Quantifying sampling noise and parametric uncertainty in atomistic-to-continuum simulations using surrogate models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salloum, Maher N.; Sargsyan, Khachik; Jones, Reese E.

2015-08-11

We present a methodology to assess the predictive fidelity of multiscale simulations by incorporating uncertainty in the information exchanged between the components of an atomistic-to-continuum simulation. We account for both the uncertainty due to finite sampling in molecular dynamics (MD) simulations and the uncertainty in the physical parameters of the model. Using Bayesian inference, we represent the expensive atomistic component by a surrogate model that relates the long-term output of the atomistic simulation to its uncertain inputs. We then present algorithms to solve for the variables exchanged across the atomistic-continuum interface in terms of polynomial chaos expansions (PCEs). We alsomore » consider a simple Couette flow where velocities are exchanged between the atomistic and continuum components, while accounting for uncertainty in the atomistic model parameters and the continuum boundary conditions. Results show convergence of the coupling algorithm at a reasonable number of iterations. As a result, the uncertainty in the obtained variables significantly depends on the amount of data sampled from the MD simulations and on the width of the time averaging window used in the MD simulations.« less

Mirrored continuum and molecular scale simulations of the ignition of high-pressure phases of RDX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Kibaek; Stewart, D. Scott, E-mail: santc@illinois.edu, E-mail: dss@illinois.edu; Joshi, Kaushik

2016-05-14

We present a mirrored atomistic and continuum framework that is used to describe the ignition of energetic materials, and a high-pressure phase of RDX in particular. The continuum formulation uses meaningful averages of thermodynamic properties obtained from the atomistic simulation and a simplification of enormously complex reaction kinetics. In particular, components are identified based on molecular weight bin averages and our methodology assumes that both the averaged atomistic and continuum simulations are represented on the same time and length scales. The atomistic simulations of thermally initiated ignition of RDX are performed using reactive molecular dynamics (RMD). The continuum model ismore » based on multi-component thermodynamics and uses a kinetics scheme that describes observed chemical changes of the averaged atomistic simulations. Thus the mirrored continuum simulations mimic the rapid change in pressure, temperature, and average molecular weight of species in the reactive mixture. This mirroring enables a new technique to simplify the chemistry obtained from reactive MD simulations while retaining the observed features and spatial and temporal scales from both the RMD and continuum model. The primary benefit of this approach is a potentially powerful, but familiar way to interpret the atomistic simulations and understand the chemical events and reaction rates. The approach is quite general and thus can provide a way to model chemistry based on atomistic simulations and extend the reach of those simulations.« less

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments

NASA Astrophysics Data System (ADS)

Brodeck, M.; Alvarez, F.; Arbe, A.; Juranyi, F.; Unruh, T.; Holderer, O.; Colmenero, J.; Richter, D.

2009-03-01

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below ≈0.6 Å-1. We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments.

PubMed

Brodeck, M; Alvarez, F; Arbe, A; Juranyi, F; Unruh, T; Holderer, O; Colmenero, J; Richter, D

2009-03-07

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below approximately 0.6 A(-1). We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations.

PubMed

Gu, Ruo-Xu; Ingólfsson, Helgi I; de Vries, Alex H; Marrink, Siewert J; Tieleman, D Peter

2017-04-20

Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level.

Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

PubMed Central

2016-01-01

Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level. PMID:27610460

Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks.

PubMed

Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus

2015-05-01

The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled. All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

Towards validated chemistry at extreme conditions: reactive MD simulations of shocked Polyvinyl Nitrate and Nitromethane

NASA Astrophysics Data System (ADS)

Islam, Md Mahbubul; Strachan, Alejandro

A detailed atomistic-level understanding of the ultrafast chemistry of detonation processes of high energy materials is crucial to understand their performance and safety. Recent advances in laser shocks and ultra-fast spectroscopy is yielding the first direct experimental evidence of chemistry at extreme conditions. At the same time, reactive molecular dynamics (MD) in current high-performance computing platforms enable an atomic description of shock-induced chemistry with length and timescales approaching those of experiments. We use MD simulations with the reactive force field ReaxFF to investigate the shock-induced chemical decomposition mechanisms of polyvinyl nitrate (PVN) and nitromethane (NM). The effect of shock pressure on chemical reaction mechanisms and kinetics of both the materials are investigated. For direct comparison of our simulation results with experimentally derived IR absorption data, we performed spectral analysis using atomistic velocity at various shock conditions. The combination of reactive MD simulations and ultrafast spectroscopy enables both the validation of ReaxFF at extreme conditions and contributes to the interpretation of the experimental data relating changes in spectral features to atomic processes. Office of Naval Research MURI program.

Passing waves from atomistic to continuum

NASA Astrophysics Data System (ADS)

Chen, Xiang; Diaz, Adrian; Xiong, Liming; McDowell, David L.; Chen, Youping

2018-02-01

Progress in the development of coupled atomistic-continuum methods for simulations of critical dynamic material behavior has been hampered by a spurious wave reflection problem at the atomistic-continuum interface. This problem is mainly caused by the difference in material descriptions between the atomistic and continuum models, which results in a mismatch in phonon dispersion relations. In this work, we introduce a new method based on atomistic dynamics of lattice coupled with a concurrent atomistic-continuum method to enable a full phonon representation in the continuum description. This permits the passage of short-wavelength, high-frequency phonon waves from the atomistic to continuum regions. The benchmark examples presented in this work demonstrate that the new scheme enables the passage of all allowable phonons through the atomistic-continuum interface; it also preserves the wave coherency and energy conservation after phonons transport across multiple atomistic-continuum interfaces. This work is the first step towards developing a concurrent atomistic-continuum simulation tool for non-equilibrium phonon-mediated thermal transport in materials with microstructural complexity.

Atomistic to continuum modeling of solidification microstructures

DOE PAGES

Karma, Alain; Tourret, Damien

2015-09-26

We summarize recent advances in modeling of solidification microstructures using computational methods that bridge atomistic to continuum scales. We first discuss progress in atomistic modeling of equilibrium and non-equilibrium solid–liquid interface properties influencing microstructure formation, as well as interface coalescence phenomena influencing the late stages of solidification. The latter is relevant in the context of hot tearing reviewed in the article by M. Rappaz in this issue. We then discuss progress to model microstructures on a continuum scale using phase-field methods. We focus on selected examples in which modeling of 3D cellular and dendritic microstructures has been directly linked tomore » experimental observations. Finally, we discuss a recently introduced coarse-grained dendritic needle network approach to simulate the formation of well-developed dendritic microstructures. The approach reliably bridges the well-separated scales traditionally simulated by phase-field and grain structure models, hence opening new avenues for quantitative modeling of complex intra- and inter-grain dynamical interactions on a grain scale.« less

Langevin Equation for DNA Dynamics

NASA Astrophysics Data System (ADS)

Grych, David; Copperman, Jeremy; Guenza, Marina

Under physiological conditions, DNA oligomers can contain well-ordered helical regions and also flexible single-stranded regions. We describe the site-specific motion of DNA with a modified Rouse-Zimm Langevin equation formalism that describes DNA as a coarse-grained polymeric chain with global structure and local flexibility. The approach has successfully described the protein dynamics in solution and has been extended to nucleic acids. Our approach provides diffusive mode analytical solutions for the dynamics of global rotational diffusion and internal motion. The internal DNA dynamics present a rich energy landscape that accounts for an interior where hydrogen bonds and base-stacking determine structure and experience limited solvent exposure. We have implemented several models incorporating different coarse-grained sites with anisotropic rotation, energy barrier crossing, and local friction coefficients that include a unique internal viscosity and our models reproduce dynamics predicted by atomistic simulations. The models reproduce bond autocorrelation along the sequence as compared to that directly calculated from atomistic molecular dynamics simulations. The Langevin equation approach captures the essence of DNA dynamics without a cumbersome atomistic representation.

Stabilization of Model Membrane Systems by Disaccharides. Quasielastic Neutron Scattering Experiments and Atomistic Simulations

NASA Astrophysics Data System (ADS)

Doxastakis, Emmanouil; Garcia Sakai, Victoria; Ohtake, Satoshi; Maranas, Janna K.; de Pablo, Juan J.

2006-03-01

Trehalose, a disaccharide of glucose, is often used for the stabilization of cell membranes in the absence of water. This work studies the effects of trehalose on model membrane systems as they undergo a melting transition using a combination of experimental methods and atomistic molecular simulations. Quasielastic neutron scattering experiments on selectively deuterated samples provide the incoherent dynamic structure over a wide time range. Elastic scans probing the lipid tail dynamics display clear evidence of a main melting transition that is significantly lowered in the presence of trehalose. Lipid headgroup mobility is considerably restricted at high temperatures and directly associated with the dynamics of the sugar in the mixture. Molecular simulations provide a detailed overview of the dynamics and their spatial and time dependence. The combined simulation and experimental methodology offers a unique, molecular view of the physics of systems commonly employed in cryopreservation and lyophilization processes.

Primary radiation damage of an FeCr alloy under pressure: Atomistic simulation

NASA Astrophysics Data System (ADS)

Tikhonchev, M. Yu.; Svetukhin, V. V.

2017-05-01

The primary radiation damage of a binary FeCr alloy deformed by applied mechanical loading is studied by an atomistic molecular dynamics simulation. Loading is simulated by specifying an applied pressure of 0.25, 1.0, and 2.5 GPa of both signs. Hydrostatic and uniaxial loading is considered along the [001], [111], [112], and [210] directions. The influence of loading on the energy of point defect formation and the threshold atomic displacement energy in single-component bcc iron is investigated. The 10-keV atomic displacement cascades in a "random" binary Fe-9 at % Cr alloy are simulated at an initial temperature of 300 K. The number of the point defects generated in a cascade is estimated, and the clustering of point defects and the spatial orientation of interstitial configurations are analyzed. Our results agree with the results of other researchers and supplement them.

Molecular Simulations of Adsorption and Diffusion in Silicalite.

NASA Astrophysics Data System (ADS)

Snurr, Randall Quentin

The adsorption and diffusion of hydrocarbons in the zeolite silicalite have been studied using molecular simulations. The simulations use an atomistic description of zeolite/sorbate interactions and are based on principles of statistical mechanics. Emphasis was placed on developing new simulation techniques to allow complex systems relevant to industrial applications in catalysis and separations processes to be studied. Adsorption isotherms and heats of sorption for methane in silicalite were calculated from grand canonical Monte Carlo (GCMC) simulations and also from molecular dynamics (MD) simulations accompanied by Widom test particle insertions. Good agreement with experimental data from the literature was found. The adsorption thermodynamics of aromatic species in silicalite at low loading was predicted by direct evaluation of the configurational integrals. Good agreement with experiment was obtained for the Henry's constants and the heats of adsorption. Molecules were predicted to be localized in the channel intersections at low loading. At higher loading, conventional GCMC simulations were found to be infeasible. Several variations of the GCMC technique were developed incorporating biased insertion moves. These new techniques are much more efficient than conventional GCMC and allow for the prediction of adsorption isotherms of tightly-fitting aromatic molecules in silicalite. Our simulations when combined with experimental evidence of a phase change in the zeolite structure at intermediate loading provide an explanation of the characteristic steps seen in the experimental isotherms. A hierarchical atomistic/lattice model for studying these systems was also developed. The hierarchical model is more than an order of magnitude more efficient computationally than direct atomistic simulation. Diffusion of benzene in silicalite was studied using transition-state theory (TST). Such an approach overcomes the time-scale limitations of using MD simulations for studying sorbate dynamics. Predicted diffusion coefficients were found to be too low compared to experiment. This was attributed to the assumption of a rigid zeolite structure in the calculations and the use of a harmonic approximation for calculating the TST rate constants. Details of sorbate motion were also investigated.

LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

NASA Astrophysics Data System (ADS)

Walter, Nathan P.; Jaiswal, Abhishek; Cai, Zhikun; Zhang, Yang

2018-07-01

Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However, the interpretation of experimental data from neutron scattering is oftentimes not trivial, partly because scattering methods probe ensemble-averaged information in the reciprocal space. Therefore, computer simulations, such as classical and ab initio molecular dynamics, are frequently used to unravel the time-dependent atomistic configurations that can reproduce the scattering patterns and thus assist in the understanding of the microscopic origin of certain properties of materials. LiquidLib is a post-processing package for analyzing the trajectory of atomistic simulations of liquids and liquid-like matter with application to neutron scattering experiments. From an atomistic simulation, LiquidLib provides the computation of various statistical quantities including the pair distribution function, the weighted and unweighted structure factors, the mean squared displacement, the non-Gaussian parameter, the four-point correlation function, the velocity auto correlation function, the self and collective van Hove correlation functions, the self and collective intermediate scattering functions, and the bond orientational order parameter. LiquidLib analyzes atomistic trajectories generated from packages such as LAMMPS, GROMACS, and VASP. It also offers an extendable platform to conveniently integrate new quantities into the library and integrate simulation trajectories of other file formats for analysis. Weighting the quantities by element-specific neutron-scattering lengths provides results directly comparable to neutron scattering measurements. Lastly, LiquidLib is independent of dimensionality, which allows analysis of trajectories in two, three, and higher dimensions. The code is beginning to find worldwide use.

On coarse projective integration for atomic deposition in amorphous systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chuang, Claire Y., E-mail: yungc@seas.upenn.edu, E-mail: meister@unm.edu, E-mail: zepedaruiz1@llnl.gov; Sinno, Talid, E-mail: talid@seas.upenn.edu; Han, Sang M., E-mail: yungc@seas.upenn.edu, E-mail: meister@unm.edu, E-mail: zepedaruiz1@llnl.gov

2015-10-07

Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the “equation-free” framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to themore » application of this technique in realistic settings is the “lifting” operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO{sub 2} substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO{sub 2} using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.« less

On Coarse Projective Integration for Atomic Deposition in Amorphous Systems

DOE PAGES

Chuang, Claire Y.; Han, Sang M.; Zepeda-Ruiz, Luis A.; ...

2015-10-02

Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of timescales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity and computational efficiency. Coarse projective integration, an example application of the ‘equation-free’ framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute gradients of slowly-evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of thismore » technique in realistic settings is the ‘lifting’ operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO 2 substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO 2 using only a few measures of the island size distribution. In conclusion, the approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.« less

Coarse graining atomistic simulations of plastically deforming amorphous solids

NASA Astrophysics Data System (ADS)

Hinkle, Adam R.; Rycroft, Chris H.; Shields, Michael D.; Falk, Michael L.

2017-05-01

The primary mode of failure in disordered solids results from the formation and persistence of highly localized regions of large plastic strains known as shear bands. Continuum-level field theories capable of predicting this mechanical response rely upon an accurate representation of the initial and evolving states of the amorphous structure. We perform molecular dynamics simulations of a metallic glass and propose a methodology for coarse graining discrete, atomistic quantities, such as the potential energies of the elemental constituents. A strain criterion is established and used to distinguish the coarse-grained degrees-of-freedom inside the emerging shear band from those of the surrounding material. A signal-to-noise ratio provides a means of evaluating the strength of the signal of the shear band as a function of the coarse graining. Finally, we investigate the effect of different coarse graining length scales by comparing a two-dimensional, numerical implementation of the effective-temperature description in the shear transformation zone (STZ) theory with direct molecular dynamics simulations. These comparisons indicate the coarse graining length scale has a lower bound, above which there is a high level of agreement between the atomistics and the STZ theory, and below which the concept of effective temperature breaks down.

Multiscale Modeling of Damage Processes in Aluminum Alloys: Grain-Scale Mechanisms

NASA Technical Reports Server (NTRS)

Hochhalter, J. D.; Veilleux, M. G.; Bozek, J. E.; Glaessgen, E. H.; Ingraffea, A. R.

2008-01-01

This paper has two goals related to the development of a physically-grounded methodology for modeling the initial stages of fatigue crack growth in an aluminum alloy. The aluminum alloy, AA 7075-T651, is susceptible to fatigue cracking that nucleates from cracked second phase iron-bearing particles. Thus, the first goal of the paper is to validate an existing framework for the prediction of the conditions under which the particles crack. The observed statistics of particle cracking (defined as incubation for this alloy) must be accurately predicted to simulate the stochastic nature of microstructurally small fatigue crack (MSFC) formation. Also, only by simulating incubation of damage in a statistically accurate manner can subsequent stages of crack growth be accurately predicted. To maintain fidelity and computational efficiency, a filtering procedure was developed to eliminate particles that were unlikely to crack. The particle filter considers the distributions of particle sizes and shapes, grain texture, and the configuration of the surrounding grains. This filter helps substantially reduce the number of particles that need to be included in the microstructural models and forms the basis of the future work on the subsequent stages of MSFC, crack nucleation and microstructurally small crack propagation. A physics-based approach to simulating fracture should ultimately begin at nanometer length scale, in which atomistic simulation is used to predict the fundamental damage mechanisms of MSFC. These mechanisms include dislocation formation and interaction, interstitial void formation, and atomic diffusion. However, atomistic simulations quickly become computationally intractable as the system size increases, especially when directly linking to the already large microstructural models. Therefore, the second goal of this paper is to propose a method that will incorporate atomistic simulation and small-scale experimental characterization into the existing multiscale framework. At the microscale, the nanoscale mechanics are represented within cohesive zones where appropriate, i.e. where the mechanics observed at the nanoscale can be represented as occurring on a plane such as at grain boundaries or slip planes at a crack front. Important advancements that are yet to be made include: 1. an increased fidelity in cohesive zone modeling; 2. a means to understand how atomistic simulation scales with time; 3. a new experimental methodology for generating empirical models for CZMs and emerging materials; and 4. a validation of simulations of the damage processes at the nano-micro scale. With ever-increasing computer power, the long-term ability to employ atomistic simulation for the prognosis of structural components will not be limited by computation power, but by our lack of knowledge in incorporating atomistic models into simulations of MSFC into a multiscale framework.

Understanding the interfacial behavior of lysozyme on Au (111) surfaces with multiscale simulations

NASA Astrophysics Data System (ADS)

Samieegohar, Mohammadreza; Ma, Heng; Sha, Feng; Jahan Sajib, Md Symon; Guerrero-García, G. Iván; Wei, Tao

2017-02-01

The understanding of the adsorption and interfacial behavior of proteins is crucial to the development of novel biosensors and biomaterials. By using bottom-up atomistic multiscale simulations, we study here the adsorption of lysozyme on Au(111) surfaces in an aqueous environment. Atomistic simulations are used to calculate the inhomogeneous polarization of the gold surface, which is induced by the protein adsorption, and by the presence of an interfacial layer of water molecules and monovalent salts. The corresponding potential of mean force between the protein and the gold surface including polarization effects is used in Langevin Dynamics simulations to study the time dependent behavior of proteins at finite concentration. These simulations display a rapid adsorption and formation of a first-layer of proteins at the interface. Proteins are initially adsorbed directly on the gold surface due to the strong protein-surface attractive interaction. A subsequent interfacial weak aggregation of proteins leading to multilayer build-up is also observed at long times.

Advances in first-principles calculations of thermodynamic properties of planetary materials (Invited)

NASA Astrophysics Data System (ADS)

Wilson, H. F.

2013-12-01

First-principles atomistic simulation is a vital tool for understanding the properties of materials at the high-pressure high-temperature conditions prevalent in giant planet interiors, but properties such as solubility and phase boundaries are dependent on entropy, a quantity not directly accessible in simulation. Determining entropic properties from atomistic simulations is a difficult problem typically requiring a time-consuming integration over molecular dynamics trajectories. Here I will describe recent advances in first-principles thermodynamic calculations which substantially increase the simplicity and efficiency of thermodynamic integration and make entropic properties more readily accessible. I will also describe the use of first-principles thermodynamic calculations for understanding problems including core solubility in gas giants and superionic phase changes in ice giants, as well as future prospects for combining first-principles thermodynamics with planetary-scale models to help us understand the origin and consequences of compositional inhomogeneity in giant planet interiors.

Proton transport in functionalised additives for PEM fuel cells: contributions from atomistic simulations.

PubMed

Tölle, Pia; Köhler, Christof; Marschall, Roland; Sharifi, Monir; Wark, Michael; Frauenheim, Thomas

2012-08-07

The conventional polymer electrolyte membrane (PEM) materials for fuel cell applications strongly rely on temperature and pressure conditions for optimal performance. In order to expand the range of operating conditions of these conventional PEM materials, mesoporous functionalised SiO(2) additives are developed. It has been demonstrated that these additives themselves achieve proton conductivities approaching those of conventional materials. However, the proton conduction mechanisms and especially factors influencing charge carrier mobility under different hydration conditions are not well known and difficult to separate from concentration effects in experiments. This tutorial review highlights contributions of atomistic computer simulations to the basic understanding and eventual design of these materials. Some basic introduction to the theoretical and computational framework is provided to introduce the reader to the field, the techniques are in principle applicable to a wide range of other situations as well. Simulation results are directly compared to experimental data as far as possible.

Molecular dynamics simulations investigating consecutive nucleation, solidification and grain growth in a twelve-million-atom Fe-system

NASA Astrophysics Data System (ADS)

Okita, Shin; Verestek, Wolfgang; Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi

2017-09-01

Continuous processes of homogeneous nucleation, solidification and grain growth are spontaneously achieved from an undercooled iron melt without any phenomenological parameter in the molecular dynamics (MD) simulation with 12 million atoms. The nucleation rate at the critical temperature is directly estimated from the atomistic configuration by cluster analysis to be of the order of 1034 m-3 s-1. Moreover, time evolution of grain size distribution during grain growth is obtained by the combination of Voronoi and cluster analyses. The grain growth exponent is estimated to be around 0.3 from the geometric average of the grain size distribution. Comprehensive understanding of kinetic properties during continuous processes is achieved in the large-scale MD simulation by utilizing the high parallel efficiency of a graphics processing unit (GPU), which is shedding light on the fundamental aspects of production processes of materials from the atomistic viewpoint.

Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics

PubMed Central

Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott

2015-01-01

We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling. PMID:25637963

Atomistic Simulations of Graphene Growth: From Kinetics to Mechanism.

PubMed

Qiu, Zongyang; Li, Pai; Li, Zhenyu; Yang, Jinlong

2018-03-20

Epitaxial growth is a promising strategy to produce high-quality graphene samples. At the same time, this method has great flexibility for industrial scale-up. To optimize growth protocols, it is essential to understand the underlying growth mechanisms. This is, however, very challenging, as the growth process is complicated and involves many elementary steps. Experimentally, atomic-scale in situ characterization methods are generally not feasible at the high temperature of graphene growth. Therefore, kinetics is the main experimental information to study growth mechanisms. Theoretically, first-principles calculations routinely provide atomic structures and energetics but have a stringent limit on the accessible spatial and time scales. Such gap between experiment and theory can be bridged by atomistic simulations using first-principles atomic details as input and providing the overall growth kinetics, which can be directly compared with experiment, as output. Typically, system-specific approximations should be applied to make such simulations computationally feasible. By feeding kinetic Monte Carlo (kMC) simulations with first-principles parameters, we can directly simulate the graphene growth process and thus understand the growth mechanisms. Our simulations suggest that the carbon dimer is the dominant feeding species in the epitaxial growth of graphene on both Cu(111) and Cu(100) surfaces, which enables us to understand why the reaction is diffusion limited on Cu(111) but attachment limited on Cu(100). When hydrogen is explicitly considered in the simulation, the central role hydrogen plays in graphene growth is revealed, which solves the long-standing puzzle into why H 2 should be fed in the chemical vapor deposition of graphene. The simulation results can be directly compared with the experimental kinetic data, if available. Our kMC simulations reproduce the experimentally observed quintic-like behavior of graphene growth on Ir(111). By checking the simulation results, we find that such nonlinearity is caused by lattice mismatch, and the induced growth front inhomogeneity can be universally used to predict growth behaviors in other heteroepitaxial systems. Notably, although experimental kinetics usually gives useful insight into atomic mechanisms, it can sometimes be misleading. Such pitfalls can be avoided via atomistic simulations, as demonstrated in our study of the graphene etching process. Growth protocols can be designed theoretically with computational kinetic and mechanistic information. By contrasting the different activation energies involved in an atom-exchange-based carbon penetration process for monolayer and bilayer graphene, we propose a three-step strategy to grow high-quality bilayer graphene. Based on first-principles parameters, a kinetic pathway toward the high-density, ordered N doping of epitaxial graphene on Cu(111) using a C 5 NCl 5 precursor is also identified. These studies demonstrate that atomistic simulations can unambiguously produce or reproduce the kinetic information on graphene growth, which is pivotal to understanding the growth mechanism and designing better growth protocols. A similar strategy can be used in growth mechanism studies of other two-dimensional atomic crystals.

Simulation of dense amorphous polymers by generating representative atomistic models

NASA Astrophysics Data System (ADS)

Curcó, David; Alemán, Carlos

2003-08-01

A method for generating atomistic models of dense amorphous polymers is presented. The generated models can be used as starting structures of Monte Carlo and molecular dynamics simulations, but also are suitable for the direct evaluation physical properties. The method is organized in a two-step procedure. First, structures are generated using an algorithm that minimizes the torsional strain. After this, an iterative algorithm is applied to relax the nonbonding interactions. In order to check the performance of the method we examined structure-dependent properties for three polymeric systems: polyethyelene (ρ=0.85 g/cm3), poly(L,D-lactic) acid (ρ=1.25 g/cm3), and polyglycolic acid (ρ=1.50 g/cm3). The method successfully generated representative packings for such dense systems using minimum computational resources.

Ab Initio Analysis of Auger-Assisted Electron Transfer.

PubMed

Hyeon-Deuk, Kim; Kim, Joonghan; Prezhdo, Oleg V

2015-01-15

Quantum confinement in nanoscale materials allows Auger-type electron-hole energy exchange. We show by direct time-domain atomistic simulation and analytic theory that Auger processes give rise to a new mechanism of charge transfer (CT) on the nanoscale. Auger-assisted CT eliminates the renown Marcus inverted regime, rationalizing recent experiments on CT from quantum dots to molecular adsorbates. The ab initio simulation reveals a complex interplay of the electron-hole and charge-phonon channels of energy exchange, demonstrating a variety of CT scenarios. The developed Marcus rate theory for Auger-assisted CT describes, without adjustable parameters, the experimental plateau of the CT rate in the region of large donor-acceptor energy gap. The analytic theory and atomistic insights apply broadly to charge and energy transfer in nanoscale systems.

Multiscale Modeling of Carbon/Phenolic Composite Thermal Protection Materials: Atomistic to Effective Properties

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Murthy, Pappu L.; Bednarcyk, Brett A.; Lawson, John W.; Monk, Joshua D.; Bauschlicher, Charles W., Jr.

2016-01-01

Next generation ablative thermal protection systems are expected to consist of 3D woven composite architectures. It is well known that composites can be tailored to achieve desired mechanical and thermal properties in various directions and thus can be made fit-for-purpose if the proper combination of constituent materials and microstructures can be realized. In the present work, the first, multiscale, atomistically-informed, computational analysis of mechanical and thermal properties of a present day - Carbon/Phenolic composite Thermal Protection System (TPS) material is conducted. Model results are compared to measured in-plane and out-of-plane mechanical and thermal properties to validate the computational approach. Results indicate that given sufficient microstructural fidelity, along with lowerscale, constituent properties derived from molecular dynamics simulations, accurate composite level (effective) thermo-elastic properties can be obtained. This suggests that next generation TPS properties can be accurately estimated via atomistically informed multiscale analysis.

How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

PubMed

Šponer, Jiří; Krepl, Miroslav; Banáš, Pavel; Kührová, Petra; Zgarbová, Marie; Jurečka, Petr; Havrila, Marek; Otyepka, Michal

2017-05-01

We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems. Fundamental limitations are the short physical time-scale of simulations, which can be partially alleviated by enhanced-sampling techniques, and the highly approximate atomistic force fields describing the simulated molecules. The applicability and present limitations of MD are demonstrated on studies of tetranucleotides, tetraloops, ribozymes, riboswitches and protein/RNA complexes. Wisely applied simulations respecting the approximations of the model can successfully complement structural and biochemical experiments. WIREs RNA 2017, 8:e1405. doi: 10.1002/wrna.1405 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

Cross-scale MD simulations of dynamic strength of tantalum

NASA Astrophysics Data System (ADS)

Bulatov, Vasily

2017-06-01

Dislocations are ubiquitous in metals where their motion presents the dominant and often the only mode of plastic response to straining. Over the last 25 years computational prediction of plastic response in metals has relied on Discrete Dislocation Dynamics (DDD) as the most fundamental method to account for collective dynamics of moving dislocations. Here we present first direct atomistic MD simulations of dislocation-mediated plasticity that are sufficiently large and long to compute plasticity response of single crystal tantalum while tracing the underlying dynamics of dislocations in all atomistic details. Where feasible, direct MD simulations sidestep DDD altogether thus reducing uncertainties of strength predictions to those of the interatomic potential. In the specific context of shock-induced material dynamics, the same MD models predict when, under what conditions and how dislocations interact and compete with other fundamental mechanisms of dynamic response, e.g. twinning, phase-transformations, fracture. In collaboration with: Luis Zepeda-Ruiz, Lawrence Livermore National Laboratory; Alexander Stukowski, Technische Universitat Darmstadt; Tomas Oppelstrup, Lawrence Livermore National Laboratory. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Multiscale Modeling of Intergranular Fracture in Aluminum: Constitutive Relation For Interface Debonding

NASA Technical Reports Server (NTRS)

Yamakov, V.; Saether, E.; Glaessgen, E. H.

2008-01-01

Intergranular fracture is a dominant mode of failure in ultrafine grained materials. In the present study, the atomistic mechanisms of grain-boundary debonding during intergranular fracture in aluminum are modeled using a coupled molecular dynamics finite element simulation. Using a statistical mechanics approach, a cohesive-zone law in the form of a traction-displacement constitutive relationship, characterizing the load transfer across the plane of a growing edge crack, is extracted from atomistic simulations and then recast in a form suitable for inclusion within a continuum finite element model. The cohesive-zone law derived by the presented technique is free of finite size effects and is statistically representative for describing the interfacial debonding of a grain boundary (GB) interface examined at atomic length scales. By incorporating the cohesive-zone law in cohesive-zone finite elements, the debonding of a GB interface can be simulated in a coupled continuum-atomistic model, in which a crack starts in the continuum environment, smoothly penetrates the continuum-atomistic interface, and continues its propagation in the atomistic environment. This study is a step towards relating atomistically derived decohesion laws to macroscopic predictions of fracture and constructing multiscale models for nanocrystalline and ultrafine grained materials.

Atomistic Cohesive Zone Models for Interface Decohesion in Metals

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.; Saether, Erik; Glaessgen, Edward H.

2009-01-01

Using a statistical mechanics approach, a cohesive-zone law in the form of a traction-displacement constitutive relationship characterizing the load transfer across the plane of a growing edge crack is extracted from atomistic simulations for use within a continuum finite element model. The methodology for the atomistic derivation of a cohesive-zone law is presented. This procedure can be implemented to build cohesive-zone finite element models for simulating fracture in nanocrystalline or ultrafine grained materials.

Protein free energy landscapes from long equilibrium simulations

NASA Astrophysics Data System (ADS)

Piana-Agostinetti, Stefano

Many computational techniques based on molecular dynamics (MD) simulation can be used to generate data to aid in the construction of protein free energy landscapes with atomistic detail. Unbiased, long, equilibrium MD simulations--although computationally very expensive--are particularly appealing, as they can provide direct kinetic and thermodynamic information on the transitions between the states that populate a protein free energy surface. It can be challenging to know how to analyze and interpret even results generated by this direct technique, however. I will discuss approaches we have employed, using equilibrium MD simulation data, to obtain descriptions of the free energy landscapes of proteins ranging in size from tens to thousands of amino acids.

Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

NASA Astrophysics Data System (ADS)

Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kibaek

2017-01-01

We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link.

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis.

PubMed

Euro, Liliya; Haapanen, Outi; Róg, Tomasz; Vattulainen, Ilpo; Suomalainen, Anu; Sharma, Vivek

2017-03-07

DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform in the "intrinsic processivity" subdomain of the enzyme. Our data indicate that noncatalytic mutations may disrupt replisomal interactions, thereby causing Pol γ-associated neurodegenerative disorders.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport.

PubMed

Komarov, Pavel V; Khalatur, Pavel G; Khokhlov, Alexei R

2013-01-01

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25-50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

Mapping strain rate dependence of dislocation-defect interactions by atomistic simulations

PubMed Central

Fan, Yue; Osetskiy, Yuri N.; Yip, Sidney; Yildiz, Bilge

2013-01-01

Probing the mechanisms of defect–defect interactions at strain rates lower than 106 s−1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation–defect interactions at virtually any strain rate, exemplified within 10−7 to 107 s−1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIAs) under shear deformation. Using an activation–relaxation algorithm [Kushima A, et al. (2009) J Chem Phys 130:224504], we uncover a unique strain-rate–dependent trigger mechanism that allows the SIA cluster to be absorbed during the process, leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain rate and temperature. Our predictions of a crossover from a defect recovery at the low strain-rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s−1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed. PMID:24114271

Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

PubMed Central

Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter

2014-01-01

Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes. PMID:24411253

Sequential slip transfer of mixed-character dislocations across Σ3 coherent twin boundary in FCC metals: a concurrent atomistic-continuum study

DOE PAGES

Xu, Shuozhi; Xiong, Liming; Chen, Youping; ...

2016-01-29

Sequential slip transfer across grain boundaries (GB) has an important role in size-dependent propagation of plastic deformation in polycrystalline metals. For example, the Hall–Petch effect, which states that a smaller average grain size results in a higher yield stress, can be rationalised in terms of dislocation pile-ups against GBs. In spite of extensive studies in modelling individual phases and grains using atomistic simulations, well-accepted criteria of slip transfer across GBs are still lacking, as well as models of predicting irreversible GB structure evolution. Slip transfer is inherently multiscale since both the atomic structure of the boundary and the long-range fieldsmore » of the dislocation pile-up come into play. In this work, concurrent atomistic-continuum simulations are performed to study sequential slip transfer of a series of curved dislocations from a given pile-up on Σ3 coherent twin boundary (CTB) in Cu and Al, with dominant leading screw character at the site of interaction. A Frank-Read source is employed to nucleate dislocations continuously. It is found that subject to a shear stress of 1.2 GPa, screw dislocations transfer into the twinned grain in Cu, but glide on the twin boundary plane in Al. Moreover, four dislocation/CTB interaction modes are identified in Al, which are affected by (1) applied shear stress, (2) dislocation line length, and (3) dislocation line curvature. Our results elucidate the discrepancies between atomistic simulations and experimental observations of dislocation-GB reactions and highlight the importance of directly modeling sequential dislocation slip transfer reactions using fully 3D models.« less

Sequential slip transfer of mixed-character dislocations across Σ3 coherent twin boundary in FCC metals: a concurrent atomistic-continuum study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Shuozhi; Xiong, Liming; Chen, Youping

Sequential slip transfer across grain boundaries (GB) has an important role in size-dependent propagation of plastic deformation in polycrystalline metals. For example, the Hall–Petch effect, which states that a smaller average grain size results in a higher yield stress, can be rationalised in terms of dislocation pile-ups against GBs. In spite of extensive studies in modelling individual phases and grains using atomistic simulations, well-accepted criteria of slip transfer across GBs are still lacking, as well as models of predicting irreversible GB structure evolution. Slip transfer is inherently multiscale since both the atomic structure of the boundary and the long-range fieldsmore » of the dislocation pile-up come into play. In this work, concurrent atomistic-continuum simulations are performed to study sequential slip transfer of a series of curved dislocations from a given pile-up on Σ3 coherent twin boundary (CTB) in Cu and Al, with dominant leading screw character at the site of interaction. A Frank-Read source is employed to nucleate dislocations continuously. It is found that subject to a shear stress of 1.2 GPa, screw dislocations transfer into the twinned grain in Cu, but glide on the twin boundary plane in Al. Moreover, four dislocation/CTB interaction modes are identified in Al, which are affected by (1) applied shear stress, (2) dislocation line length, and (3) dislocation line curvature. Our results elucidate the discrepancies between atomistic simulations and experimental observations of dislocation-GB reactions and highlight the importance of directly modeling sequential dislocation slip transfer reactions using fully 3D models.« less

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

NASA Astrophysics Data System (ADS)

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-04-01

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices.We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr00459g

Molecular-dynamics Simulation-based Cohesive Zone Representation of Intergranular Fracture Processes in Aluminum

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.; Saether, Erik; Phillips, Dawn R.; Glaessgen, Edward H.

2006-01-01

A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation

Predicting the Macroscopic Fracture Energy of Epoxy Resins from Atomistic Molecular Simulations

DOE PAGES

Meng, Zhaoxu; Bessa, Miguel A.; Xia, Wenjie; ...

2016-12-06

Predicting the macroscopic fracture energy of highly crosslinked glassy polymers from atomistic simulations is challenging due to the size of the process zone being large in these systems. Here, we present a scale-bridging approach that links atomistic molecular dynamics simulations to macroscopic fracture properties on the basis of a continuum fracture mechanics model for two different epoxy materials. Our approach reveals that the fracture energy of epoxy resins strongly depends on the functionality of epoxy resin and the component ratio between the curing agent (amine) and epoxide. The most intriguing part of our study is that we demonstrate that themore » fracture energy exhibits a maximum value within the range of conversion degrees considered (from 65% to 95%), which can be attributed to the combined effects of structural rigidity and post-yield deformability. Our study provides physical insight into the molecular mechanisms that govern the fracture characteristics of epoxy resins and demonstrates the success of utilizing atomistic molecular simulations towards predicting macroscopic material properties.« less

Elastic dipoles of point defects from atomistic simulations

NASA Astrophysics Data System (ADS)

Varvenne, Céline; Clouet, Emmanuel

2017-12-01

The interaction of point defects with an external stress field or with other structural defects is usually well described within continuum elasticity by the elastic dipole approximation. Extraction of the elastic dipoles from atomistic simulations is therefore a fundamental step to connect an atomistic description of the defect with continuum models. This can be done either by a fitting of the point-defect displacement field, by a summation of the Kanzaki forces, or by a linking equation to the residual stress. We perform here a detailed comparison of these different available methods to extract elastic dipoles, and show that they all lead to the same values when the supercell of the atomistic simulations is large enough and when the anharmonic region around the point defect is correctly handled. But, for small simulation cells compatible with ab initio calculations, only the definition through the residual stress appears tractable. The approach is illustrated by considering various point defects (vacancy, self-interstitial, and hydrogen solute atom) in zirconium, using both empirical potentials and ab initio calculations.

Predicting the Macroscopic Fracture Energy of Epoxy Resins from Atomistic Molecular Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Zhaoxu; Bessa, Miguel A.; Xia, Wenjie

Predicting the macroscopic fracture energy of highly crosslinked glassy polymers from atomistic simulations is challenging due to the size of the process zone being large in these systems. Here, we present a scale-bridging approach that links atomistic molecular dynamics simulations to macroscopic fracture properties on the basis of a continuum fracture mechanics model for two different epoxy materials. Our approach reveals that the fracture energy of epoxy resins strongly depends on the functionality of epoxy resin and the component ratio between the curing agent (amine) and epoxide. The most intriguing part of our study is that we demonstrate that themore » fracture energy exhibits a maximum value within the range of conversion degrees considered (from 65% to 95%), which can be attributed to the combined effects of structural rigidity and post-yield deformability. Our study provides physical insight into the molecular mechanisms that govern the fracture characteristics of epoxy resins and demonstrates the success of utilizing atomistic molecular simulations towards predicting macroscopic material properties.« less

Fermi-level effects in semiconductor processing: A modeling scheme for atomistic kinetic Monte Carlo simulators

NASA Astrophysics Data System (ADS)

Martin-Bragado, I.; Castrillo, P.; Jaraiz, M.; Pinacho, R.; Rubio, J. E.; Barbolla, J.; Moroz, V.

2005-09-01

Atomistic process simulation is expected to play an important role for the development of next generations of integrated circuits. This work describes an approach for modeling electric charge effects in a three-dimensional atomistic kinetic Monte Carlo process simulator. The proposed model has been applied to the diffusion of electrically active boron and arsenic atoms in silicon. Several key aspects of the underlying physical mechanisms are discussed: (i) the use of the local Debye length to smooth out the atomistic point-charge distribution, (ii) algorithms to correctly update the charge state in a physically accurate and computationally efficient way, and (iii) an efficient implementation of the drift of charged particles in an electric field. High-concentration effects such as band-gap narrowing and degenerate statistics are also taken into account. The efficiency, accuracy, and relevance of the model are discussed.

CG2AA: backmapping protein coarse-grained structures.

PubMed

Lombardi, Leandro E; Martí, Marcelo A; Capece, Luciana

2016-04-15

Coarse grain (CG) models allow long-scale simulations with a much lower computational cost than that of all-atom simulations. However, the absence of atomistic detail impedes the analysis of specific atomic interactions that are determinant in most interesting biomolecular processes. In order to study these phenomena, it is necessary to reconstruct the atomistic structure from the CG representation. This structure can be analyzed by itself or be used as an onset for atomistic molecular dynamics simulations. In this work, we present a computer program that accurately reconstructs the atomistic structure from a CG model for proteins, using a simple geometrical algorithm. The software is free and available online at http://www.ic.fcen.uba.ar/cg2aa/cg2aa.py Supplementary data are available at Bioinformatics online. lula@qi.fcen.uba.ar. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Development of Directional Decohesion Finite Elements for Multiscale Failure Analysis of Metallic Polycrystals

NASA Technical Reports Server (NTRS)

Saether, Erik; Glaessgen, Edward H.

2009-01-01

Atomistic simulations of intergranular fracture have indicated that grain-scale crack growth in polycrystalline metals can be direction dependent. At these material length scales, the atomic environment greatly influences the nature of intergranular crack propagation, through either brittle or ductile mechanisms, that are a function of adjacent grain orientation and direction of crack propagation. Methods have been developed to obtain cohesive zone models (CZM) directly from molecular dynamics simulations. These CZMs may be incorporated into decohesion finite element formulations to simulate fracture at larger length scales. A new directional decohesion element is presented that calculates the direction of Mode I opening and incorporates a material criterion for dislocation emission based on the local crystallographic environment to automatically select the CZM that best represents crack growth. The simulation of fracture in 2-D and 3-D aluminum polycrystals is used to illustrate the effect of parameterized CZMs and the effectiveness of directional decohesion finite elements.

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

PubMed

Ostermeir, Katja; Zacharias, Martin

2014-12-01

Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations. © 2014 Wiley Periodicals, Inc.

Computer Simulations of Ion Transport in Polymer Electrolyte Membranes.

PubMed

Mogurampelly, Santosh; Borodin, Oleg; Ganesan, Venkat

2016-06-07

Understanding the mechanisms and optimizing ion transport in polymer membranes have been the subject of active research for more than three decades. We present an overview of the progress and challenges involved with the modeling and simulation aspects of the ion transport properties of polymer membranes. We are concerned mainly with atomistic and coarser level simulation studies and discuss some salient work in the context of pure binary and single ion conducting polymer electrolytes, polymer nanocomposites, block copolymers, and ionic liquid-based hybrid electrolytes. We conclude with an outlook highlighting future directions.

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

PubMed

Yang, Shengfeng; Chen, Youping

2015-03-08

In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

Quantifying chain reptation in entangled polymer melts: Topological and dynamical mapping of atomistic simulation results onto the tube model

NASA Astrophysics Data System (ADS)

Stephanou, Pavlos S.; Baig, Chunggi; Tsolou, Georgia; Mavrantzas, Vlasis G.; Kröger, Martin

2010-03-01

The topological state of entangled polymers has been analyzed recently in terms of primitive paths which allowed obtaining reliable predictions of the static (statistical) properties of the underlying entanglement network for a number of polymer melts. Through a systematic methodology that first maps atomistic molecular dynamics (MD) trajectories onto time trajectories of primitive chains and then documents primitive chain motion in terms of a curvilinear diffusion in a tubelike region around the coarse-grained chain contour, we are extending these static approaches here even further by computing the most fundamental function of the reptation theory, namely, the probability ψ(s,t) that a segment s of the primitive chain remains inside the initial tube after time t, accounting directly for contour length fluctuations and constraint release. The effective diameter of the tube is independently evaluated by observing tube constraints either on atomistic displacements or on the displacement of primitive chain segments orthogonal to the initial primitive path. Having computed the tube diameter, the tube itself around each primitive path is constructed by visiting each entanglement strand along the primitive path one after the other and approximating it by the space of a small cylinder having the same axis as the entanglement strand itself and a diameter equal to the estimated effective tube diameter. Reptation of the primitive chain longitudinally inside the effective constraining tube as well as local transverse fluctuations of the chain driven mainly from constraint release and regeneration mechanisms are evident in the simulation results; the latter causes parts of the chains to venture outside their average tube surface for certain periods of time. The computed ψ(s,t) curves account directly for both of these phenomena, as well as for contour length fluctuations, since all of them are automatically captured in the atomistic simulations. Linear viscoelastic properties such as the zero shear rate viscosity and the spectra of storage and loss moduli obtained on the basis of the obtained ψ(s,t) curves for three different polymer melts (polyethylene, cis-1,4-polybutadiene, and trans-1,4-polybutadiene) are consistent with experimental rheological data and in qualitative agreement with the double reptation and dual constraint models. The new methodology is general and can be routinely applied to analyze primitive path dynamics and chain reptation in atomistic trajectories (accumulated through long MD simulations) of other model polymers or polymeric systems (e.g., bidisperse, branched, grafted, etc.); it is thus believed to be particularly useful in the future in evaluating proposed tube models and developing more accurate theories for entangled systems.

Atomistic observation and simulation analysis of spatio-temporal fluctuations during radiation-induced amorphization.

PubMed

Watanabe, Seiichi; Hoshino, Misaki; Koike, Takuto; Suda, Takanori; Ohnuki, Soumei; Takahashi, Heishichirou; Lam, Nighi Q

2003-01-01

We performed a dynamical-atomistic study of radiation-induced amorphization in the NiTi intermetallic compound using in situ high-resolution high-voltage electron microscopy and molecular dynamics simulations in connection with image simulation. Spatio-temporal fluctuations as non-equilibrium fluctuations in an energy-dissipative system, due to transient atom-cluster formation during amorphization, were revealed by the present spatial autocorrelation analysis.

A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide).

PubMed

Abbott, Lauren J; Stevens, Mark J

2015-12-28

A coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil-globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

PubMed Central

Komarov, Pavel V; Khokhlov, Alexei R

2013-01-01

Summary Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity. PMID:24205452

Effect of Single-Electron Interface Trapping in Decanano MOSFETs: A 3D Atomistic Simulation Study

NASA Technical Reports Server (NTRS)

Asenov, Asen; Balasubramaniam, R.; Brown, A. R.; Davies, J. H.

2000-01-01

We study the effect of trapping/detrapping of a single-electron in interface states in the channel of n-type MOSFETs with decanano dimensions using 3D atomistic simulation techniques. In order to highlight the basic dependencies, the simulations are carried out initially assuming continuous doping charge, and discrete localized charge only for the trapped electron. The dependence of the random telegraph signal (RTS) amplitudes on the device dimensions and on the position of the trapped charge in the channel are studied in detail. Later, in full-scale, atomistic simulations assuming discrete charge for both randomly placed dopants and the trapped electron, we highlight the importance of current percolation and of traps with strategic position where the trapped electron blocks a dominant current path.

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS.

PubMed

Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector; Rissanen, Sami; Lolicato, Fabio; Róg, Tomasz; Vattulainen, Ilpo

2017-10-23

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS.

Robust mode space approach for atomistic modeling of realistically large nanowire transistors

NASA Astrophysics Data System (ADS)

Huang, Jun Z.; Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard

2018-01-01

Nanoelectronic transistors have reached 3D length scales in which the number of atoms is countable. Truly atomistic device representations are needed to capture the essential functionalities of the devices. Atomistic quantum transport simulations of realistically extended devices are, however, computationally very demanding. The widely used mode space (MS) approach can significantly reduce the numerical cost, but a good MS basis is usually very hard to obtain for atomistic full-band models. In this work, a robust and parallel algorithm is developed to optimize the MS basis for atomistic nanowires. This enables engineering-level, reliable tight binding non-equilibrium Green's function simulation of nanowire metal-oxide-semiconductor field-effect transistor (MOSFET) with a realistic cross section of 10 nm × 10 nm using a small computer cluster. This approach is applied to compare the performance of InGaAs and Si nanowire n-type MOSFETs (nMOSFETs) with various channel lengths and cross sections. Simulation results with full-band accuracy indicate that InGaAs nanowire nMOSFETs have no drive current advantage over their Si counterparts for cross sections up to about 10 nm × 10 nm.

Prediction of Thermal Transport Properties of Materials with Microstructural Complexity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Youping

This project aims at overcoming the major obstacle standing in the way of progress in dynamic multiscale simulation, which is the lack of a concurrent atomistic-continuum method that allows phonons, heat and defects to pass through the atomistic-continuum interface. The research has led to the development of a concurrent atomistic-continuum (CAC) methodology for multiscale simulations of materials microstructural, mechanical and thermal transport behavior. Its efficacy has been tested and demonstrated through simulations of dislocation dynamics and phonon transport coupled with microstructural evolution in a variety of materials and through providing visual evidences of the nature of phonon transport, such asmore » showing the propagation of heat pulses in single and polycrystalline solids is partially ballistic and partially diffusive. In addition to providing understanding on phonon scattering with phase interface and with grain boundaries, the research has contributed a multiscale simulation tool for understanding of the behavior of complex materials and has demonstrated the capability of the tool in simulating the dynamic, in situ experimental studies of nonequilibrium transient transport processes in material samples that are at length scales typically inaccessible by atomistically resolved methods.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Haixuan; Osetskiy, Yury N; Stoller, Roger E

The fundamentals of the framework and the details of each component of the self-evolving atomistic kinetic Monte Carlo (SEAKMC) are presented. The strength of this new technique is the ability to simulate dynamic processes with atomistic fidelity that is comparable to molecular dynamics (MD) but on a much longer time scale. The observation that the dimer method preferentially finds the saddle point (SP) with the lowest energy is investigated and found to be true only for defects with high symmetry. In order to estimate the fidelity of dynamics and accuracy of the simulation time, a general criterion is proposed andmore » applied to two representative problems. Applications of SEAKMC for investigating the diffusion of interstitials and vacancies in bcc iron are presented and compared directly with MD simulations, demonstrating that SEAKMC provides results that formerly could be obtained only through MD. The correlation factor for interstitial diffusion in the dumbbell configuration, which is extremely difficult to obtain using MD, is predicted using SEAKMC. The limitations of SEAKMC are also discussed. The paper presents a comprehensive picture of the SEAKMC method in both its unique predictive capabilities and technically important details.« less

Probing the character of ultra-fast dislocations

DOE PAGES

Rudd, R. E.; Ruestes, C. J.; Bringa, E. M.; ...

2015-11-23

Plasticity is often controlled by dislocation motion, which was first measured for low pressure, low strain rate conditions decades ago. However, many applications require knowledge of dislocation motion at high stress conditions where the data are sparse, and come from indirect measurements dominated by the effect of dislocation density rather than velocity. Here we make predictions based on atomistic simulations that form the basis for a new approach to measure dislocation velocities directly at extreme conditions using three steps: create prismatic dislocation loops in a near-surface region using nanoindentation, drive the dislocations with a shockwave, and use electron microscopy tomore » determine how far the dislocations moved and thus their velocity at extreme stress and strain rate conditions. We report on atomistic simulations of tantalum that make detailed predictions of dislocation flow, and find that the approach is feasible and can uncover an exciting range of phenomena, such as transonic dislocations and a novel form of loop stretching. Furthermore, the simulated configuration enables a new class of experiments to probe average dislocation velocity at very high applied shear stress.« less

On the Reduction of Molecular Degrees of Freedom in Computer Simulations

NASA Astrophysics Data System (ADS)

Lyubartsev, Alexander P.; Laaksonen, Aatto

Molecular simulations, based on atomistic force fields are a standard theoretical tool in materials, polymers and biosciences. While various methods, with quantum chemistry incorporated, have been developed for condensed phase simulations during the last decade, there is another line of development with the purpose to bridge the time and length scales based on coarse-graining. This is expected to lead to some very interesting breakthroughs in the near future. In this lecture we will first give some background to common atomistic force fields. After that, we review a few common simple techniques for reducing the number of motional degrees of freedom to speed up the simulations. Finally, we present a powerful method for reducing uninteresting degrees of freedom. This is done by solving the Inverse Problem to obtain the interaction potentials. More precisely, we make use of the radial distribution functions, and by using the method of Inverse Monte Carlo [Lyubartsev & Laaksonen, Phys. Rev. E. 52, 3730 (1995)], we can construct effective potentials which are consistent with the original RDFs. This makes it possible to simulate much larger system than would have been possible by using atomistic force fields. We present many examples: How to simulate aqueous electrolyte solutions without any water molecules but still having the hydration structure around the ions - at the speed of a primitive electrolyte model calculation. We demonstrate how a coarse-grained model can be constructed for a double-helix DNA and how it can be used. It is accurate enough to reproduce the experimental results for ion condensation around DNA for several different counterions. We also show how we can construct site-site potentials for large-scale atomistic classical simulations of arbitrary liquids from smaller scale ab initio simulations. This methodology allows us to start from a simulation with the electrons and atomic nuclei, to construct a set of atomistic effective interaction potentials, and to use them in classical simulations. As a next step we can construct a new set of potentials beyond the atomistic description and carry out mesoscopic simulations, for example by using Dissipative Particle Dynamics. In this way we can tie together three different levels of description. The Dissipative Particle Dynamics method appears as a very promising tool to use with our coarse-grained potentials.

Surface Adsorption in Nonpolarizable Atomic Models.

PubMed

Whitmer, Jonathan K; Joshi, Abhijeet A; Carlton, Rebecca J; Abbott, Nicholas L; de Pablo, Juan J

2014-12-09

Many ionic solutions exhibit species-dependent properties, including surface tension and the salting-out of proteins. These effects may be loosely quantified in terms of the Hofmeister series, first identified in the context of protein solubility. Here, our interest is to develop atomistic models capable of capturing Hofmeister effects rigorously. Importantly, we aim to capture this dependence in computationally cheap "hard" ionic models, which do not exhibit dynamic polarization. To do this, we have performed an investigation detailing the effects of the water model on these properties. Though incredibly important, the role of water models in simulation of ionic solutions and biological systems is essentially unexplored. We quantify this via the ion-dependent surface attraction of the halide series (Cl, Br, I) and, in so doing, determine the relative importance of various hypothesized contributions to ionic surface free energies. Importantly, we demonstrate surface adsorption can result in hard ionic models combined with a thermodynamically accurate representation of the water molecule (TIP4Q). The effect observed in simulations of iodide is commensurate with previous calculations of the surface potential of mean force in rigid molecular dynamics and polarizable density-functional models. Our calculations are direct simulation evidence of the subtle but sensitive role of water thermodynamics in atomistic simulations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ortoleva, Peter J.

Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

Modeling Amorphous Microporous Polymers for CO2 Capture and Separations.

PubMed

Kupgan, Grit; Abbott, Lauren J; Hart, Kyle E; Colina, Coray M

2018-06-13

This review concentrates on the advances of atomistic molecular simulations to design and evaluate amorphous microporous polymeric materials for CO 2 capture and separations. A description of atomistic molecular simulations is provided, including simulation techniques, structural generation approaches, relaxation and equilibration methodologies, and considerations needed for validation of simulated samples. The review provides general guidelines and a comprehensive update of the recent literature (since 2007) to promote the acceleration of the discovery and screening of amorphous microporous polymers for CO 2 capture and separation processes.

Extending atomistic simulation timescale in solid/liquid systems: crystal growth from solution by a parallel-replica dynamics and continuum hybrid method.

PubMed

Lu, Chun-Yaung; Voter, Arthur F; Perez, Danny

2014-01-28

Deposition of solid material from solution is ubiquitous in nature. However, due to the inherent complexity of such systems, this process is comparatively much less understood than deposition from a gas or vacuum. Further, the accurate atomistic modeling of such systems is computationally expensive, therefore leaving many intriguing long-timescale phenomena out of reach. We present an atomistic/continuum hybrid method for extending the simulation timescales of dynamics at solid/liquid interfaces. We demonstrate the method by simulating the deposition of Ag on Ag (001) from solution with a significant speedup over standard MD. The results reveal specific features of diffusive deposition dynamics, such as a dramatic increase in the roughness of the film.

doGlycans–Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

PubMed Central

2017-01-01

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell–cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS. PMID:28906114

Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations

NASA Astrophysics Data System (ADS)

Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.

2016-07-01

Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.

Atomistic simulation of frictional anisotropy on quasicrystal approximant surfaces

DOE PAGES

Ye, Zhijiang; Martini, Ashlie; Thiel, Patricia; ...

2016-06-23

J. Y. Park et al. [Science 309, 1354 (2005)] have reported eight times greater atomic-scale friction in the periodic than in the quasiperiodic direction on the twofold face of a decagonal Al-Ni-Co quasicrystal. Here we present results of molecular-dynamics simulations intended to elucidate mechanisms behind this giant frictional anisotropy. Simulations of a bare atomic-force-microscope tip on several model substrates and under a variety of conditions failed to reproduce experimental results. On the other hand, including the experimental passivation of the tip with chains of hexadecane thiol, we reproduce qualitatively the experimental anisotropy in friction, finding evidence for entrainment of themore » organic chains in surface furrows parallel to the periodic direction.« less

Impact of asymmetric martensite and austenite nucleation and growth behavior on the phase stability and hysteresis of freestanding shape-memory nanoparticles

NASA Astrophysics Data System (ADS)

Ko, Won-Seok; Grabowski, Blazej; Neugebauer, Jörg

2018-03-01

Martensitic transformations in nanoscaled shape-memory alloys exhibit characteristic features absent for the bulk counterparts. Detailed understanding is required for applications in micro- and nanoelectromechanical systems, and experimental limitations render atomistic simulation an important complementary approach. Using a recently developed, accurate potential we investigate the phase transformation in freestanding Ni-Ti shape-memory nanoparticles with molecular-dynamics simulations. The results confirm that the decrease in the transformation temperature with decreasing particle size is correlated with an overstabilization of the austenitic surface energy over the martensitic surface energy. However, a detailed atomistic analysis of the nucleation and growth behavior reveals an unexpected difference in the mechanisms determining the austenite finish and martensite start temperature. While the austenite finish temperature is directly affected by a contribution of the surface energy difference, the martensite start temperature is mostly affected by the transformation strain, contrary to general expectations. This insight not only explains the reduced transformation temperature but also the reduced thermal hysteresis in freestanding nanoparticles.

A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulations.

PubMed

Ghaemi, Zhaleh; Minozzi, Manuela; Carloni, Paolo; Laio, Alessandro

2012-07-26

Predicting the permeability coefficient (P) of drugs permeating through the cell membrane is of paramount importance in drug discovery. We here propose an approach for calculating P based on bias-exchange metadynamics. The approach allows constructing from atomistic simulations a model of permeation taking explicitly into account not only the "trivial" reaction coordinate, the position of the drug along the direction normal to the lipid membrane plane, but also other degrees of freedom, for example, the torsional angles of the permeating molecule, or variables describing its solvation/desolvation. This allows deriving an accurate picture of the permeation process, and constructing a detailed molecular model of the transition state, making a rational control of permeation properties possible. We benchmarked this approach on the permeation of ethanol molecules through a POPC membrane, showing that the value of P calculated with our model agrees with the one calculated by a long unbiased molecular dynamics of the same system.

Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation

NASA Astrophysics Data System (ADS)

Qin, Sanbo; Mittal, Jeetain; Zhou, Huan-Xiang

2013-08-01

We have developed a ‘postprocessing’ method for modeling biochemical processes such as protein folding under crowded conditions (Qin and Zhou 2009 Biophys. J. 97 12-19). In contrast to the direct simulation approach, in which the protein undergoing folding is simulated along with crowders, the postprocessing method requires only the folding simulation without crowders. The influence of the crowders is then obtained by taking conformations from the crowder-free simulation and calculating the free energies of transferring to the crowders. This postprocessing yields the folding free energy surface of the protein under crowding. Here the postprocessing results for the folding of three small proteins under ‘repulsive’ crowding are validated by those obtained previously by the direct simulation approach (Mittal and Best 2010 Biophys. J. 98 315-20). This validation confirms the accuracy of the postprocessing approach and highlights its distinct advantages in modeling biochemical processes under cell-like crowded conditions, such as enabling an atomistic representation of the test proteins.

Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

PubMed

Kang, Myungshim; Chakraborty, Kaushik; Loverde, Sharon M

2018-06-25

We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assembly mechanism from random with ∼0.4 μs molecular dynamics simulations. Furthermore, we also computationally characterize the interfacial structure, directionality of π-π stacking, and water dynamics within several peptide-drug nanotubes with diameters consistent with the reported experimental nanotube diameter. Insight gained should inform the future design of these novel anticancer drug delivery systems.

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

PubMed Central

Abriata, Luciano A.; Dal Peraro, Matteo

2015-01-01

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin’s noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations. PMID:26023027

Comparative simulations of microjetting using atomistic and continuous approaches in presence of viscosity and surface tension

NASA Astrophysics Data System (ADS)

Durand, Olivier; Soulard, Laurent; Jaouen, Stephane; Heuze, Olivier; Colombet, Laurent; Cieren, Emmanuel

2017-06-01

We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and they use an equation of state calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of the viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with a very good agreement the distributions, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes exhibit also a similar phenomenology of fragmentation of the metallic liquid sheets ejected.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fogarty, Aoife C., E-mail: fogarty@mpip-mainz.mpg.de; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de; Kremer, Kurt, E-mail: kremer@mpip-mainz.mpg.de

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

An Embedded Statistical Method for Coupling Molecular Dynamics and Finite Element Analyses

NASA Technical Reports Server (NTRS)

Saether, E.; Glaessgen, E.H.; Yamakov, V.

2008-01-01

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

A New Concurrent Multiscale Methodology for Coupling Molecular Dynamics and Finite Element Analyses

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin; Saether, Erik; Glaessgen, Edward H/.

2008-01-01

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Lattice Thermal Conductivity of Ultra High Temperature Ceramics ZrB2 and HfB2 from Atomistic Simulations

NASA Technical Reports Server (NTRS)

Lawson, John W.; Murray, Daw S.; Bauschlicher, Charles W., Jr.

2011-01-01

Atomistic Green-Kubo simulations are performed to evaluate the lattice thermal conductivity for single crystals of the ultra high temperature ceramics ZrB2 and HfB2 for a range of temperatures. Recently developed interatomic potentials are used for these simulations. Heat current correlation functions show rapid oscillations which can be identified with mixed metal-Boron optical phonon modes. Agreement with available experimental data is good.

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

NASA Astrophysics Data System (ADS)

Fogarty, Aoife C.; Potestio, Raffaello; Kremer, Kurt

2015-05-01

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

Phase transformations at interfaces: Observations from atomistic modeling

DOE PAGES

Frolov, T.; Asta, M.; Mishin, Y.

2016-10-01

Here, we review the recent progress in theoretical understanding and atomistic computer simulations of phase transformations in materials interfaces, focusing on grain boundaries (GBs) in metallic systems. Recently developed simulation approaches enable the search and structural characterization of GB phases in single-component metals and binary alloys, calculation of thermodynamic properties of individual GB phases, and modeling of the effect of the GB phase transformations on GB kinetics. Atomistic simulations demonstrate that the GB transformations can be induced by varying the temperature, loading the GB with point defects, or varying the amount of solute segregation. The atomic-level understanding obtained from suchmore » simulations can provide input for further development of thermodynamics theories and continuous models of interface phase transformations while simultaneously serving as a testing ground for validation of theories and models. They can also help interpret and guide experimental work in this field.« less

Coarse-grained molecular dynamics simulations for giant protein-DNA complexes

NASA Astrophysics Data System (ADS)

Takada, Shoji

Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and the fluctuation matching algorithm. CG molecular dynamics methods enable us to simulate much longer time scale motions of much larger molecular systems than fully atomistic models. After broad sampling of structures with CG models, we can easily reconstruct atomistic models, from which one can continue conventional molecular dynamics simulations if desired. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

PubMed

Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

Atomistic potentials based energy flux integral criterion for dynamic adiabatic shear banding

NASA Astrophysics Data System (ADS)

Xu, Yun; Chen, Jun

2015-02-01

The energy flux integral criterion based on atomistic potentials within the framework of hyperelasticity-plasticity is proposed for dynamic adiabatic shear banding (ASB). System Helmholtz energy decomposition reveals that the dynamic influence on the integral path dependence is originated from the volumetric strain energy and partial deviatoric strain energy, and the plastic influence only from the rest part of deviatoric strain energy. The concept of critical shear banding energy is suggested for describing the initiation of ASB, which consists of the dynamic recrystallization (DRX) threshold energy and the thermal softening energy. The criterion directly relates energy flux to the basic physical processes that induce shear instability such as dislocation nucleations and multiplications, without introducing ad-hoc parameters in empirical constitutive models. It reduces to the classical path independent J-integral for quasi-static loading and elastic solids. The atomistic-to-continuum multiscale coupling method is used to simulate the initiation of ASB. Atomic configurations indicate that DRX induced microstructural softening may be essential to the dynamic shear localization and hence the initiation of ASB.

Scale transition using dislocation dynamics and the nudged elastic band method

DOE PAGES

Sobie, Cameron; Capolungo, Laurent; McDowell, David L.; ...

2017-08-01

Microstructural features such as precipitates or irradiation-induced defects impede dislocation motion and directly influence macroscopic mechanical properties such as yield point and ductility. In dislocation-defect interactions both atomic scale and long range elastic interactions are involved. Thermally assisted dislocation bypass of obstacles occurs when thermal fluctuations and driving stresses contribute sufficient energy to overcome the energy barrier. The Nudged Elastic Band (NEB) method is typically used in the context of atomistic simulations to quantify the activation barriers for a given reaction. In this work, the NEB method is generalized to coarse-grain continuum representations of evolving microstructure states beyond the discretemore » particle descriptions of first principles and atomistics. The method we employed enables the calculation of activation energies for a View the MathML source glide dislocation bypassing a [001] self-interstitial atom loop of size in the range of 4-10 nm with a spacing larger than 150nm in α-iron for a range of applied stresses and interaction geometries. This study is complemented by a comparison between atomistic and continuum based prediction of barriers.« less

Implementation and evaluation of the Level Set method: Towards efficient and accurate simulation of wet etching for microengineering applications

NASA Astrophysics Data System (ADS)

Montoliu, C.; Ferrando, N.; Gosálvez, M. A.; Cerdá, J.; Colom, R. J.

2013-10-01

The use of atomistic methods, such as the Continuous Cellular Automaton (CCA), is currently regarded as a computationally efficient and experimentally accurate approach for the simulation of anisotropic etching of various substrates in the manufacture of Micro-electro-mechanical Systems (MEMS). However, when the features of the chemical process are modified, a time-consuming calibration process needs to be used to transform the new macroscopic etch rates into a corresponding set of atomistic rates. Furthermore, changing the substrate requires a labor-intensive effort to reclassify most atomistic neighborhoods. In this context, the Level Set (LS) method provides an alternative approach where the macroscopic forces affecting the front evolution are directly applied at the discrete level, thus avoiding the need for reclassification and/or calibration. Correspondingly, we present a fully-operational Sparse Field Method (SFM) implementation of the LS approach, discussing in detail the algorithm and providing a thorough characterization of the computational cost and simulation accuracy, including a comparison to the performance by the most recent CCA model. We conclude that the SFM implementation achieves similar accuracy as the CCA method with less fluctuations in the etch front and requiring roughly 4 times less memory. Although SFM can be up to 2 times slower than CCA for the simulation of anisotropic etchants, it can also be up to 10 times faster than CCA for isotropic etchants. In addition, we present a parallel, GPU-based implementation (gSFM) and compare it to an optimized, multicore CPU version (cSFM), demonstrating that the SFM algorithm can be successfully parallelized and the simulation times consequently reduced, while keeping the accuracy of the simulations. Although modern multicore CPUs provide an acceptable option, the massively parallel architecture of modern GPUs is more suitable, as reflected by computational times for gSFM up to 7.4 times faster than for cSFM.

Chemical dynamics simulations of the monohydrated OH-(H2O) + CH3I reaction. Atomic-level mechanisms and comparison with experiment

NASA Astrophysics Data System (ADS)

Xie, Jing; Otto, Rico; Wester, Roland; Hase, William L.

2015-06-01

Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH-(H2O) + CH3I reaction. The SN2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH2I-, and to a lesser extent CH2I- (H2O), becomes important. The SN2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of SN2 and proton transfer pre-reaction complexes and intermediates, including [CH3--I--OH]-. In contrast, for the unsolvated OH- + CH3I SN2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH-(H2O) + CH3IߙSN2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the SN2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H2O molecule is unimportant. The SN2 reaction is dominated by events in which H2O leaves the reactive system as CH3OH is formed or before CH3OH formation. Formation of solvated products is unimportant and participation of the (H2O)CH3OH---I- post-reaction complex for the SN2 reaction is negligible.

Atomistic modeling of Mg/Nb interfaces: shear strength and interaction with lattice glide dislocations

DOE PAGES

Yadav, Satyesh Kumar; Shao, S.; Chen, Youxing; ...

2017-10-17

Here, using a newly developed embedded-atom-method potential for Mg–Nb, the semi-coherent Mg/Nb interface with the Kurdjumov–Sachs orientation relationship is studied. Atomistic simulations have been carried out to understand the shear strength of the interface, as well as the interaction between lattice glide dislocations and the interface. The interface shear mechanisms are dependent on the shear loading directions, through either interface sliding between Mg and Nb atomic layers or nucleation and gliding of Shockley partial dislocations in between the first two atomic planes in Mg at the interface. The shear strength for the Mg/Nb interface is found to be generally high,more » in the range of 0.9–1.3 GPa depending on the shear direction. As a consequence, the extents of dislocation core spread into the interface are considerably small, especially when compared to the case of other “weak” interfaces such as the Cu/Nb interface.« less

Atomistic and coarse-grained computer simulations of raft-like lipid mixtures.

PubMed

Pandit, Sagar A; Scott, H Larry

2007-01-01

Computer modeling can provide insights into the existence, structure, size, and thermodynamic stability of localized raft-like regions in membranes. However, the challenges in the construction and simulation of accurate models of heterogeneous membranes are great. The primary obstacle in modeling the lateral organization within a membrane is the relatively slow lateral diffusion rate for lipid molecules. Microsecond or longer time-scales are needed to fully model the formation and stability of a raft in a membra ne. Atomistic simulations currently are not able to reach this scale, but they do provide quantitative information on the intermolecular forces and correlations that are involved in lateral organization. In this chapter, the steps needed to carry out and analyze atomistic simulations of hydrated lipid bilayers having heterogeneous composition are outlined. It is then shown how the data from a molecular dynamics simulation can be used to construct a coarse-grained model for the heterogeneous bilayer that can predict the lateral organization and stability of rafts at up to millisecond time-scales.

Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

DTIC Science & Technology

2014-10-01

the angles and dihedrals that are truly unique will be indicated by the user by editing NewAngleTypesDump and NewDihedralTypesDump. The program ...Atomistic Molecular Simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Robert M Elder, Timothy W Sirk, and...Antechamber program in Assisted Model Building with Energy Refinement (AMBER) Tools to assign partial charges (using the Austin Model 1 [AM1]-bond charge

Exceptional ion rejection ability of directional solvent for non-membrane desalination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rish, Daniel; Department of Civil Engineering, University of Notre Dame, Notre Dame, Indiana 46556; Luo, Shirui

2014-01-13

The recently demonstrated directional solvent extraction (DSE) is promising for very low temperature, membrane-free water desalination. In this paper, we combine atomistic simulations and experimental validation to demonstrate that the currently used directional solvent, decanoic acid, can reject all major salt ions in seawater, with very high rejection rates. The salinities of the DSE recovered water show that ion rejection rates are ∼98%–99%—similar to those of the best reverse osmosis membranes. Our test also shows that the DSE process can desalt seawater to produce fresh water that meets drinking water standards.

A kinetic Monte Carlo approach to diffusion-controlled thermal desorption spectroscopy

NASA Astrophysics Data System (ADS)

Schablitzki, T.; Rogal, J.; Drautz, R.

2017-06-01

Atomistic simulations of thermal desorption spectra for effusion from bulk materials to characterize binding or trapping sites are a challenging task as large system sizes as well as extended time scales are required. Here, we introduce an approach where we combine kinetic Monte Carlo with an analytic approximation of the superbasins within the framework of absorbing Markov chains. We apply our approach to the effusion of hydrogen from BCC iron, where the diffusion within bulk grains is coarse grained using absorbing Markov chains, which provide an exact solution of the dynamics within a superbasin. Our analytic approximation to the superbasin is transferable with respect to grain size and elliptical shapes and can be applied in simulations with constant temperature as well as constant heating rate. The resulting thermal desorption spectra are in close agreement with direct kinetic Monte Carlo simulations, but the calculations are computationally much more efficient. Our approach is thus applicable to much larger system sizes and provides a first step towards an atomistic understanding of the influence of structural features on the position and shape of peaks in thermal desorption spectra. This article is part of the themed issue 'The challenges of hydrogen and metals'.

A Site Density Functional Theory for Water: Application to Solvation of Amino Acid Side Chains.

PubMed

Liu, Yu; Zhao, Shuangliang; Wu, Jianzhong

2013-04-09

We report a site density functional theory (SDFT) based on the conventional atomistic models of water and the universality ansatz of the bridge functional. The excess Helmholtz energy functional is formulated in terms of a quadratic expansion with respect to the local density deviation from that of a uniform system and a universal functional for all higher-order terms approximated by that of a reference hard-sphere system. With the atomistic pair direct correlation functions of the uniform system calculated from MD simulation and an analytical expression for the bridge functional from the modified fundamental measure theory, the SDFT can be used to predict the structure and thermodynamic properties of water under inhomogeneous conditions with a computational cost negligible in comparison to that of brute-force simulations. The numerical performance of the SDFT has been demonstrated with the predictions of the solvation free energies of 15 molecular analogs of amino acid side chains in water represented by SPC/E, SPC, and TIP3P models. For theTIP3P model, a comparison of the theoretical predictions with MD simulation and experimental data shows agreement within 0.64 and 1.09 kcal/mol on average, respectively.

Random Dopant Induced Threshold Voltage Lowering and Fluctuations in Sub-0.1 (micron)meter MOSFET's: A 3-D 'Atomistic' Simulation Study

NASA Technical Reports Server (NTRS)

Asenov, Asen

1998-01-01

A three-dimensional (3-D) "atomistic" simulation study of random dopant induced threshold voltage lowering and fluctuations in sub-0.1 microns MOSFET's is presented. For the first time a systematic analysis of random dopant effects down to an individual dopant level was carried out in 3-D on a scale sufficient to provide quantitative statistical predictions. Efficient algorithms based on a single multigrid solution of the Poisson equation followed by the solution of a simplified current continuity equation are used in the simulations. The effects of various MOSFET design parameters, including the channel length and width, oxide thickness and channel doping, on the threshold voltage lowering and fluctuations are studied using typical samples of 200 atomistically different MOSFET's. The atomistic results for the threshold voltage fluctuations were compared with two analytical models based on dopant number fluctuations. Although the analytical models predict the general trends in the threshold voltage fluctuations, they fail to describe quantitatively the magnitude of the fluctuations. The distribution of the atomistically calculated threshold voltage and its correlation with the number of dopants in the channel of the MOSFET's was analyzed based on a sample of 2500 microscopically different devices. The detailed analysis shows that the threshold voltage fluctuations are determined not only by the fluctuation in the dopant number, but also in the dopant position.

Atomistic simulation and XAS investigation of Mn induced defects in Bi{sub 12}TiO{sub 20}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rezende, Marcos V dos S.; Santos, Denise J.; Jackson, Robert A.

2016-06-15

This work reports an investigation of the valence and site occupancy of Mn dopants in Bi{sub 12}TiO{sub 20} (BTO: Mn) host using X-ray Absorption (XAS) and atomistic simulation techniques based on energy minimisation. X-ray Absorption Near Edge Structure (XANES) at the Mn K-edges gave typical results for Mn ions with mixed valences of 3+ and 4+. Extended X-ray Absorption Fine Structure (EXAFS) results indicated that Mn ions are probably substituted at Ti sites. Atomistic simulation was performed assuming the incorporation of Mn{sup 2+}, Mn{sup 3+} and Mn{sup 4+} ions at either Bi{sup 3+} or Ti{sup 4+} sites, and the resultsmore » were compared to XANES and EXAFS measurements. Electrical conductivity for pure and doped samples was used to evaluate the consistency of the proposed model. - Graphical abstract: The structure of Bi{sub 12}TiO{sub 20} (BTO). Display Omitted - Highlights: • Pure and Mn-doped Bi{sub 12}TiO{sub 20} samples were studied by experimental techniques combined with atomistic simulation. • Good agreement between experimental and simulation results was obtained. • XANES results suggest a mixture of 3+ and 4+ valences for Mn, occupying the Ti4+ site in both cases. • Charge compensation by holes is most energetically favoured, explaining the enhancement observed in AC dark conductivity.« less

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

PubMed Central

Mariani, Simona; Dell'Orco, Daniele; Felline, Angelo; Raimondi, Francesco; Fanelli, Francesca

2013-01-01

A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions. PMID:24009494

Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

DOE PAGES

Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; ...

2015-01-29

The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies ismore » illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.« less

Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoover, W. G.; Hoover, C. G.

1993-08-01

Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

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

PubMed

Rapaport, D C

2009-04-01

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

Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations.

PubMed

Numazawa, Satoshi; Smith, Roger

2011-10-01

Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ′ Microstructures

PubMed Central

Prakash, Aruna; Bitzek, Erik

2017-01-01

Single-crystal Ni-base superalloys, consisting of a two-phase γ/γ′ microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ′ phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ/γ′ microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ′ particles with planar γ/γ′ interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples—the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions. PMID:28772453

Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ' Microstructures.

PubMed

Prakash, Aruna; Bitzek, Erik

2017-01-23

Single-crystal Ni-base superalloys, consisting of a two-phase γ / γ ' microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ ' phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ / γ ' microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ ' particles with planar γ / γ ' interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples-the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions.

The Matter Simulation (R)evolution

PubMed Central

2018-01-01

To date, the program for the development of methods and models for atomistic and continuum simulation directed toward chemicals and materials has reached an incredible degree of sophistication and maturity. Currently, one can witness an increasingly rapid emergence of advances in computing, artificial intelligence, and robotics. This drives us to consider the future of computer simulation of matter from the molecular to the human length and time scales in a radical way that deliberately dares to go beyond the foreseeable next steps in any given discipline. This perspective article presents a view on this future development that we believe is likely to become a reality during our lifetime. PMID:29532014

Physically representative atomistic modeling of atomic-scale friction

NASA Astrophysics Data System (ADS)

Dong, Yalin

Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the interesting physical process is buried between the two contact interfaces, thus makes a direct measurement more difficult. Atomistic simulation is able to simulate the process with the dynamic information of each single atom, and therefore provides valuable interpretations for experiments. In this, we will systematically to apply Molecular Dynamics (MD) simulation to optimally model the Atomic Force Microscopy (AFM) measurement of atomic friction. Furthermore, we also employed molecular dynamics simulation to correlate the atomic dynamics with the friction behavior observed in experiments. For instance, ParRep dynamics (an accelerated molecular dynamic technique) is introduced to investigate velocity dependence of atomic friction; we also employ MD simulation to "see" how the reconstruction of gold surface modulates the friction, and the friction enhancement mechanism at a graphite step edge. Atomic stick-slip friction can be treated as a rate process. Instead of running a direction simulation of the process, we can apply transition state theory to predict its property. We will have a rigorous derivation of velocity and temperature dependence of friction based on the Prandtl-Tomlinson model as well as transition theory. A more accurate relation to prediction velocity and temperature dependence is obtained. Furthermore, we have included instrumental noise inherent in AFM measurement to interpret two discoveries in experiments, suppression of friction at low temperature and the attempt frequency discrepancy between AFM measurement and theoretical prediction. We also discuss the possibility to treat wear as a rate process.

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

PubMed

Papaleo, Elena

2015-01-01

In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

Multiscale investigation of chemical interference in proteins

NASA Astrophysics Data System (ADS)

Samiotakis, Antonios; Homouz, Dirar; Cheung, Margaret S.

2010-05-01

We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in better exploring the energy landscape of a small protein under chemical interference such as chemical denaturation. An excessive amount of water molecules in all-atomistic molecular dynamics simulations often negatively impacts the sampling efficiency of some advanced sampling techniques such as the replica exchange method and it makes the investigation of chemical interferences on protein dynamics difficult. Thus, there is a need to develop an effective strategy that focuses on sampling structural changes in protein conformations rather than solvent molecule fluctuations. In this work, we address this issue by devising a multiscale simulation scheme (MultiSCAAL) that bridges the gap between all-atomistic molecular dynamics simulation and coarse-grained molecular simulation. The two key features of this scheme are the Boltzmann inversion and a protein atomistic reconstruction method we previously developed (SCAAL). Using MultiSCAAL, we were able to enhance the sampling efficiency of proteins solvated by explicit water molecules. Our method has been tested on the folding energy landscape of a small protein Trp-cage with explicit solvent under 8M urea using both the all-atomistic replica exchange molecular dynamics and MultiSCAAL. We compared computational analyses on ensemble conformations of Trp-cage with its available experimental NOE distances. The analysis demonstrated that conformations explored by MultiSCAAL better agree with the ones probed in the experiments because it can effectively capture the changes in side-chain orientations that can flip out of the hydrophobic pocket in the presence of urea and water molecules. In this regard, MultiSCAAL is a promising and effective sampling scheme for investigating chemical interference which presents a great challenge when modeling protein interactions in vivo.

A DMPA Langmuir monolayer study: from gas to solid phase. An atomistic description by molecular dynamics Simulation.

PubMed

Giner-Casares, J J; Camacho, L; Martín-Romero, M T; Cascales, J J López

2008-03-04

In this work, a DMPA Langmuir monolayer at the air/water interface was studied by molecular dynamics simulations. Thus, an atomistic picture of a Langmuir monolayer was drawn from its expanded gas phase to its final solid condensed one. In this sense, some properties of monolayers that were traditionally poorly or even not reproduced in computer simulations, such as lipid domain formation or pressure-area per lipid isotherm, were properly reproduced in this work. Thus, the physical laws that control the lipid domain formation in the gas phase and the structure of lipid monolayers from the gas to solid condensed phase were studied. Thanks to the atomistic information provided by the molecular dynamics simulations, we were able to add valuable information to the experimental description of these processes and to access experimental data related to the lipid monolayers in their expanded phase, which is difficult or inaccessible to study by experimental techniques. In this sense, properties such as lipids head hydration and lipid structure were studied.

Analysis of an optimization-based atomistic-to-continuum coupling method for point defects

DOE PAGES

Olson, Derek; Shapeev, Alexander V.; Bochev, Pavel B.; ...

2015-11-16

Here, we formulate and analyze an optimization-based Atomistic-to-Continuum (AtC) coupling method for problems with point defects. Application of a potential-based atomistic model near the defect core enables accurate simulation of the defect. Away from the core, where site energies become nearly independent of the lattice position, the method switches to a more efficient continuum model. The two models are merged by minimizing the mismatch of their states on an overlap region, subject to the atomistic and continuum force balance equations acting independently in their domains. We prove that the optimization problem is well-posed and establish error estimates.

Time scale bridging in atomistic simulation of slow dynamics: viscous relaxation and defect activation

NASA Astrophysics Data System (ADS)

Kushima, A.; Eapen, J.; Li, Ju; Yip, S.; Zhu, T.

2011-08-01

Atomistic simulation methods are known for timescale limitations in resolving slow dynamical processes. Two well-known scenarios of slow dynamics are viscous relaxation in supercooled liquids and creep deformation in stressed solids. In both phenomena the challenge to theory and simulation is to sample the transition state pathways efficiently and follow the dynamical processes on long timescales. We present a perspective based on the biased molecular simulation methods such as metadynamics, autonomous basin climbing (ABC), strain-boost and adaptive boost simulations. Such algorithms can enable an atomic-level explanation of the temperature variation of the shear viscosity of glassy liquids, and the relaxation behavior in solids undergoing creep deformation. By discussing the dynamics of slow relaxation in two quite different areas of condensed matter science, we hope to draw attention to other complex problems where anthropological or geological-scale time behavior can be simulated at atomic resolution and understood in terms of micro-scale processes of molecular rearrangements and collective interactions. As examples of a class of phenomena that can be broadly classified as materials ageing, we point to stress corrosion cracking and cement setting as opportunities for atomistic modeling and simulations.

Understanding the physical metallurgy of the CoCrFeMnNi high-entropy alloy: an atomistic simulation study

NASA Astrophysics Data System (ADS)

Choi, Won-Mi; Jo, Yong Hee; Sohn, Seok Su; Lee, Sunghak; Lee, Byeong-Joo

2018-01-01

Although high-entropy alloys (HEAs) are attracting interest, the physical metallurgical mechanisms related to their properties have mostly not been clarified, and this limits wider industrial applications, in addition to the high alloy costs. We clarify the physical metallurgical reasons for the materials phenomena (sluggish diffusion and micro-twining at cryogenic temperatures) and investigate the effect of individual elements on solid solution hardening for the equiatomic CoCrFeMnNi HEA based on atomistic simulations (Monte Carlo, molecular dynamics and molecular statics). A significant number of stable vacant lattice sites with high migration energy barriers exists and is thought to cause the sluggish diffusion. We predict that the hexagonal close-packed (hcp) structure is more stable than the face-centered cubic (fcc) structure at 0 K, which we propose as the fundamental reason for the micro-twinning at cryogenic temperatures. The alloying effect on the critical resolved shear stress (CRSS) is well predicted by the atomistic simulation, used for a design of non-equiatomic fcc HEAs with improved strength, and is experimentally verified. This study demonstrates the applicability of the proposed atomistic approach combined with a thermodynamic calculation technique to a computational design of advanced HEAs.

Improved atomistic simulation of diffusion and sorption in metal oxides

NASA Astrophysics Data System (ADS)

Skouras, E. D.; Burganos, V. N.; Payatakes, A. C.

2001-01-01

Gas diffusion and sorption on the surface of metal oxides are investigated using atomistic simulations, that make use of two different force fields for the description of the intramolecular and intermolecular interactions. MD and MC computations are presented and estimates of the mean residence time, Henry's constant, and the heat of adsorption are provided for various common gases (CO, CO2, O2, CH4, Xe), and semiconducting substrates that hold promise for gas sensor applications (SnO2, BaTiO3). Comparison is made between the performance of a simple, first generation force field (Universal) and a more detailed, second generation field (COMPASS) under the same conditions and the same assumptions regarding the generation of the working configurations. It is found that the two force fields yield qualitatively similar results in all cases examined here. However, direct comparison with experimental data reveals that the accuracy of the COMPASS-based computations is not only higher than that of the first generation force field but exceeds even that of published specialized methods, based on ab initio computations.

A Method for Combining Experimentation and Molecular Dynamics Simulation to Improve Cohesive Zone Models for Metallic Microstructures

NASA Technical Reports Server (NTRS)

Hochhalter, J. D.; Glaessgen, E. H.; Ingraffea, A. R.; Aquino, W. A.

2009-01-01

Fracture processes within a material begin at the nanometer length scale at which the formation, propagation, and interaction of fundamental damage mechanisms occur. Physics-based modeling of these atomic processes quickly becomes computationally intractable as the system size increases. Thus, a multiscale modeling method, based on the aggregation of fundamental damage processes occurring at the nanoscale within a cohesive zone model, is under development and will enable computationally feasible and physically meaningful microscale fracture simulation in polycrystalline metals. This method employs atomistic simulation to provide an optimization loop with an initial prediction of a cohesive zone model (CZM). This initial CZM is then applied at the crack front region within a finite element model. The optimization procedure iterates upon the CZM until the finite element model acceptably reproduces the near-crack-front displacement fields obtained from experimental observation. With this approach, a comparison can be made between the original CZM predicted by atomistic simulation and the converged CZM that is based on experimental observation. Comparison of the two CZMs gives insight into how atomistic simulation scales.

A Statistical Approach for the Concurrent Coupling of Molecular Dynamics and Finite Element Methods

NASA Technical Reports Server (NTRS)

Saether, E.; Yamakov, V.; Glaessgen, E.

2007-01-01

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, increasing the size of the MD domain quickly presents intractable computational demands. A robust approach to surmount this computational limitation has been to unite continuum modeling procedures such as the finite element method (FEM) with MD analyses thereby reducing the region of atomic scale refinement. The challenging problem is to seamlessly connect the two inherently different simulation techniques at their interface. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the typical boundary value problem used to define a coupled domain. The method uses statistical averaging of the atomistic MD domain to provide displacement interface boundary conditions to the surrounding continuum FEM region, which, in return, generates interface reaction forces applied as piecewise constant traction boundary conditions to the MD domain. The two systems are computationally disconnected and communicate only through a continuous update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM) as opposed to a direct coupling method where interface atoms and FEM nodes are individually related. The methodology is inherently applicable to three-dimensional domains, avoids discretization of the continuum model down to atomic scales, and permits arbitrary temperatures to be applied.

Mesoscale mechanics of twisting carbon nanotube yarns.

PubMed

Mirzaeifar, Reza; Qin, Zhao; Buehler, Markus J

2015-03-12

Fabricating continuous macroscopic carbon nanotube (CNT) yarns with mechanical properties close to individual CNTs remains a major challenge. Spinning CNT fibers and ribbons for enhancing the weak interactions between the nanotubes is a simple and efficient method for fabricating high-strength and tough continuous yarns. Here we investigate the mesoscale mechanics of twisting CNT yarns using full atomistic and coarse grained molecular dynamics simulations, considering concurrent mechanisms at multiple length-scales. To investigate the mechanical response of such a complex structure without losing insights into the molecular mechanism, we applied a multiscale strategy. The full atomistic results are used for training a coarse grained model for studying larger systems consisting of several CNTs. The mesoscopic model parameters are updated as a function of the twist angle, based on the full atomistic results, in order to incorporate the atomistic scale deformation mechanisms in larger scale simulations. By bridging across two length scales, our model is capable of accurately predicting the mechanical behavior of twisted yarns while the atomistic level deformations in individual nanotubes are integrated into the model by updating the parameters. Our results focused on studying a bundle of close packed nanotubes provide novel mechanistic insights into the spinning of CNTs. Our simulations reveal how twisting a bundle of CNTs improves the shear interaction between the nanotubes up to a certain level due to increasing the interaction surface. Furthermore, twisting the bundle weakens the intertube interactions due to excessive deformation in the cross sections of individual CNTs in the bundle.

Literature review report on atomistic modeling tools for FeCrAl alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yongfeng; Schwen, Daniel; Martinez, Enrique

2015-12-01

This reports summarizes the literature review results on atomistic tools, particularly interatomic potentials used in molecular dynamics simulations, for FeCrAl ternary alloys. FeCrAl has recently been identified as a possible cladding concept for accident tolerant fuels for its superior corrosion resistance. Along with several other concepts, an initial evaluation and recommendation are desired for FeCrAl before it’s used in realistic fuels. For this purpose, sufficient understanding on the in-reactor behavior of FeCrAl needs to be grained in a relatively short timeframe, and multiscale modeling and simulations have been selected as an efficient measure to supplement experiments and in-reactor testing formore » better understanding on FeCrAl. For the limited knowledge on FeCrAl alloys, the multiscale modeling approach relies on atomistic simulations to obtain the missing material parameters and properties. As a first step, atomistic tools have to be identified and this is the purpose of the present report. It was noticed during the literature survey that no interatomic potentials currently available for FeCrAl. Here, we summarize the interatomic potentials available for FeCr alloys for possible molecular dynamics studies using FeCr as surrogate materials. Other atomistic methods such as lattice kinetic Monte Carlo are also included in this report. A couple of research topics at the atomic scale are suggested based on the literature survey.« less

Scalable nanohelices for predictive studies and enhanced 3D visualization.

PubMed

Meagher, Kwyn A; Doblack, Benjamin N; Ramirez, Mercedes; Davila, Lilian P

2014-11-12

Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing applications. For predictive simulations, it has become increasingly important to be able to model the structure of nanohelices accurately. To study the effect of local structure on the properties of these complex geometries one must develop realistic models. To date, software packages are rather limited in creating atomistic helical models. This work focuses on producing atomistic models of silica glass (SiO₂) nanoribbons and nanosprings for molecular dynamics (MD) simulations. Using an MD model of "bulk" silica glass, two computational procedures to precisely create the shape of nanoribbons and nanosprings are presented. The first method employs the AWK programming language and open-source software to effectively carve various shapes of silica nanoribbons from the initial bulk model, using desired dimensions and parametric equations to define a helix. With this method, accurate atomistic silica nanoribbons can be generated for a range of pitch values and dimensions. The second method involves a more robust code which allows flexibility in modeling nanohelical structures. This approach utilizes a C++ code particularly written to implement pre-screening methods as well as the mathematical equations for a helix, resulting in greater precision and efficiency when creating nanospring models. Using these codes, well-defined and scalable nanoribbons and nanosprings suited for atomistic simulations can be effectively created. An added value in both open-source codes is that they can be adapted to reproduce different helical structures, independent of material. In addition, a MATLAB graphical user interface (GUI) is used to enhance learning through visualization and interaction for a general user with the atomistic helical structures. One application of these methods is the recent study of nanohelices via MD simulations for mechanical energy harvesting purposes.

Quantum Corrections to the 'Atomistic' MOSFET Simulations

NASA Technical Reports Server (NTRS)

Asenov, Asen; Slavcheva, G.; Kaya, S.; Balasubramaniam, R.

2000-01-01

We have introduced in a simple and efficient manner quantum mechanical corrections in our 3D 'atomistic' MOSFET simulator using the density gradient formalism. We have studied in comparison with classical simulations the effect of the quantum mechanical corrections on the simulation of random dopant induced threshold voltage fluctuations, the effect of the single charge trapping on interface states and the effect of the oxide thickness fluctuations in decanano MOSFETs with ultrathin gate oxides. The introduction of quantum corrections enhances the threshold voltage fluctuations but does not affect significantly the amplitude of the random telegraph noise associated with single carrier trapping. The importance of the quantum corrections for proper simulation of oxide thickness fluctuation effects has also been demonstrated.

Structural behavior of supercritical fluids under confinement

NASA Astrophysics Data System (ADS)

Ghosh, Kanka; Krishnamurthy, C. V.

2018-01-01

The existence of the Frenkel line in the supercritical regime of a Lennard-Jones (LJ) fluid shown through molecular dynamics (MD) simulations initially and later corroborated by experiments on argon opens up possibilities of understanding the structure and dynamics of supercritical fluids in general and of the Frenkel line in particular. The location of the Frenkel line, which demarcates two distinct physical states, liquidlike and gaslike within the supercritical regime, has been established through MD simulations of the velocity autocorrelation (VACF) and radial distribution function (RDF). We, in this article, explore the changes in the structural features of supercritical LJ fluid under partial confinement using atomistic walls. The study is carried out across the Frenkel line through a series of MD simulations considering a set of thermodynamics states in the supercritical regime (P =5000 bar, 240 K ≤T ≤1500 K ) of argon well above the critical point. Confinement is partial, with atomistic walls located normal to z and extending to "infinity" along the x and y directions. In the "liquidlike" regime of the supercritical phase, particles are found to be distributed in distinct layers along the z axis with layer spacing less than one atomic diameter and the lateral RDF showing amorphous-like structure for specific spacings (packing frustration) and non-amorphous-like structure for other spacings. Increasing the rigidity of the atomistic walls is found to lead to stronger layering and increased structural order. For confinement with reflective walls, layers are found to form with one atomic diameter spacing and the lateral RDF showing close-packed structure for the smaller confinements. Translational order parameter and excess entropy assessment confirms the ordering taking place for atomistic wall and reflective wall confinements. In the "gaslike" regime of the supercritical phase, particle distribution along the spacing and the lateral RDF exhibit features not significantly different from that due to normal gas regime. The heterogeneity across the Frenkel line, found to be present both in bulk and confined systems, might cause the breakdown of the universal scaling between structure and dynamics of fluids necessitating the determination of a unique relationship between them.

Structural behavior of supercritical fluids under confinement.

PubMed

Ghosh, Kanka; Krishnamurthy, C V

2018-01-01

The existence of the Frenkel line in the supercritical regime of a Lennard-Jones (LJ) fluid shown through molecular dynamics (MD) simulations initially and later corroborated by experiments on argon opens up possibilities of understanding the structure and dynamics of supercritical fluids in general and of the Frenkel line in particular. The location of the Frenkel line, which demarcates two distinct physical states, liquidlike and gaslike within the supercritical regime, has been established through MD simulations of the velocity autocorrelation (VACF) and radial distribution function (RDF). We, in this article, explore the changes in the structural features of supercritical LJ fluid under partial confinement using atomistic walls. The study is carried out across the Frenkel line through a series of MD simulations considering a set of thermodynamics states in the supercritical regime (P=5000 bar, 240K≤T≤1500K) of argon well above the critical point. Confinement is partial, with atomistic walls located normal to z and extending to "infinity" along the x and y directions. In the "liquidlike" regime of the supercritical phase, particles are found to be distributed in distinct layers along the z axis with layer spacing less than one atomic diameter and the lateral RDF showing amorphous-like structure for specific spacings (packing frustration) and non-amorphous-like structure for other spacings. Increasing the rigidity of the atomistic walls is found to lead to stronger layering and increased structural order. For confinement with reflective walls, layers are found to form with one atomic diameter spacing and the lateral RDF showing close-packed structure for the smaller confinements. Translational order parameter and excess entropy assessment confirms the ordering taking place for atomistic wall and reflective wall confinements. In the "gaslike" regime of the supercritical phase, particle distribution along the spacing and the lateral RDF exhibit features not significantly different from that due to normal gas regime. The heterogeneity across the Frenkel line, found to be present both in bulk and confined systems, might cause the breakdown of the universal scaling between structure and dynamics of fluids necessitating the determination of a unique relationship between them.

Exploring Beta-Amyloid Protein Transmembrane Insertion Behavior and Residue-Specific Lipid Interactions in Lipid Bilayers Using Multiscale MD Simulations

NASA Astrophysics Data System (ADS)

Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

2013-03-01

Beta-amyloid (Abeta) interactions with neurons are linked to Alzheimer's. Using a multiscale MD simulation strategy that combines the high efficiency of phase space sampling of coarse-grained MD (CGD) and the high spatial resolution of Atomistic MD (AMD) simulations, we studied the Abeta insertion dynamics in cholesterol-enriched and -depleted lipid bilayers that mimic the neuronal membranes domains. Forward (AMD-CGD) and reverse (CGD-AMD) mappings were used. At the atomistic level, cholesterol promoted insertion of Abeta with high (folded) or low (unfolded) helical contents of the lipid insertion domain (Lys28-Ala42), and the insertions were stabilized by the Lys28 snorkeling and Ala42-anchoring to the polar lipid groups of the bilayer up to 200ns. After the forward mapping, the folded inserted state switched to a new extended inserted state with the Lys28 descended to the middle of the bilayer while the unfolded inserted state migrated to the membrane surface up to 4000ns. The two new states remained stable for 200ns at the atomistic scale after the reverse mapping. Our results suggested that different Abeta membrane-orientation states separated by free energy barriers can be explored by the multiscale MD more effectively than by Atomistic MD simulations alone. NIH RC1-GM090897-02

Comparative simulations of microjetting using atomistic and continuous approaches in the presence of viscosity and surface tension

NASA Astrophysics Data System (ADS)

Durand, O.; Jaouen, S.; Soulard, L.; Heuzé, O.; Colombet, L.

2017-10-01

We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations with systems containing up to 700 × 106 atoms. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and the equation of state is calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with very good agreement the profiles, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes also exhibit a similar fragmentation phenomenology of the metallic liquid sheets ejected, although the fragmentation seed is different. We show in particular, that it depends on the mesh size in the continuous approach.

Atomistic Modeling of Corrosion Events at the Interface between a Metal and Its Environment

DOE PAGES

Taylor, Christopher D.

2012-01-01

Atomistic simulation is a powerful tool for probing the structure and properties of materials and the nature of chemical reactions. Corrosion is a complex process that involves chemical reactions occurring at the interface between a material and its environment and is, therefore, highly suited to study by atomistic modeling techniques. In this paper, the complex nature of corrosion processes and mechanisms is briefly reviewed. Various atomistic methods for exploring corrosion mechanisms are then described, and recent applications in the literature surveyed. Several instances of the application of atomistic modeling to corrosion science are then reviewed in detail, including studies ofmore » the metal-water interface, the reaction of water on electrified metallic interfaces, the dissolution of metal atoms from metallic surfaces, and the role of competitive adsorption in controlling the chemical nature and structure of a metallic surface. Some perspectives are then given concerning the future of atomistic modeling in the field of corrosion science.« less

Application of bi-Helmholtz nonlocal elasticity and molecular simulations to the dynamical response of carbon nanotubes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koutsoumaris, C. Chr.; Tsamasphyros, G. J.; Vogiatzis, G. G.

2015-12-31

The nonlocal theory of elasticity is employed for the study of the free vibrations of carbon nanotubes (CNT). For the first time, a bi-Helmholtz operator has been used instead of the standard Helmholtz operator in a nonlocal beam model. Alongside the continuum formulation and its numerical solution, atomistic Molecular Dynamics (MD) simulations have been conducted in order to directly evaluate the eigenfrequencies of vibrating CNTs with a minimum of adjustable parameters. Our results show that the bi-Helmholtz operator is the most appropriate one to fit MD simulation results. However, the estimation of vibration eigenfrequencies from molecular simulations still remains anmore » open (albeit well-posed) problem.« less

Constraint methods that accelerate free-energy simulations of biomolecules.

PubMed

Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A

2015-12-28

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations

PubMed Central

2015-01-01

Many commonly used coarse-grained models for proteins are based on simplified interaction sites and consequently may suffer from significant limitations, such as the inability to properly model protein secondary structure without the addition of restraints. Recent work on a benzene fluid (LettieriS.; ZuckermanD. M.J. Comput. Chem.2012, 33, 268−27522120971) suggested an alternative strategy of tabulating and smoothing fully atomistic orientation-dependent interactions among rigid molecules or fragments. Here we report our initial efforts to apply this approach to the polar and covalent interactions intrinsic to polypeptides. We divide proteins into nearly rigid fragments, construct distance and orientation-dependent tables of the atomistic interaction energies between those fragments, and apply potential energy smoothing techniques to those tables. The amount of smoothing can be adjusted to give coarse-grained models that range from the underlying atomistic force field all the way to a bead-like coarse-grained model. For a moderate amount of smoothing, the method is able to preserve about 70–90% of the α-helical structure while providing a factor of 3–10 improvement in sampling per unit computation time (depending on how sampling is measured). For a greater amount of smoothing, multiple folding–unfolding transitions of the peptide were observed, along with a factor of 10–100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations. For a β hairpin, secondary structure is also preserved, albeit for a narrower range of the smoothing parameter and, consequently, for a more modest improvement in sampling. We have also applied the new method in a “resolution exchange” setting, in which each replica runs a Monte Carlo simulation with a different degree of smoothing. We obtain exchange rates that compare favorably to our previous efforts at resolution exchange (LymanE.; ZuckermanD. M.J. Chem. Theory Comput.2006, 2, 656−666). PMID:25400525

A relationship between three-dimensional surface hydration structures and force distribution measured by atomic force microscopy.

PubMed

Miyazawa, Keisuke; Kobayashi, Naritaka; Watkins, Matthew; Shluger, Alexander L; Amano, Ken-ichi; Fukuma, Takeshi

2016-04-07

Hydration plays important roles in various solid-liquid interfacial phenomena. Very recently, three-dimensional scanning force microscopy (3D-SFM) has been proposed as a tool to visualise solvated surfaces and their hydration structures with lateral and vertical (sub) molecular resolution. However, the relationship between the 3D force map obtained and the equilibrium water density, ρ(r), distribution above the surface remains an open question. Here, we investigate this relationship at an interface of an inorganic mineral, fluorite, and water. The force maps measured in pure water are directly compared to force maps generated using the solvent tip approximation (STA) model and from explicit molecular dynamics simulations. The results show that the simulated STA force map describes the major features of the experimentally obtained force image. The agreement between the STA data and the experiment establishes the correspondence between the water density used as an input to the STA model and the experimental hydration structure and thus provides a tool to bridge the experimental force data and atomistic solvation structures. Further applications of this method should improve the accuracy and reliability of both interpretation of 3D-SFM force maps and atomistic simulations in a wide range of solid-liquid interfacial phenomena.

Atomistic- and Meso-Scale Computational Simulations for Developing Multi-Timescale Theory for Radiation Degradation in Electronic and Optoelectronic Devices

DTIC Science & Technology

2017-02-13

3550 Aberdeen Ave., SE 11. SPONSOR/MONITOR’S REPORT Kirtland AFB, NM 87117-5776 NUMBER(S) AFRL -RV-PS-TR-2016-0161 12. DISTRIBUTION / AVAILABILITY...RVIL Kirtland AFB, NM 87117-5776 2 cys Official Record Copy AFRL /RVSW/David Cardimona 1 cy 22 Approved for public release; distribution is unlimited. ... AFRL -RV-PS- AFRL -RV-PS- TR-2016-0161 TR-2016-0161 ATOMISTIC- AND MESO-SCALE COMPUTATIONAL SIMULATIONS FOR DEVELOPING MULTI-TIMESCALE THEORY FOR

Modelling irradiation-induced softening in BCC iron by crystal plasticity approach

NASA Astrophysics Data System (ADS)

Xiao, Xiazi; Terentyev, Dmitry; Yu, Long; Song, Dingkun; Bakaev, A.; Duan, Huiling

2015-11-01

Crystal plasticity model (CPM) for BCC iron to account for radiation-induced strain softening is proposed. CPM is based on the plastically-driven and thermally-activated removal of dislocation loops. Atomistic simulations are applied to parameterize dislocation-defect interactions. Combining experimental microstructures, defect-hardening/absorption rules from atomistic simulations, and CPM fitted to properties of non-irradiated iron, the model achieves a good agreement with experimental data regarding radiation-induced strain softening and flow stress increase under neutron irradiation.

Dissolution Processes at Step Edges of Calcite in Water Investigated by High-Speed Frequency Modulation Atomic Force Microscopy and Simulation.

PubMed

Miyata, Kazuki; Tracey, John; Miyazawa, Keisuke; Haapasilta, Ville; Spijker, Peter; Kawagoe, Yuta; Foster, Adam S; Tsukamoto, Katsuo; Fukuma, Takeshi

2017-07-12

The microscopic understanding of the crystal growth and dissolution processes have been greatly advanced by the direct imaging of nanoscale step flows by atomic force microscopy (AFM), optical interferometry, and X-ray microscopy. However, one of the most fundamental events that govern their kinetics, namely, atomistic events at the step edges, have not been well understood. In this study, we have developed high-speed frequency modulation AFM (FM-AFM) and enabled true atomic-resolution imaging in liquid at ∼1 s/frame, which is ∼50 times faster than the conventional FM-AFM. With the developed AFM, we have directly imaged subnanometer-scale surface structures around the moving step edges of calcite during its dissolution in water. The obtained images reveal that the transition region with typical width of a few nanometers is formed along the step edges. Building upon insight in previous studies, our simulations suggest that the transition region is most likely to be a Ca(OH) 2 monolayer formed as an intermediate state in the dissolution process. On the basis of this finding, we improve our understanding of the atomistic dissolution model of calcite in water. These results open up a wide range of future applications of the high-speed FM-AFM to the studies on various dynamic processes at solid-liquid interfaces with true atomic resolution.

Implications for plastic flow in the deep mantle from modelling dislocations in MgSiO3 minerals.

PubMed

Carrez, Philippe; Ferré, Denise; Cordier, Patrick

2007-03-01

The dynamics of the Earth's interior is largely controlled by mantle convection, which transports radiogenic and primordial heat towards the surface. Slow stirring of the deep mantle is achieved in the solid state through high-temperature creep of rocks, which are dominated by the mineral MgSiO3 perovskite. Transformation of MgSiO3 to a 'post-perovskite' phase may explain the peculiarities of the lowermost mantle, such as the observed seismic anisotropy, but the mechanical properties of these mineralogical phases are largely unknown. Plastic flow of solids involves the motion of a large number of crystal defects, named dislocations. A quantitative description of flow in the Earth's mantle requires information about dislocations in high-pressure minerals and their behaviour under stress. This property is currently out of reach of direct atomistic simulations using either empirical interatomic potentials or ab initio calculations. Here we report an alternative to direct atomistic simulations based on the framework of the Peierls-Nabarro model. Dislocation core models are proposed for MgSiO3 perovskite (at 100 GPa) and post-perovskite (at 120 GPa). We show that in perovskite, plastic deformation is strongly influenced by the orthorhombic distortions of the unit cell. In silicate post-perovskite, large dislocations are relaxed through core dissociation, with implications for the mechanical properties and seismic anisotropy of the lowermost mantle.

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

PubMed

McCarty, J; Clark, A J; Copperman, J; Guenza, M G

2014-05-28

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

Intergranular fracture in UO{sub 2}: derivation of traction-separation law from atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yongfeng; Millett, P.C.; Tonks, M.R.

2013-07-01

In this study, the intergranular fracture behavior of UO{sub 2} was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt Σ5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at themore » propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior. (authors)« less

Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yongfeng Zhang; Paul C Millett; Michael R Tonks

2013-10-01

In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagatingmore » crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.« less

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

Coarse-Grained Molecular Models of Water: A Review

PubMed Central

Hadley, Kevin R.; McCabe, Clare

2012-01-01

Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regards to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. Finally, how the models are parameterized depends on their application, so, while some are fitted to experimental properties such as surface tension and density, others are fitted to radial distribution functions extracted from atomistic simulations. PMID:22904601

Chemical dynamics simulations of the monohydrated OH{sup −}(H{sub 2}O) + CH{sub 3}I reaction. Atomic-level mechanisms and comparison with experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Jing; Hase, William L., E-mail: bill.hase@ttu.edu; Otto, Rico

2015-06-28

Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH{sup −}(H{sub 2}O) + CH{sub 3}I reaction. The S{sub N}2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH{sub 2}I{sup −}, and to a lesser extent CH{sub 2}I{sup −} (H{sub 2}O), becomes important. The S{sub N}2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of S{sub N}2 and proton transfer pre-reaction complexes and intermediates, includingmore » [CH{sub 3}--I--OH]{sup −}. In contrast, for the unsolvated OH{sup −} + CH{sub 3}I S{sub N}2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH{sup −}(H{sub 2}O) + CH{sub 3}I S{sub N}2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the S{sub N}2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H{sub 2}O molecule is unimportant. The S{sub N}2 reaction is dominated by events in which H{sub 2}O leaves the reactive system as CH{sub 3}OH is formed or before CH{sub 3}OH formation. Formation of solvated products is unimportant and participation of the (H{sub 2}O)CH{sub 3}OH---I{sup −} post-reaction complex for the S{sub N}2 reaction is negligible.« less

Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations.

PubMed

Ithuralde, Raúl Esteban; Roitberg, Adrián Enrique; Turjanski, Adrián Gustavo

2016-07-20

Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs.

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

PubMed

May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

2014-02-01

To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure. We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR-pMHC complex and the MP1-p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of >500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein-protein interaction strength. The python analysis framework and data files are available for download at http://www.ibi.vu.nl/downloads/bioinformatics-2013-btt675.tgz.

Cascade Defect Evolution Processes: Comparison of Atomistic Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Haixuan; Stoller, Roger E; Osetskiy, Yury N

2013-11-01

Determining the defect evolution beyond the molecular dynamics (MD) time scale is critical in bridging the gap between atomistic simulations and experiments. The recently developed self-evolving atomistic kinetic Monte Carlo (SEAKMC) method provides new opportunities to simulate long-term defect evolution with MD-like fidelity. In this study, SEAKMC is applied to investigate the cascade defect evolution in bcc iron. First, the evolution of a vacancy rich region is simulated and compared with results obtained using autonomous basin climbing (ABC) +KMC and kinetic activation-relaxation technique (kART) simulations. Previously, it is found the results from kART are orders of magnitude faster than ABC+KMC.more » The results obtained from SEAKMC are similar to kART but the time predicted is about one order of magnitude faster than kART. The fidelity of SEAKMC is confirmed by statistically relevant MD simulations at multiple higher temperatures, which proves that the saddle point sampling is close to complete in SEAKMC. The second is the irradiation-induced formation of C15 Laves phase nano-size defect clusters. In contrast to previous studies, which claim the defects can grow by capturing self-interstitials, we found these highly stable clusters can transform to <111> glissile configuration on a much longer time scale. Finally, cascade-annealing simulations using SEAKMC is compared with traditional object KMC (OKMC) method. SEAKMC predicts substantially fewer surviving defects compared with OKMC. The possible origin of this difference is discussed and a possible way to improve the accuracy of OKMC based on SEAKMC results is outlined. These studies demonstrate the atomistic fidelity of SEAKMC in comparison with other on-the-fly KMC methods and provide new information on long-term defect evolution in iron.« less

Atomistic study on the FCC/BCC interface structure with {112}KS orientation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Keonwook; Beyerlein, Irene; Han, Weizhong

2011-09-23

In this study, atomistic simulation is used to explore the atomic interface structure, the intrinsic defect network, and mechanism of twin formation from the {112}KS Cu-Nb interface. The interface structure of different material systems AI-Fe and AI-Nb are also compared with Cu-Nb interface.

Atomistic simulation of the coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface

NASA Astrophysics Data System (ADS)

Xiao, HuiFang; Huang, Bin; Yao, Ge; Kang, WenBin; Gong, Sheng; Pan, Hai; Cao, Yi; Wang, Jun; Zhang, Jian; Wang, Wei

2018-03-01

Understanding the processes of protein adsorption/desorption on nanoparticles' surfaces is important for the development of new nanotechnology involving biomaterials; however, an atomistic resolution picture for these processes and for the simultaneous protein conformational change is missing. Here, we report the adsorption of protein GB1 on a polystyrene nanoparticle surface using atomistic molecular dynamic simulations. Enabled by metadynamics, we explored the relevant phase space and identified three protein states, each involving both the adsorbed and desorbed modes. We also studied the change of the secondary and tertiary structures of GB1 during adsorption and the dominant interactions between the protein and surface in different adsorption stages. The results we obtained from simulation were found to be more adequate and complete than the previous one. We believe the model presented in this paper, in comparison with the previous ones, is a better theoretical model to understand and explain the experimental results.

Assessing the fracture strength of geological and related materials via an atomistically based J-integral

NASA Astrophysics Data System (ADS)

Jones, R. E.; Criscenti, L. J.; Rimsza, J.

2016-12-01

Predicting fracture initiation and propagation in low-permeability geomaterials is a critical yet un- solved problem crucial to assessing shale caprocks at carbon dioxide sequestration sites, and controlling fracturing for gas and oil extraction. Experiments indicate that chemical reactions at fluid-geomaterial interfaces play a major role in subcritical crack growth by weakening the material and altering crack nu- cleation and growth rates. Engineering the subsurface fracture environment, however, has been hindered by a lack of understanding of the mechanisms relating chemical environment to mechanical outcome, and a lack of capability directly linking atomistic insight to macroscale observables. We have developed a fundamental atomic-level understanding of the chemical-mechanical mecha- nisms that control subcritical cracks through coarse-graining data from reactive molecular simulations. Previous studies of fracture at the atomic level have typically been limited to producing stress-strain curves, quantifying either the system-level stress or energy at which fracture propagation occurs. As such, these curves are neither characteristic of nor insightful regarding fracture features local to the crack tip. In contrast, configurational forces, such as the J-integral, are specific to the crack in that they measure the energy available to move the crack and truly quantify fracture resistance. By development and use of field estimators consistent with the continuum conservation properties we are able to connect the data produced by atomistic simulation to the continuum-level theory of fracture mechanics and thus inform engineering decisions. In order to trust this connection we have performed theoretical consistency tests and validation with experimental data. Although we have targeted geomaterials, this capability can have direct impact on other unsolved technological problems such as predicting the corrosion and embrittlement of metals and ceramics. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corpo- ration, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Alloy Design Workbench-Surface Modeling Package Developed

NASA Technical Reports Server (NTRS)

Abel, Phillip B.; Noebe, Ronald D.; Bozzolo, Guillermo H.; Good, Brian S.; Daugherty, Elaine S.

2003-01-01

NASA Glenn Research Center's Computational Materials Group has integrated a graphical user interface with in-house-developed surface modeling capabilities, with the goal of using computationally efficient atomistic simulations to aid the development of advanced aerospace materials, through the modeling of alloy surfaces, surface alloys, and segregation. The software is also ideal for modeling nanomaterials, since surface and interfacial effects can dominate material behavior and properties at this level. Through the combination of an accurate atomistic surface modeling methodology and an efficient computational engine, it is now possible to directly model these types of surface phenomenon and metallic nanostructures without a supercomputer. Fulfilling a High Operating Temperature Propulsion Components (HOTPC) project level-I milestone, a graphical user interface was created for a suite of quantum approximate atomistic materials modeling Fortran programs developed at Glenn. The resulting "Alloy Design Workbench-Surface Modeling Package" (ADW-SMP) is the combination of proven quantum approximate Bozzolo-Ferrante-Smith (BFS) algorithms (refs. 1 and 2) with a productivity-enhancing graphical front end. Written in the portable, platform independent Java programming language, the graphical user interface calls on extensively tested Fortran programs running in the background for the detailed computational tasks. Designed to run on desktop computers, the package has been deployed on PC, Mac, and SGI computer systems. The graphical user interface integrates two modes of computational materials exploration. One mode uses Monte Carlo simulations to determine lowest energy equilibrium configurations. The second approach is an interactive "what if" comparison of atomic configuration energies, designed to provide real-time insight into the underlying drivers of alloying processes.

An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era.

PubMed

Spinello, Angelo; Magistrato, Alessandra

2017-08-01

Metallo-drugs have attracted enormous interest for cancer treatment. The achievements of this drug-type are summarized by the success story of cisplatin. That being said, there have been many drawbacks with its clinical use, which prompted decades worth of research efforts to move towards safer and more effective agents, either containing platinum or different metals. Areas covered: In this review, the authors provide an atomistic picture of the molecular mechanisms involving selected metallo-drugs from structural and molecular simulation studies. They also provide an omics perspective, pointing out many unsettled aspects of the most relevant families of metallo-drugs at an epigenetic level. Expert opinion: Molecular simulations are able to provide detailed information at atomistic and temporal (ps) resolutions that are rarely accessible to experiments. The increasing accuracy of computational methods and the growing performance of computational platforms, allow us to mirror wet lab experiments in silico. Consequently, the molecular mechanisms of drugs action/failure can be directly viewed on a computer screen, like a 'computational microscope', allowing us to harness this knowledge for the design of the next-generation of metallo-drugs.

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neilson, James R.; McQueen, Tyrel M.

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE PAGES

Neilson, James R.; McQueen, Tyrel M.

2015-09-20

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Structure identification methods for atomistic simulations of crystalline materials

DOE PAGES

Stukowski, Alexander

2012-05-28

Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

Heterogeneous path ensembles for conformational transitions in semi–atomistic models of adenylate kinase

PubMed Central

Bhatt, Divesh; Zuckerman, Daniel M.

2010-01-01

We performed “weighted ensemble” path–sampling simulations of adenylate kinase, using several semi–atomistic protein models. The models have an all–atom backbone with various levels of residue interactions. The primary result is that full statistically rigorous path sampling required only a few weeks of single–processor computing time with these models, indicating the addition of further chemical detail should be readily feasible. Our semi–atomistic path ensembles are consistent with previous biophysical findings: the presence of two distinct pathways, identification of intermediates, and symmetry of forward and reverse pathways. PMID:21660120

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;

Simulating the flow of entangled polymers.

PubMed

Masubuchi, Yuichi

2014-01-01

To optimize automation for polymer processing, attempts have been made to simulate the flow of entangled polymers. In industry, fluid dynamics simulations with phenomenological constitutive equations have been practically established. However, to account for molecular characteristics, a method to obtain the constitutive relationship from the molecular structure is required. Molecular dynamics simulations with atomic description are not practical for this purpose; accordingly, coarse-grained models with reduced degrees of freedom have been developed. Although the modeling of entanglement is still a challenge, mesoscopic models with a priori settings to reproduce entangled polymer dynamics, such as tube models, have achieved remarkable success. To use the mesoscopic models as staging posts between atomistic and fluid dynamics simulations, studies have been undertaken to establish links from the coarse-grained model to the atomistic and macroscopic simulations. Consequently, integrated simulations from materials chemistry to predict the macroscopic flow in polymer processing are forthcoming.

Atomistic Monte Carlo Simulation of Lipid Membranes

PubMed Central

Wüstner, Daniel; Sklenar, Heinz

2014-01-01

Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol. PMID:24469314

Atomistic simulation of laser-pulse surface modification: Predictions of models with various length and time scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starikov, Sergey V., E-mail: starikov@ihed.ras.ru; Pisarev, Vasily V.; Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412

2015-04-07

In this work, the femtosecond laser pulse modification of surface is studied for aluminium (Al) and gold (Au) by use of two-temperature atomistic simulation. The results are obtained for various atomistic models with different scales: from pseudo-one-dimensional to full-scale three-dimensional simulation. The surface modification after laser irradiation can be caused by ablation and melting. For low energy laser pulses, the nanoscale ripples may be induced on a surface by melting without laser ablation. In this case, nanoscale changes of the surface are due to a splash of molten metal under temperature gradient. Laser ablation occurs at a higher pulse energymore » when a crater is formed on the surface. There are essential differences between Al ablation and Au ablation. In the first step of shock-wave induced ablation, swelling and void formation occur for both metals. However, the simulation of ablation in gold shows an additional athermal type of ablation that is associated with electron pressure relaxation. This type of ablation takes place at the surface layer, at a depth of several nanometers, and does not induce swelling.« less

Adaptive resolution simulation of an atomistic protein in MARTINI water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecularmore » dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.« less

Adaptive resolution simulation of an atomistic protein in MARTINI water.

PubMed

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J; Praprotnik, Matej

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

Atomistic simulations of graphite etching at realistic time scales.

PubMed

Aussems, D U B; Bal, K M; Morgan, T W; van de Sanden, M C M; Neyts, E C

2017-10-01

Hydrogen-graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe time-scale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of ∼10 20 m -2 s -1 . The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C-C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching - chemical erosion - is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.

Penetration scaling in atomistic simulations of hypervelocity impact

NASA Astrophysics Data System (ADS)

Ruestes, C. J.; Bringa, E. M.; Fioretti, F.; Higginbotham, A.; Taylor, E. A.; Graham, G.

2011-06-01

We present atomistic molecular dynamics simulations of the impact of copper nano particles at 5 km/s on copper films ranging in thickness from 0.5 to 4 times the projectile diameter. We access both penetration and cratering regimes with final cratering morphologies showing considerable similarity to experimental impacts on both micron and millimeter scales. Both craters and holes are formed from a molten region, with relatively low defect densities remaining after cooling and recrystallisation. Crater diameter and penetration limits are compared to analytical scaling models: in agreement with some models we find the onset of penetration occurs for 1.0 < f/d < 1.5, where f is the film thickness and d is the projectile diameter. However, our results for the hole size agree well with scaling laws based on macroscopic experiments providing enhanced strength of a nano-film that melts completely at the impact region is taken into account. Penetration in films with pre-existing nanocracks is qualitatively similar to penetration in perfect films, including the lack of back-spall. Simulations using ``peridynamics'' are also described and compared to the atomistic simulations. Work supported by PICT2007-PRH, PICT-2008 1325, and SeCTyP.

Physics and performances of III-V nanowire broken-gap heterojunction TFETs using an efficient tight-binding mode-space NEGF model enabling million-atom nanowire simulations.

PubMed

Afzalian, A; Vasen, T; Ramvall, P; Shen, T-M; Wu, J; Passlack, M

2018-06-27

We report the capability to simulate in a quantum-mechanical atomistic fashion record-large nanowire devices, featuring several hundred to millions of atoms and a diameter up to 18.2 nm. We have employed a tight-binding mode-space NEGF technique demonstrating by far the fastest (up to 10 000  ×  faster) but accurate (error  <  1%) atomistic simulations to date. Such technique and capability opens new avenues to explore and understand the physics of nanoscale and mesoscopic devices dominated by quantum effects. In particular, our method addresses in an unprecedented way the technologically-relevant case of band-to-band tunneling (BTBT) in III-V nanowire broken-gap heterojunction tunnel-FETs (HTFETs). We demonstrate an accurate match of simulated BTBT currents to experimental measurements in a 12 nm diameter InAs NW and in an InAs/GaSb Esaki tunneling diode. We apply our TB MS simulations and report the first in-depth atomistic study of the scaling potential of III-V GAA nanowire HTFETs including the effect of electron-phonon scattering and discrete dopant impurity band tails, quantifying the benefits of this technology for low-power low-voltage CMOS applications.

Physics and performances of III–V nanowire broken-gap heterojunction TFETs using an efficient tight-binding mode-space NEGF model enabling million-atom nanowire simulations

NASA Astrophysics Data System (ADS)

Afzalian, A.; Vasen, T.; Ramvall, P.; Shen, T.-M.; Wu, J.; Passlack, M.

2018-06-01

We report the capability to simulate in a quantum-mechanical atomistic fashion record-large nanowire devices, featuring several hundred to millions of atoms and a diameter up to 18.2 nm. We have employed a tight-binding mode-space NEGF technique demonstrating by far the fastest (up to 10 000  ×  faster) but accurate (error  <  1%) atomistic simulations to date. Such technique and capability opens new avenues to explore and understand the physics of nanoscale and mesoscopic devices dominated by quantum effects. In particular, our method addresses in an unprecedented way the technologically-relevant case of band-to-band tunneling (BTBT) in III–V nanowire broken-gap heterojunction tunnel-FETs (HTFETs). We demonstrate an accurate match of simulated BTBT currents to experimental measurements in a 12 nm diameter InAs NW and in an InAs/GaSb Esaki tunneling diode. We apply our TB MS simulations and report the first in-depth atomistic study of the scaling potential of III–V GAA nanowire HTFETs including the effect of electron–phonon scattering and discrete dopant impurity band tails, quantifying the benefits of this technology for low-power low-voltage CMOS applications.

Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

NASA Technical Reports Server (NTRS)

Asenov, Asen; Brown, Andrew R.; Davies, John H.; Saini, Subhash

1999-01-01

We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

The indispensable role of the transversal spin fluctuations mechanism in laser-induced demagnetization of Co/Pt multilayers with nanoscale magnetic domains.

PubMed

Zhang, Wei; He, Wei; Peng, Li-Cong; Zhang, Ying; Cai, Jian-Wang; Evans, Richard F L; Zhang, Xiang-Qun; Cheng, Zhao-Hua

2018-07-06

The switching of magnetic domains induced by an ultrashort laser pulse has been demonstrated in nanostructured ferromagnetic films. This leads to the dawn of a new era in breaking the ultimate physical limit for the speed of magnetic switching and manipulation, which is relevant to current and future information storage. However, our understanding of the interactions between light and spins in magnetic heterostructures with nanoscale domain structures is still lacking. Here, both time-resolved magneto-optical Kerr effect experiments and atomistic simulations are carried out to investigate the dominant mechanism of laser-induced ultrafast demagnetization in [Co/Pt] 20 multilayers with nanoscale magnetic domains. It is found that the ultrafast demagnetization time remains constant with various magnetic configurations, indicating that the domain structures play a minor role in laser-induced ultrafast demagnetization. In addition, both in experiment and atomistic simulations, we find a dependence of ultrafast demagnetization time τ M on the laser fluence, which is in contrast to the observations of spin transport within magnetic domains. The remarkable agreement between experiment and atomistic simulations indicates that the local dissipation of spin angular momentum is the dominant demagnetization mechanism in this system. More interestingly, we made a comparison between the atomistic spin dynamic simulation and the longitudinal spin flip model, highlighting that the transversal spin fluctuations mechanism is responsible for the ultrafast demagnetization in the case of inhomogeneous magnetic structures. This is a significant advance in clarifying the microscopic mechanism underlying the process of ultrafast demagnetization in inhomogeneous magnetic structures.

Accelerating molecular Monte Carlo simulations using distance and orientation dependent energy tables: tuning from atomistic accuracy to smoothed “coarse-grained” models

PubMed Central

Lettieri, S.; Zuckerman, D.M.

2011-01-01

Typically, the most time consuming part of any atomistic molecular simulation is due to the repeated calculation of distances, energies and forces between pairs of atoms. However, many molecules contain nearly rigid multi-atom groups such as rings and other conjugated moieties, whose rigidity can be exploited to significantly speed up computations. The availability of GB-scale random-access memory (RAM) offers the possibility of tabulation (pre-calculation) of distance and orientation-dependent interactions among such rigid molecular bodies. Here, we perform an investigation of this energy tabulation approach for a fluid of atomistic – but rigid – benzene molecules at standard temperature and density. In particular, using O(1) GB of RAM, we construct an energy look-up table which encompasses the full range of allowed relative positions and orientations between a pair of whole molecules. We obtain a hardware-dependent speed-up of a factor of 24-50 as compared to an ordinary (“exact”) Monte Carlo simulation and find excellent agreement between energetic and structural properties. Second, we examine the somewhat reduced fidelity of results obtained using energy tables based on much less memory use. Third, the energy table serves as a convenient platform to explore potential energy smoothing techniques, akin to coarse-graining. Simulations with smoothed tables exhibit near atomistic accuracy while increasing diffusivity. The combined speed-up in sampling from tabulation and smoothing exceeds a factor of 100. For future applications greater speed-ups can be expected for larger rigid groups, such as those found in biomolecules. PMID:22120971

Imaging dynamic fingerprints of competing E2 and SN2 reactions.

PubMed

Carrascosa, Eduardo; Meyer, Jennifer; Zhang, Jiaxu; Stei, Martin; Michaelsen, Tim; Hase, William L; Yang, Li; Wester, Roland

2017-06-21

The competition between bimolecular nucleophilic substitution and base-induced elimination is of fundamental importance for the synthesis of pure samples in organic chemistry. Many factors that influence this competition have been identified over the years, but the underlying atomistic dynamics have remained difficult to observe. We present product velocity distributions for a series of reactive collisions of the type X -  + RY with X and Y denoting the halogen atoms fluorine, chlorine and iodine. By increasing the size of the residue R from methyl to tert-butyl in several steps, we find that the dynamics drastically change from backward to dominant forward scattering of the leaving ion relative to the reactant RY velocity. This characteristic fingerprint is also confirmed by direct dynamics simulations for ethyl as residue and attributed to the dynamics of elimination reactions. This work opens the door to a detailed atomistic understanding of transformation reactions in even larger systems.The competition between chemical reactions critically affects our natural environment and the synthesis of new materials. Here, the authors present an approach to directly image distinct fingerprints of essential organic reactions and monitor their competition as a function of steric substitution.

Enhanced calculation of eigen-stress field and elastic energy in atomistic interdiffusion of alloys

NASA Astrophysics Data System (ADS)

Cecilia, José M.; Hernández-Díaz, A. M.; Castrillo, Pedro; Jiménez-Alonso, J. F.

2017-02-01

The structural evolution of alloys is affected by the elastic energy associated to eigen-stress fields. However, efficient calculations of the elastic energy in evolving geometries are actually a great challenge in promising atomistic simulation techniques such as Kinetic Monte Carlo (KMC) methods. In this paper, we report two complementary algorithms to calculate the eigen-stress field by linear superposition (a.k.a. LSA, Lineal Superposition Algorithm) and the elastic energy modification in atomistic interdiffusion of alloys (the Atom Exchange Elastic Energy Evaluation (AE4) Algorithm). LSA is shown to be appropriated for fast incremental stress calculation in highly nanostructured materials, whereas AE4 provides the required input for KMC and, additionally, it can be used to evaluate the accuracy of the eigen-stress field calculated by LSA. Consequently, they are suitable to be used on-the-fly with KMC. Both algorithms are massively parallel by their definition and thus well-suited for their parallelization on modern Graphics Processing Units (GPUs). Our computational studies confirm that we can obtain significant improvements compared to conventional Finite Element Methods, and the utilization of GPUs opens up new possibilities for the development of these methods in atomistic simulation of materials.

Validation of the Concurrent Atomistic-Continuum Method on Screw Dislocation/Stacking Fault Interactions

DOE PAGES

Xu, Shuozhi; Xiong, Liming; Chen, Youping; ...

2017-04-26

Dislocation/stacking fault interactions play an important role in the plastic deformation of metallic nanocrystals and polycrystals. These interactions have been explored in atomistic models, which are limited in scale length by high computational cost. In contrast, multiscale material modeling approaches have the potential to simulate the same systems at a fraction of the computational cost. In this paper, we validate the concurrent atomistic-continuum (CAC) method on the interactions between a lattice screw dislocation and a stacking fault (SF) in three face-centered cubic metallic materials—Ni, Al, and Ag. Two types of SFs are considered: intrinsic SF (ISF) and extrinsic SF (ESF).more » For the three materials at different strain levels, two screw dislocation/ISF interaction modes (annihilation of the ISF and transmission of the dislocation across the ISF) and three screw dislocation/ESF interaction modes (transformation of the ESF into a three-layer twin, transformation of the ESF into an ISF, and transmission of the dislocation across the ESF) are identified. Here, our results show that CAC is capable of accurately predicting the dislocation/SF interaction modes with greatly reduced DOFs compared to fully-resolved atomistic simulations.« less

Validation of the Concurrent Atomistic-Continuum Method on Screw Dislocation/Stacking Fault Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Shuozhi; Xiong, Liming; Chen, Youping

Dislocation/stacking fault interactions play an important role in the plastic deformation of metallic nanocrystals and polycrystals. These interactions have been explored in atomistic models, which are limited in scale length by high computational cost. In contrast, multiscale material modeling approaches have the potential to simulate the same systems at a fraction of the computational cost. In this paper, we validate the concurrent atomistic-continuum (CAC) method on the interactions between a lattice screw dislocation and a stacking fault (SF) in three face-centered cubic metallic materials—Ni, Al, and Ag. Two types of SFs are considered: intrinsic SF (ISF) and extrinsic SF (ESF).more » For the three materials at different strain levels, two screw dislocation/ISF interaction modes (annihilation of the ISF and transmission of the dislocation across the ISF) and three screw dislocation/ESF interaction modes (transformation of the ESF into a three-layer twin, transformation of the ESF into an ISF, and transmission of the dislocation across the ESF) are identified. Here, our results show that CAC is capable of accurately predicting the dislocation/SF interaction modes with greatly reduced DOFs compared to fully-resolved atomistic simulations.« less

Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

NASA Astrophysics Data System (ADS)

Postila, Pekka A.; Kaszuba, Karol; Kuleta, Patryk; Vattulainen, Ilpo; Sarewicz, Marcin; Osyczka, Artur; Róg, Tomasz

2016-09-01

The cytochrome (cyt) bc1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Qi-site of the cyt bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Qi-site to facilitate binding of half-protonated semiquinone - a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Qi-site.

Multiscale Modeling of Grain-Boundary Fracture: Cohesive Zone Models Parameterized From Atomistic Simulations

NASA Technical Reports Server (NTRS)

Glaessgen, Edward H.; Saether, Erik; Phillips, Dawn R.; Yamakov, Vesselin

2006-01-01

A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

PubMed Central

2017-01-01

The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments. PMID:28666087

Addressing uncertainty in atomistic machine learning.

PubMed

Peterson, Andrew A; Christensen, Rune; Khorshidi, Alireza

2017-05-10

Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility of the predictions. In this perspective, we address the types of errors that might arise in atomistic machine learning, the unique aspects of atomistic simulations that make machine-learning challenging, and highlight how uncertainty analysis can be used to assess the validity of machine-learning predictions. We suggest this will allow researchers to more fully use machine learning for the routine acceleration of large, high-accuracy, or extended-time simulations. In our demonstrations, we use a bootstrap ensemble of neural network-based calculators, and show that the width of the ensemble can provide an estimate of the uncertainty when the width is comparable to that in the training data. Intriguingly, we also show that the uncertainty can be localized to specific atoms in the simulation, which may offer hints for the generation of training data to strategically improve the machine-learned representation.

Atomistic simulation of defect formation and structure transitions in U-Mo alloys in swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Kolotova, L. N.; Starikov, S. V.

2017-11-01

In irradiation of swift heavy ions, the defects formation frequently takes place in crystals. High energy transfer into the electronic subsystem and relaxations processes lead to the formation of structural defects and cause specific effects, such as the track formation. There is a large interest to understanding of the mechanisms of defects/tracks formation due to the heating of the electron subsystem. In this work, the atomistic simulation of defects formation and structure transitions in U-Mo alloys in irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes in irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation in irradiation in the various conditions are calculated.

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

PubMed

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs

PubMed Central

Krepl, Miroslav; Cléry, Antoine; Blatter, Markus; Allain, Frederic H.T.; Sponer, Jiri

2016-01-01

RNA recognition motif (RRM) proteins represent an abundant class of proteins playing key roles in RNA biology. We present a joint atomistic molecular dynamics (MD) and experimental study of two RRM-containing proteins bound with their single-stranded target RNAs, namely the Fox-1 and SRSF1 complexes. The simulations are used in conjunction with NMR spectroscopy to interpret and expand the available structural data. We accumulate more than 50 μs of simulations and show that the MD method is robust enough to reliably describe the structural dynamics of the RRM–RNA complexes. The simulations predict unanticipated specific participation of Arg142 at the protein–RNA interface of the SRFS1 complex, which is subsequently confirmed by NMR and ITC measurements. Several segments of the protein–RNA interface may involve competition between dynamical local substates rather than firmly formed interactions, which is indirectly consistent with the primary NMR data. We demonstrate that the simulations can be used to interpret the NMR atomistic models and can provide qualified predictions. Finally, we propose a protocol for ‘MD-adapted structure ensemble’ as a way to integrate the simulation predictions and expand upon the deposited NMR structures. Unbiased μs-scale atomistic MD could become a technique routinely complementing the NMR measurements of protein–RNA complexes. PMID:27193998

An atomistic-continuum hybrid simulation of fluid flows over superhydrophobic surfaces

PubMed Central

Li, Qiang; He, Guo-Wei

2009-01-01

Recent experiments have found that slip length could be as large as on the order of 1 μm for fluid flows over superhydrophobic surfaces. Superhydrophobic surfaces can be achieved by patterning roughness on hydrophobic surfaces. In the present paper, an atomistic-continuum hybrid approach is developed to simulate the Couette flows over superhydrophobic surfaces, in which a molecular dynamics simulation is used in a small region near the superhydrophobic surface where the continuum assumption is not valid and the Navier-Stokes equations are used in a large region for bulk flows where the continuum assumption does hold. These two descriptions are coupled using the dynamic coupling model in the overlap region to ensure momentum continuity. The hybrid simulation predicts a superhydrophobic state with large slip lengths, which cannot be obtained by molecular dynamics simulation alone. PMID:19693344

Compression deformation of WC: atomistic description of hard ceramic material

NASA Astrophysics Data System (ADS)

Feng, Qing; Song, Xiaoyan; Liu, Xuemei; Liang, Shuhua; Wang, Haibin; Nie, Zuoren

2017-11-01

The deformation characteristics of WC, as a typical hard ceramic material, were studied on the nanoscale using atomistic simulations for both the single-crystal and polycrystalline forms under uniaxial compression. In particular, the effects of crystallographic orientation, grain boundary coordination and grain size on the origin of deformation were investigated. The deformation behavior of the single-crystal and polycrystalline WC both depend strongly on the orientation towards the loading direction. The grain boundaries play a significant role in the deformation coordination and the potential high fracture toughness of the nanocrystalline WC. In contrast to conventional knowledge of ceramics, maximum strength was obtained at a critical grain size corresponding to the turning point from a Hall-Petch to an inverse Hall-Petch relationship. For this the mechanism of the combined effect of dislocation motion within grains and the coordination of stress concentration at the grain boundaries were proposed. The present work has moved forward our understanding of plastic deformability and the possibility of achieving a high strength of nanocrystalline ceramic materials.

Compression deformation of WC: atomistic description of hard ceramic material.

PubMed

Feng, Qing; Song, Xiaoyan; Liu, Xuemei; Liang, Shuhua; Wang, Haibin; Nie, Zuoren

2017-11-24

The deformation characteristics of WC, as a typical hard ceramic material, were studied on the nanoscale using atomistic simulations for both the single-crystal and polycrystalline forms under uniaxial compression. In particular, the effects of crystallographic orientation, grain boundary coordination and grain size on the origin of deformation were investigated. The deformation behavior of the single-crystal and polycrystalline WC both depend strongly on the orientation towards the loading direction. The grain boundaries play a significant role in the deformation coordination and the potential high fracture toughness of the nanocrystalline WC. In contrast to conventional knowledge of ceramics, maximum strength was obtained at a critical grain size corresponding to the turning point from a Hall-Petch to an inverse Hall-Petch relationship. For this the mechanism of the combined effect of dislocation motion within grains and the coordination of stress concentration at the grain boundaries were proposed. The present work has moved forward our understanding of plastic deformability and the possibility of achieving a high strength of nanocrystalline ceramic materials.

BDA: A novel method for identifying defects in body-centered cubic crystals.

PubMed

Möller, Johannes J; Bitzek, Erik

2016-01-01

The accurate and fast identification of crystallographic defects plays a key role for the analysis of atomistic simulation output data. For face-centered cubic (fcc) metals, most existing structure analysis tools allow for the direct distinction of common defects, such as stacking faults or certain low-index surfaces. For body-centered cubic (bcc) metals, on the other hand, a robust way to identify such defects is currently not easily available. We therefore introduce a new method for analyzing atomistic configurations of bcc metals, the BCC Defect Analysis (BDA). It uses existing structure analysis algorithms and combines their results to uniquely distinguish between typical defects in bcc metals. In essence, the BDA method offers the following features:•Identification of typical defect structures in bcc metals.•Reduction of erroneously identified defects by iterative comparison to the defects in the atom's neighborhood.•Availability as ready-to-use Python script for the widespread visualization tool OVITO [http://ovito.org].

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

NASA Astrophysics Data System (ADS)

Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

2014-01-01

Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.

Atomistic polarizable force field for molecular dynamics simulations of azide anion containing ionic liquids and crystals.

NASA Astrophysics Data System (ADS)

Starovoytov, Oleg; Hooper, Justin; Borodin, Oleg; Smith, Grant

2010-03-01

Atomistic polarizable force field has been developed for a number of azide anion containing ionic liquids and crystals. Hybrid Molecular Dynamics/Monte Carlo (MD/MC) simulations were performed on methylguanazinium azide and 1-(2-butynyl)-3-methyl-imidazolium azide crystals, while 1-butyl-2,3-dimethylimidazolium azide and 1-amino-3-methyl-1,2,3-triazolium azide ionic liquids were investigated using MD simulations. Crystal cell parameters and crystal structures of 1-(2-butynyl)-3-methyl-imidazolium azide were found in good agreement with X-ray experimental data. Density and ion transport of 1-butyl-2,3-dimethylimidazolium azide predicted from MD simulations were in good agreement with experiments. Details of the ionic liquid structure and relaxation mechanism will be discussed.

A Configurational-Bias-Monte-Carlo Back-Mapping Algorithm for Efficient and Rapid Conversion of Coarse-Grained Water Structures Into Atomistic Models.

PubMed

Loeffler, Troy David; Chan, Henry; Narayanan, Badri; Cherukara, Mathew J; Gray, Stephen K; Sankaranarayanan, Subramanian K R S

2018-06-20

Coarse-grained molecular dynamics (MD) simulations represent a powerful approach to simulate longer time scale and larger length scale phenomena than those accessible to all-atom models. The gain in efficiency, however, comes at the cost of atomistic details. The reverse transformation, also known as back-mapping, of coarse grained beads into their atomistic constituents represents a major challenge. Most existing approaches are limited to specific molecules or specific force-fields and often rely on running a long time atomistic MD of the back-mapped configuration to arrive at an optimal solution. Such approaches are problematic when dealing with systems with high diffusion barriers. Here, we introduce a new extension of the configurational-bias-Monte-Carlo (CBMC) algorithm, which we term the crystalline-configurational-bias-Monte-Carlo (C-CBMC) algortihm, that allows rapid and efficient conversion of a coarse-grained model back into its atomistic representation. Although the method is generic, we use a coarse-grained water model as a representative example and demonstrate the back-mapping or reverse transformation for model systems ranging from the ice-liquid water interface to amorphous and crystalline ice configurations. A series of simulations using the TIP4P/Ice model are performed to compare the new CBMC method to several other standard Monte Carlo and Molecular Dynamics based back-mapping techniques. In all the cases, the C-CBMC algorithm is able to find optimal hydrogen bonded configuration many thousand evaluations/steps sooner than the other methods compared within this paper. For crystalline ice structures such as a hexagonal, cubic, and cubic-hexagonal stacking disorder structures, the C-CBMC was able to find structures that were between 0.05 and 0.1 eV/water molecule lower in energy than the ground state energies predicted by the other methods. Detailed analysis of the atomistic structures show a significantly better global hydrogen positioning when contrasted with the existing simpler back-mapping methods. Our results demonstrate the efficiency and efficacy of our new back-mapping approach, especially for crystalline systems where simple force-field based relaxations have a tendency to get trapped in local minima.

Atomistic methodologies for material properties of 2D materials at the nanoscale

NASA Astrophysics Data System (ADS)

Zhang, Zhen

Research on two dimensional (2D) materials, such as graphene and MoS2, now involves thousands of researchers worldwide cutting across physics, chemistry, engineering and biology. Due to the extraordinary properties of 2D materials, research extends from fundamental science to novel applications of 2D materials. From an engineering point of view, understanding the material properties of 2D materials under various conditions is crucial for tailoring the electrical and mechanical properties of 2D-material-based devices at the nanoscale. Even at the nanoscale, molecular systems typically consist of a vast number of atoms. Molecular dynamics (MD) simulations enable us to understand the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. From a continuum approach, mechanical properties and thermal properties, such as strain, stress, and heat capacity, are well defined and experimentally measurable. In MD simulations, material systems are considered to be discrete, and only interatomic potential, interatomic forces, and atom positions are directly obtainable. Besides, most of the fracture mechanics concepts, such as stress intensity factors, are not applicable since there is no singularity in MD simulations. However, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at the nanoscale. Therefore, equivalent definition of a physical quantity both in atomic scale and macroscopic scale is necessary in order to understand molecular and continuum scale phenomena concurrently. This work introduces atomistic simulation methodologies, based on interatomic potential and interatomic forces, as a tool to unveil the mechanical properties, thermal properties and fracture mechanical properties of 2D materials at the nanoscale. Among many 2D materials, graphene and MoS2 have attracted intense interest. Therefore, we applied our methodologies to graphene and MoS2 as examples. Young's modulus, Poison's ratio, heat conductivity, heat capacity, and energy release rate at the nanoscale are studied. These findings lend compelling insights into the atomistic mechanisms of graphene and MoS2, and provide useful guidelines for the design of 2D-material-based nanodevices.

Temperature Dependence of the OH- + CH3I Reaction Kinetics. Experimental and Simulation Studies and Atomic-Level Dynamics (Postprint)

DTIC Science & Technology

2013-11-25

reaction time, the core of the flow was sampled through a small orifice in a rounded nose cone, while the bulk of the gas was pumped by an oil free...than rebound for the latter. Calculations were performed with the OW quantum number J equal to 0, 3, and 6 to investigate the effect of OH-rotational...have little dependence on J. Possible effects on the atomistic mechanisms were investigated for the S(N)2 pathway and the probability of the direct

Suppression of Random Dopant-Induced Threshold Voltage Fluctuations in Sub-0.1-(micron)meter MOSFET's with Epitaxial and (delta)-Doped Channels

NASA Technical Reports Server (NTRS)

Asenov, Asen; Saini, Subhash

1999-01-01

A detailed three-dimensional (3-D) statistical 'atomistic' simulation study of fluctuation-resistant sub-0.1-(micron)meter MOSFET architectures with epitaxial channels and delta doping is presented. The need for enhancing the fluctuation resistance of the sub-0.1-(micron)meter generation transistors is highlighted by presenting summarized results from atomistic simulations of a wide range of conventional devices with uniformly doped channel. According to our atomistic results, the doping concentration dependence of the random dopant-induced threshold voltage fluctuations in conventional devices is stronger than the analytically predicted fourth-root dependence. As a result of this, the scaling of such devices will be restricted by the "intrinsic" random dopant-induced fluctuations earlier than anticipated. Our atomistic simulations confirm that the introduction of a thin epitaxial layer in the MOSFET's channel can efficiently suppress the random dopant-induced threshold voltage fluctuations in sub-0.1-(micron)meter devices. For the first time, we observe an "anomalous" reduction in the threshold voltage fluctuations with an increase in the doping concentration behind the epitaxial channel, which we attribute to screening effects. Also, for the first time we study the effect of a delta-doping, positioned behind the epitaxial layer, on the intrinsic threshold voltage fluctuations. Above a certain thickness of epitaxial layer, we observe a pronounced anomalous decrease in the threshold voltage fluctuation with the increase of the delta doping. This phenomenon, which is also associated with screening, enhances the importance of the delta doping in the design of properly scaled fluctuation-resistant sub-0.1-(micron)meter MOSFET's. Index Terms-Doping, fluctuations, MOSFET, semiconductor device simulation, silicon devices, threshold.

Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer.

PubMed

Pluhackova, Kristyna; Wassenaar, Tsjerk A; Kirsch, Sonja; Böckmann, Rainer A

2015-03-26

A molecular description of the lipid-protein interactions underlying the adsorption of proteins to membranes is crucial for understanding, for example, the specificity of adsorption or the binding strength of a protein to a bilayer, or for characterizing protein-induced changes of membrane properties. In this paper, we extend an automated in silico assay (DAFT) for binding studies and apply it to characterize the adsorption of the model fusion peptides E and K to a mixed phospholipid/cholesterol membrane using coarse-grained molecular dynamics simulations. In addition, we couple the coarse-grained protocol to reverse transformation to atomistic resolution, thereby allowing to study molecular interactions with high detail. The experimentally observed differential binding of the peptides E and K to membranes, as well as the increased binding affinity of helical over unstructered peptides, could be well reproduced using the polarizable Martini coarse-grained (CG) force field. Binding to neutral membranes is shown to be dominated by initial binding of the positively charged N-terminus to the phospholipid headgroup region, followed by membrane surface-aligned insertion of the peptide at the interface between the hydrophobic core of the membrane and its polar headgroup region. Both coarse-grained and atomistic simulations confirm a before hypothesized snorkeling of lysine side chains for the membrane-bound state of the peptide K. Cholesterol was found to be enriched in peptide vicinity, which is probably of importance for the mechanism of membrane fusion. The applied sequential multiscale method, using coarse-grained simulations for the slow adsorption process of peptides to membranes followed by backward transformation to atomistic detail and subsequent atomistic simulations of the preformed peptide-lipid complexes, is shown to be a versatile approach to study the interactions of peptides or proteins with biomembranes.

A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide)

DOE PAGES

Abbott, Lauren J.; Stevens, Mark J.

2015-12-22

In this study, a coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil–globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomisticmore » simulations.« less

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

PubMed

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

PubMed

Shen, Lin; Hu, Hao

2014-06-10

We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

A universal strategy for the creation of machine learning-based atomistic force fields

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

2017-09-01

Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.

Revealing Nanostructures through Plasmon Polarimetry.

PubMed

Kleemann, Marie-Elena; Mertens, Jan; Zheng, Xuezhi; Cormier, Sean; Turek, Vladimir; Benz, Felix; Chikkaraddy, Rohit; Deacon, William; Lombardi, Anna; Moshchalkov, Victor V; Vandenbosch, Guy A E; Baumberg, Jeremy J

2017-01-24

Polarized optical dark-field spectroscopy is shown to be a versatile noninvasive probe of plasmonic structures that trap light to the nanoscale. Clear spectral polarization splittings are found to be directly related to the asymmetric morphology of nanocavities formed between faceted gold nanoparticles and an underlying gold substrate. Both experiment and simulation show the influence of geometry on the coupled system, with spectral shifts Δλ = 3 nm from single atoms. Analytical models allow us to identify the split resonances as transverse cavity modes, tightly confined to the nanogap. The direct correlation of resonance splitting with atomistic morphology allows mapping of subnanometre structures, which is crucial for progress in extreme nano-optics involving chemistry, nanophotonics, and quantum devices.

Consistent Temperature Coupling with Thermal Fluctuations of Smooth Particle Hydrodynamics and Molecular Dynamics

PubMed Central

Ganzenmüller, Georg C.; Hiermaier, Stefan; Steinhauser, Martin O.

2012-01-01

We propose a thermodynamically consistent and energy-conserving temperature coupling scheme between the atomistic and the continuum domain. The coupling scheme links the two domains using the DPDE (Dissipative Particle Dynamics at constant Energy) thermostat and is designed to handle strong temperature gradients across the atomistic/continuum domain interface. The fundamentally different definitions of temperature in the continuum and atomistic domain – internal energy and heat capacity versus particle velocity – are accounted for in a straightforward and conceptually intuitive way by the DPDE thermostat. We verify the here-proposed scheme using a fluid, which is simultaneously represented as a continuum using Smooth Particle Hydrodynamics, and as an atomistically resolved liquid using Molecular Dynamics. In the case of equilibrium contact between both domains, we show that the correct microscopic equilibrium properties of the atomistic fluid are obtained. As an example of a strong non-equilibrium situation, we consider the propagation of a steady shock-wave from the continuum domain into the atomistic domain, and show that the coupling scheme conserves both energy and shock-wave dynamics. To demonstrate the applicability of our scheme to real systems, we consider shock loading of a phospholipid bilayer immersed in water in a multi-scale simulation, an interesting topic of biological relevance. PMID:23300586

Nanoscale deicing by molecular dynamics simulation.

PubMed

Xiao, Senbo; He, Jianying; Zhang, Zhiliang

2016-08-14

Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.

Atomistic modeling of carbon Cottrell atmospheres in bcc iron

NASA Astrophysics Data System (ADS)

Veiga, R. G. A.; Perez, M.; Becquart, C. S.; Domain, C.

2013-01-01

Atomistic simulations with an EAM interatomic potential were used to evaluate carbon-dislocation binding energies in bcc iron. These binding energies were then used to calculate the occupation probability of interstitial sites in the vicinity of an edge and a screw dislocation. The saturation concentration due to carbon-carbon interactions was also estimated by atomistic simulations in the dislocation core and taken as an upper limit for carbon concentration in a Cottrell atmosphere. We obtained a maximum concentration of 10 ± 1 at.% C at T = 0 K within a radius of 1 nm from the dislocation lines. The spatial carbon distributions around the line defects revealed that the Cottrell atmosphere associated with an edge dislocation is denser than that around a screw dislocation, in contrast with the predictions of the classical model of Cochardt and colleagues. Moreover, the present Cottrell atmosphere model is in reasonable quantitative accord with the three-dimensional atom probe data available in the literature.

Atomistic simulation of hydrophobin HFBII conformation in aqueous and fluorous media and at the water/vacuum interface.

PubMed

Raffaini, Giuseppina; Milani, Roberto; Ganazzoli, Fabio; Resnati, Giuseppe; Metrangolo, Pierangelo

2016-01-01

Hydrophobins are proteins of interest for numerous applications thanks to their unique conformational and surface properties and their ability to self-assemble at interfaces. Here we report fully atomistic molecular mechanics and molecular dynamics results together with circular dichroism experimental data, aimed to study the conformational properties of the hydrophobin HFBII in a fluorinated solvent in comparison with a water solution and/or at an aqueous/vacuum interface. Both the atomistic simulations and the circular dichroism data show the remarkable structural stability of HFBII at all scales in all these environments, with no significant structural change, although a small cavity is formed in the fluorinated solvent. The combination of theoretical calculations and circular dichroism data can describe in detail the protein conformation and flexibility in different solvents and/or at an interface, and constitutes a first step towards the study of their self-assembly. Copyright © 2015 Elsevier Inc. All rights reserved.

New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

NASA Technical Reports Server (NTRS)

Saether, E.; Yamakov, V.; Glaessgen, E.

2008-01-01

A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique

NASA Astrophysics Data System (ADS)

Shadrack Jabes, B.; Krekeler, C.; Klein, R.; Delle Site, L.

2018-05-01

We employ the Grand Canonical Adaptive Resolution Simulation (GC-AdResS) molecular dynamics technique to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS, atomistic details are kept only in an open sub-region of the system while the environment is treated at coarse-grained level; thus, if spatial quantities calculated in such a sub-region agree with the equivalent quantities calculated in a full atomistic simulation, then the atomistic degrees of freedom outside the sub-region play a negligible role. The size of the sub-region fixes the degree of spatial locality of a certain quantity. We show that even for sub-regions whose radius corresponds to the size of a few molecules, spatial properties are reasonably reproduced thus suggesting a higher degree of spatial locality, a hypothesis put forward also by other researchers and that seems to play an important role for the characterization of fundamental properties of a large class of ionic liquids.

Multiscale Modeling of UHTC: Thermal Conductivity

NASA Technical Reports Server (NTRS)

Lawson, John W.; Murry, Daw; Squire, Thomas; Bauschlicher, Charles W.

2012-01-01

We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

NASA Technical Reports Server (NTRS)

Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

2009-01-01

Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora

2016-02-05

Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly modeled. In this paper, we probe the degree of coarse graining required to simultaneously retain significant atomistic details and access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using linear polyethylene as a model system, we probe how the coarse-graining scale affects the measured dynamics. Iterative Boltzmann inversion ismore » used to derive coarse-grained potentials with 2–6 methylene groups per coarse-grained bead from a fully atomistic melt simulation. We show that atomistic detail is critical to capturing large-scale dynamics. Finally, using these models we simulate polyethylene melts for times over 500 μs to study the viscoelastic properties of well-entangled polymer melts.« less

Secondary water pore formation for proton transport in a ClC exchanger revealed by an atomistic molecular-dynamics simulation.

PubMed

Ko, Youn Jo; Jo, Won Ho

2010-05-19

Several prokaryotic ClC proteins have been demonstrated to function as exchangers that transport both chloride ions and protons simultaneously in opposite directions. However, the path of the proton through the ClC exchanger, and how the protein brings about the coupled movement of both ions are still unknown. In this work, we use an atomistic molecular dynamics (MD) simulation to demonstrate that a previously unknown secondary water pore is formed inside an Escherichia coli ClC exchanger. The secondary water pore is bifurcated from the chloride ion pathway at E148. From the systematic simulations, we determined that the glutamate residue exposed to the intracellular solution, E203, plays an important role as a trigger for the formation of the secondary water pore, and that the highly conserved tyrosine residue Y445 functions as a barrier that separates the proton from the chloride ion pathways. Based on our simulation results, we conclude that protons in the ClC exchanger are conducted via a water network through the secondary water pore, and we propose a new mechanism for the coupled transport of chloride ions and protons. It has been reported that several members of ClC proteins are not just channels that simply transport chloride ions across lipid bilayers; rather, they are exchangers that transport both the chloride ion and proton in opposite directions. However, the ion transit pathways and the mechanism of the coupled movement of these two ions have not yet been unveiled. In this article, we report a new finding (to our knowledge) of a water pore inside a prokaryotic ClC protein as revealed by computer simulation. This water pore is bifurcated from the putative chloride ion, and water molecules inside the new pore connect two glutamate residues that are known to be key residues for proton transport. On the basis of our simulation results, we conclude that the water wire that is formed inside the newly found pore acts as a proton pathway, which enables us to resolve many problems that could not be addressed by previous experimental studies. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Final Report for DE-FG02-99ER45795

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, John Warren

The research supported by this grant focuses on atomistic studies of defects, phase transitions, electronic and magnetic properties, and mechanical behaviors of materials. We have been studying novel properties of various emerging nanoscale materials on multiple levels of length and time scales, and have made accurate predictions on many technologically important properties. A significant part of our research has been devoted to exploring properties of novel nano-scale materials by pushing the limit of quantum mechanical simulations, and development of a rigorous scheme to design accurate classical inter-atomic potentials for larger scale atomistic simulations for many technologically important metals and metalmore » alloys.« less

Atomistic simulation of graphene-based polymer nanocomposites

NASA Astrophysics Data System (ADS)

Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

2016-05-01

Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

Atomistic simulations of bulk, surface and interfacial polymer properties

NASA Astrophysics Data System (ADS)

Natarajan, Upendra

In chapter I, quasi-static molecular mechanics based simulations are used to estimate the activation energy of phenoxy rings flips in the amorphous region of a semicrystalline polyimide. Intra and intermolecular contributions to the flip activation energy, the torsional cooperativity accompanying the flip, and the effect of the flip on the motion in the glassy bulk state, are looked at. Also, comparison of the weighted mean activation energy is made with experimental data from solid state NMR measurements; the simulated value being 17.5 kcal/mol., while the experimental value was observed to be 10.5 kcal/mol. Chapter II deals with construction of random copolymer thin films of styrene-butadiene (SB) and styrene-butadiene-acrylonitrile (SBA). The structure and properties of the free surfaces presented by these thin films are analysed by, the atom mass density profiles, backbone bond orientation function, and the spatial distribution of acrylonitrile groups and styrene rings. The surface energies of SB and SBA are calculated using an atomistic equation and are compared with experimental data in the literature. In chapter III, simulations of polymer-polymer interfaces between like and unlike polymers, specifically cis-polybutadiene (PBD) and atatic polypropylene (PP), are presented. The structure of an incompatible polymer-polymer interface, and the estimation of the thermodynamic work of adhesion and interfacial energy between different incompatible polymers, form the focus here. The work of adhesion is calculated using an atomistic equation and is further used in a macroscopic equation to estimate the interfacial energy. The interfacial energy is compared with typical values for other immiscible systems in the literature. The interfacial energy compared very well with interfacial energy values for a few other immiscible hydrocarbon pairs. In chapter IV, the study proceeds to look at the interactions between nonpolar and polar small molecules with SB and SBA thin film surfaces. Toluene, hexadecane and water molecules are separately simulated to interact with SB and SBA surfaces in vacuum. The energetics of interaction are calculated atomistically and used in the atomistic equation to calculate the interfacial energy or the interaction energy. Comparisons with experimental data are not made due to the small concentrations of the molecules on the polymer surface. However, fundamental understanding of the structure of the system and the breakup of the energetics are provided by such a study.

Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues

NASA Astrophysics Data System (ADS)

Fiorentini, Raffaele; Kremer, Kurt; Potestio, Raffaello; Fogarty, Aoife C.

2017-06-01

The calculation of free energy differences is a crucial step in the characterization and understanding of the physical properties of biological molecules. In the development of efficient methods to compute these quantities, a promising strategy is that of employing a dual-resolution representation of the solvent, specifically using an accurate model in the proximity of a molecule of interest and a simplified description elsewhere. One such concurrent multi-resolution simulation method is the Adaptive Resolution Scheme (AdResS), in which particles smoothly change their resolution on-the-fly as they move between different subregions. Before using this approach in the context of free energy calculations, however, it is necessary to make sure that the dual-resolution treatment of the solvent does not cause undesired effects on the computed quantities. Here, we show how AdResS can be used to calculate solvation free energies of small polar solutes using Thermodynamic Integration (TI). We discuss how the potential-energy-based TI approach combines with the force-based AdResS methodology, in which no global Hamiltonian is defined. The AdResS free energy values agree with those calculated from fully atomistic simulations to within a fraction of kBT. This is true even for small atomistic regions whose size is on the order of the correlation length, or when the properties of the coarse-grained region are extremely different from those of the atomistic region. These accurate free energy calculations are possible because AdResS allows the sampling of solvation shell configurations which are equivalent to those of fully atomistic simulations. The results of the present work thus demonstrate the viability of the use of adaptive resolution simulation methods to perform free energy calculations and pave the way for large-scale applications where a substantial computational gain can be attained.

Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding.

PubMed

Tamura, Koichi; Hayashi, Shigehiko

2015-07-14

Molecular functions of proteins are often fulfilled by global conformational changes that couple with local events such as the binding of ligand molecules. High molecular complexity of proteins has, however, been an obstacle to obtain an atomistic view of the global conformational transitions, imposing a limitation on the mechanistic understanding of the functional processes. In this study, we developed a new method of molecular dynamics (MD) simulation called the linear response path following (LRPF) to simulate a protein's global conformational changes upon ligand binding. The method introduces a biasing force based on a linear response theory, which determines a local reaction coordinate in the configuration space that represents linear coupling between local events of ligand binding and global conformational changes and thus provides one with fully atomistic models undergoing large conformational changes without knowledge of a target structure. The overall transition process involving nonlinear conformational changes is simulated through iterative cycles consisting of a biased MD simulation with an updated linear response force and a following unbiased MD simulation for relaxation. We applied the method to the simulation of global conformational changes of the yeast calmodulin N-terminal domain and successfully searched out the end conformation. The atomistically detailed trajectories revealed a sequence of molecular events that properly lead to the global conformational changes and identified key steps of local-global coupling that induce the conformational transitions. The LRPF method provides one with a powerful means to model conformational changes of proteins such as motors and transporters where local-global coupling plays a pivotal role in their functional processes.

Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

PubMed

Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

2016-08-25

The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

Continuous description of a grain boundary in olivine from atomic scale simulations: the role of disclinations

NASA Astrophysics Data System (ADS)

Cordier, P.; Sun, X.; Fressengeas, C.; Taupin, V.

2015-12-01

A crossover between atomistic description and continuous representation of grain boundaries in polycrystals is set-up to model the periodic arrays of structural units by using dislocation and disclination dipole arrays along grain boundaries. Continuous modeling of the boundary is built by bottom-up processing, meaning that the strain, rotation, curvature, disclination and dislocation density fields are calculated by using the discrete atomic positions generated by molecular dynamics simulations. Continuous modeling of a 18.9° symmetric tilt boundary in copper [1] is conducted as a benchmark case. Its accuracy is validated by comparison with a similar recent technique [2]. Then, results on the 60.8° Mg2SiO4 tilt boundary [3-4] are presented. By linking the atomistic description with continuum mechanics representations, they provide new insights into the structure of the grain boundary. [1] Fressengeas, C., Taupin, V., Capolungo, L., 2014. Continuous modelling of the structure of symmetric tilt boundaries. Int. J. Solids Struct. 51, 1434-1441. [2] Zimmerman, J.A., Bammann, D.J., Gao, H., 2009. Deformation gradients for continuum mechanical analysis of atomistic simulations. Int. J. Solids Struct. 46, 238-253. [3] Cordier, P., Demouchy, S., Beausir, B., Taupin, V., Barou, F., Fressengeas, C., 2014. Disclinations provide the missing mechanism for deforming olivine-rich rocks in the mantle. Nature 507, 51-56. [4] Adjaoud, O., Marquardt, K., Jahn, S., 2012. Atomic structures and energies of grain boundaries in Mg2SiO4 forsterite from atomistic modeling. Phys. Chem. Miner. 39, 749-760.

An atomistic simulation scheme for modeling crystal formation from solution.

PubMed

Kawska, Agnieszka; Brickmann, Jürgen; Kniep, Rüdiger; Hochrein, Oliver; Zahn, Dirk

2006-01-14

We present an atomistic simulation scheme for investigating crystal growth from solution. Molecular-dynamics simulation studies of such processes typically suffer from considerable limitations concerning both system size and simulation times. In our method this time-length scale problem is circumvented by an iterative scheme which combines a Monte Carlo-type approach for the identification of ion adsorption sites and, after each growth step, structural optimization of the ion cluster and the solvent by means of molecular-dynamics simulation runs. An important approximation of our method is based on assuming full structural relaxation of the aggregates between each of the growth steps. This concept only holds for compounds of low solubility. To illustrate our method we studied CaF2 aggregate growth from aqueous solution, which may be taken as prototypes for compounds of very low solubility. The limitations of our simulation scheme are illustrated by the example of NaCl aggregation from aqueous solution, which corresponds to a solute/solvent combination of very high salt solubility.

Giant electrocaloric response in the prototypical Pb(Mg,Nb)O3 relaxor ferroelectric from atomistic simulations

NASA Astrophysics Data System (ADS)

Jiang, Zhijun; Nahas, Y.; Prokhorenko, S.; Prosandeev, S.; Wang, D.; Íñiguez, Jorge; Bellaiche, L.

2018-03-01

An atomistic effective Hamiltonian is used to investigate electrocaloric (EC) effects of Pb (Mg1 /3Nb2 /3) O3 relaxor ferroelectrics in its ergodic regime, and subject to electric fields applied along the pseudocubic [111] direction. Such a Hamiltonian qualitatively reproduces (i) the electric field-versus-temperature phase diagram, including the existence of a critical point where first-order and second-order transitions meet each other; and (ii) a giant EC response near such a critical point. It also reveals that such giant response around this critical point is microscopically induced by field-induced percolation of polar nanoregions. Moreover, it is also found that, for any temperature above the critical point, the EC coefficient-versus-electric-field curve adopts a maximum (and thus larger electrocaloric response too), that can be well described by the general Landau-like model proposed by Jiang et al., [Phys. Rev. B 96, 014114 (2017)], 10.1103/PhysRevB.96.014114, and that is further correlated with specific microscopic features related to dipoles lying along different rhombohedral directions. Furthermore, for temperatures being at least 40 K higher than the critical temperature, the (electric field, temperature) line associated with this maximal EC coefficient is below both the Widom line and the line representing percolation of polar nanoregions.

Mathematical modeling of the crack growth in linear elastic isotropic materials by conventional fracture mechanics approaches and by molecular dynamics method: crack propagation direction angle under mixed mode loading

NASA Astrophysics Data System (ADS)

Stepanova, Larisa; Bronnikov, Sergej

2018-03-01

The crack growth directional angles in the isotropic linear elastic plane with the central crack under mixed-mode loading conditions for the full range of the mixity parameter are found. Two fracture criteria of traditional linear fracture mechanics (maximum tangential stress and minimum strain energy density criteria) are used. Atomistic simulations of the central crack growth process in an infinite plane medium under mixed-mode loading using Large-scale Molecular Massively Parallel Simulator (LAMMPS), a classical molecular dynamics code, are performed. The inter-atomic potential used in this investigation is Embedded Atom Method (EAM) potential. The plane specimens with initial central crack were subjected to Mixed-Mode loadings. The simulation cell contains 400000 atoms. The crack propagation direction angles under different values of the mixity parameter in a wide range of values from pure tensile loading to pure shear loading in a wide diapason of temperatures (from 0.1 К to 800 К) are obtained and analyzed. It is shown that the crack propagation direction angles obtained by molecular dynamics method coincide with the crack propagation direction angles given by the multi-parameter fracture criteria based on the strain energy density and the multi-parameter description of the crack-tip fields.

Coarse-Grained MD Simulations and Protein-Protein Interactions: The Cohesin-Dockerin System.

PubMed

Hall, Benjamin A; Sansom, Mark S P

2009-09-08

Coarse-grained molecular dynamics (CG-MD) may be applied as part of a multiscale modeling approach to protein-protein interactions. The cohesin-dockerin interaction provides a valuable test system for evaluation of the use of CG-MD, as structural (X-ray) data indicate a dual binding mode for the cohesin-dockerin pair. CG-MD simulations (of 5 μs duration) of the association of cohesin and dockerin identify two distinct binding modes, which resemble those observed in X-ray structures. For each binding mode, ca. 80% of interfacial residues are predicted correctly. Furthermore, each of the binding modes identified by CG-MD is conformationally stable when converted to an atomistic model and used as the basis of a conventional atomistic MD simulation of duration 20 ns.

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

PubMed

Hess, Berk; Kutzner, Carsten; van der Spoel, David; Lindahl, Erik

2008-03-01

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.

Adaptive resolution simulation of oligonucleotides

NASA Astrophysics Data System (ADS)

Netz, Paulo A.; Potestio, Raffaello; Kremer, Kurt

2016-12-01

Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods.

Realistic finite temperature simulations of magnetic systems using quantum statistics

NASA Astrophysics Data System (ADS)

Bergqvist, Lars; Bergman, Anders

2018-01-01

We have performed realistic atomistic simulations at finite temperatures using Monte Carlo and atomistic spin dynamics simulations incorporating quantum (Bose-Einstein) statistics. The description is much improved at low temperatures compared to classical (Boltzmann) statistics normally used in these kind of simulations, while at higher temperatures the classical statistics are recovered. This corrected low-temperature description is reflected in both magnetization and the magnetic specific heat, the latter allowing for improved modeling of the magnetic contribution to free energies. A central property in the method is the magnon density of states at finite temperatures, and we have compared several different implementations for obtaining it. The method has no restrictions regarding chemical and magnetic order of the considered materials. This is demonstrated by applying the method to elemental ferromagnetic systems, including Fe and Ni, as well as Fe-Co random alloys and the ferrimagnetic system GdFe3.

Soil Organic Matter (SOM): Molecular Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Amity

Molecular simulation is a powerful tool used to gain an atomistic, molecular, and nanoscale level understanding of the structure, dynamics, and interactions from adsorption on minerals and assembly in aggregates of soil organic matter (SOM). Given the importance of SOM fate and persistence in soils and the current knowledge gaps, applications of atomistic scale simulations to study the complex compounds in SOM and their interactions in self-assembled aggregates composed of different organic matter compounds and with mineral surfaces of different types common in soils are few and far between. Here, we describe various molecular simulation methods that are currently inmore » use in various areas and applicable to SOM research, followed by a brief survey of specific applications to SOM research and an illustration with our own recent efforts in this area. We conclude with an outlook and the challenges for future research in this area.« less

Effect of strain field on displacement cascade in tungsten studied by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Wang, D.; Gao, N.; Wang, Z. G.; Gao, X.; He, W. H.; Cui, M. H.; Pang, L. L.; Zhu, Y. B.

2016-10-01

Using atomistic methods, the coupling effect of strain field and displacement cascade in body-centered cubic (BCC) tungsten is directly simulated by molecular dynamics (MD) simulations at different temperatures. The values of the hydrostatic and uniaxial (parallel or perpendicular to primary knock-on atom (PKA) direction) strains are from -2% to 2% and the temperature is from 100 to 1000 K. Because of the annealing effect, the influence of strain on radiation damage at low temperature has been proved to be more significant than that at high temperature. When the cascade proceeds under the hydrostatic strain, the Frenkel Pair (FP) production, the fraction of defect in cluster and the average size of the defect cluster, all increase at tensile state and decrease at compressive state. When the cascade is under uniaxial strain, the effect of strain parallel to PKA direction is less than the effect of hydrostatic strain, while the effect of strain perpendicular to PKA direction can be negligible. Under the uniaxial strain along <1 1 1> direction, the SIA and SIA cluster is observed to orientate along the strain direction at tensile state and the uniaxial compressive strain with direction perpendicular to <1 1 1> has led to the similar preferred nucleation. All these results indicate that under irradiation, the tensile state should be avoided for materials used in nuclear power plants.

Twist-writhe partitioning in a coarse-grained DNA minicircle model

NASA Astrophysics Data System (ADS)

Sayar, Mehmet; Avşaroǧlu, Barış; Kabakçıoǧlu, Alkan

2010-04-01

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular-dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality, and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion; therefore, our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.

A Coarse Grained Model for Methylcellulose: Spontaneous Ring Formation at Elevated Temperature

NASA Astrophysics Data System (ADS)

Huang, Wenjun; Larson, Ronald

Methylcellulose (MC) is widely used as food additives and pharma applications, where its thermo-reversible gelation behavior plays an important role. To date the gelation mechanism is not well understood, and therefore attracts great research interest. In this study, we adopted coarse-grained (CG) molecular dynamics simulations to model the MC chains, including the homopolymers and random copolymers that models commercial METHOCEL A, in an implicit water environment, where each MC monomer modeled with a single bead. The simulations are carried using a LAMMPS program. We parameterized our CG model using the radial distribution functions from atomistic simulations of short MC oligomers, extrapolating the results to long chains. We used dissociation free energy to validate our CG model against the atomistic model. The CG model captured the effects of monomer substitution type and temperature from the atomistic simulations. We applied this CG model to simulate single chains up to 1000 monomers long and obtained persistence lengths that are close to those determined from experiment. We observed the chain collapse transition for random copolymer at 600 monomers long at 50C. The chain collapsed into a stable ring structure with outer diameter around 14nm, which appears to be a precursor to the fibril structure observed in the methylcellulose gel observed by Lodge et al. in the recent studies. Our CG model can be extended to other MC derivatives for studying the interaction between these polymers and small molecules, such as hydrophobic drugs.

Folding and insertion thermodynamics of the transmembrane WALP peptide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de; Bennett, W. F. Drew; Pfaendtner, Jim

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of meanmore » force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.« less

Folding and insertion thermodynamics of the transmembrane WALP peptide

NASA Astrophysics Data System (ADS)

Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

2015-12-01

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

Directional pair distribution function for diffraction line profile analysis of atomistic models

PubMed Central

Leonardi, Alberto; Leoni, Matteo; Scardi, Paolo

2013-01-01

The concept of the directional pair distribution function is proposed to describe line broadening effects in powder patterns calculated from atomistic models of nano-polycrystalline microstructures. The approach provides at the same time a description of the size effect for domains of any shape and a detailed explanation of the strain effect caused by the local atomic displacement. The latter is discussed in terms of different strain types, also accounting for strain field anisotropy and grain boundary effects. The results can in addition be directly read in terms of traditional line profile analysis, such as that based on the Warren–Averbach method. PMID:23396818

Molecular Simulation Studies of Covalently and Ionically Grafted Nanoparticles

NASA Astrophysics Data System (ADS)

Hong, Bingbing

Solvent-free covalently- or ionically-grafted nanoparticles (CGNs and IGNs) are a new class of organic-inorganic hybrid composite materials exhibiting fluid-like behaviors around room temperature. With similar structures to prior systems, e.g. nanocomposites, neutral or charged colloids, ionic liquids, etc, CGNs and IGNs inherit the functionality of inorganic nanopariticles, the facile processibility of polymers, as well as conductivity and nonvolatility from their constituent materials. In spite of the extensive prior experimental research having covered synthesis and measurements of thermal and dynamic properties, little progress in understanding of these new materials at the molecular level has been achieved, because of the lack of simulation work in this new area. Atomistic and coarse-grained molecular dynamics simulations have been performed in this thesis to investigate the thermodynamics, structure, and dynamics of these systems and to seek predictive methods predictable for their properties. Starting from poly(ethylene oxide) oligomers (PEO) melts, we established atomistic models based on united-atom representations of methylene. The Green-Kubo and Einstein-Helfand formulas were used to calculate the transport properties. The simulations generate densities, viscosities, diffusivities, in good agreement with experimental data. The chain-length dependence of the transport properties suggests that neither Rouse nor reptation models are applicable in the short-chain regime investigated. Coupled with thermodynamic integration methods, the models give good predictions of pressure-composition-density relations for CO 2 + PEO oligomers. Water effects on the Henry's constant of CO 2 in PEO have also been investigated. The dependence of the calculated Henry's constants on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. CGNs are modeled by the inclusion of solid-sphere nanoparticles into the atomistic oligomers. The calculated viscosities from Green-Kubo relationships and temperature extrapolation are of the same order of magnitude as experimental values, but show a smaller activation energy relative to real CGNs systems. Grafted systems have higher viscosities, smaller diffusion coefficients, and slower chain dynamics than the ungrafted counterparts - nanocomposites - at high temperatures. At lower temperatures, grafted systems exhibit faster dynamics for both nanoparticles and chains relative to ungrafted systems, because of lower aggregation of nanoparticles and enhanced correlations between nanoparticles and chains. This agrees with the experimental observation that the new materials have liquid-like behavior in the absence of a solvent. To lower the simulated temperatures into the experimental range, we established a coarse-grained CGNs model by matching structural distribution functions to atomistic simulation data. In contrast with linear polymer systems, for which coarse-graining always accelerate dynamics, coarse-graining of grafted nanoparticles can either accelerate or slowdown the core motions, depending on the length of the grafted chains. This can be qualitatively predicted by a simple transition-state theory. Similar atomistic models to CGNs were developed for IGNs, with ammonium counterions described by an explicit-hydrogen way; these were in turn compared with "generic" coarse-grained IGNs. The elimination of chemical details in the coarse-grained models does not bring in qualitative changes to the radial distribution functions and diffusion of atomistic IGNs, but saves considerable simulation resources and make simulations near room temperatures affordable. The chain counterions in both atomistic and coarse-grained models are mobile, moving from site to site and from nanoparticle to nanoparticle. At the same temperature and the same core volume fractions, the nanoparticle diffusivities in coarse-grained IGNs are slower by a factor ten than the cores of CGNs. The coarse-grained IGNs models are later used to investigate the system dynamics through analysis of the dependence on temperature and structural parameters of the transport properties (self-diffusion coefficients, viscosities and conductivities). Further, migration kinetics of oligomeric counterions is analyzed in a manner analogous to unimer exchange between micellar aggregates. The counterion migrations follow the "double-core" mechanism and are kinetically controlled by neighboring-core collisions. (Abstract shortened by UMI.)

Atomistic mechanisms of rapid energy transport in light-harvesting molecules

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Koga, Shiro; Akai, Ichiro; Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2011-03-01

Synthetic supermolecules such as π-conjugated light-harvesting dendrimers efficiently harvest energy from sunlight, which is of significant importance for the global energy problem. Key to their success is rapid transport of electronic excitation energy from peripheral antennas to photochemical reaction cores, the atomistic mechanisms of which remains elusive. Here, quantum-mechanical molecular dynamics simulation incorporating nonadiabatic electronic transitions reveals the key molecular motion that significantly accelerates the energy transport based on the Dexter mechanism.

Coarse-grained modeling of polyethylene melts: Effect on dynamics

DOE PAGES

Peters, Brandon L.; Salerno, K. Michael; Agrawal, Anupriya; ...

2017-05-23

The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with three to six methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully atomistic melt simulations and the transferability of CG potentials across temperatures. While IBI produces nonbonded pair potentials thatmore » give excellent agreement between the atomistic and CG pair correlation functions, the resulting pressure for the CG models is large compared with the pressure of the atomistic system. We find that correcting the potential to match the reference pressure leads to nonbonded interactions with much deeper minima and slightly smaller effective bead diameter. However, simulations with potentials generated by IBI and pressure-corrected IBI result in similar mean-square displacements (MSDs) and stress autocorrelation functions G( t) for PE melts. While the time rescaling factor required to match CG and atomistic models is the same for pressure- and non-pressure-corrected CG models, it strongly depends on temperature. Furthermore, transferability was investigated by comparing the MSDs and stress autocorrelation functions for potentials developed at different temperatures.« less

Coarse-grained modeling of polyethylene melts: Effect on dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, Brandon L.; Salerno, K. Michael; Agrawal, Anupriya

The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with three to six methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully atomistic melt simulations and the transferability of CG potentials across temperatures. While IBI produces nonbonded pair potentials thatmore » give excellent agreement between the atomistic and CG pair correlation functions, the resulting pressure for the CG models is large compared with the pressure of the atomistic system. We find that correcting the potential to match the reference pressure leads to nonbonded interactions with much deeper minima and slightly smaller effective bead diameter. However, simulations with potentials generated by IBI and pressure-corrected IBI result in similar mean-square displacements (MSDs) and stress autocorrelation functions G( t) for PE melts. While the time rescaling factor required to match CG and atomistic models is the same for pressure- and non-pressure-corrected CG models, it strongly depends on temperature. Furthermore, transferability was investigated by comparing the MSDs and stress autocorrelation functions for potentials developed at different temperatures.« less

Investigations on the mechanical behavior of nanowires with twin boundaries by atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Xia, E-mail: tianxia@lsec.cc.ac.cn

2015-03-10

Atomistic simulations are used to study the deformation behavior of twinned Cu nanowires with a <111> growth orientation under tension. Due to the existence of the twin boundaries, the strength of the twinned nanowires is higher than that of the twin-free nanowire and the yielding stress of twinned nanowires is inversely proportional to the spacings of the twin boundaries. Moreover, The ductility of the twin-free nanowire is the highest of all and it grows with the increasing spacings of the twin boundaries for twinned nanowires. Besides, we find that the twin boundaries can be served as dislocation sources as wellmore » as the free surfaces and grain boundaries.« less

Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCarty, Keven F.; Zhou, Xiaowang; Ward, Donald K.

2015-09-01

In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expandmore » the number of potential types of graphene electronic devices.« less

Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin.

PubMed

Tiwary, Pratyush

2017-12-07

Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its exceptionally high kinetic stability, being one of the strongest known noncovalent interactions in nature, and it is heavily used across the biotechnological industry. In this work, we gain understanding of the molecular determinants and bottlenecks in the dissociation of the dimeric biotin-streptavidin system in wild type and with a point mutation. Using recently proposed enhanced sampling methods with full atomistic resolution, we reproduce the experimentally reported effect of the mutation on the dissociation rate. We also answer a longstanding question regarding cause/effect in the coupled events of bond stretching and bond hydration during dissociation and establish that in this system, it is the bond stretching and not hydration which forms the bottleneck in the early parts of the dissociation process. We believe these calculations represent a step forward in the use of atomistic simulations to study pharmacokinetics. An improved understanding of biotin-streptavidin dissociation dynamics should also have direct benefits in biotechnological and nanobiotechnological applications.

Scaling of elongation transition thickness during thin-film growth on weakly interacting substrates

NASA Astrophysics Data System (ADS)

Lü, B.; Souqui, L.; Elofsson, V.; Sarakinos, K.

2017-08-01

The elongation transition thickness ( θElong) is a central concept in the theoretical description of thin-film growth dynamics on weakly interacting substrates via scaling relations of θElong with respect to rates of key atomistic film-forming processes. To date, these scaling laws have only been confirmed quantitatively by simulations, while experimental proof has been left ambiguous as it has not been possible to measure θElong. Here, we present a method for determining experimentally θElong for Ag films growing on amorphous SiO2: an archetypical weakly interacting film/substrate system. Our results confirm the theoretically predicted θElong scaling behavior, which then allow us to calculate the rates of adatom diffusion and island coalescence completion, in good agreement with the literature. The methodology presented herein casts the foundation for studying growth dynamics and cataloging atomistic-process rates for a wide range of weakly interacting film/substrate systems. This may provide insights into directed growth of metal films with a well-controlled morphology and interfacial structure on 2D crystals—including graphene and MoS2—for catalytic and nanoelectronic applications.

Modeling of crack growth under mixed-mode loading by a molecular dynamics method and a linear fracture mechanics approach

NASA Astrophysics Data System (ADS)

Stepanova, L. V.

2017-12-01

Atomistic simulations of the central crack growth process in an infinite plane medium under mixed-mode loading using Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), a classical molecular dynamics code, are performed. The inter-atomic potential used in this investigation is the Embedded Atom Method (EAM) potential. Plane specimens with an initial central crack are subjected to mixed-mode loadings. The simulation cell contains 400,000 atoms. The crack propagation direction angles under different values of the mixity parameter in a wide range of values from pure tensile loading to pure shear loading in a wide range of temperatures (from 0.1 K to 800 K) are obtained and analyzed. It is shown that the crack propagation direction angles obtained by molecular dynamics coincide with the crack propagation direction angles given by the multi-parameter fracture criteria based on the strain energy density and the multi-parameter description of the crack-tip fields. The multi-parameter fracture criteria are based on the multi-parameter stress field description taking into account the higher order terms of the Williams series expansion of the crack tip fields.

The relative entropy is fundamental to adaptive resolution simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kreis, Karsten; Graduate School Materials Science in Mainz, Staudingerweg 9, 55128 Mainz; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de

Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy withmore » respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner.« less

The relative entropy is fundamental to adaptive resolution simulations

NASA Astrophysics Data System (ADS)

Kreis, Karsten; Potestio, Raffaello

2016-07-01

Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy with respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner.

Lattice Thermal Conductivity of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2 from Atomistic Simulations

NASA Technical Reports Server (NTRS)

Lawson, JOhn W.; Daw, Murray S.; Bauschlicher, Charles W.

2011-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 are candidate materials for applications in extreme environments because of their high melting point, good mechanical properties and reasonable oxidation resistance. Unlike many ceramics, these materials have high thermal conductivity which can be advantageous, for example, to reduce thermal shock. Recently, we developed Tersoff style interatomic potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current. Results at room temperature and at elevated temperatures will be reported.

Atomistic simulations of contact area and conductance at nanoscale interfaces.

PubMed

Hu, Xiaoli; Martini, Ashlie

2017-11-09

Atomistic simulations were used to study conductance across the interface between a nanoscale gold probe and a graphite surface with a step edge. Conductance on the graphite terrace was observed to increase with load and be approximately proportional to contact area calculated from the positions of atoms in the interface. The relationship between area and conductance was further explored by varying the position of the contact relative to the location of the graphite step edge. These simulations reproduced a previously-reported current dip at step edges measured experimentally and the trend was explained by changes in both contact area and the distribution of distances between atoms in the interface. The novel approach reported here provides a foundation for future studies of the fundamental relationships between conductance, load and surface topography at the atomic scale.

Atomistic Simulation of High-Density Uranium Fuels

DOE PAGES

Garcés, Jorge Eduardo; Bozzolo, Guillermo

2011-01-01

We apply an atomistic modeling approach to deal with interfacial phenomena in high-density uranium fuels. The effects of Si, as additive to Al or as U-Mo-particles coating, on the behavior of the Al/U-Mo interface is modeled by using the Bozzolo-Ferrante-Smith (BFS) method for alloys. The basic experimental features characterizing the real system are identified, via simulations and atom-by-atom analysis. These include (1) the trend indicating formation of interfacial compounds, (2) much reduced diffusion of Al into U-Mo solid solution due to the high Si concentration, (3) Si depletion in the Al matrix, (4) an unexpected interaction between Mo and Simore » which inhibits Si diffusion to deeper layers in the U-Mo solid solution, and (5) the minimum amount of Si needed to perform as an effective diffusion barrier. Simulation results related to alternatives to Si dispersed in the Al matrix, such as the use of C coating of U-Mo particles or Zr instead of the Al matrix, are also shown. Recent experimental results confirmed early theoretical proposals, along the lines of the results reported in this work, showing that atomistic computational modeling could become a valuable tool to aid the experimental work in the development of nuclear fuels.« less

Multiscale Modeling of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2: Application to Lattice Thermal Conductivity

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Squire, Thomas H.; Bauschlicher, Charles W.

2012-01-01

We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkins, Stephen J.; Wright, David W.; Zhang, Hailiang

2016-10-14

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-artmore » molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in whichGenAppprovides the deployment infrastructure for running applications on both standard and high-performance computing hardware, andSASSIEprovides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data.GenAppproduces the accessible web-based front end termedSASSIE-web, andGenAppandSASSIEalso make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.« less

Parallel multiscale simulations of a brain aneurysm

PubMed Central

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

2012-01-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work. PMID:23734066

Parallel multiscale simulations of a brain aneurysm.

PubMed

Grinberg, Leopold; Fedosov, Dmitry A; Karniadakis, George Em

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr . The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

PubMed

Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

2016-12-01

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web , and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

Parallel multiscale simulations of a brain aneurysm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em, E-mail: george_karniadakis@brown.edu

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm.more » The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.« less

Small-angle neutron scattering study of a monoclonal antibody using free-energy constraints.

PubMed

Clark, Nicholas J; Zhang, Hailiang; Krueger, Susan; Lee, Hyo Jin; Ketchem, Randal R; Kerwin, Bruce; Kanapuram, Sekhar R; Treuheit, Michael J; McAuley, Arnold; Curtis, Joseph E

2013-11-14

Monoclonal antibodies (mAbs) contain hinge-like regions that enable structural flexibility of globular domains that have a direct effect on biological function. A subclass of mAbs, IgG2, have several interchain disulfide bonds in the hinge region that could potentially limit structural flexibility of the globular domains and affect the overall configuration space available to the mAb. We have characterized human IgG2 mAb in solution via small-angle neutron scattering (SANS) and interpreted the scattering data using atomistic models. Molecular Monte Carlo combined with molecular dynamics simulations of a model mAb indicate that a wide range of structural configurations are plausible, spanning radius of gyration values from ∼39 to ∼55 Å. Structural ensembles and representative single structure solutions were derived by comparison of theoretical SANS profiles of mAb models to experimental SANS data. Additionally, molecular mechanical and solvation free-energy calculations were carried out on the ensemble of best-fitting mAb structures. The results of this study indicate that low-resolution techniques like small-angle scattering combined with atomistic molecular simulations with free-energy analysis may be helpful to determine the types of intramolecular interactions that influence function and could lead to deleterious changes to mAb structure. This methodology will be useful to analyze small-angle scattering data of many macromolecular systems.

A continuously growing web-based interface structure databank

NASA Astrophysics Data System (ADS)

Erwin, N. A.; Wang, E. I.; Osysko, A.; Warner, D. H.

2012-07-01

The macroscopic properties of materials can be significantly influenced by the presence of microscopic interfaces. The complexity of these interfaces coupled with the vast configurational space in which they reside has been a long-standing obstacle to the advancement of true bottom-up material behavior predictions. In this vein, atomistic simulations have proven to be a valuable tool for investigating interface behavior. However, before atomistic simulations can be utilized to model interface behavior, meaningful interface atomic structures must be generated. The generation of structures has historically been carried out disjointly by individual research groups, and thus, has constituted an overlap in effort across the broad research community. To address this overlap and to lower the barrier for new researchers to explore interface modeling, we introduce a web-based interface structure databank (www.isdb.cee.cornell.edu) where users can search, download and share interface structures. The databank is intended to grow via two mechanisms: (1) interface structure donations from individual research groups and (2) an automated structure generation algorithm which continuously creates equilibrium interface structures. In this paper, we describe the databank, the automated interface generation algorithm, and compare a subset of the autonomously generated structures to structures currently available in the literature. To date, the automated generation algorithm has been directed toward aluminum grain boundary structures, which can be compared with experimentally measured population densities of aluminum polycrystals.

Amp: A modular approach to machine learning in atomistic simulations

NASA Astrophysics Data System (ADS)

Khorshidi, Alireza; Peterson, Andrew A.

2016-10-01

Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which makes it compatible with a wide variety of commercial and open-source electronic structure codes. We finally demonstrate that the neural network model inside Amp can accurately interpolate electronic structure energies as well as forces of thousands of multi-species atomic systems.

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations.

PubMed

Quevillon, Michael J; Whitmer, Jonathan K

2018-01-02

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure-constant temperature ensemble. These materials exhibit a distinct "smectic" liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications.

Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well. The robustness of the algorithm with respect to the only free parameter it involves is ascertained. The method is then applied to perform tensile tests on gold nanopillars on strain rates as low as 100/s, bringing out the perils of high strain-rate molecular dynamics calculations. We also calculate temperature and stress dependence of activation free energy for surface nucleation of dislocations in pristine gold nanopillars under realistic loads. While maintaining fully atomistic resolution, we reach the fraction-of-a-second time scale regime. It is found that the activation free energy depends significantly and nonlinearly on the driving force (stress or strain) and temperature, leading to very high activation entropies for surface dislocation nucleation.

Mechanical response of collagen molecule under hydrostatic compression.

PubMed

Saini, Karanvir; Kumar, Navin

2015-04-01

Proteins like collagen are the basic building blocks of various body tissues (soft and hard). Collagen molecules find their presence in the skeletal system of the body where they bear mechanical loads from different directions, either individually or along with hydroxy-apatite crystals. Therefore, it is very important to understand the mechanical behavior of the collagen molecule which is subjected to multi-axial state of loading. The estimation of strains of collagen molecule along different directions resulting from the changes in hydrostatic pressure magnitude, can provide us new insights into its mechanical behavior. In the present work, full atomistic simulations have been used to study global (volumetric) as well as local (along different directions) mechanical properties of the hydrated collagen molecule which is subjected to different hydrostatic pressure magnitudes. To estimate the local mechanical properties, the strains of collagen molecule along its longitudinal and transverse directions have been acquired at different hydrostatic pressure magnitudes. In spite of non-homogeneous distribution of atoms within the collagen molecule, the calculated values of local mechanical properties have been found to carry the same order of magnitude along the longitudinal and transverse directions. It has been demonstrated that the values of global mechanical properties like compressibility, bulk modulus, etc. as well as local mechanical properties like linear compressibility, linear elastic modulus, etc. are functions of magnitudes of applied hydrostatic pressures. The mechanical characteristics of collagen molecule based on the atomistic model have also been compared with that of the continuum model in the present work. The comparison showed up orthotropic material behavior for the collagen molecule. The information on collagen molecule provided in the present study can be very helpful in designing the future bio-materials. Copyright © 2015 Elsevier B.V. All rights reserved.

Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

NASA Astrophysics Data System (ADS)

Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank

2017-10-01

Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.

Coarse-Grained Simulation of Solvated Cellulose Ib Microfibril

NASA Astrophysics Data System (ADS)

Fan, Bingxin; Maranas, Janna; Zhong, Linghao; Zhen Zhao Collaboration

2013-03-01

We construct a coarse-grained (CG) model of cellulose microfibrils in water. The force field is derived from atomistic simulation of a 40 glucose-unit-long microfibril by requiring consistency between the chain configuration, intermolecular packing and hydrogen bonding of the two levels of modeling. Intermolecular interactions such as hydrogen bonding are added sequentially until the force field holds the microfibril crystal structure. This stepwise process enables us to evaluate the importance of each potential and provides insight to ordered and disordered regions. We simulate cellulose microfibrils with 100 to 400 residues, comparable to the smallest observed microfibrils. Microfibrils longer than 100nm would form a bending region along their longitudinal direction. Multiple bends are observed in the microfibril containing 400 residues. Although the cause is not clear, the bending regions may provide us insights about the periodicity and the behavior of the disordered regions in the microfibril.

Nanoscale Stress-Corrosion of Geomaterials in Aqueous Solutions

NASA Astrophysics Data System (ADS)

Criscenti, L. J.; Rimsza, J. M.; Matteo, E. N.; Jones, R. E.

2017-12-01

Predicting subcritical crack propagation in low-permeability geo-materials is an unsolved problem crucial to assessing shale caprocks at CO2 sequestration sites, and controlling fracturing for gas and oil extraction. Experiments indicate that chemical reactions at fluid-material interfaces play a major role in subcritical crack growth by weakening the material and altering crack nucleation and growth rates. However, understanding subsurface fracture has been hindered by a lack of understanding of the mechanisms relating chemical environment to mechanical outcome, and a lack of capability directly linking atomistic insight to macroscale observables. We are using both molecular simulation and experiment to develop an atomistic-level understanding of the chemical-mechanical coupling that controls subcritical crack propagation. We are investigating fracture of isotropic silica glass in different environments (air, distilled water, and Na+-rich solutions) and will extend our research to include clay minerals in shales. Molecular simulations are performed with ReaxFF, a reactive force field that allows for explicit modeling of bond breaking and formation processes during crack propagation. A coarse-graining method produces calculated fracture toughness values from the atomistic data. We are performing double cleavage drilled compression (DCDC) experiments in aqueous environmental chambers and monitoring crack propagation with either a confocal or atomic force microscope. Our results show that silica fracture toughness decreases as the environment changes from air to distilled water to Na+-rich solutions. These results suggest that our newly developed computational and experimental techniques can be used to investigate the impact of fluid composition on crack growth in geo-materials and that we will be able to use these methods to understand coupled chemo-mechanical processes and predict crack propagation in shale minerals. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia LLC, a wholly owned subsidiary of Honeywell International Inc. for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Femtosecond visualization of lattice dynamics in shock-compressed matter.

PubMed

Milathianaki, D; Boutet, S; Williams, G J; Higginbotham, A; Ratner, D; Gleason, A E; Messerschmidt, M; Seibert, M M; Swift, D C; Hering, P; Robinson, J; White, W E; Wark, J S

2013-10-11

The ultrafast evolution of microstructure is key to understanding high-pressure and strain-rate phenomena. However, the visualization of lattice dynamics at scales commensurate with those of atomistic simulations has been challenging. Here, we report femtosecond x-ray diffraction measurements unveiling the response of copper to laser shock-compression at peak normal elastic stresses of ~73 gigapascals (GPa) and strain rates of 10(9) per second. We capture the evolution of the lattice from a one-dimensional (1D) elastic to a 3D plastically relaxed state within a few tens of picoseconds, after reaching shear stresses of 18 GPa. Our in situ high-precision measurement of material strength at spatial (<1 micrometer) and temporal (<50 picoseconds) scales provides a direct comparison with multimillion-atom molecular dynamics simulations.

Dislocations in bilayer graphene

NASA Astrophysics Data System (ADS)

Butz, Benjamin; Dolle, Christian; Niekiel, Florian; Weber, Konstantin; Waldmann, Daniel; Weber, Heiko B.; Meyer, Bernd; Spiecker, Erdmann

2014-01-01

Dislocations represent one of the most fascinating and fundamental concepts in materials science. Most importantly, dislocations are the main carriers of plastic deformation in crystalline materials. Furthermore, they can strongly affect the local electronic and optical properties of semiconductors and ionic crystals. In materials with small dimensions, they experience extensive image forces, which attract them to the surface to release strain energy. However, in layered crystals such as graphite, dislocation movement is mainly restricted to the basal plane. Thus, the dislocations cannot escape, enabling their confinement in crystals as thin as only two monolayers. To explore the nature of dislocations under such extreme boundary conditions, the material of choice is bilayer graphene, the thinnest possible quasi-two-dimensional crystal in which such linear defects can be confined. Homogeneous and robust graphene membranes derived from high-quality epitaxial graphene on silicon carbide provide an ideal platform for their investigation. Here we report the direct observation of basal-plane dislocations in freestanding bilayer graphene using transmission electron microscopy and their detailed investigation by diffraction contrast analysis and atomistic simulations. Our investigation reveals two striking size effects. First, the absence of stacking-fault energy, a unique property of bilayer graphene, leads to a characteristic dislocation pattern that corresponds to an alternating ABAC change of the stacking order. Second, our experiments in combination with atomistic simulations reveal a pronounced buckling of the bilayer graphene membrane that results directly from accommodation of strain. In fact, the buckling changes the strain state of the bilayer graphene and is of key importance for its electronic properties. Our findings will contribute to the understanding of dislocations and of their role in the structural, mechanical and electronic properties of bilayer and few-layer graphene.

Dislocations in bilayer graphene.

PubMed

Butz, Benjamin; Dolle, Christian; Niekiel, Florian; Weber, Konstantin; Waldmann, Daniel; Weber, Heiko B; Meyer, Bernd; Spiecker, Erdmann

2014-01-23

Dislocations represent one of the most fascinating and fundamental concepts in materials science. Most importantly, dislocations are the main carriers of plastic deformation in crystalline materials. Furthermore, they can strongly affect the local electronic and optical properties of semiconductors and ionic crystals. In materials with small dimensions, they experience extensive image forces, which attract them to the surface to release strain energy. However, in layered crystals such as graphite, dislocation movement is mainly restricted to the basal plane. Thus, the dislocations cannot escape, enabling their confinement in crystals as thin as only two monolayers. To explore the nature of dislocations under such extreme boundary conditions, the material of choice is bilayer graphene, the thinnest possible quasi-two-dimensional crystal in which such linear defects can be confined. Homogeneous and robust graphene membranes derived from high-quality epitaxial graphene on silicon carbide provide an ideal platform for their investigation. Here we report the direct observation of basal-plane dislocations in freestanding bilayer graphene using transmission electron microscopy and their detailed investigation by diffraction contrast analysis and atomistic simulations. Our investigation reveals two striking size effects. First, the absence of stacking-fault energy, a unique property of bilayer graphene, leads to a characteristic dislocation pattern that corresponds to an alternating AB B[Symbol: see text]AC change of the stacking order. Second, our experiments in combination with atomistic simulations reveal a pronounced buckling of the bilayer graphene membrane that results directly from accommodation of strain. In fact, the buckling changes the strain state of the bilayer graphene and is of key importance for its electronic properties. Our findings will contribute to the understanding of dislocations and of their role in the structural, mechanical and electronic properties of bilayer and few-layer graphene.

Scale-dependent diffusion anisotropy in nanoporous silicon

PubMed Central

Kondrashova, Daria; Lauerer, Alexander; Mehlhorn, Dirk; Jobic, Hervé; Feldhoff, Armin; Thommes, Matthias; Chakraborty, Dipanjan; Gommes, Cedric; Zecevic, Jovana; de Jongh, Petra; Bunde, Armin; Kärger, Jörg; Valiullin, Rustem

2017-01-01

Nanoporous silicon produced by electrochemical etching of highly B-doped p-type silicon wafers can be prepared with tubular pores imbedded in a silicon matrix. Such materials have found many technological applications and provide a useful model system for studying phase transitions under confinement. This paper reports a joint experimental and simulation study of diffusion in such materials, covering displacements from molecular dimensions up to tens of micrometers with carefully selected probe molecules. In addition to mass transfer through the channels, diffusion (at much smaller rates) is also found to occur in directions perpendicular to the channels, thus providing clear evidence of connectivity. With increasing displacements, propagation in both axial and transversal directions is progressively retarded, suggesting a scale-dependent, hierarchical distribution of transport resistances (“constrictions” in the channels) and of shortcuts (connecting “bridges”) between adjacent channels. The experimental evidence from these studies is confirmed by molecular dynamics (MD) simulation in the range of atomistic displacements and rationalized with a simple model of statistically distributed “constrictions” and “bridges” for displacements in the micrometer range via dynamic Monte Carlo (DMC) simulation. Both ranges are demonstrated to be mutually transferrable by DMC simulations based on the pore space topology determined by electron tomography. PMID:28106047

Computational Modeling of Hydroxypropyl-Methylcellulose Acetate Succinate (HPMCAS) and Phenytoin Interactions: A Systematic Coarse-Graining Approach.

PubMed

Huang, Wenjun; Mandal, Taraknath; Larson, Ronald G

2017-03-06

We present coarse-grained (CG) force fields for hydroxypropyl-methylcellulose acetate succinate (HPMCAS) polymers and the drug molecule phenytoin using a bead/stiff spring model, with each bead representing a HPMCAS monomer or monomer side group (hydroxypropyl acetyl, acetyl, or succinyl) or a single phenytoin ring. We obtain the bonded and nonbonded interaction parameters in our CG model using the RDFs from atomistic simulations of short HPMCAS model oligomers (20-mer) and atomistic simulations of phenytoin molecules. The nonbonded interactions are modeled using a LJ 12-6 potential, with separate parameters for each monomer substitution type, which allows heterogeneous polymer chains to be modeled. The cross interaction terms between the polymer and phenytoin CG beads are obtained explicitly from atomistic level polymer-phenytoin simulations, rather than from mixing rules. We study the solvation behavior of 50-mer and 100-mer polymer chains and find chain-length-dependent aggregation. We also compare the phenytoin CG force field developed in this work with that in Mandal et al. (Soft Matter, 2016, 12, 8246-8255) and conclude both are suitable for studying the interaction between polymer and drug in solvated solid dispersion formulation, in the absence of drug crystallization. Finally, we present simulations of heterogeneous HPMCAS model polymer chains and phenytoin molecules. Polymer and drug form a complex in a short period of simulation time due to strong intermolecular interactions. Moreover, the protonated polymer chains are more effective than deprotonated ones in inhibiting the drug aggregation in the polymer-drug complex.

A Coarse-grained Model of Stratum Corneum Lipids: Free Fatty Acids and Ceramide NS

PubMed Central

Moore, Timothy C.; Iacovella, Christopher R.; Hartkamp, Remco; Bunge, Annette L.; McCabe, Clare

2017-01-01

Ceramide (CER)-based biological membranes are used both experimentally and in simulations as simplified model systems of the skin barrier. Molecular dynamics studies have generally focused on simulating preassembled structures using atomistically detailed models of CERs, which limit the system sizes and timescales that can practically be probed, rendering them ineffective for studying particular phenomena, including self-assembly into bilayer and lamellar superstructures. Here, we report on the development of a coarse-grained (CG) model for CER NS, the most abundant CER in human stratum corneum. Multistate iterative Boltzmann inversion is used to derive the intermolecular pair potentials, resulting in a force field that is applicable over a range of state points and suitable for studying ceramide self-assembly. The chosen CG mapping, which includes explicit interaction sites for hydroxyl groups, captures the directional nature of hydrogen bonding and allows for accurate predictions of several key structural properties of CER NS bilayers. Simulated wetting experiments allow the hydrophobicity of CG beads to be accurately tuned to match atomistic wetting behavior, which affects the whole system since inaccurate hydrophobic character is found to unphysically alter the lipid packing in hydrated lamellar states. We find that CER NS can self-assemble into multilamellar structures, enabling the study of lipid systems more representative of the multilamellar lipid structures present in the skin barrier. The coarse-grained force field derived herein represents an important step in using molecular dynamics to study the human skin barrier, which gives a resolution not available through experiment alone. PMID:27564869

Multimillion to billion atom simulations of nanosystems under extreme conditions

NASA Astrophysics Data System (ADS)

Vashishta, P.

2008-12-01

Advanced materials and devices with nanometer grain/feature sizes are being developed to achieve higher strength and toughness in ceramic materials and greater speeds in electronic devices. Below 100 nm, however, continuum description of materials and devices must be supplemented by atomistic descriptions. Current state of the art atomistic simulations involve 10 million - 1 billion atoms. We investigate initiation, growth and healing of wing cracks in confined silica glass by multimillion atom molecular dynamics (MD) simulations. Under dynamic compression, frictional sliding of pre-crack surfaces nucleates nanovoids, which evolve into nanocrack columns at the pre-crack tip. Nanocrack columns merge to form a wing crack, which grows via coalescence with nanovoids in the direction of maximum compression. Lateral confinement arrests the growth and partially heals the wing crack. Growth and arrest of the wing crack occur repeatedly, as observed in dynamic compression experiments on brittle solids under lateral confinement. MD simulation of hypervelocity projectile impact in aluminum nitride and alumina has also been studied. The simulations reveal strong interplay between shock- induced structural phase transformation, plastic deformation and brittle cracks. The shock wave splits into an elastic precursor and a wurtzite-to-rocksalt structural transformation wave. When the elastic wave reflected from the boundary of the sample interacts with the transformation wave front, nanocavities are generated along the penetration path of the projectile and dislocations in adjacent regions. The nanocavities coalesce to form mode I brittle cracks while dislocations generate kink bands that give rise to mode II cracks. These simulations provide a microscopic view of defects associated with simultaneous tensile and shear cracking at the structural phase transformation boundary due to shock impact in high-strength ceramics. Initiation of chemical reactions at shock fronts prior to detonation and dynamic transition in the shock structure of an energetic material (RDX) and reaction of aluminium nanoparticles in oxygen atmosphere followed by explosive burning is also discussed.

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

PubMed Central

Petrov, Drazen; Zagrovic, Bojan

2014-01-01

The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the picture of protein behavior in biologically relevant crowded environments. PMID:24854339

Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pratihar, Subha; Barnes, George L.; Laskin, Julia

In this Perspective mass spectrometry experiments and chemical dynamics simulations are described which have explored the atomistic dynamics of protonated peptide ions, peptide-H+, colliding with organic surfaces. These studies have investigated surface-induced dissociation (SID) for which peptide-H+ fragments upon collision with the surface, peptide-H+ physisorption on the surface, soft landing (SL), and peptide-H+ reaction with the surface, reactive landing (RL). The simulations include QM+MM and QM/MM direct dynamics. For collisions with self-assembled monolayer (SAM) surfaces there is quite good agreement between experiment and simulation in the efficiency of energy transfer to the peptide-H+ ion’s internal degrees of freedom. Both themore » experiments and simulations show two mechanisms for peptide-H+ fragmentation, i.e. shattering and statistical, RRKM dynamics. Mechanisms for SL are probed in simulations of collisions of protonated dialanine with a perfluorinated SAM surface. RL has been studied experimentally for a number of peptide-H+ + surface systems, and qualitative agreement between simulation and experiment is found for two similar systems.« less

Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

NASA Astrophysics Data System (ADS)

Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

2017-01-01

This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.

NEAMS FPL M2 Milestone Report: Development of a UO₂ Grain Size Model using Multicale Modeling and Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tonks, Michael R; Zhang, Yongfeng; Bai, Xianming

2014-06-01

This report summarizes development work funded by the Nuclear Energy Advanced Modeling Simulation program's Fuels Product Line (FPL) to develop a mechanistic model for the average grain size in UO₂ fuel. The model is developed using a multiscale modeling and simulation approach involving atomistic simulations, as well as mesoscale simulations using INL's MARMOT code.

Long-time atomistic simulations with the Parallel Replica Dynamics method

NASA Astrophysics Data System (ADS)

Perez, Danny

Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2018-04-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2017-12-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

Free-Energy Landscape of the Dissolution of Gibbsite at High pH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Zhizhang; Kerisit, Sebastien N.; Stack, Andrew G.

The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of suitable, direct experimental probes. In this regard, we have applied atomistic simulations to map the free energy landscape of the dissolution of gibbsite from a step edge, as a model of metal hydroxide dissolution. The overall reaction combines kink site formation and kink site propagation. Two individual reactions were found to be rate-limiting for kink site formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sitesmore » into the solution. As a result, a pool of mobile and labile Al adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, the simulation results will enable the development of microscopic mechanistic models of metal oxide dissolution.« less

Multiscale modelling of precipitation in concentrated alloys: from atomistic Monte Carlo simulations to cluster dynamics I thermodynamics

NASA Astrophysics Data System (ADS)

Lépinoux, J.; Sigli, C.

2018-01-01

In a recent paper, the authors showed how the clusters free energies are constrained by the coagulation probability, and explained various anomalies observed during the precipitation kinetics in concentrated alloys. This coagulation probability appeared to be a too complex function to be accurately predicted knowing only the cluster distribution in Cluster Dynamics (CD). Using atomistic Monte Carlo (MC) simulations, it is shown that during a transformation at constant temperature, after a short transient regime, the transformation occurs at quasi-equilibrium. It is proposed to use MC simulations until the system quasi-equilibrates then to switch to CD which is mean field but not limited by a box size like MC. In this paper, we explain how to take into account the information available before the quasi-equilibrium state to establish guidelines to safely predict the cluster free energies.

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

PubMed

Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

2015-01-01

Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

Atomistic models of vacancy-mediated diffusion in silicon

NASA Astrophysics Data System (ADS)

Dunham, Scott T.; Wu, Can Dong

1995-08-01

Vacancy-mediated diffusion of dopants in silicon is investigated using Monte Carlo simulations of hopping diffusion, as well as analytic approximations based on atomistic considerations. Dopant/vacancy interaction potentials are assumed to extend out to third-nearest neighbor distances, as required for pair diffusion theories. Analysis focusing on the third-nearest neighbor sites as bridging configurations for uncorrelated hops leads to an improved analytic model for vacancy-mediated dopant diffusion. The Monte Carlo simulations of vacancy motion on a doped silicon lattice verify the analytic results for moderate doping levels. For very high doping (≳2×1020 cm-3) the simulations show a very rapid increase in pair diffusivity due to interactions of vacancies with more than one dopant atom. This behavior has previously been observed experimentally for group IV and V atoms in silicon [Nylandsted Larsen et al., J. Appl. Phys. 73, 691 (1993)], and the simulations predict both the point of onset and doping dependence of the experimentally observed diffusivity enhancement.

Development of a Coarse-grained Model of Polypeptoids for Studying Self-assembly in Solution

NASA Astrophysics Data System (ADS)

Du, Pu; Rick, Steven; Kumar, Revati

Polypeptoid, a class of highly tunable biomimetic analogues of peptides, are used as a prototypical model system to study self-assembly. The focus of this work is to glean insight into the effect of electrostatic and other non-covalent secondary interactions on the self-assembly of sequence-defined polypeptoids, with different charged and uncharged side groups, in solution that will complement experiments. Atomistic (AA) molecular dynamics simulation can provide a complete description of self-assembly of polypeptoid systems. However, the long simulation length and time scales needed for these processes require the development of a computationally cheaper alternative, namely coarse-grained (CG) models. A CG model for studying polypeptoid micellar interactions is being developed, parameterized on atomistic simulations, using a hybridized approach involving the OPLS-UA force filed and the Stillinger-Weber (SW) potential form. The development of the model as well as the results from the simulations on the self-assembly as function of polypeptoid chemical structure and sequences will be presented.

Molecular Dynamics Studies of Self-Assembling Biomolecules and DNA-functionalized Gold Nanoparticles

NASA Astrophysics Data System (ADS)

Cho, Vince Y.

This thesis is organized as following. In Chapter 2, we use fully atomistic MD simulations to study the conformation of DNA molecules that link gold nanoparticles to form nanoparticle superlattice crystals. In Chapter 3, we study the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber by using CGMD simulations. Compared to fully atomistic MD simulations, CGMD simulations prove to be computationally cost-efficient and reasonably accurate for exploring self-assembly, and are used in all subsequent chapters. In Chapter 4, we apply CGMD methods to study the self-assembly of small molecule-DNA hybrid (SMDH) building blocks into well-defined cage-like dimers, and reveal the role of kinetics and thermodynamics in this process. In Chapter 5, we extend the CGMD model for this system and find that the assembly of SMDHs can be fine-tuned by changing parameters. In Chapter 6, we explore superlattice crystal structures of DNA-functionalized gold nanoparticles (DNA-AuNP) with the CGMD model and compare the hybridization.

Giant and Tunable Anisotropy of Nanoscale Friction in Graphene

NASA Astrophysics Data System (ADS)

Capaz, Rodrigo; Menezes, Marcos; Almeida, Clara; de Cicco, Marcelo; Achete, Carlos; Fragneaud, Benjamin; Cançado, Luiz Gustavo; Paupitz, Ricardo; Galvão, Douglas; Prioli, Rodrigo

The nanoscale friction between an atomic force microscopy tip and graphene is investigated using friction force microscopy (FFM). During the tip movement, friction forces are observed to increase and then saturate in a highly anisotropic manner. As a result, the friction coefficient of graphene is highly dependent on the scanning direction: Under some conditions, the energy dissipated along the armchair direction can be 80% higher than along the zigzag direction. In comparison, for highly-oriented pyrolitic graphite (HOPG), the friction anisotropy between armchair and zigzag directions is only 15%. This giant friction anisotropy in graphene results from anisotropies in the amplitudes of flexural deformations of the graphene sheet driven by the tip movement, not present in HOPG. The effect can be seen as a novel manifestation of the classical phenomenon of Euler buckling at the nanoscale, which provides the non-linear ingredients that amplify friction anisotropy. Simulations based on a novel version of the 2D Tomlinson model (modified to include the effects of flexural deformations), as well as fully atomistic molecular dynamics simulations and first-principles density-functional theory (DFT) calculations, are able to reproduce and explain the experimental observations.

Giant and Tunable Anisotropy of Nanoscale Friction in Graphene

NASA Astrophysics Data System (ADS)

Almeida, Clara M.; Prioli, Rodrigo; Fragneaud, Benjamin; Cançado, Luiz Gustavo; Paupitz, Ricardo; Galvão, Douglas S.; de Cicco, Marcelo; Menezes, Marcos G.; Achete, Carlos A.; Capaz, Rodrigo B.

2016-08-01

The nanoscale friction between an atomic force microscopy tip and graphene is investigated using friction force microscopy (FFM). During the tip movement, friction forces are observed to increase and then saturate in a highly anisotropic manner. As a result, the friction forces in graphene are highly dependent on the scanning direction: under some conditions, the energy dissipated along the armchair direction can be 80% higher than along the zigzag direction. In comparison, for highly-oriented pyrolitic graphite (HOPG), the friction anisotropy between armchair and zigzag directions is only 15%. This giant friction anisotropy in graphene results from anisotropies in the amplitudes of flexural deformations of the graphene sheet driven by the tip movement, not present in HOPG. The effect can be seen as a novel manifestation of the classical phenomenon of Euler buckling at the nanoscale, which provides the non-linear ingredients that amplify friction anisotropy. Simulations based on a novel version of the 2D Tomlinson model (modified to include the effects of flexural deformations), as well as fully atomistic molecular dynamics simulations and first-principles density-functional theory (DFT) calculations, are able to reproduce and explain the experimental observations.

Designing Free Energy Surfaces That Match Experimental Data with Metadynamics

DOE PAGES

White, Andrew D.; Dama, James F.; Voth, Gregory A.

2015-04-30

Creating models that are consistent with experimental data is essential in molecular modeling. This is often done by iteratively tuning the molecular force field of a simulation to match experimental data. An alternative method is to bias a simulation, leading to a hybrid model composed of the original force field and biasing terms. Previously we introduced such a method called experiment directed simulation (EDS). EDS minimally biases simulations to match average values. We also introduce a new method called experiment directed metadynamics (EDM) that creates minimal biases for matching entire free energy surfaces such as radial distribution functions and phi/psimore » angle free energies. It is also possible with EDM to create a tunable mixture of the experimental data and free energy of the unbiased ensemble with explicit ratios. EDM can be proven to be convergent, and we also present proof, via a maximum entropy argument, that the final bias is minimal and unique. Examples of its use are given in the construction of ensembles that follow a desired free energy. Finally, the example systems studied include a Lennard-Jones fluid made to match a radial distribution function, an atomistic model augmented with bioinformatics data, and a three-component electrolyte solution where ab initio simulation data is used to improve a classical empirical model.« less

Designing free energy surfaces that match experimental data with metadynamics.

PubMed

White, Andrew D; Dama, James F; Voth, Gregory A

2015-06-09

Creating models that are consistent with experimental data is essential in molecular modeling. This is often done by iteratively tuning the molecular force field of a simulation to match experimental data. An alternative method is to bias a simulation, leading to a hybrid model composed of the original force field and biasing terms. We previously introduced such a method called experiment directed simulation (EDS). EDS minimally biases simulations to match average values. In this work, we introduce a new method called experiment directed metadynamics (EDM) that creates minimal biases for matching entire free energy surfaces such as radial distribution functions and phi/psi angle free energies. It is also possible with EDM to create a tunable mixture of the experimental data and free energy of the unbiased ensemble with explicit ratios. EDM can be proven to be convergent, and we also present proof, via a maximum entropy argument, that the final bias is minimal and unique. Examples of its use are given in the construction of ensembles that follow a desired free energy. The example systems studied include a Lennard-Jones fluid made to match a radial distribution function, an atomistic model augmented with bioinformatics data, and a three-component electrolyte solution where ab initio simulation data is used to improve a classical empirical model.

Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

PubMed

van der Vaart, Arjan

2015-05-01

Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

Exploring the Ability of a Coarse-grained Potential to Describe the Stress-strain Response of Glassy Polystyrene

DTIC Science & Technology

2012-10-01

using the open-source code Large-scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) (http://lammps.sandia.gov) (23). The commercial...parameters are proprietary and cannot be ported to the LAMMPS 4 simulation code. In our molecular dynamics simulations at the atomistic resolution, we...IBI iterative Boltzmann inversion LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator MAPS Materials Processes and Simulations MS

Anharmonicity and self-similarity of the free energy landscape of protein G.

PubMed

Pontiggia, F; Colombo, G; Micheletti, C; Orland, H

2007-01-26

The near-native free-energy landscape of protein G is investigated through 0.4-micros-long atomistic molecular dynamics simulations in an explicit solvent. A theoretical and computational framework is used to assess the time dependence of salient thermodynamical features. While the quasiharmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free-energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them.

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

NASA Astrophysics Data System (ADS)

Zhang, Zhiwei; Chen, Pei; Qin, Fei; An, Tong; Yu, Huiping

2018-05-01

Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD) layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young's modulus, ultimate tensile strength (UTS), and strain at fracture is observed.

Modeling the atomistic growth behavior of gold nanoparticles in solution

NASA Astrophysics Data System (ADS)

Turner, C. Heath; Lei, Yu; Bao, Yuping

2016-04-01

The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions.

Adhesion of single- and multi-walled carbon nanotubes to silicon substrate: atomistic simulations and continuum analysis

NASA Astrophysics Data System (ADS)

Yuan, Xuebo; Wang, Youshan

2017-10-01

The radial deformation of carbon nanotubes (CNTs) adhering to a substrate may prominently affect their mechanical and physical properties. In this study, both classical atomistic simulations and continuum analysis are carried out, to investigate the lateral adhesion of single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs) to a silicon substrate. A linear elastic model for analyzing the adhesion of 2D shells to a rigid semi-infinite substrate is constructed in the framework of continuum mechanics. Good agreement is achieved between the cross-section profiles of adhesive CNTs obtained by the continuum model and by the atomistic simulation approach. It is found that the adhesion of a CNT to the silicon substrate is significantly influenced by its initial diameter and the number of walls. CNTs with radius larger than a certain critical radius are deformed radially on the silicon substrate with flat contact regions. With increasing number of walls, the extent of radial deformation of a MWCNT on the substrate decreases dramatically, and the flat contact area reduces—and eventually vanishes—due to increasing equivalent bending stiffness. It is analytically predicted that large-diameter MWCNTs with a large number of walls are likely to ‘stand’ on the silicon substrate. The present work can be useful for understanding the radial deformation of CNTs adhering to a solid planar substrate.

Sensitivity of Force Fields on Mechanical Properties of Metals Predicted by Atomistic Simulations

NASA Astrophysics Data System (ADS)

Rassoulinejad-Mousavi, Seyed Moein; Zhang, Yuwen

Increasing number of micro/nanoscale studies for scientific and engineering applications, leads to huge deployment of atomistic simulations such as molecular dynamics and Monte-Carlo simulation. Many complains from users in the simulation community arises for obtaining wrong results notwithstanding of correct simulation procedure and conditions. Improper choice of force field, known as interatomic potential is the likely causes. For the sake of users' assurance, convenience and time saving, several interatomic potentials are evaluated by molecular dynamics. Elastic properties of multiple FCC and BCC pure metallic species are obtained by LAMMPS, using different interatomic potentials designed for pure species and their alloys at different temperatures. The potentials created based on the Embedded Atom Method (EAM), Modified EAM (MEAM) and ReaX force fields, adopted from available open databases. Independent elastic stiffness constants of cubic single crystals for different metals are obtained. The results are compared with the experimental ones available in the literature and deviations for each force field are provided at each temperature. Using current work, users of these force fields can easily judge on the one they are going to designate for their problem.

A method for generating reliable atomistic models of amorphous polymers based on a random search of energy minima

NASA Astrophysics Data System (ADS)

Curcó, David; Casanovas, Jordi; Roca, Marc; Alemán, Carlos

2005-07-01

A method for generating atomistic models of dense amorphous polymers is presented. The method is organized in a two-steps procedure. First, structures are generated using an algorithm that minimizes the torsional strain. After this, a relaxation algorithm is applied to minimize the non-bonding interactions. Two alternative relaxation methods, which are based simple minimization and Concerted Rotation techniques, have been implemented. The performance of the method has been checked by simulating polyethylene, polypropylene, nylon 6, poly(L,D-lactic acid) and polyglycolic acid.

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations

PubMed Central

2018-01-01

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure–constant temperature ensemble. These materials exhibit a distinct “smectic” liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications. PMID:29301305

Enhanced densification under shock compression in porous silicon

NASA Astrophysics Data System (ADS)

Lane, J. Matthew D.; Thompson, Aidan P.; Vogler, Tracy J.

2014-10-01

Under shock compression, most porous materials exhibit lower densities for a given pressure than that of a full-dense sample of the same material. However, some porous materials exhibit an anomalous, or enhanced, densification under shock compression. We demonstrate a molecular mechanism that drives this behavior. We also present evidence from atomistic simulation that silicon belongs to this anomalous class of materials. Atomistic simulations indicate that local shear strain in the neighborhood of collapsing pores nucleates a local solid-solid phase transformation even when bulk pressures are below the thermodynamic phase transformation pressure. This metastable, local, and partial, solid-solid phase transformation, which accounts for the enhanced densification in silicon, is driven by the local stress state near the void, not equilibrium thermodynamics. This mechanism may also explain the phenomenon in other covalently bonded materials.

Calculating the enthalpy of vaporization for ionic liquid clusters.

PubMed

Kelkar, Manish S; Maginn, Edward J

2007-08-16

Classical atomistic simulations are used to compute the enthalpy of vaporization of a series of ionic liquids composed of 1-alkyl-3-methylimidazolium cations paired with the bis(trifluoromethylsulfonyl)imide anion. The calculations show that the enthalpy of vaporization is lowest for neutral ion pairs. The enthalpy of vaporization increases by about 40 kJ/mol with the addition of each ion pair to the vaporizing cluster. Non-neutral clusters have much higher vaporization enthalpies than their neutral counterparts and thus are not expected to make up a significant fraction of volatile species. The enthalpy of vaporization increases slightly as the cation alkyl chain length increases and as temperature decreases. The calculated vaporization enthalpies are consistent with two sets of recent experimental measurements as well as with previous atomistic simulations.

Atomistic simulations of the optical absorption of type-II CdSe/ZnTe superlattices

PubMed Central

2012-01-01

We perform accurate tight binding simulations to design type-II short-period CdSe/ZnTe superlattices suited for photovoltaic applications. Absorption calculations demonstrate a very good agreement with optical results with threshold strongly depending on the chemical species near interfaces. PMID:23031315

Melting processes of oligomeric α and β isotactic polypropylene crystals at ultrafast heating rates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ji, Xiaojing; He, Xuehao, E-mail: xhhe@tju.edu.cn, E-mail: scjiang@tju.edu.cn; Jiang, Shichun, E-mail: xhhe@tju.edu.cn, E-mail: scjiang@tju.edu.cn

The melting behaviors of α (stable) and β (metastable) isotactic polypropylene (iPP) crystals at ultrafast heating rates are simulated with atomistic molecular dynamics method. Quantitative information about the melting processes of α- and β-iPP crystals at atomistic level is achieved. The result shows that the melting process starts from the interfaces of lamellar crystal through random dislocation of iPP chains along the perpendicular direction of lamellar crystal structure. In the melting process, the lamellar crystal gradually expands but the corresponding thickness decreases. The analysis shows that the system expansion lags behind the crystallinity decreasing and the lagging extents for α-more » and β-iPP are significantly different. The apparent melting points of α- and β-iPP crystals rise with the increase of the heating rate and lamellar crystal thickness. The apparent melting point of α-iPP crystal is always higher than that of β-iPP at differently heating rates. Applying the Gibbs-Thomson rule and the scaling property of the melting kinetics, the equilibrium melting points of perfect α- and β-iPP crystals are finally predicted and it shows a good agreement with experimental result.« less

Accessible, almost ab initio multi-scale modeling of entangled polymers via slip-links

NASA Astrophysics Data System (ADS)

Andreev, Marat

It is widely accepted that dynamics of entangled polymers can be described by the tube model. Here we advocate for an alternative approach to entanglement modeling known as slip-links. Recently, slip-links were shown to possess important advantages over tube models, namely they have strong connections to atomistic, multichain levels of description, agree with non-equilibrium thermodynamics, are applicable to any chain architecture and can be used in linear or non-linear rheology. We present a hierarchy of slip-link models that are connected to each other through successive coarse graining. Models in the hierarchy are consistent in their overlapping domains of applicability in order to allow a straightforward mapping of parameters. In particular, the most--detailed level of description has four parameters, three of which can be determined directly from atomistic simulations. On the other hand, the least--detailed member of the hierarchy is numerically accessible, and allows for non-equilibrium flow predictions of complex chain architectures. Using GPU implementation these predictions can be obtained in minutes of computational time on a single desktop equipped with a mainstream gaming GPU. The GPU code is available online for free download.

Effective Particle Size From Molecular Dynamics Simulations in Fluids

DOE PAGES

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov; ...

2017-12-08

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses.

PubMed

Huber, Roland G; Marzinek, Jan K; Holdbrook, Daniel A; Bond, Peter J

2017-09-01

Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals. In recent years, advances in computing architecture and algorithms have begun to allow us to use simulations to study the structure and dynamics of viral ultrastructures at various stages of their life cycle in atomistic or near-atomistic detail. In this review, we outline specific challenges and solutions that have emerged to allow for structurally detailed modelling of viruses in silico. We focus on the history and state of the art of atomistic and coarse-grained approaches to simulate the dynamics of the large, macromolecular structures associated with viral infection, and on their usefulness in explaining and expanding upon experimental data. We discuss the types of interactions that need to be modeled to describe major components of the virus particle and advances in modelling techniques that allow for the treatment of these systems, highlighting recent key simulation studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effective Particle Size From Molecular Dynamics Simulations in Fluids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Improving the Thermodynamic Stability of Aluminate Spinel Nanoparticles with Rare Earths

DOE PAGES

Hasan, M. M.; Dey, Sanchita; Nafsin, Nazia; ...

2016-06-29

Surface energy is a key parameter to understand and predict the stability of catalysts. In this work, the surface energy of MgAl 2O 4, an important base material for catalyst support, was reduced by using dopants prone to form surface excess (surface segregation): Y 3+, Gd 3+, and La 3+. The energy reduction was predicted by atomistic simulations of spinel surfaces and experimentally demonstrated by using microcalorimetry. The surface energy of undoped MgAl 2O 4 was directly measured as 1.65 ± 0.04 J/m 2 and was reduced by adding 2 mol % of the dopants to 1.55 ± 0.04 J/mmore » 2 for Y-doping, 1.45 ± 0.05 J/m 2 for Gd-doping, and 1.26 ± 0.06 J/m 2 for La-doping. Atomistic simulations are qualitatively consistent with the experiments, reinforcing the link between the role of dopants in stabilizing the surface and the energy of segregation. Surface segregation was experimentally assessed using electron energy loss spectroscopy mapping in a scanning transmission electron microscopy image. Finally, the reduced energy resulted in coarsening inhibition for the doped samples and, hence, systematically smaller particle sizes (larger surface areas), meaning increased stability for catalytic applications. Moreover, both experiment and modeling reveal preferential dopant segregation to specific surfaces, which leads to the preponderance of {111} surface planes and suggests a strategy to enhance the area of desired surfaces in nanoparticles for better catalyst support activity.« less

Atomistic modeling of thermomechanical properties of SWNT/Epoxy nanocomposites

NASA Astrophysics Data System (ADS)

Fasanella, Nicholas; Sundararaghavan, Veera

2015-09-01

Molecular dynamics simulations are performed to compute thermomechanical properties of cured epoxy resins reinforced with pristine and covalently functionalized carbon nanotubes. A DGEBA-DDS epoxy network was built using the ‘dendrimer’ growth approach where 75% of available epoxy sites were cross-linked. The epoxy model is verified through comparisons to experiments, and simulations are performed on nanotube reinforced cross-linked epoxy matrix using the CVFF force field in LAMMPS. Full stiffness matrices and linear coefficient of thermal expansion vectors are obtained for the nanocomposite. Large increases in stiffness and large decreases in thermal expansion were seen along the direction of the nanotube for both nanocomposite systems when compared to neat epoxy. The direction transverse to nanotube saw a 40% increase in stiffness due to covalent functionalization over neat epoxy at 1 K whereas the pristine nanotube system only saw a 7% increase due to van der Waals effects. The functionalized SWNT/epoxy nanocomposite showed an additional 42% decrease in thermal expansion along the nanotube direction when compared to the pristine SWNT/epoxy nanocomposite. The stiffness matrices are rotated over every possible orientation to simulate the effects of an isotropic system of randomly oriented nanotubes in the epoxy. The randomly oriented covalently functionalized SWNT/Epoxy nanocomposites showed substantial improvements over the plain epoxy in terms of higher stiffness (200% increase) and lower thermal expansion (32% reduction). Through MD simulations, we develop means to build simulation cells, perform annealing to reach correct densities, compute thermomechanical properties and compare with experiments.

Quantum dynamical simulations of local field enhancement in metal nanoparticles.

PubMed

Negre, Christian F A; Perassi, Eduardo M; Coronado, Eduardo A; Sánchez, Cristián G

2013-03-27

Field enhancements (Γ) around small Ag nanoparticles (NPs) are calculated using a quantum dynamical simulation formalism and the results are compared with electrodynamic simulations using the discrete dipole approximation (DDA) in order to address the important issue of the intrinsic atomistic structure of NPs. Quite remarkably, in both quantum and classical approaches the highest values of Γ are located in the same regions around single NPs. However, by introducing a complete atomistic description of the metallic NPs in optical simulations, a different pattern of the Γ distribution is obtained. Knowing the correct pattern of the Γ distribution around NPs is crucial for understanding the spectroscopic features of molecules inside hot spots. The enhancement produced by surface plasmon coupling is studied by using both approaches in NP dimers for different inter-particle distances. The results show that the trend of the variation of Γ versus inter-particle distance is different for classical and quantum simulations. This difference is explained in terms of a charge transfer mechanism that cannot be obtained with classical electrodynamics. Finally, time dependent distribution of the enhancement factor is simulated by introducing a time dependent field perturbation into the Hamiltonian, allowing an assessment of the localized surface plasmon resonance quantum dynamics.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khabaz, Fardin, E-mail: rajesh.khare@ttu.edu; Khare, Ketan S., E-mail: rajesh.khare@ttu.edu; Khare, Rajesh, E-mail: rajesh.khare@ttu.edu

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 Young’s 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 themore » 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.« less

Perspective: Machine learning potentials for atomistic simulations

NASA Astrophysics Data System (ADS)

Behler, Jörg

2016-11-01

Nowadays, computer simulations have become a standard tool in essentially all fields of chemistry, condensed matter physics, and materials science. In order to keep up with state-of-the-art experiments and the ever growing complexity of the investigated problems, there is a constantly increasing need for simulations of more realistic, i.e., larger, model systems with improved accuracy. In many cases, the availability of sufficiently efficient interatomic potentials providing reliable energies and forces has become a serious bottleneck for performing these simulations. To address this problem, currently a paradigm change is taking place in the development of interatomic potentials. Since the early days of computer simulations simplified potentials have been derived using physical approximations whenever the direct application of electronic structure methods has been too demanding. Recent advances in machine learning (ML) now offer an alternative approach for the representation of potential-energy surfaces by fitting large data sets from electronic structure calculations. In this perspective, the central ideas underlying these ML potentials, solved problems and remaining challenges are reviewed along with a discussion of their current applicability and limitations.

Multi-million atom electronic structure calculations for quantum dots

NASA Astrophysics Data System (ADS)

Usman, Muhammad

Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined stark shift, coherent coupling of electronic states in a quantum dot molecule etc.; (3) to assess the potential use of the quantum dots in real device implementation and to provide physical insight to the experimentalists. Full three dimensional strain and electronic structure simulations of quantum dot structures containing multi-million atoms are done using NEMO 3-D. Both single and vertically stacked quantum dot structures are analyzed in detail. The results show that the strain and the piezoelectricity significantly impact the electronic structure of these devices. This work shows that the InAs quantum dots when placed in the InGaAs quantum well red shifts the emission wavelength. Such InAs/GaAs-based optical devices can be used for optical-fiber based communication systems at longer wavelengths (1.3um -- 1.5um). Our atomistic simulations of InAs/InGaAs/GaAs quantum dots quantitatively match with the experiment and give the critical insight of the physics involved in these structures. A single quantum dot molecule is studied for coherent quantum coupling of electronic states under the influence of static electric field applied in the growth direction. Such nanostructures can be used in the implementation of quantum information technologies. A close quantitative match with the experimental optical measurements allowed us to get a physical insight into the complex physics of quantum tunnel couplings of electronic states as the device operation switches between atomic and molecular regimes. Another important aspect is to design the quantum dots for a desired isotropic polarization of the optical emissions. Both single and coupled quantum dots are studied for TE/TM ratio engineering. The atomistic study provides a detailed physical analysis of these computationally expensive large nanostructures and serves as a guide for the experimentalists for the design of the polarization independent devices for the optical communication systems.

Accurate atomistic first-principles calculations of electronic stopping

DOE PAGES

Schleife, André; Kanai, Yosuke; Correa, Alfredo A.

2015-01-20

In this paper, we show that atomistic first-principles calculations based on real-time propagation within time-dependent density functional theory are capable of accurately describing electronic stopping of light projectile atoms in metal hosts over a wide range of projectile velocities. In particular, we employ a plane-wave pseudopotential scheme to solve time-dependent Kohn-Sham equations for representative systems of H and He projectiles in crystalline aluminum. This approach to simulate nonadiabatic electron-ion interaction provides an accurate framework that allows for quantitative comparison with experiment without introducing ad hoc parameters such as effective charges, or assumptions about the dielectric function. Finally, our work clearlymore » shows that this atomistic first-principles description of electronic stopping is able to disentangle contributions due to tightly bound semicore electrons and geometric aspects of the stopping geometry (channeling versus off-channeling) in a wide range of projectile velocities.« less

Molecular Modeling for Calculation of Mechanical Properties of Epoxies with Moisture Ingress

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Frankland, Sarah J.; Hinkley, J. A.; Gates, T. S.

2009-01-01

Atomistic models of epoxy structures were built in order to assess the effect of crosslink degree, moisture content and temperature on the calculated properties of a typical representative generic epoxy. Each atomistic model had approximately 7000 atoms and was contained within a periodic boundary condition cell with edge lengths of about 4 nm. Four atomistic models were built with a range of crosslink degree and moisture content. Each of these structures was simulated at three temperatures: 300 K, 350 K, and 400 K. Elastic constants were calculated for these structures by monitoring the stress tensor as a function of applied strain deformations to the periodic boundary conditions. The mechanical properties showed reasonably consistent behavior with respect to these parameters. The moduli decreased with decreasing crosslink degree with increasing temperature. The moduli generally decreased with increasing moisture content, although this effect was not as consistent as that seen for temperature and crosslink degree.

Dislocation dynamics simulations of plasticity at small scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Caizhi

2010-01-01

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

Effects of applied strain on nanoscale self-interstitial cluster formation in BCC iron

NASA Astrophysics Data System (ADS)

Gao, Ning; Setyawan, Wahyu; Kurtz, Richard J.; Wang, Zhiguang

2017-09-01

The effect of applied strains on the configurational evolution of self-interstitial clusters in BCC iron (Fe) is explored with atomistic simulations. A novel cluster configuration is discovered at low temperatures (<600 K), which consists of 〈 110 〉 dumbbells and 〈 111 〉 crowdions in a specific configuration, resulting in an immobile defect. The stability and diffusion of this cluster at higher temperatures is explored. In addition, an anisotropy distribution factor of a particular [ hkl ] interstitial loop within the family of 〈 hkl 〉 loops is calculated as a function of strain. The results show that loop anisotropy is governed by the angle between the stress direction and the orientation of the 〈 111 〉 crowdions in the loop, and directly linked to the stress induced preferred nucleation of self-interstitial atoms.

The Development of Models to Optimize Selection of Nuclear Fuels through Atomic-Level Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prof. Simon Phillpot; Prof. Susan B. Sinnott; Prof. Hans Seifert

2009-01-26

Demonstrated that FRAPCON can be modified to accept data generated from first principles studies, and that the result obtained from the modified FRAPCON make sense in terms of the inputs. Determined the temperature dependence of the thermal conductivity of single crystal UO2 from atomistic simulation.

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, T.

1986-01-01

During this reporting period three investigations were carried out. The first area of research concerned the analysis of the structure-energy relationship in small clusters. This study is very closely related to the improvement of the potential energy functions which are suitable and simple enough to be used in atomistic simulation studies. Parameters obtained from ab initio calculations for dimers and trimers of Al were used to estimate energetics and global minimum energy structures of clusters continuing up to 15 Al atoms. The second research topic addressed modeling of the collision process for atoms impinging on surfaces. In this simulation study qualitative aspects of the O atom collision with a graphite surface were analyzed. Four different O/graphite systems were considered and the aftermath of the impact was analyzed. The final area of investigation was related to the simulation of thin amorphous Si films on crystalline Si substrates. Parameters obtained in an earlier study were used to model an exposed amorphous Si surface and an a-Si/c-Si interface. Structural details for various film thicknesses were investigated at an atomistic level.

Atomistic minimal model for estimating profile of electrodeposited nanopatterns

NASA Astrophysics Data System (ADS)

Asgharpour Hassankiadeh, Somayeh; Sadeghi, Ali

2018-06-01

We develop a computationally efficient and methodologically simple approach to realize molecular dynamics simulations of electrodeposition. Our minimal model takes into account the nontrivial electric field due a sharp electrode tip to perform simulations of the controllable coating of a thin layer on a surface with an atomic precision. On the atomic scale a highly site-selective electrodeposition of ions and charged particles by means of the sharp tip of a scanning probe microscope is possible. A better understanding of the microscopic process, obtained mainly from atomistic simulations, helps us to enhance the quality of this nanopatterning technique and to make it applicable in fabrication of nanowires and nanocontacts. In the limit of screened inter-particle interactions, it is feasible to run very fast simulations of the electrodeposition process within the framework of the proposed model and thus to investigate how the shape of the overlayer depends on the tip-sample geometry and dielectric properties, electrolyte viscosity, etc. Our calculation results reveal that the sharpness of the profile of a nano-scale deposited overlayer is dictated by the normal-to-sample surface component of the electric field underneath the tip.

AACSD: An atomistic analyzer for crystal structure and defects

NASA Astrophysics Data System (ADS)

Liu, Z. R.; Zhang, R. F.

2018-01-01

We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vögele, Martin; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M.; Holm, Christian

2015-12-28

We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models aremore » able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.« less

Structured water in polyelectrolyte dendrimers: Understanding small angle neutron scattering results through atomistic simulation

NASA Astrophysics Data System (ADS)

Wu, Bin; Kerkeni, Boutheïna; Egami, Takeshi; Do, Changwoo; Liu, Yun; Wang, Yongmei; Porcar, Lionel; Hong, Kunlun; Smith, Sean C.; Liu, Emily L.; Smith, Gregory S.; Chen, Wei-Ren

2012-04-01

Based on atomistic molecular dynamics (MD) simulations, the small angle neutron scattering (SANS) intensity behavior of a single generation-4 polyelectrolyte polyamidoamine starburst dendrimer is investigated at different levels of molecular protonation. The SANS form factor, P(Q), and Debye autocorrelation function, γ(r), are calculated from the equilibrium MD trajectory based on a mathematical approach proposed in this work. The consistency found in comparison against previously published experimental findings (W.-R. Chen, L. Porcar, Y. Liu, P. D. Butler, and L. J. Magid, Macromolecules 40, 5887 (2007)) leads to a link between the neutron scattering experiment and MD computation, and fresh perspectives. The simulations enable scattering calculations of not only the hydrocarbons but also the contribution from the scattering length density fluctuations caused by structured, confined water within the dendrimer. Based on our computational results, we explore the validity of using radius of gyration RG for microstructure characterization of a polyelectrolyte dendrimer from the scattering perspective.

Large-scale atomistic simulations of helium-3 bubble growth in complex palladium alloys

DOE PAGES

Hale, Lucas M.; Zimmerman, Jonathan A.; Wong, Bryan M.

2016-05-18

Palladium is an attractive material for hydrogen and hydrogen-isotope storage applications due to its properties of large storage density and high diffusion of lattice hydrogen. When considering tritium storage, the material’s structural and mechanical integrity is threatened by both the embrittlement effect of hydrogen and the creation and evolution of additional crystal defects (e.g., dislocations, stacking faults) caused by the formation and growth of helium-3 bubbles. Using recently developed inter-atomic potentials for the palladium-silver-hydrogen system, we perform large-scale atomistic simulations to examine the defect-mediated mechanisms that govern helium bubble growth. Our simulations show the evolution of a distribution of materialmore » defects, and we compare the material behavior displayed with expectations from experiment and theory. In conclusion, we also present density functional theory calculations to characterize ideal tensile and shear strengths for these materials, which enable the understanding of how and why our developed potentials either meet or confound these expectations.« less

A generalized Poisson solver for first-principles device simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bani-Hashemian, Mohammad Hossein; VandeVondele, Joost, E-mail: joost.vandevondele@mat.ethz.ch; Brück, Sascha

2016-01-28

Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices. Dirichlet conditions are enforced as constraints in a variational framework giving rise to a saddle point problem. The resulting system of equations is then solved using a stationary iterative methodmore » in which the generalized Poisson operator is preconditioned with the standard Laplace operator. The solver can make use of any sufficiently smooth function modelling the dielectric constant, including density dependent dielectric continuum models. For all the boundary conditions, consistent derivatives are available and molecular dynamics simulations can be performed. The convergence behaviour of the scheme is investigated and its capabilities are demonstrated.« less

Improved Atomistic Monte Carlo Simulations Demonstrate that Poly-L-Proline Adopts Heterogeneous Ensembles of Conformations of Semi-Rigid Segments Interrupted by Kinks

PubMed Central

Radhakrishnan, Aditya; Vitalis, Andreas; Mao, Albert H.; Steffen, Adam T.; Pappu, Rohit V.

2012-01-01

Poly-L-proline (PLP) polymers are useful mimics of biologically relevant proline-rich sequences. Biophysical and computational studies of PLP polymers in aqueous solutions are challenging because of the diversity of length scales and the slow time scales for conformational conversions. We describe an atomistic simulation approach that combines an improved ABSINTH implicit solvation model, with conformational sampling based on standard and novel Metropolis Monte Carlo moves. Refinements to forcefield parameters were guided by published experimental data for proline-rich systems. We assessed the validity of our simulation results through quantitative comparisons to experimental data that were not used in refining the forcefield parameters. Our analysis shows that PLP polymers form heterogeneous ensembles of conformations characterized by semi-rigid, rod-like segments interrupted by kinks, which result from a combination of internal cis peptide bonds, flexible backbone ψ-angles, and the coupling between ring puckering and backbone degrees of freedom. PMID:22329658

Atomistic Modeling of RuAl and (RuNi) Al Alloys

NASA Technical Reports Server (NTRS)

Gargano, Pablo; Mosca, Hugo; Bozzolo, Guillermo; Noebe, Ronald D.; Gray, Hugh R. (Technical Monitor)

2002-01-01

Atomistic modeling of RuAl and RuAlNi alloys, using the BFS (Bozzolo-Ferrante-Smith) method for alloys is performed. The lattice parameter and energy of formation of B2 RuAl as a function of stoichiometry and the lattice parameter of (Ru(sub 50-x)Ni(sub x)Al(sub 50)) alloys as a function of Ni concentration are computed. BFS based Monte Carlo simulations indicate that compositions close to Ru25Ni25Al50 are single phase with no obvious evidence of a miscibility gap and separation of the individual B2 phases.

Atomistic insights into deep eutectic electrolytes: the influence of urea on the electrolyte salt LiTFSI in view of electrochemical applications.

PubMed

Lesch, Volker; Heuer, Andreas; Rad, Babak R; Winter, Martin; Smiatek, Jens

2016-10-19

The influence of urea on the conducting salt lithium bis-(trifluoromethanesulfonyl)-imide (LiTFSI) in terms of lithium ion coordination numbers and lithium ion transport properties is studied via atomistic molecular dynamics simulations. Our results indicate that the presence of urea favors the formation of a deep eutectic electrolyte with pronounced ion conductivities which can be explained by a competition between urea and TFSI in occupying the first coordination shell around lithium ions. All simulation findings verify that high urea concentrations lead to a significant increase of ionic diffusivities and an occurrence of relatively high lithium transference numbers in good agreement with experimental results. The outcomes of our study point at the possible application of deep eutectic electrolytes as ion conducting materials in lithium ion batteries.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Man, Viet Hoang; Pan, Feng; Sagui, Celeste, E-mail: sagui@ncsu.edu

We explore the use of a fast laser melting simulation approach combined with atomistic molecular dynamics simulations in order to determine the melting and healing responses of B-DNA and Z-DNA dodecamers with the same d(5′-CGCGCGCGCGCG-3′){sub 2} sequence. The frequency of the laser pulse is specifically tuned to disrupt Watson-Crick hydrogen bonds, thus inducing melting of the DNA duplexes. Subsequently, the structures relax and partially refold, depending on the field strength. In addition to the inherent interest of the nonequilibrium melting process, we propose that fast melting by an infrared laser pulse could be used as a technique for a fastmore » comparison of relative stabilities of same-sequence oligonucleotides with different secondary structures with full atomistic detail of the structures and solvent. This could be particularly useful for nonstandard secondary structures involving non-canonical base pairs, mismatches, etc.« less

Thin films structural properties: results of the full-atomistic supercomputer simulation

NASA Astrophysics Data System (ADS)

Grigoriev, F. V.; Sulimov, V. B.; Tikhonravov, A. V.

2017-12-01

The previously developed full-atomistic approach to the thin film growth simulation is applied for the investigation of the dependence of silicon dioxide films properties on deposition conditions. It is shown that the surface roughness and porosity are essentially reduced with the growth of energy of deposited silicon atoms. The growth of energy from 0.1 eV to 10 eV results in the increase of the film density for 0.2 - 0.4 g/cm3 and of the refractive index for 0.04-0.08. The compressive stress in films structures is observed for all deposition conditions. Absolute values of the stress tensor components increase with the growth of e energy of deposited atoms. The increase of the substrate temperature results in smoothing of the density profiles of the deposited films.

Multiscale atomistic simulation of metal-oxygen surface interactions: Methodological development, theoretical investigation, and correlation with experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Judith C.

The purpose of this grant is to develop the multi-scale theoretical methods to describe the nanoscale oxidation of metal thin films, as the PI (Yang) extensive previous experience in the experimental elucidation of the initial stages of Cu oxidation by primarily in situ transmission electron microscopy methods. Through the use and development of computational tools at varying length (and time) scales, from atomistic quantum mechanical calculation, force field mesoscale simulations, to large scale Kinetic Monte Carlo (KMC) modeling, the fundamental underpinings of the initial stages of Cu oxidation have been elucidated. The development of computational modeling tools allows for acceleratedmore » materials discovery. The theoretical tools developed from this program impact a wide range of technologies that depend on surface reactions, including corrosion, catalysis, and nanomaterials fabrication.« less

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

3d visualization of atomistic simulations on every desktop

NASA Astrophysics Data System (ADS)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-08-01

Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

PubMed

Riniker, Sereina; van Gunsteren, Wilfred F

2011-02-28

The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostatic interactions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and all-atom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectric permittivity were chosen as primary target properties. The model properties are compared with those obtained from experiment, from clusters of simple-point-charge water molecules of appropriate size in the liquid phase, and for other CG water models if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine-grained atomistic water models.

Understanding luminescence properties of grain boundaries in GaN thin films and their atomistic origin

NASA Astrophysics Data System (ADS)

Yoo, Hyobin; Yoon, Sangmoon; Chung, Kunook; Kang, Seoung-Hun; Kwon, Young-Kyun; Yi, Gyu-Chul; Kim, Miyoung

2018-03-01

We report our findings on the optical properties of grain boundaries in GaN films grown on graphene layers and discuss their atomistic origin. We combine electron backscatter diffraction with cathodoluminescence to directly correlate the structural defects with their optical properties, enabling the high-precision local luminescence measurement of the grain boundaries in GaN films. To further understand the atomistic origin of the luminescence properties, we carefully probed atomic core structures of the grain boundaries by exploiting aberration-corrected scanning transmission electron microscopy. The atomic core structures of grain boundaries show different ordering behaviors compared with those observed previously in threading dislocations. Energetics of the grain boundary core structures and their correlation with electronic structures were studied by first principles calculation.

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary

PubMed Central

Yang, Shengfeng; Chen, Youping

2015-01-01

In this paper, we present the development of a concurrent atomistic–continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic–continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress–strain responses, the GB–crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB–crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation. PMID:25792957

ReaxFF based molecular dynamics simulations of ignition front propagation in hydrocarbon/oxygen mixtures under high temperature and pressure conditions.

PubMed

Ashraf, Chowdhury; Jain, Abhishek; Xuan, Yuan; van Duin, Adri C T

2017-02-15

In this paper, we present the first atomistic-scale based method for calculating ignition front propagation speed and hypothesize that this quantity is related to laminar flame speed. This method is based on atomistic-level molecular dynamics (MD) simulations with the ReaxFF reactive force field. Results reported in this study are for supercritical (P = 55 MPa and T u = 1800 K) combustion of hydrocarbons as elevated pressure and temperature are required to accelerate the dynamics for reactive MD simulations. These simulations are performed for different types of hydrocarbons, including alkyne, alkane, and aromatic, and are able to successfully reproduce the experimental trend of reactivity of these hydrocarbons. Moreover, our results indicate that the ignition front propagation speed under supercritical conditions has a strong dependence on equivalence ratio, similar to experimentally measured flame speeds at lower temperatures and pressures which supports our hypothesis that ignition front speed is a related quantity to laminar flame speed. In addition, comparisons between results obtained from ReaxFF simulation and continuum simulations performed under similar conditions show good qualitative, and reasonable quantitative agreement. This demonstrates that ReaxFF based MD-simulations are a promising tool to study flame speed/ignition front speed in supercritical hydrocarbon combustion.

Multiscale Modeling and Simulation of Material Processing

DTIC Science & Technology

2006-07-01

As a re- GIMP simulations . Fig. 2 illustrates the contact algo- suit, MPM using a single mesh tends to induce early con- rithm for the contact pair ...21-07-2006 Final Performance Report 05-01-2003 - 04-30-2006 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Multiscale Modeling and Simulation of Material...development of scaling laws for multiscale simulations from atomistic to continuum using material testing techniques, such as tension and indentation

Homogeneous nucleation and microstructure evolution in million-atom molecular dynamics simulation

PubMed Central

Shibuta, Yasushi; Oguchi, Kanae; Takaki, Tomohiro; Ohno, Munekazu

2015-01-01

Homogeneous nucleation from an undercooled iron melt is investigated by the statistical sampling of million-atom molecular dynamics (MD) simulations performed on a graphics processing unit (GPU). Fifty independent instances of isothermal MD calculations with one million atoms in a quasi-two-dimensional cell over a nanosecond reveal that the nucleation rate and the incubation time of nucleation as functions of temperature have characteristic shapes with a nose at the critical temperature. This indicates that thermally activated homogeneous nucleation occurs spontaneously in MD simulations without any inducing factor, whereas most previous studies have employed factors such as pressure, surface effect, and continuous cooling to induce nucleation. Moreover, further calculations over ten nanoseconds capture the microstructure evolution on the order of tens of nanometers from the atomistic viewpoint and the grain growth exponent is directly estimated. Our novel approach based on the concept of “melting pots in a supercomputer” is opening a new phase in computational metallurgy with the aid of rapid advances in computational environments. PMID:26311304

Transient Spectra in TDDFT: Corrections and Correlations

NASA Astrophysics Data System (ADS)

Parkhill, John; Nguyen, Triet

We introduce an atomistic, all-electron, black-box electronic structure code to simulate transient absorption (TA) spectra and apply it to simulate pyrazole and a GFP chromophore derivative. The method is an application of OSCF2, our dissipative extension of time-dependent density functional theory. We compare our simulated spectra directly with recent ultra-fast spectroscopic experiments, showing that they are usefully predicted. We also relate bleaches in the TA signal to Fermi-blocking which would be missed in a simplified model. An important ingredient in the method is the stationary-TDDFT correction scheme recently put forwards by Fischer, Govind, and Cramer which allows us to overcome a limitation of adiabatic TDDFT. We demonstrate that OSCF2 is able to predict both the energies of bleaches and induced absorptions, as well as the decay of the transient spectrum, with only the molecular structure as input. With remaining time we will discuss corrections which resolve the non-resonant behavior of driven TDDFT, and correlated corrections to mean-field dynamics.

Probing the limits of metal plasticity with molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zepeda-Ruiz, Luis A.; Stukowski, Alexander; Oppelstrup, Tomas; Bulatov, Vasily V.

2017-10-01

Ordinarily, the strength and plasticity properties of a metal are defined by dislocations--line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocation dynamics models are usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive to perform routinely. However, atomistic simulations accurately capture every possible mechanism of material response, resolving every ``jiggle and wiggle'' of atomic motion, whereas dislocation dynamics models do not. Here we present fully dynamic atomistic simulations of bulk single-crystal plasticity in the body-centred-cubic metal tantalum. Our goal is to quantify the conditions under which the limits of dislocation-mediated plasticity are reached and to understand what happens to the metal beyond any such limit. In our simulations, the metal is compressed at ultrahigh strain rates along its [001] crystal axis under conditions of constant pressure, temperature and strain rate. To address the complexity of crystal plasticity processes on the length scales (85-340 nm) and timescales (1 ns-1μs) that we examine, we use recently developed methods of in situ computational microscopy to recast the enormous amount of transient trajectory data generated in our simulations into a form that can be analysed by a human. Our simulations predict that, on reaching certain limiting conditions of strain, dislocations alone can no longer relieve mechanical loads; instead, another mechanism, known as deformation twinning (the sudden re-orientation of the crystal lattice), takes over as the dominant mode of dynamic response. Below this limit, the metal assumes a strain-path-independent steady state of plastic flow in which the flow stress and the dislocation density remain constant as long as the conditions of straining thereafter remain unchanged. In this distinct state, tantalum flows like a viscous fluid while retaining its crystal lattice and remaining a strong and stiff metal.

Simulating the Physical World

NASA Astrophysics Data System (ADS)

Berendsen, Herman J. C.

2004-06-01

The simulation of physical systems requires a simplified, hierarchical approach which models each level from the atomistic to the macroscopic scale. From quantum mechanics to fluid dynamics, this book systematically treats the broad scope of computer modeling and simulations, describing the fundamental theory behind each level of approximation. Berendsen evaluates each stage in relation to its applications giving the reader insight into the possibilities and limitations of the models. Practical guidance for applications and sample programs in Python are provided. With a strong emphasis on molecular models in chemistry and biochemistry, this book will be suitable for advanced undergraduate and graduate courses on molecular modeling and simulation within physics, biophysics, physical chemistry and materials science. It will also be a useful reference to all those working in the field. Additional resources for this title including solutions for instructors and programs are available online at www.cambridge.org/9780521835275. The first book to cover the wide range of modeling and simulations, from atomistic to the macroscopic scale, in a systematic fashion Providing a wealth of background material, it does not assume advanced knowledge and is eminently suitable for course use Contains practical examples and sample programs in Python

Study of Structure and Deformation Pathways in Ti-7Al Using Atomistic Simulations, Experiments, and Characterization

NASA Astrophysics Data System (ADS)

Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.

2017-05-01

Ti-7Al is a good model material for mimicking the α phase response of near- α and α+ β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.

Perspectives on the simulation of protein–surface interactions using empirical force field methods

PubMed Central

Latour, Robert A.

2014-01-01

Protein–surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein–surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation. PMID:25028242

Structure, Kinetics, and Thermodynamics of the Aqueous Uranyl(VI) Cation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerisit, Sebastien N.; Liu, Chongxuan

2013-08-20

Molecular simulation techniques are employed to gain insights into the structural, kinetic, and thermodynamic properties of the uranyl(VI) cation (UO22+) in aqueous solution. The simulations make use of an atomistic potential model (force field) derived in this work and based on the model of Guilbaud and Wipff (Guilbaud, P.; Wipff, G. J. Mol. Struct. (THEOCHEM) 1996, 366, 55-63). Reactive flux and thermodynamic integration calculations show that the derived potential model yields predictions for the water exchange rate and free energy of hydration, respectively, that are in agreement with experimental data. The water binding energies, hydration shell structure, and self-diffusion coefficientmore » are also calculated and discussed. Finally, a combination of metadynamics and transition path sampling simulations is employed to probe the mechanisms of water exchange reactions in the first hydration shell of the uranyl ion. These atomistic simulations indicate, based on two-dimensional free energy surfaces, that water exchanges follow an associative interchange mechanism. The nature and structure of the water exchange transition states are also determined. The improved potential model is expected to lead to more accurate predictions of uranyl adsorption energies at mineral surfaces using potential-based molecular dynamics simulations.« less

Cascade debris overlap mechanism of 〈100〉 dislocation loop formation in Fe and FeCr

NASA Astrophysics Data System (ADS)

Granberg, F.; Byggmästar, J.; Sand, A. E.; Nordlund, K.

2017-09-01

Two types of dislocation loops are observed in irradiated α-Fe, the 1/2〈111〉 loop and the 〈100〉 loop. Atomistic simulations consistently predict that only the energetically more favourable 1/2〈111〉 loops are formed directly in cascades, leaving the formation mechanism of 〈100〉 loops an unsolved question. We show how 〈100〉 loops can be formed when cascades overlap with random pre-existing primary radiation damage in Fe and FeCr. This indicates that there are no specific constraints involved in the formation of 〈100〉 loops, and can explain their common occurrence.

Ion Transport via Structural Relaxations in Polymerized Ionic Liquids

NASA Astrophysics Data System (ADS)

Ganesan, Venkat; Mogurampelly, Santosh

We study the mechanisms underlying ion transport in poly(1-butyl-3-vinylimidazolium-hexafluorophosphate) polymer electrolytes. We consider polymer electrolytes of varying polymerized ionic liquid to ionic liquid (polyIL:IL) ratios and use atomistic molecular dynamics (MD) simulations to probe the dynamical and structural characteristics of the electrolyte. Our results reveal that anion diffusion along polymer backbone occurs primarily viathe formation and breaking of ion-pairs involving threepolymerized cationic monomers of twodifferent polymer chains. Moreover, we observe that the ionic diffusivities exhibit a direct correlation with the structural relaxation times of the ion-pairs and hydrogen bonds (H-bonds). These results provide new insights into the mechanisms underlying ion transport in polymerized ionic liquid electrolytes.

Atomistic insights on the nanoscale single grain scratching mechanism of silicon carbide ceramic based on molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Liu, Yao; Li, Beizhi; Kong, Lingfei

2018-03-01

The precision and crack-free surface of brittle silicon carbide (SiC) ceramic was achieved in the nanoscale ductile grinding. However, the nanoscale scratching mechanism and the root causes of SiC ductile response, especially in the atomistic aspects, have not been fully understood yet. In this study, the SiC atomistic scale scratching mechanism was investigated by single diamond grain scratching simulation based on molecular dynamics. The results indicated that the ductile scratching process of SiC could be achieved in the nanoscale depth of cut through the phase transition to an amorphous structure with few hexagonal diamond structure. Furthermore, the silicon atoms in SiC could penetrate into diamond grain which may cause wear of diamond grain. It was further found out that the chip material in the front of grain flowed along the grain side surface to form the groove protrusion as the scratching speed increases. The higher scratching speed promoted more atoms to transfer into the amorphous structure and reduced the hexagonal diamond and dislocation atoms number, which resulted in higher temperature, smaller scratching force, smaller normal stress, and thinner subsurface damage thickness, due to larger speed impaction causing more bonds broken which makes the SiC more ductile.

Protein-Backbone Thermodynamics across the Membrane Interface.

PubMed

Bereau, Tristan; Kremer, Kurt

2016-07-07

The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups.

Multiscale simulations of defect dipole-enhanced electromechanical coupling at dilute defect concentrations

NASA Astrophysics Data System (ADS)

Liu, Shi; Cohen, R. E.

2017-08-01

The role of defects in solids of mixed ionic-covalent bonds such as ferroelectric oxides is complex. Current understanding of defects on ferroelectric properties at the single-defect level remains mostly at the empirical level, and the detailed atomistic mechanisms for many defect-mediated polarization-switching processes have not been convincingly revealed quantum mechanically. We simulate the polarization-electric field (P-E) and strain-electric field (ɛ-E) hysteresis loops for BaTiO3 in the presence of generic defect dipoles with large-scale molecular dynamics and provide a detailed atomistic picture of the defect dipole-enhanced electromechanical coupling. We develop a general first-principles-based atomistic model, enabling a quantitative understanding of the relationship between macroscopic ferroelectric properties and dipolar impurities of different orientations, concentrations, and dipole moments. We find that the collective orientation of dipolar defects relative to the external field is the key microscopic structure feature that strongly affects materials hardening/softening and electromechanical coupling. We show that a small concentration (≈0.1 at. %) of defect dipoles dramatically improves electromechanical responses. This offers the opportunity to improve the performance of inexpensive polycrystalline ferroelectric ceramics through defect dipole engineering for a range of applications including piezoelectric sensors, actuators, and transducers.

In silico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level

PubMed Central

Yang, Changwon; Kulkarni, Mandar; Lim, Manho

2017-01-01

Abstract The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged time scale (10–12 μs) parallel tempering metadynamics (PTMetaD) simulation method in conjunction with a modified version of the AMBER bsc1 force field. For unbiased descriptions of the folding free energy landscape of TBA-15, this force field was minimally modified. From this direct folding simulation using the modified bsc1 force field, reasonably converged free energy landscapes were obtained in K+-rich aqueous solution (150 mM), providing detailed atomistic pictures of GQ folding mechanisms for TBA-15. This study found that the TBA folding occurred via multiple folding pathways with two major free energy barriers of 13 and 15 kcal/mol in the presence of several intermediate states of G-triplex variants. The early formation of these intermediates was associated with a single K+ ion capturing. Interestingly, these intermediate states appear to undergo facile transitions among themselves through relatively small energy barriers. PMID:29112755

Interaction of 〈1 0 0〉 dislocation loops with dislocations studied by dislocation dynamics in α-iron

NASA Astrophysics Data System (ADS)

Shi, X. J.; Dupuy, L.; Devincre, B.; Terentyev, D.; Vincent, L.

2015-05-01

Interstitial dislocation loops with Burgers vector of 〈1 0 0〉 type are formed in α-iron under neutron or heavy ion irradiation. As the density and size of these loops increase with radiation dose and temperature, these defects are thought to play a key role in hardening and subsequent embrittlement of iron-based steels. The aim of the present work is to study the pinning strength of the loops on mobile dislocations. Prior to run massive Dislocation Dynamics (DD) simulations involving experimentally representative array of radiation defects and dislocations, the DD code and its parameterization are validated by comparing the individual loop-dislocation reactions with those obtained from direct atomistic Molecular Dynamics (MD) simulations. Several loop-dislocation reaction mechanisms are successfully reproduced as well as the values of the unpinning stress to detach mobile dislocations from the defects.

Atomistic simulations of shock-induced alloying reactions in Ni /Al nanolaminates

NASA Astrophysics Data System (ADS)

Zhao, Shijin; Germann, Timothy C.; Strachan, Alejandro

2006-10-01

We employ molecular dynamics simulations with a first principles-based many body potential to characterize the exothermic alloying reactions of nanostructured Ni /Al multilayers induced by shock loading. We introduce a novel technique that captures both the initial shock transit as well as the subsequent longer-time-scale Ni3Al alloy formation. Initially, the softer Al layers are shock heated to a higher temperature than the harder Ni layers as a result of a series of shock reflections from the impedance-mismatched interfaces. Once initiated, the highly exothermic alloying reactions can propagate in a self-sustained manner by mass and thermal diffusion. We also characterize the role of voids on the initiation of alloying. The interaction of the shock wave with the voids leads not only to significant local heating (hot spots) but also directly aids the intermixing between Al and Ni; both of these phenomena contribute to a significant acceleration of the alloying reactions.

Atomistic material behavior at extreme pressures

DOE PAGES

Beland, Laurent K.; Osetskiy, Yury N.; Stoller, Roger E.

2016-08-05

Computer simulations are routinely performed to model the response of materials to extreme environments, such as neutron (or ion) irradiation. The latter involves high-energy collisions from which a recoiling atom creates a so-called atomic displacement cascade. These cascades involve coordinated motion of atoms in the form of supersonic shockwaves. These shockwaves are characterized by local atomic pressures >15 GPa and interatomic distances <2 Å. Similar pressures and interatomic distances are observed in other extreme environment, including short-pulse laser ablation, high-impact ballistic collisions and diamond anvil cells. Displacement cascade simulations using four different force fields, with initial kinetic energies ranging frommore » 1 to 40 keV, show that there is a direct relationship between these high-pressure states and stable defect production. An important shortcoming in the modeling of interatomic interactions at these short distances, which in turn determines final defect production, is brought to light.« less

Polymer Architecture Effects in Confined Geometry: Molecular Dynamics Simulation Study

NASA Astrophysics Data System (ADS)

Wijesinghe, Sidath; Perahia, Dvora; Grest, Gary

Luminescent rigid polymers confined into nanoparticles, or polydots, are emerging as a promising tool for nano medicine. The constrained architecture of a rigid backbone trapped in nano-dimensions results in photophysics that differs from that of spontaneously assembled rigid polymers. Incorporating ionizable functionalities in the polymers, often required for therapeutics, impacts the polymer conformation in solution. Here we report fully atomistic molecular dynamics simulations on the structure of dialkyl p-phenylene ethynylene confined into polydots. We find that the structure and thermal stability of polydots are sensitive to both the molecular weight n and the carboxylation fraction f. At room temperature , polydots remain confined regardless of n and f . However, as temperature is increased, polydots with lower n or f rearrange whereas polydots with higher n or fremain confined, though no direct clustering of the ionic groups was observed. NSF CHE 1308298 is acknowledged.

Critical length scale controls adhesive wear mechanisms

PubMed Central

Aghababaei, Ramin; Warner, Derek H.; Molinari, Jean-Francois

2016-01-01

The adhesive wear process remains one of the least understood areas of mechanics. While it has long been established that adhesive wear is a direct result of contacting surface asperities, an agreed upon understanding of how contacting asperities lead to wear debris particle has remained elusive. This has restricted adhesive wear prediction to empirical models with limited transferability. Here we show that discrepant observations and predictions of two distinct adhesive wear mechanisms can be reconciled into a unified framework. Using atomistic simulations with model interatomic potentials, we reveal a transition in the asperity wear mechanism when contact junctions fall below a critical length scale. A simple analytic model is formulated to predict the transition in both the simulation results and experiments. This new understanding may help expand use of computer modelling to explore adhesive wear processes and to advance physics-based wear laws without empirical coefficients. PMID:27264270

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daily, Michael D.; Baer, Marcel D.; Mundy, Christopher J.

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids usingmore » a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical forcefield (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through sidechain-sidechain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described. MDD was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. Research was funded by the Laboratory Directed Research and Development program at Pacific Northwest National Laboratory. MDB acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Material & Engineering. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

NASA Astrophysics Data System (ADS)

Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kiabek

2015-06-01

We consider the ignition of a high-pressure gamma-phase of an explosive crystal of RDX which forms during overdriven shock initiation. Molecular dynamics (MD), with first-principles based or reactive force field based molecular potentials, provides a description of the chemistry as an extremely complex reaction network. The results of the molecular simulation is analyzed by sorting molecular product fragments into high and low molecular groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation, that has a single temperature and stress state for the mixture is used to represent the same RDX material and its chemistry. Each component in the continuum model has a corresponding Gibbs continuum potential, that are in turn inferred from molecular MD informed equation of state libraries such as CHEETAH, or are directly simulated by Monte Carlo MD simulations. Information about transport, kinetic rates and diffusion are derived from the MD simulation and the growth of a reactive hot spot in the RDX is studied with both simulations that mirror the other results to provide an essential, continuum/atomistic link. Supported by N000014-12-1-0555, subaward-36561937 (ONR).

Large scale atomistic simulation of single-layer graphene growth on Ni(111) surface: molecular dynamics simulation based on a new generation of carbon-metal potential

NASA Astrophysics Data System (ADS)

Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng

2015-12-01

To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results.To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06016h

In Silico Determination of Gas Permeabilities by Non-Equilibrium Molecular Dynamics: CO2 and He through PIM-1

PubMed Central

Frentrup, Hendrik; Hart, Kyle E.; Colina, Coray M.; Müller, Erich A.

2015-01-01

We study the permeation dynamics of helium and carbon dioxide through an atomistically detailed model of a polymer of intrinsic microporosity, PIM-1, via non-equilibrium molecular dynamics (NEMD) simulations. This work presents the first explicit molecular modeling of gas permeation through a high free-volume polymer sample, and it demonstrates how permeability and solubility can be obtained coherently from a single simulation. Solubilities in particular can be obtained to a very high degree of confidence and within experimental inaccuracies. Furthermore, the simulations make it possible to obtain very specific information on the diffusion dynamics of penetrant molecules and yield detailed maps of gas occupancy, which are akin to a digital tomographic scan of the polymer network. In addition to determining permeability and solubility directly from NEMD simulations, the results shed light on the permeation mechanism of the penetrant gases, suggesting that the relative openness of the microporous topology promotes the anomalous diffusion of penetrant gases, which entails a deviation from the pore hopping mechanism usually observed in gas diffusion in polymers. PMID:25764366

Direct Prediction of EPR Spectra from Lipid Bilayers: Understanding Structure and Dynamics in Biological Membranes.

PubMed

Catte, Andrea; White, Gaye F; Wilson, Mark R; Oganesyan, Vasily S

2018-06-02

Of the many biophysical techniques now being brought to bear on studies of membranes, electron paramagnetic resonance (EPR) of nitroxide spin probes was the first to provide information about both mobility and ordering in lipid membranes. Here, we report the first prediction of variable temperature EPR spectra of model lipid bilayers in the presence and absence of cholesterol from the results of large scale fully atomistic molecular dynamics (MD) simulations. Three types of structurally different spin probes were employed in order to study different parts of the bilayer. Our results demonstrate very good agreement with experiment and thus confirm the accuracy of the latest lipid force fields. The atomic resolution of the simulations allows the interpretation of the molecular motions and interactions in terms of their impact on the sensitive EPR line shapes. Direct versus indirect effects of cholesterol on the dynamics of spin probes are analysed. Given the complexity of structural organisation in lipid bilayers, the advantage of using a combined MD-EPR simulation approach is two-fold. Firstly, prediction of EPR line shapes directly from MD trajectories of actual phospholipid structures allows unambiguous interpretation of EPR spectra of biological membranes in terms of complex motions. Secondly, such an approach provides an ultimate test bed for the up-to-date MD simulation models employed in the studies of biological membranes, an area that currently attracts great attention. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomistic Simulation of Frictional Sliding Between Cellulose Iß Nanocrystals

Treesearch

Xiawa Wu; Robert J. Moon; Ashlie Martini

2013-01-01

Sliding friction between cellulose Iß nanocrystals is studied using molecular dynamics simulation. The effects of sliding velocity, normal load, and relative angle between sliding surface are predicted, and the results analyzed in terms of the number of hydrogen bonds within and between the cellulose chains. We find that although the observed friction trends can be...

Multi-Scale Simulation of High Energy Density Ionic Liquids

DTIC Science & Technology

2007-06-19

and simulation of ionic liquids (ILs). A polarizable model was developed to simulate ILs more accurately at the atomistic level. A multiscale coarse...propellant, 1- hydroxyethyl-4-amino-1, 2, 4-triazolium nitrate (HEATN), were studied with the all-atom polarizable model. The mechanism suggested for HEATN...with this AFOSR-supported project, a polarizable forcefield for the ionic liquids such as 1-ethyl-3-methylimidazolium nitrate (EMIM*/NO3-) was

Molecular Simulation of the Free Energy for the Accurate Determination of Phase Transition Properties of Molecular Solids

NASA Astrophysics Data System (ADS)

Sellers, Michael; Lisal, Martin; Brennan, John

2015-06-01

Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.

The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian

2015-12-28

We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, butmore » increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.« less

Atomistic modeling of La 3+ doping segregation effect on nanocrystalline yttria-stabilized zirconia

DOE PAGES

Zhang, Shenli; Sha, Haoyan; Castro, Ricardo H. R.; ...

2018-01-01

The effect of La 3+ doping on the structure and ionic conductivity change in nanocrystalline yttria-stabilized zirconia (YSZ) was studied using a combination of Monte Carlo and molecular dynamics simulations.

Nanoscale structure and morphology of sulfonated polyphenylenes via atomistic simulations

DOE PAGES

Abbott, Lauren J.; Frischknecht, Amalie L.

2017-01-23

We performed atomistic simulations on a series of sulfonated polyphenylenes systematically varying the degree of sulfonation and water content to determine their effect on the nanoscale structure, particularly for the hydrophilic domains formed by the ionic groups and water molecules. We found that the local structure around the ionic groups depended on the sulfonation and hydration levels, with the sulfonate groups and hydronium ions less strongly coupled at higher water contents. In addition, we characterized the morphology of the ionic domains employing two complementary clustering algorithms. At low sulfonation and hydration levels, clusters were more elongated in shape and poorlymore » connected throughout the system. As the degree of sulfonation and water content were increased, the clusters became more spherical, and a fully percolated ionic domain was formed. As a result, these structural details have important implications for ion transport.« less

Origin of tension-compression asymmetry in ultrafine-grained fcc metals

NASA Astrophysics Data System (ADS)

Tsuru, T.

2017-08-01

A mechanism of anomalous tension-compression (T-C) asymmetry in ultrafine-grained (UFG) metals is proposed using large-scale atomistic simulations and dislocation theory. Unlike coarse-grained metals, UFG Al exhibits remarkable T-C asymmetry of the yield stress. The atomistic simulations reveal that the yield event is not related to intragranular dislocations but caused by dislocation nucleation from the grain boundaries (GBs). The dislocation core structure associated with the stacking fault energy in Al is strongly affected by the external stress compared with Cu; specifically, high tensile stress stabilizes the dissociation into partial dislocations. These dislocations are more likely to be nucleated from GBs and form deformation twins from an energetic viewpoint. The mechanism, which is different from well-known mechanisms for nanocrystalline and amorphous metals, is unique to high-strength UFG metals and can explain the difference in T-C asymmetry between UFG Cu and Al.

Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

DOE PAGES

Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; ...

2017-01-26

When using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. Furthermore, by calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. A comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnonsmore » leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.« less

Solute-defect interactions in Al-Mg alloys from diffusive variational Gaussian calculations

NASA Astrophysics Data System (ADS)

Dontsova, E.; Rottler, J.; Sinclair, C. W.

2014-11-01

Resolving atomic-scale defect topologies and energetics with accurate atomistic interaction models provides access to the nonlinear phenomena inherent at atomic length and time scales. Coarse graining the dynamics of such simulations to look at the migration of, e.g., solute atoms, while retaining the rich atomic-scale detail required to properly describe defects, is a particular challenge. In this paper, we present an adaptation of the recently developed "diffusive molecular dynamics" model to describe the energetics and kinetics of binary alloys on diffusive time scales. The potential of the technique is illustrated by applying it to the classic problems of solute segregation to a planar boundary (stacking fault) and edge dislocation in the Al-Mg system. Our approach provides fully dynamical solutions in situations with an evolving energy landscape in a computationally efficient way, where atomistic kinetic Monte Carlo simulations are difficult or impractical to perform.

Molecular design and MD simulations of epitaxial superlattice of self-assembling ternary lipid bilayers

NASA Astrophysics Data System (ADS)

Chou, George; Vaughn, Mark; Cheng, K.

2011-10-01

Multicomponent lipid bilayers represent an important model system for studying cell membranes. At present, an ordered multicomponent phospholipid/cholesterol bilayer system involving charged lipid is still not available. Using a lipid superlattice (SL) model, a 13 x 15 x 15 nm^3 ternary phosphatidylcholine/phosphatidylserine/cholesterol bilayer system in water with simultaneous headgroup SL and acyl chain SL at different depths, or epitaxial SL, of the bilayer has been designed with atomistic detail. The arrangements of this epitaxial SL system were optimized by only two molecular parameters, lattice space and rotational angle of the lipids. Using atomistic MD simulations, we demonstrated the stability of the ordered structures for more than 100 ns. A positional restrained system was also used as a control. This system will provide new insights into understanding the nanodomain structures of cell membranes at the molecular level.

Docking 90Sr radionuclide in cement: An atomistic modeling study

NASA Astrophysics Data System (ADS)

Youssef, Mostafa; Pellenq, Roland J.-M.; Yildiz, Bilge

Cementitious materials are considered to be a waste form for the ultimate disposal of radioactive materials in geological repositories. We investigated by means of atomistic simulations the encapsulation of strontium-90, an important radionuclide, in calcium-silicate-hydrate (C-S-H) and its crystalline analog, the 9 Å-tobermorite. C-S-H is the major binding phase of cement. Strontium was shown to energetically favor substituting calcium in the interlayer sites in C-S-H and 9 Å-tobermorite with the trend more pronounced in the latter. The integrity of the silicate chains in both cementitious waste forms were not affected by strontium substitution within the time span of molecular dynamics simulation. Finally, we observed a limited degradation of the mechanical properties in the strontium-containing cementitious waste form with the increasing strontium concentration. These results suggest the cement hydrate as a good candidate for immobilizing radioactive strontium.

Basal-plane dislocations in bilayer graphene - Peculiarities in a quasi-2D material

NASA Astrophysics Data System (ADS)

Butz, Benjamin

2015-03-01

Dislocations represent one of the most fascinating and fundamental concepts in materials science. First and foremost, they are the main carriers of plastic deformation in crystalline materials. Furthermore, they can strongly alter the local electronic or optical properties of semiconductors and ionic crystals. In layered crystals like graphite dislocation movement is restricted to the basal plane. Thus, those basal-plane dislocations cannot escape enabling their confinement in between only two atomic layers of the material. So-called bilayer graphene is the thinnest imaginable quasi-2D crystal to explore the nature and behavior of dislocations under such extreme boundary conditions. Robust graphene membranes derived from epitaxial graphene on SiC provide an ideal platform for their investigation. The presentation will give an insight in the direct observation of basal-plane partial dislocations by transmission electron microscopy and their detailed investigation by diffraction contrast analysis and atomistic simulations. The investigation reveals striking size effects. First, the absence of stacking fault energy, a unique property of bilayer graphene, leads to a characteristic dislocation pattern, which corresponds to an alternating AB <--> BA change of the stacking order. Most importantly, our experiments in combination with atomistic simulations reveal a pronounced buckling of the bilayer graphene membrane, which directly results from accommodation of strain. In fact, the buckling completely changes the strain state of the bilayer graphene and is of key importance for its electronic/spin transport properties. Due to the high degree of disorder in our quasi-2D material it is one of the very few examples for a perfect linear magnetoresistance, i.e. the linear dependency of the in-plane electrical resistance on a magnetic field applied perpendicular to the graphene sheet up to field strengths of more than 60 T. This research is financed by the German Research Foundation through the SFB 953 ``Synthetic Carbon Allotropes.''

Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

PubMed

Buchner, Ginka S; Murphy, Ronan D; Buchete, Nicolae-Viorel; Kubelka, Jan

2011-08-01

The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at multiple levels, from atomistic to coarse-grained representations. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches. Copyright © 2010 Elsevier B.V. All rights reserved.

Coarse-Grained Models for Protein-Cell Membrane Interactions

PubMed Central

Bradley, Ryan; Radhakrishnan, Ravi

2015-01-01

The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes. PMID:26613047

Computational modeling and simulation of spall fracture in polycrystalline solids by an atomistic-based interfacial zone model

PubMed Central

Lin, Liqiang; Zeng, Xiaowei

2015-01-01

The focus of this work is to investigate spall fracture in polycrystalline materials under high-speed impact loading by using an atomistic-based interfacial zone model. We illustrate that for polycrystalline materials, increases in the potential energy ratio between grain boundaries and grains could cause a fracture transition from intergranular to transgranular mode. We also found out that the spall strength increases when there is a fracture transition from intergranular to transgranular. In addition, analysis of grain size, crystal lattice orientation and impact speed reveals that the spall strength increases as grain size or impact speed increases. PMID:26435546

Strain field determination in III-V heteroepitaxy coupling finite elements with experimental and theoretical techniques at the nanoscale

NASA Astrophysics Data System (ADS)

Florini, Nikoletta; Dimitrakopulos, George P.; Kioseoglou, Joseph; Pelekanos, Nikos T.; Kehagias, Thomas

2017-04-01

We are briefly reviewing the current status of elastic strain field determination in III-V heteroepitaxial nanostructures, linking finite elements (FE) calculations with quantitative nanoscale imaging and atomistic calculation techniques. III-V semiconductor nanostructure systems of various dimensions are evaluated in terms of their importance in photonic and microelectronic devices. As elastic strain distribution inside nano-heterostructures has a significant impact on the alloy composition, and thus their electronic properties, it is important to accurately map its components both at the interface plane and along the growth direction. Therefore, we focus on the determination of the stress-strain fields in III-V heteroepitaxial nanostructures by experimental and theoretical methods with emphasis on the numerical FE method by means of anisotropic continuum elasticity (CE) approximation. Subsequently, we present our contribution to the field by coupling FE simulations on InAs quantum dots (QDs) grown on (211)B GaAs substrate, either uncapped or buried, and GaAs/AlGaAs core-shell nanowires (NWs) grown on (111) Si, with quantitative high-resolution transmission electron microscopy (HRTEM) methods and atomistic molecular dynamics (MD) calculations. Full determination of the elastic strain distribution can be exploited for band gap tailoring of the heterostructures by controlling the content of the active elements, and thus influence the emitted radiation.

High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.

PubMed

Haxton, Thomas K

2015-03-10

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are accurately approximated by their average values, while retaining soft degrees of freedom (unconstrained dihedral angles) mostly responsible for conformational variability. We demonstrate that our scheme retains nearly atomistic resolution by mapping all experimental protein configurations in the Protein Data Bank onto coarse-grained configurations and then analytically backmapping those configurations back to all-atom configurations. This roundtrip mapping throws away all information associated with the eliminated (stiff) degrees of freedom except for their average values, which we use to construct optimal backmapping functions. Despite the 4:1 reduction in the number of degrees of freedom, we find that heavy atoms move only 0.051 Å on average during the roundtrip mapping, while hydrogens move 0.179 Å on average, an unprecedented combination of efficiency and accuracy among coarse-grained protein models. We discuss the advantages of such a high-resolution model for parametrizing effective interactions and accurately calculating observables through direct or multiscale simulations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yadav, Satyesh Kumar; Shao, S.; Chen, Youxing

Here, using a newly developed embedded-atom-method potential for Mg–Nb, the semi-coherent Mg/Nb interface with the Kurdjumov–Sachs orientation relationship is studied. Atomistic simulations have been carried out to understand the shear strength of the interface, as well as the interaction between lattice glide dislocations and the interface. The interface shear mechanisms are dependent on the shear loading directions, through either interface sliding between Mg and Nb atomic layers or nucleation and gliding of Shockley partial dislocations in between the first two atomic planes in Mg at the interface. The shear strength for the Mg/Nb interface is found to be generally high,more » in the range of 0.9–1.3 GPa depending on the shear direction. As a consequence, the extents of dislocation core spread into the interface are considerably small, especially when compared to the case of other “weak” interfaces such as the Cu/Nb interface.« less

Opposite correlations between cation disordering and amorphization resistance in spinels versus pyrochlores

PubMed Central

Uberuaga, Blas Pedro; Tang, Ming; Jiang, Chao; Valdez, James A.; Smith, Roger; Wang, Yongqiang; Sickafus, Kurt E.

2015-01-01

Understanding and predicting radiation damage evolution in complex materials is crucial for developing next-generation nuclear energy sources. Here, using a combination of ion beam irradiation, transmission electron microscopy and X-ray diffraction, we show that, contrary to the behaviour observed in pyrochlores, the amorphization resistance of spinel compounds correlates directly with the energy to disorder the structure. Using a combination of atomistic simulation techniques, we ascribe this behaviour to structural defects on the cation sublattice that are present in spinel but not in pyrochlore. Specifically, because of these structural defects, there are kinetic pathways for the relaxation of disorder in spinel that are absent in pyrochlore. This leads to a direct correlation between amorphization resistance and disordering energetics in spinel, the opposite of that observed in pyrochlores. These results provide new insight into the origins of amorphization resistance in complex oxides beyond fluorite derivatives. PMID:26510750

Characterizing the boundary lateral to the shear direction of deformation twins in magnesium

DOE PAGES

Liu, Y.; Li, N.; Shao, S.; ...

2016-06-01

The three-dimensional nature of twins, especially the atomic structures and motion mechanisms of the boundary lateral to the shear direction of the twin, has never been characterized at the atomic level, because such boundary is, in principle, crystallographically unobservable. We thus refer to it here as the dark side of the twin. Here, using high-resolution transmission electron microscopy and atomistic simulations, we characterize the dark side of {101 ⁻2} deformation twins in magnesium. It is found that the dark side is serrated and comprised of {101 ⁻2} coherent twin boundaries and semi-coherent twist prismatic–prismatic {211 ⁻0} boundaries that control twinmore » growth. The conclusions we find in this work apply to the same twin mode in other hexagonal close-packed materials, and the conceptual ideas discussed here should hold for all twin modes in crystalline materials.« less

Opposite correlations between cation disordering and amorphization resistance in spinels versus pyrochlores

DOE PAGES

Uberuaga, Blas Pedro; Tang, Ming; Jiang, Chao; ...

2015-10-29

Understanding and predicting radiation damage evolution in complex materials is crucial for developing next-generation nuclear energy sources. Here, using a combination of ion beam irradiation, transmission electron microscopy and X-ray diffraction, we show that, contrary to the behaviour observed in pyrochlores, the amorphization resistance of spinel compounds correlates directly with the energy to disorder the structure. Using a combination of atomistic simulation techniques, we ascribe this behaviour to structural defects on the cation sublattice that are present in spinel but not in pyrochlore. Specifically, because of these structural defects, there are kinetic pathways for the relaxation of disorder in spinelmore » that are absent in pyrochlore. This leads to a direct correlation between amorphization resistance and disordering energetics in spinel, the opposite of that observed in pyrochlores. Furthermore, these results provide new insight into the origins of amorphization resistance in complex oxides beyond fluorite derivatives.« less

Opposite correlations between cation disordering and amorphization resistance in spinels versus pyrochlores.

PubMed

Uberuaga, Blas Pedro; Tang, Ming; Jiang, Chao; Valdez, James A; Smith, Roger; Wang, Yongqiang; Sickafus, Kurt E

2015-10-29

Understanding and predicting radiation damage evolution in complex materials is crucial for developing next-generation nuclear energy sources. Here, using a combination of ion beam irradiation, transmission electron microscopy and X-ray diffraction, we show that, contrary to the behaviour observed in pyrochlores, the amorphization resistance of spinel compounds correlates directly with the energy to disorder the structure. Using a combination of atomistic simulation techniques, we ascribe this behaviour to structural defects on the cation sublattice that are present in spinel but not in pyrochlore. Specifically, because of these structural defects, there are kinetic pathways for the relaxation of disorder in spinel that are absent in pyrochlore. This leads to a direct correlation between amorphization resistance and disordering energetics in spinel, the opposite of that observed in pyrochlores. These results provide new insight into the origins of amorphization resistance in complex oxides beyond fluorite derivatives.

Free-Energy Landscape of the Dissolution of Gibbsite at High pH.

PubMed

Shen, Zhizhang; Kerisit, Sebastien N; Stack, Andrew G; Rosso, Kevin M

2018-04-05

The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of direct experimental probes. In this regard, we have applied atomistic simulations to map the free-energy landscape of the dissolution of gibbsite from a step edge as a model of metal hydroxide dissolution. The overall reaction combines kink formation and kink propagation. Two individual reactions were found to be rate-limiting for kink formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sites into the solution. As a result, a pool of mobile and labile adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, our results will enable the development of microscopic mechanistic models of metal oxide dissolution.

Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex

PubMed Central

Bian, Yunqiang; Tan, Cheng; Wang, Jun; Sheng, Yuebiao; Zhang, Jian; Wang, Wei

2014-01-01

In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and ions explicitly modeled. Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations, the free energy landscape of this G-DNA was obtained for the first time and four folding intermediates were identified, including a triplex and a basically formed quadruplex. The simulations also provided atomistic pictures for the structures and cation binding patterns of the intermediates. The results showed that the structure formation and cation binding are cooperative and mutually supporting each other. The syn/anti reorientation dynamics of the intermediates was also investigated. It was found that the nucleotides usually take correct syn/anti configurations when they form native and stable hydrogen bonds with the others, while fluctuating between two configurations when they do not. Misfolded intermediates with wrong syn/anti configurations were observed in the early intermediates but not in the later ones. Based on the simulations, we also discussed the roles of the non-native interactions. Besides, the formation process of the parallel conformation in the first two G-repeats and the associated reversal loop were studied. Based on the above results, we proposed a folding pathway for the hybrid-1 type G-quadruplex with atomistic details, which is new and more complete compared with previous ones. The knowledge gained for this type of G-DNA may provide a general insight for the folding of the other G-quadruplexes. PMID:24722458

Thermal conductance of Teflon and Polyethylene: Insight from an atomistic, single-molecule level

PubMed Central

Buerkle, Marius; Asai, Yoshihiro

2017-01-01

The thermal transport properties of teflon (polytetrafluoroethylene) and its polyethylene counterparts are, while highly desirable and widely used, only superficially understood. Here, we aim therefore to provide rigorous insight from an atomistic point of view in context of single-molecule devices. We show that for vinyl polymers adsorbed on metal-surfaces the thermal transport strongly depends on the properties of the metal-molecule interface and that the reduced thermal conductance observed for teflon derivatives originates in a reduced phonon injection life time. In asymmetric molecules phonon blocking on the intra molecular interface leads to a further reduction of thermal conductance. For hetrojunctions with different electrode materials we find that thermal conductance is suppressed due to a reduced overlap of the available phonon modes in the different electrodes. A detailed atomistic picture is thereby provided by studying the transport through perfluorooctane and octane on a single-molecule level using first principles transport calculations and nonequilibrium molecular dynamic simulations. PMID:28150738

Spontaneous Athermal Cross-Slip Nucleation at Screw Dislocation Intersections in FCC Metals and L1(2) Intermetallics Investigated via Atomistic Simulations

DTIC Science & Technology

2013-01-01

LAMMPS [12], developed at Sandia National Labora- tory. The simulation cell is a rectangular parallelepiped having the x-axis oriented along the [1 1 0...cross-slip during deformation. Acknowledgements The authors acknowledge use of the 3d molecular dynamics code, LAMMPS , which was developed at Sandia

Atomic scale simulations for improved CRUD and fuel performance modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersson, Anders David Ragnar; Cooper, Michael William Donald

2017-01-06

A more mechanistic description of fuel performance codes can be achieved by deriving models and parameters from atomistic scale simulations rather than fitting models empirically to experimental data. The same argument applies to modeling deposition of corrosion products on fuel rods (CRUD). Here are some results from publications in 2016 carried out using the CASL allocation at LANL.

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

PubMed

Reshetnikov, Roman V; Sponer, Jiri; Rassokhina, Olga I; Kopylov, Alexei M; Tsvetkov, Philipp O; Makarov, Alexander A; Golovin, Andrey V

2011-12-01

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. © The Author(s) 2011. Published by Oxford University Press.

Pressure control in interfacial systems: Atomistic simulations of vapor nucleation

NASA Astrophysics Data System (ADS)

Marchio, S.; Meloni, S.; Giacomello, A.; Valeriani, C.; Casciola, C. M.

2018-02-01

A large number of phenomena of scientific and technological interest involve multiple phases and occur at constant pressure of one of the two phases, e.g., the liquid phase in vapor nucleation. It is therefore of great interest to be able to reproduce such conditions in atomistic simulations. Here we study how popular barostats, originally devised for homogeneous systems, behave when applied straightforwardly to heterogeneous systems. We focus on vapor nucleation from a super-heated Lennard-Jones liquid, studied via hybrid restrained Monte Carlo simulations. The results show a departure from the trends predicted for the case of constant liquid pressure, i.e., from the conditions of classical nucleation theory. Artifacts deriving from standard (global) barostats are shown to depend on the size of the simulation box. In particular, for Lennard-Jones liquid systems of 7000 and 13 500 atoms, at conditions typically found in the literature, we have estimated an error of 10-15 kBT on the free-energy barrier, corresponding to an error of 104-106 s-1σ-3 on the nucleation rate. A mechanical (local) barostat is proposed which heals the artifacts for the considered case of vapor nucleation.

Multipolar electrostatics.

PubMed

Cardamone, Salvatore; Hughes, Timothy J; Popelier, Paul L A

2014-06-14

Atomistic simulation of chemical systems is currently limited by the elementary description of electrostatics that atomic point-charges offer. Unfortunately, a model of one point-charge for each atom fails to capture the anisotropic nature of electronic features such as lone pairs or π-systems. Higher order electrostatic terms, such as those offered by a multipole moment expansion, naturally recover these important electronic features. The question remains as to why such a description has not yet been widely adopted by popular molecular mechanics force fields. There are two widely-held misconceptions about the more rigorous formalism of multipolar electrostatics: (1) Accuracy: the implementation of multipole moments, compared to point-charges, offers little to no advantage in terms of an accurate representation of a system's energetics, structure and dynamics. (2) Efficiency: atomistic simulation using multipole moments is computationally prohibitive compared to simulation using point-charges. Whilst the second of these may have found some basis when computational power was a limiting factor, the first has no theoretical grounding. In the current work, we disprove the two statements above and systematically demonstrate that multipole moments are not discredited by either. We hope that this perspective will help in catalysing the transition to more realistic electrostatic modelling, to be adopted by popular molecular simulation software.

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

PubMed Central

Reshetnikov, Roman V.; Sponer, Jiri; Rassokhina, Olga I.; Kopylov, Alexei M.; Tsvetkov, Philipp O.; Makarov, Alexander A.; Golovin, Andrey V.

2011-01-01

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. PMID:21893589

Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations

PubMed Central

Baumketner, Andrij; Nesmelov, Yuri

2011-01-01

The recovery stroke is a key step in the functional cycle of muscle motor protein myosin, during which pre-recovery conformation of the protein is changed into the active post-recovery conformation, ready to exersice force. We study the microscopic details of this transition using molecular dynamics simulations of atomistic models in implicit and explicit solvent. In more than 2 μs of aggregate simulation time, we uncover evidence that the recovery stroke is a two-step process consisting of two stages separated by a time delay. In our simulations, we directly observe the first stage at which switch II loop closes in the presence of adenosine triphosphate at the nucleotide binding site. The resulting configuration of the nucleotide binding site is identical to that detected experimentally. Distribution of inter-residue distances measured in the force generating region of myosin is in good agreement with the experimental data. The second stage of the recovery stroke structural transition, rotation of the converter domain, was not observed in our simulations. Apparently it occurs on a longer time scale. We suggest that the two parts of the recovery stroke need to be studied using separate computational models. PMID:21922589

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

PubMed Central

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-01-01

We studied the microsecond folding dynamics of three β hairpins (Trp zippers 1–3, TZ1–TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1–TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations. PMID:15020773

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-03-01

We studied the microsecond folding dynamics of three hairpins (Trp zippers 1-3, TZ1-TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1-TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations.

Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations.

PubMed

Stock, Philipp; Monroe, Jacob I; Utzig, Thomas; Smith, David J; Shell, M Scott; Valtiner, Markus

2017-03-28

Interactions between hydrophobic moieties steer ubiquitous processes in aqueous media, including the self-organization of biologic matter. Recent decades have seen tremendous progress in understanding these for macroscopic hydrophobic interfaces. Yet, it is still a challenge to experimentally measure hydrophobic interactions (HIs) at the single-molecule scale and thus to compare with theory. Here, we present a combined experimental-simulation approach to directly measure and quantify the sequence dependence and additivity of HIs in peptide systems at the single-molecule scale. We combine dynamic single-molecule force spectroscopy on model peptides with fully atomistic, both equilibrium and nonequilibrium, molecular dynamics (MD) simulations of the same systems. Specifically, we mutate a flexible (GS) 5 peptide scaffold with increasing numbers of hydrophobic leucine monomers and measure the peptides' desorption from hydrophobic self-assembled monolayer surfaces. Based on the analysis of nonequilibrium work-trajectories, we measure an interaction free energy that scales linearly with 3.0-3.4 k B T per leucine. In good agreement, simulations indicate a similar trend with 2.1 k B T per leucine, while also providing a detailed molecular view into HIs. This approach potentially provides a roadmap for directly extracting qualitative and quantitative single-molecule interactions at solid/liquid interfaces in a wide range of fields, including interactions at biointerfaces and adhesive interactions in industrial applications.

Atomistic simulations of dislocation dynamics in δ-Pu-Ga alloys

NASA Astrophysics Data System (ADS)

Karavaev, A. V.; Dremov, V. V.; Ionov, G. V.

2017-12-01

Molecular dynamics with the modified embedded atom model (MEAM) for interatomic interaction is applied to direct simulations of dislocation dynamics in fcc δ-phase Pu-Ga alloys. First, parameters of the MEAM potential are fitted to accurately reproduce experimental phonon dispersion curves and phonon density of states at ambient conditions. Then the stress-velocity dependence for edge dislocations as well as Pierls stress are obtained in direct MD modeling of dislocation motion using the shear stress relaxation technique. The simulations are performed for different gallium concentrations and the dependence of static yield stress on Ga concentration derived demonstrates good agreement with experimental data. Finally, the influence of radiation defects (primary radiation defects, nano-pores, and radiogenic helium bubbles) on dislocation dynamics is investigated. It is demonstrated that uniformly distributed vacancies and nano-pores have little effect on dislocation dynamics in comparison with that of helium bubbles. The results of the MD simulations evidence that the accumulation of the radiogenic helium in the form of nanometer-sized bubbles is the main factor affecting strength properties during long-term storage. The calculated dependence of static yield stress on helium bubbles concentration for fcc Pu 1 wt .% Ga is in good agreement with that obtained in experiments on accelerated aging. The developed technique of static yield stress evaluation is applicable to δ-phase Pu-Ga alloys with arbitrary Ga concentrations.

Using Molecular Dynamics to quantify the electrical double layer and examine the potential for its direct observation in the in-situ TEM

DOE PAGES

Welch, David A.; Mehdi, Beata L.; Hatchell, Hanna J.; ...

2015-03-25

Understanding the fundamental processes taking place at the electrode-electrolyte interface in batteries will play a key role in the development of next generation energy storage technologies. One of the most fundamental aspects of the electrode-electrolyte interface is the electrical double layer (EDL). Given the recent development of high spatial resolution in-situ electrochemical cells for scanning transmission electron microscopy (STEM), there now exists the possibility that we can directly observe the formation and dynamics of the EDL. In this paper we predict electrolyte structure within the EDL using classical models and atomistic Molecular Dynamics (MD) simulations. The MD simulations show thatmore » the classical models fail to accurately reproduce concentration profiles that exist within the electrolyte. It is thus suggested that MD must be used in order to accurately predict STEM images of the electrode-electrolyte interface. Using MD and image simulations together for a high contrast electrolyte (the high atomic number CsCl electrolyte), it is determined that, for a smooth interface, concentration profiles within the EDL should be visible experimentally. When normal experimental parameters such as rough interfaces and low-Z electrolytes (like those used in Li-ion batteries) are considered, observation of the EDL appears to be more difficult.« less

Proposed correlation of structure network inherited from producing techniques and deformation behavior for Ni-Ti-Mo metallic glasses via atomistic simulations

PubMed Central

Yang, M. H.; Li, J. H.; Liu, B. X.

2016-01-01

Based on the newly constructed n-body potential of Ni-Ti-Mo system, Molecular Dynamics and Monte Carlo simulations predict an energetically favored glass formation region and an optimal composition sub-region with the highest glass-forming ability. In order to compare the producing techniques between liquid melt quenching (LMQ) and solid-state amorphization (SSA), inherent hierarchical structure and its effect on mechanical property were clarified via atomistic simulations. It is revealed that both producing techniques exhibit no pronounced differences in the local atomic structure and mechanical behavior, while the LMQ method makes a relatively more ordered structure and a higher intrinsic strength. Meanwhile, it is found that the dominant short-order clusters of Ni-Ti-Mo metallic glasses obtained by LMQ and SSA are similar. By analyzing the structural evolution upon uniaxial tensile deformation, it is concluded that the gradual collapse of the spatial structure network is intimately correlated to the mechanical response of metallic glasses and acts as a structural signature of the initiation and propagation of shear bands. PMID:27418115

Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule.

PubMed

Mandal, Taraknath; Marson, Ryan L; Larson, Ronald G

2016-10-04

We describe a systematic coarse-graining method to study crystallization and predict possible polymorphs of small organic molecules. In this method, a coarse-grained (CG) force field is obtained by inverse-Boltzmann iteration from the radial distribution function of atomistic simulations of the known crystal. With the force field obtained by this method, we show that CG simulations of the drug phenytoin predict growth of a crystalline slab from a melt of phenytoin, allowing determination of the fastest-growing surface, as well as giving the correct lattice parameters and crystal morphology. By applying meta-dynamics to the coarse-grained model, a new crystalline form of phenytoin (monoclinic, space group P2 1 ) was predicted which is different from the experimentally known crystal structure (orthorhombic, space group Pna2 1 ). Atomistic simulations and quantum calculations then showed the polymorph to be meta-stable at ambient temperature and pressure, and thermodynamically more stable than the conventional orthorhombic crystal at high pressure. The results suggest an efficient route to study crystal growth of small organic molecules that could also be useful for identification of possible polymorphs as well.

Lattice Thermal Conductivity of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2 from Atomistic Simulations

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success.

PubMed

Xiao, Xingqing; Agris, Paul F; Hall, Carol K

2016-05-01

A computational strategy that integrates our peptide search algorithm with atomistic molecular dynamics simulation was used to design rational peptide drugs that recognize and bind to the anticodon stem and loop domain (ASL(Lys3)) of human tRNAUUULys3 for the purpose of interrupting HIV replication. The score function of the search algorithm was improved by adding a peptide stability term weighted by an adjustable factor λ to the peptide binding free energy. The five best peptide sequences associated with five different values of λ were determined using the search algorithm and then input in atomistic simulations to examine the stability of the peptides' folded conformations and their ability to bind to ASL(Lys3). Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASL(Lys3). Thus, addition of a peptide stability term significantly improves the success rate for our peptide design search. © 2016 Wiley Periodicals, Inc.

Atomistic simulation of flow-induced crystallization at constant temperature

NASA Astrophysics Data System (ADS)

Baig, C.; Edwards, B. J.

2010-02-01

Semi-crystalline fibers, such as nylon, orlon, and spectra, play a crucial role in modern society in applications including clothing, medical devices, and aerospace technology. These applications rely on the enhanced properties that are generated in these fibers through the orientation and deformation of the constituent molecules of a molten liquid undergoing flow prior to crystallization; however, the atomistic mechanisms of flow-induced crystallization are not understood, and macroscopic theories that have been developed in the past to describe this behavior are semi-empirical. We present here the results of the first successful simulation of flow-induced crystallization at constant temperature using a nonequilibrium Monte Carlo algorithm for a short-chain polyethylene liquid. A phase transition between the liquid and crystalline phases was observed at a critical flow rate in elongational flow. The simulation results quantitatively matched experimental X-ray diffraction data of the crystalline phase. Examination of the configurational temperature generated under flow confirmed for the first time the hypothesis that flow-induced stresses within the liquid effectively raised the crystallization temperature of the liquid.

Ion beam nanopatterning of III-V semiconductors: Consistency of experimental and simulation trends within a chemistry-driven theory

DOE PAGES

El-Atwani, O.; Norris, S. A.; Ludwig, K.; ...

2015-12-16

In this study, several proposed mechanisms and theoretical models exist concerning nanostructure evolution on III-V semiconductors (particularly GaSb) via ion beam irradiation. However, making quantitative contact between experiment on the one hand and model-parameter dependent predictions from different theories on the other is usually difficult. In this study, we take a different approach and provide an experimental investigation with a range of targets (GaSb, GaAs, GaP) and ion species (Ne, Ar, Kr, Xe) to determine new parametric trends regarding nanostructure evolution. Concurrently, atomistic simulations using binary collision approximation over the same ion/target combinations were performed to determine parametric trends onmore » several quantities related to existing model. A comparison of experimental and numerical trends reveals that the two are broadly consistent under the assumption that instabilities are driven by chemical instability based on phase separation. Furthermore, the atomistic simulations and a survey of material thermodynamic properties suggest that a plausible microscopic mechanism for this process is an ion-enhanced mobility associated with energy deposition by collision cascades.« less

Shock Simulations of Single-Site Coarse-Grain RDX using the Dissipative Particle Dynamics Method with Reactivity

NASA Astrophysics Data System (ADS)

Sellers, Michael; Lisal, Martin; Schweigert, Igor; Larentzos, James; Brennan, John

2015-06-01

In discrete particle simulations, when an atomistic model is coarse-grained, a trade-off is made: a boost in computational speed for a reduction in accuracy. Dissipative Particle Dynamics (DPD) methods help to recover accuracy in viscous and thermal properties, while giving back a small amount of computational speed. One of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. Today, pairing the current evolution of DPD-RX with a coarse-grained potential and its chemical decomposition reactions allows for the simulation of the shock behavior of energetic materials at a timescale faster than an atomistic counterpart. In 2007, Maillet et al. introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We have recently extended the DPD-RX method and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its tranition to hot product gases within DPD-RX will be presented. Additionally, examples of the effect of microstructure on shock behavior will be shown. Approved for public release. Distribution is unlimited.

Components for Atomistic-to-Continuum Multiscale Modeling of Flow in Micro- and Nanofluidic Systems

DOE PAGES

Adalsteinsson, Helgi; Debusschere, Bert J.; Long, Kevin R.; ...

2008-01-01

Micro- and nanofluidics pose a series of significant challenges for science-based modeling. Key among those are the wide separation of length- and timescales between interface phenomena and bulk flow and the spatially heterogeneous solution properties near solid-liquid interfaces. It is not uncommon for characteristic scales in these systems to span nine orders of magnitude from the atomic motions in particle dynamics up to evolution of mass transport at the macroscale level, making explicit particle models intractable for all but the simplest systems. Recently, atomistic-to-continuum (A2C) multiscale simulations have gained a lot of interest as an approach to rigorously handle particle-levelmore » dynamics while also tracking evolution of large-scale macroscale behavior. While these methods are clearly not applicable to all classes of simulations, they are finding traction in systems in which tight-binding, and physically important, dynamics at system interfaces have complex effects on the slower-evolving large-scale evolution of the surrounding medium. These conditions allow decomposition of the simulation into discrete domains, either spatially or temporally. In this paper, we describe how features of domain decomposed simulation systems can be harnessed to yield flexible and efficient software for multiscale simulations of electric field-driven micro- and nanofluidics.« less

Continuous modeling of a grain boundary in MgO and its disclination induced grain-boundary migration mechanism

NASA Astrophysics Data System (ADS)

Cordier, P.; Sun, X.; Taupin, V.; Fressengeas, C.

2016-12-01

Grain boundaries (GBs) are thin material layers where the lattice rotates from one orientation to the next one within a few nanometers. Because they treat these layers as infinitely thin interfaces, large-scale polycrystalline representations fail to describe their structure. Conversely, atomistic representations provide a detailed description of the GBs, but their character remains discrete and not prone to coarse-graining procedures. Continuum descriptions based on kinematic and crystal defect fields defined at interatomic scale are appealing because they can provide smooth and thorough descriptions of GBs, recovering in some sense the atomistic description and potentially serving as a basis for coarse-grained polycrystalline representations. In this work, a crossover between atomistic description and continuous representation of a MgO tilt boundary in polycrystals is set-up to model the periodic arrays of structural units by using dislocation and disclination dipole arrays along GBs. The strain, rotation, curvature, disclination and dislocation density fields are determined in the boundary area by using the discrete atomic positions generated by molecular dynamics simulations. Then, this continuous disclination/dislocation model is used as part of the initial conditions in elasto-plastic continuum mechanics simulations to investigate the shear-coupled boundary migration of tilt boundaries. The present study leads to better understanding of the structure and mechanical architecture of grain boundaries.

Parallel algorithm for multiscale atomistic/continuum simulations using LAMMPS

NASA Astrophysics Data System (ADS)

Pavia, F.; Curtin, W. A.

2015-07-01

Deformation and fracture processes in engineering materials often require simultaneous descriptions over a range of length and time scales, with each scale using a different computational technique. Here we present a high-performance parallel 3D computing framework for executing large multiscale studies that couple an atomic domain, modeled using molecular dynamics and a continuum domain, modeled using explicit finite elements. We use the robust Coupled Atomistic/Discrete-Dislocation (CADD) displacement-coupling method, but without the transfer of dislocations between atoms and continuum. The main purpose of the work is to provide a multiscale implementation within an existing large-scale parallel molecular dynamics code (LAMMPS) that enables use of all the tools associated with this popular open-source code, while extending CADD-type coupling to 3D. Validation of the implementation includes the demonstration of (i) stability in finite-temperature dynamics using Langevin dynamics, (ii) elimination of wave reflections due to large dynamic events occurring in the MD region and (iii) the absence of spurious forces acting on dislocations due to the MD/FE coupling, for dislocations further than 10 Å from the coupling boundary. A first non-trivial example application of dislocation glide and bowing around obstacles is shown, for dislocation lengths of ∼50 nm using fewer than 1 000 000 atoms but reproducing results of extremely large atomistic simulations at much lower computational cost.

Detonation initiation in a model of explosive: Comparative atomistic and hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Murzov, S. A.; Sergeev, O. V.; Dyachkov, S. A.; Egorova, M. S.; Parshikov, A. N.; Zhakhovsky, V. V.

2016-11-01

Here we extend consistent simulations to reactive materials by the example of AB model explosive. The kinetic model of chemical reactions observed in a molecular dynamics (MD) simulation of self-sustained detonation wave can be used in hydrodynamic simulation of detonation initiation. Kinetic coefficients are obtained by minimization of difference between profiles of species calculated from the kinetic model and observed in MD simulations of isochoric thermal decomposition with a help of downhill simplex method combined with random walk in multidimensional space of fitting kinetic model parameters.

Simulation of the optical coating deposition

NASA Astrophysics Data System (ADS)

Grigoriev, Fedor; Sulimov, Vladimir; Tikhonravov, Alexander

2018-04-01

A brief review of the mathematical methods of thin-film growth simulation and results of their applications is presented. Both full-atomistic and multi-scale approaches that were used in the studies of thin-film deposition are considered. The results of the structural parameter simulation including density profiles, roughness, porosity, point defect concentration, and others are discussed. The application of the quantum level methods to the simulation of the thin-film electronic and optical properties is considered. Special attention is paid to the simulation of the silicon dioxide thin films.

All-atom Simulation of Amyloid Aggregates

NASA Astrophysics Data System (ADS)

Berhanu, Workalemahu M.; Alred, Erik J.; Bernhardt, Nathan A.; Hansmann, Ulrich H. E.

Molecular simulations are now commonly used to complement experiments in the investigation of amyloid formation and their role in human diseases. While various simulations based on enhanced sampling techniques are used in amyloid formation simulations, this article will focus on those using standard atomistic simulations to evaluate the stability of fibril models. Such studies explore the limitations that arise from the choice of force field or polymorphism; and explore the stability of in vivo and in vitro forms of Aβ fibril aggregates, and the role of heterologous seeding as a link between different amyloid diseases.

A Fast Algorithm for Massively Parallel, Long-Term, Simulation of Complex Molecular Dynamics Systems

NASA Technical Reports Server (NTRS)

Jaramillo-Botero, Andres; Goddard, William A, III; Fijany, Amir

1997-01-01

The advances in theory and computing technology over the last decade have led to enormous progress in applying atomistic molecular dynamics (MD) methods to the characterization, prediction, and design of chemical, biological, and material systems,.

Computer Science Techniques Applied to Parallel Atomistic Simulation

NASA Astrophysics Data System (ADS)

Nakano, Aiichiro

1998-03-01

Recent developments in parallel processing technology and multiresolution numerical algorithms have established large-scale molecular dynamics (MD) simulations as a new research mode for studying materials phenomena such as fracture. However, this requires large system sizes and long simulated times. We have developed: i) Space-time multiresolution schemes; ii) fuzzy-clustering approach to hierarchical dynamics; iii) wavelet-based adaptive curvilinear-coordinate load balancing; iv) multilevel preconditioned conjugate gradient method; and v) spacefilling-curve-based data compression for parallel I/O. Using these techniques, million-atom parallel MD simulations are performed for the oxidation dynamics of nanocrystalline Al. The simulations take into account the effect of dynamic charge transfer between Al and O using the electronegativity equalization scheme. The resulting long-range Coulomb interaction is calculated efficiently with the fast multipole method. Results for temperature and charge distributions, residual stresses, bond lengths and bond angles, and diffusivities of Al and O will be presented. The oxidation of nanocrystalline Al is elucidated through immersive visualization in virtual environments. A unique dual-degree education program at Louisiana State University will also be discussed in which students can obtain a Ph.D. in Physics & Astronomy and a M.S. from the Department of Computer Science in five years. This program fosters interdisciplinary research activities for interfacing High Performance Computing and Communications with large-scale atomistic simulations of advanced materials. This work was supported by NSF (CAREER Program), ARO, PRF, and Louisiana LEQSF.

Interwell Connectivity Evaluation Using Injection and Production Fluctuation Data

NASA Astrophysics Data System (ADS)

Shang, Barry Zhongqi

The development of multiscale methods for computational simulation of biophysical systems represents a significant challenge. Effective computational models that bridge physical insights obtained from atomistic simulations and experimental findings are lacking. An accurate passing of information between these scales would enable: (1) an improved physical understanding of structure-function relationships, and (2) enhanced rational strategies for molecular engineering and materials design. Two approaches are described in this dissertation to facilitate these multiscale goals. In Part I, we develop a lattice kinetic Monte Carlo model to simulate cellulose decomposition by cellulase enzymes and to understand the effects of spatial confinement on enzyme kinetics. An enhanced mechanistic understanding of this reaction system could enhance the design of cellulose bioconversion technologies for renewable and sustainable energy. Using our model, we simulate the reaction up to experimental conversion times of days, while simultaneously capturing the microscopic kinetic behaviors. Therefore, the influence of molecular-scale kinetics on the macroscopic conversion rate is made transparent. The inclusion of spatial constraints in the kinetic model represents a significant advance over classical mass-action models commonly used to describe this reaction system. We find that restrictions due to enzyme jamming and substrate heterogeneity at the molecular level play a dominate role in limiting cellulose conversion. We identify that the key rate limitations are the slow rates of enzyme complexation with glucan chains and the competition between enzyme processivity and jamming. We show that the kinetics of complexation, which involves extraction of a glucan chain end from the cellulose surface and threading through the enzyme active site, occurs slowly on the order of hours, while intrinsic hydrolytic bond cleavage occurs on the order of seconds. We also elucidate the subtle trade-off between processivity and jamming. Highly processive enzymes cleave a large fraction of a glucan chain during each processive run but are prone to jamming at obstacles. Less processive enzymes avoid jamming but cleave only a small fraction of a chain. Optimizing this trade-off maximizes the cellulose conversion rate. We also elucidate the molecular-scale kinetic origins for synergy among cellulases in enzyme mixtures. In contrast to the currently accepted theory, we show that the ability of an endoglucanase to increase the concentration of chain ends for exoglucanases is insufficient for synergy to occur. Rather, endoglucanases must enhance the rate of complexation between exoglucanases and the newly created chain ends. This enhancement occurs when the endoglucanase is able to partially decrystallize the cellulose surface. We show generally that the driving forces for complexation and jamming, which govern the kinetics of pure exoglucanases, also control the degree of synergy in endo-exo mixtures. In Part II, we focus our attention on a different multiscale problem. This challenge is the development of coarse-grained models from atomistic models to access larger length- and time-scales in a simulation. This problem is difficult because it requires a delicate balance between maintaining (1) physical simplicity in the coarse-grained model and (2) physical consistency with the atomistic model. To achieve these goals, we develop a scheme to coarse-grain an atomistic fluid model into a fluctuating hydrodynamics (FHD) model. The FHD model describes the solvent as a field of fluctuating mass, momentum, and energy densities. The dynamics of the fluid are governed by continuum balance equations and fluctuation-dissipation relations based on the constitutive transport laws. The incorporation of both macroscopic transport and microscopic fluctuation phenomena could provide richer physical insight into the behaviors of biophysical systems driven by hydrodynamic fluctuations, such as hydrophobic assembly and crystal nucleation. We further extend our coarse-graining method by developing an interfacial FHD model using information obtained from simulations of an atomistic liquid-vapor interface. We illustrate that a phenomenological Ginzburg-Landau free energy employed in the FHD model can effectively represent the attractive molecular interactions of the atomistic model, which give rise to phase separation. For argon and water, we show that the interfacial FHD model can reproduce the compressibility, surface tension, and capillary wave spectrum of the atomistic model. Via this approach, simulations that explore the coupling between hydrodynamic fluctuations and phase equilibria with molecular-scale consistency are now possible. In both Parts I and II, the emerging theme is that the combination of bottom-up coarse graining and top-down phenomenology is essential for enabling a multiscale approach to remain physically consistent with molecular-scale interactions while simultaneously capturing the collective macroscopic behaviors. This hybrid strategy enables the resulting computational models to be both physically insightful and practically meaningful. (Abstract shortened by UMI.).

Protein displacements under external forces: An atomistic Langevin dynamics approach.

PubMed

Gnandt, David; Utz, Nadine; Blumen, Alexander; Koslowski, Thorsten

2009-02-28

We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.

Reaction pathways in atomistic models of thin film growth

NASA Astrophysics Data System (ADS)

Lloyd, Adam L.; Zhou, Ying; Yu, Miao; Scott, Chris; Smith, Roger; Kenny, Steven D.

2017-10-01

The atomistic processes that form the basis of thin film growth often involve complex multi-atom movements of atoms or groups of atoms on or close to the surface of a substrate. These transitions and their pathways are often difficult to predict in advance. By using an adaptive kinetic Monte Carlo (AKMC) approach, many complex mechanisms can be identified so that the growth processes can be understood and ultimately controlled. Here the AKMC technique is briefly described along with some special adaptions that can speed up the simulations when, for example, the transition barriers are small. Examples are given of such complex processes that occur in different material systems especially for the growth of metals and metallic oxides.

Author Correction: Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations.

PubMed

Paul, Fabian; Wehmeyer, Christoph; Abualrous, Esam T; Wu, Hao; Crabtree, Michael D; Schöneberg, Johannes; Clarke, Jane; Freund, Christian; Weikl, Thomas R; Noé, Frank

2018-03-09

In the original version of this Article, the Acknowledgement section omitted financial support from the Deutsche Forschungsgemeinschaft grant SFB 958/A4. This error has now been corrected in both the PDF and HTML versions of the Article.

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

NASA Astrophysics Data System (ADS)

Henke, Paul S.; Mak, Chi H.

2014-08-01

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

A Perspective on Coupled Multiscale Simulation and Validation in Nuclear Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

M. P. Short; D. Gaston; C. R. Stanek

2014-01-01

The field of nuclear materials encompasses numerous opportunities to address and ultimately solve longstanding industrial problems by improving the fundamental understanding of materials through the integration of experiments with multiscale modeling and high-performance simulation. A particularly noteworthy example is an ongoing study of axial power distortions in a nuclear reactor induced by corrosion deposits, known as CRUD (Chalk River unidentified deposits). We describe how progress is being made toward achieving scientific advances and technological solutions on two fronts. Specifically, the study of thermal conductivity of CRUD phases has augmented missing data as well as revealed new mechanisms. Additionally, the developmentmore » of a multiscale simulation framework shows potential for the validation of a new capability to predict the power distribution of a reactor, in effect direct evidence of technological impact. The material- and system-level challenges identified in the study of CRUD are similar to other well-known vexing problems in nuclear materials, such as irradiation accelerated corrosion, stress corrosion cracking, and void swelling; they all involve connecting materials science fundamentals at the atomistic- and mesoscales to technology challenges at the macroscale.« less

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping.

PubMed

Henke, Paul S; Mak, Chi H

2014-08-14

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg(2+) that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

Exploration of the folding dynamics of human telomeric G-quadruplex with a hybrid atomistic structure-based model

NASA Astrophysics Data System (ADS)

Bian, Yunqiang; Ren, Weitong; Song, Feng; Yu, Jiafeng; Wang, Jihua

2018-05-01

Structure-based models or Gō-like models, which are built from one or multiple particular experimental structures, have been successfully applied to the folding of proteins and RNAs. Recently, a variant termed the hybrid atomistic model advances the description of backbone and side chain interactions of traditional structure-based models, by borrowing the description of local interactions from classical force fields. In this study, we assessed the validity of this model in the folding problem of human telomeric DNA G-quadruplex, where local dihedral terms play important roles. A two-state model was developed and a set of molecular dynamics simulations was conducted to study the folding dynamics of sequence Htel24, which was experimentally validated to adopt two different (3 + 1) hybrid G-quadruplex topologies in K+ solution. Consistent with the experimental observations, the hybrid-1 conformation was found to be more stable and the hybrid-2 conformation was kinetically more favored. The simulations revealed that the hybrid-2 conformation folded in a higher cooperative manner, which may be the reason why it was kinetically more accessible. Moreover, by building a Markov state model, a two-quartet G-quadruplex state and a misfolded state were identified as competing states to complicate the folding process of Htel24. Besides, the simulations also showed that the transition between hybrid-1 and hybrid-2 conformations may proceed an ensemble of hairpin structures. The hybrid atomistic structure-based model reproduced the kinetic partitioning folding dynamics of Htel24 between two different folds, and thus can be used to study the complex folding processes of other G-quadruplex structures.

Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal.

PubMed

Huang, Liangliang; Seredych, Mykola; Bandosz, Teresa J; van Duin, Adri C T; Lu, Xiaohua; Gubbins, Keith E

2013-11-21

The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O∕H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O∕H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.

Atomistic Modeling of the Fluid-Solid Interface in Simple Fluids

NASA Astrophysics Data System (ADS)

Hadjiconstantinou, Nicolas; Wang, Gerald

2017-11-01

Fluids can exhibit pronounced structuring effects near a solid boundary, typically manifested in a layered structure that has been extensively shown to directly affect transport across the interface. We present and discuss several results from molecular-mechanical modeling and molecular-dynamics (MD) simulations aimed at characterizing the structure of the first fluid layer directly adjacent to the solid. We identify a new dimensionless group - termed the Wall number - which characterizes the degree of fluid layering, by comparing the competing effects of wall-fluid interaction and thermal energy. We find that in the layering regime, several key features of the first layer layer - including its distance from the solid, its width, and its areal density - can be described using mean-field-energy arguments, as well as asymptotic analysis of the Nernst-Planck equation. For dense fluids, the areal density and the width of the first layer can be related to the bulk fluid density using a simple scaling relation. MD simulations show that these results are broadly applicable and robust to the presence of a second confining solid boundary, different choices of wall structure and thermalization, strengths of fluid-solid interaction, and wall geometries.

Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level.

PubMed

Yang, Changwon; Kulkarni, Mandar; Lim, Manho; Pak, Youngshang

2017-12-15

The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged time scale (10-12 μs) parallel tempering metadynamics (PTMetaD) simulation method in conjunction with a modified version of the AMBER bsc1 force field. For unbiased descriptions of the folding free energy landscape of TBA-15, this force field was minimally modified. From this direct folding simulation using the modified bsc1 force field, reasonably converged free energy landscapes were obtained in K+-rich aqueous solution (150 mM), providing detailed atomistic pictures of GQ folding mechanisms for TBA-15. This study found that the TBA folding occurred via multiple folding pathways with two major free energy barriers of 13 and 15 kcal/mol in the presence of several intermediate states of G-triplex variants. The early formation of these intermediates was associated with a single K+ ion capturing. Interestingly, these intermediate states appear to undergo facile transitions among themselves through relatively small energy barriers. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Atomistic simulation of cubic and tetragonal phases of U-Mo alloy: Structure and thermodynamic properties

NASA Astrophysics Data System (ADS)

Starikov, S. V.; Kolotova, L. N.; Kuksin, A. Yu.; Smirnova, D. E.; Tseplyaev, V. I.

2018-02-01

We studied structure and thermodynamic properties of cubic and tetragonal phases of pure uranium and U-Mo alloys using atomistic simulations: molecular dynamics and density functional theory. The main attention was paid to the metastable γ0 -phase that is formed in U-Mo alloys at low temperature. Structure of γ0 -phase is similar to body-centered tetragonal (bct) lattice with displacement of a central atom in the basic cell along [ 001 ] direction. Such displacements have opposite orientations for part of the neighbouring basic cells. In this case, such ordering of the displacements can be designated as antiferro-displacement. Formation of such complex structure may be interpreted through forming of short U-U bonds. At heating, the tetragonal structure transforms into cubic γs -phase, still showing ordering of central atom displacements. With rise in temperature, γs -phase transforms to γ-phase with a quasi body-centered cubic (q-bcc) lattice. The local positions of uranium atoms in γ-phase correspond to γs -phase, however, orientations of the central atom displacements become disordered. Transition from γ0 to γ can be considered as antiferro-to paraelastic transition of order-disorder type. This approach to the structure description of uranium alloy allows to explain a number of unusual features found in the experiments: anisotropy of lattice at low temperature; remarkably high self-diffusion mobility in γ-phase; decreasing of electrical resistivity at heating for some alloys. In addition, important part of this work is the development of new interatomic potential for U-Mo system made with taking into account details of studied structures.

Molecular simulations of self-assembly processes of amphiphiles in dilute solutions: the challenge for quantitative modelling

NASA Astrophysics Data System (ADS)

Jusufi, Arben

2013-11-01

We report on two recent developments in molecular simulations of self-assembly processes of amphiphilic solutions. We focus on the determination of micelle formation of ionic surfactants which exhibit the archetype of self-assembling compounds in solution. The first approach is centred on the challenge in predicting micellisation properties through explicit solvent molecular dynamics simulations. Even with a coarse-grained (CG) approach and the use of highly optimised software packages run on graphics processing unit hardware, it remains in many cases computationally infeasible to directly extract the critical micelle concentration (cmc). However, combined with a recently presented theoretical mean-field model this task becomes resolved. An alternative approach to study self-assembly is through implicit solvent modelling of the surfactants. Here we review some latest results and present new ones regarding capabilities of such a modelling approach in determining the cmc, and the aggregate structures in the dilute regime, that is currently not accessible through explicit solvent simulations, neither through atomistic nor through CG approaches. A special focus is put on surfactant concentration effects and surfactant correlations quantified by scattering intensities that are compared to recently published small-angle X-ray scattering data.

Large fraction of crystal directions leads to ion channeling

NASA Astrophysics Data System (ADS)

Nordlund, K.; Djurabekova, F.; Hobler, G.

2016-12-01

It is well established that when energetic ions are moving in crystals, they may penetrate much deeper if they happen to be directed in some specific crystal directions. This `channeling' effect is utilized for instance in certain ion beam analysis methods and has been described by analytical theories and atomistic computer simulations. However, there have been very few systematic studies of channeling in directions other than the principal low-index ones. We present here a molecular dynamics-based approach to calculate ion channeling systematically over all crystal directions, providing ion `channeling maps' that easily show in which directions channeling is expected. The results show that channeling effects can be quite significant even at energies below 1 keV, and that in many cases, significant planar channeling occurs also in a wide range of crystal directions between the low-index principal ones. In all of the cases studied, a large fraction (˜20 -60 % ) of all crystal directions show channeling. A practical implication of this is that modern experiments on randomly oriented nanostructures will have a large probability of channeling. It also means that when ion irradiations are carried out on polycrystalline samples, channeling effects on the results cannot a priori be assumed to be negligible. The maps allow for easy selection of good `nonchanneling' directions in experiments or alternatively finding wide channels for beneficial uses of channeling. We implement channeling theory to also give the fraction of channeling directions in a manner directly comparable to the simulations. The comparison shows good qualitative agreement. In particular, channeling theory is very good at predicting which channels are active at a given energy. This is true down to sub-keV energies, provided the penetration depth is not too small.

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes

PubMed Central

Covino, Roberto; Coifman, Ronald R.; Gear, C. William; Georgiou, Anastasia S.; Kevrekidis, Ioannis G.

2017-01-01

We describe and implement a computer-assisted approach for accelerating the exploration of uncharted effective free-energy surfaces (FESs). More generally, the aim is the extraction of coarse-grained, macroscopic information from stochastic or atomistic simulations, such as molecular dynamics (MD). The approach functionally links the MD simulator with nonlinear manifold learning techniques. The added value comes from biasing the simulator toward unexplored phase-space regions by exploiting the smoothness of the gradually revealed intrinsic low-dimensional geometry of the FES. PMID:28634293

Critical Issues on Materials for Gen-IV Reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caro, M; Marian, J; Martinez, E

2009-02-27

Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that seeks to relate in a near-term effort dislocation dynamics to polycrystal plasticity. The requirements originated in the reactor systems under consideration today for future sources of nuclear energy. These requirements are beyond the present day performance of nuclear materials andmore » calls for the development of new, high temperature, radiation resistant materials. Fe-Cr alloys with 9-12% Cr content are the base matrix of advanced ferritic/martensitic (FM) steels envisaged as fuel cladding and structural components of Gen-IV reactors. Predictive tools are needed to calculate structural and mechanical properties of these steels. This project represents a contribution in that direction. The synergy between the continuous progress of parallel computing and the spectacular advances in the theoretical framework that describes materials have lead to a significant advance in our comprehension of materials properties and their mechanical behavior. We took this progress to our advantage and within this LDRD were able to provide a detailed physical understanding of iron-chromium alloys microstructural behavior. By combining ab-initio simulations, many-body interatomic potential development, and mesoscale dislocation dynamics we were able to describe their microstructure evolution. For the first time in the case of Fe-Cr alloys, atomistic and mesoscale were merged and the first steps taken towards incorporating ordering and precipitation effects into dislocation dynamics (DD) simulations. Molecular dynamics (MD) studies of the transport of self-interstitial, vacancy and point defect clusters in concentrated Fe-Cr alloys were performed for future diffusion data calculations. A recently developed parallel MC code with displacement allowed us to predict the evolution of the defect microstructures, local chemistry changes, grain boundary segregation and precipitation resulting from radiation enhanced diffusion. We showed that grain boundaries, dislocations and free surfaces are not preferential for alpha-prime precipitation, and explained experimental observations of short-range order (SRO) in Fe-rich FeCr alloys. Our atomistic studies of dislocation hardening allowed us to obtain dislocation mobility functions for BCC pure iron and Fe-Cr and determine for FCC metals the dislocation interaction with precipitates with a description to be used in Dislocation Dynamic (DD) codes. A Synchronous parallel Kinetic Monte Carlo code was developed and tested which promises to expand the range of applicability of kMC simulations. This LDRD furthered the limits of the available science on the thermodynamic and mechanic behavior of metallic alloys and extended the application of physically-based multiscale materials modeling to cases of severe temperature and neutron fluence conditions in advanced future nuclear reactors. The report is organized as follows: after a brief introduction, we present the research activities, and results obtained. We give recommendations on future LLNL activities that may contribute to the progress in this area, together with examples of possible research lines to be supported.« less

Solubilization of Therapeutic Agents in Micellar Nanomedicines

PubMed Central

Vuković, Lela; Madriaga, Antonett; Kuzmis, Antonina; Banerjee, Amrita; Tang, Alan; Tao, Kevin; Shah, Neil; Král, Petr; Onyuksel, Hayat

2014-01-01

We use atomistic molecular dynamics simulations to reveal the binding mechanisms of therapeutic agents in PEG-ylated micellar nanocarriers (SSM). In our experiments, SSM in buffer solutions can solubilize either ≈ 11 small bexarotene molecules or ≈ 6 (2 in low ionic strength buffer) human vasoactive intestinal peptide (VIP) molecules. Free energy calculations reveal that molecules of the poorly water soluble drug bexarotene can reside at the micellar ionic interface of the PEG corona, with their polar ends pointing out. Alternatively, they can reside in the alkane core center, where several bexarotene molecules can self-stabilize by forming a cluster held together by a network of hydrogen bonds. We also show that highly charged molecules, such as VIP, can be stabilized at the SSM ionic interface by Coulombic coupling between their positively charged residues and the negatively charged phosphate head-groups of the lipids. The obtained results illustrate that atomistic simulations can reveal drug solubilization character in nanocarriers and be used in efficient optimization of novel nanomedicines. PMID:24283508

DOE Office of Scientific and Technical Information (OSTI.GOV)

El-Atwani, O.; Norris, S. A.; Ludwig, K.

In this study, several proposed mechanisms and theoretical models exist concerning nanostructure evolution on III-V semiconductors (particularly GaSb) via ion beam irradiation. However, making quantitative contact between experiment on the one hand and model-parameter dependent predictions from different theories on the other is usually difficult. In this study, we take a different approach and provide an experimental investigation with a range of targets (GaSb, GaAs, GaP) and ion species (Ne, Ar, Kr, Xe) to determine new parametric trends regarding nanostructure evolution. Concurrently, atomistic simulations using binary collision approximation over the same ion/target combinations were performed to determine parametric trends onmore » several quantities related to existing model. A comparison of experimental and numerical trends reveals that the two are broadly consistent under the assumption that instabilities are driven by chemical instability based on phase separation. Furthermore, the atomistic simulations and a survey of material thermodynamic properties suggest that a plausible microscopic mechanism for this process is an ion-enhanced mobility associated with energy deposition by collision cascades.« less

Atomistic modeling and simulation of the role of Be and Bi in Al diffusion in U-Mo fuel

NASA Astrophysics Data System (ADS)

Hofman, G. L.; Bozzolo, G.; Mosca, H. O.; Yacout, A. M.

2011-07-01

Within the RERTR program, previous experimental and modeling studies identified Si as the alloying addition to the Al cladding responsible for inhibiting Al interdiffusion in the UMo fuel. However, difficulties with reprocessing have rendered this choice inappropriate, leading to the need to study alternative elements. In this work, we discuss the results of an atomistic modeling effort which allows for the systematic study of several possible alloying additions. Based on the behavior observed in the phase diagrams, beryllium or bismuth additions suggest themselves as possible options to replace Si. The results of temperature-dependent simulations using the Bozzolo-Ferrante-Smith (BFS) method for the energetics for varying concentrations of either element are shown, indicating that Be could have a substantial effect in stopping Al interdiffusion, while Bi does not. Details of the calculations and the dependence of the role of each alloying addition as a function of temperature and concentration (of beryllium or bismuth in Al) are shown.

Revealing spatially heterogeneous relaxation in a model nanocomposite.

PubMed

Cheng, Shiwang; Mirigian, Stephen; Carrillo, Jan-Michael Y; Bocharova, Vera; Sumpter, Bobby G; Schweizer, Kenneth S; Sokolov, Alexei P

2015-11-21

The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility gradient shows no "glassy" layer, but the α-relaxation time near the nanoparticle grows with cooling faster than the α-relaxation time in the bulk and is ∼20 times longer at low temperatures. The interfacial layer thickness increases from ∼1.8 nm at higher temperatures to ∼3.5 nm upon cooling to near bulk Tg. A real space microscopic description of the mobility gradient is constructed by synergistically combining high temperature atomistic simulation with theory. Our analysis suggests that the interfacial slowing down arises mainly due to an increase of the local cage scale barrier for activated hopping induced by enhanced packing and densification near the nanoparticle surface. The theory is employed to predict how local surface densification can be manipulated to control layer dynamics and shear rigidity over a wide temperature range.

Atomistic simulation of CO2 solubility in poly(ethylene oxide) oligomers

NASA Astrophysics Data System (ADS)

Hong, Bingbing; Panagiotopoulos, Athanassios Z.

2014-06-01

We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henry's constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henry's constant. Dependence of the calculated Henry's constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length.

Molecular mechanism of polyacrylate helix sense switching across its free energy landscape.

PubMed

Pietropaolo, Adriana; Nakano, Tamaki

2013-04-17

Helical polymers with switchable screw sense are versatile frameworks for chiral functional materials. In this work, we reconstructed the free energy landscape of helical poly(2,7-bis(4-tert-butylphenyl)fluoren-9-yl acrylate) [poly(BBPFA)], as its racemization is selectively driven by light without any rearrangement of chemical bonds. The chirality inversion was enforced by atomistic free energy simulations using chirality indices as reaction coordinates. The free energy landscape reproduced the experimental electronic circular dichroism spectra. We propose that the chirality inversion of poly(BBPFA) proceeds from a left-handed 31 helix via multistate free energy pathways to reach the right-handed 31 helix. The inversion is triggered by the rotation of biphenyl units with an activation barrier of 38 kcal/mol. To the best of our knowledge, this is the first report on the chiral inversion mechanism of a helical polymer determined in a quantitative way in the framework of atomistic free energy simulations.

Simulations of noble gases adsorbed on graphene

NASA Astrophysics Data System (ADS)

Maiga, Sidi; Gatica, Silvina

2014-03-01

We present results of Grand Canonical Monte Carlo simulations of adsorption of Kr, Ar and Xe on a suspended graphene sheet. We compute the adsorbate-adsorbate interaction by a Lennard-Jones potential. We adopt a hybrid model for the graphene-adsorbate force; in the hybrid model, the potential interaction with the nearest carbon atoms (within a distance rnn) is computed with an atomistic pair potential Ua; for the atoms at r>rnn, we compute the interaction energy as a continuous integration over a carbon uniform sheet with the density of graphene. For the atomistic potential Ua, we assume the anisotropic LJ potential adapted from the graphite-He interaction proposed by Cole et.al. This interaction includes the anisotropy of the C atoms on graphene, which originates in the anisotropic π-bonds. The adsorption isotherms, energy and structure of the layer are obtained and compared with experimental results. We also compare with the adsorption on graphite and carbon nanotubes. This research was supported by NSF/PRDM (Howard University) and NSF (DMR 1006010).

Revealing spatially heterogeneous relaxation in a model nanocomposite

DOE PAGES

Cheng, Shiwang; Mirigian, Stephen; Carrillo, Jan-Michael Y.; ...

2015-11-18

The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility gradient shows no glassy layer, but the -relaxation time near the nanoparticle grows with cooling faster than the -relaxation time in the bulk and is ~20 times longer at low temperatures. The interfacial layer thickness increases from ~1.8 nm at higher temperatures to ~3.5 nm upon cooling to near bulk T g. A real space microscopic description of the mobility gradient is constructed by synergistically combining high temperature atomistic simulation with theory.more » Our analysis suggests that the interfacial slowing down arises mainly due to an increase of the local cage scale barrier for activated hopping induced by enhanced packing and densification near the nanoparticle surface. As a result, the theory is employed to predict how local surface densification can be manipulated to control layer dynamics and shear rigidity over a wide temperature range.« less

A transformation theory of stochastic evolution in Red Moon methodology to time evolution of chemical reaction process in the full atomistic system.

PubMed

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H 2 + I 2  ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H 2 and I 2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H 2 ] eq and equilibrium constants K eq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H 2 ] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

Inclusion Complexes Behavior at the Air-Water Interface. Molecular Dynamic Simulation Study.

NASA Astrophysics Data System (ADS)

Gargallo, L.; Vargas, D.; Sandoval, C.; Saavedra, M.; Becerra, N.; Leiva, A.; Radić, D.

2008-08-01

The interfacial properties of the inclusion complexes (ICs), obtained from the threading of α-cyclodextrin (α-CD) onto poly(ethylene-oxide)(PEO), poly(ɛ-caprolactone)(PEC) and poly(tetrahydrofuran)(PTHF) and their precursor homopolymers (PHPoly), were studied at the air-water interface. The free surface energy was determined by wettability measurements. The experimental behavior of these systems was described by an atomistic molecular dynamics simulation (MDS).

Coarse graining of atactic polystyrene and its derivatives

NASA Astrophysics Data System (ADS)

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

2014-03-01

Capturing large length scales in polymers and soft matter while retaining atomistic properties is imperative to computational studies of dynamic systems. Here we present a new methodology developing coarse-grain model based on atomistic simulation of atactic polystyrene (PS). Similar to previous work by Fritz et al., each monomer is described by two coarse grained beads. In contrast to this earlier work where intramolecular potentials were based on Monte Carlo simulation of both isotactic and syndiotactic single PS molecule to capture stereochemistry, we obtained intramolecular interactions from a single molecular dynamics simulation of an all-atom atactic PS melts. The non-bonded interactions are obtained using the iterative Boltzmann inversion (IBI) scheme. This methodology has been extended to coarse graining of poly-(t-butyl-styrene) (PtBS). An additional coarse-grained bead is used to describe the t-butyl group. Similar to the process for PS, the intramolecular interactions are obtained from a single all atom atactic melt simulation. Starting from the non-bonded interactions for PS, we show that the IBI method for the non-bonded interactions of PtBS converges relatively fast. A generalized scheme for substituted PS is currently in development. We would like to acknowledge Prof. Kurt Kremer for helpful discussions during this work.

Characterizing single isolated radiation-damage events from molecular dynamics via virtual diffraction methods

DOE PAGES

Stewart, James A.; Brookman, G.; Price, Patrick Michael; ...

2018-04-25

In this study, the evolution and characterization of single-isolated-ion-strikes are investigated by combining atomistic simulations with selected-area electron diffraction (SAED) patterns generated from these simulations. Five molecular dynamics simulations are performed for a single 20 keV primary knock-on atom in bulk crystalline Si. The resulting cascade damage is characterized in two complementary ways. First, the individual cascade events are conventionally quantified through the evolution of the number of defects and the atomic (volumetric) strain associated with these defect structures. These results show that (i) the radiation damage produced is consistent with the Norgett, Robinson, and Torrens model of damage productionmore » and (ii) there is a net positive volumetric strain associated with the cascade structures. Second, virtual SAED patterns are generated for the resulting cascade-damaged structures along several zone axes. The analysis of the corresponding diffraction patterns shows the SAED spots approximately doubling in size, on average, due to broadening induced by the defect structures. Furthermore, the SAED spots are observed to exhibit an average radial outward shift between 0.33% and 0.87% depending on the zone axis. Finally, this characterization approach, as utilized here, is a preliminary investigation in developing methodologies and opportunities to link experimental observations with atomistic simulations to elucidate microstructural damage states.« less

A kinetic Monte Carlo simulation method of van der Waals epitaxy for atomistic nucleation-growth processes of transition metal dichalcogenides.

PubMed

Nie, Yifan; Liang, Chaoping; Cha, Pil-Ryung; Colombo, Luigi; Wallace, Robert M; Cho, Kyeongjae

2017-06-07

Controlled growth of crystalline solids is critical for device applications, and atomistic modeling methods have been developed for bulk crystalline solids. Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW) heterostructures has not yet been developed. Specifically, the growth of single-layered transition metal dichalcogenides (TMDs) is currently facing tremendous challenges, and a detailed understanding based on KMC simulations would provide critical guidance to enable controlled growth of vdW heterostructures. In this work, a KMC simulation method is developed for the growth modeling on the vdW epitaxy of TMDs. The KMC method has introduced full material parameters for TMDs in bottom-up synthesis: metal and chalcogen adsorption/desorption/diffusion on substrate and grown TMD surface, TMD stacking sequence, chalcogen/metal ratio, flake edge diffusion and vacancy diffusion. The KMC processes result in multiple kinetic behaviors associated with various growth behaviors observed in experiments. Different phenomena observed during vdW epitaxy process are analysed in terms of complex competitions among multiple kinetic processes. The KMC method is used in the investigation and prediction of growth mechanisms, which provide qualitative suggestions to guide experimental study.

Characterizing single isolated radiation-damage events from molecular dynamics via virtual diffraction methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, James A.; Brookman, G.; Price, Patrick Michael

In this study, the evolution and characterization of single-isolated-ion-strikes are investigated by combining atomistic simulations with selected-area electron diffraction (SAED) patterns generated from these simulations. Five molecular dynamics simulations are performed for a single 20 keV primary knock-on atom in bulk crystalline Si. The resulting cascade damage is characterized in two complementary ways. First, the individual cascade events are conventionally quantified through the evolution of the number of defects and the atomic (volumetric) strain associated with these defect structures. These results show that (i) the radiation damage produced is consistent with the Norgett, Robinson, and Torrens model of damage productionmore » and (ii) there is a net positive volumetric strain associated with the cascade structures. Second, virtual SAED patterns are generated for the resulting cascade-damaged structures along several zone axes. The analysis of the corresponding diffraction patterns shows the SAED spots approximately doubling in size, on average, due to broadening induced by the defect structures. Furthermore, the SAED spots are observed to exhibit an average radial outward shift between 0.33% and 0.87% depending on the zone axis. Finally, this characterization approach, as utilized here, is a preliminary investigation in developing methodologies and opportunities to link experimental observations with atomistic simulations to elucidate microstructural damage states.« less

Characterizing single isolated radiation-damage events from molecular dynamics via virtual diffraction methods

NASA Astrophysics Data System (ADS)

Stewart, J. A.; Brookman, G.; Price, P.; Franco, M.; Ji, W.; Hattar, K.; Dingreville, R.

2018-04-01

The evolution and characterization of single-isolated-ion-strikes are investigated by combining atomistic simulations with selected-area electron diffraction (SAED) patterns generated from these simulations. Five molecular dynamics simulations are performed for a single 20 keV primary knock-on atom in bulk crystalline Si. The resulting cascade damage is characterized in two complementary ways. First, the individual cascade events are conventionally quantified through the evolution of the number of defects and the atomic (volumetric) strain associated with these defect structures. These results show that (i) the radiation damage produced is consistent with the Norgett, Robinson, and Torrens model of damage production and (ii) there is a net positive volumetric strain associated with the cascade structures. Second, virtual SAED patterns are generated for the resulting cascade-damaged structures along several zone axes. The analysis of the corresponding diffraction patterns shows the SAED spots approximately doubling in size, on average, due to broadening induced by the defect structures. Furthermore, the SAED spots are observed to exhibit an average radial outward shift between 0.33% and 0.87% depending on the zone axis. This characterization approach, as utilized here, is a preliminary investigation in developing methodologies and opportunities to link experimental observations with atomistic simulations to elucidate microstructural damage states.

Atomistic simulation of mineral-melt trace-element partitioning

NASA Astrophysics Data System (ADS)

Allan, Neil L.; Du, Zhimei; Lavrentiev, Mikhail Yu.; Blundy, Jon D.; Purton, John A.; van Westrenen, Wim

2003-09-01

We discuss recent advances in computational approaches to trace-element incorporation in minerals and melts. It is crucial to take explicit account of the local structural environment of each ion in the solid and the change in this environment following the introduction of a foreign atom or atoms. Particular attention is paid to models using relaxation (strain) energies and solution energies, and the use of these different models for isovalent and heterovalent substitution in diopside and forsterite. Solution energies are also evaluated for pyrope and grossular garnets, and pyrope-grossular solid solutions. Unfavourable interactions between dodecahedral sites containing ions of the same size and connected by an intervening tetrahedron lead to larger solubilities of trace elements in the garnet solid solution than in either end member compound and to the failure of Goldschmidt's first rule. Our final two examples are the partitioning behaviour of noble gases, which behave as 'ions of zero charge' and the direct calculation of high-temperature partition coefficients between CaO solid and melt via Monte Carlo simulations.

First-principles simulation on Seebeck coefficient in silicon nanowires

NASA Astrophysics Data System (ADS)

Nakamura, Koichi

2017-06-01

The Seebeck coefficients of silicon nanowires (SiNWs) were simulated on the basis of first-principles calculation using various atomistic structure models. The electronic band structures of fully hydrogen-terminated SiNW models give the correct image of quantum mechanical confinement from bulk silicon to SiNW for each axial direction, and the change in the density of states by dimensional reduction to SiNW enhances the thermoelectric performance in terms of the Seebeck coefficient, compared with those of bulk silicon and silicon nanosheets. The uniaxial tensile strain for the SiNW models does not strongly affect the Seebeck coefficient even for the SiNW system with giant piezoresistivity. In contrast, dangling bonds on a wire wall sharply reduce the Seebeck coefficient of SiNW and totally degrade thermoelectric performance from the viewpoint of the power factor. The exclusion of dangling bonds is a key element for the design and application of high-performance thermoelectric nanowires of semiconducting materials.

Modeling radiation induced segregation in Iron-Chromium alloys

DOE PAGES

Senninger, Oriane; Soisson, Frederic; Martinez Saez, Enrique; ...

2015-10-16

Radiation induced segregation in ferritic Fe-Cr alloys is studied by Atomistic Kinetic Monte Carlo simulations that include di usion of chemical species by vacancy and interstitial migration, recombination, and elimination at sinks. The parameters of the di usion model are tted to DFT calculations. Transport coe cients that control the coupling between di usion of defects and chemical species are measured in dilute and concentrated alloys. Radiation induced segregation near grain boundaries is directly simulated with this model. We nd that the di usion of vacancies toward sinks leads to a Cr depletion. Meanwhile, the di usion of self-interstitials causesmore » an enrichment of Cr in the vicinity of sinks. For concentrations lower than 15%Cr, we predict that sinks will be enriched with Cr for temperatures lower than a threshold. When the temperature is above this threshold value, the sinks will be depleted in Cr. These results are compared to previous experimental studies and models. Cases of radiation induced precipitation and radiation accelerated precipitation are considered.« less

Formation and emission mechanisms of Ag nanoclusters in the Ar matrix assembly cluster source

NASA Astrophysics Data System (ADS)

Zhao, Junlei; Cao, Lu; Palmer, Richard E.; Nordlund, Kai; Djurabekova, Flyura

2017-11-01

In this paper, we study the mechanisms of growth of Ag nanoclusters in a solid Ar matrix and the emission of these nanoclusters from the matrix by a combination of experimental and theoretical methods. The molecular dynamics simulations show that the cluster growth mechanism can be described as "thermal spike-enhanced clustering" in multiple sequential ion impact events. We further show that experimentally observed large sputtered metal clusters cannot be formed by direct sputtering of Ag mixed in the Ar. Instead, we describe the mechanism of emission of the metal nanocluster that, at first, is formed in the cryogenic matrix due to multiple ion impacts, and then is emitted as a result of the simultaneous effects of interface boiling and spring force. We also develop an analytical model describing this size-dependent cluster emission. The model bridges the atomistic simulations and experimental time and length scales, and allows increasing the controllability of fast generation of nanoclusters in experiments with a high production rate.

The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.

PubMed

Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele

2017-09-14

In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.

Effect of the barometric phase transition of a DMPA bilayer on the lipid/water interface. An atomistic description by molecular dynamics simulation.

PubMed

Casares, J J Giner; Camacho, L; Romero, M T Martín; Cascales, J J López

2007-12-13

Understanding the structure and dynamics of phospholipid bilayers is of fundamental relevance in biophysics, biochemistry, and chemical physics. Lipid Langmuir monolayers are used as a model of lipid bilayers, because they are much more easily studied experimentally, although some authors question the validity of this model. With the aim of throwing light on this debate, we used molecular dynamics simulations to obtain an atomistic description of a membrane of dimyristoylphosphatidic acid under different surface pressures. Our results show that at low surface pressure the interdigitation between opposite lipids (that is, back-to-back interactions) controls the system structure. In this setting and due to the absence of this effect in the Langmuir monolayers, the behavior between these two systems differs considerably. However, when the surface pressure increases the lipid interdigitation diminishes and so monolayer and bilayer behavior converges. In this work, four computer simulations were carried out, subjecting the phospholipids to lateral pressures ranging from 0.17 to 40 mN/m. The phospholipids were studied in their charged state because this approach is closer to the experimental situation. Special attention was paid to validating our simulation results by comparison with available experimental data, therebeing in general excellent agreement between experimental and simulation data. In addition, the properties of the lipid/solution interface associated with the lipid barometric phase transition were studied.

Atomistic Simulation of Initiation in Hexanitrostilbene

NASA Astrophysics Data System (ADS)

Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

2015-06-01

We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Dynamics in entangled polyethylene melts [Multi time scale dynamics in entangled polyethylene melts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salerno, K. Michael; Agrawal, Anupriya; Peters, Brandon L.

Polymer dynamics creates distinctive viscoelastic behavior as a result of a coupled interplay of motion at the atomic length scale and motion of the entire macromolecule. Capturing the broad time and length scales of polymeric motion however, remains a challenge. Using linear polyethylene as a model system, we probe the effects of the degree of coarse graining on polymer dynamics. Coarse-grained (CG) potentials are derived using iterative Boltzmann inversion with λ methylene groups per CG bead (denoted CGλ) with λ = 2,3,4 and 6 from a fully-atomistic polyethylene melt simulation. By rescaling time in the CG models by a factormore » α, the chain mobility for the atomistic and CG models match. We show that independent of the degree of coarse graining, all measured static and dynamic properties are essentially the same once the dynamic scaling factor α and a non-crossing constraint for the CG6 model are included. The speedup of the CG4 model is about 3 times that of the CG3 model and is comparable to that of the CG6 model. Furthermore, using these CG models we were able to reach times of over 500 μs, allowing us to measure a number of quantities, including the stress relaxation function, plateau modulus and shear viscosity, and compare directly to experiment.« less

Dynamics in entangled polyethylene melts [Multi time scale dynamics in entangled polyethylene melts

DOE PAGES

Salerno, K. Michael; Agrawal, Anupriya; Peters, Brandon L.; ...

2016-10-10

Polymer dynamics creates distinctive viscoelastic behavior as a result of a coupled interplay of motion at the atomic length scale and motion of the entire macromolecule. Capturing the broad time and length scales of polymeric motion however, remains a challenge. Using linear polyethylene as a model system, we probe the effects of the degree of coarse graining on polymer dynamics. Coarse-grained (CG) potentials are derived using iterative Boltzmann inversion with λ methylene groups per CG bead (denoted CGλ) with λ = 2,3,4 and 6 from a fully-atomistic polyethylene melt simulation. By rescaling time in the CG models by a factormore » α, the chain mobility for the atomistic and CG models match. We show that independent of the degree of coarse graining, all measured static and dynamic properties are essentially the same once the dynamic scaling factor α and a non-crossing constraint for the CG6 model are included. The speedup of the CG4 model is about 3 times that of the CG3 model and is comparable to that of the CG6 model. Furthermore, using these CG models we were able to reach times of over 500 μs, allowing us to measure a number of quantities, including the stress relaxation function, plateau modulus and shear viscosity, and compare directly to experiment.« less

Atomistic Simulation Derived Insight on the Irreversible Structural Changes of Si Electrode during Fast and Slow Delithiation.

PubMed

Kim, Kwang Jin; Wortman, James; Kim, Sung-Yup; Qi, Yue

2017-07-12

Quantifying the irreversible chemical and structural changes of Si during cycling remains challenging. In this study, a continuous reactive molecular dynamics delithiation algorithm, with well-controlled potential gradient and delithiation rate, was developed and used to investigate the "natural" delithiation responses of an aluminum-oxide coated silicon thin-film. Fast delithiation led to the formation of dense Si network near the surface and nanoporosity inside the a-Li x Si, resulting in 141% volume dilation and significant amount of Li trapped inside (a-Li 1.2 Si) at the end of delithiation process. In contrast, slow delithiation allowed the a-Li x Si to shrink by near-equilibrium condition, demonstrating no permanent inner pore with nearly Li-free structure (a-Li 0.2 Si) and minimal volume dilation (44%). However, even without trapped Li, the delithiated a-Li x Si still exhibited higher volume (lower density) than the equilibrium structure with the same Li concentration, despite delithiation rate. The origin of this excess volume is the loss of directly bonded Si-Si pairs, which made the subsequent relithiation faster. On the basis of the atomistic modeling and the quantified degradation mechanism, battery operating guidelines, including the delithiation rate and the depth of charge to avoid trapped Li and coating delamination, were suggested to improve the durability Si electrodes.

Atomistic Simulation of the Rate-Dependent Ductile-to-Brittle Failure Transition in Bicrystalline Metal Nanowires.

PubMed

Tao, Weiwei; Cao, Penghui; Park, Harold S

2018-02-14

The mechanical properties and plastic deformation mechanisms of metal nanowires have been studied intensely for many years. One of the important yet unresolved challenges in this field is to bridge the gap in properties and deformation mechanisms reported for slow strain rate experiments (∼10 -2 s -1 ), and high strain rate molecular dynamics (MD) simulations (∼10 8 s -1 ) such that a complete understanding of strain rate effects on mechanical deformation and plasticity can be obtained. In this work, we use long time scale atomistic modeling based on potential energy surface exploration to elucidate the atomistic mechanisms governing a strain-rate-dependent incipient plasticity and yielding transition for face centered cubic (FCC) copper and silver nanowires. The transition occurs for both metals with both pristine and rough surfaces for all computationally accessible diameters (<10 nm). We find that the yield transition is induced by a transition in the incipient plastic event from Shockley partials nucleated on primary slip systems at MD strain rates to the nucleation of planar defects on non-Schmid slip planes at experimental strain rates, where multiple twin boundaries and planar stacking faults appear in copper and silver, respectively. Finally, we demonstrate that, at experimental strain rates, a ductile-to-brittle transition in failure mode similar to previous experimental studies on bicrystalline silver nanowires is observed, which is driven by differences in dislocation activity and grain boundary mobility as compared to the high strain rate case.

Acceleration of saddle-point searches with machine learning.

PubMed

Peterson, Andrew A

2016-08-21

In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the number of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.

Acceleration of saddle-point searches with machine learning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peterson, Andrew A., E-mail: andrew-peterson@brown.edu

In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the numbermore » of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.« less

Effects of applied strain on nanoscale self-interstitial cluster formation in BCC iron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Ning; Setyawan, Wahyu; Kurtz, Richard J.

2017-09-01

The effect of applied strains on the configurational evolution of self-interstitial clusters in BCC iron (Fe) is explored with atomistic simulations. A novel cluster configuration is discovered at low temperatures (<600 K), which consists of <110> dumbbells and <111> crowdions in a specific configuration, resulting in an immobile defect. The stability and diffusion of this cluster at higher temperatures is explored. In addition, an anisotropy distribution factor of a particular [hkl] interstitial loop within the family of loops is calculated as a function of strain. The results show that loop anisotropy is governed by the angle between the stress directionmore » and the orientation of the <111> crowdions in the loop, and directly linked to the stress induced preferred nucleation of self-interstitial atoms.« less

Wormlike Chain Theory and Bending of Short DNA

NASA Astrophysics Data System (ADS)

Mazur, Alexey K.

2007-05-01

The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. The computed distributions remarkably agree with the wormlike chain theory and qualitatively differ from predictions of the subelastic chain model. The computed data exhibit only small anomalies in the apparent flexibility of short DNA and cannot account for the recently reported AFM data. It is possible that the current atomistic DNA models miss some essential mechanisms of DNA bending on intermediate length scales. Analysis of bent DNA structures reveal, however, that the bending motion is structurally heterogeneous and directionally anisotropic on the length scales where the experimental anomalies were detected. These effects are essential for interpretation of the experimental data and they also can be responsible for the apparent discrepancy.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de; Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de

We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in moremore » efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.« less

Dynamics of Surfactant Clustering at Interfaces and Its Influence on the Interfacial Tension: Atomistic Simulation of a Sodium Hexadecane-Benzene Sulfonate-Tetradecane-Water System.

PubMed

Paredes, Ricardo; Fariñas-Sánchez, Ana Isabel; Medina-Rodrı Guez, Bryan; Samaniego, Samantha; Aray, Yosslen; Álvarez, Luis Javier

2018-03-06

The process of equilibration of the tetradecane-water interface in the presence of sodium hexadecane-benzene sulfonate is studied using intensive atomistic molecular dynamics simulations. Starting as an initial point with all of the surfactants at the interface, it is obtained that the equilibration time of the interface (several microseconds) is orders of magnitude higher than previously reported simulated times. There is strong evidence that this slow equilibration process is due to the aggregation of surfactants molecules on the interface. To determine this fact, temporal evolution of interfacial tension and interfacial formation energy are studied and their temporal variations are correlated with cluster formation. To study cluster evolution, the mean cluster size and the probability that a molecule of surfactant chosen at random is free are obtained as a function of time. Cluster size distribution is estimated, and it is observed that some of the molecules remain free, whereas the rest agglomerate. Additionally, the temporal evolution of the interfacial thickness and the structure of the surfactant molecules on the interface are studied. It is observed how this structure depends on whether the molecules agglomerate or not.

Tunnel Field-Effect Transistors in 2-D Transition Metal Dichalcogenide Materials

NASA Astrophysics Data System (ADS)

Ilatikhameneh, Hesameddin; Tan, Yaohua; Novakovic, Bozidar; Klimeck, Gerhard; Rahman, Rajib; Appenzeller, Joerg

2015-12-01

In this work, the performance of Tunnel Field-Effect Transistors (TFETs) based on two-dimensional Transition Metal Dichalcogenide (TMD) materials is investigated by atomistic quantum transport simulations. One of the major challenges of TFETs is their low ON-currents. 2D material based TFETs can have tight gate control and high electric fields at the tunnel junction, and can in principle generate high ON-currents along with a sub-threshold swing smaller than 60 mV/dec. Our simulations reveal that high performance TMD TFETs, not only require good gate control, but also rely on the choice of the right channel material with optimum band gap, effective mass and source/drain doping level. Unlike previous works, a full band atomistic tight binding method is used self-consistently with 3D Poisson equation to simulate ballistic quantum transport in these devices. The effect of the choice of TMD material on the performance of the device and its transfer characteristics are discussed. Moreover, the criteria for high ON-currents are explained with a simple analytic model, showing the related fundamental factors. Finally, the subthreshold swing and energy-delay of these TFETs are compared with conventional CMOS devices.

Free vibration analysis of single-walled boron nitride nanotubes based on a computational mechanics framework

NASA Astrophysics Data System (ADS)

Yan, J. W.; Tong, L. H.; Xiang, Ping

2017-12-01

Free vibration behaviors of single-walled boron nitride nanotubes are investigated using a computational mechanics approach. Tersoff-Brenner potential is used to reflect atomic interaction between boron and nitrogen atoms. The higher-order Cauchy-Born rule is employed to establish the constitutive relationship for single-walled boron nitride nanotubes on the basis of higher-order gradient continuum theory. It bridges the gaps between the nanoscale lattice structures with a continuum body. A mesh-free modeling framework is constructed, using the moving Kriging interpolation which automatically satisfies the higher-order continuity, to implement numerical simulation in order to match the higher-order constitutive model. In comparison with conventional atomistic simulation methods, the established atomistic-continuum multi-scale approach possesses advantages in tackling atomic structures with high-accuracy and high-efficiency. Free vibration characteristics of single-walled boron nitride nanotubes with different boundary conditions, tube chiralities, lengths and radii are examined in case studies. In this research, it is pointed out that a critical radius exists for the evaluation of fundamental vibration frequencies of boron nitride nanotubes; opposite trends can be observed prior to and beyond the critical radius. Simulation results are presented and discussed.

Multiscale Molecular Dynamics Simulations of Model Hydrophobically Modified Ethylene Oxide Urethane Micelles.

PubMed

Yuan, Fang; Larson, Ronald G

2015-09-24

The flower-like micelles of various aggregation numbers of a model hydrophobically modified ethylene oxide urethane (HEUR) molecule, C16E45C16, and their corresponding starlike micelles, containing the surfactants C16E22 and C16E23, were studied by atomistic and coarse-grained molecular dynamic (MD) simulations. We used free energies from umbrella sampling to calculate the size distribution of micelle sizes and the average time for escape of a hydrophobic group from the micelle. Using the coarse-grained MARTINI force field, the most probable size of the model HEUR molecule was thereby determined to be about 80 hydrophobes per micelle and the average hydrophobe escape time to be about 0.1 s, both of which are consistent with previous experimental studies. Atomistic simulations reveal that hydrogen bond formation and the mean lifetime of hydration waters of the poly(ethylene oxide) (or PEO) groups are location-dependent in the HEUR micelle, with PEO groups immediately adjacent to the C16 groups forming the fewest hydrogen bonds with water and having hydration waters with longer lifetimes than those of the PEO groups located further away from the C16 groups.

Impact of the A2V Mutation on the Heterozygous and Homozygous Aβ1-40 Dimer Structures from Atomistic Simulations.

PubMed

Nguyen, Phuong H; Sterpone, Fabio; Campanera, Josep M; Nasica-Labouze, Jessica; Derreumaux, Philippe

2016-06-15

The A2V mutation was reported to protect from Alzheimer's disease in its heterozygous form and cause an early Alzheimer's disease type dementia in its homozygous form. Experiments showed that the aggregation rate follows the order A2V > WT (wild-type) > A2V-WT. To understand the impact of this mutation, we carried out replica exchange molecular dynamics simulations of Aβ1-40 WT-A2V and A2V-A2V dimers and compared to the WT dimer. Our atomistic simulations reveal that the mean secondary structure remains constant, but there are substantial differences in the intramolecular and intermolecular conformations upon single and double A2V mutation. Upon single mutation, the intrinsic disorder is reduced, the intermolecular potential energies are reduced, the population of intramolecular three-stranded β-sheets is increased, and the number of all α dimer topologies is decreased. Taken together, these results offer an explanation for the reduced aggregation rate of the Aβ1-40 A2V-WT peptides and the protective effect of A2V in heterozygotes.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

Summation rules for a fully nonlocal energy-based quasicontinuum method

NASA Astrophysics Data System (ADS)

Amelang, J. S.; Venturini, G. N.; Kochmann, D. M.

2015-09-01

The quasicontinuum (QC) method coarse-grains crystalline atomic ensembles in order to bridge the scales from individual atoms to the micro- and mesoscales. A crucial cornerstone of all QC techniques, summation or quadrature rules efficiently approximate the thermodynamic quantities of interest. Here, we investigate summation rules for a fully nonlocal, energy-based QC method to approximate the total Hamiltonian of a crystalline atomic ensemble by a weighted sum over a small subset of all atoms in the crystal lattice. Our formulation does not conceptually differentiate between atomistic and coarse-grained regions and thus allows for seamless bridging without domain-coupling interfaces. We review traditional summation rules and discuss their strengths and weaknesses with a focus on energy approximation errors and spurious force artifacts. Moreover, we introduce summation rules which produce no residual or spurious force artifacts in centrosymmetric crystals in the large-element limit under arbitrary affine deformations in two dimensions (and marginal force artifacts in three dimensions), while allowing us to seamlessly bridge to full atomistics. Through a comprehensive suite of examples with spatially non-uniform QC discretizations in two and three dimensions, we compare the accuracy of the new scheme to various previous ones. Our results confirm that the new summation rules exhibit significantly smaller force artifacts and energy approximation errors. Our numerical benchmark examples include the calculation of elastic constants from completely random QC meshes and the inhomogeneous deformation of aggressively coarse-grained crystals containing nano-voids. In the elastic regime, we directly compare QC results to those of full atomistics to assess global and local errors in complex QC simulations. Going beyond elasticity, we illustrate the performance of the energy-based QC method with the new second-order summation rule by the help of nanoindentation examples with automatic mesh adaptation. Overall, our findings provide guidelines for the selection of summation rules for the fully nonlocal energy-based QC method.

Universal mechanism of thermo-mechanical deformation in metallic glasses

DOE PAGES

Dmowski, W.; Tong, Y.; Iwashita, T.; ...

2015-02-11

Here we investigated the atomistic structure of metallic glasses subjected to thermo-mechanical creep deformation using high energy x-ray diffraction and molecular dynamics simulation. The experiments were performed in-situ, at high temperatures as a time dependent deformation in the elastic regime, and ex-situ on samples quenched under stress. We show that all the anisotropic structure functions of the samples undergone thermo-mechanical creep can be scaled into a single curve, regardless of the magnitude of anelastic strain, stress level and the sign of the stress, demonstrating universal behavior and pointing to unique atomistic unit of anelastic deformation. The structural changes due tomore » creep are strongly localized within the second nearest neighbors, involving only a small group of atoms.« less

Thermochemistry of organic reactions in microporous oxides by atomistic simulations: benchmarking against periodic B3LYP.

PubMed

Bleken, Francesca; Svelle, Stian; Lillerud, Karl Petter; Olsbye, Unni; Arstad, Bjørnar; Swang, Ole

2010-07-15

The methylation of ethene by methyl chloride and methanol in the microporous materials SAPO-34 and SSZ-13 has been studied using different periodic atomistic modeling approaches based on density functional theory. The RPBE functional, which earlier has been used successfully in studies of surface reactions on metals, fails to yield a qualitatively correct description of the transition states under study. Employing B3LYP as functional gives results in line with experimental data: (1) Methanol is adsorbed more strongly than methyl chloride to the acid site. (2) The activation energies for the methylation of ethene are slightly lower for SSZ-13. Furthermore, the B3LYP activation energies are lower for methyl chloride than for methanol.

The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood-Buff approaches.

PubMed

Kobayashi, Takeshi; Reid, Joshua E S J; Shimizu, Seishi; Fyta, Maria; Smiatek, Jens

2017-07-26

We study the properties of residual water molecules at different mole fractions in dialkylimidazolium based ionic liquids (ILs), namely 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM/BF 4 ) and 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM/BF 4 ) by means of atomistic molecular dynamics (MD) simulations. The corresponding Kirkwood-Buff (KB) integrals for the water-ion and ion-ion correlation behavior are calculated by a direct evaluation of the radial distribution functions. The outcomes are compared to the corresponding KB integrals derived by an inverse approach based on experimental data. Our results reveal a quantitative agreement between both approaches, which paves a way towards a more reliable comparison between simulation and experimental results. The simulation outcomes further highlight that water even at intermediate mole fractions has a negligible influence on the ion distribution in the solution. More detailed analysis on the local/bulk partition coefficients and the partial structure factors reveal that water molecules at low mole fractions mainly remain in the monomeric state. A non-linear increase of higher order water clusters can be found at larger water concentrations. For both ILs, a more pronounced water coordination around the cations when compared to the anions can be observed, which points out that the IL cations are mainly responsible for water pairing mechanisms. Our simulations thus provide detailed insights in the properties of dialkylimidazolium based ILs and their effects on water binding.

Multiscale modeling and simulation for nano/micro materials

NASA Astrophysics Data System (ADS)

Wang, Xianqiao

Continuum description and atomic description used to be two distinct methods in the community of modeling and simulations. Science and technology have become so advanced that our understanding of many physical phenomena involves the concepts of both. So our goal now is to build a bridge to make atoms and continua communicate with each other. Micromorphic theory (MMT) envisions a material body as a continuous collection of deformable particles; each possesses finite size and inner structure. It is considered as the most successful top-down formulation of a two-level continuum model to bridge the gap between the micro level and macro level. Therefore MMT can be expected to unveil many new classes of physical phenomena that fall beyond classical field theories. In this work, the constitutive equations for generalized Micromorphic thermoviscoelastic solid and generalized Micromorphic fluid have been formulated. To enlarge the domain of applicability of MMT, from nano, micro to macro, we take a bottom-up approach to re-derive the generalized atomistic field theory (AFT) comprehensively and completely and establish the relationship between AFT and MMT. Finite element (FE) method is then implemented to pursue the numerical solutions of the governing equations derived in AFT. When the finest mesh is used, i.e., the size of FE mesh is equal to the lattice constant of the material, the computational model becomes identical to molecular dynamics simulation. When a coarse mesh is used, the resulting model is a coarse-grained model, the majority of the degrees of freedom are eliminated and the computational cost is largely reduced. When the coarse mesh and finest mesh exist concurrently, i.e., the finest mesh is used in the critical regions and the coarser mesh is used in the far field, it leads naturally to a concurrent atomistic/continuum model. Atomic scale, coarse-grained scale and concurrent atomistic/continuum simulations have demonstrated the potential capability of AFT to simulate most grand challenging problems in nano/micro physics, and shown that AFT has the advantages of both atomic model and MMT. Therefore, AFT has accomplished the mission to bridge the gap between continuum mechanics and atomic physics.

Simulation of clustering and anisotropy due to Co step-edge segregation in vapor-deposited CoPt3

NASA Astrophysics Data System (ADS)

Maranville, B. B.; Schuerman, M.; Hellman, F.

2006-03-01

An atomistic mechanism is proposed for the creation of structural anisotropy and consequent large perpendicular magnetic anisotropy in vapor-deposited films of CoPt3 . Energetic considerations of bonding in Co-Pt suggest that Co segregates to step edges due to their low coordination, for all film orientations, while Pt segregates to the two low index surfaces. Coalescence of islands during growth cause these Co-rich step edges to become flat thin Co platelets in a Pt rich matrix, giving rise to the experimentally observed magnetic anisotropy. This proposed model is tested with kinetic Monte Carlo simulation of the vapor deposition growth. A tight-binding, second-moment approximation to the interatomic potential is used to calculate the probability of an atom hopping from one surface site to another, assuming an Arrhenius-like activation model of surface motion. Growth is simulated by allowing many hopping events per adatom. The simulated as-grown films show an asymmetry in Co-Co bonding between the in-plane and out-of-plane directions, in good agreement with experimental data. The growth temperature dependence found in the simulations is strong and similar to that seen in experiments, and an increase in Co edge segregation with increasing temperature is also observed.

Harnessing atomistic simulations to predict the rate at which dislocations overcome obstacles

NASA Astrophysics Data System (ADS)

Saroukhani, S.; Nguyen, L. D.; Leung, K. W. K.; Singh, C. V.; Warner, D. H.

2016-05-01

Predicting the rate at which dislocations overcome obstacles is key to understanding the microscopic features that govern the plastic flow of modern alloys. In this spirit, the current manuscript examines the rate at which an edge dislocation overcomes an obstacle in aluminum. Predictions were made using different popular variants of Harmonic Transition State Theory (HTST) and compared to those of direct Molecular Dynamics (MD) simulations. The HTST predictions were found to be grossly inaccurate due to the large entropy barrier associated with the dislocation-obstacle interaction. Considering the importance of finite temperature effects, the utility of the Finite Temperature String (FTS) method was then explored. While this approach was found capable of identifying a prominent reaction tube, it was not capable of computing the free energy profile along the tube. Lastly, the utility of the Transition Interface Sampling (TIS) approach was explored, which does not need a free energy profile and is known to be less reliant on the choice of reaction coordinate. The TIS approach was found capable of accurately predicting the rate, relative to direct MD simulations. This finding was utilized to examine the temperature and load dependence of the dislocation-obstacle interaction in a simple periodic cell configuration. An attractive rate prediction approach combining TST and simple continuum models is identified, and the strain rate sensitivity of individual dislocation obstacle interactions is predicted.

Microscopic origin of gating current fluctuations in a potassium channel voltage sensor.

PubMed

Freites, J Alfredo; Schow, Eric V; White, Stephen H; Tobias, Douglas J

2012-06-06

Voltage-dependent ion channels open and close in response to changes in membrane electrical potential due to the motion of their voltage-sensing domains (VSDs). VSD charge displacements within the membrane electric field are observed in electrophysiology experiments as gating currents preceding ionic conduction. The elementary charge motions that give rise to the gating current cannot be observed directly, but appear as discrete current pulses that generate fluctuations in gating current measurements. Here we report direct observation of gating-charge displacements in an atomistic molecular dynamics simulation of the isolated VSD from the KvAP channel in a hydrated lipid bilayer on the timescale (10-μs) expected for elementary gating charge transitions. The results reveal that gating-charge displacements are associated with the water-catalyzed rearrangement of salt bridges between the S4 arginines and a set of conserved acidic side chains on the S1-S3 transmembrane segments in the hydrated interior of the VSD. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Qingcheng, E-mail: qiy9@pitt.edu; To, Albert C., E-mail: albertto@pitt.edu

Surface effects have been observed to contribute significantly to the mechanical response of nanoscale structures. The newly proposed energy-based coarse-grained atomistic method Multiresolution Molecular Mechanics (MMM) (Yang, To (2015), ) is applied to capture surface effect for nanosized structures by designing a surface summation rule SR{sup S} within the framework of MMM. Combined with previously proposed bulk summation rule SR{sup B}, the MMM summation rule SR{sup MMM} is completed. SR{sup S} and SR{sup B} are consistently formed within SR{sup MMM} for general finite element shape functions. Analogous to quadrature rules in finite element method (FEM), the key idea to themore » good performance of SR{sup MMM} lies in that the order or distribution of energy for coarse-grained atomistic model is mathematically derived such that the number, position and weight of quadrature-type (sampling) atoms can be determined. Mathematically, the derived energy distribution of surface area is different from that of bulk region. Physically, the difference is due to the fact that surface atoms lack neighboring bonding. As such, SR{sup S} and SR{sup B} are employed for surface and bulk domains, respectively. Two- and three-dimensional numerical examples using the respective 4-node bilinear quadrilateral, 8-node quadratic quadrilateral and 8-node hexahedral meshes are employed to verify and validate the proposed approach. It is shown that MMM with SR{sup MMM} accurately captures corner, edge and surface effects with less 0.3% degrees of freedom of the original atomistic system, compared against full atomistic simulation. The effectiveness of SR{sup MMM} with respect to high order element is also demonstrated by employing the 8-node quadratic quadrilateral to solve a beam bending problem considering surface effect. In addition, the introduced sampling error with SR{sup MMM} that is analogous to numerical integration error with quadrature rule in FEM is very small. - Highlights: • Surface effect captured by Multiresolution Molecular Mechanics (MMM) is presented. • A novel surface summation rule within the framework of MMM is proposed. • Surface, corner and edges effects are accuterly captured in two and three dimension. • MMM with less 0.3% degrees of freedom of atomistics reproduces atomistic results.« less

Formation mechanism of gas bubble superlattice in UMo metal fuels: Phase-field modeling investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Shenyang; Burkes, Douglas E.; Lavender, Curt A.

2016-07-08

Nano-gas bubble superlattices are often observed in irradiated UMo nuclear fuels. However, the for- mation mechanism of gas bubble superlattices is not well understood. A number of physical processes may affect the gas bubble nucleation and growth; hence, the morphology of gas bubble microstructures including size and spatial distributions. In this work, a phase-field model integrating a first-passage Monte Carlo method to investigate the formation mechanism of gas bubble superlattices was devel- oped. Six physical processes are taken into account in the model: 1) heterogeneous generation of gas atoms, vacancies, and interstitials informed from atomistic simulations; 2) one-dimensional (1-D) migration of interstitials; 3) irradiation-induced dissolution of gas atoms; 4) recombination between vacancies and interstitials; 5) elastic interaction; and 6) heterogeneous nucleation of gas bubbles. We found that the elastic interaction doesn’t cause the gas bubble alignment, and fast 1-D migration of interstitials alongmore » $$\\langle$$110$$\\rangle$$ directions in the body-centered cubic U matrix causes the gas bubble alignment along $$\\langle$$110$$\\rangle$$ directions. It implies that 1-D interstitial migration along [110] direction should be the primary mechanism of a fcc gas bubble superlattice which is observed in bcc UMo alloys. Simulations also show that fission rates, saturated gas concentration, and elastic interaction all affect the morphology of gas bubble microstructures.« less

Atomistic Simulation of Interfaces in Materials of Solid State Ionics

NASA Astrophysics Data System (ADS)

Ivanov-Schitz, A. K.; Mazo, G. N.

2018-01-01

The possibilities of describing correctly interfaces of different types in solids within a computer experiment using molecular statics simulation, molecular dynamics simulation, and quantum chemical calculations are discussed. Heterophase boundaries of various types, including grain boundaries and solid electrolyte‒solid electrolyte and ionic conductor‒electrode material interfaces, are considered. Specific microstructural features and mechanisms of the ion transport in real heterophase structures (cationic conductor‒metal anode and anionic conductor‒cathode) existing in solid state ionics devices (such as solid-state batteries and fuel cells) are discussed.

Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Junghans, Christoph; Agarwal, Animesh; Delle Site, Luigi

Here, we discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within 10%–15% accuracy, is given by the Amdahl’s Law adapted to the specific quantities involved in the problem. The derivation of the predictive formula is general enough that it may be applied to the general case of molecular dynamics approaches where a reduction of degrees of freedom in a multi scale fashion occurs.

Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique

DOE PAGES

Junghans, Christoph; Agarwal, Animesh; Delle Site, Luigi

2017-06-01

Here, we discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within 10%–15% accuracy, is given by the Amdahl’s Law adapted to the specific quantities involved in the problem. The derivation of the predictive formula is general enough that it may be applied to the general case of molecular dynamics approaches where a reduction of degrees of freedom in a multi scale fashion occurs.

Mimicking coarse-grained simulations without coarse-graining: enhanced sampling by damping short-range interactions.

PubMed

Wei, Dongshan; Wang, Feng

2010-08-28

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Mimicking coarse-grained simulations without coarse-graining: Enhanced sampling by damping short-range interactions

NASA Astrophysics Data System (ADS)

Wei, Dongshan; Wang, Feng

2010-08-01

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

PubMed

Prior, C; Danilāne, L; Oganesyan, V S

2018-05-16

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

Computer simulation of thermal conductivity in vulcanized polyisoprene at variable strain and temperature

NASA Astrophysics Data System (ADS)

Engelmann, Sven; Meyer, Jan; Hentschke, Reinhard

2017-08-01

We study the thermal conductivity tensor in an atomistic model of vulcanized cis-1,4-polyisoprene (PI) rubber via molecular dynamics simulations. Our polymer force field is based on V. A. Harmandaris et al. [J. Chem. Phys. 116, 436 (2002), 10.1063/1.1416872], whereas the polymerization algorithm follows the description in J. Hager et al. [Macromolecules 48, 9039 (2015), 10.1021/acs.macromol.5b01864]. The polymer chains are chemically cross linked via sulfur bridges of adjustable cross-link density. A volume-conserving uniaxial strain of up to 200% is applied to the systems. The widely used GROMACS simulation package is adapted to allow using the Green-Kubo approach to calculate the thermal conductivity tensor components. Our analysis of the heat flux autocorrelation functions leads to the conclusion that the thermal conductivity in PI is governed by short-lived phonon modes at low wave numbers due to deformation of the monomers along the polymer backbone. Applying uniaxial strain causes increased orientation of monomers along the strain direction, which enhances the attendant thermal conductivity component. We find an exponential increase of the conductivity in stretch direction in terms of an attendant orientation order parameter. This is accompanied by a simultaneous decline of thermal conductivity in the orthogonal directions. Increase of the cross-link density only has a weak effect on thermal conductivity in the unstrained system, even at high cross-link density. In the strained system we do observed a rising thermal conductivity in the limit of high stress. This increase is attributed to enhanced coupling between chains rather than to their orientation.

Molecular Dynamics Simulations of Hugoniot Relations for Poly[methyl methacrylate

DTIC Science & Technology

2011-11-01

A Method for Atomistic Simulations of Shocked Materials. Physical Review E 2000, 63, 016121. 5. Plimpton , S . Fast Parallel Algorithms for Short...5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) Tanya L. Chantawansri, Edward F. C. Byrd, Betsy M. Rice, and Jan W. Andzelm 5d. PROJECT NUMBER 5e. TASK...NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) U.S. Army Research Laboratory ATTN: RDRL-WMM-G Aberdeen

Quantifying the influence of twin boundaries on the deformation of nanocrystalline copper using atomistic simulations

DOE PAGES

Tucker, Garritt J.; Foiles, Stephen Martin

2014-09-22

Over the past decade, numerous efforts have sought to understand the influence of twin boundaries on the behavior of polycrystalline materials. Early results suggested that twin boundaries within nanocrystalline face-centered cubic metals have a considerable effect on material behavior by altering the activated deformation mechanisms. In this work, we employ molecular dynamics simulations to elucidate the role of twin boundaries on the deformation of <100> columnar nanocrystalline copper at room temperature under uniaxial strain. We leverage non-local kinematic metrics, formulated from continuum mechanics theory, to compute atomically-resolved rotational and strain fields during plastic deformation. These results are then utilized tomore » compute the distribution of various nanoscale mechanisms during straining, and quantitatively resolve their contribution to the total strain accommodation within the microstructure, highlighting the fundamental role of twin boundaries. Our results show that nanoscale twins influence nanocrystalline copper by altering the cooperation of fundamental deformation mechanisms and their contributed role in strain accommodation, and we present new methods for extracting useful information from atomistic simulations. The simulation results suggest a tension–compression asymmetry in the distribution of deformation mechanisms and strain accommodation by either dislocations or twin boundary mechanisms. In highly twinned microstructures, twin boundary migration can become a significant deformation mode, in comparison to lattice dislocation plasticity in non-twinned columnar microstructures, especially during compression.« less

Multiscale equation-free algorithms for molecular dynamics

NASA Astrophysics Data System (ADS)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nomura, K; Seymour, R; Wang, W

2009-02-17

A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based onmore » hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).« less

Atomistic and Coarse-Grained Modeling of the Adsorption of Graphene Nanoflakes at the Oil-Water Interface.

PubMed

Ardham, Vikram Reddy; Leroy, Frédéric

2018-03-01

The high interfacial tension between two immiscible liquids can provide the necessary driving force for the self-assembly of nanoparticles at the interface. Particularly, the interface between water and oily liquids (hydrocarbon chains) has been exploited to prepare networks of highly interconnected graphene sheets of only a few layers thickness, which are well suited for industrial applications. Studying such complex systems through particle-based simulations could greatly enhance the understanding of the various driving forces in action and could possibly give more control over the self-assembly process. However, the interaction potentials used in particle-based simulations are typically derived by reproducing bulk properties and are therefore not suitable for describing systems dominated by interfaces. To address this issue, we introduce a methodology to derive solid-liquid interaction potentials that yield an accurate representation of the balance between interfacial interactions at atomistic and coarse-grained resolutions. Our approach is validated through its ability to lead to the adsorption of graphene nanoflakes at the interface between water and n-hexane. The development of accurate coarse-grained potentials that our approach enables will allow us to perform large-scale simulations to study the assembly of graphene nanoparticles at the interface between immiscible liquids. Our methodology is illustrated through a simulation of many graphene nanoflakes adsorbing at the interface.

Room temperature deformation mechanisms of alumina particles observed from in situ micro-compression and atomistic simulations.

DOE PAGES

Sarobol, Pylin; Chandross, Michael E.; Carroll, Jay D.; ...

2015-09-22

Aerosol deposition (AD) is a solid-state deposition technology that has been developed to fabricate ceramic coatings nominally at room temperature. Sub-micron ceramic particles accelerated by pressurized gas impact, deform, and consolidate on substrates under vacuum. Ceramic particle consolidation in AD coatings is highly dependent on particle deformation and bonding; these behaviors are not well understood. In this work, atomistic simulations and in situ micro-compressions in the scanning electron microscope, and the transmission electron microscope (TEM) were utilized to investigate fundamental mechanisms responsible for plastic deformation/fracture of particles under applied compression. Results showed that highly defective micron-sized alumina particles, initially containingmore » numerous dislocations or a grain boundary, exhibited no observable shape change before fracture/fragmentation. Simulations and experimental results indicated that particles containing a grain boundary only accommodate low strain energy per unit volume before crack nucleation and propagation. In contrast, nearly defect-free, sub-micron, single crystal alumina particles exhibited plastic deformation and fracture without fragmentation. Dislocation nucleation/motion, significant plastic deformation, and shape change were observed. Simulation and TEM in situ micro-compression results indicated that nearly defect-free particles accommodate high strain energy per unit volume associated with dislocation plasticity before fracture. As a result, the identified deformation mechanisms provide insight into feedstock design for AD.« less

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

Evaluating variability with atomistic simulations: the effect of potential and calculation methodology on the modeling of lattice and elastic constants

NASA Astrophysics Data System (ADS)

Hale, Lucas M.; Trautt, Zachary T.; Becker, Chandler A.

2018-07-01

Atomistic simulations using classical interatomic potentials are powerful investigative tools linking atomic structures to dynamic properties and behaviors. It is well known that different interatomic potentials produce different results, thus making it necessary to characterize potentials based on how they predict basic properties. Doing so makes it possible to compare existing interatomic models in order to select those best suited for specific use cases, and to identify any limitations of the models that may lead to unrealistic responses. While the methods for obtaining many of these properties are often thought of as simple calculations, there are many underlying aspects that can lead to variability in the reported property values. For instance, multiple methods may exist for computing the same property and values may be sensitive to certain simulation parameters. Here, we introduce a new high-throughput computational framework that encodes various simulation methodologies as Python calculation scripts. Three distinct methods for evaluating the lattice and elastic constants of bulk crystal structures are implemented and used to evaluate the properties across 120 interatomic potentials, 18 crystal prototypes, and all possible combinations of unique lattice site and elemental model pairings. Analysis of the results reveals which potentials and crystal prototypes are sensitive to the calculation methods and parameters, and it assists with the verification of potentials, methods, and molecular dynamics software. The results, calculation scripts, and computational infrastructure are self-contained and openly available to support researchers in performing meaningful simulations.

Atomistic Modeling of Quaternary Alloys: Ti and Cu in NiAl

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Mosca, Hugo O.; Wilson, Allen W.; Noebe, Ronald D.; Garces, Jorge E.

2002-01-01

The change in site preference in NiAl(Ti,Cu) alloys with concentration is examined experimentally via ALCHEMI and theoretically using the Bozzolo-Ferrante-Smith (BFS) method for alloys. Results for the site occupancy of Ti and Cu additions as a function of concentration are determined experimentally for five alloys. These results are reproduced with large-scale BFS-based Monte Carlo atomistic simulations. The original set of five alloys is extended to 25 concentrations, which are modeled by means of the BFS method for alloys, showing in more detail the compositional range over which major changes in behavior occur. A simple but powerful approach based on the definition of atomic local environments also is introduced to describe energetically the interactions between the various elements and therefore to explain the observed behavior.

Redox reactions with empirical potentials: atomistic battery discharge simulations.

PubMed

Dapp, Wolf B; Müser, Martin H

2013-08-14

Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

Identification of atomic-level mechanisms for gas-phase X- + CH3Y SN2 reactions by combined experiments and simulations.

PubMed

Xie, Jing; Otto, Rico; Mikosch, Jochen; Zhang, Jiaxu; Wester, Roland; Hase, William L

2014-10-21

For the traditional model of gas-phase X(-) + CH3Y SN2 reactions, C3v ion-dipole pre- and postreaction complexes X(-)---CH3Y and XCH3---Y(-), separated by a central barrier, are formed. Statistical intramolecular dynamics are assumed for these complexes, so that their unimolecular rate constants are given by RRKM theory. Both previous simulations and experiments have shown that the dynamics of these complexes are not statistical and of interest is how these nonstatistical dynamics affect the SN2 rate constant. This work also found there was a transition from an indirect, nonstatistical, complex forming mechanism, to a direct mechanism, as either the vibrational and/or relative translational energy of the reactants was increased. The current Account reviews recent collaborative studies involving molecular beam ion-imaging experiments and direct (on-the-fly) dynamics simulations of the SN2 reactions for which Cl(-), F(-), and OH(-) react with CH3I. Also considered are reactions of the microsolvated anions OH(-)(H2O) and OH(-)(H2O)2 with CH3I. These studies have provided a detailed understanding of the atomistic mechanisms for these SN2 reactions. Overall, the atomistic dynamics for the Cl(-) + CH3I SN2 reaction follows those found in previous studies. The reaction is indirect, complex forming at low reactant collision energies, and then there is a transition to direct reaction between 0.2 and 0.4 eV. The direct reaction may occur by rebound mechanism, in which the ClCH3 product rebounds backward from the I(-) product or a stripping mechanism in which Cl(-) strips CH3 from the I atom and scatters in the forward direction. A similar indirect to direct mechanistic transition was observed in previous work for the Cl(-) + CH3Cl and Cl(-) + CH3Br SN2 reactions. At the high collision energy of 1.9 eV, a new indirect mechanism, called the roundabout, was discovered. For the F(-) + CH3I reaction, there is not a transition from indirect to direct reaction as Erel is increased. The indirect mechanism, with prereaction complex formation, is important at all the Erel investigated, contributing up ∼60% of the reaction. The remaining direct reaction occurs by the rebound and stripping mechanisms. Though the potential energy curve for the OH(-) + CH3I reaction is similar to that for F(-) + CH3I, the two reactions have different dynamics. They are akin, in that for both there is not a transition from an indirect to direct reaction. However, for F(-) + CH3I indirect reaction dominates at all Erel, but it is less important for OH(-) + CH3I and becomes negligible as Erel is increased. Stripping is a minor channel for F(-) + CH3I, but accounts for more than 60% of the OH(-) + CH3I reaction at high Erel. Adding one or two H2O molecules to OH(-) alters the reaction dynamics from that for unsolvated OH(-). Adding one H2O molecule enhances indirect reaction at low Erel, and changes the reaction mechanism from primarily stripping to rebound at high Erel. With two H2O molecules the dynamics is indirect and isotropic at all collision energies.

Coarse-grained hydrodynamics from correlation functions

NASA Astrophysics Data System (ADS)

Palmer, Bruce

2018-02-01

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is demonstrated on a discrete particle simulation of diffusion with a spatially dependent diffusion coefficient. Correlation functions are calculated from the particle simulation and the spatially varying diffusion coefficient is recovered using a fitting procedure.