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Sample records for molecular dynamics simulations

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  3. 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:...

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

    Broader source: Energy.gov (indexed) [DOE]

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

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

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

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

  6. Molecular dynamics simulations of microscale fluid transport

    SciTech Connect (OSTI)

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

    1998-02-01

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

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

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

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

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

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

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

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

    Broader source: Energy.gov (indexed) [DOE]

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Broader source: Energy.gov (indexed) [DOE]

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

  12. 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.

  13. Multi million-to-Billion Atom Molecular Dynamics Simulations of

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

    Cavitation-Induced Damage on a Silica Slab | Argonne Leadership Computing Facility Multi million-to-Billion Atom Molecular Dynamics Simulations of Cavitation-Induced Damage on a Silica Slab Authors: Shekhar, A., Nomura, K., Rajiv, K., Nakano, A., Vashishta, P Cavitation bubble collapse causes severe damage to materials. For example, cavitation erosion is a major threat to the safety of nuclear power plants. The cavitation bubbles may also be utilized for preventing stress corrosion cracking

  14. Molecular dynamics simulation of radiation damage cascades in diamond

    SciTech Connect (OSTI)

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

    2015-06-28

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

  15. Molecular dynamics simulations of hydrogen diffusion in aluminum

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

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

    2016-03-23

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

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

    Office of Scientific and Technical Information (OSTI)

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

  17. 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.

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

    SciTech Connect (OSTI)

    Mugnai, Mauro L.; Elber, Ron

    2015-01-07

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

  19. Clustering effects in ionic polymers: Molecular dynamics simulations

    SciTech Connect (OSTI)

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

    2015-08-18

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

  20. Clustering effects in ionic polymers: Molecular dynamics simulations

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

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

    2015-08-18

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

  1. 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.

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

    SciTech Connect (OSTI)

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

    1996-08-01

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

  3. 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.

  4. Molecular dynamics simulation of annealed ZnO surfaces

    SciTech Connect (OSTI)

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

    2015-04-24

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

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

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

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

    2015-01-06

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

  6. Molecular Dynamics Simulation of Thermodynamic Properties in Uranium Dioxide

    SciTech Connect (OSTI)

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

    2014-03-01

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

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

    SciTech Connect (OSTI)

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

    2015-12-07

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

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

    2014-01-01

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

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

    SciTech Connect (OSTI)

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

    2015-08-17

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

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

    SciTech Connect (OSTI)

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

    2014-07-15

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

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

    SciTech Connect (OSTI)

    Valone, S.M.

    1995-07-01

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

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

    SciTech Connect (OSTI)

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

    2007-09-11

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

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

    SciTech Connect (OSTI)

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

    2009-12-18

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

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

    SciTech Connect (OSTI)

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

    2015-04-24

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

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

    SciTech Connect (OSTI)

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

    2015-08-01

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

  16. 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

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

    SciTech Connect (OSTI)

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

    2011-10-01

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

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

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

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

    2015-11-24

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

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

    SciTech Connect (OSTI)

    Holkundkar, Amol R.

    2013-11-15

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

  20. 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.

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

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

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

    2015-01-29

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

  2. 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}

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

    SciTech Connect (OSTI)

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

    2015-03-15

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

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

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

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

    2015-10-22

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

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

    SciTech Connect (OSTI)

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

    2015-10-22

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

  6. 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.

  7. 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.

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

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

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

    2016-03-22

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

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

    SciTech Connect (OSTI)

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

    2015-04-14

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

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

    SciTech Connect (OSTI)

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

    2014-11-17

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

  11. Substructured multibody molecular dynamics.

    SciTech Connect (OSTI)

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

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

    SciTech Connect (OSTI)

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

    2008-11-01

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

  13. 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.

  14. 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

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

    SciTech Connect (OSTI)

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

    1997-10-01

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

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

    SciTech Connect (OSTI)

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

    2015-04-28

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

  17. 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.

  18. 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.

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

    SciTech Connect (OSTI)

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

    2015-06-14

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

  20. 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.

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

    SciTech Connect (OSTI)

    Mester, Zoltan; Panagiotopoulos, Athanassios Z.

    2015-01-28

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

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

    SciTech Connect (OSTI)

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

    2015-01-05

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

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

    SciTech Connect (OSTI)

    Chen Shilu; Fang Weihai

    2009-08-07

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

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

    SciTech Connect (OSTI)

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

    1995-04-01

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

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

    SciTech Connect (OSTI)

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

    2014-05-14

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

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

    SciTech Connect (OSTI)

    Jakse, N.; Pasturel, A.

    2014-12-21

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

  7. 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

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

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

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

    2016-01-20

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

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

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

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

    2016-02-04

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

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

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

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

    2015-02-17

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

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

    SciTech Connect (OSTI)

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

    2015-04-24

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

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

    SciTech Connect (OSTI)

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-28

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

  13. 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.

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

    SciTech Connect (OSTI)

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

    2015-03-04

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

  15. 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

  16. 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.

  17. 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.

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

    SciTech Connect (OSTI)

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

    2015-11-16

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

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

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

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

    2015-11-16

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

  20. 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.

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

    SciTech Connect (OSTI)

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

    2014-12-01

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

  2. 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-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less

  3. Molecular Dynamics Simulations of Tri-n-butyl-phosphate/n-Dodecane Mixture: Thermophysical Properties and Molecular Structure

    SciTech Connect (OSTI)

    de Almeida, Valmor F; Cui, Shengting; Khomami, Bamin

    2014-01-01

    Molecular dynamics simulations of tri-n-butyl-phosphate (TBP)/n-dodecane mixture in the liquid phase have been carried out using two recently developed TBP force field models (J. Phys. Chem. B 2012, 116, 305) in combination with the all-atom optimized potentials for liquid simulations (OPLS-AA) force field model for n-dodecane. Specifically, the electric dipole moment of TBP, mass density of the mixture, and the excess volume of mixing were computed with TBP mole fraction ranging from 0 to 1. It is found that the aforementioned force field models accurately predict the mass density of the mixture in the entire mole fraction range. Commensurate with experimental measurements, the electric dipole moment of the TBP was found to slightly increase with the mole fraction of TBP in the mixture. Also, in accord with experimental data, the excess volume of mixing is positive in the entire mole fraction range, peaking at TBP mole fraction range 0.3 0.5. Finally, a close examination of the spatial pair correlation functions between TBP molecules, and between TBP and n-dodecane molecules, revealed formation of TBP dimers through self-association at close distance, a phenomenon with ample experimental evidence.

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

    SciTech Connect (OSTI)

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

    2014-04-10

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

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

    SciTech Connect (OSTI)

    Rudd, R E

    2009-02-05

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

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

    SciTech Connect (OSTI)

    Zhang, B.

    1993-08-01

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

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

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

    Barrows, Wesley; Dingreville, Rémi; Spearot, Douglas

    2015-10-19

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

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

    SciTech Connect (OSTI)

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

    2015-02-01

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

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

    SciTech Connect (OSTI)

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

    2011-05-05

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

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

    SciTech Connect (OSTI)

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

    2014-01-14

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

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

    SciTech Connect (OSTI)

    Barrows, Wesley; Dingreville, Rmi; Spearot, Douglas

    2015-10-19

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

  12. 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.

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

    SciTech Connect (OSTI)

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

    2014-07-01

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

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

    SciTech Connect (OSTI)

    Zhang, Wenjin; Peng, Yufeng; Liu, Zhongli

    2014-05-15

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

  15. 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.

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

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

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

    2014-02-05

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

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

    SciTech Connect (OSTI)

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

    2015-07-21

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

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

    SciTech Connect (OSTI)

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

    2014-02-05

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

  19. 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.

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

    SciTech Connect (OSTI)

    Hyeon-Deuk, Kim; Ando, Koji

    2014-05-07

    Liquid para-hydrogen (p-H{sub 2}) is a typical quantum liquid which exhibits strong nuclear quantum effects (NQEs) and thus anomalous static and dynamic properties. We propose a real-time simulation method of wave packet (WP) molecular dynamics (MD) based on non-empirical intra- and inter-molecular interactions of non-spherical hydrogen molecules, and apply it to condensed-phase p-H{sub 2}. The NQEs, such as WP delocalization and zero-point energy, are taken into account without perturbative expansion of prepared model potential functions but with explicit interactions between nuclear and electron WPs. The developed MD simulation for 100 ps with 1200 hydrogen molecules is realized at feasible computational cost, by which basic experimental properties of p-H{sub 2} liquid such as radial distribution functions, self-diffusion coefficients, and shear viscosities are all well reproduced.

  1. Mass transport properties of Pu/DT mixtures from orbital free molecular dynamics simulations

    SciTech Connect (OSTI)

    Kress, Joel David; Ticknor, Christopher; Collins, Lee A.

    2015-09-16

    Mass transport properties (shear viscosity and diffusion coefficients) for Pu/DT mixtures were calculated with Orbital Free Molecular Dynamics (OFMD). The results were fitted to simple functions of mass density (for ρ=10.4 to 62.4 g/cm3) and temperature (for T=100 up to 3,000 eV) for Pu/DT mixtures consisting of 100/0, 25/75, 50/50, and 75/25 by number.

  2. Lenard-Balescu calculations and classical molecular dynamics simulations of electrical and thermal conductivities of hydrogen plasmas

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

    Whitley, Heather D.; Scullard, Christian R.; Benedict, Lorin X.; Castor, John I.; Randles, Amanda; Glosli, James N.; Richards, David F.; Desjarlais, Michael P.; Graziani, Frank R.

    2015-12-04

    Here, we present a discussion of kinetic theory treatments of linear electrical and thermal transport in hydrogen plasmas, for a regime of interest to inertial confinement fusion applications. In order to assess the accuracy of one of the more involved of these approaches, classical Lenard-Balescu theory, we perform classical molecular dynamics simulations of hydrogen plasmas using 2-body quantum statistical potentials and compute both electrical and thermal conductivity from out particle trajectories using the Kubo approach. Our classical Lenard-Balescu results employing the identical statistical potentials agree well with the simulations.

  3. Molecular dynamics simulations of D{sub 2}O ice photodesorption

    SciTech Connect (OSTI)

    Arasa, C.; Andersson, S.; Cuppen, H. M.; Dishoeck, E. F. van; Kroes, G. J.

    2011-04-28

    Molecular dynamics (MD) calculations have been performed to study the ultraviolet (UV) photodissociation of D{sub 2}O in an amorphous D{sub 2}O ice surface at 10, 20, 60, and 90 K, in order to investigate the influence of isotope effects on the photodesorption processes. As for H{sub 2}O, the main processes after UV photodissociation are trapping and desorption of either fragments or D{sub 2}O molecules. Trapping mainly takes place in the deeper monolayers of the ice, whereas desorption occurs in the uppermost layers. There are three desorption processes: D atom, OD radical, and D{sub 2}O molecule photodesorption. D{sub 2}O desorption takes places either by direct desorption of a recombined D{sub 2}O molecule, or when an energetic D atom produced by photodissociation kicks a surrounding D{sub 2}O molecule out of the surface by transferring part of its momentum. Desorption probabilities are calculated for photoexcitation of D{sub 2}O in the top four monolayers and are compared quantitatively with those for H{sub 2}O obtained from previous MD simulations of UV photodissociation of amorphous water ice at different ice temperatures [Arasa et al., J. Chem. Phys. 132, 184510 (2010)]. The main conclusions are the same, but the average D atom photodesorption probability is smaller than that of the H atom (by about a factor of 0.9) because D has lower kinetic energy than H, whereas the average OD radical photodesorption probability is larger than that of OH (by about a factor of 2.5-2.9 depending on ice temperature) because OD has higher translational energy than OH for every ice temperature studied. The average D{sub 2}O photodesorption probability is larger than that of H{sub 2}O (by about a factor of 1.4-2.3 depending on ice temperature), and this is entirely due to a larger contribution of the D{sub 2}O kick-out mechanism. This is an isotope effect: the kick-out mechanism is more efficient for D{sub 2}O ice, because the D atom formed after D{sub 2}O photodissociation

  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. Assessment of Molecular Modeling & Simulation

    SciTech Connect (OSTI)

    2002-01-03

    This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.

  6. Accelerated Molecular Dynamics Methods

    Broader source: Energy.gov [DOE]

    This presentation on Accelerated Molecular Dynamics Methods was given at the DOE Theory Focus Session on Hydrogen Storage Materials on May 18, 2006.

  7. Hybrid Quantum Mechanics/Molecular Mechanics-Based Molecular Dynamics Simulation of Acid-Catalyzed Dehydration of Polyols in Liquid Water

    SciTech Connect (OSTI)

    Caratzoulas, Stavros; Courtney, Timothy; Vlachos, Dionisios G.

    2011-01-01

    We use the conversion of protonated glycerol to acrolein for a case study of the mechanism of acid-catalyzed dehydration of polyols in aqueous environments. We employ hybrid Quamtum Mechanics/Molecular Mechanics Molecular Dynamics (QM/MM MD) simulations with biased sampling and perform free energy calculations for the elementary steps of the reaction. We investigate the effects of solvent dynamics and in particular the role of quantum mechanical water in the dehydration mechanism. We present results supporting a mechanism that proceeds via water-mediated proton transfers and thus through an enol intermediate. We find that the first dehydration may take place by two, low-energy pathways requiring, respectively, 20.9 and 18.8 kcal/mol of activation free energy. The second dehydration requires 19.9 kcal/mol of activation free energy while for the overall reaction we compute a free energy change of -8 kcal/mol.

  8. Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

    SciTech Connect (OSTI)

    Jakobtorweihen, S. Ingram, T.; Gerlach, T.; Smirnova, I.; Zuniga, A. Chaides; Keil, F. J.

    2014-07-28

    Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations.

  9. Molecular dynamics simulation of Coulomb explosion, melting and shock wave creation in silicon after an ionization pulse

    SciTech Connect (OSTI)

    Li, Zhongyu; Shao, Lin; Chen, Di; Wang, Jing

    2014-04-14

    Strong electronic stopping power of swift ions in a semiconducting or insulating substrate can lead to localized electron stripping. The subsequent repulsive interactions among charged target atoms can cause Coulomb explosion. Using molecular dynamics simulation, we simulate Coulomb explosion in silicon by introducing an ionization pulse lasting for different periods, and at different substrate temperatures. We find that the longer the pulse period, the larger the melting radius. The observation can be explained by a critical energy density model assuming that melting required thermal energy density is a constant value and the total thermal energy gained from Coulomb explosion is linearly proportional to the ionization period. Our studies also show that melting radius is larger at higher substrate temperatures. The temperature effect is explained due to a longer structural relaxation above the melting temperature at original ionization boundary due to lower heat dissipation rates. Furthermore, simulations show the formation of shock waves, created due to the compression from the melting core.

  10. An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water

    SciTech Connect (OSTI)

    Fanourgakis, Georgios S.; Tipparaju, Vinod; Nieplocha, Jarek; Xantheas, Sotiris S.

    2007-01-01

    An efficient parallelization scheme for classical Molecular Dynamics simulations with flexible polarizable empirical potentials is presented. It is based on the standard Ewald summation technique to handle the long-range electrostatic and induction interactions. The algorithm for this parallelization scheme is designed for systems containing several thousands of polarizable sites in the simulation box. Its performance is evaluated during Molecular Dynamics simulations under periodic boundary conditions with unit cell sizes ranging from 128-512 water molecules employing two exible, polarizable water models [POL1(F) and TTM2-F] containing 1 and 3 polarizable sites respectively. The efficiency of the algorithm, is evaluated against a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient calculations of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed in several cases. To the best of our knowledge, this is the first attempt for a parallel implementation of a polarizable potential under periodic boundary conditions. Guidelines for adapting the algorithm for larger systems are also discussed. This research was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences laboratory, a national scientific user facility sponsored by the U.S. Department of Energys Office of Biological and Environmental Research located at the Pacific Northwest National Laboratory. The Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy under contract DE-AC05-76RL01830.

  11. Three-dimensional ordering of cold ion beams in a storage ring: A molecular-dynamics simulation study

    SciTech Connect (OSTI)

    Yuri, Yosuke

    2015-06-29

    Three-dimensional (3D) ordering of a charged-particle beams circulating in a storage ring is systematically studied with a molecular-dynamics simulation code. An ion beam can exhibit a 3D ordered configuration at ultralow temperature as a result of powerful 3D laser cooling. Various unique characteristics of the ordered beams, different from those of crystalline beams, are revealed in detail, such as the single-particle motion in the transverse and longitudinal directions, and the dependence of the tune depression and the Coulomb coupling constant on the operating points.

  12. Radiation damage in cubic ZrO2 and yttria-stabilized zirconia from molecular dynamics simulations

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

    Aidhy, Dilpuneet S.; Zhang, Yanwen; Weber, William J.

    2014-11-20

    Here, we perform molecular dynamics simulation on cubic ZrO2 and yttria-stabilized zirconia (YSZ) to elucidate defect cluster formation resulting from radiation damage, and evaluate the impact of Y-dopants. Interstitial clusters composed of split-interstitial building blocks, i.e., Zr-Zr or Y-Zr are formed. Moreover, oxygen vacancies control cation defect migration; in their presence, Zr interstitials aggregate to form split-interstitials whereas in their absence Zr interstitials remain immobile, as isolated single-interstitials. Y-doping prevents interstitial cluster formation due to sequestration of oxygen vacancies.

  13. Radiation damage in cubic-ZrO2 and yttria-stabilized zirconia from molecular dynamics simulations

    SciTech Connect (OSTI)

    Aidhy, Dilpuneet S; Zhang, Yanwen; Weber, William J

    2015-01-01

    We perform molecular dynamics simulation on cubic ZrO2 and yttria-stabilized zirconia (YSZ) to elucidate defect cluster formation resulting from radiation damage, and evaluate the impact of Y-dopants. Interstitial clusters composed of split-interstitial building blocks, i.e., Zr-Zr or Y-Zr are formed. Oxygen vacancies control cation defect migration; in their presence, Zr interstitials aggregate to form split-interstitials whereas in their absence Zr interstitials remain immobile, as isolated single-interstitials. Y-doping prevents interstitial cluster formation due to sequestration of oxygen vacancies.

  14. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    SciTech Connect (OSTI)

    Lee, Mal Soon; McGrail, B. Peter; Rousseau, Roger J.; Glezakou, Vassiliki Alexandra

    2015-10-12

    The interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivity and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T=323 K and P=90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences, Geosciences and Biosciences

  15. 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.

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

    SciTech Connect (OSTI)

    Lan, Tian; Li, Chen; Niedziela, Jennifer L; Smith, Hillary; Abernathy, Douglas L; Rossman, George; Fultz, B.

    2014-01-01

    Inelastic neutron scattering measurements on silver oxide (Ag2O) with the cuprite structure were performed at temperatures from 40 to 400 K, and Fourier transform far-infrared spectra were measured from 100 to 300 K. The measured phonon densities of states and the infrared spectra showed unusually large energy shifts with temperature, and large linewidth broadenings. First principles molecular dynamics (MD) calculations were performed at various temperatures, successfully accounting for the negative thermal expansion (NTE) and local dynamics. Using the Fourier-transformed velocity autocorrelation method, the MD calculations reproduced the large anharmonic effects of Ag2O, and were in excellent agreement with the neutron scattering data. The quasiharmonic approximation (QHA) was less successful in accounting for much of the phonon behavior. The QHA could account for some of the NTE below 250 K, although not at higher temperatures. Strong anharmonic effects were found for both phonons and for the NTE. The lifetime broadenings of Ag2O were explained by anharmonic perturbation theory, which showed rich interactions between the Ag-dominated modes and the O-dominated modes in both up- and down-conversion processes.

  17. Effect of Cu2+ Activation on Interfacial Water Structure at the Sphalerite Surface as Studied by Molecular Dynamics Simulation

    SciTech Connect (OSTI)

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

    2015-12-10

    In the first part of this paper, an experimental contact angle study of the fresh and Cu2+ activated sphalerite-ZnS surface as well as the covellite-CuS (001) surface is reported describing the increased hydrophobic character of the surface during Cu2+ activation. In addition to these experimental results, the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite- CuS2 (100), and covellite-CuS (001) surfaces were examined using Molecular Dynamics Simulation (MDS). Our MDS results on the behavior of interfacial water at the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite-CuS2 (100), and covellite-CuS (001) surfaces include simulated contact angles, water number density distribution, water dipole orientation, water residence time, and hydrogen-bonding considerations. The copper content at the Cu2+ activated sphalerite surface seems to account for the increased hydrophobicity as revealed by both experimental and MD simulated contact angle measurements. The relatively greater hydrophobic character developed at the Cu2+ activated sphalerite surface and at the copper-zinc sulfide surface has been described by MDS, based on the structure of interfacial water and its dynamic properties. L.X.D. acknowledges funding from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

  18. 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.

  19. The liquid surface of chiral ionic liquids as seen from molecular dynamics simulations combined with intrinsic analysis

    SciTech Connect (OSTI)

    Lísal, Martin

    2013-12-07

    We present molecular-level insight into the liquid/gas interface of two chiral room-temperature ionic liquids (RTILs) derived from 1-n-butyl-3-methylimidazolium bromide ([bmim][Br]); namely, (R)-1-butyl-3-(3-hydroxy-2-methylpropyl)imidazolium bromide (hydroxypropyl) and 1-butyl-3-[(1R)-nopyl]imidazolium bromide (nopyl). We use our currently developed force field which was validated against the experimental bulk density, heat of vaporization, and surface tension of [bmim][Br]. The force field for the RTILs adopts the Chemistry at Harvard Molecular Mechanics (CHARMM) parameters for the intramolecular and repulsion-dispersion interactions along with the reduced partial atomic charges based on ab initio calculations. The net charges of the ions are around ±0.8e, which mimic the anion to cation charge transfer and many-body effects. Molecular dynamics simulations in the slab geometry combined with the intrinsic interface analysis are employed to provide a detailed description of the RTIL/gas interface in terms of the structural and dynamic properties of the interfacial, sub-interfacial, and central layers at a temperature of 300 K. The focus is on the comparison of the liquid/gas interface for the chiral RTILs with the interface for parent [bmim][Br]. The structure of the interface is elucidated by evaluating the surface roughness, intrinsic atomic density profiles, and orientation ordering of the cations. The dynamics of the ions at the interfacial region is characterized by computing the survival probability, and normal and lateral self-diffusion coefficients in the layers.

  20. 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.

  1. Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

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

    Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; Opper, Kathleen L.; Wagener, Kenneth B.; Stevens, Mark J.; Frischknecht, Amalie Lucile; Winey, Karen I.

    2015-02-09

    Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the

  2. Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations

    SciTech Connect (OSTI)

    Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro

    2015-12-31

    Ab initio molecular dynamics simulations have been used to inspect the adsorption of O{sub 2} to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O{sub 2} and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O{sub 2} adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.

  3. Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

    SciTech Connect (OSTI)

    Lisal, Martin; Izak, Pavel

    2013-07-07

    Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf{sub 2}N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 {mu}mol/m{sup 2} at 300 K. For [bmim][Tf{sub 2}N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are {+-}0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf{sub 2}N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

  4. Accelerated Molecular Dynamics Methods

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

    ... Los Alamos Parallel Replica Dynamics Procedure Start clock and run thermostatted MD on ... Sum the trajectory times over all M processors. Advance simulation clock by this t sum Los ...

  5. Neutron Scattering of Residual Hydrogen in 1,4-Dioxane-D8 Liquid. Understanding Measurements with Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    de Almeida, Valmor F.; Liu, Hongjun; Herwig, Kenneth W.; Kidder, Michelle

    2016-01-01

    That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to inter-molecular scattering and that uncertainty in the extent of deuteration account for discrepancies between simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen-deuterium pair, and complementary interference from the deuterium-deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298K and at 343K) protiated mole fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. Although we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids and similar systematic experimental/computational studies can be performed to either

  6. Effect of Surface Oxidation on Interfacial Water Structure at a Pyrite (100) Surface as Studied by Molecular Dynamics Simulation

    SciTech Connect (OSTI)

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

    2015-06-01

    In the first part of this paper, a Scanning Electron Microscopy and contact angle study of a pyrite surface (100) is reported describing the relationship between surface oxidation and the hydrophilic surface state. In addition to these experimental results, the following simulated surface states were examined using Molecular Dynamics Simulation (MDS): fresh unoxidized (100) surface; polysulfide at the (100) surface; elemental sulfur at the (100) surface. Crystal structures for the polysulfide and elemental sulfur at the (100) surface were simulated using Density Functional Theory (DFT) quantum chemical calculations. The well known oxidation mechanism which involves formation of a metal deficient layer was also described with DFT. Our MDS results of the behavior of interfacial water at the fresh and oxidized pyrite (100) surfaces without/with the presence of ferric hydroxide include simulated contact angles, number density distribution for water, water dipole orientation, water residence time, and hydrogen-bonding considerations. The significance of the formation of ferric hydroxide islands in accounting for the corresponding hydrophilic surface state is revealed not only from experimental contact angle measurements but also from simulated contact angle measurements using MDS. The hydrophilic surface state developed at oxidized pyrite surfaces has been described by MDS, on which basis the surface state is explained based on interfacial water structure. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE funded work performed by Liem X. Dang. Battelle operates the Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.

  7. Homogeneous hydride formation path in α-Zr: Molecular dynamics simulations with the charge-optimized many-body potential

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

    Zhang, Yongfeng; Bai, Xian-Ming; Yu, Jianguo; Tonks, Michael R.; Noordhoek, Mark J.; Phillpot, Simon R.

    2016-06-01

    A formation path for homogeneous γ hydride formation in hcp α-Zr, from solid solution to the ζ and then the γ hydride, was demonstrated using molecular static calculations and molecular dynamic simulations with the charge-optimized many-body (COMB) potential. Hydrogen has limited solubility in α-Zr. Once the solubility limit is exceeded, the stability of solid solution gives way to that of coherent hydride phases such as the ζ hydride by planar precipitation of hydrogen. At finite temperatures, the ζ hydride goes through a partial hcp-fcc transformation via 1/3 <1¯100> slip on the basal plane, and transforms into a mixture of γmore » hydride and α-Zr. In the ζ hydride, slip on the basal plane is favored thermodynamically with negligible barrier, and is therefore feasible at finite temperatures without mechanical loading. The transformation process involves slips of three equivalent shear partials, in contrast to that proposed in the literature where only a single shear partial was involved. The adoption of multiple slip partials minimizes the macroscopic shape change of embedded hydride clusters and the shear strain accumulation in the matrix, and thus reduces the overall barrier needed for homogeneous γ hydride formation. In conclusion, this formation path requires finite temperatures for hydrogen diffusion without mechanical loading. Therefore, it should be effective at the cladding operating conditions.« less

  8. 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.

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

    SciTech Connect (OSTI)

    Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean -Luc; Emigh, Aiyana; Lightstone, Felice C.; Salsbury , Jr, Freddie

    2015-04-13

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.

  10. 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

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

    SciTech Connect (OSTI)

    Mabuchi, Takuya; Tokumasu, Takashi

    2014-09-14

    We have performed a detailed analysis of the structural properties of the sulfonate groups in terms of isolated and overlapped solvation shells in the nanostructure of hydrated Nafion membrane using classical molecular dynamics simulations. Our simulations have demonstrated the correlation between the two different areas in bound water region, i.e., the first solvation shell, and the vehicular transport of hydronium ions at different water contents. We have employed a model of the Nafion membrane using the improved force field, which is newly modified and validated by comparing the density and water diffusivity with those obtained experimentally. The first solvation shells were classified into the two types, the isolated area and the overlapped area. The mean residence times of solvent molecules explicitly showed the different behaviors in each of those areas in terms of the vehicular transport of protons: the diffusivity of classical hydronium ions in the overlapped area dominates their total diffusion at lower water contents while that in the isolated area dominates for their diffusion at higher water contents. The results provided insights into the importance role of those areas in the solvation shells for the diffusivity of vehicular transport of hydronium ions in hydrated Nafion membrane.

  12. Neutron scattering of residual hydrogen in 1,4-dioxane d8 liquid: Understanding measurements with molecular dynamics simulations

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

    Liu, Hongjun; Herwig, Kenneth W.; Kidder, Michelle K.; de Almeida, Valmor F.

    2016-06-08

    That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well-known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to intermolecular scattering and that uncertainty in the extent of deuteration account for discrepancies betweenmore » simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen–deuterium pair, and complementary interference from the deuterium–deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298 K and at 343 K) protiated molar fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here, we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. As a result, we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids, and similar systematic experimental/computational studies can be

  13. 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.

  14. Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

    SciTech Connect (OSTI)

    Parkes, Marie V.; Demir, Hakan; Teich-McGoldrick, Stephanie L.; Sholl, David S.; Greathouse, Jeffery A.; Allendorf, Mark D.

    2014-03-28

    Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of framework force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.

  15. Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

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

    Parkes, Marie V.; Demir, Hakan; Teich-McGoldrick, Stephanie L.; Sholl, David S.; Greathouse, Jeffery A.; Allendorf, Mark D.

    2014-03-28

    Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of frameworkmore » force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.« less

  16. On computing stress in polymer systems involving multi-body potentials from molecular dynamics simulation

    SciTech Connect (OSTI)

    Fu, Yao E-mail: jhsong@cec.sc.edu; Song, Jeong-Hoon E-mail: jhsong@cec.sc.edu

    2014-08-07

    Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.

  17. Reliable Viscosity Calculation from Equilibrium Molecular Dynamics

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

    Simulations: A Time Decomposition Method - Joint Center for Energy Storage Research July 7, 2015, Research Highlights Reliable Viscosity Calculation from Equilibrium Molecular Dynamics Simulations: A Time Decomposition Method Schematic demonstration of the time decomposition method Scientific Achievement An equilibrium molecular dynamics-based computational method is developed and tested for the reliable calculation of viscosity. Significance and Impact Viscosity is one of the key properties

  18. Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

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

    Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.; Valdez, Carlos A.

    2016-02-04

    Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

  19. Preparation, temperature dependent structural, molecular dynamics simulations studies and electrochemical properties of LiFePO{sub 4}

    SciTech Connect (OSTI)

    Rao, R. Prasada; Reddy, M.V.; Adams, S.; Chowdari, B.V.R.

    2015-06-15

    Highlights: • LiFePO{sub 4} compound was prepared by carbothermal reduction method. • In-situ XRD studies were carried out on LiFePO{sub 4} at various temperatures. • Dedicated imperial potentials used to explain the variation of lattice constants. • It exhibited reversible capacity of 140 (±5) mAh g{sup −1}, stable up to 400 cycles. - Abstract: LiFePO{sub 4} was prepared using carbothermal reduction method. In-situ temperature dependent structural studies were carried using X-ray diffraction. Molecular dynamics simulations were conducted for the LiFePO{sub 4} using empirical potentials developed using bond valence approach to investigate the structural variations. Electrochemical behaviour of LiFePO{sub 4} was evaluated using cyclic voltammetry and galvanostatic cycling studies at room temperature. Charge–discharge cycling studies showed a reversible capacities 140 (±5) mAh g{sup −1} at the end of 50th cycle and these capacity values were stable up to 400 cycles and almost nil capacity fade between 50 and 400 cycles, showing excellent capacity retention, low capacity fading. The cyclic voltammetry studies showed a main cathodic and anodic redox peaks at 3.34 and 3.5 V vs. Li, respectively.

  20. Molecular dynamics simulation of self-rotation effects on ultra-precision polishing of single-crystal copper

    SciTech Connect (OSTI)

    Yang, Yihan; Zhao, Hongwei; Zhang, Lin; Shao, Mingkun; Liu, Hongda; Huang, Hu

    2013-10-15

    Understanding the behaviors of the material removal mechanism of ultra-precision polishing process has been a critical issue of generating well-formed surface. In order to make clear the abrasive self-rotation effects on material removal at the atomic level, a three-dimensional molecular dynamics (MD) model is conducted to study the mechanics of ultra-precision polishing on single-crystal copper with a diamond abrasive and the effects of abrasive self-rotation velocity and direction. Morse potential energy function and EAM potential energy function are applied to model the copper/diamond and copper/copper interactions, respectively. The simulation results show that the deformation mechanism of single-crystal copper is due to the formation and movement of dislocations in the specimen. In addition, with the increasing of abrasive self-rotation velocity, the deformation mechanism falls from cutting to plowing regimes. The abrasive self-rotation velocity and direction have effects on the morphology and quality of the specimen surface, distribution and evolution of defects under the surface of the specimen. Also, the interatomic force between abrasive and specimen is studied to account for the effects of different polishing conditions.

  1. Molecular dynamical simulation of the behavior of early precipitated stage in aging process in dilute Cu-Cr alloy

    SciTech Connect (OSTI)

    Feng, J.; Liu, L.; Chen, J.; Du, Y.; Zhou, R.; Xiao, B.

    2010-06-15

    The aging behaviors of Cu-Cr alloys in the early stage at different temperatures are investigated by molecular dynamics simulations. First principles potentials are used for the interactions between Cu and Cr atoms. The initial behavior of precipitation is characterized by transmission electron microscope and electron energy disperse spectroscopy. The results showed that Cu-Cr supersaturated solid solution is thermodynamically unstable. The mean-square displacements of the atoms are used to describe the diffusivity. At room temperature, the atoms only show harmonic vibrations near the equilibrium positions. The mutual diffusion at 873 K is different from the unidirectional diffusion in low temperatures. The calculation shows that aging process is accelerated with increasing temperature, which is not only due to the lower diffusion activation energy of Cr at higher temperature, but also because Cu atoms are also participated in the aging process. When ''aging'' at 1073 K, the precipitation of Cr element is dissolved again into Cu matrix, which is an ''over-aging'' state of Cu-Cr alloy at high temperature.

  2. Anisotropy of the solid–liquid interface properties of the Ni–Zr B33 phase from molecular dynamics simulation

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

    Wilson, S. R.; Mendelev, M. I.

    2015-01-08

    Solid–liquid interface (SLI) properties of the Ni–Zr B33 phase were determined from molecular dynamics simulations. In order to perform these measurements, a new semi-empirical potential for Ni–Zr alloy was developed that well reproduces the material properties required to model SLIs in the Ni50.0Zr50.0 alloy. In particular, the developed potential is shown to provide that the solid phase emerging from the liquid Ni50.0Zr50.0alloy is B33 (apart from a small fraction of point defects), in agreement with the experimental phase diagram. The SLI properties obtained using the developed potential exhibit an extraordinary degree of anisotropy. It is observed that anisotropies in bothmore » the interfacial free energy and mobility are an order of magnitude larger than those measured to date in any other metallic compound. Moreover, the [0 1 0] interface is shown to play a significant role in the observed anisotropy. Our data suggest that the [0 1 0] interface simultaneously corresponds to the lowest mobility, the lowest free energy and the highest stiffness of all inclinations in B33 Ni–Zr. This finding can be understood by taking into account a rather complicated crystal structure in this crystallographic direction.« less

  3. Effect of surface free energies on the heterogeneous nucleation of water droplet: A molecular dynamics simulation approach

    SciTech Connect (OSTI)

    Xu, W.; Lan, Z.; Peng, B. L.; Wen, R. F.; Ma, X. H.

    2015-02-07

    Heterogeneous nucleation of water droplet on surfaces with different solid-liquid interaction intensities is investigated by molecular dynamics simulation. The interaction potentials between surface atoms and vapor molecules are adjusted to obtain various surface free energies, and the nucleation process and wetting state of nuclei on surfaces are investigated. The results indicate that near-constant contact angles are already established for nano-scale nuclei on various surfaces, with the contact angle decreasing with solid-liquid interaction intensities linearly. Meanwhile, noticeable fluctuation of vapor-liquid interfaces can be observed for the nuclei that deposited on surfaces, which is caused by the asymmetric forces from vapor molecules. The formation and growth rate of nuclei are increasing with the solid-liquid interaction intensities. For low energy surface, the attraction of surface atoms to water molecules is comparably weak, and the pre-existing clusters can depart from the surface and enter into the bulk vapor phase. The distribution of clusters within the bulk vapor phase becomes competitive as compared with that absorbed on surface. For moderate energy surfaces, heterogeneous nucleation predominates and the formation of clusters within bulk vapor phase is suppressed. The effect of high energy particles that embedded in low energy surface is also discussed under the same simulation system. The nucleation preferably initiates on the high energy particles, and the clusters that formed on the heterogeneous particles are trapped around their original positions instead of migrating around as that observed on smooth surfaces. This feature makes it possible for the heterogeneous particles to act as fixed nucleation sites, and simulation results also suggest that the number of nuclei increases monotonously with the number of high energy particles. The growth of nuclei on high energy particles can be divided into three sub-stages, beginning with the formation

  4. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    SciTech Connect (OSTI)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  5. Adapting SAFT-? perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

    SciTech Connect (OSTI)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-07-14

    In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-? WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-? refers to the particular form of statistical associating fluid theory that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A new chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH{sub 2} and CH{sub 3} and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ?2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ?1% from simulation data while the theory reproduces

  6. Molecular dynamics of membrane proteins.

    SciTech Connect (OSTI)

    Woolf, Thomas B.; Crozier, Paul Stewart; Stevens, Mark Jackson

    2004-10-01

    Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.

  7. Simulations of the quart (101-bar1)/water interface: A comparison of classical force fields, ab initi molecular dynamics, and x-ray reflectivity experiments.

    SciTech Connect (OSTI)

    Skelton, Adam; Fenter, Paul; Kubicki, James D.; Wesolowski, David J; Cummings, Peter T

    2011-01-01

    Classical molecular dynamics (CMD) simulations of the (1011) surface of quartz interacting with bulk liquid water are performed using three different classical force fields, Lopes et al., ClayFF, and CHARMM water contact angle (CWCA), and compared to ab initio molecular dynamics (AIMD) and X-ray reflectivity (XR) results. The axial densities of the water and surface atoms normal to the surface are calculated and compared to previous XR experiments. Favorable agreement is shown for all the force fields with respect to the position of the water atoms. Analyses such as the radial distribution functions between water and hydroxyl atoms and the average cosine of the angle between the water dipole vector and the normal of the surface are also calculated for each force field. Significant differences are found between the different force fields from such analyses, indicating differing descriptions of the structured water in the near vicinity of the surface. AIMD simulations are also performed to obtain the water and hydroxyl structure for comparison among the predictions of the three classical force fields to better understand which force field is most accurate. It is shown that ClayFF exhibits the best agreement with the AIMD simulations for water hydroxyl radial distribution functions, suggesting that ClayFF treats the hydrogen bonding more accurately.

  8. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    SciTech Connect (OSTI)

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

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

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

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

  10. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

    SciTech Connect (OSTI)

    MacDermaid, Christopher M. Klein, Michael L.; Fiorin, Giacomo; Kashyap, Hemant K.; DeVane, Russell H.; Shinoda, Wataru; Klauda, Jeffery B.

    2015-12-28

    The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.

  11. Geochemical Reaction Mechanism Discovery from Molecular Simulation

    SciTech Connect (OSTI)

    Stack, Andrew G.; Kent, Paul R. C.

    2014-11-10

    Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineral surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.

  12. Geochemical Reaction Mechanism Discovery from Molecular Simulation

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

    Stack, Andrew G.; Kent, Paul R. C.

    2014-11-10

    Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less

  13. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

    SciTech Connect (OSTI)

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-03-07

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeperthe binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnOit has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.

  14. Application of computational fluid dynamics for the simulation of cryogenic molecular sieve bed absorber of hydrogen isotopes recovery system for Indian LLCB-TBM

    SciTech Connect (OSTI)

    Gayathri Devi, V.; Sircar, A.; Sarkar, B.

    2015-03-15

    One of the most challenging tasks in the design of the fuel cycle system lies in the effective design of Tritium Extraction System (TES) which involves proper extraction and purification of tritium in the fuel cycle of the fusion reactor. Indian Lead Lithium cooled Ceramic Breeder Test Blanket Module (LLCB-TBM) would extract hydrogen isotopes through Cryogenic Molecular Sieve Bed (CMSB) adsorber system. A prototype Hydrogen Isotopes Recovery System (HIRS) is being developed to validate the concepts for tritium extraction by adsorption mass transfer mechanism. In this study, a design model has been developed and analyzed to simulate the adsorption mass transfer kinetics in a fixed bed adsorption column. The simulation leads primarily to effective design of HIRS, which is a state-of-the-art technology. The paper describes the process simulation approach and the results of Computational Fluid Dynamics (CFD) analysis. The effects of different operating conditions are studied to investigate their influence on the hydrogen isotopes adsorption capacity. The results of the present simulation study would be used to understand the best optimized transport phenomenon before realizing the TES as a system for LLCB-TBM. (authors)

  15. Look-ahead Dynamic Simulation

    Energy Science and Technology Software Center (OSTI)

    2015-10-20

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

  16. Molecular dynamics simulation of radiation damage in CaCd{sub 6} quasicrystal cubic approximant up to 10 keV

    SciTech Connect (OSTI)

    Chen, P. H.; Avchachov, K.; Nordlund, K.; Pussi, K.

    2013-06-21

    Due to the peculiar nature of the atomic order in quasicrystals, examining phase transitions in this class of materials is of particular interest. Energetic particle irradiation can provide a way to modify the structure locally in a quasicrystal. To examine irradiation-induced phase transitions in quasicrystals on the atomic scale, we have carried out molecular dynamics simulations of collision cascades in CaCd{sub 6} quasicrystal cubic approximant with energies up to 10 keV at 0 and 300 K. The results show that the threshold energies depend surprisingly strongly on the local coordination environments. The energy dependence of stable defect formation exhibits a power-law dependence on cascade energy, and surviving defects are dominated by Cd interstitials and vacancies. Only a modest effect of temperature is observed on defect survival, while irradiation temperature increases lead to a slight increase in the average size of both vacancy clusters and interstitial clusters.

  17. Spectral shapes of Ar-broadened HCl lines in the fundamental band by classical molecular dynamics simulations and comparison with experiments

    SciTech Connect (OSTI)

    Tran, H.; Domenech, J.-L.

    2014-08-14

    Spectral shapes of isolated lines of HCl perturbed by Ar are investigated for the first time using classical molecular dynamics simulations (CMDS). Using reliable intermolecular potentials taken from the literature, these CMDS provide the time evolution of the auto-correlation function of the dipole moment, whose Fourier-Laplace transform leads to the absorption spectrum. In order to test these calculations, room temperature spectra of various lines in the fundamental band of HCl diluted in Ar are measured, in a large pressure range, with a difference-frequency laser spectrometer. Comparisons between measured and calculated spectra show that the CMDS are able to predict the large Dicke narrowing effect on the shape of HCl lines and to satisfactorily reproduce the shapes of HCl spectra at different pressures and for various rotational quantum numbers.

  18. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

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

    | Argonne Leadership Computing Facility Computationally Efficient Multiconfigurational Reactive Molecular Dynamics Authors: Takefumi Yamashita, Yuxing Peng, Chris Knight, Gregory A. Voth It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial

  19. Cantera Aerosol Dynamics Simulator

    Energy Science and Technology Software Center (OSTI)

    2004-09-01

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

  20. CO{sub 2} isolated line shapes by classical molecular dynamics simulations: Influence of the intermolecular potential and comparison with new measurements

    SciTech Connect (OSTI)

    Larcher, G.; Tran, H. Schwell, M.; Chelin, P.; Landsheere, X.; Hartmann, J.-M.; Hu, S.-M.

    2014-02-28

    Room temperature absorption spectra of various transitions of pure CO{sub 2} have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 μm and 0.8 μm regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO{sub 2} lines, in terms of both the Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO{sub 2} transitions are almost independent of the rotational quantum number of the considered lines.

  1. A molecular dynamics investigation of the unusual concentration...

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

    138, 228-234 (2011) DOI: 10.1016j.micromeso.2010.09.032 Full-size image (19 K) Abstract: Molecular Dynamics (MD) simulations were carried out to determine the self-diffusivitiy,...

  2. A molecular dynamics investigation of the diffusion characteristics...

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

    137, 83-91 (2011) DOI: 10.1016j.micromeso.2010.08.026 Full-size image (36 K) Abstract: Molecular dynamics (MD) simulations are used to investigate the diffusion characteristics...

  3. Nanoparticle generation and transport resulting from femtosecond laser ablation of ultrathin metal films: Time-resolved measurements and molecular dynamics simulations

    SciTech Connect (OSTI)

    Rouleau, C. M. Puretzky, A. A.; Geohegan, D. B.; Shih, C.-Y.; Wu, C.; Zhigilei, L. V.

    2014-05-12

    The synthesis of metal nanoparticles by ultrafast laser ablation of nanometers-thick metal films has been studied experimentally and computationally. Near-threshold backside laser ablation of 2–20 nm-thick Pt films deposited on fused silica substrates was found to produce nanoparticles with size distributions that were bimodal for the thicker films, but collapsed into a single mode distribution for the thinnest film. Time-resolved imaging of blackbody emission from the Pt nanoparticles was used to reveal the nanoparticle propagation dynamics and estimate their temperatures. The observed nanoparticle plume was compact and highly forward-directed with a well-defined collective velocity that permitted multiple rebounds with substrates to be revealed. Large-scale molecular dynamics simulations were used to understand the evolution of compressive and tensile stresses in the thicker melted liquid films that lead to their breakup and ejection of two groups of nanoparticles with different velocity and size distributions. Ultrafast laser irradiation of ultrathin (few nm) metal films avoids the splitting of the film and appears to be a method well-suited to cleanly synthesize and deposit nanoparticles from semitransparent thin film targets in highly directed beams.

  4. Molecular dynamics simulations and thermochemistry of reactive ion etching of silicon by chlorine, chlorine dimer, bromine, and bromine dimer cations

    SciTech Connect (OSTI)

    Valone, S.M.; Hanson, D.E.; Kress, J.D.

    1998-05-08

    Simulations of Cl plasma etch of Si surfaces with MD techniques agree reasonably well with the available experimental information on yields and surface morphologies. This information has been supplied to a Monte Carlo etch profile resulting in substantial agreement with comparable inputs provided through controlled experiments. To the extent that more recent measurements of etch rates are more reliable than older ones, preliminary MD simulations using bond-order corrections to the atomic interactions between neighboring Si atoms on the surface improves agreement with experiment through an increase in etch rate and improved agreement with XPS measurements of surface stoichiometry. Thermochemical and geometric analysis of small Si-Br molecules is consistent with the current notions of the effects of including brominated species in etchant gases.

  5. Thermal transport in UO2 with defects and fission products by molecular dynamics simulations

    SciTech Connect (OSTI)

    Liu, Xiang-Yang; Cooper, Michael William Donald; Mcclellan, Kenneth James; Lashley, Jason Charles; Byler, Darrin David; Stanek, Christopher Richard; Andersson, Anders David Ragnar

    2015-10-14

    The importance of the thermal transport in nuclear fuel has motivated a wide range of experimental and modelling studies. In this report, the reduction of thermal transport in UO2 due to defects and fission products has been investigated using non-equilibrium MD simulations, with two sets of empirical potentials for studying the degregation of UO2 thermal conductivity including a Buckingham type interatomic potential and a recently developed EAM type interatomic potential. Additional parameters for U5+ and Zr4+ in UO2 have been developed for the EAM potential. The thermal conductivity results from MD simulations are then corrected for the spin-phonon scattering through Callaway model formulations. To validate the modelling results, comparison was made with experimental measurements on single crystal hyper-stoichiometric UO2+x samples.

  6. 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 −}.

  7. Ab initio molecular dynamics simulations of short-range order in Zr50Cu45Al5 and Cu50Zr45Al5 metallic glasses

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

    Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

    2016-02-01

    Comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0 > is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2 > and < 0,2,8,1 >, are prominent. And the < 0,2,8,2 > polyhedra in Cu50Zr45Al5more » MG mainly originate from Al-centered clusters, while the < 0,0,12,0 > in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. Lastly, the relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.« less

  8. Ab initio molecular dynamics simulations of short-range order in Zr50Cu45Al5 and Cu50Zr45Al5 metallic glasses

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

    Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

    2016-02-01

    In this study, comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons <0,0,12,0> is dominant, and in the Cu-rich one the distorted icosahedral orders, especially <0,2,8,2> and <0,2,8,1>, are prominent. And the <0,2,8,2> polyhedra in Cu50Zr45Al5 MG mainly originate from Al-centeredmore » clusters, while the <0,0,12,0> in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. The relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.« less

  9. Quantitative in-situ scanning electron microscope pull-out experiments and molecular dynamics simulations of carbon nanotubes embedded in palladium

    SciTech Connect (OSTI)

    Hartmann, S., E-mail: steffen.hartmann@etit.tu-chemnitz.de; Blaudeck, T.; Hermann, S.; Wunderle, B. [Technische Universitt Chemnitz, Reichenhainer Str. 70, 09126 Chemnitz (Germany); Hlck, O. [Technische Universitt Chemnitz, Reichenhainer Str. 70, 09126 Chemnitz (Germany); Fraunhofer IZM Berlin, Gustav-Meyer-Allee 25, 13355 Berlin (Germany); Schulz, S. E.; Gessner, T. [Technische Universitt Chemnitz, Reichenhainer Str. 70, 09126 Chemnitz (Germany); Fraunhofer ENAS Chemnitz, Technologie-Campus 3, 09126 Chemnitz (Germany)

    2014-04-14

    In this paper, we present our results of experimental and numerical pull-out tests on carbon nanotubes (CNTs) embedded in palladium. We prepared simple specimens by employing standard silicon wafers, physical vapor deposition of palladium and deposition of CNTs with a simple drop coating technique. An AFM cantilever with known stiffness connected to a nanomanipulation system was utilized inside a scanning electron microscope (SEM) as a force sensor to determine forces acting on a CNT during the pull-out process. SEM-images of the cantilever attached to a CNT have been evaluated for subsequent displacement steps with greyscale correlation to determine the cantilever deflection. We compare the experimentally obtained pull-out forces with values of numerical investigations by means of molecular dynamics and give interpretations for deviations according to material impurities or defects and their influence on the pull-out data. We find a very good agreement of force data from simulation and experiment, which is 17 nN and in the range of 1061 nN, respectively. Our findings contribute to the ongoing research of the mechanical characterization of CNT-metal interfaces. This is of significant interest for the design of future mechanical sensors utilizing the intrinsic piezoresistive effect of CNTs or other future devices incorporating CNT-metal interfaces.

  10. The thermal conductivity of mixed fuel UxPu1-xO2: molecular dynamics simulations

    SciTech Connect (OSTI)

    Liu, Xiang-Yang; Cooper, Michael William Donald; Stanek, Christopher Richard; Andersson, Anders David Ragnar

    2015-10-16

    Mixed oxides (MOX), in the context of nuclear fuels, are a mixture of the oxides of heavy actinide elements such as uranium, plutonium and thorium. The interest in the UO2-PuO2 system arises from the fact that these oxides are used both in fast breeder reactors (FBRs) as well as in pressurized water reactors (PWRs). The thermal conductivity of UO2 fuel is an important material property that affects fuel performance since it is the key parameter determining the temperature distribution in the fuel, thus governing, e.g., dimensional changes due to thermal expansion, fission gas release rates, etc. For this reason it is important to understand the thermal conductivity of MOX fuel and how it differs from UO2. Here, molecular dynamics (MD) simulations are carried out to determine quantitatively, the effect of mixing on the thermal conductivity of UxPu1-xO2, as a function of PuO2 concentrations, for a range of temperatures, 300 – 1500 K. The results will be used to develop enhanced continuum thermal conductivity models for MARMOT and BISON by INL. These models express the thermal conductivity as a function of microstructure state-variables, thus enabling thermal conductivity models with closer connection to the physical state of the fuel.

  11. Large-Scale Condensed Matter and Fluid Dynamics Simulations in Three

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

    Diverse Areas: Part II: Molecular Dynamics Study of Clay-Polymer Nanocomposites | Argonne Leadership Computing Facility Snapshot from a molecular dynamics simulation of a system containing 16 isolated clay sheets immersed in a polymer melt. , Snapshot from a molecular dynamics simulation of an isolated clay platelet (consisting of two sheets) immersed in water. Top image: Snapshot from a molecular dynamics simulation of a system containing 16 isolated clay sheets immersed in a polymer melt.

  12. Dynamic Power Grid Simulation

    Energy Science and Technology Software Center (OSTI)

    2015-09-14

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

  13. Entropy of Liquid Water from Ab Initio Molecular Dynamics | Argonne

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

    Leadership Computing Facility Entropy of Liquid Water from Ab Initio Molecular Dynamics Authors: Zhang, C., Spanu,L., Galli, G. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations. We present the results obtained with semilocal, hybrid, and van der Waals density functionals. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the

  14. Application of optimal prediction to molecular dynamics

    SciTech Connect (OSTI)

    Barber IV, John Letherman

    2004-12-01

    Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is {delta}-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.

  15. Evaluating mixture adsorption models using molecular simulation...

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

    molecular simulation Previous Next List Joseph A. Swisher, Li-Chiang Lin, Jihan Kim, Berend Smit, AICHE J., 59, 3054-3064 (2013) DOI: 10.1002aic.14058 Abstract: The design of ...

  16. Dynamic Simulation Nuclear Power Plants

    Energy Science and Technology Software Center (OSTI)

    1992-03-03

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

  17. Molecular Simulation of Carbon Dioxide, Brine, and Clay Mineral...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Molecular Simulation of Carbon Dioxide, Brine, and Clay Mineral Citation Details In-Document Search Title: Molecular Simulation of Carbon Dioxide, Brine, and Clay ...

  18. Parallel Molecular Dynamics Program for Molecules

    Energy Science and Technology Software Center (OSTI)

    1995-03-07

    ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.

  19. On Eliminating Synchronous Communication in Molecular Simulations to Improve Scalability

    SciTech Connect (OSTI)

    Straatsma, TP; Chavarría-Miranda, Daniel

    2013-12-01

    Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular systems as it provides access to properties that are difficult, impossible or prohibitively expensive to obtain experimentally. Many of the available software packages have been parallelized to take advantage of modern massively concurrent processing resources. The challenge in achieving parallel efficiency is commonly attributed to the fact that molecular dynamics algorithms are communication intensive. This paper illustrates how an appropriately chosen data distribution and asynchronous one-sided communication approach can be used to effectively deal with the data movement within the Global Arrays/ARMCI programming model framework. A new put_notify capability is presented here, allowing the implementation of the molecular dynamics algorithm without any explicit global or local synchronization or global data reduction operations. In addition, this push-data model is shown to very effectively allow hiding data communication behind computation. Rather than data movement or explicit global reductions, the implicit synchronization of the algorithm becomes the primary challenge for scalability. Without any explicit synchronous operations, the scalability of molecular simulations is shown to depend only on the ability to evenly balance computational load.

  20. Optimizing legacy molecular dynamics software with directive-based offload

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

    Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

    2015-05-14

    The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.« less

  1. Optimizing legacy molecular dynamics software with directive-based offload

    SciTech Connect (OSTI)

    Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

    2015-05-14

    The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.

  2. First principles molecular dynamics without self-consistent field optimization

    SciTech Connect (OSTI)

    Souvatzis, Petros; Niklasson, Anders M. N.

    2014-01-28

    We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.

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

    SciTech Connect (OSTI)

    Loyalka, Sudarshan

    2015-04-09

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

  4. Molecular Dynamics and Energy Minimization Based on Embedded Atom Method

    Energy Science and Technology Software Center (OSTI)

    1995-03-01

    This program performs atomic scale computer simulations of the structure and dynamics of metallic system using energetices based on the Embedded Atom Method. The program performs two types of calculations. First, it performs local energy minimization of all atomic positions to determine ground state and saddle point energies and structures. Second, it performs molecular dynamics simulations to determine thermodynamics or miscroscopic dynamics of the system. In both cases, various constraints can be applied to themore » system. The volume of the system can be varied automatically to achieve any desired external pressure. The temperature in molecular dynamics simulations can be controlled by a variety of methods. Further, the temperature control can be applied either to the entire system or just a subset of the atoms that would act as a thermal source/sink. The motion of one or more of the atoms can be constrained to either simulate the effects of bulk boundary conditions or to facilitate the determination of saddle point configurations. The simulations are performed with periodic boundary conditions.« less

  5. 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.

  6. Molecular dynamics simulations of the electrical double layer on smectite surfaces contacting concentrated mixed electrolyte (NaCl-CaCl?) solutions

    SciTech Connect (OSTI)

    Bourg, Ian C.; Sposito, Garrison

    2011-01-01

    We report new molecular dynamics results elucidating the structure of the electrical double layer (EDL) on smectite surfaces contacting mixed NaClCaCl2 electrolyte solutions in the range of concentrations relevant to pore waters in geologic repositories for CO2 or high-level radioactive waste (0.341.83 molc dm-3). Our results confirm the existence of three distinct ion adsorption planes (0-, ?-, and d-planes), often assumed in EDL models, but with two important qualifications: (1) the location of the ?- and d-planes are independent of ionic strength or ion type and (2) indifferent electrolyte ions can occupy all three planes. Charge inversion occurred in the diffuse ion swarm because of the affinity of the clay surface for CaCl+ ion pairs. Therefore, at concentrations {>=0.34 molc dm-3}, properties arising from long-range electrostatics at interfaces (electrophoresis, electro-osmosis, co-ion exclusion, colloidal aggregation) will not be correctly predicted by most EDL models. Co-ion exclusion, typically neglected by surface speciation models, balanced a large part of the clay mineral structural charge in the more concentrated solutions. Water molecules and ions diffused relatively rapidly even in the first statistical water monolayer, contradicting reports of rigid ice-like structures for water on clay mineral surfaces.

  7. Multiscale reactive molecular dynamics | Argonne Leadership Computing

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

    Facility reactive molecular dynamics Authors: Chris KnighT, Gerrick E. Lindberg, Gregory A. Voth Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data

  8. Structure, solvation, and dynamics of Mg{sup 2+}, Ca{sup 2+}, Sr{sup 2+}, and Ba{sup 2+} complexes with 3-hydroxyflavone and perchlorate anion in acetonitrile medium: A molecular dynamics simulation study

    SciTech Connect (OSTI)

    Agieienko, Vira N.; Kolesnik, Yaroslav V.; Kalugin, Oleg N.

    2014-05-21

    Molecular dynamics simulations of complexes of Mg{sup 2+}, Ca{sup 2+}, Sr{sup 2+}, and Ba{sup 2+} with 3-hydroxyflavone (flavonol, 3HF) and ClO {sub 4}{sup ?} in acetonitrile were performed. The united atoms force field model was proposed for the 3HF molecule using the results of DFT quantum chemical calculations. 3HF was interpreted as a rigid molecule with two internal degrees of freedom, i.e., rotation of the phenyl ring and of the OH group with respect to the chromone moiety. The interatomic radial distribution functions showed that interaction of the cations with flavonol occurs via the carbonyl group of 3HF and it is accompanied with substitution of one of the acetonitrile molecules in the cations first solvation shells. Formation of the cation3HF complexes does not have significant impact on the rotation of the phenyl ring with respect to the chromone moiety. However, the orientation of the flavonol's OH-group is more sensitive to the interaction with doubly charged cations. When complex with Mg{sup 2+} is formed, the OH-group turns out of the plane of the chromone moiety that leads to rupture of intramolecular H-bond in the ligand molecule. Complexation of Ca{sup 2+}, Sr{sup 2+}, and BaClO {sub 4}{sup +} with 3HF produces two structures with different OH-positions, as in the free flavonol with the intramolecular H-bond and as in the complex with Mg{sup 2+} with disrupted H-bonding. It was shown that additional stabilization of the [MgClO{sub 4}(3HF)]{sup +} and [BaClO{sub 4}(3HF)]{sup +} complexes is determined by strong affinity of perchlorate anion to interact with flavonol via intracomplex hydrogen bond between an oxygen atom of the anion and the hydrogen atom of the 3-hydroxyl group. Noticeable difference in the values of the self-diffusion coefficients for Kt{sup 2+} from one side and ClO {sub 4}{sup ?}, 3HF, and AN in the cations coordination shell from another side implies quite weak interaction between cation, anion, and ligands in the

  9. Analysis of Molecular Clusters in Simulations of Lithium-Ion...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Analysis of Molecular Clusters in Simulations of Lithium-Ion Battery Electrolytes. Citation Details In-Document Search Title: Analysis of Molecular Clusters in ...

  10. Reaction dynamics in polyatomic molecular systems

    SciTech Connect (OSTI)

    Miller, W.H.

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  11. Dynamics Simulation in a Wave Environment

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

    focus: Advanced Naval concepts Also have projects in: Offshore Platforms Wave Energy Converters Wind Power 3 Coupled Dynamics (AEGIR Co-simulation Capability) * Interprocess ...

  12. A molecular dynamics study of polymer/graphene interfacial systems

    SciTech Connect (OSTI)

    Rissanou, Anastassia N.; Harmandaris, Vagelis

    2014-05-15

    Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

  13. simulate the dynamic distribution of lithium in the electrode

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

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

  14. 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.

  15. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect (OSTI)

    Nesbitt, David J.

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

  16. Molecular Dynameomics

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

    Dynameomics Molecular Dynameomics DaggettHiResWhitebg.png Key Challenges: Perform molecular dynamics simulations to characterize both native (i.e. biologically active) and...

  17. Nano-crystallization and magnetic mechanisms of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy by ab initio molecular dynamics simulation

    SciTech Connect (OSTI)

    Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro; Liang, Yunye; Kawazoe, Yoshiyuki

    2014-05-07

    Iron-based amorphous and nano-crystalline alloys have attracted a growing interest due to their potential in the application of magnetic coil production. However, fundamental understanding of the nano-crystallization mechanisms and magnetic features in the amorphous structure are still lack of knowledge. In the present work, we performed ab initio molecular dynamics simulation to clarify the ionic and electronic structure in atomic scale, and to derive the origin of the good magnetic property of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy. The simulation gave a direct evidence of the Cu-P bonding preference in the amorphous alloy, which may promote nucleation in nano-crystallization process. On the other hand, the electron transfer and the band/orbital features in the amorphous alloy suggests that alloying elements with large electronegativity and the potential to expand Fe disordered matrix are preferred for enhancing the magnetization.

  18. Investigation of Interfacial and Bulk Dissociation of HBr, HCl, and HNO3 Using Density Functional Theory-Based Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    Baer, Marcel; Tobias, Douglas J.; Mundy, Christopher J.

    2014-12-18

    In this study we investigate the free energy barrier associated with the dissociation of strong acids, XH (HBr, HCl and HNO3) deprotonation, and subsequent formation of ionpairs, X___H3O+ in the vicinity of the air-water interface. We will show that the free energy for acid dissociation for HCl and HNO3 show significant differences at the air-water than under bulk solvation conditions producing a picture where at the interface associated molecular species can be stable. For the strongest acid we consider, HBr the more traditional picture of acids is preserved in the vicinity of the air-water interface. Our results have implications for our understanding of acids, and their surface tensions at the air-water interface.

  19. Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo

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

    White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry

    2015-07-07

    Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficientmore » as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.« less

  20. Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo

    SciTech Connect (OSTI)

    White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry

    2015-07-07

    Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.

  1. Accelerated molecular dynamics methods: introduction and recent developments

    SciTech Connect (OSTI)

    Uberuaga, Blas Pedro; Voter, Arthur F; Perez, Danny; Shim, Y; Amar, J G

    2009-01-01

    A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what

  2. United polarizable multipole water model for molecular mechanics simulation

    SciTech Connect (OSTI)

    Qi, Rui; Wang, Qiantao; Ren, Pengyu; Wang, Lee-Ping; Pande, Vijay S.

    2015-07-07

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

  3. Molecular Simulation of Carbon Dioxide Brine and Clay Mineral...

    Office of Scientific and Technical Information (OSTI)

    of Carbon Dioxide Brine and Clay Mineral Interactions and Determination of Contact Angles. Citation Details In-Document Search Title: Molecular Simulation of Carbon Dioxide ...

  4. Molecular Simulation of Carbon Dioxide Nanodroplets on Clay in...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Molecular Simulation of Carbon Dioxide Nanodroplets on Clay in Deep Saline Aquifers. Authors: Tenney, Craig M. Publication Date: ...

  5. Molecular Simulation of Carbon Dioxide Nanodroplets on Clay Surfaces...

    Office of Scientific and Technical Information (OSTI)

    Surfaces in Deep Saline Aquifers. Citation Details In-Document Search Title: Molecular Simulation of Carbon Dioxide Nanodroplets on Clay Surfaces in Deep Saline Aquifers. Authors: ...

  6. Reactive Molecular Simulations of Protonation of Water Clusters...

    Office of Scientific and Technical Information (OSTI)

    of Water Clusters and Depletion of Acidity in H-ZSM-5 Zeolite Citation Details In-Document Search Title: Reactive Molecular Simulations of Protonation of Water Clusters ...

  7. The high pressure structure and equation of state of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) up to 20 GPa: X-ray diffraction measurements and first principles molecular dynamics simulations

    SciTech Connect (OSTI)

    Stavou, Elissaios; Manaa, M. Riad; Zaug, Joseph M.; Kuo, I-Feng W.; Pagoria, Philip F.; Crowhurst, Jonathan C.; Armstrong, Michael R.; Kalkan, Bora

    2015-10-14

    Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. As a result, we find very good agreement between the experimental and theoretically derived EOS.

  8. The high pressure structure and equation of state of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) up to 20 GPa: X-ray diffraction measurements and first principles molecular dynamics simulations

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

    Stavou, Elissaios; Manaa, M. Riad; Zaug, Joseph M.; Kuo, I-Feng W.; Pagoria, Philip F.; Crowhurst, Jonathan C.; Armstrong, Michael R.; Kalkan, Bora

    2015-10-14

    Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phasemore » transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. As a result, we find very good agreement between the experimental and theoretically derived EOS.« less

  9. Isomorphic phase transformation in shocked cerium using molecular dynamics

    SciTech Connect (OSTI)

    Dupont, Virginie; Germann, Timothy C; Chen, Shao - Ping

    2010-08-12

    Cerium (Ce) undergoes a significant ({approx}16%) volume collapse associated with an isomorphic fcc-fcc phase transformation when subject to compressive loading. We present here a new Embedded Atom Method (EAM) potential for Cerium that models two minima for the two fcc phases. We show results from its use in Molecular Dynamics (MD) simulations of Ce samples subjected to shocks with pressures ranging from 0.5 to 25 GPa. A split wave structure is observed, with an elastic precursor followed by a plastic wave. The plastic wave causes the expected fcc-fcc phase transformation. Comparisons to experiments and MD simulations on Cesium (Cs) indicate that three waves could be observed. The construction of the EAM potential may be the source of the difference.

  10. Mechanical unfolding of a beta-hairpin using molecular dynamics

    SciTech Connect (OSTI)

    Bryant, Zev; Pande, Vijay S.; Rokhsar, Daniel S.

    1999-10-16

    Single molecule mechanical unfolding experiments have the potential to provide insights into the details of protein folding pathways. To investigate the relationship between force-extension unfolding curves and microscopic events, we performed molecular dynamics simulations of the mechanical unfolding of the C-terminal hairpin of protein G. We have studied the dependence of the unfolding pathway on pulling speed, cantilever stiffness, and attachment points. Under conditions which generate low forces, the unfolding trajectory mimics the untethered, thermally accessible pathway previously proposed based on high temperature studies. In this stepwise pathway, complete breakdown of backbone hydrogen bonds precedes dissociation of the hydrophobic cluster. Under more extreme conditions, the cluster and hydrogen bonds break simultaneously. Transitions between folding intermediates can be identified in our simulations as features of the calculated force-extension curves.

  11. Dynamic procedure for filtered gyrokinetic simulations

    SciTech Connect (OSTI)

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

    2012-01-15

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

  12. Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

    SciTech Connect (OSTI)

    Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M.

    2014-10-15

    The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

  13. Dynamic Fracture Simulations of Explosively Loaded Cylinders

    SciTech Connect (OSTI)

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

    2015-11-30

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

  14. Dynamic simulation gives 20-20 foresight

    SciTech Connect (OSTI)

    Womack, J.W.

    1986-04-07

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

  15. Molecular beam studies of reaction dynamics

    SciTech Connect (OSTI)

    Lee, Y.T.

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

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

    Office of Scientific and Technical Information (OSTI)

    DOE Contract Number: DE-AC52-07NA27344 Resource Type: Conference Resource Relation: Conference: Presented at: SPIE Photonics West LASE 2015, San Francisco, CA, United States, Feb ...

  17. Nonequilibrium Molecular Dynamics Simulations of the Rheology...

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

    ... usage N*100 bytes <10GB >10GB Current LAMMPS, GROMACS, NAMD, DLPOLY,.... VASP, Qbox, Pwscf VASP, PEtot Future Library... requiring 1000 to 10000 energy evaluations Typical ...

  18. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

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

    Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

  19. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    SciTech Connect (OSTI)

    Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology.

  20. Final report [Molecular simulations of complex fluids in confined geometrics

    SciTech Connect (OSTI)

    Gehrke, Stevin H.; Jiang, Shaoyi

    2002-07-22

    This award supports collaborative research between Kansas State University and Sandia National Laboratories on the topic ''Molecular simulations of complex fluids in confined geometries.'' The objectives of this work are to develop new methodologies for fast and accurate simulations, and to apply simulations to various problems of interest to DOE. The success of this work will address several deficiencies in Sandia's capabilities in the area of molecular simulations. In addition, it provides educational opportunities for students and will enhance the science and technology capabilities at Kansas State through partnership with the national laboratories.

  1. On Extended-Term Dynamic Simulations

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

    Extended-Term Dynamic Simulations with High Penetrations of Photovoltaic Generation Ricky Concepcion, Ryan Elliott Sandia National Laboratories Albuquerque, NM 87185 {rconcep, rtellio}@sandia.gov Matt Donnelly Montana Tech Butte, MT 59701 mdonnelly@mtech.edu Juan Sanchez-Gasca GE Energy Schenectady, NY 12345 juan1.sanchez@ge.com Abstract-The uncontrolled intermittent availability of renew- able energy sources makes integration of such devices into today's grid a challenge. Thus, it is imperative

  2. Integrated computer simulation on FIR FEL dynamics

    SciTech Connect (OSTI)

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

    1995-12-31

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

  3. Multiscale Molecular Simulations at the Petascale (Parallelization of

    Office of Scientific and Technical Information (OSTI)

    Reactive Force Field Model for Blue Gene/Q): ALCF-2 Early Science Program Technical Report (Technical Report) | SciTech Connect Multiscale Molecular Simulations at the Petascale (Parallelization of Reactive Force Field Model for Blue Gene/Q): ALCF-2 Early Science Program Technical Report Citation Details In-Document Search Title: Multiscale Molecular Simulations at the Petascale (Parallelization of Reactive Force Field Model for Blue Gene/Q): ALCF-2 Early Science Program Technical Report

  4. Computational simulation of dynamic impact problems

    SciTech Connect (OSTI)

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

    1996-12-31

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

  5. Atomic, molecular, and nuclear quantum dynamics and control in...

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

    Atomic, molecular, and nuclear quantum dynamics and control in (strong) visible to x-ray (laser) fields Wednesday, July 20, 2016 - 3:00pm SLAC, Redtail Hawk Conference Room 108A ...

  6. Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics...

    Office of Scientific and Technical Information (OSTI)

    Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C-H Region of DMSO as a Case Study Citation Details In-Document Search Title: ...

  7. 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.

  8. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics

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

    for Absolute Ligand Binding | Argonne Leadership Computing Facility Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics for Absolute Ligand Binding Authors: Jiang, W., Roux, B. Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of

  9. Deposition of cobalt atoms onto Alq 3 films: A molecular dynamics...

    Office of Scientific and Technical Information (OSTI)

    Deposition of cobalt atoms onto Alq 3 films: A molecular dynamics study Prev Next Title: Deposition of cobalt atoms onto Alq 3 films: A molecular dynamics study Authors: ...

  10. Dynamical analysis of highly excited molecular spectra

    SciTech Connect (OSTI)

    Kellman, M.E.

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  11. Temperature dependence of creep compliance of highly cross-linked epoxy: A molecular simulation study

    SciTech Connect (OSTI)

    Khabaz, Fardin Khare, Ketan S. Khare, Rajesh

    2014-05-15

    We have used molecular dynamics (MD) simulations to study the effect of temperature on the creep compliance of neat cross-linked epoxy. Experimental studies of mechanical behavior of cross-linked epoxy in literature commonly report creep compliance values, whereas molecular simulations of these systems have primarily focused on the Youngs modulus. In this work, in order to obtain a more direct comparison between experiments and simulations, atomistically detailed models of the cross-linked epoxy are used to study their creep compliance as a function of temperature using MD simulations. The creep tests are performed by applying a constant tensile stress and monitoring the resulting strain in the system. Our results show that simulated values of creep compliance increase with an increase in both time and temperature. We believe that such calculations of the creep compliance, along with the use of time temperature superposition, hold great promise in connecting the molecular insight obtained from molecular simulation at small length- and time-scales with the experimental behavior of such materials. To the best of our knowledge, this work is the first reported effort that investigates the creep compliance behavior of cross-linked epoxy using MD simulations.

  12. Filaments in simulations of molecular cloud formation

    SciTech Connect (OSTI)

    Gmez, Gilberto C.; Vzquez-Semadeni, Enrique

    2014-08-20

    We report on the filaments that develop self-consistently in a new numerical simulation of cloud formation by colliding flows. As in previous studies, the forming cloud begins to undergo gravitational collapse because it rapidly acquires a mass much larger than the average Jeans mass. Thus, the collapse soon becomes nearly pressureless, proceeding along its shortest dimension first. This naturally produces filaments in the cloud and clumps within the filaments. The filaments are not in equilibrium at any time, but instead are long-lived flow features through which the gas flows from the cloud to the clumps. The filaments are long-lived because they accrete from their environment while simultaneously accreting onto the clumps within them; they are essentially the locus where the flow changes from accreting in two dimensions to accreting in one dimension. Moreover, the clumps also exhibit a hierarchical nature: the gas in a filament flows onto a main, central clump but other, smaller-scale clumps form along the infalling gas. Correspondingly, the velocity along the filament exhibits a hierarchy of jumps at the locations of the clumps. Two prominent filaments in the simulation have lengths ?15 pc and masses ?600 M {sub ?} above density n ? 10{sup 3} cm{sup 3} (?2 10{sup 3} M {sub ?} at n > 50 cm{sup 3}). The density profile exhibits a central flattened core of size ?0.3 pc and an envelope that decays as r {sup 2.5} in reasonable agreement with observations. Accretion onto the filament reaches a maximum linear density rate of ?30 M {sub ?} Myr{sup 1} pc{sup 1}.

  13. Dynamics of micelle-nanoparticle systems undergoing shear: a coarse-grained molecular dynamics approach

    SciTech Connect (OSTI)

    Rolfe, Bryan A.; Chun, Jaehun; Joo, Yong L.

    2013-09-05

    Recent experimental work has shown that polymeric micelles can template nanoparticles via interstitial sites in shear-ordered micelle solutions. In the current study, we report simulation results based on a coarse-grained molecular dynamics (CGMD) model of a solvent/polymer/nanoparticle system. Our results demonstrate the importance of polymer concentration and the micelle corona length in 2D shear-ordering of neat block copolymer solutions. Although our results do not show strong 3D ordering during shear, we find that cessation of shear allows the system to relax into a 3D configuration of greater order than without shear. It is further shown that this post-shear relaxation is strongly dependent on the length of the micelle corona. For the first time, we demonstrate the presence and importance of a flow disturbance surrounding micelles in simple shear flow at moderate Pclet numbers. This disturbance is similar to what is observed around simulated star polymers and ellipsoids. The extent of the flow disturbance increases as expected with a longer micelle corona length. It is further suggested that without proper consideration of these dynamics, a stable nanoparticle configuration would be difficult to obtain.

  14. VUV studies of molecular photofragmentation dynamics

    SciTech Connect (OSTI)

    White, M.G.

    1993-12-01

    State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.

  15. 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.

  16. Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

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

    Borreguero Calvo, Jose M.; Lynch, Vickie E.

    2015-11-23

    Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulationmore » due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.« less

  17. Comparison of binary collision approximation and molecular dynamics for displacement cascades in GaAs.

    SciTech Connect (OSTI)

    Foiles, Stephen Martin

    2011-10-01

    The predictions of binary collision approximation (BCA) and molecular dynamics (MD) simulations of displacement cascades in GaAs are compared. There are three issues addressed in this work. The first is the optimal choice of the effective displacement threshold to use in the BCA calculations to obtain the best agreement with MD results. Second, the spatial correlations of point defects are compared. This is related to the level of clustering that occurs for different types of radiation. Finally, the size and structure of amorphous zones seen in the MD simulations is summarized. BCA simulations are not able to predict the formation of amorphous material.

  18. State-to-state dynamics of molecular energy transfer

    SciTech Connect (OSTI)

    Gentry, W.R.; Giese, C.F.

    1993-12-01

    The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

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

    Office of Scientific and Technical Information (OSTI)

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

  20. Input File Creation for the Molecular Dynamics Program LAMMPS.

    Energy Science and Technology Software Center (OSTI)

    2001-05-30

    The program creates an input data file for the molecular dynamics program LAMMPS. The input file created is a liquid mixture between two walls explicitly composed of particles. The liquid molecules are modeled as a bead-spring molecule. The input data file specifies the position and topology of the starting state. The data structure of input allows for dynamic bond creation (cross-linking) within the LAMMPS code.

  1. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

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

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-He

    2015-02-25

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Moreover, our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of themore » substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, furthermore, we predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  2. Molecular dynamics investigation of the substrate binding mechanism in carboxylesterase

    SciTech Connect (OSTI)

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-he

    2015-01-01

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of the substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, we further predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase rPPEs, which will help guide

  3. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

    SciTech Connect (OSTI)

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-He

    2015-02-25

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Moreover, our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of the substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, furthermore, we predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  4. Rotational Brownian Dynamics simulations of clathrin cage formation

    SciTech Connect (OSTI)

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

    2014-08-14

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

  5. Self-consistent field theory based molecular dynamics with linear system-size scaling

    SciTech Connect (OSTI)

    Richters, Dorothee; Khne, Thomas D.

    2014-04-07

    We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

  6. Expansion techniques for collisionless stellar dynamical simulations

    SciTech Connect (OSTI)

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

    2014-09-10

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

  7. Kinetic simulations of plasmoid chain dynamics

    SciTech Connect (OSTI)

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

    2013-08-15

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

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

    SciTech Connect (OSTI)

    Concepcion, Ricky James; Elliott, Ryan Thomas

    2015-12-01

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

  9. Cell multipole method for molecular simulations in bulk and confined systems

    SciTech Connect (OSTI)

    Zheng, Jie; Balasundaram, Ramkumar; Gehrke, Stevin H.; Heffelfinger, Grant S.; Goddard, William A. III; Jiang, Shaoyi

    2002-08-01

    One of the bottlenecks in molecular simulations is to treat large systems involving electrostatic interactions. Computational time in conventional molecular simulation methods scales with O(N{sup 2}), where N is the number of atoms. With the emergence of the cell multipole method (CMM) and massively parallel supercomputers, simulations of 10 million atoms have been performed. In this work, the optimal hierarchy cell level and the algorithm for Taylor expansion were recommended for fast and accurate molecular dynamics (MD) simulations of three-dimensional (3D) systems. CMM was then extended to treat quasi-two-dimensional (2D) systems, which is very important for condensed matter physics problems. In addition, CMM was applied to grand canonical ensemble Monte Carlo (GCMC) simulations for both 3D and 2D systems. Under the optimal conditions, the results show that computational time is approximately linear with N for large systems, average error in total potential energy is less than {approx}1%, and RMS force is about 0.015 for 3D and 2D systems when compared with the Ewald summation.

  10. Wetting kinetics of water nano-droplet containing non-surfactant nanoparticles: A molecular dynamics study

    SciTech Connect (OSTI)

    Lu, Gui; Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104 ; Hu, Han; Sun, Ying E-mail: ysun@coe.drexel.edu; Duan, Yuanyuan E-mail: ysun@coe.drexel.edu

    2013-12-16

    In this Letter, dynamic wetting of water nano-droplets containing non-surfactant gold nanoparticles on a gold substrate is examined via molecular dynamics simulations. The results show that the addition of non-surfactant nanoparticles hinders the nano-second droplet wetting process, attributed to the increases in both surface tension of the nanofluid and friction between nanofluid and substrate. The droplet wetting kinetics decreases with increasing nanoparticle loading and water-particle interaction energy. The observed wetting suppression and the absence of nanoparticle ordering near the contact line of nano-sized droplets differ from the wetting behaviors reported from nanofluid droplets of micron size or larger.