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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 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Molecular Simulations Probing the Adsorption and Diffusion of Ammonia, Nitrogen, Hydrogen, and Their Mixtures in Bulk MFI Zeolite and MFI Nanosheets at High Temperature and Pressure

Recent advances in the synthesis of MFI zeolite nanosheets have led to highly selective membranes that are promising candidates for small-scale ammonia separation from ammonia/nitrogen/hydrogen mixtures in distributed green ammonia production plants. Using force-field-based molecular simulations, we evaluate the performance of bulk all-silica MFI zeolite and a 3 nm thick all-silica MFI nanosheet for ammonia/nitrogen/hydrogen separations at moderate temperature and pressure conditions (T = 373 K, p = 5 bar) as well as conditions relevant for a membrane-based reactor–separator process (T = 523 or 623 K, p = 80 bar). Isobaric–isothermal Gibbs ensemble Monte Carlo (GEMC) simulations were carried out to understand the selective adsorption behavior for these mixtures. Molecular dynamics simulations in the canonical ensemble were performed to examine the transport behavior of ammonia in a mixture with nitrogen or hydrogen at loadings obtained from the GEMC simulations. Our results show that both bulk MFI and the nanosheet with explicit surface silanols are highly selective toward ammonia adsorption, but the adsorption selectivity decreases by factors of 4 and 10 for ammonia/nitrogen and ammonia/hydrogen mixtures as the temperature is increased from 373 to 623 K. Conversely, the diffusion selectivities toward ammonia are more favorable at process-relevant temperatures and for the MFI nanosheet. Here, at T = 523 K and p = 80 bar, our simulations predict overall separation factors of 3.8 ± 0.2 and 4.5 ± 0.3 for ammonia/nitrogen and ammonia/hydrogen mixtures, respectively, in the bulk MFI zeolite, and separation factors of 8.6 ± 0.4 and 12.5 ± 0.8, respectively, for the MFI nanosheet.

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

Quantum fluctuations in dense plasma simulations

Molecular dynamics (MD) simulations are a powerful tool for modeling warm and hot dense matter. Density functional theory (DFT) MD simulations are often preferred in dense plasmas in order to accurately model quantum electronic structure. However, DFT-MD simulations neglect interaction effects due to fluctuations in excited states. In this work, we present an MD approach that uses excited state method pseudoatoms to run dense plasma simulations with many different core-electron configurations at classical MD speeds. We also allow for transitions between different configurations in our simulations and find that these fluctuations are especially important for highly excited states. Our results suggest that finite configuration lifetimes that are comparable to the inverse ion plasma frequency need to be accounted for in order to accurately model ion distributions in dense plasma simulations. We also demonstrate that excited state fluctuations have a direct impact on ion plasma microfields, generate different plasma microfields for different excitation levels, and thereby induce absorption–emission line shape asymmetries even in steady-state plasmas.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The importance of long-timescale simulations for driven systems: An example of He bubble growth at a W GB

Accelerated Molecular Dynamics (AMD) is used to study complex systems under realistic conditions by extending the timescales accessible by Molecular Dynamics. However, some studies rely instead on driving atomic systems harder with higher temperature, faster growth, etc. Here, we study He bubble growth at a W grain boundary as an illustration of harnessing AMD methods to avoid consequences of over-driving the system. The growth mechanisms observed for a He bubble grown under realistic conditions are compared to bubbles-grown orders of magnitude faster, at rates typical of conventional molecular dynamics simulations. We find that progressive growth mechanisms and bubble structures depend on the rate at which the bubble is grown providing further evidence that care must be taken when simulating the dynamics of driven systems such as this one.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Quantum Simulation of Molecular Dynamics Processes─A Benchmark Study Using a Classical Simulator and Present-Day Quantum Hardware

Here, we explore how the fundamental problems in quantum molecular dynamics can be modeled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes propagation of a free wave packet, vibration of a harmonic oscillator, and tunneling through a barrier. Each of these problems starts with the initial wave packet setup. Although Qiskit provides a general method for initializing wave functions, in most cases it generates deep quantum circuits. While these circuits perform well on noiseless simulators, they suffer from excessive noise on quantum hardware. To overcome this issue, we designed a shallower quantum circuit for preparing a Gaussian-like initial wave packet, which improves the performance of real hardware. Next, quantum circuits are implemented to apply the kinetic and potential energy operators for the evolution of a wave function over time. The results of our modeling on classical emulators of quantum hardware agree perfectly with the results obtained using the traditional (classical) methods. This serves as a benchmark and demonstrates that the quantum algorithms and Qiskit codes we developed are accurate. However, the results obtained on the actual quantum hardware available today, such as IBM’s superconducting qubits and IonQ’s trapped ions, indicate large discrepancies due to hardware limitations. This work highlights both the potential and challenges of using quantum computers to solve fundamental quantum molecular dynamics problems.

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

Granular Flow

LIGGGHTS-INL is a capability-extended version of LIGGGHTS. LIGGGHTS is an Open Source Discrete Element Method Particle Simulation Software (https://www.cfdem.com/media/DEM/docu/Manual.html). LIGGGHTS stands for LAMMPS improved for general granular and granular heat transfer simulations. LAMMPS is a classical molecular dynamics simulator. It is widely used in the field of Molecular Dynamics (https://lammps.sandia.gov/doc/Manual.html). Thanks to physical and algorithmic analogies, LAMMPS is a very good platform for DEM simulations. LAMMPS offers a GRANULAR package to perform these kinds of simulations. LIGGGHTS aims to improve those capability with the goal to apply it to industrial applications.

Xia, Yidong↗
DOE OSTI2020

Conformation and dynamics of ring polymers under symmetric thin film confinement

Understanding the structure and dynamics of polymers under confinement has been of widespread interest, and one class of polymers that have received comparatively little attention under confinement is that of ring polymers. The properties of non-concatenated ring polymers can also be important in biological fields because ring polymers have been proven to be a good model to study DNA organization in the cell nucleus. From our previous study, linear polymers in a cylindrically confined polymer melt were found to segregate from each other as a result of the strong correlation hole effect that is enhanced by the confining surfaces. By comparison, our subsequent study of linear polymers in confined thin films at similar levels of confinements found only the onset of segregation. Here, we use molecular dynamics simulation to investigate the chain conformations and dynamics of ring polymers under planar (1D) confinement as a function of film thickness. Our results show that conformations of ring polymers are similar to the linear polymers under planar confinement, except that ring polymers are less compressed in the direction normal to the walls. While we find that the correlation hole effect is enhanced under confinement, it is not as pronounced as the linear polymers under 2D confinement. Finally, we show that chain dynamics far above Tg are primarily affected by the friction from walls based on the monomeric friction coefficient we get from the Rouse mode analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Mechanism of DNA origami folding elucidated by mesoscopic simulations

Abstract Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Dynamics modeling of molten salt reactor with reduced and expanded representations of delayed neutron precursors

Molten salt reactors (MSRs) present unique challenges in dynamic behavior due to the mobility of their fuel. In these reactors, delayed neutron precursors (DNPs) drift with the fuel circulation through the primary loop. As a result, a fraction of DNPs decays outside the core, effectively reducing the available delayed neutron population for reactivity control. Consequently, precise modeling of the distribution and behavior of DNPs is critical for accurate reactor dynamics simulations. In this study, the System Dynamics Analysis Tool (SDAT) was used to simulate a thermal-spectrum MSR under steady-state conditions and following transients. The effects of using reduced and expanded representations of DNPs with fewer or more groups than the conventional 6-group model were investigated. Their impact on the simulated distribution of precursors in the primary loop, reactivity loss value, and reactor response to transients was analyzed. Simulation results showed that reduced models lead to the loss of the actual DNPs distribution data, resulting in less accurate estimates of reactivity loss. Reactor power predictions using these reduced models showed significant deviations compared to those using the conventional 6-group model in transient simulations. Expanded models offered a more accurate representation of the distribution of DNPs and reactivity loss estimates. Reactor power predictions using expanded models showed minimal deviation from the conventional 6-group model during the simulated transients.

analysis↗
DOE OSTI2022

Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering

Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, in this study, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ~20–50 cm –1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2

Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic’s evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (M pro ), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. Here, this work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic “warhead” to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of M pro with micromolar affinities (K I of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Abstract Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli , AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Microstructural impacts on ionic conductivity of oxide solid electrolytes from a combined atomistic-mesoscale approach

Abstract Although multiple oxide-based solid electrolyte materials with intrinsically high ionic conductivities have emerged, practical processing and synthesis routes introduce grain boundaries and other interfaces that can perturb primary conduction channels. To directly probe these effects, we demonstrate an efficient and general mesoscopic computational method capable of predicting effective ionic conductivity through a complex polycrystalline oxide-based solid electrolyte microstructure without relying on simplified equivalent circuit description. We parameterize the framework for Li 7- x La 3 Zr 2 O 12 (LLZO) garnet solid electrolyte by combining synthetic microstructures from phase-field simulations with diffusivities from molecular dynamics simulations of ordered and disordered systems. Systematically designed simulations reveal an interdependence between atomistic and mesoscopic microstructural impacts on the effective ionic conductivity of polycrystalline LLZO, quantified by newly defined metrics that characterize the complex ionic transport mechanism. Our results provide fundamental understanding of the physical origins of the reported variability in ionic conductivities based on an extensive analysis of literature data, while simultaneously outlining practical design guidance for achieving desired ionic transport properties based on conditions for which sensitivity to microstructural features is highest. Additional implications of our results are discussed, including a possible connection between ion conduction behavior and dendrite formation.

25 ENERGY STORAGE↗
DOE OSTI2021

Vascular K ATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides

Vascular tone is dependent on smooth muscle K ATP channels comprising pore-forming Kir6.1 and regulatory SUR2B subunits, in which mutations cause Cantú syndrome. Unique among K ATP isoforms, they lack spontaneous activity and require Mg-nucleotides for activation. Structural mechanisms underlying these properties are unknown. Here, we determined cryogenic electron microscopy structures of vascular K ATP channels bound to inhibitory ATP and glibenclamide, which differ informatively from similarly determined pancreatic K ATP channel isoform (Kir6.2/SUR1). Unlike SUR1, SUR2B subunits adopt distinct rotational “propeller” and “quatrefoil” geometries surrounding their Kir6.1 core. The glutamate/aspartate-rich linker connecting the two halves of the SUR-ABC core is observed in a quatrefoil-like conformation. Molecular dynamics simulations reveal MgADP-dependent dynamic tripartite interactions between this linker, SUR2B, and Kir6.1. The structures captured implicate a progression of intermediate states between MgADP-free inactivated, and MgADP-bound activated conformations wherein the glutamate/aspartate-rich linker participates as mobile autoinhibitory domain, suggesting a conformational pathway toward K ATP channel activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Two-dimensional coherent spectrum of high-spin models via a quantum computing approach

Here in this work we present and benchmark a quantum computing approach to calculate the two-dimensional coherent spectrum (2DCS) of high-spin models. Our approach is based on simulating their real-time dynamics in the presence of several magnetic field pulses, which are spaced in time. We utilize the adaptive variational quantum dynamics simulation algorithm for the study due to its compact circuits, which enables simulations over sufficiently long times to achieve the required resolution in frequency space. Specifically, we consider an antiferromagnetic quantum spin model that incorporates Dzyaloshinskii-Moriya interactions and single-ion anisotropy. The obtained 2DCS spectra exhibit distinct peaks at multiples of the magnon frequency, arising from transitions between different eigenstates of the unperturbed Hamiltonian. By comparing the one-dimensional coherent spectrum with 2DCS, we demonstrate that 2DCS provides a higher resolution of the energy spectrum. We further investigate how the quantum resources scale with the magnitude of the spin using two different binary encodings of the high-spin operators: the standard binary encoding and the Gray code. At low magnetic fields both encodings require comparable quantum resources, but at larger field strengths the Gray code is advantageous. Numerical simulations for spin models with increasing number of sites indicate a polynomial system-size scaling for quantum resources. Lastly, we compare the numerical 2DCS with experimental results on a rare-earth orthoferrite system. The observed strength of the magnonic high-harmonic generation signals in the 2DCS of the quantum high-spin model aligns well with the experimental data, showing significant improvement over the corresponding mean-field results.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

High-fidelity, hyper-accurate, and evolved mutants rewire atomic-level communication in CRISPR-Cas9

The high-fidelity (HF1), hyper-accurate (Hypa), and evolved (Evo) variants of the CRISPR-associated protein 9 (Cas9) endonuclease are critical tools to mitigate off-target effects in the application of CRISPR-Cas9 technology. The mechanisms by which mutations in recognition subdomain 3 (Rec3) mediate specificity in these variants are poorly understood. Here, solution nuclear magnetic resonance and molecular dynamics simulations establish the structural and dynamic effects of high-specificity mutations in Rec3, and how they propagate the allosteric signal of Cas9. We reveal conserved structural changes and dynamic differences at regions of Rec3 that interface with the RNA:DNA hybrid, transducing chemical signals from Rec3 to the catalytic His-Asn-His (HNH) domain. The variants remodel the communication sourcing from the Rec3 α helix 37, previously shown to sense target DNA complementarity, either directly or allosterically. This mechanism increases communication between the DNA mismatch recognition helix and the HNH active site, shedding light on the structure and dynamics underlying Cas9 specificity and providing insight for future engineering principles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Imaging Wavepackets in Real-Space & Disentangling Ultrafast Solvation Dynamics with High-Energy Ultrafast X-ray Scattering

The microscopic information of solute and solute-solvent motions can be measured using ultrafast diffuse x-ray scattering, and compared to molecular dynamics simulations, as demonstrated in studies of solvated molecular systems done in X-ray free-electron lasers. However, for the typical photon energies used in these experiments, the photon momentum transfer range was limited to lower Q values where the signals arising from different parts of the studied system overlap significantly. Recently, this limitation was greatly alleviated by extending the photon energy at the Linac Coherent Light-Source (LCLS), significantly increasing the accessible momentum transfer range. This improvement is transformative for ultrafast diffuse x-ray scattering measurements, enabling for the first time to disentangle the solute scattering difference signal, that persists to higher Q values, from the bulk solvent and solute-solvent cross-terms difference signals. In addition, it enhances the prediction ability of modeling and simulation methods such as the hybrid QM/MM approach. The extended Q range also opens the way to resolve in real-space details regarding coherent wavepackets motions beyond their center-of-mass positions. Here, we present the first results on high-energy (18keV) diffuse x-ray scattering in solution, demonstrating high fidelity time-resolved scattering and analysis of the photoexcited model photocatalysts PtPOP ([Pt2(POP)4]4-), and IrDimen ([Ir2(dimen)4]2+) in several solvents. These complexes provide ideal systems for demonstrating the ability of high-Q ultrafast scattering and QM/MM simulations to decompose ultrafast solvation dynamics into specific changes in the solute-solvent pair distribution function with a particular focus on how electronically excited states change the interaction between the solvent and photo-catalytically active metal sites. We introduce an approach to further utilize the high-energy capability and demonstrate a single-shot ultra-wide-angle X-ray Scattering modality using two perpendicular detectors, spanning a scattering angle range of more than 100 degrees, allowing to extend the accessible momentum transfer range up to Q~14 Å-1. We develop a model-free method to invert the x-ray scattering signals and enable the recovery of multiple pair-density motions that happen simultaneously, allowing us to directly measure in real-space nuclear wavepacket motions. . [1] Natan, Adi. "Real-Space Inversion and Super-Resolution of Ultrafast X-ray Scattering using Natural Scattering Kernels." arXiv preprint arXiv:2107.05576 (2021)

Natan, Adi↗
DOE OSTI2022

Provably accurate simulation of gauge theories and bosonic systems

Quantum many-body systems involving bosonic modes or gauge fields have infinite-dimensional local Hilbert spaces which must be truncated to perform simulations of real-time dynamics on classical or quantum computers. To analyze the truncation error, we develop methods for bounding the rate of growth of local quantum numbers such as the occupation number of a mode at a lattice site, or the electric field at a lattice link. Our approach applies to various models of bosons interacting with spins or fermions, and also to both abelian and non-abelian gauge theories. We show that if states in these models are truncated by imposing an upper limit Λ on each local quantum number, and if the initial state has low local quantum numbers, then an error at most ϵ can be achieved by choosing Λ to scale polylogarithmically with ϵ − 1 , an exponential improvement over previous bounds based on energy conservation. For the Hubbard-Holstein model, we numerically compute a bound on Λ that achieves accuracy ϵ , obtaining significantly improved estimates in various parameter regimes. We also establish a criterion for truncating the Hamiltonian with a provable guarantee on the accuracy of time evolution. Building on that result, we formulate quantum algorithms for dynamical simulation of lattice gauge theories and of models with bosonic modes; the gate complexity depends almost linearly on spacetime volume in the former case, and almost quadratically on time in the latter case. We establish a lower bound showing that there are systems involving bosons for which this quadratic scaling with time cannot be improved. By applying our result on the truncation error in time evolution, we also prove that spectrally isolated energy eigenstates can be approximated with accuracy ϵ by truncating local quantum numbers at Λ = polylog ( ϵ − 1 ) .

Tong, Yu↗
DOE OSTI2024

Increasing thermostability of the key photorespiratory enzyme glycerate 3‐kinase by structure‐based recombination

As global temperatures rise, improving crop yields will require enhancing the thermotolerance of crops. One approach for improving thermotolerance is using bioengineering to increase the thermostability of enzymes catalysing essential biological processes. Photorespiration is an essential recycling process in plants that is integral to photosynthesis and crop growth. The enzymes of photorespiration are targets for enhancing plant thermotolerance as this pathway limits carbon fixation at elevated temperatures. We explored the effects of temperature on the activity of the photorespiratory enzyme glycerate kinase (GLYK) from various organisms and the homologue from the thermophilic alga Cyanidioschyzon merolae was more thermotolerant than those from mesophilic plants, including Arabidopsis thaliana. To understand enzyme features underlying the thermotolerance of C. merolae GLYK (CmGLYK), we performed molecular dynamics simulations using AlphaFold-predicted structures, which revealed greater movement of loop regions of mesophilic plant GLYKs at higher temperatures compared to CmGLYK. Based on these simulations, hybrid proteins were produced and analysed. These hybrid enzymes contained loop regions from CmGLYK replacing the most mobile corresponding loops of AtGLYK. Two of these hybrid enzymes had enhanced thermostability, with melting temperatures increased by 6 °C. One hybrid with three grafted loops maintained higher activity at elevated temperatures. Whilst this hybrid enzyme exhibited enhanced thermostability and a similar Km for ATP compared to AtGLYK, its Km for glycerate increased threefold. This study demonstrates that molecular dynamics simulation-guided structure-based recombination offers a promising strategy for enhancing the thermostability of other plant enzymes with possible application to increasing the thermotolerance of plants under warming climates.

59 BASIC BIOLOGICAL SCIENCES↗