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At least 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
NASA NTRS1998

Computer Simulation of the far Infrared Collision Induced Absorption Spectra of Gaseous CO2

Far infrared collision induced absorption spectra of gaseous CO2 were computed using molecular dynamics simulations. The quadrupole and hexadecapole multipolar induction, through the trace, and the anisotropy of the molecular polarizability were found to be insufficient to represent properly the dipole induction mechanism. For a detailed analysis of the induction process the spectra obtained were decomposed into components resulting from different terms of the induced dipole. Based on this decomposition, all additional overlap contribution for each term was proposed. When spectra were recomputed including such overlap, good agreement between experiment and simulation was achieved over the temperature range at which measurements exist (233-400 K). The use of an anisotropic intermolecular potential was found to be of critical importance for obtaining the right shape of the far wings of the spectra.

Gruszka, Marcin↗
DOE OSTI2021

Phase evolution in two-phase alloys during severe plastic deformation

Herein, phase evolution in FCC metals with strongly interacting alloy components during severe plastic deformation is investigated using molecular dynamics simulations. Specifically, we study the alloy microstructure in steady state, nucleation and growth of precipitates in supersaturated alloys, and the decomposition of precipitates in undersaturated alloys. The results are compared to a modified effective temperature model, providing a physical understanding for the atomic processes underlying the model and a perspective on its strengths and weaknesses. Key observations in this work are nucleation and growth of precipitates during SPD at a temperature of 100 K; Gibbs-Thomson-like behavior relating solubility to precipitate size under steady-state shearing; a direct relationship between the effective temperature and the shear modulus; and the importance of cluster agglomeration during precipitate growth. The study also reveals that the mechanisms of forced chemical mixing depends on precipitate size, adding complications for effective temperature models describing inhomogeneous systems. The simulations are shown to provide good semiquantitative agreement with experimental findings reported in the literature.

36 MATERIALS SCIENCE↗
DOE OSTI2024

eReaxFF force field development for BaZr 0.8 Y 0.2 O 3-δ solid oxide electrolysis cells applications

The use of solid-oxide materials in electrocatalysis applications, especially in hydrogen-evolution reactions, is promising. However, further improvements are warranted to overcome the fundamental bottlenecks to enhancing the performance of solid-oxide electrolysis cells (SOECs), which is directly linked to the more-refined fundamental understanding of complex physical and chemical phenomena and mass exchanges that take place at the surfaces and in the bulk of electrocatalysis materials. Here, we developed an eReaxFF force field for barium zirconate doped with 20 mol% of yttrium, BaZr 0.8 Y 0.2 O 3-δ (BZY20) to enable a systematic, large-length-scale, and longer-timescale atomistic simulation of solid-oxide electrocatalysis for hydrogen generation. All parameters for the eReaxFF were optimized to reproduce quantum-mechanical (QM) calculations on relevant condensed phase and cluster systems describing oxygen vacancies, vacancy migrations, electron localization, water adsorption, water splitting, and hydrogen generation on the surfaces of the BZY20 solid oxide. Using the developed force field, we performed both zero-voltage (excess electrons absent) and non-zero-voltage (excess electrons present) molecular dynamics simulations to observe water adsorption, water splitting, proton migration, oxygen-vacancy migrations, and eventual hydrogen-production reactions. Based on investigations offered in the present study, we conclude that the eReaxFF force field-based approach can enable computationally efficient simulations for electron conductivity, electron leakage, and other non-zero-voltage effects on the solid oxide materials using the explicit-electron concept. Moreover, we demonstrate how the eReaxFF force field-based atomistic-simulation approach can enhance our understanding of processes in SOEC applications and potentially other renewable-energy applications.

08 HYDROGEN↗
DOE OSTI2021

Effect of sink strength on coherency loss of precipitates in dilute Cu-base alloys during in situ ion irradiation

In situ irradiations with 1 MeV Kr ions at 50~613 K up to a fluence of 6.25 × 10 14 ions/cm 2 (~1.25 displacements per atom, dpa) have been performed on pre-aged dilute Cu-0.9%Co, Cu-0.9%Fe and Cu-0.8%Cr alloys containing uniform matrix dispersions of coherent precipitates in order to study the effects of initial precipitate sink strength, damage dose and irradiation temperature on radiation-induced coherency loss of precipitates. Coherent precipitates with different point defect sink strengths (2πNd, where N and d are the precipitate density and diameter) were used in this work to examine potential differences in atomic relaxation during absorption of point defects. In all cases, irradiation to low doses (<~1 dpa) was very effective at inducing loss of precipitate coherency. At low sink strengths (~10 13 m -2 ), loss of precipitate coherency could be induced for doses ~0.01 dpa. This suggests there might be an efficient preferential medium-range strain-induced bias for absorption of interstitial defects due to tensile strains emanating from the undersized precipitates, which induces relatively rapid loss of coherency at low precipitate sink strengths. High precipitate sink strength (~10 14 m -2 ) conditions were relatively resistant to the radiation-induced loss of coherency (requiring higher doses approaching ~1 dpa) and this might be due to nearly equal numbers of interstitial and vacancy defects arriving at the precipitate interface for such high sink strength conditions. The precipitate coherency loss was observed to have a weak dependence on irradiation temperature. Molecular dynamics simulations confirm a strong effect of precipitate sink strength on the probability of interstitial absorption at precipitates.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Building and Breaking Carbon Composites with REACTER

Carbon composites have become indispensable for aerospace and other high-performance applications, and a detailed picture of their morphology and failure mechanisms remains difficult to obtain through experiment. REACTER is a versatile computational modeling tool for atomistic molecular dynamics designed to model chemical reactions at the speed and length scales of classical force fields.1 In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites, carbon-fiber reinforced polymers (CFRP) and carbon nanotube (CNT) composites. Carbon fiber core morphologies were created by the method of Desai et al.,2 but using the advanced reaction constraints framework of REACTER, their proposed multistep procedure was reduced to a single uninterrupted molecular dynamics simulation. The carbon fiber filler was embedded into a polymer matrix by simulated in situ polymerization of several thermosetting resins, including bismaleimide and polyarylacetylene, to obtain the final CFRP model. To generate the second class of carbon composite, CNT networks were grown dynamically using the new ‘create atoms’ feature of REACTER, and similarly infiltrated with resin to obtain CNT composites. The resulting models were compared directly to experiment using simulated high resolution transmission electron microscopy and x-ray diffraction. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a reaction constraint on the total potential energy of the involved atoms.

Molecular Dynamics↗
DOE OSTI2023

Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N -1-Phenylethyl Sidechains

N-substituted glycines (polypeptoids) containing chiral hydrophobic sidechains are known to fold into biomimetic alpha helices. These helix formers often produce conformationally heterogeneous structures and are difficult to characterize at a sub-nanometer resolution. Previously, peptoid N-1-phenylethyl (S)-enantiomer sidechains (Nspe) were inferred from various experiments to form right-handed helices and (R)-enantiomers (Nrpe), left-handed helices. Prior computational work for N(s/r)pe oligomers has struggled to reproduce this trend. Herein, quantum mechanics calculations and molecular dynamics simulations are used to understand the origins of this discrepancy. Results from DFT and molecular mechanics calculations on a variety of Nspe and Nrpe oligomers as a function of chain length are in agreement, showing that Nspe and Nrpe prefer left- and right-handed helices, respectively. Additional metadynamics simulations are used to study Nrpe and Nspe oligomers folding in water. These results show that the free-energy driving forces for assembly into a helical backbone configuration are very small (within ~k B T). Lastly, we compare DFT calculations for other experimentally characterized peptoid sidechains, N(r/s)sb, N(r/s)tbe, and N(r/s)npe. In this analysis, we show that peptoid sidechains determined to be more robust experimentally (tbe and npe) have helical preferences opposite the trend seen in less robust assemblies formed by N(r/s)pe and N(r/s)sb chemistries. Furthermore, the more robust tbe and nnpe favor the (S)-enantiomer to right-handed and the (R)-enantiomers to left-handed helices.

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

Direct Monte Carlo Simulations of Chemical Equilibrium Composition of Molecular Fluid Mixtures Under Shock Conditions

A new Monte Carlo simulation method is implemented which holds the number and kind of atoms constant rather than the number and kind of molecules for a molecular fluid mixture. Chemical reactions are allowed as a correlated move of atoms such as an interchange of atoms between molecules. Equilibrium chemical composition is determined as an average over the simulation along with equation of state quantities. Results are presented for N 2 + O 2 → 2NO at 30GPa and 3000K. The equilibrium composition is shown to be sensitive to the potentials between unlike species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1996

Mechanism of unassisted ion transport across membrane bilayers

To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.

NASA Discipline Exobiology↗
DOE OSTI2023

Composition-dependent fracture energy in metallic glasses

The interplay between metallic glasses (MGs) mechanical properties, fracture energy (G), and glass-forming ability (GFA) and their dependence on alloy composition remain poorly understood. Here, we perform molecular dynamics simulations to investigate the intrinsic composition-dependence of G in Cu x Zr 100-x MGs (x = 20, 30, 40, 50, 64). The results indicate that the value of G increases with Cu content. In addition, it is revealed that MGs with higher G values display higher Poisson’s ratio (ν) and GFA, suggesting a close correlation between fracture toughness, mechanical properties, and GFA. This correlation between G, ν and GFA can be understood based on the fragility (m) of supercooled liquids, which is directly related to the structural heterogeneity in MGs. Larger m values are related to dynamic slowdown and supercooled liquid stabilization, which enhance GFA and the formation of pronounced structural heterogeneity, comprised of loosely packed regions that favor β-relaxation and the activation of shear transformation zones. Those concurrently promote the expansion of the plastic zone at the crack tip, enhancing the observed value of G. Furthermore, these simulation results shed light on the intrinsic relationship between fracture toughness, mechanical properties, and alloy composition in MGs.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Three-Dimensional Mass Spectrometric Imaging of Biological Structures Using a Vacuum-Compatible Microfluidic Device

Three-dimensional (3D) molecular imaging of biological structures is important for a wide range of research. In recent decades, secondary ion mass spectrometry (SIMS) has been recognized as a powerful technique for both two-dimensional (2D) and 3D molecular imaging. Sample fixations (e. g., chemical fixation and cryogenic fixation methods) are necessary to adapt biological samples to the vacuum condition in the SIMS chamber, which has been demonstrated to be non-trivial and less controllable, thus limiting the wider application of SIMS on 3D molecular analysis of biological samples. Our group recently developed in situ liquid SIMS that offers great opportunities for the molecular study of various liquids and liquid interfaces. In this work, we demonstrate that a further development of the vacuum-compatible microfluidic device used in in situ liquid SIMS provides a convenient freeze-fixation of biological samples and leads to more controllable and convenient 3D molecular imaging. The special design of this new vacuum-compatible liquid chamber allows an easy determination of sputter rates of ice, which is critical for calibrating the depth scale of frozen biological samples. Sputter yield of a 20 keV Ar 1800 + ion on ice has been determined as 1500 (± 8%) water molecules per Ar 1800 + ion, consistent with our results from molecular dynamics simulations. Moreover, using the information of ice sputter yield, we successfully conduct 3D molecular imaging of frozen homogenized milk and observe network structures of interesting organic and inorganic species. Finally, taken together, our results will significantly benefit various research fields relying on 3D molecular imaging of biological structures.

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

Self-Assembled Oligomers Facilitate Amino Acid-Driven CO 2 Capture at the Air–Aqueous Interface

Direct air capture of CO 2 using amino acid absorbents, such as glycine or sarcosine, is constrained by the relatively slow mass transfer of CO 2 through the air–aqueous interface. Our recent study showed a marked improvement in CO 2 capture by introducing CO 2 -permeable oligo-dimethylsiloxane (ODMS-MIM + ) oligomers with cationic (imidazolium, MIM + ) headgroups. Here, in this work, we have employed all-atom molecular dynamics simulations in combination with subensemble analysis using network theory to provide a detailed molecular picture of the behavior of CO 2 and the glycinate anions (Gly – ) at the ODMS-MIM + decorated air–aqueous interfaces. We show that the cationic head groups of the surfactants enhance the concentration and lifetime of Gly – in the interfacial region, while ODMS tails promote the physisorption of CO 2 in the interfacial region. Together, these two factors increase the effective region of contact and the probability of interactions between CO 2 and Gly – compared to that of the pure air–aqueous interface. The fundamental insights gained in this work establish essential foundations for developing hybrid systems with oligomer-decorated interfaces to maximize the overall CO 2 capture rates.

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

Probing Molecular Assembly of Small Organic Molecules during Meniscus-Guided Coating Using Experimental and Molecular Dynamics Approaches

Evaporation-based thin-film coating processes are ubiquitous in fields such as organic electronics, dye coatings, and the pharmaceutical industry. Based on experimental observations of enhanced thin-film alignment during meniscus-guided coating (MGC), a molecular dynamics simulation was developed to describe the thin-film formation that occurs due to the interplay between evaporation and fluid dynamics. The process of solvent evaporation from solution is first examined, which leads to the formation of a solid thin film after evaporation is complete. Next, an MGC process was simulated by introducing a flow profile coupled with the evaporative system. In this work, we gain insights into how molecules respond and reorient in the presence of a flow profile. These results indicate that both the evaporation and the flow profile have an impact on orienting small molecules in a thin film during the MCG process. Combining experimental techniques with simulations helps enhance the understanding of the forces that are significant in directing molecular aggregation during coating processes.

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

The Work of Mechanical Degradation in Elongating Polymer Melts

Molecular dynamics simulations are used to study the mechanical degradation of well-entangled polymer melts during uniaxial extensional flow. Simulations measure the transient rise in extensional stresses and relate them to the molecular alignment and scission of chain backbones. Intermolecular entanglements couple chain scission in space and time, making degradation sensitive to deformation history and strain rate in ways not displayed by dilute polymer solutions. The rate of chain scission is nonmonotonic and peaks at strains corresponding to the maximum extensibility of entanglement segments but prior to the full extension of chain backbones. We measure a specific work per scission event w* and decompose it into separate contributions associated with chain alignment, chemical bond breaking, and scission-induced plasticity. We find chain scission in melts requires activating plastic dissipation that is multiple orders of magnitude larger than the chemical work required to break a covalent backbone bond. Our findings underscore the critical need to consider bulk polymer mechanics and rheology in designing efficient mechanical degradation and mechanochemical processes.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The Energetic Origins of Pi–Pi Contacts in Proteins

Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein’s stability and structure. Pi–pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi–pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi–pi contact motifs. We find that neutral pi–pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter–Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi–pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi–pi contacts in polar media and like typical ion–pi interactions in nonpolar environments. Like-charged pairs such as arginine–arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi–pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.

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

Nanoscale simulation of the thylakoid membrane response to extreme temperatures

Abstract The thylakoid membrane is in a temperature‐sensitive equilibrium that shifts repeatedly during the life cycle in response to ambient temperature or solar irradiance. Plants respond to seasonal temperature variation by changing their thylakoid lipid composition, while a more rapid mechanism for short‐term heat exposure is required. The emission of the small organic molecule isoprene has been postulated as one such possible rapid mechanism. The protective mechanism of isoprene is unknown, but some plants emit isoprene at high temperature. We investigate the dynamics and structure for lipids within a thylakoid membrane across temperatures and varied isoprene content using classical molecular dynamics simulations. The results are compared with experimental findings for temperature‐dependent changes in the lipid composition and shape of thylakoids. The surface area, volume, and flexibility of the membrane, as well as the lipid diffusion, increase with temperature, while the membrane thickness decreases. Saturated thylakoid 34:3 glycolipids derived from eukaryotic synthesis pathways exhibit altered dynamics relative to lipids from prokaryotic synthesis paths, which could explain the upregulation of specific lipid synthesis pathways at different temperatures. Increasing isoprene concentration was not observed to have a significant thermoprotective effect on the thylakoid membranes, and that isoprene readily permeated the membrane models tested.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

High Energy Density Physics of Inertial Confinement Fusion Ablator Materials

The historic December 5, 2022 experiment at Lawrence Livermore National Lab’s (LLNL) National Ignition Facility (NIF) reached fusion energy ignition for the first time. This is the most important scientific breakthrough of the 21st century paves the way to future clean inertial fusion energy (IFE). The diamond (high density carbon (HDC)) ablator material used in this experiment displays detrimental effects due to the development of hydrodynamic instabilities at the diamond/fuel interface under shock compression. New alternatives to diamond ablators are required to step up the energy yield in ICF experiments. The unique combination of mechanical strength (approaching that of diamond), the ability to accommodate high-Z dopants (in contrast to diamond), and the tunability of the properties (through synthesis material with varying sp 3 content) make amorphous carbon (a-C) a promising material for next-generation IFE ablative capsules. However, despite its critical importance to the IFE program, the behavior of a-C carbon at extreme temperatures and pressures remains largely unexplored. The primary goals of this project were to perform groundbreaking dynamic compression experiments and predictive simulations to uncover the fundamental high-energy-density physics of amorphous carbon. Our goals were (1) to uncover the metastability range of amorphous carbon and probe phase transitions to diamond or metastable supercooled liquid carbon; (2) to acquire high-quality equation of state (EOS) data and develop an experimentally validated EOS from machine-learning MD simulations of the complex states of carbon; and (3) to uncover the complex behavior of carbon liquid in both thermodynamically stable and metastable supercooled states by accessing large areas of carbon phase diagram with amorphous samples with variable sp 3 content. Our proposed experimental program included measurements of equation of state and diffraction measurements using the Omega EP laser at the Laboratory of Laser Energetics at the University of Rochester. The theoretical/simulation program involved the development of machine-learning models of the complex response of amorphous carbon under dynamic compression by performing molecular dynamics simulations at experimental time and length scales using leadership class DOE supercomputers. Simulations guided experiments to observe predicted phenomena and acquire critical experimental data in specific pressure-temperature domains to validate theoretical models. This research delivered fundamental properties of novel amorphous carbon IFE ablator material, including phase diagram and EOS. These results will aid in IFE target design and implosion experiments. A unique combination of predictive simulations and dynamic and static experiments provided a highly inspirational intellectual environment for graduate students and postdocs involved in this project.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRSDate not supplied

Modeling Ring-Opening Polymerization with Machine-Learned Committors

Many important industrial and biological processes depend on ring-opening polymerization (ROP), including large-scale production polymers, such as nylon 6, and a variety of biodegradable polymers and high-performance resins. Large-scale simulations (>200K atoms) of ROP were performed using a deep neural network-based method that captured the effect of the local chemical environment of the reactive sites using training data from quantum chemical methods. The utility of this method was demonstrated by modeling the cationic ROP of bis-benzoxazine, a promising resin for use in advanced high-temperature application composites (>200°C). Density functional theory calculations were used to map out the various ring opening and polymerization reaction paths that occur during the thermal processing of bis-benzoxazine. The probabilities of these reactions, as a function of local atomic configurations, were used to construct committor functions using a neural network approach. The learned committor functions were then used to determine when a particular reaction occurred within the REACTER framework for reactive molecular dynamics simulations. The experimentally observed exotherm that occurs during bis-benzoxazine ROP was captured in an effective manner in the simulations by imposing a local heating of the system that corresponds to the enthalpy of reaction for each reaction. The dependence of the final polymer morphology on the ROP reaction temperature was analyzed at the molecular scale. The results presented in this work indicate that machine-learned committor functions are a promising approach for incorporating high-fidelity reactivity criteria that capture the effect of local chemical environments into large-scale polymerization simulations.

machine learning, polymer simulations, molecular d↗
DOE OSTI2021

SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories)

Protein-only trajectories of the lowest-temperature window (310K) extracted from temperature replica-exchange molecular dynamics simulations of 23 different SARS CoV-2 systems, including S Protein ACE2-receptor binding-domain, MPro, PLPro, NSP3 ADRP (X-domain/macrodomain/phosphatase), NSP15 (endoribonuclease), NSP9, NSP10, NSP16, and N-protein N-terminus. Systems were prepared with charmm-gui and simulated using the GROMACS simulation software suite. Trajectories are provided in compressed dcd format with accompanying coordinate/topology files in pdb and psf formats. This data supplements the data release, DOI: 10.13139/OLCF/1650650 ('SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)')

59 BASIC BIOLOGICAL SCIENCES↗