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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication

Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with viral genome replication. Here in this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can initially bind in a comparatively stabilized state to the viral RdRp active site, as it primarily forms base stacking with the template uracil nucleotide (nt +1), which under freely fluctuations supports a low free energy barrier of the RDV-TP insertion (~1.5 kcal mol -1 ). In comparison, the corresponding natural substrate ATP binds initially to the RdRp active site in Watson–Crick base pairing with the template nt, and inserts into the active site with a medium low free energy barrier (~2.6 kcal mol -1 ), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be specifically stabilized by motif C-S759, S682 (near motif B) with the base, and motif G-K500 with the template backbone. Although the RDV-TP insertion can be hindered by motif F-R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif A-D623, respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Molecular engineering of fluoroether electrolytes for lithium metal batteries

Fluoroether solvents are promising electrolyte candidates for high-energy-density lithium metal batteries, where high ionic conductivity and oxidative stability are important metrics for design of new systems. Recent experiments have shown that these performance metrics, particularly stability, can be tuned by changing the fraction of ether and fluorine content. However, little is known about how different molecular architectures influence the underlying ion transport mechanisms and conductivity. Here, we use all-atom molecular dynamics simulations to elucidate the ion transport and solvation characteristics of fluoroether chains of varying length, and having different ether segment and fluorine terminal group contents. The design rules that emerge from this effort are that solvent size determines lithium-ion transport kinetics, solvation structure, and solvation energy. In particular, the mechanism for lithium-ion transport is found to shift from ion hopping between solvation sites located in different fluoroether chains in short-chain solvents, to ion–solvent co-diffusion in long-chain solvents, indicating that an optimum exists for molecules of intermediate length, where hopping is possible but solvent diffusion is fast. Consistent with these findings, our experimental measurements reveal a non-monotonic behavior of the effects of solvent size on lithium-ion conductivity, with a maximum occurring for medium-length solvent chains. Finally, a key design principle for achieving high ionic conductivity is that a trade-off is required between relying on shorter fluoroether chains having high self-diffusivity, and relying on longer chains that increase the stability of local solvation shells.

25 ENERGY STORAGE↗
DOE OSTI2023

Activation of atomic transport via vibrational coupling-induced force fluctuations

Vibrational coupling, although well-explored in many fields, has seldom been investigated in the context of mass transport. In this Letter, we examine the impact of vibrational coupling on atomic transport using simple molecular dynamics simulations. Our study shows that the atomic transport can be activated when the natural frequency of the atomic slit is close to the natural frequency of the atom being transported. We uncover the presence of fluctuating forces induced by vibrational coupling with higher amplitudes observed when the coupling is strong. We show that the transport activation mechanism is due to the high force fluctuations that arise during strong vibrational coupling allowing the atom to temporarily surpass the transport barrier of the slit. Our findings will serve as a foundation for the continued examination of vibrational coupling in the realm of mass transport.

Physics↗
DOE OSTI2025

Molecular understanding of ion transport in a zwitterionic electrolyte

Zwitterions (ZIs) are unique molecules that carry both positive and negative charges, resulting in overall charge neutrality and high dielectric constants. These distinctive properties have enabled broad applications of zwitterionic functionality, including the emerging use of ZIs in lithium-ion battery electrolytes. As a contribution to this developing field, we use all-atom molecular dynamics simulations to investigate the ion transport mechanisms in amorphous mixtures of a zwitterionic liquid containing a range of LiTFSI salt concentrations. Furthermore, the local coordination environment around the Li + ions plays a strong role in governing ionic conductivity, as well as the enhancement of Li + transport numbers with increasing salt concentration. Addition of small amounts of water leads to increased conductivity and ion mobilities due to the water coordinating with the Li + ions, which reduces direct interactions with larger charged species.

Classical molecular dynamic simulations↗
DOE OSTI2022

Bivalent recognition of fatty acyl-CoA by a human integral membrane palmitoyltransferase

S-acylation, also known as palmitoylation, is the most abundant form of protein lipidation in humans. This reversible posttranslational modification, which targets thousands of proteins, is catalyzed by 23 members of the DHHC family of integral membrane enzymes. DHHC enzymes use fatty acyl-CoA as the ubiquitous fatty acyl donor and become autoacylated at a catalytic cysteine; this intermediate subsequently transfers the fatty acyl group to a cysteine in the target protein. Protein S-acylation intersects with almost all areas of human physiology, and several DHHC enzymes are considered as possible therapeutic targets against diseases such as cancer. These efforts would greatly benefit from a detailed understanding of the molecular basis for this crucial enzymatic reaction. Here, in this study, we combine X-ray crystallography with all-atom molecular dynamics simulations to elucidate the structure of the precatalytic complex of human DHHC20 in complex with palmitoyl CoA. The resulting structure reveals that the fatty acyl chain inserts into a hydrophobic pocket within the transmembrane spanning region of the protein, whereas the CoA headgroup is recognized by the cytosolic domain through polar and ionic interactions. Biochemical experiments corroborate the predictions from our structural model. We show, using both computational and experimental analyses, that palmitoyl CoA acts as a bivalent ligand where the interaction of the DHHC enzyme with both the fatty acyl chain and the CoA headgroup is important for catalytic chemistry to proceed. This bivalency explains how, in the presence of high concentrations of free CoA under physiological conditions, DHHC enzymes can efficiently use palmitoyl CoA as a substrate for autoacylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Preface to the JPCM special issue on intense radiation sources in condensed matter and materials physics

This special issue is designed to honour the contributions of our colleague Neville Greaves who was among the first to apply newly-available synchrotron x-ray techniques to study the synthesis, structures and properties of advanced materials [1, 2]. His wide ranging work on ceramics, glasses and nanomaterials was celebrated in a recent issue of the J. Non-Cryst. Solids [3]. Neville's contributions to synchrotron research, highlighted here, focussed on design and construction of new beamline capabilities and sample environments to probe materials under different physical and chemical conditions, integrating various techniques to obtain complementary data on structure and bonding. The innovative nature of his work is illustrated by his studies of liquids and glasses, where he incorporated aerodynamic levitation into these experimental techniques, using both synchrotron x-ray and neutron beams to probe the structural transformations and dynamics combined with molecular dynamics simulations to study atomic scale organisation. His work has had a major impact on fundamental condensed matter physics and chemistry as well as applied materials science; and in this issue, we present contributions from colleagues using and developing new experimental techniques at current and next-generation synchrotron, neutron and free-electron laser sources and in their own laboratories, that probe the fundamental physics, chemistry and functional properties of novel materials and processes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Learning to classify quantum phases of matter with a few measurements

We study the identification of quantum phases of matter, at zero temperature, when only part of the phase diagram is known in advance. Following a supervised learning approach, we show how to use our previous knowledge to construct an observable capable of classifying the phase even in the unknown region. By using a combination of classical and quantum techniques, such as tensor networks, kernel methods, generalization bounds, quantum algorithms, and shadow estimators, we show that, in some cases, the certification of new ground states can be obtained with a polynomial number of measurements. An important application of our findings is the classification of the phases of matter obtained in quantum simulators, e.g. cold atom experiments, capable of efficiently preparing ground states of complex many-particle systems and applying simple measurements, e.g. single qubit measurements, but unable to perform a universal set of gates.

quantum machine learning↗
DOE OSTI2022

Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.

Okoto, Patience S.↗
DOE OSTI2024

Unexpected Observation of Disorder and Multiple Phase-Transition Pathways in Shock-Compressed Zr

The response of materials under dynamic compression involves a complex interplay of various deformation mechanisms aimed at relieving shear stresses, yielding a remarkable diversity in material behavior. Here, in this Letter, we utilize femtosecond x-ray diffraction coupled with nanosecond laser compression to reveal an intricate competition between multiple shear-relieving mechanisms within an elemental metal. Our observations in shocked-compressed single-crystal Zr indicate a disorder-mediated shear relaxation at lower pressures. Above the phase-transition pressure, we observe the increasing contribution of structural phase transition in relieving shear stress. We detect not one but three concurrent pathways during the transition from the hcp to a hex-3 structure. These complex dynamics are partially corroborated through multimillion-atom molecular dynamics simulations employing a machine-learned interatomic potential. Our observation of multiple concurrent pathways and disorder during shock compression underscore the far greater intricacies in the dynamic response of metals than previously assumed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

How Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets

The emergence and rapid worldwide spread of the novel coronavirus disease, COVID-19, has prompted concerted efforts to find successful treatments. The causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), uses its spike (S) protein to gain entry into host cells. Therefore, the S protein presents a viable target to develop a directed therapy. Here, we deployed an integrated artificial intelligence with all-atom molecular dynamics simulation approach to provide new details of the S protein structure. Based on a comprehensive structural analysis of S proteins from SARS-CoV-2 and previous human coronaviruses, we found that the protomer state of S proteins is structurally flexible. Without the presence of a stabilizing beta sheet from another protomer chain, two regions in the S2 domain and the hinge connecting the S1 and S2 subunits lose their secondary structures. Interestingly, the region in the S2 domain was previously identified as an immunodominant site in the SARS-CoV-1 S protein. We anticipate that the molecular details elucidated here will assist in effective therapeutic development for COVID-19.

Chen, Serena↗
DOE OSTI2026

Stellarator Design Exploration Using Symbolic-Regression Neutronics Surrogates

Systems codes require fast, simplified models to rapidly evaluate fusion power plant concepts, but neutronics analyses are often a computational bottleneck. Here, to address this, surrogate models for key neutronics responses have been developed using 3-D neutronics-ready models built with the open-source code ParaStell from a database of stellarator equilibria. Neutronics responses such as tritium breeding ratio (TBR), nuclear heating, and neutron-induced radiation damage displacements per atom (dpa) were simulated using OpenMC. Through sensitivity analysis and symbolic regression (SR), simple power-law formulas were derived connecting these neutronics responses to global stellarator parameters, including fusion power, plasma surface area, and plasma elongation. Validation shows these formulas can predict the simulation results with low error, enabling quick and accurate assessment of neutronics requirements in stellarator design exploration activities with systems codes.

Modeling↗
DOE OSTI2024

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Residing in the 5' untranslated region of the mRNA, the 2'-deoxyguanosine (2'-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2'-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg 2+ ). We have quantitatively explored the combined effect of ligand (2'-dG) and Mg 2+ binding on the energy landscape of the aptamer domain of the 2'-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg 2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg 2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2'-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg 2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg 2+ and ligand also facilitate a more compact structure in the three-way junction region.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Two-photon Rydberg EIT resonances in non-collinear beam configurations

We study the modifications of Rydberg EIT resonances in non-collinear geometry in which the two required optical fields cross at a small non-zero angle. We observe a strong broadening and amplitude reduction even for small angles when compared to exact counter-propagating and co-propagating collinear geometries. We confirm that such EIT peak deterioration results from the additional Doppler broadening due to the transverse velocity distribution of atoms. The numerical simulation closely matches the experimental measurements. While a non-collinear geometry provides improved spatial resolution for Rydberg EIT electrometry, we conclude that the crossing angle must be small to maintain field sensitivity.

Su, Kevin↗
DOE OSTI2021

Pathways and Mechanism of Caffeine Binding to Human Adenosine A 2A Receptor

Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the pathways and mechanism of CFF binding to the target receptors remain unclear. In this study, we have performed all-atom-enhanced sampling simulations using a robust Gaussian-accelerated molecular dynamics (GaMD) method to elucidate the binding mechanism of CFF to human adenosine A 2A receptor (A 2A AR). Multiple 500–1,000 ns GaMD simulations captured both binding and dissociation of CFF in the A 2A AR. The GaMD-predicted binding poses of CFF were highly consistent with the x-ray crystal conformations with a characteristic hydrogen bond formed between CFF and residue N6.55 in the receptor. In addition, a low-energy intermediate binding conformation was revealed for CFF at the receptor extracellular mouth between ECL2 and TM1. While the ligand-binding pathways of the A 2A AR were found similar to those of other class A GPCRs identified from previous studies, the ECL2 with high sequence divergence serves as an attractive target site for designing allosteric modulators as selective drugs of the A 2A AR.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2021

Evolution of Thyroglobulin Loop Kinetics in EpCAM

Epithelial cell-activating molecule (EpCAM) is an important cancer biomarker and therapeutic target given its elevated expression in epithelial cancers. EpCAM is a type I transmembrane protein that forms cis-dimers along the thyroglobulin type-1A-like domain (TYD) in the extracellular region. The thyroglobulin loop (TY loop) within the TYD is structurally dynamic in the monomer state of human EpCAM, binding reversibly to a TYD site. However, it is not known if this flexibility is prevalent across different species. Here, we conduct over 17 μs of all-atom molecular dynamics simulations to study EpCAM TY loop kinetics of five different species, including human, mouse, chicken, frog, and fish. We find that the TY loop remains dynamic across evolution. In addition to the TYD binding site, we discover a second binding site for the TY loop in the C-terminal domain (CTD). Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms. Whereas fish TY loop has comparable binding for both TYD and CTD sites, the TY loops of other species preferably bind the TYD site. A hybrid construct of fish EpCAM with human TY loop restores the TYD binding preference, suggesting robust effects of the TY loop sequence on its dynamic behavior. Our findings provide insights into the structural dynamics of EpCAM and its implication in physiological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Chapter 21. Atomic-Level Dislocation Dynamics in Irradiated Metals

Primary damage and microstructure evolution in structural nuclear materials operating under conditions of a high flux of energetic atomic particles and high temperature and stress lead to the formation of a high concentration, non-homogeneous distribution of defect clusters in the form of dislocation loops, voids, gas-filled bubbles and radiation-induced precipitates of nanometer scale. They cause changes in many material properties. Being obstacles to dislocation glide, they strongly affect the mechanical properties, with an increase in yield and flow stresses and a reduction in ductility. Atomic-scale computer simulations can provide details of how these effects are influenced by the obstacle structure, applied stress, strain rate and temperature. Processes such as obstacle cutting, transformation, absorption and drag are observed. Some recent results for body-centered and face-centered cubic metals are described in this review and, where appropriate, comparisons are drawn with predictions based on the elasticity theory of crystal defects. Perspectives on how to use this information at higher scales and in particular in mesoscale, dislocation dynamics simulations are also discussed.

Osetskiy, Yury N.↗