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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
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

Coupling of Flavonoid Initiation Sites with Monolignols Studied by Density Functional Theory

Lignin recalcitrance presents a challenge for the development of a bioeconomy that employs lignocellulosic feedstocks. The efficiency of lignin deconstruction is improved by a reduction of molecular weight, and given the discovery that flavones serve as initiation sites in lignin biosynthesis, these molecular weight reductions could potentially be achieved with plant metabolic engineering to over-express flavonoids. Upon increasing the flavonoid content in lignin, the bond strengths and properties of flavonoid-monolignol linkages become increasingly important. To that end, the current work applies density functional theory calculations to elucidate the bond dissociation enthalpies (BDEs) of flavonoid-monolignol linkages, including dimers with oxidized monolignols. Specifically, the dimer bond strengths and monomer hydrogen abstraction energies for the flavonoids tricin, chrysoeriol, luteolin, apigenin, catechin, epicatechin, epigallocatechin, and epigallocatechin gallate are calculated, when coupled to seven natural and engineered monolignols. Results indicate that 4'-O-ß linkage strengths between flavonoids and monolignols are of comparable strength to inter-monolignol ß-O-4 linkages, with average flavonoid-monolignol BDEs of 70.7 kcal/mol relative to ~69.3 kcal/mol in analogous canonical monolignols. Epigallocatechin yielded the lowest 4'-O-ß bond strength of 52.3 kcal/mol when coupled to an oxidized monolignol, while the flavones overall produced lower average BDEs, relative to the flavanols. Substituents at the 3'-C and 5'-C positions on flavonoids affected the dimer linkage strengths to a greater extent than glycosylation or substituents further from the linkage. Erythro and threo stereochemistry across the flavonoid-monolignol linkage library exhibited only small energetic differences and no pronounced correlations. Taken together, the predictions from this work support the concept that higher concentrations of flavonoid initiation sites in lignin may afford linkage properties conducive to more facile lignin depolymerization.

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

Tricyclononenes and tricyclononadienes as efficient monomers for controlled ROMP: understanding structure–propagation rate relationships and enabling facile post-polymerization modification

Grubbs 3rd-generation (G3) pre-catalyst-initiated ring-opening metathesis polymerization (ROMP) remains an indispensable tool in the polymer chemist's toolbox. Tricyclononenes (TCN) and tricyclononadienes (TCND) represent under-explored classes of monomers for ROMP that have the potential to both advance fundamental knowledge (e.g., structure-polymerization kinetics relationships) and serve as practical tools for the polymer chemist (e.g., post-polymerization functionalization). In this work, a library of TCN and TCND imides, monoesters, and diesters, along with their exo-norbornene counterparts, were synthesized to compare their behaviors in G3-initiated ROMP. Real-time 1 H NMR was used to study their polymerization kinetics; propagation rates ( k p ) were extracted for each monomer. To understand the relationships between monomer structure and ROMP propagation rates, density functional theory methods were used to calculate a variety of electronic and steric parameters for each monomer. While electronic parameters (e.g., HOMO energy levels) correlated positively with the measured k p values, steric parameters generally gave improved correlations, which indicates that monomer size and shape are better predictors for k p than electronic parameters for this data set. Furthermore, the TCND diester—which contains an electron-deficient cyclobutene that is resistant to ROMP—and its polymer p(TCND) are shown to be highly reactive toward DBU-catalyzed conjugate addition reactions with thiols, providing a protecting- and activating-group free strategy for post-polymerization modification.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A split luciferase system for studying coronavirus Mpro dimerization in vitro and in living cells

The main protease enzyme (Mpro) of coronaviruses cleaves the viral polyprotein into functional units essential for virus replication. Prior work has demonstrated that Mpro functions as a homodimer. However, studies on the mechanism of dimerization have been challenging because the purified protease is mostly dimeric, dimerization-defective mutants lack proteolytic activity, and robust cell-based assays have yet to be reported. To enable work on Mpro dimerization, we have developed a quantitative luciferase-based SARS-CoV-2 (SARS2) Mpro biosensor that accurately reports protein dimerization in living cells and, upon purification, also in vitro. Co-transfection of cells with a construct expressing Mpro fused to the 18 kDa LargeBiT of luciferase (LgBiT) and a second construct with Mpro fused to the 1 kDa SmallBiT of luciferase (SmBiT) results in a reconstitution of luciferase activity in a dose-dependent manner that requires conserved residues within the dimerization interface. Proteolytic activity is dispensable for dimerization and, uniquely, a C145A catalytically inactive mutant exhibits enhanced dimerization signal likely due to lower cytotoxicity. Mpro enzymes from multiple different coronaviruses also dimerize in this system, indicating mechanistic conservation. Interestingly, this dimerization biosensor also provides a quantitative read-out of inhibitor-facilitated dimerization. Covalent SARS2 Mpro inhibitors such as nirmatrelvir cause a 3- to 5-fold increase in luciferase activity. Together with corroborating structural, biophysical, and molecular dynamics experiments, our studies support a model in which covalent Mpro inhibitors such as nirmatrelvir simultaneously block catalytic activity and induce allosteric stabilization of the dimeric complex.

SARS-CoV-2 main protease (Mpro/3CLpro)↗
DOE OSTI2020

Optimization of Energy Flow through Synthetic Metabolic Modules and Regulatory Networks in a Model Photosynthetic Eukaryotic Microbe

Photosynthetic organisms have recently gained considerable attention for a role in development of renewable energy sources. Genome-enabled systems biology methods, coupled with functional and synthetic genomics, present opportunities to develop sustainable and economical applications such as fuel production within the next 10 to 15 years. However, optimization of light-driven metabolism for biomass or biofuel production will require a detailed systems biology understanding of photosynthetic processes and cellular metabolism. Genome-scale metabolic models (GEMs) are at the core of systems analysis of cellular processes and form a common organizational framework for analyses of data resulting from functional genomics experimental work and computational studies. Therefore, there is a clear demand for high quality photosynthetic model organisms and the appropriate computational tools that enable systems analysis of light-driven metabolism. Through research conducted we expanded the currently available repertoire of photosynthetic GEMs to include the commercially valuable model diatom Phaeoctylum tricornutum. Diatoms have a peculiar and distinct evolutionary footprint and represent a major eukaryotic lineage that is taxonomically and functionally distinct from green and red algae and vascular plants. Therefore, the true potential for light-driven metabolism aimed at biofuel production remains poorly understood at a systems level for a large subset of the global diversity of photosynthetic organisms. The metabolic capabilities of P. tricornutum were comparatively modeled with those from other photosynthetic groups in order to elucidate the occurrence of metabolic traits within and between phototrophs. Additionally, this research resulted in significant extension of the COnstraints Based Reconstruction and Analysis (COBRA) Toolbox to accommodate the crucial need for infrastructure required for ‘omics data integration and analysis in the context of genome-scale models. Therefore, the proposed research achieved two important goals. First, within the broad scope of photosynthetic organisms, we functionally compared and, as a result, identified cellular processes that require optimization in order to enable deployment as biofuel feedstock. Second, the proposed research resulted in development of key computational infrastructure, which can be further extended to other biological systems, that is currently lacking but necessary for multiple ‘omics data integration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Multipartite entanglement in the one-dimensional spin- 1 2 Heisenberg antiferromagnet

Multipartite entanglement refers to the simultaneous entanglement between multiple subsystems of a many-body quantum system. While multipartite entanglement can be difficult to quantify analytically, it is known that it can be witnessed through the quantum Fisher information (QFI), a quantity that can also be related to dynamical Kubo response functions. In this work, we first show that the finite temperature QFI can generally be expressed in terms of a static structure factor of the system, plus a correction that vanishes as T→0. This implies that the static structure factor witnesses multipartite entanglement near quantum critical points at temperatures below a characteristic energy scale of the system. Therefore, in systems with a known static structure factor, we can deduce finite temperature scaling of multipartite entanglement and low temperature entanglement depth without knowledge of the full dynamical response function of the system. This is particularly useful to study 1D quantum critical systems in which sub-power-law divergences can dominate entanglement growth, where the conventional scaling theory of the QFI breaks down. Furthermore, the 1D spin- 1 2 antiferromagnetic Heisenberg model is an important example of such a system, and we show that multipartite entanglement in the Heisenberg chain diverges nontrivially as ~ln(1/T) 3/2 . We verify these predictions with calculations of the QFI using conformal field theory and matrix product state simulations. Finally, we discuss the implications of our results for experiments to probe entanglement in quantum materials, comparing to neutron scattering data in KCuF 3 , a material well described by the Heisenberg chain.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Coal polymer composites prepared by fused deposition modeling (FDM) 3D printing

Coal is a vital energy resource worldwide, but pollutants and greenhouse gases from its combustion cause environmental problems. To explore the non-combustion approach to use and valorize coal, anthracite and lignite were blended with polyamide 12 (PA 12) through FDM printing in this work and compared in the composites. By adding lignite, Young’s modulus improved with increasing loading to 50 wt% while tensile strength leveled off among the composites, compared to that of PA 12. By contrast, the addition of anthracite decreased the tensile performance at all loadings. Rheology tests and morphology analyses suggested that the interactions between fillers (anthracite and lignite) and PA 12 may cause differences in tensile properties. In addition, the printed lignite composites showed improved thermal conductivity (~ twofold), indicating lignite demonstrates the potential to build functional composites. This work provides a strategy to use lignite in composites by 3D printing for value-added products and reduces the demand for petroleum-based polymers. Overall, our approach diverts lignite from combustion processes and alleviates the negative impact of lignite use on the environment.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Emergence of topological and trivial interface states in VSe 2 films coupled to Bi 2 Se 3

Coupling ordinary metals with topological Bi 2 Se 3 can instigate the long-range migration of the spin-polarized Dirac states. Instead, for trivial metallic VSe 2 films on Bi 2 Se 3 , topological and trivial Rashba-type interface states emerge, each strongly localized at the VSe 2 /Bi 2 Se 3 interface. Their rapidly decaying spectral weights are uncovered by thickness-dependent band mappings of VSe 2 films and replicated by a phenomenological first-principles model of the spectral function. In this work, the results are pertinent to spintronic devices requiring spin transmission across metal/topological insulator interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2024

On the practical usefulness of the Hardware Efficient Ansatz

Variational Quantum Algorithms (VQAs) and Quantum Machine Learning (QML) models train a parametrized quantum circuit to solve a given learning task. The success of these algorithms greatly hinges on appropriately choosing an ansatz for the quantum circuit. Perhaps one of the most famous ansatzes is the one-dimensional layered Hardware Efficient Ansatz (HEA), which seeks to minimize the effect of hardware noise by using native gates and connectives. The use of this HEA has generated a certain ambivalence arising from the fact that while it suffers from barren plateaus at long depths, it can also avoid them at shallow ones. In this work, we attempt to determine whether one should, or should not, use a HEA. We rigorously identify scenarios where shallow HEAs should likely be avoided (e.g., VQA or QML tasks with data satisfying a volume law of entanglement). More importantly, we identify a Goldilocks scenario where shallow HEAs could achieve a quantum speedup: QML tasks with data satisfying an area law of entanglement. We provide examples for such scenario (such as Gaussian diagonal ensemble random Hamiltonian discrimination), and we show that in these cases a shallow HEA is always trainable and that there exists an anti-concentration of loss function values. Our work highlights the crucial role that input states play in the trainability of a parametrized quantum circuit, a phenomenon that is verified in our numerics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

The impacts of charge transfer, localization, and metallicity on hydrogen retention and transport capacity

Solid state hydrides such as early transition metal hydrides are of inestimable importance for the future of hydrogen energy and are actively being investigated for energy conversion and storage applications such as fuel cells, solid-state batteries and neutron moderators. The retention and transport behavior of hydrogen in these hydrides has a huge role on the extended performance of components. While early transition-metal-based compounds exhibit many peculiar properties due to their unique correlated electronic signatures arising from -orbital electrons, the fundamental chemistry and transport behavior of hydrogen in such hydrides is not well understood. In the present work, using density functional theory, a highly intricate bonding feature is revealed through the theoretical investigation of the electronic structure of early transition metal hydrides YH 2 and ZrH 2 . In particular, a pronounced charge transfer from the transition element to H, results in localized electron densities at deep energy levels. The interplay between intrinsic charge transfer, charge localization, and metallicity in YH 2 and ZrH 2 leads to strong chemical bonding between metal and hydrogen atoms and large energy barriers for the migration of hydrogen vacancies. Specifically, hydrogen vacancies are found to be stable in the neutral state due to electron screening effects, accompanied by substantially high migration barriers between 0.8–1.2 eV along different crystallographic directions. In contrast, recent literature shows the migration barrier for charged H vacancies in insulating s-block metal hydrides lie between 0.1–0.4 eV, which is suitable for fast conduction applications. This pivotal electron structure difference exploited between early transition metal hydrides and alkali/alkaline earth metal hydrides determines extended hydrogen retention in these early transition metal hydrides. Finally, this work explains fundamental differences between the electronic structure of s-block and d-block metal hydrides, and its impact on the mobility of hydrogen vacancies.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

3D spherical functional expansion tallies in Serpent 2 Monte Carlo code

This work extends the application of functional expansion tallies to 3D spherical geometries. The 3D Zernike polynomials are set as an orthonormal polynomials basis for the functional reconstruction. The study describes the construction of the complete set of polynomials, a natural expansion of the spherical harmonics polynomials where 3D Zernike moments can be evaluated as a linear combination of the geometrical moments. The 3D Zernike polynomials formulation and the computational approach implemented in Serpent 2 are presented and tested through the Godiva model from the ICSBEP criticality benchmark test cases. The implementation results are in agreement with a reference solution described in a fine-resolution mesh, enhancing also the performance and memory demand. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Density-related properties from self-interaction corrected density functional theory calculations

The Perdew–Zunger self-interaction correction (PZ-SIC) removes unphysical electron self-interaction from calculations employing standard density functional approximations. Doing so improves many computed properties, bringing them into better agreement with experimental observations or with results from high-level quantum chemistry calculations. However, while PZ-SIC generally corrects in the right direction relative to the corresponding reference values, in many cases, it over-corrects. For this reason, scaled-down versions of PZ-SIC have been proposed and investigated. These approaches have mostly employed exterior scaling in which SIC correction terms are scaled in the same way at every point in space. Recently, a new local, or interior, scaling SIC method was proposed on non-empirical grounds to restore a property of the exact, but unknown, density functional that is broken in PZ-SIC. Here, the scaling at each point depends on the character of the charge density at that point. However, the local scaling can be done in various ways while still restoring the behavior of the exact functional. In this work, we compare and contrast the performance of various interior scaling approaches for addressing over-corrections of calculated molecular dipole moments and atomic polarizabilities and properties that reflect the nature of the electronic charge density.

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

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

Abstract Background Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the Na V 1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations in SCN1A are associated with epilepsy, including Dravet syndrome (DS). The majority of DS patients harbor coding mutations causing SCN1A haploinsufficiency; however, putative causal non-coding promoter mutations have been identified. Methods To determine the functional role of one of these potentially redundant Scn1a promoters, we focused on the non-coding Scn1a 1b regulatory region, previously described as a non-canonical alternative transcriptional start site. We generated a transgenic mouse line with deletion of the extended evolutionarily conserved 1b non-coding interval and characterized changes in gene and protein expression, and assessed seizure activity and alterations in behavior. Results Mice harboring a deletion of the 1b non-coding interval exhibited surprisingly severe reductions of Scn1a and Na V 1.1 expression throughout the brain. This was accompanied by electroencephalographic and thermal-evoked seizures, and behavioral deficits. Conclusions This work contributes to functional dissection of the regulatory wiring of a major epilepsy risk gene, SCN1A . We identified the 1b region as a critical disease-relevant regulatory element and provide evidence that non-canonical and seemingly redundant promoters can have essential function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Leveraging Actinide Hydrolysis Chemistry for Targeted Th and U Separations using Amidoxime-Functionalized Poly(HIPE)s

Polymerized high internal phase emulsions (poly(HIPE)s) are porous polymer monoliths whose synthesis can easily be tailored to allow incorporation of functional units. In this work, nitrile containing poly(HIPE)s have been prepared with either acrylonitrile (AN) or 4-cyanostyrene (4CS) comonomers. Post-synthetic modification of these nitrile-containing poly(HIPE)s yields their corresponding amidoximated analogues, which were studied for actinide uptake. These amidoxime-functionalized, porous polymers were shown to adsorb 95 % Th4+ species from aqueous solution within 30 minutes. In contrast to other amidoxime containing polymers the uptake of UO22+ in these poly(HIPE)s is lower under similar conditions. A critical analysis of actinide separations and high-energy X-ray scattering data provides insight into the polymers’ selectivity, enabled by the uptake of multinuclear Th clusters.

actinides↗
DOE OSTI2020

Reconfigurable Pinwheel Artificial-Spin-Ice and Superconductor Hybrid Device

The ability to control the potential landscape in a medium of interacting particles could lead to intriguing collective behavior and innovative functionalities. In this work, we utilize spatially reconfigurable magnetic potentials of a pinwheel artificial-spin-ice (ASI) structure to tailor the motion of superconducting vortices. The reconstituted chain structures of the magnetic charges in the pinwheel ASI and the strong interaction between magnetic charges and superconducting vortices allow significant modification of the transport properties of the underlying superconducting thin film, resulting in a reprogrammable resistance state that enables a reversible and switchable vortex Hall effect. Our results highlight an effective and simple method of using ASI as an in situ reconfigurable nanoscale energy landscape to design reprogrammable superconducting electronics, which could also be applied to the in situ control of properties and functionalities in other magnetic particle systems, such as magnetic skyrmions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Bifacial_Radiance v0.4.2 [SWR-18-03]

The bifacial_radiance software contains a series of Python wrapper functions to make working with RADIANCE easier, particularly for the PV researcher interested in bifacial PV performance. For more information, check out our documentation, Tutorials in the form of Jupyter Notebooks, or refer to our Wiki and Issues page. Installation https://youtu.be/4A9GocfHKyM This video shows how to install the bifacial_radiance software and all associated software needed. More info on the Wiki. Instructions are also shown below. For detailed instructions of how to install bifacial_radiance, you can also refer to the installation guide. A GUI has been added in version 3.0. The GUI reads/writes all input parameters necessary to run a simulation, and runs the specified simulation by calling the correct functions with the specified parameters. So no need to use a journal or a script! But you still need to install following the procedure below.

Deline, Chris↗
DOE OSTI2023

Complex defect chemistry of hydrothermally-synthesized Nb-substituted β$'$-LiVOPO 4

Lithium vanadyl phosphate (LiVOPO 4 ) is a next-generation multielectron battery cathode that can intercalate up to two Li-ions per V-ion through the redox couples of V 4+ /V 3+ and V 5+ /V 4+ . However, its rate capacity is undermined by the sluggish Li-ion diffusion in the high-voltage region (4 V for V 5+ /V 4+ redox). Nb substitution was used to expand the crystal lattice to facilitate Li-ion diffusion. Here, in this work, Nb substitution was achieved via hydrothermal synthesis, which resulted in a new, lower symmetry β'-LiVOPO 4 phase with preferential Nb occupation of one of the two V sites. This phase presents complex defect chemistries, including cation vacancies and hydrogen interstitials, characterized by a combination of X-ray and neutron diffraction, elemental and thermogravimetric analyses, X-ray absorption spectroscopy, and magnetic susceptibility measurements. The Nb-substituted samples demonstrated improved capacity retention and rate capabilities in the high-voltage region, albeit an enlarged voltage hysteresis related to a partial V 4+ /V 3+ redox reaction, as evidenced by ex situ X-ray absorption spectroscopy and pair distribution function analysis. This work highlights the importance of understanding the complex defect chemistry and its consequence on electrochemistry in polyanionic intercalation compounds.

36 MATERIALS SCIENCE↗