Search NASA⌕ Search

SEARCH · Search NASA

Results for “classical 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.

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

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Tuning the Functionalities of Porous Liquids for Emergent Gas-Capture Properties

Type 3 Porous Liquids (PLs) are a class of materials with the potential to revolutionize gas capture, storage, and utilization. These PLs are formed by suspending sorbent nanoparticles (e.g., metal−organic frameworks) in sterically excluded solvents, creating permanent porosity for gas capture in a processable, low-viscosity phase. Herein, a computational study revealed sorbent surface functionalization strategies to enhance CO 2 sorption, and the molecular structural signatures underpinning the enhancements in gas uptake. PLs composed of a ZIF-8 surface functionalized with 3-amino-1,2,4-triazole (Atz) in glyceryl triacetate were targeted for emergent CO 2 capture, exceeding that of the unfunctionalized ZIF-8 PL. ZIF-8 was surface functionalized with Atz at various surface coverage fractions (f), and classical molecular dynamics simulations predicted an increase in CO 2 sorption capacity with increasing f, up to f = 0.75. Additionally, detailed structural analyses revealed that solvent orientational order, derived from the solvent triplet-angle distribution, can identify the gas-capture potential of a PL without requiring computationally expensive direct modeling of the CO 2 sorption. Combined with experimental validation, initial computational screening of PL compositions promises to accelerate the discovery of PL compositions for novel gas separation materials platforms.

gas capture↗
DOE OSTI2025

Quantum Monte Carlo and Density Functional Theory Study of Strain and Magnetism in 2D 1T-VSe 2 with Charge Density Wave States

Two-dimensional (2D) 1T-VSe 2 has prompted significant interest due to the discrepancies regarding alleged ferromagnetism (FM) at room temperature, charge density wave (CDW) states, and the interplay between the two. We employed a combined Diffusion Monte Carlo (DMC) and density functional theory (DFT) approach to accurately investigate the magnetic properties, CDW states, and their responses to strain in monolayer 1T-VSe 2 . Our calculations show the delicate competition between various phases, revealing critical insights into the relationship between their energetic and structural properties. Here, we performed classical Monte Carlo simulations informed by our DMC and DFT results and found the magnetic transition temperature (T c ) of the undistorted (non-CDW) FM phase to be 228 K and the distorted (CDW) phase to be 68 K. Additionally, we studied the response of biaxial strain on the energetic stability and magnetic properties of various phases of 2D 1T-VSe 2 and found that small amounts of strain can increase the T c , suggesting a promising route for engineering and enhancing magnetic behavior. Finally, we synthesized 1T-VSe 2 and performed Raman spectroscopy measurements, which were in close agreement with our calculated results, validating our computational approach. Our work emphasizes the role of highly accurate DMC methods in advancing the understanding of monolayer 1T-VSe 2 and provides a robust framework for future studies of 2D magnetic materials.

2D magnets↗
DOE OSTI2024

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria that encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo , the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We used molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo . Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed the overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceu m model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.

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

Visualizing the Three-Dimensional Arrangement of Hydrogen Atoms in Organic Molecules by Coulomb Explosion Imaging

Structure-sensitive methods based on femtosecond light or electron pulses are now making it possible to measure how molecular structures change during light-induced processes. Despite significant progress, high-fidelity imaging of nuclear positions remains a challenge even for relatively small molecular systems and, notably, regarding the positions of hydrogen atoms. As demonstrated in recent work, X-ray-induced Coulomb explosion imaging (CEI) may overcome this obstacle, as its sensitivity does not depend on the mass of the imaged atoms. The photoinduced ring opening of the heterocyclic molecule 2(5 H )-thiophenone has attracted recent interest. Here, in this work, we show that CEI offers a powerful route to imaging the peripheral H atoms in this molecule and thus, more generally, to tracking detailed nuclear motions (e.g., isomerizations) in organic molecules on ultrafast time scales. Specifically, we record momentum-space Coulomb explosion images that report on the three-dimensional positioning of all nuclei within the molecule, for instance, distinguishing H atoms in C–H bonds that lie within or are directed out of the plane defined by the heavy atoms. The prospect of imaging peripheral H atoms to probe photochemical dynamics is explored by coupling ab initio molecular dynamics with classical Coulomb explosion simulations, thereby differentiating potential photoproduct isomers, including those whose structures primarily differ in the position of the hydrogens.

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

Structure and mechanical properties of grain boundaries in molybdenum disulfide (MoS 2 )

Molybdenum disulfide (MoS 2 ) is a two-dimensional material widely used as a lubricant in many applications involving mechanical loading under a wide range of operating temperatures. Since many synthesis and processing techniques yield MoS 2 in its polycrystalline form, establishing grain boundary (GB) structure–property relations is key to designing MoS 2 microstructures with tailored properties. Here, we employ classical, reactive atomistic simulations to investigate the structure and mechanical behavior of a wide range of GBs in MoS 2 as a function of temperature. Using a bicrystal MoS 2 geometry, we characterize the atomic structure and calculate the energy of several low-angle GBs. Then, we simulate the tensile deformation behavior of MoS 2 bicrystals at several temperatures. Our results reveal that at temperatures above 100 K, the deformation of MoS 2 bicrystals is characterized by the nucleation of shear bands from GBs that grow, with subsequent loading, into the MoS 2 crystals. At low temperatures, the tensile deformation is characterized by the nucleation and propagation of deformation fronts, resulting in altered bond angles and bond lengths. Quantitative analysis reveals a decrease in the ultimate tensile stress and ultimate failure strain of MoS 2 bicrystals with the increase in temperature. Furthermore, our simulations of the mechanical behavior of metastable GBs reveal that the strength and ductility decrease with the increase in energy of these boundary structures. In broad terms, our work provides future avenues to employ GB engineering as a strategy to tailor the properties of MoS 2 microstructures.

Moore, Robert D. [Lehigh Univ., Bethlehem, PA (Uni↗
DOE OSTI2025

Water under hydrophobic confinement: entropy and diffusion

The properties of liquid water are known to change drastically in confined geometries. A most interesting and intriguing phenomenon is that the diffusion of water is found to be strongly enhanced by the proximity of a hydrophobic confining wall relative to the bulk diffusion. We report a molecular dynamics simulation using a classical water model investigating the water diffusion near a non-interacting smooth confining wall, which is assumed to imitate a hydrophobic surface, revealing a pronounced diffusion enhancement within several water layers adjacent to the wall. We present evidence that the observed diffusion enhancement can be accounted for, with a quantitative accuracy, using the universal scaling law for liquid diffusion that relates the diffusion rate to the excess entropy. These results show that the scaling law, which has so far only been used for the description of the diffusion in simple liquids, can successfully describe the diffusion in water. It is shown that the law can be used for the analysis of water dynamics under nanoscale hydrophobic confinement, which is currently a subject of intense research activity.

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

Stoichiometry dependent properties of cerium hydride: An active learning developed interatomic potential study

Cerium hydride has a variety of interesting properties, including a known lattice contraction and densification with increasing hydrogen content. However, precise stoichiometric control is not experimentally straightforward and ab initio approaches are not computationally feasible for many properties such as melting and low temperature diffusion. Therefore, we develop a machine-learned interatomic potential for cerium hydride that is valid for H to Ce ratios from 2.0 to 3.0. A query-by-committee active learning approach is used to develop the training set. Leveraging classical molecular dynamics simulations, we assess a range of properties and provide fundamental mechanisms for the trends with stoichiometry. Finally, a majority of the properties follow the trend of lattice contraction, being governed by the stronger lattice binding induced by adding octahedral atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Diffuse scattering from dynamically compressed single-crystal zirconium following the pressure-induced α → ω phase transition

The prototypical α → ω phase transition in zirconium is an ideal test bed for our understanding of polymorphism under extreme loading conditions. After half a century of study, a consensus had emerged that the transition is realized via one of two distinct displacive mechanisms, depending on the nature of the compression path. However, recent dynamic-compression experiments equipped with diffraction diagnostics performed in the past few years have revealed new transition mechanisms, demonstrating that our understanding of the underlying atomistic dynamics and transition kinetics is in fact far from complete. We present classical molecular dynamics simulations of the α → ω phase transition in single-crystal zirconium shock compressed along the [0001] axis using a machine-learning-class potential. The transition is predicted to proceed primarily via a modified version of the two-stage Usikov-Zilberstein mechanism, whereby the high-pressure ω phase heterogeneously nucleates at boundaries between grains of an intermediate β phase. We further observe the fomentation of atomistic disorder at the junctions between β grains, leading to the formation of highly defective interstitial material between the ω grains. We directly compare synthetic x-ray diffraction patterns generated from our simulations with those obtained using femtosecond diffraction in recent dynamic-compression experiments, and show that the simulations produce the same unique, anisotropic diffuse scattering signal unlike any previously seen from an elemental metal. Our simulations suggest that the diffuse signal arises from a combination of thermal diffuse scattering, nanoparticlelike scattering from residual kinetically stabilized α and β grains, and scattering from interstitial defective structures. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗
DOE OSTI2024

Coordinate versus momentum cuts and effects of collective flow on critical fluctuations

We analyze particle number fluctuations in the crossover region near the critical endpoint of a first-order phase transition by utilizing molecular dynamics simulations of the classical Lennard-Jones fluid. We extend our previous study [V. A. Kuznietsov , ] by incorporating longitudinal collective flow. The scaled variance of particle number distribution inside different coordinate and momentum space acceptances is computed through ensemble averaging and found to agree with earlier results obtained using time averaging, validating the ergodic hypothesis for fluctuation observables. Presence of a sizable collective flow is found to be essential for observing large fluctuations from the critical point in momentum space acceptances. We discuss our findings in the context of heavy-ion collisions. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Anharmonic phonons, thermal expansion, and nuclear quantum effects in Zn

The anharmonic behavior of phonons and thermal expansion of hexagonal zinc were studied from 15 to 690 K by inelastic neutron scattering (INS) and ab initio simulations. Phonon spectra were measured for Q-points covering the full Brillouin zone, giving the phonon density of states (DOS) and dispersions along high-symmetry directions. The dispersions were sharp at 15 K, but diffuse intensity was observed at energies above them. The dispersions broadened with temperature T and the diffuse intensity became stronger. This diffuse intensity appeared in all INS measurements and simulations, except for classical molecular dynamics at 15 K. The temperature-dependent effective potential (TDEP) method, which included the nuclear quantum effect from zero-point vibrational dynamics, was used to calculate the free energy and thermal expansion. For T < 100 K nuclear quantum effects were important for obtaining the correct negative thermal expansion, and path integral molecular dynamics (PIMD) was particularly effective for obtaining the negative thermal expansion in the basal plane. A Heisenberg-Langevin model for interacting phonons coupled to a thermal bath was able to reproduce the shape and intensity of the diffuse spectral features.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

High-order cumulants and correlation functions near the critical point from molecular dynamics

We present a systematic investigation of particle-number fluctuations in the crossover region near the critical end point of a first-order phase transition using molecular dynamics simulations of the classical Lennard-Jones fluid. We extend our prior studies to third- and fourth-order cumulants in both coordinate- and momentum-space acceptances and integrated correlation functions (factorial cumulants). We find that, even near the critical point, non-Gaussian cumulants equilibrate on timescales comparable to those of the second-order cumulants, but show stronger finite-size effects. The presence of interactions and of the critical point leads to strong deviations of the cumulants from the ideal-gas baseline in coordinate space; these deviations are expected to persist in momentum space in the presence of collective expansion. In particular, the kurtosis becomes strongly negative, κσ 2 ≪ − 1 , on the crossover side of the critical point. However, this signal is significantly diluted once an efficiency cut used to distinguish protons from baryons is applied, leading to |κσ 2 | ≲ 1 even in the presence of the critical point. We discuss our results in the context of ongoing measurements of proton-number cumulants in heavy-ion collisions in RHIC-BES-II.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

On the role of α-alumina in the origin of life: Surface-driven assembly of amino acids

We investigate the hypothesis that mineral/water interfaces played a crucial catalytic role in peptide formation by promoting the self-assembly of amino acids. Using classical molecular dynamics simulations, we demonstrate that the α-alumina(0001) surface exhibits an affinity of 4k B Tfor individual glycine or GG dipeptide molecules due to hydrogen bonds. In simulations with multiple glycine molecules, surface-bound glycine enhances further adsorption, leading to the formation of long chains connected by hydrogen bonds between the carboxyl and amine groups of glycine molecules. We find that the likelihood of observing chains longer than 10 glycine units increases by at least five orders of magnitude at the surface compared to the bulk. This surface-driven assembly is primarily due to local high density and alignment with the alumina surface pattern. Together, these results propose a model for how mineral surfaces can induce configuration-specific assembly of amino acids, thereby promoting condensation reactions.

Science & Technology - Other Topics↗
DOE OSTI2024

DRIFT: Diffusivity Regulation of Isotopes by nanoconFinementT

Spontaneous isotope fractionation has been reported under nanoconfinement conditions in naturally occurring systems, but the origin of this phenomena is currently unknown. Two existing hypotheses have been proposed, one based on changes in the solvation environment of the isotopes that reduces the non-mass dependent hydrodynamics contribution to diffusion. The other is that isotopes have mass-dependent surface adsorption, varying their total diffusion through nanoconfined channels. To investigate these hypotheses, benchtop experiments, nuclear magnetic resonance (NMR) spectroscopy, and molecule scale modeling were applied. Classical molecular dynamics simulations identified that the Na + and Cl - hydration shells across the three different salt solutions ( 22 Na 35 Cl, 23 Na 35 Cl, 24 Na 35 Cl) did not vary as a function of the Na + isotope, but that there was a significant pore size effect, with larger hydration shells at larger pore sizes. Additionally, while total adsorption times did not vary as a function of the Na + isotope or pore size, the free ion concentration, or those adsorbed on the surface for <5% of the simulation time did exhibit isotope dependence. Experimentally, challenges occurred developing a repeatable experiment, but NMR characterization of water diffusion rates through ordered alumina membranes was able to identify the existence of two distinct water environments associated with water inside and outside the pore. Further NMR studies could be used to confirm variation in hydration shells and diffusion rates of dissolved ions in water. Ultimately, mass-dependence adsorption is a primary driver of variations in isotope diffusion rates, rather than variation in hydration shells that occur under nanoconfinement.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1988

Equivalent linearization for fatigue life estimates of a nonlinear structure

An adaptation of the method of equivalent linearization is developed in order to estimate the fatigue life of a nonlinear structure excited by Gaussian white noise. While conventional equivalent linearization has been successfully applied to approximate the mean square responses of the variety of complex nonlinear systems, it has not been possible to apply the method for fatigue predictions. This limitation results from the assumption that the probability density of the response of the nonlinear system is Gaussian, which is not generally true. In the present effort, a modification of equivalent linearization, developed by the author, is employed which has been shown in recent studies to provide a much more accurate description of the random response of a nonlinear structure than provided by conventional equivalent linearization. A method is presented for estimating fatigue life based on this approach and results are compared with those obtained using both numerical simulation and the classical method. The fatigue life is estimated for a nonlinear plate vibrating in a single resonant mode with random white noise excitation. Excellent agreement is found between all three methods. These results indicate that equivalent linearization may be extended to predict the fatigue life of more complex nonlinear systems than can be analyzed at present.

Miles, R. N.↗
NASA NTRS1998

Nanoscale Etching and Indentation of Silicon(001) Surface with Carbon Nanotube Tips

The possibility of nanoscale etching and indentation of Si(001)(2x1) surface by (8,0) and (10,10) carbon nanotube tips is demonstrated, for the first time, by classical molecular dynamics simulations employing Tersoff's many-body potential for a mixed C/Si/Ge system. In the nanotube tip barely touching the surface scenario atomistic etching is observed, where as in the nanoindentation scenario nanotube tip penetrates the surface without much hindrance. The results are explained in terms of the relative strength of C-C, C-Si, and Si-Si bonds.

Dzegilenko, Fendor N.↗
NASA NTRS2017

Path Profiles of Cn2 Derived from Radiometer Temperature Measurements and Geometrical Ray Tracing

Atmospheric turbulence has significant impairments on the operation of Free-Space Optical (FSO) communication systems, in particular temporal and spatial intensity fluctuations at the receiving aperture resulting in power surges and fades, changes in angle of arrival, spatial coherence degradation, etc. The refractive index structure parameter Cn2 is a statistical measure of the strength of turbulence in the atmosphere and is highly dependent upon vertical height. Therefore to understand atmospheric turbulence effects on vertical FSO communication links such as space-to-ground links, it is necessary to specify Cn2 profiles along the atmospheric propagation path. To avoid the limitations on the applicability of classical approaches, propagation simulation through geometrical ray tracing is applied. This is achieved by considering the atmosphere along the optical propagation path as a spatial distribution of spherical bubbles with varying relative refractive index deviations representing turbulent eddies. The relative deviations of the refractive index are statistically determined from altitude-dependent and time-varying temperature fluctuations, as measured by a microwave profiling radiometer. For each representative atmosphere ray paths are analyzed using geometrical optics, which is particularly advantageous in situations of strong turbulence where there is severe wavefront distortion and discontinuity. The refractive index structure parameter is then determined as a function of height and time.

Atmospheric turbulence↗
NASA NTRS2018

Stochastic Reduced Order Models with Python (SROMPy)

Stochastic Reduced Order Models with Python (SROMPy) is a software package developed to enable user-friendly utilization of the stochastic reduced order model (SROM) approach for uncertainty quantification. A SROM is a low dimensional, discrete approximation to a random quantity that enables efficient and non-intrusive stochastic computations. With SROMPy, a user can easily generate a SROM to approximate a random variable or vector described by several different types of probability distributions using the Python programming language. Once a SROM is constructed, the software can be used to propagate uncertainty through a user-defined computational model to estimate statistics of a given quantity of interest. This report is meant to introduce the SROMPy module and brie y demonstrate its capabilities. A simple example of a spring-mass system with a random input is included to illustrate the practicality of the SROM approach to uncertainty quantification and relative ease of applying it with SROMPy. The example includes a comparison with a solution obtained using classical Monte Carlo simulation, demonstrating the similarities and advantages of using the SROM approach.

Warner, James E.↗
NASA NTRSDate not supplied

REACTER 2.0: Quantum-Informed Reaction Constraints and Automated Interaction Typing

REACTER is a heuristic method for modeling chemical reactions in classical molecular dynamics simulations, implemented in LAMMPS as fix bond/react. The authors recently extended LAMMPS to support alphanumeric labels for atom types, bond types etc., which enables the pre- and post-reaction templates required by the REACTER protocol to be portable between different simulations and greatly simplifies the task of creating simulation-ready reaction templates. To further increase the generality of reaction templates, support for wildcard characters within atom types has been added, along with the automatic assignment of interaction types for new bonds, angles, etc. based on the involved atom types. In some cases, this feature can express a class of reactions with one pair of reaction templates, where previously dozens may have been required. Advanced reaction constraints have also been added, including an Arrhenius constraint to enforce an effective activation energy, a root-mean-square-deviation option for complex geometrical constraints, as well as a custom constraint that leverages LAMMPS’ powerful built-in variable framework. Other new features include variable support for various inputs (e.g., to allow reaction rates or cutoffs to be dependent on overall conversion), on-the-fly update of molecule IDs, and the ability to create new atoms positioned with respect to the reaction site. The new features are applied to modeling polymeric, thermosetting and composite materials, and advanced applications of the new reaction constraints are demonstrated. For example, REACTER is shown to accurately reproduce mechanically-induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a constraint on the total potential energy of the involved atoms.

polymer simulations↗