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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structure, dynamics, and electrochemistry of choline chloride/ethylene glycol eutectic solvents at an electrode surface explored by molecular dynamics simulations

Choline chloride and ethylene glycol mixtures with 1:2, 1:4, and 1:6 molar ratios on the surfaces of graphite and gold electrodes were studied using classical molecular dynamics simulations. Both neutral and charged electrodes were considered. The liquid composition, solvation structure, molecular orientation, and dynamics at the electrode surface are significantly different from those of the bulk liquid. These properties strongly depend on the electrode material and charge density, whereas they are less sensitive to the overall solvent composition. The effect of the electrode on the composition, structure, and orientation of the liquid fades beyond ∼10 Å from the surface of the electrode. This distance corresponds to about two layers of the structured solvent, despite the fact that the layered structure extends to at least five layers or about 25 Å. However, the electrode influences solvent dynamics over a longer distance. The electrochemical properties of the eutectic solvent at both electrode surfaces were also studied. The simulations captured the experimental differential capacitance shapes for both electrode systems, although the magnitudes and exact shapes differ. The simulations further revealed that the solvent in the first solvation layer can both overscreen and underscreen the electrode charges depending on the electrode material and electrode potential.

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

Insights on the structure and properties of sodium iron phosphate glasses from molecular dynamics simulations

Iron phosphate glasses are promising nuclear waste forms while more detailed understanding of their structures and structure-property relations are still needed to better design waste glass compositions. In this work we report studies of three series of sodium iron phosphate (NFP) glasses: 60P 2 O 5 -(40-x)Fe 2 O 3 -xNa 2 O (x = 0→40), (100–2x)P 2 O 5 -xFe 2 O 3 -xNa 2 O (x = 5→17.5) and one with different iron redox ratio, to understand the composition as well as the iron redox effects on the structure and properties of these glasses using molecular dynamics simulations with effective two-body and three-body potentials. Structural analyses, including pair distribution function, bond angle distribution, Q n distribution, and polyhedral connectivity, were performed to obtain in-depth information on short-range and medium-range structural features. The P-O pair distributions showed a first peak splitting with phosphorus-bridging and non-bridging oxygen contributions. This and the average P-O and other cation-oxygen bond distances are in excellent agreement with experiments. The coordination number of P 5+ remained four while that of Fe 3+ increased from 4.30 to 4.72 with decreasing Fe/Na ratio. Polyhedral linkage analysis showed [PO 4 ] units linked with [PO 4 ] and [FeO x ] through corner-sharing while the [PO 4 ]-[FeO x ] linkages become dominant for compositions with Fe 2 O 3 larger than 15 mol%. The effect of iron redox ratio on the structure of NFP glasses was also studied and it was found that bond lengths and coordination numbers were not strongly affected, while the reduction of iron introduced higher network distortions, as evident by O-P-O bond angle and Q n distribution. The glass transition temperature (T g ) showed a monotonic increase with Fe 2 O 3 in the first series, in good agreement with experiments, while those of the second series showed a maximum at P 2 O 5 = 82 mol%. Here, calculated elastic moduli were found to increase with Fe 2 O 3 in the first glass series, which was be explained by the increase of network connectivity, while those of the second series decrease with Fe 2 O 3 due to decrease of P 2 O 5 .

36 MATERIALS SCIENCE↗
DOE OSTI2021

Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2022

A high-dimensional neural network potential for molecular dynamics simulations of condensed phase nickel and phase transitions

A high-dimensional neural network interatomic potential was developed and used in molecular dynamics simulations of condensed phase Ni and Ni systems with liquid–solid phase coexistence. The reference data set was generated by sampling the potential energy surface over a broad temperature-pressure domain using ab initio MD simulations to train a unified potential. Excellent agreement was achieved between bulk face-centered cubic nickel thermal expansion simulations and relevant experimental data. The same potential also yields accurate structures and diffusivities in the liquid state. The phase transition between liquid and solid phases was simulated using the two-phase interface method. The predicted melting point temperature is within a few kelvins of the literature value. Here, the general methodology could be applied to describe crystals with much more complex phase behaviors.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations

We study the phase equilibrium between liquid water and ice Ih modeled by the TIP4P/Ice interatomic potential using enhanced sampling molecular dynamics simulations. Our approach is based on the calculation of ice Ih-liquid free energy differences from simulations that visit reversibly both phases. The reversible interconversion is achieved by introducing a static bias potential as a function of an order parameter. The order parameter was tailored to crystallize the hexagonal diamond structure of oxygen in ice Ih. Furthermore, we analyze the effect of the system size on the ice Ih-liquid free energy differences, and we obtain a melting temperature of 270 K in the thermodynamic limit. This result is in agreement with estimates from thermodynamic integration (272 K) and coexistence simulations (270 K). Since the order parameter does not include information about the coordinates of the protons, the spontaneously formed solid configurations contain proton disorder as expected for ice Ih.

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

Ab-Initio molecular dynamics simulations of binary NaCl-ThCl 4 and ternary NaCl-ThCl 4 -UCl 3 molten salts

Molten salt reactor (MSR) with Thorium (Th) fuel cycle has attracted growing attention due to its merits such as safety, low radioactive waste production, and non-proliferation. The design and safe operation of MSR rely on a thorough understanding of the thermophysical properties of molten salts over a wide range of composition and temperature. However, experimental data of Th-based molten salts are limited due to the inherent challenges of dealing with corrosive molten salts and the radioactive nature of actinides. Here, in this work, thermophysical properties including density, heat capacity, thermal expansion coefficient, and mixing energy of binary NaCl-ThCl 4 and ternary NaCl-ThCl 4 -UCl 3 molten salts are explored using ab-initio molecular dynamic simulations (AIMD) with the dDsC dispersion correction. The calculated mixing energy of binary NaCl-ThCl 4 exhibits a minimum close to the eutectic composition. The heat capacity of the mixtures is linearly dependent on the mole fraction of each component. 7-fold and 6-fold coordinated Th complexes are dominant in the mixtures. 8-fold coordinated Th complex increases with ThCl 4 fraction due to the formation of network structures. The average coordination number of Th exhibits a minimum near the eutectic composition. The minimum mixing energy for the ternary mixtures is observed in systems with a composition close to [NaCl] 0.5 [ThCl 4 ] 0.25 [UCl 3 ] 0.25 . The density positively deviates from the ideal solution in mixtures near this composition. These results are important to fill the data and knowledge gap of ThCl 4 molten salts.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Data and Code for Atomic Scale Etching of Diamond: Insights from Molecular Dynamics Simulations

This work investigates the effects of argon ions, hydrogen atoms, and hydrogen ions on the diamond (100) surface using classical molecular dynamics simulations. The purpose of this investigation was to asses plasma processing techniques for applications in quantum device manufacturing. The simulations suggest that combining argon ion smoothing with selective, near threshold energy H removal of amorphous C could be an effective strategy for diamond surface engineering, leading to more reliable and sensitive diamond color center devices. Results were found to differ significantly with interatomic potential, and an analysis of these differences was also carried out. Included in this repository are LAMMPS source files, input scripts, and plotting scripts required to reproduce the data. Also included are the output data required to make all the plots included in the associated publication.

Brenner↗
DOE OSTI2023

X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula

Here, we study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Combined molecular and spin dynamics simulation of BCC iron with vacancy defects

Utilizing an atomistic computational model, which handles both translational and spin degrees of freedom, combined molecular and spin dynamics simulations have been performed to investigate the effect of vacancy defects on spin wave excitations in ferromagnetic iron. Fourier transforms of space- and time-displaced correlation functions yield the dynamic structure factor, providing characteristic frequencies and lifetimes of the spin wave modes. A comparison of the system with a 5% vacancy concentration with pure lattice data shows a decrease in frequency and a decrease in lifetime for all transverse spin wave excitations observed. In addition, the clearly defined transverse spin wave excitations are distorted with the introduction of vacancy defects, and we observe reduced excitation lifetimes due to increased magnon–magnon scattering. We observe further evidence of increased magnon–magnon scattering, as the peaks in the longitudinal spin wave spectrum become less distinct. Finally, similar impacts are observed in the vibrational subsystem, with a decrease in characteristic phonon frequency and flattening of lattice excitation signals due to vacancy defects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Collective Vibrational Strong Coupling Effects on Molecular Vibrational Relaxation and Energy Transfer: Numerical Insights via Cavity Molecular Dynamics Simulations**

Abstract For a small fraction of hot CO 2 molecules immersed in a liquid‐phase CO 2 thermal bath, classical cavity molecular dynamics simulations show that forming collective vibrational strong coupling (VSC) between the C=O asymmetric stretch of CO 2 molecules and a cavity mode accelerates hot‐molecule relaxation. This acceleration stems from the fact that polaritons can be transiently excited during the nonequilibrium process, which facilitates intermolecular vibrational energy transfer. The VSC effects on these rates 1) resonantly depend on the cavity mode detuning, 2) cooperatively depend on Rabi splitting, and 3) collectively scale with the number of hot molecules. For larger cavity volumes, the average VSC effect per molecule can remain meaningful for up to N ≈10 4 molecules forming VSC. Moreover, the transiently excited lower polariton prefers to relax by transferring its energy to the tail of the molecular energy distribution rather than distributing it equally to all thermal molecules. As far as the parameter dependence is concerned, the vibrational relaxation data presented here appear analogous to VSC catalysis in Fabry–Pérot microcavities.

Li, Tao E.↗
DOE OSTI2021

Collective Vibrational Strong Coupling Effects on Molecular Vibrational Relaxation and Energy Transfer: Numerical Insights via Cavity Molecular Dynamics Simulations**

Abstract For a small fraction of hot CO 2 molecules immersed in a liquid‐phase CO 2 thermal bath, classical cavity molecular dynamics simulations show that forming collective vibrational strong coupling (VSC) between the C=O asymmetric stretch of CO 2 molecules and a cavity mode accelerates hot‐molecule relaxation. This acceleration stems from the fact that polaritons can be transiently excited during the nonequilibrium process, which facilitates intermolecular vibrational energy transfer. The VSC effects on these rates 1) resonantly depend on the cavity mode detuning, 2) cooperatively depend on Rabi splitting, and 3) collectively scale with the number of hot molecules. For larger cavity volumes, the average VSC effect per molecule can remain meaningful for up to N ≈10 4 molecules forming VSC. Moreover, the transiently excited lower polariton prefers to relax by transferring its energy to the tail of the molecular energy distribution rather than distributing it equally to all thermal molecules. As far as the parameter dependence is concerned, the vibrational relaxation data presented here appear analogous to VSC catalysis in Fabry–Pérot microcavities.

Li, Tao E.↗
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 OSTI2022

Molecular dynamics simulation of seeded crystal growth in glass

The mechanism of non-congruent growth of a crystal from glass has been sought using molecular dynamics simulations. Specifically, as a model of this process, the growth of a lithium niobate (LiNbO 3 ) crystal seed sandwiched between two lithium niobosilicate (LNS) glass slabs has been simulated as a function of time and temperature. The growth of pre-existing crystal is strongly affected by the orientation of crystal seed, temperature, and the SiO 2 concentration in the surrounding LNS glass matrix. The orientation of LiNbO 3 seed surface that has inherently larger interplanar distance results in a relatively slower crystal growth. The addition of SiO 2 to LNS system significantly decreases the crystal growth, which primarily occurs in the region devoid of Si. The suppressive effect of SiO 2 on growth rate can be traced to the existence of defect complex comprising of Si substituted at the Nb site and a nearby Nb vacancy.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Molecular-gas-dynamics simulations of turbulent Couette flow over a mean-free-path-scale permeable substrate

Here we report flow statistics and visualizations from molecular-gas-dynamics simulations using the direct simulation Monte Carlo (DSMC) method for turbulent Couette flow in a minimal domain where the lower wall is replaced by an idealized permeable fibrous substrate representative of thermal-protection-system materials for which the Knudsen number is O(10 -1 ). Comparisons are made with smooth-wall DSMC simulations and smooth-wall direct numerical simulations (DNS) of the Navier-Stokes equations for the same conditions. Roughness, permeability, and noncontinuum effects are assessed. In the range of Reynolds numbers considered herein, the scalings of the skin friction on the permeable substrate and of the mean flow within the substrate suggest that they are dominated by viscous effects. While the regenerative cycle characteristic of smooth-wall turbulence remains intact for all cases considered, we observe that the near-wall velocity fluctuations are modulated by the permeable substrate with a wavelength equal to the pore spacing. Additionally, the flow within the substrate shows significant rarefaction effects, resulting in an apparent permeability that is 13% larger than the intrinsic permeability. In contrast, the smooth-wall DSMC and DNS simulations exhibit remarkably good agreement for the statistics examined, despite the Knudsen number based on the viscous length scale being as large as O(10 -1 ). This latter result is at variance with classical estimates for the breakdown of the continuum assumption and calls for further investigations into the interaction of noncontinuum effects and turbulence.

42 ENGINEERING↗
DOE OSTI2024

Beam Dynamics simulations for ERDC project -- SRF linac for industrial use

Compact conductively cooled SRF industrial linacs can provide unique parameters of the electron beam for industrial applications. (up to 10MeV, 1MW). For ERDC project we designed normal conducting RF injector with thermal RF gridded gun integrated in first cell of multi-cell cavities. For design of the RF gun we used MICHELLE software to simulate and optimize parameters of the beam. Output file was converted to ASTRA format and most beam dynamic simulations in multi-cell normal conducting cavity and cryomodule were performed by using ASTRA software. For cross-checking we compare results of MICHELLE and AS-TRA in first few cells. At the end of injector beam reach ~250keV energy which allow to trap bunch in acceleration regime without losses in TESLA like 1.3 GHz cavity. Short solenoid at the end of injector allow to regulate transverse beam size in cryomodule to match beam to extraction system and also reduce charge losses in accelerator.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Molecular dynamics simulations of inelastic x-ray scattering from shocked copper

By taking the spatial and temporal Fourier transforms of the coordinates of the atoms in molecular dynamics simulations conducted using an embedded-atom-method potential, we calculate the inelastic scattering of x rays from copper single crystals shocked along [001] to pressures of up to 70 GPa. Above the Hugoniot elastic limit, we find that the copious stacking faults generated at the shock front introduce strong quasi-elastic scattering (QES) that competes with the inelastic scattering signal, which remains discernible within the first Brillouin zone; for specific directions in reciprocal space outside the first zone, the QES dominates the inelastic signal overwhelmingly. The synthetic scattering spectra we generate from our Fourier transforms suggest that energy resolutions of order 10 meV would be required to distinguish inelastic from quasi-elastic scattering within the first Brillouin zone of shock-loaded copper. We further note that high-resolution inelastic scattering also affords the possibility of directly measuring particle velocities via the Doppler shift. These simulations are of relevance to future planned inelastic scattering experiments at x-ray Free Electron Laser facilities.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗