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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 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Multi-reward Reinforcement Learning Based Bond-Order Potential to Study Strain-Assisted Phase Transitions in Phosphorene

Here, we introduce a multi-reward reinforcement learning (RL) approach to train a flexible bond-order potential (BOP) for 2D phosphorene based on ab initio training data sets. Our approach is based on a continuous action space Monte Carlo tree search algorithm that is general and scalable and presents an efficient multiobjective optimization scheme for high-dimensional materials design problems. As a proof-of-concept, we deploy this scheme to parametrize multiple structural and dynamical properties of 2D phosphorene polymorphs. Our RL-trained BOP model adequately captures the structure, energetics, transformation barriers, equation of state, elastic constants, and phonon dispersions of various 2D P polymorphs. We use this model to probe the impact of temperature and strain rate on the phase transition from black (α-P) to blue phosphorene (β-P) through molecular dynamics simulations. A decrease in critical strain for this phase transition with increase in temperature is observed, and the underlying atomistic mechanisms are discussed.

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

Interfacial Response and Structural Adaptation of Structured Polyelectrolyte Thin Films

Ionizable block copolymers with distinctive block characteristics display the diversity crucial for the design of macromolecules for targeted applications. In contrast to van der Waals copolymers, their interfaces, which are critical to their function, consist of nanodomains, each of a different nature and thus unique interfacial behavior. Here, the interfacial response of a symmetric block copolymer with a sulfonated polystyrene polyelectrolyte center, tethered to polyethylene-r-propylene and terminated by poly(t-butyl styrene) is probed as polymer films are exposed to three polar solvents, water, propanol, and tetrahydrofuran (THF), using molecular dynamics simulations. Each of the solvents captures a distinctive interaction with the individual blocks. We find that at the film boundary, the interfacial response is initially dominated by that of the hydrophobic blocks to all solvents. At later times, the solvent distribution among the blocks, where water molecules associate predominantly with the sulfonated groups and propanol and THF reside at multiple different sites, determines the chemical composition and the polymer conformation at the interface. Altogether, these simulations provide the first direct molecular insight into the interfacial response of ionizable copolymers.

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

Reconstruction of effective potential from statistical analysis of dynamic trajectories

The broad incorporation of microscopic methods is yielding a wealth of information on the atomic and mesoscale dynamics of individual atoms, molecules, and particles on surfaces and in open volumes. Analysis of such data necessitates statistical frameworks to convert observed dynamic behaviors to effective properties of materials. Here, we develop a method for the stochastic reconstruction of effective local potentials solely from observed structural data collected from molecular dynamics simulations (i.e., data analogous to those obtained via atomically resolved microscopies). Using the silicon vacancy defect in graphene as a model, we apply the statistical framework presented herein to reconstruct the free energy landscape from the calculated atomic displacements. Evidence of consistency between the reconstructed local potential and the trajectory data from which it was produced is presented, along with a quantitative assessment of the uncertainty in the inferred parameters.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Manipulating Organic Semiconductor Morphology with Visible Light

A method is presented to manipulate the final morphology of roll-to-roll slot-die coated poly(3-hexylthiophene) (P3HT) by optically exciting the p-type polymer in solution while coating. These results provide a comprehensive picture of the entire knowledge chain, from demonstrating how to apply the authors’ method to a fundamental understanding of the changes in morphology and physical properties induced by exciting P3HT while coating. By combining results from density functional theory and molecular dynamics simulations with a variety of X-ray experiments, absorption spectroscopy, and THz spectroscopy, the relationship between morphology and physical properties of the thin film is demonstrated. Specifically, in P3HT films excited with light during deposition, changes in crystallinity and texture with more face-on orientation and increased out-of-plane charge mobility are observed.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Graph-EAM: An Interpretable and Efficient Graph Neural Network Potential Framework

The development of deep learning interatomic potentials has enabled efficient and accurate computations in quantum chemistry and materials science, circumventing computationally expensive ab initio calculations. However, the huge number of learnable parameters in deep learning models and their complex architectures hinder physical interpretability and affect the robustness of the derived potential. In this work, we propose graph-EAM, a lightweight graph neural network (GNN) inspired by the empirical embedded atom method to model the interatomic potential of single-element structures. Four material systems: platinum, niobium, silicon, and amorphous-carbon, for which quantum simulation data sets are publicly available, are examined to demonstrate that graph-EAM can achieve high energy and force prediction accuracy-comparable or better than existing state-of-the-art machine learning models-with much fewer parameters. It is also shown that the explicit inclusion of the angular information via three-body atomic density increases the prediction accuracy. In conclusion, the accuracy and efficiency of potentials obtained from graph-EAM can help accelerate the molecular dynamics simulation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2024

Multiscale Modeling of Thermoplastics Using Atomistic-informed Micromechanics

A multiscale repeating unit cell model of a single spherulite containing four disparate length scales was developed to predict the thermoelastic behavior of semicrystalline thermoplastic materials for composite aerospace applications. The continuum level scales were fully coupled and modeled using the generalized method of cells and the high fidelity generalized method of cells micromechanics theories. Data from molecular dynamics simulations were used as inputs for the amorphous and crystalline constituents in the multiscale continuum models. Effective Young’s modulus, shear modulus, Poisson’s ratio, coefficient of thermal expansion, and thermal conductivity were predicted for polyether ether ketone and polyether ketone ketone, showing good agreement with the available experimental data from the open literature. Moreover, it is shown that predicted properties are fairly insensitive to the fidelity of the micromechanics model used at the highest continuum scale or the assumed shape of the spherulite.

thermoplastics↗
DOE OSTI2020

Entropy production in model colloidal suspensions under shear via the fluctuation theorem

Dissipative systems often exhibit novel and unexpected properties. This is, for instance, the case of simple liquids, which, when subjected to shear and after reaching a steady state, can exhibit a negative entropy production over finite length scales and timescales. This result, among others, is captured by nonequilibrium relations known as fluctuation theorems. Using nonequilibrium molecular dynamics simulations, we examine how, by fine-tuning the properties of the components of a complex fluid, we can steer the nonequilibrium response of the fluid. More specifically, we show how we control the nonequilibrium probability distribution for the shear stress and, in turn, how often states with a negative entropy production can occur. To achieve this, we start by characterizing how the size for the liquid matrix impacts the probability of observing negative entropy states, as well as the timescale over which these can be observed. We then measure how the addition of larger particles to this liquid matrix, i.e., simulating a model colloidal suspension, results in an increase in the occurrence of such states. As a result, this suggests how modifications in the composition of the mixture and in the properties of its components lead to an increase in the probability of observing states of negative entropy production and, thus, for the system to run in reverse.

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

Switching of Hybrid Improper Ferroelectricity in Oxide Double Perovskites

In ABO 3 -type perovskite oxides with Pnma symmetry, rotation (Q R+ , a 0 a 0 c + ) and tilt (Q T , a – a – c 0 ) of BO 6 octahedra are the two primary order parameters. These order parameters establish an inherent trilinear coupling with anti-ferroelectric A-site displacement (Q AFE ) to form the low-symmetry phase. The symmetry is further lowered in double perovskite oxides (DPOs) due to A/A' cation ordering. It in turn makes these systems polar via hybrid improper ferroelectric mechanism, primarily driven by Q R+ and Q T . Naturally, it has been believed that functionalities such as polarization can also be switched by tuning these primary order parameters. However, mystery around finding switching mechanism still remains. Our study based on density functional theory calculations combined with finite-temperature molecular dynamics simulations shows that the polarization switching is a two-step process, driven by out-of-phase rotation (Q R– , a 0 a 0 c – when Q T = 0 or, a – a – b – when Q T ≠ 0). A series of polar DPOs such as KLnFeOsO 6 [Ln = Sm, Gd, Dy, Tm (lanthanides) and Y (rare earth)], all belonging to P2 1 symmetry, are considered in this investigation. The polarization switching P ($\overrightarrow{P}$) occurs at a very high temperature of ~1150 K through a phase transition, from a polar (P2 1 ) phase with $\overrightarrow{P}$(+) to $\overrightarrow{P}$(-) via a non-polar P4/n phase. The switching itself is metastable in nature. The switching (both polarization and spin state) is only observed for a very short period of time (~23 ps) that poses limitation on using such a mechanism in memory device realization. We demonstrate a concurrent heating–cooling procedure to overcome such shortcoming. In conclusion, simulations conducted at 600 K further imply that long lasting switching can be achieved, at least for 1.2 ns for 600 K, and ideally for an infinite time, if the material is heated just above the T c followed by rapid cooling to a temperature below T c .

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

Roles for Countercharge in the Voltage Sensor Domain of Ion Channels

Voltage-gated ion channels share a common structure typified by peripheral, voltage sensor domains. Their S4 segments respond to alteration in membrane potential with translocation coupled to ion permeation through a central pore domain. The mechanisms of gating in these channels have been intensely studied using pioneering methods such as measurement of charge displacement across a membrane, sequencing of genes coding for voltage-gated ion channels, and the development of all-atom molecular dynamics simulations using structural information from prokaryotic and eukaryotic channel proteins. One aspect of this work has been the description of the role of conserved negative countercharges in S1, S2, and S3 transmembrane segments to promote sequential salt-bridge formation with positively charged residues in S4 segments. These interactions facilitate S4 translocation through the lipid bilayer. In this review, we describe functional and computational work investigating the role of these countercharges in S4 translocation, voltage sensor domain hydration, and in diseases resulting from countercharge mutations.

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

Influence of acid leaching surface treatment on indentation cracking of soda lime silicate glass

Past work has shown that water or acid soaking treatments can increase the mechanical strength of soda lime silicate (SLS) glasses. In this work, we show that acid leaching treatments result in an increase in the apparent crack resistance of the acid-leached surface of SLS glass during indentation. Vickers indentation tests in controlled environments show a humidity dependence of radial cracking, suggesting that the transport of water through the leached layer plays a critical role in the propagation of cracks to the glass surface. Here, molecular dynamics simulations with reactive force fields indicate that the leached surface layer can undergo pressure-induced mechanochemical reactions during indentation, which increases the bridging oxygen connectivity in the silica network of the leached layer. Such structural changes can hinder transport of water molecules from the environment to the subsurface crack tip. Based on experimental observations and simulation results, a new hypothesis is proposed that mechanochemical restructuring in the leached layer in response to the applied load may lower the transport kinetics of molecular water to critical flaws, resulting in an apparent enhancement in the crack resistance of the acid-leached surface of SLS glass.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Isolating Chemical Reaction Mechanism as a Variable with Reactive Coarse-Grained Molecular Dynamics: Step-Growth versus Chain-Growth Polymerization

Here we present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often group multiple atoms into a single “coarse-grained” interaction site, which leads to a loss of chemical resolution. In this work we convert this shortcoming into a feature and use identical coarse-grained models to represent molecules that share nonreactive characteristics but react by different mechanisms. As a proof of concept, we use this approach to simulate and investigate distinct, yet similar, trifunctional isocyanurate resin formulations that polymerize by either chain- or step-growth. Because the underlying molecular mechanics of these models are identical, all emergent differences are a function of the reaction mechanism only. We find that the microscopic morphologies resemble related all-atom simulations and that simulated mechanical testing reasonably agrees with experiment.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Stereoselective recognition of morphine enantiomers by μ -opioid receptor

Stereospecific recognition of chiral molecules plays a crucial role in biological systems. The μ-opioid receptor (MOR) exhibits binding affinity towards (-)-morphine, a well-established gold standard in pain management, while it shows minimal binding affinity for the (+)-morphine enantiomer, resulting in a lack of analgesic activity. Understanding how MOR stereoselectively recognizes morphine enantiomers has remained a puzzle in neuroscience and pharmacology for over half-a-century due to the lack of direct observation techniques. To unravel this mystery, we constructed the binding and unbinding processes of morphine enantiomers with MOR via molecular dynamics simulations to investigate the thermodynamics and kinetics governing MOR's stereoselective recognition of morphine enantiomers. Our findings reveal that the binding of (-)-morphine stabilizes MOR in its activated state, exhibiting a deep energy well and a prolonged residence time. In contrast, (+)-morphine fails to sustain the activation state of MOR. Furthermore, the results suggest that specific residues, namely D114 2.50 and D147 3.32 , are deprotonated in the active state of MOR bound to (-)-morphine. This work highlights that the selectivity in molecular recognition goes beyond binding affinities, extending into the realm of residence time.

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

Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non‐productive binding: insights from crystal structures and MD simulation

Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) ( EC3.2.1.176 ) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p‐ nitrophenyl‐β‐ d ‐cellobioside (pNPC), p‐ nitrophenyl‐β‐ d ‐lactoside (pNPL) and methylumbelliferyl‐β‐ d ‐cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o‐nitrophenyl‐β‐ d ‐cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium . Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non‐productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non‐productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates ( k cat ) than TrCel7A, but higher Michaelis–Menten ( K M ) constants as well. Furthermore, oNPC turned out to be useful as an active‐site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Crystal Structure and Preparation of Li7La3Zr2O12 (LLZO) Solid-State Electrolyte and Doping Impacts on the Conductivity: An Overview

As an essential part of solid-state lithium-ion batteries, solid electrolytes are receiving increasing interest. Among all solid electrolytes, garnet-type Li7La3Zr2O12 (LLZO) has proven to be one of the most promising electrolytes because of its high ionic conductivity at room temperature, low activation energy, good chemical and electrochemical stability, and wide potential window. Since the first report of LLZO, extensive research has been done in both experimental investigations and theoretical simulations aiming to improve its performance and make LLZO a feasible solid electrolyte. These include developing different methods for the synthesis of LLZO, using different crucibles and different sintering temperatures to stabilize the crystal structure, and adopting different methods of cation doping to achieve more stable LLZO with a higher ionic conductivity and lower activation energy. It also includes intensive efforts made to reveal the mechanism of Li ion movement and understand its determination of the ionic conductivity of the material through molecular dynamic simulations. Nonetheless, more insightful study is expected in order to obtain LLZO with a higher ionic conductivity at room temperature and further improve chemical and electrochemical stability, while optimal multiple doping is thought to be a feasible and promising route. This review summarizes recent progress in the investigations of crystal structure and preparation of LLZO, and the impacts of doping on the lithium ionic conductivity of LLZO.

Raju, Md Mozammal (ORCID:0000000319040523)↗
DOE OSTI2021

Nuclear quantum effects on the quasiparticle properties of the chloride anion aqueous solution within the GW approximation

Photoelectron spectroscopy experiments in ionic solutions reveal important electronic structure information, in which the interaction between hydrated ions and water solvent can be inferred. Based on many-body perturbation theory with GW approximation, we theoretically compute the quasiparticle electronic structure of chloride anion solution, which is modeled by path-integral abinitio molecular dynamics simulation by taking account the nuclear quantum effects (NQEs). The electronic levels of hydrated anion as well as water are determined and compared with the recent experimental photoelectron spectra. It is found that NQEs improve the agreement between theoretical prediction and experiment because NQEs effectively weaken the hybridization of the between the Cl – anion and water. Furthermore, our study indicates that NQEs plays a small but non-negligible role in predicting the electronic structure of the aqueous solvation of ions of the Hofmeister series.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Breaking up CO 2 through pressure-induced redox reaction with rhenium

We present results from density-functional-theory (DFT) based molecular dynamics simulations of fluid mixtures of carbon dioxide (CO 2 ) and rhenium (Re) metal at pressures up to 45 GPa and a temperature of 4000 K. Covalently-bonded carbon chains form as a result of a redox reaction between CO 2 and Re, whereas a pure CO 2 fluid is stable against decomposition at the same conditions. Furthermore, these findings have implications in reducing CO 2 by pressure-induced redox reactions with transition metals, which may play a role in CO 2 destruction and carbon storage as related to possible solutions to the current climate crisis.

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

Analyzing the effect of pressure on the properties of point defects in $\gamma\mathrm{U–Mo}$ through atomistic simulations

Uranium–molybdenum (U–Mo) alloys in monolithic fuel foil are the primary candidate for the conversion of high-performance research reactors in the USA. Monolithic fuel is utilized in a plate-type design with a zirconium diffusion barrier and aluminum cladding. These fuel types are unique in that they contain no plenum for the release of fission gases, which, in conjunction with the aluminum cladding, can lead to large stress states within the fuel. The nature of how fundamental processes of radiation damage, including the evolution of point defects, under such stresses occur is unknown. In this work, we present molecular dynamics simulations of the formation energy of point defects under applied stress. We report this work will allow for the implementation of stress-dependent microstructural evolution models of nuclear fuels, including those for both fission gas bubble growth and creep, which are critical to ensure the stable and predictable behavior of research reactor fuels.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS2011

Atomic Simulation of Complex DNA DSBs and the Interactions with the Ku70/80 Heterodimer

DNA double strand breaks (DSBs) induced by ionizing radiation (IR) usually contain modified bases such as 8-oxo-7,8-dihydroguanine (8-oxoG) and thymine glycol, apurinic/apyrimidinic (AP) sites, 2-deoxyribonolactone, or single-strand breaks (SSBs). The presence of such lesions in close proximity to the DSB terminus makes the DNA nicks more difficult to repair and rejoin than endogenously induced simple DSBs, and as such a major determinant of the biological effects of high linear energy transfer (LET) radiation as encountered in space travel. In this study we conducted molecular dynamics simulations on a series of DNA duplexes with various complex lesions of 8-oxoG and AP sites, in an effort to investigate the effects of such lesions to the structural integrity and stability of DNA after insulted by IR. We also simulated the interaction of such complex DSBs with the Ku70/80 heterodimer, the first protein in mammalian cells to embark the non-homologous end joining (NHEJ) DNA repair pathway. The results indicate, compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex, thus they present more deleterious effects to the genome integrity if not captured and repaired promptly in cells. Simulations also demonstrate the binding of Ku drastically reduces structural disruption and flexibility caused by the complex lesions, and the interactions of Ku with complex DSBs have a different potential energy landscape from the bound structure with simple DSB. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. This energy shift may help the Ku protein to secure at the DSB terminus for a longer time, so that other end processing factors or repair pathways can proceed at the lesions before NHEJ repair process starts. These atomic simulations may provide valuable new insight into the selective action of repair proteins on damaged DNA.

Hu, Shaowen↗