Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular dynamics”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
NASA NTRS1991

Molecular dynamics and quasidynamics simulations of the annealing of bulk and near-surface interstitials formed in molecular-beam epitaxial Si due to low-energy particle bombardment during deposition

The relaxation, diffusion, and annihilation of split and hexagonal interstitials resulting from 10 eV Si irradiation of (2x1)-terminated Si(100) are investigated. Molecular dynamics and quasidynamics simulations, utilizing the Tersoff many-body potential are used in the investigation. The interstitials are created in layers two through six, and stable atomic configurations and total potential energies are derived as a function of site symmetry and layer depth. The interstitial Si atoms are allowed to diffuse, and the total potential energy changes are calculated. Lattice configurations along each path, as well as the starting configurations, are relaxed, and minimum energy diffusion paths are derived. The results show that the minimum energy paths are toward the surface and generally involved tetrahedral sites. The calculated interstitial migration activation energies are always less than 1.4 eV and are much lower in the near-surface region than in the bulk.

Kitabatake, M.↗
DOE OSTI2021

An Investigation into the Approximations Used in Wave Packet Molecular Dynamics for the Study of Warm Dense Matter

Wave packet molecular dynamics (WPMD) has recently received a lot of attention as a computationally fast tool with which to study dynamical processes in warm dense matter beyond the Born–Oppenheimer approximation. These techniques, typically, employ many approximations to achieve computational efficiency while implementing semi-empirical scaling parameters to retain accuracy. We investigated three of the main approximations ubiquitous to WPMD: a restricted basis set, approximations to exchange, and the lack of correlation. We examined each of these approximations in regard to atomic and molecular hydrogen in addition to a dense hydrogen plasma. We found that the biggest improvement to WPMD comes from combining a two-Gaussian basis with a semi-empirical correction based on the valence-bond wave function. A single parameter scales this correction to match experimental pressures of dense hydrogen. Ultimately, we found that semi-empirical scaling parameters are necessary to correct for the main approximations in WPMD. However, reducing the scaling parameters for more ab-initio terms gives more accurate results and displays the underlying physics more readily.

Angermeier, William A. (ORCID:0000000177161564)↗
DOE OSTI2021

Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations

A generalization of the Lees-Edwards periodic boundary conditions (gLE-PBC) for molecular dynamics (MD) simulations is developed to allow for arbitrary deformations to be applied to the domain. The gLE-PBC domain remains a rectangular cuboid regardless of the applied deformation in contrast with the Lagrangian-rhomboid periodic boundary conditions (LR-PBC) where the domain deforms according to the applied deformation. Furthermore, the kinematics of gLE-PBC are validated against pure shear. The gLE-PBC method for interacting systems is then validated against the LR-PBC method and analytical solutions for a solid under isotropic compression, one-dimensional shearing, three-dimensional extension and shearing and for a liquid under Couette flow. Bulk physical properties extracted from the gLE-PBC simulations agree well with values calculated from equilibrium MD simulations. Three dimensional shearing and a deformation with a full velocity gradient matrix are also simulated, showing the range of problems gLE-PBC can explore.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRSDate not supplied

REACTER: A Heuristic Method for Reactive Molecular Dynamics

REACTER (www.reacter.org) is a heuristic protocol that enables the simulation of complex reactions using atomistic molecular dynamics (MD) with a fixed-valence force field. Incorporating reactions into classical MD with this approach allows modeling of reactive systems over greatly-increased time scales, enabling systems to be modeled with MD that would not otherwise be feasible. One or more competing multi-step reactions or series of reactions can be invoked simultaneously. Special treatment can be applied to neighboring atoms to relax high energy configurations while the simulation progresses. The original version of REACTER, which was implemented in the open-source LAMMPS simulation package as fix bond/react, was only available for serial simulations. This work describes the expansion of fix bond/react for use in parallel simulations, as well as the addition of various new options, including deletion of reaction by-products, reversible reactions, and custom reaction constraints. These new capabilities are demonstrated through large-scale simulations (200,000+ atoms) of the polymerization of polystyrene and nylon 6,6. The morphologies of both polymers are analyzed after reaching >99% extent of polymerization. Finally, the newly-added reversible reactions feature is demonstrated by rupturing these highly-entangled systems under uniaxial strain by defining a chain scission reaction.

polymer simulations, molecular dynamics↗
DOE OSTI2025

Infrared spectral signatures of interfacial water at TiO 2 –electrolyte interfaces from deep potential molecular dynamics

Vibrational spectroscopy is a powerful tool for probing water at oxide–electrolyte interfaces, but its molecular interpretation can be challenging. Here, we employ deep potential long-range molecular dynamics simulations with layer-resolved spectral analysis to investigate the microscopic origins of the infrared (IR) response of water at the interface with anatase TiO 2 (101), a prototypical oxide surface. The calculated interfacial spectra exhibit characteristic modifications compared to bulk water IR spectra, including enhanced intensities, a red shifted and broadened stretching band, and a higher-frequency shoulder, in qualitative agreement with experiments. Spectral decomposition shows that these signatures originate mainly from the first interfacial water layer, dominated by surface-bound H 2 O at Ti 5C sites, with secondary contributions from the second layer. A moderate salt concentration (0.4 M NaCl) leaves both the interfacial structure and the spectra essentially unchanged, while tuning the pH strongly modulates the spectral intensity. We establish a scaling relation linking the spectral intensity to the surface water dissociation fraction and the dipole moment, both governed by interfacial electric fields. These findings provide a microscopic framework for interpreting IR spectra of oxide–electrolyte interfaces.

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

Ab Initio Molecular Dynamics Study of Pd Nucleation on a γ-Al 2 O 3 Surface

We perform ab initio molecular dynamics (AIMD) free energy simulations to investigate the stability and dynamics of dispersed Pd atoms and subnanometer clusters on γ-Al 2 O 3 . We consider nucleation for varying Pd loadings on dry γ-Al 2 O 3 (100), dry γ-Al 2 O 3 (110) and wet γ-Al 2 O 3 (110) and examine temperature, entropy and water coverage effects on the stability and dynamics of Pd clusters. At low Pd loading (1.07 Pd atoms/nm 2 on the (100) and 0.75 Pd/nm 2 on the (110)), association of the Pd atoms is thermodynamically unfavorable on the dry surfaces and almost thermoneutral on the wet (110) owing to water blocking of the AlIII defect sites. In agreement with past studies, the Pd atoms are quite mobile but the diffusion free energy barriers do not increase with the water coverage, as previously suggested, but rather remain similar in magnitude owing to translational entropy at finite temperatures. At these Pd loadings, oxidized Pd(II) atoms on the wet (110) surface are dispersed and immobile. At higher Pd loading (1.12 and 1.5 Pd atoms/nm 2 ) on the (110) surface, Pd 3 and Pd 4 clusters are thermodynamically very stable and form fast. At the 1.12 Pd atoms/nm 2 loading, the formation of the Pd 3 cluster is two orders of magnitude slower when the surface is hydroxylated as the system becomes somewhat trapped before the dinuclear cluster Pd 2 collides with a Pd atom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Exploring cryo-electron microscopy with molecular dynamics

Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.

Biochemistry & Molecular Biology↗
DOE OSTI2025

MBX V1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations

The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the "gold standard" coupled-cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. In conclusion, these advancements enable simulations on nanosecond time scales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A review of displacement cascade simulations using molecular dynamics emphasizing interatomic potentials for TPBAR components

This review explores molecular dynamics simulations for studying radiation damage in Tritium Producing Burnable Absorber Rod (TPBAR) materials, emphasizing the role of interatomic potentials in displacement cascades. Recent machine learning potentials (MLPs), trained on quantum data, enhance prediction accuracy over traditional models like EAM. We highlight temperature, PKA energy, and composition effects on damage evolution in TPBAR components, recommending suitable potentials and discussing advancements for materials in extreme radiation environments.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Initial position optimization in molecular dynamics simulations for a Coulomb system

A new algorithm for molecular dynamics (MD) simulations is developed to optimize plasma particle distributions at given initial temperatures. By combining velocity scaling and reassignment, the method effectively eliminates the initial rise and oscillation in temperatures observed with randomly distributed positions. These rises and oscillations are undesired numerical artifacts observed in conventional plasma MD simulations, arising from unoptimized particle positions. The algorithm demonstrates temperature relaxation without initial rises or oscillations, as well as precise flow velocity relaxation, enabling accurate measurement of relaxation times. The code is accelerated using graphics processing units for parallel processing, enhancing the study of plasma dynamics. The proposed method for distributing physically valid particles in MD simulations enables accurate studies of intrinsic collision processes in plasmas, including the dynamics of strongly coupled plasmas, plasma–wave interactions, and transport phenomena in magnetized plasmas. The paper concludes with a discussion of potential applications and future enhancements to the algorithm.

Jo, Jawon (ORCID:0009000924193285)↗
DOE OSTI2023

FASDA: An FPGA-Aided, Scalable and Distributed Accelerator for Range-Limited Molecular Dynamics

Conducting long-term simulations of small molecules using Molecular Dynamics (MD) is crucial in drug design. However, traditional methods to accelerate the process including ASICs or GPUs, have limitations. ASICs are difficult to access, while publicly accessible GPU packages for MD have issues with more GPUs when processing small molecules, causing decreased performance. Conversely, FPGAs are renowned for their scalability and have been commonly used as accelerators for various applications, making them suitable for the task. Moreover, with the availability of FPGAs in the cloud, pharmaceutical developers can now access FPGA devices. The only missing piece is a design deployed for MD acceleration. Therefore, we present FASDA, the first FPGA-based MD accelerator available for community development. FASDA is designed to evaluate range-limited MD, which is the most resource-intensive and computationally demanding component in MD. It outperforms the state of-the-art GPU solution by 4.67x, significantly reducing the time for MD in drug design.

Wu, Chunshu↗
DOE OSTI2024

Solid Electrolyte Interphase Formation at the Ionic Liquid Electrolyte—Lithium-Metal Interface Using an Ab Initio Molecular Dynamics Approach

An interfacial study is performed using ab initio molecular dynamics (AIMD) simulations to elucidate the electrochemical interfacial stability of an ionic liquid (IL) as component of an electrolyte in contact with a Li-metal anode when an additive, vinylene carbonate (VC), is added to the electrolyte. The IL electrolyte is composed of 1-butyl-1-methylpyrrolidinium bis(fluoro-sulfonyl)-imide (PYR14 + FSI − ) with lithium bis(trifluoromethane-sulfonyl)imide salt (Li + TFSI − ) in a 8:2 concentration ratio. Reactions observed at the interface electrolyte/Li-metal during the AIMD simulations are verified by electronic structure calculations using density functional theory calculations considering a continuum solvent model. We found that the addition of VC to the IL prevents further reduction of the counter-ion TFSI − and retards reduction of FSI − in comparison to the case when the additive VC is absent. The PYR14 + reduction is never observed with or without the additive. The 1st, 2nd, and 3rd electron affinities of the PYR14 + are −0.08, −0.36 and −3.65 eV, indicating little to large repulsive behavior against electrons. The opposite is observed for the two negative ions, FSI − and TFSI − , which yield 1st electron affinities of 1.73 and 1.83 eV, respectively. Reactions obtained under open circuit conditions. Dissociation mechanisms are presented for all IL components reduced at the IL/Li-metal interface.

Electrochemistry↗
NASA NTRS1991

Molecular dynamics investigation of radiation damage in semiconductors

Results of a molecular dynamics investigation of the effects of radiation damage on the crystallographic structure of semiconductors are reported. Particular cosiderastion is given to the formation of point defects and small defect complexes in silicon at the end of a radiation-damage cascade. The calculations described make use of the equivalent crystal theory of Smith and Banerjea (1988). Results on the existence of an atomic displacement threshold, the defect formation energy, and some crystallographic information on the defects observed are reported.

Good, Brian S.↗
DOE OSTI2022

Structural evolution in Au- and Pd-based metallic glass forming liquids and the case for improved molecular dynamics force fields

The results of a combined experimental and computational investigation of the structural evolution of Au 81 Si 19 , Pd 82 Si 18 , and Pd 77 Cu 6 Si 17 metallic glass forming liquids are presented. Electrostatically levitated metallic liquids are prepared, and synchrotron x-ray scattering studies are combined with embedded atom method molecular dynamics simulations to probe the distribution of relevant structural units. Metal–metalloid based metallic glass forming systems are an extremely important class of materials with varied glass forming ability and mechanical processibility. High quality experimental x-ray scattering data are in poor agreement with the data from the molecular dynamics simulations, demonstrating the need for improved interatomic potentials. The first peak in the x-ray static structure factor in Pd 77 Cu 6 Si 17 displays evidence for a Curie–Weiss type behavior but also a peak in the effective Curie temperature. In conclusion, a proposed order parameter distinguishing glass forming ability, 1/(S(T,q 1 )−1, shows a peak in the effective Curie temperature near a crossover temperature established by the behavior of the viscosity, T A .

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

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

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

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Variational control forces for enhanced sampling of nonequilibrium molecular dynamics simulations

We introduce a variational algorithm to estimate the likelihood of a rare event within a nonequilibrium molecular dynamics simulation through the evaluation of an optimal control force. Optimization of a control force within a chosen basis is made possible by explicit forms for the gradients of a cost function in terms of the susceptibility of driven trajectories to changes in variational parameters. We consider probabilities of time-integrated dynamical observables as characterized by their large deviation functions and find that in many cases, the variational estimate is quantitatively accurate. Additionally, we provide expressions to exactly correct the variational estimate that can be evaluated directly. We benchmark this algorithm against the numerically exact solution of a model of a driven particle in a periodic potential, where the control force can be represented with a complete basis. Additionally, we then demonstrate the utility of the algorithm in a model of repulsive particles on a line, which undergo a dynamical phase transition, resulting in singular changes to the form of the optimal control force. In both systems, we find fast convergence and are able to evaluate large deviation functions with significant increases in statistical efficiency over alternative Monte Carlo approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗