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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
NASA NTRS1989

A model for including thermal conduction in molecular dynamics simulations

A technique is introduced for including thermal conduction in molecular dynamics simulations for solids. A model is developed to allow energy flow between the computational cell and the bulk of the solid when periodic boundary conditions cannot be used. Thermal conduction is achieved by scaling the velocities of atoms in a transitional boundary layer. The scaling factor is obtained from the thermal diffusivity, and the results show good agreement with the solution for a continuous medium at long times. The effects of different temperature and size of the system, and of variations in strength parameter, atomic mass, and thermal diffusivity were investigated. In all cases, no significant change in simulation results has been found.

Wu, Yue↗
DOE OSTI2020

Elastic Properties of Plasma-Exposed Tungsten Predicted by Molecular-Dynamics Simulations

We report results of systematic molecular-dynamics computations of the elastic properties of single-crystalline tungsten containing structural defects, voids and overpressurized He nanobubbles, related to plasma exposure of tungsten serving as a plasma- facing component (PFC) in nuclear fusion devices. Our computations reveal that the empty voids are centers of dilatation resulting in development of tensile stress in the tungsten matrix, whereas He-filled voids (nanobubbles) introduce compressive stress in the plasma-exposed tungsten. We find that the dependence of the elastic moduli of plasma-exposed tungsten, namely, the bulk, Young, and shear modulus, on its void fraction follows a universal exponential scaling relation. We also find that the elastic moduli of plasma-exposed tungsten soften substantially as a function of He content in the tungsten matrix, following an exponential scaling relation; this He-induced exponential softening is in addition to the softening caused in the matrix with increasing temperature. A systematic characterization of the dependence of the elastic moduli on the He bubble size reveals that He bubble growth affects significantly both the bulk modulus and the Poisson ratio of plasma-exposed tungsten, while its effect on the Young and shear moduli of the plasma-exposed material is weak. Our findings contribute directly to the development of a structure-properties database that is required for the predictive modeling of the dynamical response of PFCs in nuclear fusion devices.

36 MATERIALS SCIENCE↗
NASA NTRS1995

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

Jaffe, Richard↗
NASA NTRS2007

Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation

The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.

Yamakov, V.↗
DOE OSTI2026

MixPI: Mixed-time slicing path integral software for quantized molecular dynamics simulations

We introduce the MixPI software to implement path integral molecular dynamics (PIMD) simulations for the study of condensed phase systems where nuclear quantum effects (NQEs) are important. In contrast to existing PIMD simulation software, MixPI enables the implementation of mixed quantum–classical path integral simulations where only a subset of system degrees of freedom (dofs) are treated quantum mechanically in an extended phase space while the remaining dofs are described classically. We expect this software to be particularly useful for simulations of electron and proton transfer in condensed phase systems, as well as for the study of biological and material systems where only a handful of dofs contribute significantly to the observed NQEs. We demonstrate the use of MixPI in two different systems. The first is a simple water model where we implement a set of mixed quantum–classical simulations to compute average energy and radial distribution functions. We use these simulations to benchmark the effectiveness of MixPI and to demonstrate how it enables systematic investigation into the origin of observed NQEs. We then compute radial distribution functions for a system where MixPI is essential: a solvated metal (M 2+ ) cation described using an explicit quantized electron localized on an M 3+ ion in water.

chemical physics↗
DOE OSTI2020

Identification of preferred multimodal ligand‐binding regions on IgG1 F C using nuclear magnetic resonance and molecular dynamics simulations

Abstract In this study, the binding of multimodal chromatographic ligands to the IgG1 F C domain were studied using nuclear magnetic resonance and molecular dynamics simulations. Nuclear magnetic resonance experiments carried out with chromatographic ligands and a perdeuterated 15 N‐labeled F C domain indicated that while single‐mode ion exchange ligands interacted very weakly throughout the F C surface, multimodal ligands containing negatively charged and aromatic moieties interacted with specific clusters of residues with relatively high affinity, forming distinct binding regions on the F C . The multimodal ligand‐binding sites on the F C were concentrated in the hinge region and near the interface of the C H 2 and C H 3 domains. Furthermore, the multimodal binding sites were primarily composed of positively charged, polar, and aliphatic residues in these regions, with histidine residues exhibiting some of the strongest binding affinities with the multimodal ligand. Interestingly, comparison of protein surface property data with ligand interaction sites indicated that the patch analysis on F C corroborated molecular‐level binding information obtained from the nuclear magnetic resonance experiments. Finally, molecular dynamics simulation results were shown to be qualitatively consistent with the nuclear magnetic resonance results and to provide further insights into the binding mechanisms. An important contribution to multimodal ligand‐F C binding in these preferred regions was shown to be electrostatic interactions and π–π stacking of surface‐exposed histidines with the ligands. This combined biophysical and simulation approach has provided a deeper molecular‐level understanding of multimodal ligand–F C interactions and sets the stage for future analyses of even more complex biotherapeutics.

Gudhka, Ronak B.↗
NASA NTRS1995

Molecular dynamics simulation of a piston driven shock wave in a hard sphere gas

Molecular dynamics simulation is used to study the piston driven shock wave at Mach 1.5, 3, and 10. A shock tube, whose shape is a circular cylinder, is filled with hard sphere molecules having a Maxwellian thermal velocity distribution and zero mean velocity. The piston moves and a shock wave is generated. All collisions are specular, including those between the molecules and the computational boundaries, so that the shock development is entirely causal, with no imposed statistics. The structure of the generated shock is examined in detail, and the wave speed; profiles of density, velocity, and temperature; and shock thickness are determined. The results are compared with published results of other methods, especially the direct simulation Monte-Carlo method. Property profiles are similar to those generated by direct simulation Monte-Carlo method. The shock wave thicknesses are smaller than the direct simulation Monte-Carlo results, but larger than those of the other methods. Simulation of a shock wave, which is one-dimensional, is a severe test of the molecular dynamics method, which is always three-dimensional. A major challenge of the thesis is to examine the capability of the molecular dynamics methods by choosing a difficult task.

Woo, Myeung-Jouh↗
NASA NTRS1993

Evaporation kinetics of Mg2SiO4 crystals and melts from molecular dynamics simulations

Computer simulations based on the molecular dynamics (MD) technique were used to study the mechanisms and kinetics of free evaporation from crystalline and molten forsterite (i.e., Mg2SiO4) on an atomic level. The interatomic potential employed for these simulations reproduces the energetics of bonding in forsterite and in gas-phase MgO and SiO2 reasonably accurately. Results of the simulation include predicted evaporation rates, diffusion rates, and reaction mechanisms for Mg2SiO4(s or l) yields 2Mg(g) + 20(g) + SiO2(g).

Kubicki, J. D.↗
DOE OSTI2023

Molecular-dynamics simulation methods for macromolecular crystallography

It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein–solvent interface. To address this limitation, a set of MD–MX methods that combine MD simulations of protein crystals with conventional modeling and refinement tools have been developed. In an application to a cyclic adenosine monophosphate-dependent protein kinase at room temperature, the procedure improved the interpretation of ambiguous density, yielding an alternative water model and a revised protein model including multiple conformations. The revised model provides mechanistic insights into the catalytic and regulatory interactions of the enzyme. The same methods may be used in other MX studies to seek mechanistic insights.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effects of Surface Orientation and Termination Plane on Glass‐to‐Crystal Transformation of Lithium Disilicate by Molecular Dynamics Simulations

Glass‐to‐crystal transformation of lithium disilicate is studied using molecular dynamics simulations using an effective partial charge potential. The structural evolution of the interface between glassy and crystalline lithium disilicate is analyzed to simulate crystallization of glass on pre‐existing crystal seeds. Besides previously used atomic number density, the distribution of Q n species (Si tetrahedra with n bridging oxygen) is shown to be an effective parameter for following this transformation quantitatively. The early stages of crystal growth are significantly affected by the orientation and termination of the surface of adjacent crystal, as indicated by calculated atomic density, partial ordering, atomic segregation, and an increase in Q 3 concentration. In particular, under‐coordinated Si within the outer crystal layer is found to be most effective in transforming the amorphous structure toward crystallinity. The increase in Q 3 in the glass close to interface region most clearly shows the initial stage of lithium disilicate crystal growth.

Sun, Wei↗
DOE OSTI2024

Large-scale atomistic model construction of subbituminous and bituminous coals for solvent extraction simulations with reactive molecular dynamics

Large-scale atomistic models for complex polycyclic aromatic hydrocarbon systems help understand the chemical properties and behaviors of complex feedstocks such as coal or petroleum. However, the development and utilization of large-scale models remain limited due to the difficulty in achieving the varied structural characteristics necessary to capture stochastic nature of these feedstocks. Here we demonstrate a systematic workflow to construct stochastic molecular systems from a broad analytical suite: high-resolution transmission electron microscopy (HRTEM), carbon-13 nuclear magnetic resonance spectroscopy ( 13 C NMR), laser desorption ionization mass spectroscopy (LDI-MS), and elemental analysis. We present a model construction and analysis utility of a new Python-based module. We selected one subbituminous and three high-volatile bituminous coals to construct large-scale models (~40,000 atoms). The constructed models were utilized to examine the affinity for solvent extraction (naphthalene or tetralin) and the effect of structural properties (e.g., aromatic cluster size, functional groups, and cross-linking) in reactive molecular dynamics simulations. Complex chemical reactions were monitored with bond order transitions, intermediates formation, and mass distributions. Reactive molecular dynamics simulations suggest a plausible chemical extraction process and products for the complex fossil feedstocks. The results indicated that radical formations with bond breaking of bridging oxygens and carbons were required at high temperatures to facilitate hydrogeneration and extraction of gas molecules from radical-free molecules. We observed that aliphatic chains of tetralin were easily decomposed and combined with radicals to form small size of molecules with aryl bonding, mainly increasing molecules in the 500–1000 Da, while naphthalene had little impact on chemical extraction process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

RAS Protein Molecular Dynamics Simulations

This dataset contains 6401 files that describe parameters and other inputs for running molecular dynamics computer simulations of Ras proteins associated with a lipid-based cell membrane model in water, as well as resulting time-trajectories of atomic motion in these simulations. Specifically, the content includes: (a) 21 files containing generalized force field parameters, and (b) 22 files of similar format and content for each of 290 separate molecular dynamics simulations (22 ´ 290 = 6,380). The total size of this data set is 1.0 TB.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Thermophysical properties of simple liquid metals: A brief review of theory

In this paper, we review the current theory of the thermophysical properties of simple liquid metals. The emphasis is on thermodynamic properties, but we also briefly discuss the nonequilibrium properties of liquid metals. We begin by defining a 'simple liquid metal' as one in which the valence electrons interact only weakly with the ionic cores, so that the interaction can be treated by perturbation theory. We then write down the equilibrium Hamiltonian of a liquid metal as a sum of five terms: the bare ion-ion interaction, the electron-electron interaction, the bare electron-ion interaction, and the kinetic energies of electrons and ions. Since the electron-ion interaction can be treated by perturbation, the electronic part contributes in two ways to the Helmholtz free energy: it gives a density-dependent term which is independent of the arrangement of ions, and it acts to screen the ion-ion interaction, giving rise to effective ion-ion pair potentials which are density-dependent, in general. After sketching the form of a typical pair potential, we briefly enumerate some methods for calculating the ionic distribution function and hence the Helmholtz free energy of the liquid: monte Carlo simulations, molecular dynamics simulations, and thermodynamic perturbation theory. The final result is a general expression for the Helmholtz free energy of the liquid metal. It can be used to calculate a wide range of thermodynamic properties of simple metal liquids, which we enumerate. They include not only a range of thermodynamic coefficients of both metals and alloys, but also many aspects of the phase diagram, including freezing curves of pure elements and phase diagrams of liquid alloys (including liquidus and solidus curves). We briefly mention some key discoveries resulting from previous applications of this method, and point out that the same methods work for other materials not normally considered to be liquid metals (such as colloidal suspensions, in which the suspended microspheres behave like ions screened by the salt solution in which they are suspended). We conclude with a brief discussion of some non-equilibrium (i.e., transport) properties which can be treated by an extension of these methods. These include electrical resistivity, thermal conductivity, viscosity, atomic self-diffusion coefficients, concentration diffusion coefficients in alloys, surface tension and thermal emissivity. Finally, we briefly mention two methods by which the theory might be extended to non-simple liquid metals: these are empirical techniques (i.e., empirical two- and three-body potentials), and numerical many-body approaches. Both may be potentially applicable to extremely complex systems, such as nonstoichiometric liquid semiconductor alloys.

Stroud, David↗
DOE OSTI2024

Understanding and Manipulating Counterion Condensation within Charged Polymer Electrolytes for Selective and Low Resistant Membrane Separations

Polymeric ion-exchange membranes are found at the heart of numerous electrochemical systems spanning separations (electrodialysis and membrane capacitive deionization) and energy conversion and storage (flow batteries, fuel cells, and electrolyzers). The ion-exchange membrane separators need to be ion conducting but electron insulating, and in many scenarios selective for a particular ion to conduct. Because of their polymeric nature, the molecular architectures of ion-exchange membranes lack the molecular precision found in many inorganic materials. Plus, they contain numerous structural defects that impede ionic transport. As a result of their poor structure, it has been difficult to carefully probe the underlying physics that governs ion transport in ion-exchange membranes. We investigated counterion condensation phenomena in ion-exchange membranes and correlated it to bulk ionic charge transport and selectivity in precisely defined and long-range ordered materials afforded through the principles of directed self-assembly. A multi-faceted approach spanning i.) advanced metrology, two-dimensional atomic force microscopy, x-ray scattering, and ion-exchange equilibria, and ii.) molecular simulations (classical molecular dynamics and ab-inito molecular dynamics) that bridge multiple time and length scales, were employed to correlate the extent of counterion condensation to ionic conductivity and selectivity. After uncovering the extent of the condensation phenomena in this project, new macromolecular chemistries were employed to manipulate the ion pairing interactions of the condensed counterions to tethered ions on the polymer backbone so more facile and selective conduction rates can be attained. The research has aided in the rational design of polymeric ion-exchange membrane separators with high current density for electrochemical systems and subsequently better energy efficiency.

36 MATERIALS SCIENCE↗
NASA NTRS2008

Molecular Dynamics Simulations of Adhesion at Epoxy Interfaces

The effect of moisture on adhesives used in aerospace applications can be modeled with chemically specific techniques such as molecular dynamics simulation. In the present study, the surface energy and work of adhesion are calculated for epoxy surfaces and interfaces, respectively, by using molecular dynamics simulation. Modifications are made to current theory to calculate the work of adhesion at the epoxy-epoxy interface with and without water. Quantitative agreement with experimental values is obtained for the surface energy and work of adhesion at the interface without water. The work of adhesion agrees qualitatively with the experimental values for the interface with water: the magnitude is reduced 15% with respect to the value for the interface without water. A variation of 26% in the magnitude is observed depending on the water configuration at a concentration of 1.6 wt%. The methods and modifications to the method that are employed to obtain these values are expected to be applicable for other epoxy adhesives to determine the effects of moisture uptake on their work of adhesion.

Frankland, Sarah-Jane V.↗
DOE OSTI2020

ReaxFF molecular dynamics simulations of electrolyte–water systems at supercritical temperature

We have performed ReaxFF molecular dynamics simulations of alkali metal–chlorine pairs in different water densities at supercritical temperature (700 K) to elucidate the structural and dynamical properties of the system. The radial distribution function and the angular distribution function explain the inter-ionic structural and orientational arrangements of atoms during the simulation. The coordination number of water molecules in the solvation shell of ions increases with an increase in the radius of ions. We find that the self-diffusion coefficient of metal ions increases with a decrease in density under supercritical conditions due to the formation of voids within the system. The hydrogen bond dynamics has been interpreted by the residence time distribution of various ions, which shows Li+ having the highest water retaining capability. The void distribution within the system has been analyzed by using the Voronoi polyhedra algorithm providing an estimation of void formation within the system at high temperatures. We observe the formation of salt clusters of Na+ and K+ at low densities due to the loss of dielectric constants of ions. The diffusion of ions gets altered dramatically due to the formation of voids and nucleation of ions in the system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Code modernization strategies for short-range non-bonded molecular dynamics simulations

Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase in parallelism are molecular dynamics simulations. In this paper, we describe our efforts at modernizing the ESPResSo++ simulation package for molecular dynamics by restructuring its particle data layout for efficient memory accesses and applying vectorization techniques to benefit the calculation of short-range non-bonded forces, which results in an overall three times speedup and serves as a baseline for further optimizations. We also implement fine-grained parallelism for multi-core CPUs through HPX, a C++ runtime system which uses lightweight threads and an asynchronous many-task approach to maximize concurrency. Our goal is to evaluate the performance of an HPX-based approach compared to the bulk-synchronous MPI-based implementation. This requires the introduction of an additional layer to the domain decomposition scheme that defines the task granularity. On spatially inhomogeneous systems, which impose a corresponding load-imbalance in traditional MPI-based approaches, we demonstrate that by choosing an optimal task size, the efficient work-stealing mechanisms of HPX can overcome the overhead of communication resulting in an overall 1.4 times speedup compared to the baseline MPI version.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2017

Modeling Chemical Reactions in Classical Molecular Dynamics Simulations

An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics (MD) simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed.

Jacob R Gissinger↗