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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 955 records · Page 53
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DOE OSTI2024

CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation

Molecular conformer generation (MCG) is an important task in cheminformatics and drug discovery. The ability to efficiently generate low-energy 3D structures can avoid expensive quantum mechanical simulations, leading to accelerated virtual screenings and enhanced structural exploration. Several generative models have been developed for MCG, but many struggle to consistently produce high-quality conformers for meaningful downstream applications. To address these issues, we introduce CoarsenConf, which coarse-grains molecular graphs based on torsional angles and integrates them into an SE(3)-equivariant hierarchical variational autoencoder. Through equivariant coarse-graining, we aggregate the fine-grained atomic coordinates of subgraphs connected via rotatable bonds, creating a variable-length coarse-grained latent representation. Our model uses a novel aggregated attention mechanism to restore fine-grained coordinates from the coarse-grained latent representation, enabling efficient generation of accurate conformers. Furthermore, we evaluate the chemical and biochemical quality of our generated conformers on multiple downstream applications, including property prediction and large-scale oracle-based protein docking. Overall, CoarsenConf generates more accurate conformer ensembles compared to prior generative models.

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

KBKit: A Python Toolkit for Kirkwood–Buff Theory from Molecular Dynamics

Thermodynamic properties of liquid mixtures govern processes that range from drug delivery to energy storage, yet extracting these properties from molecular simulations remains challenging. Kirkwood–Buff (KB) theory offers a rigorous route by linking microscopic pair distribution functions to macroscopic free energies, but practical use of the theory has been hindered by two obstacles: (i) the long simulations needed to obtain well-converged Kirkwood-Buff integrals (KBIs) and (ii) the specialized corrections required to translate finite-size data to the thermodynamic limit. $\texttt{KBKit}$ is an open-source Python package that removes these barriers. It automatically computes KBIs and derived thermodynamic quantities from GROMACS input files, applies state-of-the-art finite-size corrections, and provides built-in diagnostic tools to quantify statistical uncertainty. Written with modern software-engineering practices—continuous integration, extensive unit testing, and thorough documentation—$\texttt{KBKit}$ is both reliable and easy to extend. By condensing complex KBI analysis into a few intuitive commands, $\texttt{KBKit}$ enables researchers to incorporate KB theory into routine simulation workflows and accelerate the discovery of solution-phase thermodynamics.

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

Semi-Empirical Shadow Molecular Dynamics: A PyTorch Implementation

Here, extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) in its most recent shadow potential energy version has been implemented in the semiempirical PyTorch-based software PySeQM. The implementation includes finite electronic temperatures, canonical density matrix perturbation theory, and an adaptive Krylov subspace approximation for the integration of the electronic equations of motion within the XL-BOMB approach (KSA-XL-BOMD). The PyTorch implementation leverages the use of GPU and machine learning hardware accelerators for the simulations. The new XL-BOMD formulation allows studying more challenging chemical systems with charge instabilities and low electronic energy gaps. The current public release of PySeQM continues our development of modular architecture for large-scale simulations employing semi-empirical quantum-mechanical treatment. Applied to molecular dynamics, simulation of 840 carbon atoms, one integration time step executes in 4 s on a single Nvidia RTX A6000 GPU.

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

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials

Silicon carbide (SiC) divacancies are attractive candidates for spin-defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model. Here, the trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multidefect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.

Computer simulations↗
DOE OSTI2019

Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration

In order to accelerate molecular dynamics simulations using polarizable force fields, we combine a new extended Lagrangian approach that eliminates the self-consistent field step (iEL/0-SCF) with a stochastic integration scheme that allows for a long time step using a multiple time scale algorithm (SIN(R)). We consider different algorithms for the combined scheme that places different components of the nonbonded forces into different time scales, as well as splitting individual nonbonded forces across time scales, to demonstrate that the combined method works well for bulk water as well as for a concentrated salt solution, aqueous peptide, and solvated protein. Depending on system and desired accuracy, the iEL/0-SCF and SIN(R) combination yields lower bound computational speed-ups of ~6–8 relative to a molecular dynamics Verlet integration using a standard SCF solver implemented in the reference program TINKER 8.1. Finally, the combined approach embodies a significant advance for equilibrium simulations in the canonical ensemble of many-body potential energy surfaces for condensed phase systems with speed-ups that exceed what is possible by either method alone.

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

Nitromethane Decomposition via Automated Reaction Discovery and an Ab Initio Corrected Kinetic Model

In the explore the systematic construction of kinetic models from in silico reaction data for the decomposition of nitromethane. Our models are constructed in a computationally affordable manner by using reactions discovered through accelerated molecular dynamics simulations using the ReaxFF reactive force field. The reaction paths are then optimized to determine reaction rate parameters. We introduce a reaction barrier correction scheme that combines accurate thermochemical data from density functional theory with ReaxFF minimal energy paths. We validate our models across different thermodynamic regimes, showing predictions of gas phase CO and NO concentrations and high-pressure induction times that are similar to experimental data. The kinetic models are analyzed to find fundamental decomposition reactions in different thermodynamic regimes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Interfacial Properties and Design of Functional Energy Materials

The vital importance of energy to society continues to demand a relentless pursuit of energy responsive materials that can bridge fundamental chemical structures at the molecular level and achieve improved functionality, such as efficient energy conversion/storage/transmission, over multiple length scales. This demand can potentially be realized by harnessing the power of self-assembly a spontaneous process where molecules or much larger entities form ordered aggregates as a consequence of predominately non-covalent (weak) interactions. Self-assembly is the key to bottom-up design of molecular devices, because the nearly atomic-level control is very difficult to realize in a top-down, e.g., lithographic approach. However, while function (e.g., charge mobility) in simple systems such as single crystals can often be predicted, predicting the function of the great variety of self-assembled molecular architectures is complicated by the lack of understanding and control over nanoscale interactions, mesoscale architectures, and macroscale (long-range) order. To establish a foundation toward delivering practical solutions, it is critical to develop an understanding of the chemical and physical mechanisms responsible for the self-assembly of molecular and hybrid materials on various substrates. Typically molecular self-assembly involves poorly understood non-covalent intermolecular and substrate-molecule interactions compounded by local and/or collective influences from the substrate atomic lattice (symmetry and/or topological features) and electronic structure. Thus, progress towards unraveling the underlying physicochemical processes that control the structure and macroscopic physical, mechanical, electrical, and transport properties of materials increasingly requires tight integration of theory, modeling and simulation with precision synthesis, advanced experimental characterization, and device measurements. In this mode, theory and simulation can greatly accelerate the process of materials discovery by providing atomic level understanding of physicochemical phenomena and for making predictions of trends. In particular, this approach can provide understanding, prediction and exploration of new materials and conditions before they are realized in the lab, to illuminate connections between experimental observations, and help identify new materials for targeted synthesis. Toward this end, Density Functional Theory (DFT) can provide a suitable computational framework for investigating the inter- and intramolecular bonding, molecular conformation, charge and spin configurations that are intrinsic to self-assembly of molecules on substrates. This Account highlights recent advances in using an integrated approach based on DFT and scanning probe microscopy [STM(s), AFM] to study/develop electronic materials formed from the self-assembly of molecules into supramolecular or polymeric architectures on substrates. Here it is the interplay between molecular interactions and surface electrons that is used to control the final architecture and subsequent bulk properties of the two-dimensional patterns/assemblies. Indeed a rich variety of functional energy materials become possible.

Sumpter, Bobby G↗
DOE OSTI2017

Evidence for percolation diffusion of cations and reordering in disordered pyrochlore from accelerated molecular dynamics

Diffusion in complex oxides is critical to ionic transport, radiation damage evolution, sintering, and aging. In complex oxides such as pyrochlores, anionic diffusion is dramatically affected by cation disorder. However, little is known about how disorder influences cation transport. Here, we report results from classical and accelerated molecular dynamics simulations of vacancy-mediated cation diffusion in Gd 2 Ti 2 O 7 pyrochlore, on the microsecond timescale. We find that diffusion is slow at low levels of disorder, while higher disorder allows for fast diffusion, which is then accompanied by antisite annihilation and reordering, and thus a slowing of cation transport. Cation diffusivity is therefore not constant, but decreases as the material reorders. We also show that fast cation diffusion is triggered by the formation of a percolation network of antisites. This is in contrast with observations from other complex oxides and disordered media models, suggesting a fundamentally different relation between disorder and mass transport.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

The role of charge in microdroplet redox chemistry

In charged water microdroplets, which occur in nature or in the lab upon ultrasonication or in electrospray processes, the thermodynamics for reactive chemistry can be dramatically altered relative to the bulk phase. Here, we provide a theoretical basis for the observation of accelerated chemistry by simulating water droplets of increasing charge imbalance to create redox agents such as hydroxyl and hydrogen radicals and solvated electrons. We compute the hydration enthalpy of OH - and H + that controls the electron transfer process, and the corresponding changes in vertical ionization energy and vertical electron affinity of the ions, to create OH • and H • reactive species. We find that at ~ 20 - 50% of the Rayleigh limit of droplet charge the hydration enthalpy of both OH - and H + have decreased by >50 kcal/mol such that electron transfer becomes thermodynamically favorable, in correspondence with the more favorable vertical electron affinity of H + and the lowered vertical ionization energy of OH - . We provide scaling arguments that show that the nanoscale calculations and conclusions extend to the experimental microdroplet length scale. The relevance of the droplet charge for chemical reactivity is illustrated for the formation of H 2 O 2 , and has clear implications for other redox reactions observed to occur with enhanced rates in microdroplets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Laboratory realization of relativistic pair-plasma beams

Relativistic electron-positron plasmas are ubiquitous in extreme astrophysical environments such as black-hole and neutron-star magnetospheres, where accretion-powered jets and pulsar winds are expected to be enriched with electron-positron pairs. Their role in the dynamics of such environments is in many cases believed to be fundamental, but their behavior differs significantly from typical electron-ion plasmas due to the matter-antimatter symmetry of the charged components. So far, our experimental inability to produce large yields of positrons in quasi-neutral beams has restricted the understanding of electron-positron pair plasmas to simple numerical and analytical studies, which are rather limited. We present the first experimental results confirming the generation of high-density, quasi-neutral, relativistic electron-positron pair beams using the 440 GeV/c beam at CERN’s Super Proton Synchrotron (SPS) accelerator. Monte Carlo simulations agree well with the experimental data and show that the characteristic scales necessary for collective plasma behavior, such as the Debye length and the collisionless skin depth, are exceeded by the measured size of the produced pair beams. Our work opens up the possibility of directly probing the microphysics of pair plasmas beyond quasi-linear evolution into regimes that are challenging to simulate or measure via astronomical observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Near-Field Corrosion Interactions between Glass and Corrosion Resistant Alloys

This study explores the corrosion interactions between model nuclear waste glass materials and corrosion resistant alloys, under conditions that simulate the near field of a nuclear waste repository. The interactions between the corrosion of stainless steel (SS) 316, alloy G30, or alloy 625, and international simple glass or soda-lime silica glass are systematically studied. The dissimilar materials were exposed in close proximity to each other in different electrolytes at 90 oC. After exposure, the glass surface exposed near metals showed different regimes of corrosion, with distinct surface morphologies and chemistries that were likely affected by the local environment created by the localized corrosion of metals. Surface and solution analyses showed that the corrosion rate of glass was enhanced by the presence of metals. Infrared spectroscopy data suggested the local build-up of stresses in the contact area of glass, which may lead to the mechanical instability of the glass alteration layer. On the other hand, the effect of glass on metal corrosion is strongly dependent on the leaching solution. In electrolytes containing abundant aggressive anions such as Cl-, glass seems to suppress the localized corrosion of SS by the precipitation of a Si-rich surface film that protects the SS substrate from solutions. However, in less aggressive electrolytes, the corrosion rate of SS was increased by the presence of glass corrosion products. Overall, our study showed that the hidden and localized damage on glass in contact with metals may enhance the release of incorporated radionuclides compared to typical uniform glass corrosion. Therefore, more attention should be paid to the corrosion interactions between metals and glass under repository conditions.

Guo, Xiaolei↗
DOE OSTI2017

The mobility of small vacancy/helium complexes in tungsten and its impact on retention in fusion-relevant conditions

Tungsten is a promising plasma facing material for fusion reactors. Despite many favorable properties, helium ions incoming from the plasma are known to dramatically affect the microstructure of tungsten, leading to bubble growth, blistering, and/or to the formation of fuzz. In order to develop mitigation strategies, it is essential to understand the atomistic processes that lead to bubble formation and subsequent microstructural changes. In this work, we use large-scale Accelerated Molecular Dynamics simulations to investigate small (N=1,2) V N He M vacancy/helium complexes, which serve as the nuclei for larger helium bubble growth, over timescales reaching into the milliseconds under conditions typical of the operation of fusion reactors. These complexes can interconvert between different I L V N+L He M variants via Frenkel pair nucleation (leading to the creation of a additional vacancy/interstitial pair) and annihilation events; sequences of these events can lead to net migration of these embryonic bubbles. The competition between nucleation and annihilation produces a very complex dependence of the diffusivity on the number of heliums. Finally, through cluster dynamics simulations, we show that diffusion of these complexes provides an efficient pathway for helium release at fluxes expected in fusion reactors, and hence that accounting for the mobility of these complexes is crucial.

36 MATERIALS SCIENCE↗
DOE OSTI2012

ISOS-3 Inter-Laboratory Collaboration Focused on the Stability of a Variety of Organic Photovoltaic Devices

Seven distinct sets (n {>=} 12) of state of the art organic photovoltaic devices were prepared by leading research laboratories in a collaboration planned at the Third International Summit on Organic Photovoltaic Stability (ISOS-3). All devices were shipped to RISO DTU and characterized simultaneously up to 1830 h in accordance with established ISOS-3 protocols under three distinct illumination conditions: accelerated full sun simulation; low level indoor fluorescent lighting; and dark storage with daily measurement under full sun simulation. Three nominally identical devices were used in each experiment both to provide an assessment of the homogeneity of the samples and to distribute samples for a variety of post soaking analytical measurements at six distinct laboratories enabling comparison at various stages in the degradation of the devices. Over 100 devices with more than 300 cells were used in the study. We present here design and fabrication details for the seven device sets, benefits and challenges associated with the unprecedented size of the collaboration, characterization protocols, and results both on individual device stability and uniformity of device sets, in the three illumination conditions.

14 SOLAR ENERGY↗
DOE OSTI2015

Insights into dynamic processes of cations in pyrochlores and other complex oxides

Complex oxides are critical components of many key technologies, from solid oxide fuel cells and superionics to inert matrix fuels and nuclear waste forms. In many cases, understanding mass transport is important for predicting performance and, thus, extensive effort has been devoted to understanding mass transport in these materials. However, most work has focused on the behavior of oxygen while cation transport has received relatively little attention, even though cation diffusion is responsible for many phenomena, including sintering, radiation damage evolution, and deformation processes. Here, we use accelerated molecular dynamics simulations to examine the kinetics of cation defects in one class of complex oxides, A₂B₂O₇ pyrochlore. In some pyrochlore chemistries, B cation defects are kinetically unstable, transforming to A cation defects and antisites at rates faster than they can diffuse. When this occurs, transport of B cations occurs through defect processes on the A sublattice. Further, these A cation defects, either interstitials or vacancies, can interact with antisite disorder, reordering the material locally, though this process is much more efficient for interstitials than vacancies. Whether this behavior occurs in a given pyrochlore depends on the A and B chemistry. Pyrochlores with a smaller ratio of cation radii exhibit this complex behavior, while those with larger ratios exhibit direct migration of B interstitials. Similar behavior has been reported in other complex oxides such as spinels and perovskites, suggesting that this coupling of transport between the A and B cation sublattices, while not universal, occurs in many complex oxide.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Localized saddle-point search and application to temperature-accelerated dynamics

We present a method for speeding up temperature-accelerated dynamics (TAD) simulations by carrying out a localized saddle-point (LSAD) search. In this method, instead of using the entire system to determine the energy barriers of activated processes, the calculation is localized by only including a small chunk of atoms around the atoms directly involved in the transition. Using this method, we have obtained N-independent scaling for the computational cost of the saddle-point search as a function of system size N. The error arising from localization is analyzed using a variety of model systems, including a variety of activated processes on Ag(100) and Cu(100) surfaces, as well as multiatom moves in Cu radiation damage and metal heteroepitaxial growth. Our results show significantly improved performance of TAD with the LSAD method, for the case of Ag/Ag(100) annealing and Cu/Cu(100) growth, while maintaining a negligibly small error in energy barriers.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Pair mobility functions for rigid spheres in concentrated colloidal dispersions: Force, torque, translation, and rotation

The formulation of detailed models for the dynamics of condensed soft matter including colloidal suspensions and other complex fluids requires accurate description of the physical forces between microstructural constituents. In dilute suspensions, pair-level interactions are sufficient to capture hydrodynamic, interparticle, and thermodynamic forces. In dense suspensions, many-body interactions must be considered. Prior analytical approaches to capturing such interactions such as mean-field approaches replace detailed interactions with averaged approximations. However, long-range coupling and effects of concentration on local structure, which may play an important role in, e.g., phase transitions, are smeared out in such approaches. An alternative to such approximations is the detailed modeling of hydrodynamic interactions utilizing precise couplings between moments of the hydrodynamic traction on a suspended particle and the motion of that or other suspended particles. For two isolated spheres, a set of these functions was calculated by Jeffrey and Onishi [J. Fluid Mech. 139, 261–290 (1984)] and Jeffrey [J. Phys. Fluids 4, 16–29 (1992)]. Along with pioneering work by Batchelor, these are the touchstone for low-Reynolds-number hydrodynamic interactions and have been applied directly in the solution of many important problems related to the dynamics of dilute colloidal dispersions [G. K. Batchelor and J. T. Green, J. Fluid Mech. 56, 375–400 (1972) and G. K. Batchelor, J. Fluid Mech. 74, 1–29 (1976)]. Toward extension of these functions to concentrated systems, here we present a new stochastic sampling technique to rapidly calculate an analogous set of mobility functions describing the hydrodynamic interactions between two hard spheres immersed in a suspension of arbitrary concentration, utilizing accelerated Stokesian dynamics simulations. These mobility functions provide precise, radially dependent couplings of hydrodynamic force and torque to particle translation and rotation, for arbitrary colloid volume fraction ϕ. The pair mobilities (describing entrainment of one particle by the disturbance flow created by another) decay slowly with separation distance: as 1/r, for volume fractions 0.05 ≤ ϕ ≤ 0.5. For the relative mobility, we find an initially rapid growth as a pair separates, followed by a slow, 1/r growth. Up to ϕ ≤ 0.4, the relative mobility does not reached the far-field value even beyond separations of many particle sizes. In the case of ϕ = 0.5, the far-field asymptote is reached but only at a separation of eight radii and after a slow 1/r growth. At these higher concentrations, the coefficients also reveal liquid-like structural effects on pair mobility at close separations. These results confirm that long-range many-body hydrodynamic interactions are an essential part of the dynamics of concentrated systems and that care must be taken when applying renormalization schemes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

The purported square ice in bilayer graphene is a nanoscale, monolayer object

The phase diagram of water is complex, and interfacial effects can stabilize unusual structures at the nanoscale. In this paper, we employ bond order accelerated molecular dynamics simulations to show that upon encapsulation within bilayer graphene, water can spontaneously adopt a two-dimensional (monomolecular) layer of “square ice” at ambient conditions, instead of an encapsulated water droplet. Free energy calculations show that this motif is thermodynamically stable up to diameters of approximately 15 nm due to enhanced hydrogen bonding and favorable binding to the graphene sheets. Entropic losses due to solidification and reduced graphene–graphene binding enthalpy are opposing thermodynamic forces that conspire to limit the maximum size, but modification of any of these thermodynamic factors should change the range of stability. Finally, simulated core-level spectroscopy reveals unambiguous orientation dependent signatures of square ice that should be discernable in experiments.

36 MATERIALS SCIENCE↗