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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 289 records · Page 16
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 OSTI2020

Re-evaluation of the TSL for Yttrium Hydride

Yttrium hydride (YH x ) is of interest as a high-temperature moderator material in advanced nuclear reactor systems because of its superior ability to retain hydrogen at elevated temperatures. Thermal neutron scattering laws (TSL) for hydrogen bound in yttrium hydride (H-YH 2 ) and yttrium bound in yttrium hydride (Y-YH 2 ) were previously evaluated by Naval Nuclear Laboratory using the ab initio approach and released in ENDF/B-VIII.0. In that work, density functional theory, incorporating the generalized gradient approximation (GGA) for the exchange-correlation energy, was used to simulate the face-centered cubic structure of YH 2 and calculate the interatomic Hellmann-Feynman forces for a 2×2×2 supercell containing 96 atoms. Lattice dynamics calculations using PHONON were used to determine the phonon density of states. The calculated phonon density of states for H and Y in YH 2 were then used to prepare H-YH 2 and Y-YH 2 TSL evaluations, in the incoherent approximation, using the LEAPR module of NJOY. In addition, elastic scattering was assumed to be incoherent for both H and Y. While the incoherent elastic scattering approximation is appropriate for H-YH 2 , it introduces an undesirable approximation for Y-YH 2 . In this work, we re-evaluate the TSL for Y-YH 2 using FLASSH (Full Law Analysis Scattering System Hub). Y-YH 2 is evaluated using the FLASSH generalized coherent elastic scattering capability in order to capture the Bragg peaks associated with the YH 2 crystal structure which were neglected in the prior NJOY-based evaluation due to limitations in LEAPR. An experimental approach to validate the Y-YH 2 TSL using neutron transmission measurements is discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Three-state harmonic models for photoinduced charge transfer

A widely used strategy for simulating the charge transfer between donor and acceptor electronic states in an all-atom anharmonic condensedphase system is based on invoking linear response theory to describe the system in terms of an effective spin-boson model Hamiltonian. Extending this strategy to photoinduced charge transfer processes requires also taking into consideration the ground electronic state in addition to the excited donor and acceptor electronic states. In this paper, we revisit the problem of describing such nonequilibrium processes in terms of an effective three-state harmonic model. We do so within the framework of nonequilibrium Fermi’s golden rule (NE-FGR) in the context of photoinduced charge transfer in the carotenoid–porphyrin–C 60 (CPC 60 ) molecular triad dissolved in explicit tetrahydrofuran (THF). To this end, we consider different ways for obtaining a three-state harmonic model from the equilibrium autocorrelation functions of the donor–acceptor, donor–ground, and acceptor–ground energy gaps, as obtained from all-atom molecular dynamics simulations of the CPC 60 /THF system. The quantum-mechanically exact time-dependent NE-FGR rate coefficients for two different charge transfer processes in two different triad conformations are then calculated using the effective three-state model Hamiltonians as well as a hierarchy of more approximate expressions that lead to the instantaneous Marcus theory limit. Our results show that the photoinduced charge transfer in CPC 60 /THF can be described accurately by the effective harmonic three-state models and that nuclear quantum effects are small in this system.

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

Low Repetition-Rate, High-Resolution Femtosecond Transmission Electron Microscopy

Spatial and energy resolutions of state-of-the-art transmission electron microscopes (TEMs) have surpassed 50 pm and 5 meV. However, with respect to the time domain, even the fastest detectors combined with the brightest sources may only be able to reach the microsecond timescale. Thus, conventional methods are incapable of resolving myriad fundamental ultrafast (i.e., attosecond to picosecond) atomic-scale dynamics. The successful demonstration of femtosecond (fs) laser-based (LB) ultrafast transmission electron microscopy (UEM) nearly 20 years ago provided a means to span this nearly 10-order-of-magnitude temporal gap. While nanometer-picosecond UEM studies of dynamics are now well established, ultrafast Å-scale imaging has gone largely unrealized. Further, while instrument development has rightly been an emphasis, and while new modalities and uses of pulsed-beam TEM continue to emerge, the overall chemical and materials application space has been only modestly explored to date. In this Perspectives article, we argue that these apparent shortfalls can be attributed to a simple lack of data and detail. We speculate that present work and continued growth of the field will ultimately lead to the realization that Å-scale fs dynamics can indeed be imaged with minimally modified UEM instrumentation and with repetition rates (f rep ) below - and perhaps even well below - 1 MHz. We further argue that use of low f rep , whether for LB UEM or for chopped/bunched beams, significantly expands the accessible application space. Furthermore, this calls for systematically establishing modality-specific limits so that especially promising technologies can be pursued, thus ultimately facilitating broader adoption as individual instrument capabilities expand.

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

Effects of interlayer spacing and applied pressure on the lanthanide transport in MoS 2 -based two-dimensional channels

Rare-earth elements (REEs) are critical to modern industry but difficult to separate due to their subtle and monotonic changes in physicochemical properties. MoS 2 -based two-dimensional (2D) materials offer novel opportunities for enhancing REE separation, exhibiting a distinct volcano-shaped transport performance distribution that peaks at Sm 3+ . However, the specific contributions of thermodynamic and kinetic factors to ion transport within 2D confinement remain unclear. In this study, we conducted a series of non-equilibrium all-atom molecular dynamics (MD) simulations to explore the effects of interlayer spacing and external pressure on the transport of lanthanide ions in Å-scale acetate functionalized 2D MoS 2 (MoS 2 -COOH) channels. We examined ion entry and permeation rates, water flux, dehydration, and binding modes. The simulation results reveal that the transport trends of lanthanide ions are jointly driven by the dehydration degree and the relative-binding strengths of ions to water and to the acetate within the 2D channels. Notably, the dehydration pattern of lanthanide ions during permeation is closely linked to kinetic factors. Overall, this study provides a detailed atomistic understanding of the mechanisms underlying lanthanide ion transport under confinement. These findings point to the significant potential for tuning confinement and chemical functionalization within Å-scale channels for more efficient REE separation.

2D channels↗
DOE OSTI2021

Electron choreography at the attosecond time scale

Abstract In this work, we report on coherent control of electron dynamics in atoms via attosecond pulse-shaping. We show that the photoelectron emission from argon gas produced by absorption of an attosecond pulse train (APT) made of odd and even harmonics can be manipulated along the direction of polarization of the light by tuning the spectral components (amplitude and phase) of the pulse. In addition, we show that APTs produced with a two-color (400- plus 800 nm) femtosecond driving field exhibit high temporal tunability, which is optimized for an intensity ratio between the two colors in the range of 0.1 to 5%.

74 ATOMIC AND MOLECULAR PHYSICS↗
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 OSTI2025

Attosecond Optical Orientation

Circularly polarized light offers opportunities to probe symmetry-dependent properties of matter such as chirality and spin. Circular-dichroic measurements typically require further intrinsic or extrinsic breaking of symmetry by, e.g., enantiomeric excess, orientation, magnetic fields, or direction-sensitive detectors. Here we introduce circular-dichroic attosecond transient absorption spectroscopy by leveraging the angular momentum of two circularly polarized pulses, both pump and probe, in an isotropic medium, optically orienting the angular momentum of excited states on an attosecond timescale. We investigate a circular-dichroic measurement of the attosecond transient absorption of He Rydberg states. By limiting the allowed pathways via dipole selection rules for co- and counterrotating circularly polarized near-infrared and extreme ultraviolet (XUV) pulses, different spectral reshapings of the XUV transient absorption due to the AC Stark effect are observed. Furthermore, paired with time-dependent Schrödinger equation calculations, the results show the role of selection and propensity rules and open up new opportunities to study coupling pathways of excited states as well as spin-dependent dynamics in atoms and beyond via attosecond optical orientation.

Angular momentum of light↗
DOE OSTI2020

Local self-motion of water through the Van Hove function

Here, we show that the self-part of the Van Hove Function the correlation function describing the dynamics of a single molecule of water can be determined through a high-resolution inelastic X-ray scattering experiment. The measurement of inelastic X-ray scattering up to 10 Å -1 makes it possible to convert the inelastic X-ray scattering spectra into the Van Hove function, and its self-part is extracted from the short-range correlations. The diffusivity estimated from the short-range dynamics of water molecules is different from the long-range diffusivity measured by other methods. This approach using the experimentally determined self-part of the Van Hove function will be useful to the study of the local dynamics of atoms and molecules in liquids.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Potential of Attosecond Coherent Diffractive Imaging

Attosecond science has been transforming our understanding of electron dynamics in atoms, molecules, and solids. However, to date almost all of the attoscience experiments have been based on spectroscopic measurements because attosecond pulses have intrinsically very broad spectra due to the uncertainty principle and are incompatible with conventional imaging systems. In this paper we report an important advance towards achieving attosecond coherent diffractive imaging. Using simulated attosecond pulses, we simultaneously reconstruct the spectrum, 17 probes, and 17 spectral images of extended objects from a set of ptychographic diffraction patterns. We further confirm the principle and feasibility of this method by successfully performing a ptychographic coherent diffractive imaging experiment using a light-emitting diode with a broad spectrum. We believe this work clears the way to an unexplored domain of attosecond imaging science, which could have a far-reaching impact across different disciplines.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Dynamics of Density Fluctuations in Atomic Nuclei

We study the spatiotemporal patterns of density fluctuations in 16,24O and 48Ca using nuclear interactions from chiral effective field theory and the time-dependent coupled-cluster method. We find that two-particle–two-hole excitations generate small-amplitude fluctuations that are fast, short-ranged, and of stochastic character.

Bonaiti, Francesca [ORNL] (ORCID:0000000239261609)↗
DOE OSTI2024

X-ray-induced piezoresponse during X-ray photon correlation spectroscopy of PbMg 1/3 Nb 2/3 O 3

X-ray photon correlation spectroscopy (XPCS) holds strong promise for observing atomic-scale dynamics in materials, both at equilibrium and during non-equilibrium transitions. Here an in situ XPCS study of the relaxor ferroelectric PbMg 1/3 Nb 2/3 O 3 (PMN) is reported. A weak applied AC electric field generates strong response in the speckle of the diffuse scattering from the polar nanodomains, which is captured using the two-time correlation function. Correlated motions of the Bragg peak are also observed, which indicate dynamic tilting of the illuminated volume. This tilting quantitatively accounts for the observed two-time speckle correlations. The magnitude of the tilting would not be expected solely from the modest applied field, since PMN is an electrostrictive material with no linear strain response to the field. A model is developed based on non-uniform static charging of the illuminated surface spot by the incident micrometre-scale X-ray beam and the electrostrictive material response to the combination of static and dynamic fields. The model qualitatively explains the direction and magnitude of the observed tilting, and predicts that X-ray-induced piezoresponse could be an important factor in correctly interpreting results from XPCS and nanodiffraction studies of other insulating materials under applied AC field or varying X-ray illumination.

36 MATERIALS SCIENCE↗
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 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↗