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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A spall and diffraction study of nanosecond pressure release across the iron ε-α phase boundary

The extreme response of polycrystalline iron at high pressures and high strain rates is revealed by means of high-power laser pulses. The compression portion of the pulse coupled with x-ray diffraction identifies the expected body-centered cubic (α) to hexagonal close packed (ε) displacive transformation. Upon release, observation shows that the complete reverse transformation takes approximately 8 ns and that the structure returns to its initial microstructural configuration, in a reversible transformation path. This is in good agreement with molecular dynamics (MD) simulations which predict an inverse dependence between transformation time and strain rate. The grain size is reduced from μm to nm range during compression and begins increasing back to the original grain size on decompression. The kinetics of the transition is dictated by heterogenous nucleation as it follows the Johnson-Mehl-Avrami-Kolmogorov equation with the appropriate time exponent of ~1. This is confirmed by MD simulations which also identify profuse twinning and dislocation generation. Here, the tensile pulse generated upon reflection at the free surface is captured by time-resolved free surface velocity measurements from which a peak tensile stress of 7 GPa is obtained, in stark contrast with its quasi-static value of ~200 MPa. At these strain rates, the strength of grain interiors, which is determined by twinning and slip exceeds the strength of the boundaries, and failure initiates preferentially in the latter.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Implementing a neural network interatomic model with performance portability for emerging exascale architectures

The two main thrusts of computational science are increasingly accurate predictions and faster calculations; to this end, the zeitgeist in molecular dynamics (MD) simulations is pursuing machine learned and data driven interatomic models, e.g. neural network potentials, and novel hardware architectures, e.g. GPUs. Current implementations of neural network potentials are orders of magnitude slower than traditional interatomic models and while looming exascale computing offers the ability to run large, accurate simulations with these models, achieving portable performance for MD with new and varied exascale hardware requires rethinking traditional algorithms, using novel data structures, and library solutions. We re-implement a neural network interatomic model in CabanaMD, an MD proxy application, built on libraries developed for performance portability. Our implementation shows significantly improved thread scaling in this complex kernel as compared to a current LAMMPS implementation, across both strong and weak scaling. Our single-source solution enables simulations up to 20 million atoms on a single CPU node and 4 million atoms with improved performance on a single GPU. Furthermore, we also explore parallelism and data layout choices (using flexible data structures called AoSoAs) and their effect on performance, seeing up to ~50% and ~5% improvements in performance on a GPU by choosing the right level of parallelism and data layout respectively.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Atomic scale etching of diamond: insights from molecular dynamics simulations

Diamond is a promising material for multiple applications in quantum information processing and sensing as well as applications in microelectronics. However, diamond devices can be limited by surface defects that compromise charge stability and spin coherence, among others. Improved strategies in plasma etching of diamond could play an important role in minimizing or eliminating these defects. In this work, we explore plasma-assisted atomic scale etching of diamond using argon ions (Ar + ), hydrogen ions (H + ) and hydrogen atoms (H). We employ classical molecular dynamics (MD) simulations and test several interatomic potentials based on the Reactive Empirical Bond Order (REBO) form with comparisons to a variety of published experimental results. We performed MD simulations of low-energy hydrogen ($\leqslant$50 eV) and argon ( $\leqslant$200 eV) ion bombardment of diamond surfaces. Ar + bombardment can be used to locally smooth initially rough diamond surfaces via the formation of an amorphous C layer, the thickness of which increases with argon ion energy. Subsequent exposure with hydrogen ions (or fast neutrals) will selectively etch this amorphous C layer, leaving the underlying diamond layer mostly intact if the H energy is maintained below about 10 eV. The simulations suggest that combining Ar + smoothing with selective, near threshold energy H removal of amorphous C can be an effective strategy for diamond surface engineering, leading to more reliable and sensitive diamond color center devices.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site

Organophosphorus hydrolase (OPH) is a metalloenzyme that can hydrolyze organophosphorus agents resulting in products that are generally of reduced toxicity. The best OPH substrate found to date is diethyl p-nitrophenyl phosphate (paraoxon). Most structural and kinetic studies assume that the binding orientation of paraoxon is identical to that of diethyl 4-methylbenzylphosphonate, which is the only substrate analog co-crystallized with OPH. In the current work, we used a combined docking and molecular dynamics (MD) approach to predict the likely binding mode of paraoxon. Then, we used the predicted binding mode to run MD simulations on the wild type (WT) OPH complexed with paraoxon, and OPH mutants complexed with paraoxon. Additionally, we identified three hot-spot residues (D253, H254, and I255) involved in the stability of the OPH active site. We then experimentally assayed single and double mutants involving these residues for paraoxon binding affinity. The binding free energy calculations and the experimental kinetics of the reactions between each OPH mutant and paraoxon show that mutated forms D253E, D253E-H254R, and D253E-I255G exhibit enhanced substrate binding affinity over WT OPH. Interestingly, our experimental results show that the substrate binding affinity of the double mutant D253E-H254R increased by 19-fold compared to WT OPH.

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

Structure of Water Adsorbed on Nanocrystalline Calcium Silicate Hydrate Determined from Neutron Scattering and Molecular Dynamics Simulations

Calcium silicate hydrate (C-S-H) is a disordered, nanocrystalline material that acts as a primary binding phase in Portland cement. Thin films of water are present on the surfaces and in nanopores of C-S-H, impacting many of its chemical and mechanical properties, such as ion transport, creep, or thermal behavior. Despite decades of research, a full understanding of the structural details of adsorbed, confined, and bulk water in C-S-H remains elusive. In this work, we applied a multitechnique study involving molecular dynamics (MD) simulations validated by neutron diffraction with isotopic substitution (NDIS) and X-ray scattering methods to investigate the structure of water in C-S-H and C-A-S-H (an Al-bearing, low-CO 2 C-S-H substitute). Direct comparison of NDIS data with the MD results reveals that the structure of confined and interfacial water differs significantly from the bulk water and exhibits a larger degree of mesoscale ordering for more hydrated C-S-H structures. As a result, this observation suggests an important role of water as a stabilizer of the atomistic-level structure of C-S-H.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Simulation of two nanoparticle melting to understand the conductivity drop of 3D-printed silver nanowires

The future flexible sensor technology will require low-temperature, fast processing 3D printing techniques that will rely heavily on the quality of nanoparticle (NP) Ink. Electrical conductivity has been found to decrease in majority of the 3D printed electronic wires. Herein we report a fundamental understanding in drop of electrical conductivity in processed silver (Ag) line wire, generally found in Ag-nanoparticle Ink, using large-scale atomistic molecular dynamics (MD) simulations of sintering of five different sizes of Ag NPs. To preserve the high conductivity of pure silver wires, the integrity of the pristine face-centered cubic (FCC) crystalline structure must be retained in the processed line wires. Simulations show that the pristine Ag FCC structures of the nanoparticles are not recovered after melting and resolidification, instead, the resolidified material is paracrystaline. The breakdown of pristine FCC structures might be the cause of the drop in conductivity of processed Ag wires. Simulation results suggest that the intermediate size nanoparticles retain highest percentage of the pristine silver face-centered cubic (FCC) structure after pulse treatments. Our results show that the most promising Ag-Ink should contain smaller to medium size silver NPs that can retain FCC structure after 3D printing of the Ag-Ink.

42 ENGINEERING↗
DOE OSTI2023

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Multiscale Concurrent Atomistic-Continuum (CAC) modeling of multicomponent alloys

We report strengthening in complex multicomponent systems such as solid solution alloys is controlled primarily by the dynamic interactions between dislocation lines and heterogeneously distributed solute species. Modeling of extended defect length scales in such multicomponent systems becomes prohibitively expensive, motivating the development of reduced order approaches. This work explores the application of the Concurrent Atomistic-Continuum (CAC) method to model dislocation mobility in random alloys at extended length scales. By employing recently developed average-atom interatomic potentials, the average “bulk” material response in coarse-grained regions interacts with true random solute species in the atomistic-scale domain. We demonstrate that spurious stresses in domain resolution transition regions are eliminated entirely due to the CAC formulation. Simultaneously, the key details of local stress fluctuation due to randomness in the dislocation core region are captured, and fluctuating stress smoothly decays to the long-range dislocation stress field response. Dislocation mobility calculations, for line lengths over 400 nm, are computed as a function of alloy composition in the model FeNiCr system and compared to full molecular dynamics (MD). The results capture the composition-dependent trends, while reducing degrees of freedom by nearly 40%. This approach can be readily extended to any system described by an EAM potential and facilitates the study of large-scale defect dynamics in complex solute environments to support computational alloy design.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Extreme Metastability of Diamond and its Transformation to the BC8 Post-Diamond Phase of Carbon

Diamond possesses exceptional physical properties due to its remarkably strong carbon–carbon bonding, leading to significant resilience to structural transformations at very high pressures and temperatures. Despite several experimental attempts, synthesis and recovery of the theoretically predicted post-diamond BC8 phase remains elusive. Through quantum-accurate multimillion atom molecular dynamics (MD) simulations, we have uncovered the extreme metastability of diamond at very high pressures, significantly exceeding its range of thermodynamic stability. We predict the post-diamond BC8 phase to be experimentally accessible only within a narrow high pressure–temperature region of the carbon phase diagram. The diamond to BC8 transformation proceeds through premelting followed by BC8 nucleation and growth in the metastable carbon liquid. Here we propose a double-shock compression pathway for BC8 synthesis, which is currently being explored in experiments at the National Ignition Facility.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Understanding the plasticity contributions during laser-shock loading and spall failure of Cu microstructures at the atomic scales

A hybrid atomic-scale and continuum modeling framework is used to study the microstructural evolution during the laser-induced shock deformation and failure (spallation) of copper microstructures. A continuum two-temperature model (TTM) is used to account for the interaction of Cu atoms with a laser in molecular dynamics (MD) simulations. The MD-TTM simulations study the effect of laser loading conditions (laser fluence) on the microstructure (defects) evolution during various stages of shock wave propagation, reflection, and interaction in single-crystal (sc) Cu systems. In addition, the role of the microstructure is investigated by comparing the defect evolution and spall response of sc-Cu and nanocrystalline (nc) Cu systems. The defect (stacking faults and twin faults) evolution behavior in the metal at various times is further characterized using virtual in situ selected area electron diffraction and x-ray diffraction during various stages of evolution of microstructure. Here, the simulations elucidate the uncertain relation between spall strength and strain-rate and the much stronger relation between the spall strength and the temperatures generated due to laser shock loading for the small Cu sample dimensions considered here.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Molecular-dynamics simulation methods for macromolecular crystallography

It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein–solvent interface. To address this limitation, a set of MD–MX methods that combine MD simulations of protein crystals with conventional modeling and refinement tools have been developed. In an application to a cyclic adenosine monophosphate-dependent protein kinase at room temperature, the procedure improved the interpretation of ambiguous density, yielding an alternative water model and a revised protein model including multiple conformations. The revised model provides mechanistic insights into the catalytic and regulatory interactions of the enzyme. The same methods may be used in other MX studies to seek mechanistic insights.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Unexpected Kinetic Solvent Effects Enhance Activity and Selectivity in Biphasic Systems

Biphasic dehydration of fructose to 5-hydroxymethylfurfural (HMF) has shown unprecedented increases in productivity, but a mechanistic understanding is lacking. Herein, we couple fast experimental reaction kinetics, multiscale modeling (phase behavior, classical molecular dynamics(MD), and quantum mechanics/molecular mechanics MD), in situ sampling, and IR and 13 C-NMR spectroscopy to elucidate the complex effects of nonpolar extracting organic solvents on the kinetics of fructose dehydration. We show that these organic solvents can reach significant mutual solubility with water at reaction temperatures, enabling the partition of the sugar and catalyst into the extracting phase. In the organic-rich environment, the dehydration of fructose proceeds faster and more selectively than in water due to increased relative abundance of the reactive furanose isomer, enhanced water–catalyst–substrate interactions driven by nanophase separation, and higher product stability stemming from preferential solvation. Furthermore, we demonstrate that these solvent effects impact other critical biphasic reactions in biomass upgrading and provide qualitative principles for solvent selection.

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

Interfacial water asymmetry at ideal electrochemical interfaces

Controlling electrochemical reactivity requires a detailed understanding of the charging behavior and thermodynamics of the electrochemical interface. Experiments can independently probe the overall charge response of the electrochemical double layer by capacitance measurements and the thermodynamics of the inner layer with potential of maximum entropy measurements. Relating these properties by computational modeling of the electrochemical interface has so far been challenging due to the low accuracy of classical molecular dynamics (MD) for capacitance and the limited time and length scales of ab initio MD. Here, we combine large ensembles of long-time-scale classical MD simulations with charge response from electronic density functional theory to predict the potential-dependent capacitance of a family of ideal aqueous electrochemical interfaces with different peak capacitances. We show that while the potential of maximum capacitance varies, this entire family exhibits an electrode charge of maximum capacitance (CMC) between -2.9 and -2.2 μC/cm 2 , regardless of the details in the electronic response. Simulated heating of the same interfaces reveals that the entropy peaks at a charge of maximum entropy (CME) of -5.1 ± 0.6 μC/cm 2 , in agreement with experimental findings for metallic electrodes. The CME and CMC both indicate asymmetric response of interfacial water that is stronger for negatively charged electrodes, while the difference between CME and CMC illustrates the richness in behavior of even the ideal electrochemical interface.

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

Effect of free surfaces on localized plastic deformation in single-crystal nickel containing helium bubbles and radiation-induced self-interstitial atom clusters

This paper presents molecular dynamics (MD) simulations of plastic deformation in single-crystal Ni models containing internal distributions of helium (He) bubbles and self-interstitial atom (SIA) clusters corresponding to experimental characterization of ex-service Inconel X-750 components. Here, we simulate single crystals with and without free surfaces at room temperature and 588K, the latter temperature corresponding to the Inconel X-750 service conditions. Both models are deformed under multiple slip to a maximum deviatoric strain of ~10 %. A dislocation slip band forms in the model without free surfaces, but not in the model with free surfaces. However, the latter exhibits nano-twin nucleation from surfaces. Helium (He) bubbles that overlap with a slip band or a nano-twinned region deform more severely than other bubbles in the model. Nevertheless, the bubbles do not link up and do not form configurations that resemble incipient cracks.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Interface and Thermophysical Properties of R 32 Refrigerant

Driven by the urgent demand for efficient cooling in microelectronics and advanced thermal management systems, difluoromethane (R32/CH 2 F 2 ) has emerged as a promising candidate owing to its favorable thermophysical properties, including high heat transfer efficiency and low viscosity. While bulk properties such as density, viscosity, and thermal conductivity have been widely studied, interfacial properties, including surface tension and interfacial thickness, remain comparatively underexplored, despite their importance in phase-transition dynamics. Here, we perform molecular dynamics (MD) simulations from 180 to 300 K using an optimized transferable force field for fluoropropenes with enhanced electrostatics to assess both bulk and interfacial behavior of R32. Simulations reproduced density within ±2.1%, viscosity within 3.05%, and thermal conductivity within 7.41% of NIST reference data. Heat capacities (C p and C v ) were predicted within 5%. For interfacial properties, surface tension trends were reproduced within 13.58% deviation, and the vapor–liquid coexistence curve closely matched reference data, yielding a critical temperature of 345.7 K (1.6% deviation) and a critical density of 0.397 g/cm 3 (6.4% deviation). Importantly, the vapor–liquid interface exhibited pronounced temperature-dependent broadening across the 180–290 K range. This behavior correlates with increasing molecular kinetic energy, reduction in intermolecular cohesive interactions, and a progressive loss of preferential dipole alignment, which collectively enhance thermal fluctuation amplitudes at elevated temperatures. These validated results provide predictive molecular-level insights, particularly for interfacial properties that remain less characterized. By reducing property prediction errors in key parameters such as critical temperature, this work provides reliable inputs for heat-exchanger and system models. Such correlations can support optimized component sizing, improved performance, and reduced refrigerant charge. Beyond R32, the methodology offers a transferable framework for blended and next-generation low-GWP refrigerants, contributing to sustainable thermal management aligned with the 2027 EU F-Gas regulation and 2030 Kigali Amendment.

Fluids↗
DOE OSTI2025

Binding Free Energy Analysis of Colicin D, E3 and E8 to Their Respective Cognate Immunity Proteins Using Computational Simulations

Colicins are antimicrobial proteins produced by bacteria for the purpose of destroying neighboring bacteria. Colicin activity is neutralized by a specific cognate immunity protein in order to protect the host. This study investigates the structural and binding mechanisms underlying the interaction of colicin-D, -E3 and -E8 to their respective immunity proteins (ImD, Im3 and Im8) using structure prediction, molecular dynamics (MD) simulations and MM-PBSA approach of free energy calculations. High-confidence colicin-immunity (Col-Im) complex structures predicted using AlphaFold2 were subjected to MD simulations of 150 ns with GROMACS and were analyzed for the binding free energy calculation using gmx_MMPBSA. Results showed that the complex of Col_E3-Im3 exhibited the most favorable binding free energy, driven by strong van der Waals and electrostatic interactions. Col_D-ImD and Col_E8-Im8 also showed the favorable binding. Electrostatics and hydrogen bonding emerged as a key factor driving binding and stability, while polar solvation acted as a destabilizing factor across all systems. These outcomes provide an understanding of the molecular mechanisms of Col-Im systems, with potential applications for developing natural antimicrobials for food safety.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Nonequilibrium effects in high-gain inertial confinement fusion

Recent experimental demonstrations of ignition and target gain in inertial confinement fusion (ICF) have stimulated interest in exploring the fundamental physics of violent deuterium-tritium (DT) burn in high-gain ICF targets. A significant DT-burn fraction is a necessary condition for high energy gain and large neutron yields (>100MJ). Using classical molecular-dynamics (MD) simulations and a hybrid fluid-kinetic model, we examine how a large fraction of low-energy 𝛼 particles can kick D and T ions out of equilibrium in high-gain ICF targets. The MD results suggest that (1) temperatures of 𝑇 𝐷 and 𝑇 𝑇 can differ by as much as ∼20% of their mean temperature and (2) the deviation of the DT energy distribution from the Maxwell-Boltzmann function can exceed ∼30%. Some of these MD observations, such as the preferential heating of D ions by low-energy 𝛼 particles and the temperature separation, can be explained by a proposed hybrid fluid-kinetic model. Furthermore, the implication of such nonequilibrium effects on the DT reactivity is also discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Mechanistic study of chemical looping reactions between solid carbon fuels and CuO

Copper (Cu) based chemical-looping combustion (CLC) is a promising process that utilizes solid carbon fuel such as coal and biomass. Understanding the reaction kinetics in this process can facilitate the industrial design of CLC units. Here, in this work, molecular dynamics (MD) simulations were performed to investigate the reaction kinetics of n-butane and two simplified solid carbon fuels (lignite and anthracite) with/without copper oxide (CuO) nanoparticle. In addition, experiments were conducted on the thermal characteristics, flammability, and flame speeds of CuO and solid carbon mixtures. For n-butane, oxidation on the CuO surface is the primary reaction since the activation energy of the surface reaction is much lower than that of oxygen (O 2 ) combustion (9.2 vs. 53.3 kcal/mol). On the other hand, for lignite, there is a smaller difference in the activation energy of O 2 combustion and surface reaction (23.04 vs. 6.34 kcal/mol). We hypothesize that some solid carbon fuels can have different reaction kinetics dependent upon temperature. This is proven by the case of a simplified anthracite coal: an Arrhenius plot shows that this solid carbon fuel has two different reaction kinetic regimes and the critical temperature for the change in kinetics is related to the oxygen uncoupling of the CuO nanoparticle. Like the modeling simulations, a change in activation energy is observed in the experimental results, where desorption of molecular oxygen from CuO becomes important.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗