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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

New pair style for molecular dynamics package LAMMPS

This pair style will enable molecular dynamics simulations of hydrogen interaction with Fe-C steels. No such simulations are possible without such a pair style. This is significant because Fe-C steels are the most commonly used steels and improving their resistance to hydrogen embrittlement has attracted wide interests. SAND2020-12230 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & 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.

Zhou, Xiaowang↗
DOE OSTI2020

Molecular dynamics and continuum analyses of the electrokinetic zeta potential in nanostructured slit channels

This work presents a theoretical and numerical study of electrokinetic flow and the zeta potential for the case of slit channels with nanoscale surface features of dimensions comparable to the Debye length, by employing molecular dynamics simulations and continuum-level analyses. Additionally, a simple analytical model for considering the average effect of such surface features producing nanoscale roughness is proposed by employing matched asymptotic solutions for the charge density and fluid flow field, and matching conditions that satisfy electroneutrality and the Onsager reciprocal relation between the electroosmotic flow rate and streaming current. The proposed analytical model quantitatively accounts for results from molecular dynamics simulations that consider the presence of ion solvation shells and surface hydration layers. Our analysis indicates that a simultaneous knowledge of the electroosmotic and pressure-driven flow rate or streaming current can be instrumental to unambiguously determine the zeta potential in the presence of nanoscale surface features.

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

Efficient perturbation-tracking method for directly probing the spectral phonon properties from molecular dynamics simulations

Existing methods for directly extracting the spectral phonon properties from molecular dynamics (MD) simulations, like the normal mode analysis (NMA) and spectral energy density analysis, all require a very long simulation time to produce reliable results with good convergence. So far, these methods are mainly applied in studies using small systems and with empirical potentials, as the heavy computational load has greatly hindered their further applications. Here we propose a perturbation-tracking (PT) method for directly probing the mode-wise phonon anharmonic frequencies and lifetimes. We show that results obtained from our method are in excellent agreement with those from the conventional NMA approach, using Si as the model material system. Comparing with the NMA approach, the PT method offers a greater accuracy and significant improvement of efficiency. It takes an average of two orders of magnitude and up to three orders of magnitude less simulation time to obtain the same lifetime result of a phonon mode with intermediate to high accuracy. Meanwhile, our method preserves all the dynamics of probed phonon mode from a particular state, which means it is capable of studying the transient thermal transport processes in a nonequilibrium system. Besides the exceptional efficiency, our method also comes with freedom to choose to probe only those modes of interest. This makes it ideal for use with large systems and in computationally demanding applications, such as ab initio MD simulations. Moreover, the PT method we propose here is very straightforward and easy to implement.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Modification of a force field for molecular dynamics simulations of silicon etching by chlorine atoms

Here, a modified classical molecular dynamics (MD) force field is presented for the interaction between silicon (Si) and chlorine (Cl). The original version of the force field is shown to significantly overestimate the probability of Si etching by thermal Cl atoms. However, the modified force field corrects this problem and results in generally good agreement with experimental data. Further, it is shown that while the modification of the force field improves the prediction of Si spontaneous etching with Cl atoms, it does not degrade predictions of atomic-layer etching of Si with Cl[Formula: see text] molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Modulating Cu electrode microenvironments with MOF coatings: insights from molecular dynamics and electrochemical experiments of CO reduction

Metal-organic frameworks (MOFs) present a compelling strategy for tuning electrochemical interfaces by reshaping interfacial solvent structure. In this study, we examine how MOF coatings influence the microenvironment at copper electrodes during the CO electroreduction reaction (CORR) using a combined approach of molecular dynamics (MD) simulations and electrochemical experiments. Two MOFs, NU-901 and ZIF-8, are selected to explore the impact of pore size and channel hydrophobicity on electrochemical activity and interfacial concentration in acetonitrile (ACN) and dimethyl sulfoxide (DMSO) electrolytes. Electrochemical measurements reveal that MOF@Cu electrodes exhibit lower Faradaic efficiencies for CO hydrogenation products (ethylene and methane) compared to bare copper but have dramatic impacts on the interfacial microenvironment. NU-901, with its larger pores and strong interactions with DMSO, traps DMSO molecules and enhances CO coordination in DMSO but suppresses CORR selectivity in favor of the hydrogen evolution reaction (HER). ZIF-8, with smaller pores and hydrophobic channels, limits the interfacial water concentration, and, in ACN, promotes CO coordination. The simulations provide insights into how MOFs can act as physical modulators of reactant delivery and interfacial structure to control electrochemical microenvironments. This work highlights the value of molecular dynamics in uncovering how structural features of MOFs influence interfacial phenomena, even when catalytic performance is not directly improved.

Copper electrode microenvironments↗
DOE OSTI2020

Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results

Herein, we present a novel method to incorporate structural results from surface-sensitive scattering, such as X-ray or neutron reflectometry, into molecular dynamics simulations. While reflectometry techniques generally provide a means to determine the molecular-scale structures of organized interfacial films, they were recently shown to offer the capability to characterize the structures of protein-membrane complexes supported by a solid substrate. One-dimensional information inherent in the experimental results is used in the form of component volume occupancy (CVO) profiles, which describe the distribution of molecular components within an interfacial architecture, to construct real-space constraints in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown in the re-evaluation of an neutron-reflection-derived structure which was approximated by an independent molecular dynamics simulation in earlier work, and it also leads to faster equilibration of ensemble structures. We further show that time averaging the CVO profile that develops in the simulation while biasing with this approach permits fluctuations about the average that are necessary for conformational exploration of the system. This method is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and may take prohibitively long to equilibrate in simulations.

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

Quantum Simulation of Molecular Dynamics Processes─A Benchmark Study Using a Classical Simulator and Present-Day Quantum Hardware

Here, we explore how the fundamental problems in quantum molecular dynamics can be modeled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes propagation of a free wave packet, vibration of a harmonic oscillator, and tunneling through a barrier. Each of these problems starts with the initial wave packet setup. Although Qiskit provides a general method for initializing wave functions, in most cases it generates deep quantum circuits. While these circuits perform well on noiseless simulators, they suffer from excessive noise on quantum hardware. To overcome this issue, we designed a shallower quantum circuit for preparing a Gaussian-like initial wave packet, which improves the performance of real hardware. Next, quantum circuits are implemented to apply the kinetic and potential energy operators for the evolution of a wave function over time. The results of our modeling on classical emulators of quantum hardware agree perfectly with the results obtained using the traditional (classical) methods. This serves as a benchmark and demonstrates that the quantum algorithms and Qiskit codes we developed are accurate. However, the results obtained on the actual quantum hardware available today, such as IBM’s superconducting qubits and IonQ’s trapped ions, indicate large discrepancies due to hardware limitations. This work highlights both the potential and challenges of using quantum computers to solve fundamental quantum molecular dynamics problems.

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

Correlations for the specific heat capacity of ( U x Pu 1 - x ) 1 - y Gd y O 2 - z derived from molecular dynamics

We report UO 2 is the primary conventional fuel used in most nuclear reactors with Gd 2 O 3 commonly added as a burnable absorber to produce a more level power distribution in the reactor core at the beginning of operation. It can also be mixed with other actinide oxides to produce mixed oxide (MOx) fuel. In this study, molecular dynamics simulations were used to predict the specific heat capacity of Gd-doped PuO 2 , UO 2 and (U, Pu)O 2 MOx accommodating Gd 3+ substituted at cation sites via two charge compensation mechanisms - oxygen vacancy formation and the oxidation of U 4+ to U 5+ . The specific heat capacity values for PuO 2 and UO 2 are in good agreement with other studies showing a distinct peak at high temperatures - above 1800 K. As Gd 3+ is added, the peak height reduces for each composition considered. An analytical fit was applied to the data where Gd 3+ was fully charge compensated by either oxygen vacancies or U 5+ . The expression was then validated by predicting the specific heat capacity for three compositions of (Ux Pu 1-x ) 1-y Gd y O 2-z containing both oxygen vacancies and U 5+ , and compared to molecular dynamics data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis

A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but trade-offs between accuracy and computational cost have limited their use. We previously developed extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) methods that leverage a negligible compromise in accuracy to substantially decrease the cost of QMD simulations. Here, we develop a reactive QMD approach using the latest XL-BOMD formulation, which enables efficient simulations of highly reactive systems, and use it to investigate mechanisms of intermediate formation in isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenyl isocyanide, forming a thioimidate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation and suggested a possible role of Asp17 as a proton donor in the early phase of ICH catalysis. To test whether the pathway seen using the reactive QMD approach might be relevant to ICH catalysis, we performed X-ray crystallography and pre-steady-state enzyme kinetics studies of wild-type and D17N mutant ICH. Both the structure and kinetics are sensitive to the D17N mutation in a manner that is consistent with the order of the reaction steps seen in the simulations. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate model reactions for the design of experiments that provide information about enzyme mechanisms involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dynamic and relativistic effects on Pt–Pt indirect spin–spin coupling in aqueous solution studied by ab initio molecular dynamics and two- vs four-component density functional NMR calculations

Treating 195Pt nuclear magnetic resonance parameters in solution remains a considerable challenge from a quantum chemistry point of view, requiring a high level of theory that simultaneously takes into account the relativistic effects, the dynamic treatment of the solvent–solute system, and the dynamic electron correlation. A combination of Car-Parrinello molecular dynamics (CPMD) and relativistic calculations based on two-component zeroth order regular approximation spin–orbit Kohn–Sham (2c-ZKS) and four-component Dirac–Kohn–Sham (4c-DKS) Hamiltonians is performed to address the solvent effect (water) on the conformational changes and JPtPt1 coupling. A series of bridged PtIII dinuclear complexes [L1–Pt2(NH3)4(Am)2–L2]n+ (Am = α–pyrrolidonate and pivalamidate; L = H2O, Cl−, and Br−) are studied. The computed Pt–Pt coupling is strongly dependent on the conformational dynamics of the complexes, which, in turn, is correlated with the trans influence among axial ligands and with the angle N–C–O from the bridging ligands. The J-coupling is decomposed in terms of dynamic contributions. The decomposition reveals that the vibrational and explicit solvation contributions reduce JPtPt1 of diaquo complexes (L1 = L2 = H2O) in comparison to the static gas-phase magnitude, whereas the implicit solvation and bulk contributions correspond to an increase in JPtPt1 in dihalo (L1 = L2 = X−) and aquahalo (L1 = H2O; L2 = X−) complexes. Relativistic treatment combined with CPMD shows that the 2c-ZKS Hamiltonian performs as well as 4c-DKS for the JPtPt1 coupling.

Chemistry↗
DOE OSTI2022

Investigation of the thermal conductivity of molten LiF-NaF-KF with experiments, theory, and equilibrium molecular dynamics

Molten salts are being proposed for numerous advanced energy applications, including advanced nuclear reactors, concentrating solar power plants, thermal energy storage, and fusion reactors. Accurate knowledge of the thermophysical properties of molten salts directly impact the performance of these energy systems and are essential for design and safety analyses. Thermal conductivity data for fluoride molten salts and mixtures are especially lacking. In this work, experimental measurements of thermal conductivity using the steady-state variable gap technique were performed on eutectic LiF-NaF-KF from 834 to 1195 K. The experiment accounts for radiative, convective, and conductive heat losses. In addition, theoretical and molecular dynamics models are used, from 750 K up to 1300 K, to estimate the thermal conductivity for comparison with the experimental results. The results of experiments show a weak negative deviation of thermal conductivity with temperature, unlike previous experimental results in the literature. The measured thermal conductivity magnitudes agree with the theoretical and molecular dynamics predictions, aside from the data above 1100 K, where heat losses and radiative errors are the most significant, having a 16% maximum deviation from theory. These experimental results provide new thermal conductivity data for the LiF-NaF-KF system and further validation of the predictive models. The theoretical model was used to map the composition and temperature dependent thermal conductivity of LiF-NaF-KF and the mapping’s deviation from a linear additivity estimation of thermal conductivity. Additionally, this mapping showed the highest deviations from linearity for KF-LiF rich mixtures and increasing deviation with temperature. Notably, the deviation from linearity near the LiF-NaF-KF eutectic composition was around 25%.

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

Sticking Coefficients of Fusion Reactor Impurities from Molecular Dynamics Simulations for the Design of Cryopumps

A cryopump can be utilized as an impurity removal component of a direct internal recirculation (DIR) system for the fusion fuel cycle. The DIR facilitates a low fuel inventory by continuously pumping unburnt fuel while removing impurities from the fusion exhaust stream. A cryopump can target multiple impurity species by maintaining a temperature lower than the gas triple-point temperature that promotes desublimation. The desublimation/condensation of gases in cryopumps can be characterized by the sticking coefficient, which is defined as the probability for a gas particle to stick to a (cryo-)surface upon collision. The sticking coefficient is one of the important design/operation parameters for cryopumps, and it depends on a variety of surface and gas properties. Here, in this study, molecular dynamics simulations were utilized to estimate the sticking coefficients of typical fusion gas impurity species N 2 , CO 2 , and CH 4 over a Cu surface for a range of gas temperatures and surface coverages. The molecular dynamics study showed that the sticking coefficients for gases decrease with an increase in gas temperature. The presence of a single full monolayer of condensate on the metallic surface showed an adverse effect on the sticking of gases; however the sticking improved with two full monolayers of condensate on the surface. The sticking of gases over the mixed condensate on a surface was more favorable than the condensate of the same species for N 2 and CH 4 , with an exception for CO 2 , which showed a decrease in sticking over the mixed condensate.

cryopump↗
DOE OSTI2025

Molecular Dynamics Simulations of a Liquid Metal Wetting Zirconia Suboxides

Molecular dynamics simulations were performed of a liquid metal (Ag) interacting with various zirconia suboxides to calculate the work of adhesion between the liquid metal and the suboxides. These simulations were then used to assess the impact of oxygen content on wetting. The results of this work show a wetting transition as oxygen content is reduced.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Molecular Dynamics Study of Creep Deformation in Nickel-based Superalloy

The present study employs molecular dynamics simulations of Ni-based superalloy to investigate the creep behavior under uniaxial compression test. Dislocation dynamics is analyzed for the nickel-based single crystal superalloy with the presence of void and with varying the distribution of gamma-prime phase The results show that multiple-void systems are more prone to yield than single-void systems and single-void systems are more prone to yield than the system withoutvoid. From the simulations, it has been determined that the creep mechanism in Ni/Ni3Al is subject to change on the applied stress depending on the distribution of gamma-prime phases change. Dislocation behavior is also observed in addition to the time evolution of dislocation nucleation and growth to quantify the propensity and mechanism of creep in nickel-based single crystal superalloy. The studies confirmed that dislocation length prior to plastic deformation decreased as the number of voids increased. In addition, the deformation behavior for finegrained nickel-based polycrystalline superalloy upon grain size variation is also investigated. Our findings show that both the movement mechanisms of the grains and grain boundaries and the relationship between grain size and yield strength are highly affected by the grain size of the materials. All the databases have then been classified to accurately predict the target class vi machine learning using the data mining tool WEKA.

creep, nickel-based superalloy, molecular dynamics↗