations and experiment, both small-angle neutron (SANS) and small-angle X-ray scattering (SAXS), to determine the precise structure of bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG), a lipid commonly encountered in bacterial membranes. Experiment and simulation are used to develop a one-dimensional scattering density profile (SDP) model suitable for the analysis of experimental data. The joint refinement of such data (i.e., SANS and SAXS) results in the area per lipid that is then used in the fixed-area simulations. In the final step, the direct comparison of simulated-to-experimental data gives rise to the detailed structure of POPG bilayers. From these studies we conclude that POPG s molecular area is 66.0 +/- 1.3 ^2, its overall bilayer thickness is 36.7 +/- 0.7 , and its hydrocarbon region thickness is 27.9 ( 0.6 , assuming a simulated value of 1203 ^3 for the total lipid volume.

  19. 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 [Warsaw University of Technology, Faculty of Materials Science and Engineering, Woloska 141, 02507 Warsaw (Poland); Caban, Piotr [Institute of Electronic Materials Technology, Wolczynska 133, 01919 Warsaw (Poland); Kurzydlowski, Krzysztof J. [Warsaw University of Technology, Faculty of Materials Science and Engineering Woloska, 141, 02507 Warsaw (Poland)

    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.

  20. Functional Domain Motions in Proteins on the 1 100 ns Timescale: Comparison of Neutron Spin-Echo Spectroscopy of Phosphoglycerate Kinase with Molecular-Dynamics Simulation

    SciTech Connect (OSTI)

    Smolin, Nikolai [ORNL; Biehl, R [Southern Methodist University, Dallas; Kneller, Gerald [University of Orleans; Richter, Dieter O [ORNL; Smith, Jeremy C [ORNL

    2011-01-01

    Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the 1 100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins.