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Results for “Molecular dynamics computer simulation”

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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Machine learning dielectric screening for the simulation of excited state properties of molecules and materials

Accurate and efficient calculations of absorption spectra of molecules and materials are essential for the understanding and rational design of broad classes of systems. Solving the Bethe–Salpeter equation (BSE) for electron–hole pairs usually yields accurate predictions of absorption spectra, but it is computationally expensive, especially if thermal averages of spectra computed for multiple configurations are required. We present a method based on machine learning to evaluate a key quantity entering the definition of absorption spectra: the dielectric screening. We show that our approach yields a model for the screening that is transferable between multiple configurations sampled during first principles molecular dynamics simulations; hence it leads to a substantial improvement in the efficiency of calculations of finite temperature spectra. We obtained computational gains of one to two orders of magnitude for systems with 50 to 500 atoms, including liquids, solids, nanostructures, and solid/liquid interfaces. Importantly, the models of dielectric screening derived here may be used not only in the solution of the BSE but also in developing functionals for time-dependent density functional theory (TDDFT) calculations of homogeneous and heterogeneous systems. Overall, our work provides a strategy to combine machine learning with electronic structure calculations to accelerate first principles simulations of excited-state properties.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Activation dynamics of a water-soluble human mu-opioid receptor

The mu-opioid receptor (MOR), a class A G protein-coupled receptor mediates opioid analgesia and remains a central target for pain therapeutics. While crystal structures of MOR exist, they provide limited insight into the receptor’s dynamic conformational landscape underlying function. Here, we engineered a thermostable water-soluble MOR variant (wsMOR) that retains native-like ligand-binding and activation dynamics. This variant enables high-yield production and detailed solution-phase structural studies that are challenging with membrane-embedded MOR, providing a valuable tool for studying receptor activation and aqueous-phase drug screening. Using a combined computational and experimental approach, we performed long-timescale all-atom molecular dynamics simulations together with neutron scattering and single-molecule FRET, revealing a structurally stable receptor with a diverse ensemble of conformations at different temporal resolutions. In the ligand-free state, wsMOR displayed high conformational flexibility, which decreased upon agonist binding, particularly in transmembrane helix 6, a hallmark of G protein-coupled receptor activation. Positive allosteric modulation and G protein binding further stabilized active-like states. These findings highlight wsMOR’s conformational plasticity across picosecond to millisecond timescales and provide a foundation for structure-guided development of next-generation opioid ligands with improved efficacy and safety.

E, Agyemang [University of Tennessee Knoxville]↗
DOE OSTI2020

Quantitative metrics for evaluating thermonuclear design codes and physics models applied to the National Ignition Campaign

In this study, physics models and design codes for hot dense plasmas undergoing thermonuclear burn are evaluated objectively using statistical metrics that compare the difference between calculations and data relative to the experimental uncertainties. The analysis is applied to the National Ignition Campaign (NIC) because it is relevant, comprehensive, and well documented. The statistics confirm that a key process afflicting NIC performance is mix driven by hydrodynamic instabilities as approximated here using the KL model [G. Dimonte and R. Tipton, Phys. Fluids 18, 085101 (2006)]. New physics models are also presented for instability-driven magnetic fields [B. Srinivasan et al., Phys. Rev. Lett. 108, 165002 (2012)] and the Coulomb logarithm for electron–ion thermal relaxation [G. Dimonte and J. Daligault, Phys. Rev. Lett. 101, 135001 (2008)]. The plasma-generated magnetic fields improve the agreement between code and data in a statistically significant manner by reducing the electron thermal conduction in the hot-spot via the Hall term. The Coulomb logarithm is presented in a numerically practical form that incorporates recent theoretical advances. However, it does not improve the agreement between the code and data because the thermal relaxation is so fast in non-ignited NIC plasmas that the typical 20% error does not change the tight coupling between electrons and ions. Even with these improved physics models, the one-dimensional simulations presented here are not able to describe the high-convergence NIC implosions in a statistically acceptable manner. Of the heroic multi-dimensional simulations of Clark et al. [Phys. Plasmas 23, 056302 (2016)], only those in three-dimensions satisfy the statistical acceptance criterion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Activated relaxation in supercooled monodisperse atomic and polymeric WCA fluids: Simulation and ECNLE theory

Here, we combine simulation and Elastically Collective Nonlinear Langevin Equation (ECNLE) theory to study the activated relaxation in monodisperse atomic and polymeric Weeks–Chandler–Andersen (WCA) liquids over a wide range of temperatures and densities in the supercooled regime under isochoric conditions. By employing novel crystal-avoiding simulations, metastable equilibrium dynamics is probed in the absence of complications associated with size polydispersity. Based on a highly accurate structural input from integral equation theory, ECNLE theory is found to describe well the simulated density and temperature dependences of the alpha relaxation time of atomic fluids using a single system-specific parameter, a c , that reflects the nonuniversal relative importance of local cage and collective elastic barriers. For polymer fluids, the explicit dynamical effect of local chain connectivity is modeled at the fundamental dynamic free energy trajectory level based on a different parameter, N c , that quantifies the degree of intramolecular correlation of bonded segment activated barrier hopping. For the flexible chain model studied, a physically intuitive value of N c ≈ 2 results in good agreement between simulation and theory. A direct comparison between atomic and polymeric systems reveals that chain connectivity can speed up activated segmental relaxation due to weakening of equilibrium packing correlations but can slow down relaxation due to local bonding constraints. The empirical thermodynamic scaling idea for the alpha time is found to work well at high densities or temperatures but fails when both density and temperature are low. The rich and subtle behaviors revealed from simulation for atomic and polymeric WCA fluids are all well captured by ECNLE theory.

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

Capacitance of Carbon Nanotube/Graphene Composite Electrodes with [BMIM + ][BF$_4^–$]/Acetonitrile: Fixed Voltage Molecular Dynamics Simulations

The capacitance of nanoporous carbon electrode materials is dictated by the physical interactions with electrolyte ions and molecules at the accessible interior electrode surface. While significant progress has been made in designing and synthesizing carbon materials with well-defined and relatively homogeneous nanoporosity, the majority of materials remain heterogeneous, and the resulting properties reflect an average over this distribution. In this regard, computer simulations can be a valuable tool to predict or validate structure/property relationships by systematically investigating well-defined, model electrode morphologies. In this work, we utilize fixed-voltage molecular dynamics simulations to predict structure/capacitance relationships for five different model morphologies of carbon nanotube/graphene (CNT/G) composite electrodes with 1-butyl-3-methylimidazolium tetrafluoroborate/acetonitrile electrolyte. The CNT/G electrode models are inspired by experimental “layer-by-layer” syntheses and strike a balance between realism and computational tractability. Comparison between different model electrode architectures elucidates important structure/property relationships. We find that CNT/graphene contact points serve as “hot spots” with significantly enhanced charge separation relative to the rest of the electrode. Furthermore, we demonstrate a specific nanoconfinement motif that provides substantial 3–4$\times$ enhancement of local capacitance, resulting in a ~40% increase of the total electrode differential capacitance. Because the accessible surface area of the model CNT/G electrodes is precisely determined, a comparison of per-area capacitance across systems is unambiguous. Our results thus complement a prior computational demonstration of capacitance enhancement in nanoconfinement while elucidating additional interaction motifs at CNT/G electrochemical interfaces.

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

Accelerating charge estimation in molecular dynamics simulations using physics-informed neural networks: corrosion applications

Molecular Dynamics (MD) simulations are used to understand the effects of corrosion on metallic materials in salt brine. Reactive force fields in classical MD enable accurate modeling of bond formation and breakage in the aqueous medium and at the metal-electrolyte interface, while also facilitating dynamic partial charge equilibration. However, MD simulations are computationally intensive and unsuitable for modeling the long time scales characteristic of corrosive phenomena. To address this, we develop reduced-order machine learning models that provide accurate and efficient predictions of charge density in corrosive environments. Specifically, we use Long Short-Term Memory (LSTM) networks to forecast charge density evolution based on atomic environments represented by Smooth Overlap of Atomic Positions (SOAP) descriptors. A physics-informed loss function enforces charge neutrality and electronegativity equivalence. The atomic charges predicted by the deep learning model trained on this work were obtained two orders of magnitude faster than those from molecular dynamics (MD) simulations, with an error of less than 3% compared to the MD-obtained charges, even in extrapolative scenarios, while adhering to physical constraints. This demonstrates the excellent accuracy, computational efficiency, and validity of the developed model. Lastly, even though developed for corrosion, these protocols are formulated in a phenomenon-agnostic manner, allowing application to various variable-charge interatomic potentials and related fields.

Atomistic models↗
DOE OSTI2021

Investigations of water/oxide interfaces by molecular dynamics simulations

Water/oxide interfaces are ubiquitous on earth and show significant influence on many chemical processes. For example, understanding water and solute adsorption as well as catalytic water splitting can help build better fuel cells and solar cells to overcome our looming energy crisis; the interaction between biomolecules and water/oxide interfaces is one hypothesis to explain the origin of life. However, knowledge in this area is still limited due to the difficulty of studying water/solid interfaces. As a result, research using increasingly sophisticated experimental techniques and computational simulations has been carried out in recent years. Although it is difficult for experimental techniques to provide detailed microscopic structural information, molecular dynamics (MD) simulations have satisfactory performance. In this report, we discuss classical and ab initio MD simulations of water/oxide interfaces. Generally, we are interested in the following questions: How do solid surfaces perturb interfacial water structure? How do interfacial water molecules and adsorbed solutes affect solid surfaces and how do interfacial environments affect solvent and solute behavior? Finally, we discuss progress in the application of neural network potential based MD simulations, which offer a promising future because this approach has already enabled ab initio level accuracy for very large systems and long trajectories.

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

AIMD‐Based Protocols for Modeling Exciplex Fluorescence Spectra and Inter‐System Crossing in Photocatalytic Chromophores

ABSTRACT This study introduces a computational protocol for modeling the emission spectra of exciplexes using excited‐state ab initio molecular dynamics (AIMD) simulations. The protocol is applied to a model exciplex formed by oligo‐p‐phenylenes (OPPs) and triethylamine (TEA), which is of interest in the context of photocatalytic reduction of . AIMD facilitates efficient sampling of the conformational space of OPP3 and OPP4 exciplexes with TEA, offering a dynamic alternative to previously employed static methods. The AIMD‐based protocol successfully reproduces experimental emission spectra for OPP‐TEA exciplexes, agreeing with previous computational and experimental findings. The results show that AIMD simulations provide an efficient means of sampling the conformational space of these exciplexes, requiring less user input and, in some instances, fewer computational resources than multiple excited‐state optimizations initiated from user‐specified initial structures. The study also evaluates the yield of intersystem crossing (ISC) using AIMD and Landau‐Zener probability. The results suggest that ISC is a minor decay channel for OPP3 and OPP4. This work provides new insights into the structural flexibility and emission characteristics of OPP‐TEA photoredox catalyst systems, potentially contributing to improved design strategies for organic chromophores in reduction applications.

Giudetti, Goran [Department of Chemistry Universit↗
DOE OSTI2020

CephFS experiments on stria.sandia.gov

This report is an institutional record of experiments conducted to explore performance of a vendor installation of CephFS on the SNL stria cluster. Comparisons between CephFS, the Lustre parallel file system, and NFS were done using the IOR and MDTEST benchmarking tools, a test program which uses the SEACAS/Trilinos IOSS library, and the checkpointing activity performed by the LAMMPS molecular dynamics simulation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Development and application of hybrid AIMD/cDFT simulations for atomic-to-mesoscale chemistry

Many important chemical processes involve reactivity and dynamics in complex solutions. Gaining a fundamental understanding of these reaction mechanisms is a challenging goal that requires advanced computational and experimental approaches. However, important techniques such as molecular simulation have limitations in terms of scales of time, length, and system complexity. Furthermore, among the currently available solvation models, there are very few designed to describe the interaction between the molecular scale and the mesoscale. To help address this challenge, here, we establish a novel hybrid approach that couples first-principles plane-wave density functional theory with classical density functional theory (cDFT). In this approach, a region of interest described by ab initio molecular dynamics (AIMD) interacts with the surrounding medium described using cDFT to arrive at a self-consistent ground state. cDFT is a robust but efficient mesoscopic approach to accurate thermodynamics of bulk electrolyte solutions over a wide concentration range (up to 2M concentrations). Benchmarking against commonly used continuum models of solvation, such as SMD, as well as experiments, demonstrates that our hybrid AIMD–cDFT method is able to produce reasonable solvation energies for a variety of molecules and ions. With this model, we also examined the solvent effects on a prototype S N 2 reaction of the nucleophilic attack of a chloride ion on methyl chloride in the solution. The resulting reaction pathway profile and the solution phase barrier agree well with experiment, showing that our AIMD/cDFT hybrid approach can provide insight into the specific role of the solvent on the reaction coordinate.

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

Keeping LAMMPS cutting edge

Since its inception 30 years ago, LAMMPS has grown to be a world-class molecular dynamics code and a cornerstone of computational materials science research. This project aimed to keep LAMMPS at the forefront of molecular dynamics simulations by adapting LAMMPS to the latest developments in machine learning technology and hardware. Initially, the project set out to provide a unified implementation of active learning for efficient training data generation in LAMMPS, but the research trajectory pivoted to address more immediate and impactful opportunities. On the hardware side, recent record-breaking molecular dynamics simulations were developed on the Cerebras wafer-scale AI chip, and this project has developed an interface between LAMMPS and the hardware-specific molecular dynamics code to accelerate and simplify development and user adoption. On the software side, PyTorch’s Ahead-of-Time (AOT) compilation features promised increased performance for state-of-the-art equivariant neural network potentials, and this project laid the groundwork for their adoption in LAMMPS, resulting in a nearly 20x acceleration in extreme cases. Combined with a comprehensive benchmark study of LAMMPS across all current exascale systems, this project has reinforced LAMMPS’s role as a versatile, high-performance tool for current and future materials science applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.

Okoto, Patience S.↗
DOE OSTI2021

Insights into scale translation of methane transport in nanopores

Accurate prediction of flow behavior in shale matrix is critical for efficient development of shale gas reservoirs. In these systems, the majority of pores are in the nano-size range. As a result, continuum-based approaches may not be appropriate to simulate flow in such systems. Molecular dynamics (MD) simulations are capable of capturing the relevant microscale physics. Their relatively high computational expense, however, restricts MD simulations to rather small systems and domains. This limitation creates a gap between computational need of macroscale systems and capabilities of MD simulations. The lattice Boltzmann method (LBM) is a suitable candidate to bridge this gap. In this work, the multiple-relaxation-time (MRT)-LBM is used to study methane transport in nano-size pores. Adsorption effects near solid boundaries, as well as non-ideal behavior of fluids, are accounted for via incorporating appropriate force terms in LBM. In this work, parameters associated with the force terms in the equation of state are studied in detail, and a workflow is proposed to determine optimal values of these parameters for gas flow in slit pores. Specifically, we establish these parameters such that the range of density values that the model is able to simulate is maximized. We demonstrate this workflow by simulating gas flow where velocity and density profiles from MD simulations are used as reference data. Results from LBM simulations are in good agreement with MD reference data for pores that are 4 nm in width or larger. Moreover, we propose a preconditioning scheme to improve the stability of LBM in dealing with complex geometries. The robustness of this scheme is demonstrated by simulating several roughness geometries. This work motivates the use of LBM in scale translation of the physics of mass transport in more complex permeable media.

03 NATURAL GAS↗
DOE OSTI2022

Exponential Water Uptake in Ionomer Membranes Results from Polymer Plasticization

Water content is the most influential factor in the performance of ion-exchange membranes (IEMs), controlling their mechanical rigidity, ionic conductivity, and degradation rates. Membranes absorb water exponentially at high water activity (a w ), making that region of the sorption isotherm the most influential on membrane properties. Plasticization of the polymer by water has been proposed to cause this exponential uptake at high a w . However, an integrated microscopic picture of the structure, thermodynamic, and mechanical properties of IEMs as a function of a w has remained elusive. In this work, we use large-scale molecular simulations validated with experimental measurements to compute the sorption isotherms, Young’s modulus, polymer dynamics, and structure of IEMs. The simulations unveil that the exponential increase in water uptake (WU) coincides in all cases with the glass to rubber transition of the membrane, as measured through its Young’s modulus and segmental polymer dynamics. Functionalization of the polymer with alkyl groups further contributes to its plasticization, increasing the WU at a given a w and ion-exchange capacity (IEC). The alkyl chains act synergistically with water to plasticize the polymer matrix and allow water penetration in the membrane. The simulations reveal that the width of the water channels depends on the ratio λ of water to ions in the polymer but is independent of its IEC. We conclude that differences in the polymer matrix–not the water channels–are responsible for the distinct uptake response of IEMs to the thermodynamic driving force of water activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Synthesis and investigation into explosive sensitivity for a series of new picramide explosives

Tailoring the molecular properties that govern energetic material sensitivity is essential to improve safety and help develop new energetic materials. Despite this need, understanding the complex chemistry and physics of explosive initiation and propagation is still a challenge. Recent work by our group has reinforced the view that explosive sensitivity under sub-shock conditions is connected to the strength of the weakest covalent bond in the molecule, that is, its “trigger linkage.” These correlations have been observed with different classes of energetic molecules and indicate that “trigger linkage” bond breaking, and heat of explosion are good indicators for the sensitivity trends. Herein we report the synthesis of aliphatic energetic materials with ethane, propane and neopentane backbones. Experimental and computational studies show that the trigger linkage model, based on results from quantum molecular dynamics simulations, correctly predicts trends observed in the impact sensitivity of the molecules. However, while the model predicts the impact sensitivities of the ethane series, the neopentane series has higher impact sensitivities than predicted, which is presumably influenced by crystal packing effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Understanding and Controlling Photoexcited Molecules in Complex Environments (Final Technical Report)

Predicting the outcome of a photochemical reaction is complicated by factors outside the scope of tradition theoretical chemistry. On such small scales, fluctuations of the environment render outcomes stochastic, nonadiabatic dynamics blur the separation between nuclear and electronic motion, and ultrafast relaxation renders typical assumptions of equilibrium inappropriate. This project aimed to elucidate and control nonadiabatic molecular dynamics in condensed phases. We developed accurate, efficient simulation tools to study irreversible molecular processes computational across a range of scales. We applied these methodological advances to study electron transfer under exotic conditions where spin and topology opened new pathways for reactivity. We also brought these ideas to bare on light harvesting systems, where energy and charge transport are coupled, and where long lifetimes can be deleterious to function. These advances helped to establish general principles for chemical efficiency and guide the design of nanoscale energy materials, molecular machines, and related technologies.

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

Spatial description of dislocation nucleation in the shock response of single-crystal aluminum

Nonequilibrium molecular dynamics simulations of shock loaded single-crystal Al in the $\langle$100$\rangle$, $\langle$110$\rangle$, $\langle$111$\rangle$, and $\langle$123$\rangle$ orientations are conducted to study elastic and plastic shockwave formation and details associated with dislocation activity. A computer vision-based approach is implemented to capture the presence of dislocations and describe their spatial characteristics in the zone of nucleation behind the propagating shockwave. The methodology developed relies on the sequences of images extracted during shock loading that show dislocation activity within a cross section of the sample. Results reveal that the spacing between activated slip systems is orientation dependent and exhibits a modest reduction for the $\langle$100$\rangle$ and $\langle$111$\rangle$ orientations as shock pressure increases. Comparisons are made to existing theoretical models. Such relationships between shock pressure and dislocation activity, extracted from molecular dynamics simulations, can be used to inform higher length scale simulations or modeling of dislocation-based plasticity during shock.

36 MATERIALS SCIENCE↗