Search NASA⌕ Search

SEARCH · Search NASA

Results for “molecular dynamics (MD)”

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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Dynamics of plasma atomic layer etching: Molecular dynamics simulations and optical emission spectroscopy

Atomic layer etching is intrinsically dynamic as it involves sequential and repeated exposures of a surface to be etched with different species at different energies. The composition and structure of the near surface region change in both time and depth. Full understanding of this process requires resolving both temporal and spatial variations. In this work, we consider silicon (Si) atomic layer etching (ALE) by alternating exposure to chlorine gas (Cl 2 ) and argon ions (Ar + ). Molecular dynamics (MD) simulations are compared to experimental measurements with the aim of better understanding the dynamics of ALE and to test the simulation procedure. The simulations help to more fully interpret the experimental measurements. Further, optical emission measured just above the surface being etched can be related to etch products and can, therefore, be directly compared to simulation predictions. The simulations capture the measured initial product distribution leaving the surface and match the measured etch per cycle reasonably well. While simulations demonstrate the importance of ion-induced surface damage and mixing into a layer below the surface, the depth of which depends mainly on ion energy, the experiments suggest there is more Cl mixed into the layer than the MD procedure predicts.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Modeling Equilibrium Solid–Liquid Interfaces under Effective Constant Chemical Potential Using Machine Learning Interatomic Potentials

The chemical potential (μ) of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot maintain constant chemical potential with reference to a targeted concentration or chemical potential under nonequilibrium or dynamic conditions, as solute species can migrate to the interface and deplete (or enrich) the bulk due to solute-interface interactions. In this study, we introduce a simple and computationally efficient approach named iterative quasi-constant chemical potential molecular dynamics (iqCμMD) simulation, which helps simulate targeted molar concentrations of species in solution. iqCμMD overcomes the limitations of conventional MD by adjusting the number of species in the solution to reach a target bulk concentration (chemical potential), which allows simulation of the interface under the bulk conditions comparable to experiment. We demonstrate our approach using machine learning interatomic potential (MLIP)-based MD simulations of the Na 2 SO 4,aq –graphene interface, and to show the transferability of our approach, we also perform classical force field-based MD simulations of NaCl aq –air and NaCl aq –graphite interfaces, which produce comparable results to previous CμMD simulations. Our results also show that the iqCμMD approach efficiently achieves the desired bulk ion concentration within two iterations, and by utilizing MLIPs, we can achieve converged results using relatively small-scale simulations compared to previous CμMD simulations. By combining iqCμMD with MLIP-driven simulations, solid–liquid interfaces can be modeled under an effective constant chemical potential with DFT-level accuracy. Here, we show that iqCμMD offers a robust and simple computational framework for constant chemical potential simulations, as its only requirement is to be able to converge interfacial simulations with a measurable bulk region.

Chemical structure↗
DOE OSTI2025

Characterization of kerogen nanopores using 2D NMR relaxation and MD simulations

The characterization of kerogen nanopores is crucial for predicting the geostorage capacity and recoverability of natural gas in unconventional gas shale reservoirs. Towards this end, a powerful technique is presented which integrates 2D NMR T 1 -T 2 relaxation measurements with molecular dynamics (MD) simulations of hydrocarbons confined in the nanopores of kerogen. The integrated NMR-MD technique is demonstrated using T 1 -T 2 measurements of kerogen isolates and organic-rich chalks saturated with heptane, together with MD simulations of heptane completely dissolved in a realistic kerogen model. The NMR-MD results are used to extract the swelling ratio and nanopore size distribution of kerogen as a function of depth in the reservoir. The effects of organic nanoconfinement on the T 1 relaxation dispersion and T 2 residual dipolar coupling of heptane are investigated, as well as the effect of downhole effective stress on the kerogen nanopore size as a function of depth and compaction. Potential applications in partially depleted gas shale reservoirs are discussed, including CO 2 utilization/geostorage, geostorage of green H 2 , and integration of the NMR-MD technique with thermodynamic models for predicting the competitive sorption of gas mixtures in kerogen.

Compaction↗
DOE OSTI2021

Fourier-like Thermal Relaxation of Nanoscale Explosive Hot Spots

Hot spots are local regions of high temperature that are widely considered to govern explosive initiation. Hot spot dynamics rests on a delicate balance between heat generation due to chemical reactions and heat loss through thermal conduction, making accurate determinations of the conductivity under extreme conditions a key component of predictive explosive models. We develop here an approach to directly determine the thermal transport properties of explosive hot spots with realistic initial structures through a combination of molecular dynamics (MD) and diffusive heat equation (HEq) modeling. Effective thermal conductivity values are determined by fitting HEq models to MD predictions of long timescale hot spot relaxation. The approach is applied to model hot spots in the molecular crystalline explosive 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) for a range of shock strengths and two limiting cases for impact orientation. Isotropic and anisotropic HEq models yield similar results, despite TATB exhibiting some of the largest and most anisotropic thermal conductivity values for explosive near normal conditions. The conductivity is found to be a strong function of density, which parametrically captures dependence on temperature, pressure, and material state. The associated root-mean-square errors of the fitted HEq models are approximately 5% of MD predicted final equilibrium temperatures. Here, the conductivity values determined here for TATB hot spots are considerably larger than those used in a prior hot spot criticality study, which may significantly impact predictions for critical hot spot sizes. The approach provides a convenient foundation for determining the effective thermal conductivity for hot spot problems in other explosives and directly yields information on reasonable approximations that might be taken in higher-level models for those materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Molecular Dynamics Simulations of Helium Bubble Formation in Palladium Tritides [Slides]

Pd readily absorbs hydrogen and its isotopes, and can be used to purify gas mixtures involving tritium. Tritium decays to He, forming He bubbles. Bubbles causes possible PCT effects swelling, He release, all leading to failures. Radioactive decay experiments take many years. Molecular dynamics (MD) studies can be quickly done. No previous MD methods can simulate He bubble nucleation and growth.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Molecular Dynamics Simulations of Helium Bubble Formation in Palladium Tritides [Slides]

Pd readily absorbs hydrogen and its isotopes, and can be used to purify gas mixtures involving tritium. Tritium decays to He, forming He bubbles. Bubbles causes possible PCT effects swelling, He release, all leading to failures. Radioactive decay experiments take many years. Molecular dynamics (MD) studies can be quickly done. No previous MD methods can simulate He bubble nucleation and growth.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Ionic Liquid-Enhanced Interfaces to Boost Reactive C O2 Capture

The addition of ionic liquids (ILs) to a mixture containing a molecular solvent and other ionic species can induce the heterogeneous redistribution of cations and anions at the gas–liquid interface. This nonuniform redistribution of cations and anions driven by the differences in the solvophilicity of ions can improve the thermophysical and interfacial properties of such mixtures, creating a local chemical environment that is conducive to some reactions. In this work, ILs are added to a mixture of potassium hydroxide (KOH) and ethylene glycol (EG), used as a reactive absorbent and electrolyte in the migration-assisted moisture-gradient (MAMG) process for CO 2 capture. Molecular dynamics (MD) simulations are employed to probe into the effects of complex ion–ion and ion–solvent interactions and to examine the chemical composition at the gas–liquid interface. A total of 12 systems are investigated using molecular simulations to identify trends in the performance of IL additives based on the choice of cation, anion, and IL concentration. The cation effects are studied using IL additives based on 1-ethyl-3-methylimidazolium ([EMIM] + ) and 1-butyl-3-methylimidazolium ([BMIM] + ), while the impact of anions is examined using additives based on dicyanamide [DCA] − , triflate [TfO] − , bistriflimide [NTf 2 ] − , and hexafluorophosphate [PF 6 ] − anions, respectively. The influence of the IL concentration is also evaluated at molar concentrations between 1% and 4%. The simulation results indicate that the use of IL additives can affect the physical CO 2 solubility, surface tension, and the localization of CO 2 around the [OH] − ions at the gas–liquid interface. It is also evident that the choice of cations, anions, and IL concentration determines the extent to which the IL additives impact the local physicochemical properties. Physical dissolution, diffusive transport, and interaction with [OH] − are critical intermediate steps toward reactive CO 2 capture using a liquid absorbent. Hence, the improvement in one or more of these properties, aided by IL additives, is expected to improve the overall CO 2 capture performance. Experiments reaffirmed the impact of IL additives on CO 2 capture performance and the sensitivity to the choice of the cation, anion, and concentration of the IL additive.

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

Reversible Physical Gelation of Thermotropic Liquid Crystals Driven by Nanoplate Self-Assembly

Physically gelled soft materials, driven by the self-assembly of low-molecular-mass gelators (LMGs), have emerged as a platform for designing advanced gels that exhibit reversible gelation and property tunability. Liquid crystal (LC) gels are of great interest due to their supramolecular orderings as gel hosts and their enhanced electro-optical properties. In this study, we demonstrate the physical gelation of a nematic LC driven by nanoplate self-assembly, expanding the concept of gelators from small molecules to nanoparticles. These nanoplates are functionalized with promesogenic ligands and form a fibrillar network in LCs with face-to-face interplate stacking, resembling LMGs. The critical gelation volume fraction in the tilt test is only 0.14 v %, comparable to values reported for LMGs. Rheological analyses confirm viscoelastic properties characteristic of gelation. In situ small-angle X-ray scattering (SAXS) characterizes the formation of nanoplate networks in the LC with decreasing temperature, wherein LC mesogens become trapped in pores. Molecular dynamics (MD) simulations reveal that the interaction between ligand-coated nanoplates and LC-forming mesogens induces a multidomain LC structure, increasing friction between LC domains and stabilizing the gel. This study establishes direct relationships among molecular interactions, nanostructures, and mechanical properties in physically gelled LCs. In conclusion, the findings inspire the future gelator design of both LMGs and nanoplates, with potential applicability in bioscaffold engineering and liquid crystalline nanocomposites.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
DOE OSTI2022

Modified Lucas-Washburn theory for fluid filling in nanotubes

Ultrafast water transport in carbon nanotubes (CNTs) has drawn a great deal of attention in a number of applications, such as water desalination, power generation, and biomolecule detection. With the recent experimental advances in water filling of isolated CNTs, the Lucas-Washburn theory for capillary rise in tubes needs to be revisited for a better understanding of the physics and dynamics of water filling in CNTs. Here, the Lucas-Washburn theory is corrected for the hydrodynamic entrance effects as well as the variation of capillary pressure and hydrodynamic properties with the radius and length of CNTs. Due to the large slippage in CNTs, inclusion of the entrance effects is important particularly for the initial stages of filling where a L ∝ t scaling, as opposed to L 2 ∝ t , is observed in our molecular dynamics (MD) simulations. The corrected Lucas-Washburn theory is shown to predict the water filling dynamics in CNTs as observed in MD simulations. With the corrected theory, we achieve a better understanding of capillary rise and water filling dynamics in CNTs.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Xe Recovery from Nuclear Power Plants Off-Gas Streams: Molecular Simulations of Gas Permeation through DD3R Zeolite Membrane

Recent experimental work has shown zeolite membrane-based separation as a promising potential technology for Kr/Xe gas mixtures due to its much lower energy requirements in comparison to cryogenic distillation, the conventional separation method for such mixtures. Such a separation is also economically rewarding because Xe is in high demand, as a valuable product for many applications/processes. In this work, we have used Molecular Dynamics (MD) simulations to study the effects of different conditions, i.e., temperature, pressure, and gas feed composition, on Kr/Xe separation performance via DD3R zeolite membranes. We provide a comprehensive study of the permeation of the different gas species, density profiles, and diffusion coefficients. Molecular simulations show that if the feed is changed from pure Kr/Xe to an equimolar mixture, the Kr/Xe separation factor increases, which agrees with experiments. In addition, when Ar is introduced as a sweep gas, the adsorption of both Kr and Xe increases, while the permeation of pure Kr increases. A similar behavior is observed with equimolar mixtures of Kr/Xe with Ar as the sweep gas. High-separation Kr/Xe selectivity is observed at 50 atm and 425 K but with low total permeation rates. Changing pressure and temperature are found to have profound effects on optimizing the separation selectivity and the permeation throughput.

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

Dislocation transmission across Σ3{112} incoherent twin boundary: a combined atomistic and phase-field study

Grain boundaries (GBs) in polycrystalline materials act as impediments to dislocation motion and result in strengthening. Understanding slip transmission through GBs, specifically twin boundaries, is essential to understand the plastic deformation behavior of polycrystalline fcc materials. Here the interaction between a glide dislocation and Σ3{112} incoherent twin boundary (ITB) in copper is investigated using a combined atomistic and mesoscale approach. The material parameters and structure of the GB in the mesoscale phase field dislocation dynamics (PFDD) model are informed from Molecular Statics (MS) simulations. The structural unit of the ITB consists of an array of three partial dislocations. The interaction between a glide dislocation impinging on each of the GB partial dislocations is investigated using both PFDD and Molecular Dynamics (MD) with two boundary conditions. Transmission planes predicted by both PFDD and MD (NVT) are in agreement, and show that not all transmission events are direct. Critical transmission stresses predicted by PFDD are in the range of 276 MPa to 1380 MPa, while MD predictions are in the range from 100 MPa to 700 MPa. The PFDD and MD predictions of slip transmission are explained using dislocation theory based on isotropic linear elasticity.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Synergistic Density Functional Theory and Molecular Dynamics Approach to Elucidate PNIPAM–Water Interaction Mechanisms

This study employs Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations to investigate interactions between water molecules and Poly(N-isopropylacrylamide) (PNIPAM). DFT reveals preferential water binding sites, with enhanced binding energy observed in the linker zone. Quantum Theory of Atoms in Molecules (QTAIM) and electron localization function (ELF) analyses highlight the roles of hydrogen bonding and steric hindrance. MD simulations unveil temperature-dependent hydration dynamics, with structural transitions marked by changes in the radius of gyration (Rg) and the radial distribution function (RDF), aligning with DFT findings. Our work goes beyond prior studies by combining a DFT, QTAIM and MD simulations approach across different PNIPAM monomer-to-30mer structures. It introduces a systematic quantification of pseudo-saturation thresholds and explores water clustering dynamics with structural specificity, which have not been previously reported in the literature. These novel insights establish a more complete molecular-level picture of PNIPAM hydration behavior and temperature responsiveness, emphasizing the importance of amide hydrogen and carbonyl oxygen sites in hydrogen bonding, which weakens above the lower critical solution temperature (LCST), resulting in increased hydrophobicity and paving the way for understanding water sorption mechanisms, offering guidance for future applications such as dehumidification and atmospheric water harvesting.

08 HYDROGEN↗
DOE OSTI2024

Evaluating Cryo–TEM Reconstruction Accuracy of Self–Assembled Polymer Nanostructures

Cryogenic transmission electron microscopy (cryo–TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA–reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo–TEM 3D reconstructions of self–assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. In conclusion, these findings confirm the fidelity of single particle analysis in accurately resolving complex structural characteristics and heterogeneous structures, exhibiting its potential as a valuable tool for detailed structural analysis of synthetic polymers and soft materials.

36 MATERIALS SCIENCE↗
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 OSTI2020

Quasi-equilibrium predictions of water desorption kinetics from rapidly-heated metal oxide surfaces

Controlling sub-microsecond desorption of water and other impurities from electrode surfaces at high heating rates is crucial for pulsed power applications. Despite the short time scales involved, quasi-equilibrium ideas based on transition state theory (TST) and Arrhenius temperature dependence have been widely applied to fit desorption activation free energies. Here, we apply molecular dynamics (MD) simulations in conjunction with equilibrium potential-of-mean-force (PMF) techniques to directly compute the activation free energies (ΔG*) associated with desorption of intact water molecules from Fe 2 O 3 and Cr 2 O 3 (0001) surfaces. The desorption free energy profiles are diffuse, without maxima, and have substantial dependences on temperature and surface water coverage. Incorporating the predicted ΔG* into an analytical form gives rate equations that are in reasonable agreement with non-equilibrium molecular dynamics desorption simulations. We also show that different ΔG* analytical functional forms which give similar predictions at a particular heating rate can yield desorption times that differ by up to a factor of four or more when the ramp rate is extrapolated by 8 orders of magnitude. This highlights the importance of constructing a physically-motivated ΔG* functional form to predict fast desorption kinetics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2016

Interfacial Structure and Capacitance of Li-doped Ionic Liquid Electrolytes from Molecular Simulations

Ionic liquids have been proposed as candidate electrolytes for high-energy density, rechargeable batteries, supercapacitors, and hybrid energy storage devices. Though Li-salt is often present in these systems, its influence on interfacial properties is largely uncharacterized. We, thereby, present an extensive computational analysis, supported by experimental comparisons, of the properties of a representative set of these electrolytesat an ideal carbon interface as a function of Li-salt doping and voltage. We have performed polarizable molecular (MD) dynamics simulations, using the APPLEP force field, to evaluate electric double layer (EDL) capacitance and distribution of Li+ in the EDL. Differential capacitance exhibits the characteristic camel profile and is insensitive to Li-doping. Li+ localizes in the second molecular layer of the EDL, which is a result of confinement from free energy barriers associated with ion layering. Joint MDelectronic structure computations show the electrochemical window of the electrolytes to be a weak function of Li-doping. Estimates of supercapacitor specific energy are made using the computed window and capacitance. The magnitude and trends in specific energy are in good agreement with experiment.

batteries↗
DOE OSTI2024

FPGA-Accelerated Range-Limited Molecular Dynamics

Long timescale Molecular Dynamics (MD) simulation of small molecules is crucial in drug design and basic science. To accelerate a small data set that is executed for a large number of iterations, high-efficiency is required. Recent work in this domain has demonstrated that among COTS devices only FPGA-centric clusters can scale beyond a few processors. The problem addressed here is that, as the number of on-chip processors has increased from fewer than 10 into the hundreds, previous intra-chip routing solutions are no longer viable. We find, however, that through various design innovations, high efficiency can be maintained. These include replacing the previous broadcast networks with ring-routing and then augmenting the rings with out-of-order and caching mechanisms. Others are adding a level of hierarchical filtering and memory recycling. Two novel optimized architectures emerge, together with a number of variations. These are validated, analyzed, and evaluated. We find that in the domain of interest speed-ups over GPUs are achieved. Finally, the potential impact is that this system promises to be the basis for scalable long timescale MD with commodity clusters.

97 MATHEMATICS AND COMPUTING↗