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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 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
NASA NTRS1991

Molecular dynamics and quasidynamics simulations of the annealing of bulk and near-surface interstitials formed in molecular-beam epitaxial Si due to low-energy particle bombardment during deposition

The relaxation, diffusion, and annihilation of split and hexagonal interstitials resulting from 10 eV Si irradiation of (2x1)-terminated Si(100) are investigated. Molecular dynamics and quasidynamics simulations, utilizing the Tersoff many-body potential are used in the investigation. The interstitials are created in layers two through six, and stable atomic configurations and total potential energies are derived as a function of site symmetry and layer depth. The interstitial Si atoms are allowed to diffuse, and the total potential energy changes are calculated. Lattice configurations along each path, as well as the starting configurations, are relaxed, and minimum energy diffusion paths are derived. The results show that the minimum energy paths are toward the surface and generally involved tetrahedral sites. The calculated interstitial migration activation energies are always less than 1.4 eV and are much lower in the near-surface region than in the bulk.

Kitabatake, M.↗
DOE OSTI2020

Coordinate transformation methodology for simulating quasistatic elastoplastic solids

Molecular dynamics simulations frequently employ periodic boundary conditions where the positions of the periodic images are manipulated in order to apply deformation to the material sample. For example, Lees-Edwards conditions use moving periodic images to apply simple shear. Here, we examine the problem of precisely comparing this type of simulation to continuum solid mechanics. We employ a hypo-elastoplastic mechanical model, and develop a projection method to enforce quasi-static equilibrium. We introduce a simulation framework that uses a fixed Cartesian computational grid on a reference domain, and imposes deformation via a time-dependent coordinate transformation to the physical domain. As a test case for our method, we consider the evolution of shear bands in a bulk metallic glass using the shear transformation zone theory of amorphous plasticity. We examine the growth of shear bands in simple shear and pure shear conditions as a function of the initial preparation of the bulk metallic glass.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Optimization of Thermal Conductance at Interfaces Using Machine Learning Algorithms

We report optimization of thermal transport across the interface of two different materials is critical to micro-/nanoscale electronic, photonic, and phononic devices. Although several examples of compositional intermixing at the interfaces having a positive effect on interfacial thermal conductance (ITC) have been reported, an optimum arrangement has not yet been determined because of the large number of potential atomic configurations and the significant computational cost of evaluation. On the other hand, computation-driven materials design efforts are rising in popularity and importance. Yet, the scalability and transferability of machine learning models remain as challenges in creating a complete pipeline for the simulation and analysis of large molecular systems. In this work we present a scalable Bayesian optimization framework, which leverages dynamic spawning of jobs through the Message Passing Interface (MPI) to run multiple parallel molecular dynamics simulations within a parent MPI job to optimize heat transfer at the silicon and aluminum (Si/Al) interface. We found a maximum of 50% increase in the ITC when introducing a two-layer intermixed region that consists of a higher percentage of Si. Because of the random nature of the intermixing, the magnitude of increase in the ITC varies. We observed that both homogeneity/heterogeneity of the intermixing and the intrinsic stochastic nature of molecular dynamics simulations account for the variance in ITC.

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

Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations

To gain molecular and mechanistic insights into initiation of the RAS-RAF signaling cascade, we developed and used a combination of multiscale simulation and experimental approaches. The influence and impact of the membrane on RAS and RAF proteins is a factor we are just beginning to understand and appreciate in more detail. Molecular simulation is an ideal methodology to further study this complicated relationship between the membrane and associated proteins. Our previous work using Multiscale Machine-learned Modeling Infrastructure investigated different lipid compositions solely around the KRAS4b protein and the interplay between protein behavior and these membrane environments. Multiscale Machine-learned Modeling Infrastructure uses machine learning to couple adjacent simulation scales and has been efficiently scaled across some of the world’s largest high-performance computers. Recently, we have expanded this multiresolution framework to include the all-atom simulation scale and to incorporate the RAF RBDCRD domains. Here, we present the overall analysis results from this new simulation campaign comprising a mixture of RAS and RAF RBDCRD proteins. Approximately 35,000 coarse-grained and 10,000 all-atom molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations that were generated from a micron-scale continuum simulation containing hundreds of copies of the proteins. Our studies suggest that orientations of the RAS-RBDCRD complex on the membrane occupy distinct configurational states, and the spatial patterns of lipid arrangements around these different protein states are unique to each state. The extent and size of lipid “fingerprints” imposed on the membrane by the RAS-RBDCRD protein complex are significantly larger than observed for just the RAS protein on its own. These protein complexes strongly associate, but we do not observe statistically significant preferred protein-protein orientations. These observations indicate that spatial colocalization of RAS-RBDCRD proteins in the same vicinity may be assisted by specific membrane environments, acting to increase the probability of signaling complex formation.

Carpenter, Timothy S. [Lawrence Livermore National↗
DOE OSTI2025

Evaluation of Density-Functional Tight-Binding Methods for Simulation of Protic Molecular Ion Pairs

In this work, we benchmark the accuracy of the density-functional tight-binding (DFTB) method, namely the long-range corrected second-order (LC-DFTB2) and third-order (DFTB3) models, for predicting energetics of imidazolium-based ionic liquid (IL) ion pairs. We compare the DFTB models against popular density functionals such as LC-ωPBE and B3LYP, using ab initio domain-based local pair-natural orbital coupled cluster (DLPNO-CC) energies as reference. Calculations were carried out in the gas phase, as well as in aqueous solution using implicit solvent methods. We find that the LC-DFTB2 model shows excellent performance in the gas phase and agrees well with reference energies in implicit solvent, often outperforming DFTB3 predictions for complexation energetics. Our study identifies a range of opportunities for use of the LC-DFTB method and quantifies its sensitivity to protonation states and the types of chemical interactions between ion pairs.

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

The carboxylation status of osteocalcin has important consequences for its structure and dynamics

The carboxylation status of Osteocalcin (Ocn) not only influences formation and structure in bones but also has important endocrine functions affecting energy metabolism and expenditure. In this study, the role of γ-carboxylation of the glutamate residues in the structure-dynamics-function relationship in Ocn is investigated. Three forms of Ocn, differentially carboxylated at the Glu-17, 21 and 24 residues, along with a mutated form of Ocn carrying Glu/Ala mutations, are modeled and simulated using molecular dynamics (MD) simulation in the presence of calcium ions. Characterization of the global conformational dynamics of Ocn, described in terms of the orientational variations within its 3-helical domain, highlights large structural variations in the non-carboxylated osteocalcin (nOcn). The bi-carboxylated Ocn (bOcn) and tri-carboxylated (tOcn) species, in contrast, display relatively rigid tertiary structures, with the dynamics of most regions strongly correlated. Radial distribution functions calculated for both bOcn and tOcn show long-range ordering of the calcium ion distribution around the carboxylated glutamate (γGlu) residues, likely playing an important role in promoting stability of these Ocns. Additionally, the same calcium ions are observed to coordinate with neighboring γGlu, better shielding their negative charges and in turn stabilizing these systems more than do the singly coordinating calcium ions observed in the case of nOcn. bOcn is also found to exhibit a more helical C-terminal structure, that has been shown to activate its cellular receptor GPRC6A, highlighting the allosteric role of Ocn carboxylation in modulating the stability and binding potential of the active C-terminal. Furthermore, the carboxylation status of Ocn as well and its calcium coordination appear to have a direct influence on Ocn structure and dynamics, possibly leading to the known differences in Ocn biological function.

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

Functionalization of Electrodes with Tunable [EMIM] x [Cl] x +1 – Ionic Liquid Clusters for Electrochemical Separations

Functionalization of electrodes with clusters of hydrophobic molecules may improve the energy efficiency and selectivity of electrochemical separations by modulating the desolvation process occurring at the interface. Ionic liquids (IL), which have a broad range of compositions and properties, are potential candidates for controlling the transport, desolvation, and adsorption of target ions at electrochemical interfaces. We report a joint experimental and theoretical investigation of the structure, stability, and selective adsorption properties of the IL clusters 1-ethyl-3-methylimidazolium chloride [EMIM] x [Cl] x+1 - (x = 1 – 10) and demonstrate their ability to adsorb and separate ions from solution. The structure and stability of the IL clusters are determined experimentally using high-mass-resolution electrospray ionization mass spectrometry, collision-induced dissociation, and negative ion photoelectron spectroscopy. Global optimization theory and ab initio molecular dynamics simulations provide molecular-level insight into the bonding and structural fluxionality of these species. Ion soft landing is used to selectively functionalize the surface of highly oriented pyrolytic graphite (HOPG) working electrodes with [EMIM] 1 [Cl] 2 - , [EMIM] 3 [Cl] 4 - , and [EMIM] 5 [Cl] 6 - clusters. Kelvin probe microscopy provides insight into the relative stability of the clusters on HOPG and their effect on the work function of IL-functionalized electrodes. Cyclic voltammetry measurements reveal irreversible adsorption of Fe(CN) 6 4-/3- anions during redox cycling, while electrochemical impedance spectroscopy indicates a substantial decrease in the electron transfer resistance of the IL-functionalized electrodes due to adsorption of Fe(CN) 6 4-/3- . Overall, our findings demonstrate that IL clusters with different size and stoichiometry may be used to increase the efficiency of electrochemical separations, opening new horizons in selective electrode functionalization.

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

Ion Pairing and Molecular Orientation at Liquid/Liquid Interfaces: Self-Assembly and Function

We report that molecular orientation plays a pivotal role in defining the functionality and chemistry of interfaces, yet accurate measurements probing this important feature are few, due, in part, to technical and analytical limitations in extracting information from molecular monolayers. For example, buried liquid/liquid interfaces, where a complex and poorly understood balance of inter- and intramolecular interactions impart structural constraints that facilitate the formation of supramolecular assemblies capable of new functions, are difficult to probe experimentally. Here, we use vibrational sum-frequency generation spectroscopy, numerical polarization analysis, and atomistic molecular dynamics simulations to probe molecular orientations at buried oil/aqueous interfaces decorated with amphiphilic oligomers. We show that the orientation of self-assembled oligomers changes upon the addition of salts in the aqueous phase. The evolution of these structures can be described by competitive ion effects in the aqueous phase altering the orientations of the tails extending into the oil phase. These specific anionic effects occur via interfacial ion pairing and associated changes in interfacial solvation and hydrogen-bonding networks. These findings provide more quantitative insight into orientational changes encountered during self-assembly and pave the way for the design of functional interfaces for chemical separations, neuromorphic computing applications, and related biomimetic systems.

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

Molecular latent space simulators

Latent space simulators learn kinetic models for atomistic simulations and generate novel trajectories at six orders of magnitude lower cost.

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

Failure of molecular dynamics to provide appropriate structures for quantum mechanical description of the aqueous chloride ion charge-transfer-to-solvent ultraviolet spectrum

The lowest band in the charge-transfer-to-solvent ultraviolet absorption spectrum of aqueous chloride ion is studied by experiment and computation. Interestingly, the experiments indicate that at concentrations up to at least 0.25 M, where calculations indicate ion pairing to be significant, there is no notable effect of ionic strength on the spectrum. The experimental spectra are fitted to aid comparison with computations. Classical molecular dynamic simulations are carried out on dilute aqueous Cl - , Na + , and NaCl, producing radial distribution functions in reasonable agreement with experiment and, for NaCl, clear evidence of ion pairing. Clusters are extracted from the simulations for quantum mechanical excited state calculations. Accurate ab initio coupled-cluster benchmark calculations on a small number of representative clusters are carried out and used to identify and validate an efficient protocol based on time-dependent density functional theory. The latter is used to carry out quantum mechanical calculations on thousands of clusters. The resulting computed spectrum is in excellent agreement with experiment for the peak position, with little influence from ion pairing, but is in qualitative disagreement on the width, being only about half as wide. It is concluded that simulation by classical molecular dynamics fails to provide an adequate variety of structures to explain the experimental CTTS spectrum of aqueous Cl - .

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

Cancer-associated somatic mutations in human phosphofructokinase-1 reveal a critical electrostatic interaction for allosteric regulation of enzyme activity

Metabolic reprogramming, including increased glucose uptake and lactic acid excretion, is a hallmark of cancer. The glycolytic ‘gatekeeper’ enzyme phosphofructokinase-1 (PFK1), which catalyzes the step committing glucose to breakdown, is dysregulated in cancers. While altered PFK1 activity and expression in tumors have been demonstrated, little is known about the effects of cancer-associated somatic mutations. Somatic mutations in PFK1 inform our understanding of allosteric regulation by identifying key amino acid residues involved in the regulation of enzyme activity. Here, we characterized mutations disrupting an evolutionarily conserved salt bridge between aspartic acid and arginine in human platelet (PFKP) and liver (PFKL) isoforms. Using purified recombinant proteins, we showed that disruption of the Asp–Arg pair in two PFK1 isoforms decreased enzyme activity and altered allosteric regulation. We determined the crystal structure of PFK1 to 3.6 Å resolution and used molecular dynamic simulations to understand molecular mechanisms of altered allosteric regulation. We showed that PFKP-D564N had a decreased total system energy and changes in the electrostatic surface potential of the effector site. Cells expressing PFKP-D564N demonstrated a decreased rate of glycolysis, while their ability to induce glycolytic flux under conditions of low cellular energy was enhanced compared with cells expressing wild-type PFKP. Taken together, these results suggest that mutations in Arg–Asp pair at the interface of the catalytic-regulatory domains stabilizes the t-state and presents novel mechanistic insight for therapeutic development in cancer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Impact of composition and symmetry energy on the temperature of quasiprojectiles simulated with antisymmetrized molecular dynamics

The equation of state describes the emergent physical properties of matter. Experimental data is needed to help constrain the equation of state for nuclear matter. These constraints can help distinguish between an “asy-stiff” and an “asy-soft” equation of state, which has astrophysical implications. One path to help constrain the models is to analyze the nuclear caloric curve; some experiments have shown dependence on neutron excess, and may thus be sensitive to the asymmetry. A difference in the caloric curve based on the asymmetry of the reconstructed quasiprojectile (QP) had been observed using 70 Zn on 70 Zn at 35 MeV/nucleon taken with the NIMROD array. Antisymmetrized molecular dynamics calculations were performed for the same system and deexcited with gemini++. Both Gogny (asy-soft) and Gogny-as (asy-stiff) data sets were generated. The particles were then filtered based on detector geometric acceptance and thresholds. From the accepted particles, the excitation energy and temperature were calculated in the same way as for experimental data. Additionally, filter effects on the observed nuclear caloric curves were investigated. A tendency for the asy-stiff nuclear caloric curves to have higher temperatures than their asy-soft counterparts was observed for a number of probes. In addition, some probes may show sensitivity to the reconstructed composition of the QP, but this is inconclusive due to high statistical fluctuations and a large dependence on the exact method of event selection.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Biexcitons are bound in CsPbBr 3 perovskite nanocrystals

Here, we study the energetics of quasiparticle excitations in CsPbBr 3 perovskite nanocrystals using path integral molecular dynamics simulations. Employing detailed molecular models, we elucidate the interplay of anharmonic lattice degrees of freedom, dielectric confinement, and electronic correlation on exciton and biexciton binding energies of a range of nanocrystal sizes. We find generally good agreement with some experimental observations of binding energies and additionally explain the observed size-dependent Stokes shift. The explicit model calculations are compared with simplified approximations to rationalize the lattice contributions to binding. We find that polaron formation significantly reduces exciton binding energies, whereas these effects are negligible for biexciton interactions. While experimentally the binding energy of biexcitons is uncertain, based on our study, we conclude that biexcitons are bound in CsPbBr 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

New experimental approach to understanding the chemical reactivity of oxide surfaces

Metal oxides have been an attractive option for a range of applications, including hydrogen sensors, microelectronics, and catalysis, due to their reactivity and tunability. The properties of metal oxides can vary greatly on their precise surface structure; however, few surface science techniques can achieve atomistic-level determinations of surface structure, and fewer yet can do so for insulator surfaces. Low energy ion beam analysis offers a potential insulator-compatible solution to characterizing the surface structure of metal oxides. As a feasibility study, we apply low energy ion beam analysis to investigate the surface structure of a magnetite single crystal, Fe 3 O 4 (100). We obtain multi-angle maps using both forward-scattering low energy ion scattering (LEIS) and backscattering impact-collision ion scattering spectroscopy (ICISS). Both sets of experimental maps have intensity patterns that reflect the symmetries of the Fe 3 O 4 (100) surface structure. However, analytical interpretation of these intensity patterns to extract details of the surface structure is significantly more complex than previous LEIS and ICISS structural studies of one-component metal crystals, which had far more symmetries to exploit. To gain further insight into the surface structure, we model our experimental measurements with ion-trajectory tracing simulations using molecular dynamics. Our simulations provide a qualitative indication that our experimental measurements agree better with a subsurface cation vacancy model than a distorted bulk model.

36 MATERIALS SCIENCE↗
DOE OSTI2021

mystic : software for autonomous discovery and design under uncertainty

Throughout the diverse range of science and engineering applications, there is a growing desire to develop computational methods that can reliably predict the behavior of complex systems. Specifically, there is a strategic need for tools that can robustly forecast the behavior of complex physical systems, where data may be high-dimensional, noisy, or sparse, and models of the system may be time-dependent or include uncertainty. We use mystic to build tools that leverage statistical learning, physics-informed learning, and active learning in the efficient generation of reliably predictive surrogates for complex physical systems. mystic is a robust, proven, open-source optimization and uncertainty quantification toolkit with over a decade of use in the design and optimization of neutron instrumentation, solar-powered drones, and gasguns, and in iterative tuning of models for Raman spectroscopy and elastoplastic materials strength. Recent developments have focused on automated learning of statistically robust surrogates under uncertainty, with applications in materials in extreme environments, nanostructures, materials simulations and strength models, and the failure of shielding under particle radiation. In 2020, McKerns demonstrated active learning of optimally robust surrogates with respect to new simulated data for molecular dynamics simulations of materials mixing in warm dense matter, and is currently applying active learning to the automated steering of particle accelerator beams and the optimal design and control of quantum optical sensor instrumentation.

42 ENGINEERING↗