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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 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Many paths, similar destinations: viruses and bacterial microcompartments form polyhedra inside cells

A large number of biological entities assemble into icosahedral structures, and these are ubiquitous throughout nature. Examples include eukaryotic and prokaryotic viral capsids and more recently discovered bacterial microcompartments. Viral capsids and bacterial microcompartments are both composed of pentameric and hexameric subunits; however, they differ in the type of cargo they encapsulate: nucleic acid or protein. Also, both depart from strict icosahedral symmetry: while this is less common in viruses, among bacterial microcompartments, diverse and heterogeneous polyhedra are common. We review shared principles and key distinctions between the self-directed assembly of various icosahedral architectures and their polyhedral variants in nature and explore the concept that there are multiple paths, influenced by their cargo, to arriving at similar protein cage morphologies.

bacterial microcompartments↗
DOE OSTI2024

Nitrogen–Rich Conjugated Macrocycles: Synthesis, Conductivity, and Application in Electrochemical CO 2 Capture

Here we report a series of nitrogen-rich conjugated macrocycles that mimic the structure and function of semiconducting 2D metal–organic and covalent organic frameworks while providing greater solution processability and surface tunability. Using a new tetraaminotriphenylene building block that is compatible with both coordination chemistry and dynamic covalent chemistry reactions, we have synthesized two distinct macrocyclic cores containing Ni–N and phenazine-based linkages, respectively. The fully conjugated macrocycle cores support strong interlayer stacking and accessible nanochannels. For the metal–organic macrocycles, good out-of-plane charge transport is preserved, with pressed pellet conductivities of 10 –3 S/cm for the nickel variants. Lastly, using electrochemically mediated CO2 capture as an example, we illustrate how colloidal phenazine-based organic macrocycles improve electrical contact and active site electrochemical accessibility relative to bulk covalent organic framework powders. Together, these results highlight how simple macrocycles can enable new synthetic directions as well as new applications by combining the properties of crystalline porous frameworks, the processability of nanomaterials, and the precision of molecular synthesis.

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

Vapor–liquid equilibrium of water with the MB-pol many-body potential

Among the many existing molecular models of water, the MB-pol many-body potential has emerged as a remarkably accurate model, capable of reproducing thermodynamic, structural, and dynamic properties across water's solid, liquid, and vapor phases. In this work, we assessed the performance of MB-pol with respect to an important set of properties related to vapor-liquid coexistence and interfacial behavior. Through direct coexistence classical molecular dynamics simulations at temperatures of 400 K < T < 600 K, we calculated properties such as equilibrium coexistence densities, vapor-liquid interfacial tension, vapor pressure, and enthalpy of vaporization and compared the MB-pol results to experimental data. We also compared rigid vs fully flexible variants of the MB-pol model and evaluated system size effects for the properties studied. We found that the MB-pol model predictions are in good agreement with experimental data, even for temperatures approaching the vapor-liquid critical point; this agreement was largely insensitive to system sizes or the rigid vs flexible treatment of the intramolecular degrees of freedom. Furthermore, these results attest to the chemical accuracy of MB-pol and its high degree of transferability, thus enabling MB-pol's application across a large swath of water's phase diagram.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Characterizing Sub-Cohorts via Data Normalization and Representation Learning

The process of identifying a cohort of interest is a very challenging task. It requires manually inspecting many patient records of complex structure that might include medical coding errors and missing data. This paper presents a computational pipeline for refining the process of cohort selection based on medical concepts recorded in the electronic health records (EHRs). The pipeline extracts EHR data for a given cohort and normalizes this data using standard vocabularies. Then a stacked denoising autoencoder is used to embed the normalized patient vectors in a low dimensional space, where the patients are subsequently clustered into sub-cohorts. The goal is to represent the cohort in a standard format and abstract variants of sub-populations. As a use-case, we applied the pipeline to 1.8 million Veterans diagnosed with major depressive disorder (MDD), and identified four meaningful sub-cohorts using the features learned by the autoencoder. Then, each sub-cohort was explored using a set of keywords for interpretation.

Rush III, Everett↗
DOE OSTI2025

Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin

Abstract The essential enzyme messenger RNA (mRNA) (guanine-N7) methyltransferase catalyzes S-adenosylmethionine (SAM)-dependent conversion of GpppRNA ends to the m7GpppRNA cap structure characteristic of eukaryal mRNAs. The antibiotic sinefungin (SFG) is a SAM analog in which the S-CH3 sulfonium moiety of SAM is replaced by a C-NH2 amine. Available evidence indicates that the antifungal activity of SFG is exerted via inhibition of fungal cap methyltransferase Abd1. Here we report that recombinant Kluyveromyces lactis and Saccharomyces cerevisiae Abd1 are 240-fold and 485-fold more sensitive to inhibition by SFG than by the reaction product S-adenosylhomocysteine (SAH). Crystal structures of K. lactis and S. cerevisiae Abd1 as binary complexes with SAH or SFG and ternary complexes with GTP•SFG highlight how SFG makes two hydrogen bonds from its C-NH2 amine to the guanine-O6 and -N7 atoms of GTP that account for its higher affinity vis-à-vis SAH and SAM. Through a genetic screen to isolate SFG-resistant S. cerevisiae strains, a conserved tyrosine (Tyr416) that interacts with the cap guanine in Abd1 was identified as a key determinant of SFG potency. Tyr416 Abd1 variants confer SFG resistance in vitro by weakening cap-assisted SFG interactions with Abd1. Our study illuminates the basis for the exquisite SFG sensitivity of fungal cap methyltransferases.

Biochemistry & Molecular Biology↗
DOE OSTI2024

An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations

Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M pro ) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 M pro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.

Westberg, Michael↗
DOE OSTI2024

Excited state electronic structure of dimethyl disulfide involved in photodissociation at ∼200 nm

Dimethyl disulfide (DMDS), one of the smallest organic molecules with an S–S bond, serves as a model system for understanding photofragmentation in polypeptides and proteins. Prior studies of DMDS photodissociation excited at ∼266 nm and ∼248 nm have elucidated the mechanisms of S–S and C–S bond cleavage, which involve the lowest excited electronic states S 1 and S 2 . Far less is known about the dissociation mechanisms and electronic structure of relevant excited states of DMDS excited at ∼200 nm. Herein we present calculations of the electronic structure and properties of electronic states S 1 –S 6 accessed when DMDS is excited at ∼200 nm. Our analysis includes a comparison of theoretical and experimental UV spectra, as well as theoretically predicted one-dimensional cuts through the singlet and triplet potential energy surfaces along the S–S and C–S bond dissociation coordinates. Finally, we present calculations of spin–orbit coupling constants at the Franck–Condon geometry to assess the likelihood of ultrafast intersystem crossing. We show that choosing an accurate yet computationally efficient electronic structure method for calculating the S 0 –S 6 potential energy surfaces along relevant dissociation coordinates is challenging due to excited states with doubly excited character and/or mixed Rydberg-valence character. Our findings demonstrate that the extended multi-state complete active space second-order perturbation theory (XMS-CASPT2) balances this computational efficiency and accuracy, as it captures both the Rydberg character of states in the Franck–Condon region and multiconfigurational character toward the bond-dissociation limits. In conclusion, we compare the performance of XMS-CASPT2 to a new variant of equation of motion coupled cluster theory with single, double, and perturbative triple corrections, EOM-CCSD(T)(a)*, finding that EOM-CCSD(T)(a)* significantly improves the treatment of doubly excited states compared to EOM-CCSD, but struggles to quantitatively capture asymptotic energies along bond dissociation coordinates for these states.

Rishi, Varun↗
DOE OSTI2025

An unusual Co–S bond links B 12 chaperones in an interprotein complex

Chaperones in trafficking pathways ensure specificity of transition metal loading and protection against adventitious side reactions. In B 12 , an essential cofactor for humans, a cobalt ion is coordinated to a >1.3 kDa tetrapyrrolic scaffold, posing logistical challenges for its translocation. In this study, we report the 3.4 Å crystal structure of the human MMACHC and MMADHC B 12 chaperones, tethered via a rarely seen covalent cobalt–sulfur bond. B 12 is bound in the base-off state to MMACHC, with Cys-261 on MMADHC serving as the upper axial ligand; the lower-axial position is vacant. The propensity of thiolato-cobalamin derivatives bound to MMACHC to undergo spontaneous decomposition via general acid catalysis or reduction/oxidation chemistry is averted in the interprotein complex with MMADHC. An exposed face in the complex suggests an exit route for B 12 . No known clinical variants localize to the interprotein interface, consistent with the cobalt–sulfur bond being key to forming the high-affinity complex.

Science & Technology - Other Topics↗
DOE OSTI2022

Data-driven Minimum Entropy Control for Stochastic Nonlinear Systems using the Cumulant-Generating Function

Here, we present a novel minimum entropy control algorithm for a class of stochastic nonlinear systems subjected to non-Gaussian noises. The entropy control can be considered as an optimization problem for the system randomness attenuation, but the mean value has to be considered separately. To overcome this disadvantage, a new representation of the system stochastic properties was given using the cumulant-generating function based on the moment-generating function, in which the mean value and the entropy was reflected by the shape of the cumulant-generating function. Based on the samples of the system output and control input, a time-variant linear model was identified, and the minimum entropy optimization was transformed to system stabilization. Then, an optimal control strategy was developed to achieve the randomness attenuation, and the boundedness of the controlled system output was analyzed. The effectiveness of the presented control algorithm was demonstrated by a numerical example. In this paper, a data-driven minimum entropy design is presented without pre-knowledge of the system model; entropy optimization is achieved by the system stabilization approach in which the stochastic distribution control and minimum entropy are unified using the same identified structure; and a potential framework is obtained since all the existing system stabilization methods can be adopted to achieve the minimum entropy objective.

42 ENGINEERING↗
DOE OSTI2021

Rational Enzyme Design for Controlled Functionalization of Acetylated Xylan for Cell-Free Polymer Biosynthesis

Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.

93 SC - Biological and Environmental Research (BER↗
DOE OSTI2022

Reduced order models for thermal radiative transfer problems based on moment equations and data-driven approximations of the Eddington tensor

Here a new group of structure and asymptotic preserving reduced-order models (ROMs) for multidimensional nonlinear thermal radiative transfer (TRT) problems is presented. They are formulated by means of the nonlinear projective approach and data compression techniques. The nonlinear projection is applied to the Boltzmann transport equation (BTE) to derive a hierarchy of low-order moment equations. Approximation of the Eddington tensor that provides exact closure for the system of moment equations is found with projection-based data-driven methodologies. These include the (i) proper orthogonal decomposition (POD), (ii) dynamic mode decomposition (DMD) and (iii) a variant of the DMD. A parameterization is derived for this ROM for the temperature of radiation incoming to the problem domain (the radiation drive temperature). This parameterization is informed from results of a dimensionless study of the TRT problem. Analysis of the ROMs is performed on the classical Fleck-Cummings TRT multigroup test problem in 2D geometry with a radiation-driven Marshak wave. Numerical results are presented to demonstrate the performance of these ROMs for the simulation of evolving radiation and heat waves. Results show these models to be sufficiently accurate for practical computations with rather low-rank representations of the Eddington tensor. As the rank of the approximation is increased, the errors of solutions generated by the ROMs gradually decreases.

42 ENGINEERING↗
DOE OSTI2020

Atomic structure and grain shape evolution of nanodiamond during annealing in oxidizing atmosphere from neutron diffraction and MD simulations

In this work, real space pair-distribution function (PDF) analysis in conjunction with molecular dynamics (MD) simulations was applied to characterize crystal structure, shape and surface structure of diamond nanoparticles annealed in air up to 880 °C. MD simulated models of individual nanodiamond particles of various shapes and sizes were used to calculate theoretical radial distribution functions G(r) for powders with different grain size distributions. The calculated curves, showing distinct differences for the explored parameter space, were compared to the experimental G(r) functions obtained from neutron scattering for annealed detonated nanodiamond samples in a search for a model best describing the actual powders. It was found that as-synthesized nanodiamond grains are terminated by equally abundant (100), (110) and (111) crystallographic faces and their structure does not change upon annealing in air up to 280 °C. The shape and size of grains annealed above 480 °C changes due to surface etching. The etching rate differs between crystals faces and depends on temperature, resulting in the observed differences in grain shape. Below 680 °C the share of the (110) facets gradually increases and at 680 °C the grains become rhombic dodecahedra terminated solely by (110) surfaces. Further increase of the annealing temperature promotes formation of (111) surfaces and at 880 °C the preferred grain shape becomes an octahedron terminated by a variant of (111) surfaces possessing three dangling sp3 bonds per atom. At lower temperatures all grains become smaller and the size distribution moves towards the lower values. Furthermore, as the annealing temperature increases, the smallest grains disappear entirely and the average grain size grows back.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Assessment of Measurement Uncertainties in the Jupiter High-240 Experiment

The Jupiter High-240 experiment performed in May of 2019 was previously discussed as a variant of the original Jupiter experiment incorporating plutonium metal alloy fuel plates with higher 240Pu content and lead plates, using both a reference configuration and a second configuration where eight lead plates were replaced with aluminum to simulate voiding. Measurements were recorded for experiment period, the “pressure” of the Comet ram upon closure for each near-critical measurement, and temperature. The experiment reactor period is the time it would take to increase the neutron population by a factor of e. For this experiment, the copper reflectors and upper third of the fuel sits upon a support structure with the lower fuel arrays raised up into the center of the reflectors using a ram (see Fig. 1). The recorded logbook temperature for each measurement corresponds to a resistance temperature detector (RTD) located at the top center of the upper fuel array. This paper summarizes the evaluated uncertainties for the Jupiter High 240 experiment as contributed via the recorded measurements and nuclear data and their assessed impact upon the computation of system reactivity and eigenvalue.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Microstructure Evolution of U–Zr System in A Thermal Cycling Neutron Diffraction Experiment: Extruded U–10Zr (wt. %)

Microstructure evolution of 1073 K extruded U–10Zr (wt. %) fuel during thermal cycling (303–1073 K with a ~9 hour hold at 873 K during cooling) was investigated using in situ neutron diffraction. Analysis was performed using Rietveld texture and crystal structure refinements from time–of–flight neutron diffraction data, with a focus on the evolution of textures and lattice parameters as a function of temperature. The α–U phase exhibits lattice contraction with increasing temperature along the b lattice direction and lattice expansion in the other directions while the other phases exhibit lattice expansion with temperature in all directions. Contrary to the established phase diagram, the β–U phase is absent at the temperatures of the thermal cycling. (001) α and (110) γ plane normals are observed with a strong preferred orientation along the extrusion direction. Finally, the variant selection of (001) α ||(110) γ is observed for the first time.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues

Drug resistance to front-line malarial treatments represents an ongoing threat to control malaria, a vector borne infectious disease. The malarial parasite, Plasmodium falciparum has developed genetic variants, conferring resistance to the current standard therapeutic artemisinin and its derivatives commonly referred to as artemisinin-combination therapies (ACTs). Emergence of multi-drug resistance parasite genotypes is a warning of potential treatment failure, reaffirming the urgent and critical need to find and validate alternate drug targets to prevent the spread of disease. An attractive and novel drug target includes glucose-regulated protein 78 kDa (GRP78, or BiP), an essential molecular chaperone protein involved in the unfolded protein response that is upregulated in ACT treated P. falciparum parasites. We have shown that both sequence and structure are closely related to human GRP78 (hGRP78), a chaperone belonging to the HSP70 class of ATPase proteins, which is often upregulated in cellular stress responses and cancer. By screening a library of nucleoside analogues, we identified eight ‘hit’ compounds binding at the active site of the ATP binding domain of P. falciparum GRP78 using a high-throughput ligand soaking screen using x-ray crystallography. These compounds were further evaluated using protein thermal shift assays to assess target binding activity. The nucleoside analogues identified from our screen provide a starting point for the development of more potent and selective antimalarial inhibitors. In addition, we have established a well-defined, high-throughput crystal-based screening approach that can be applied to many crystallizable P. falciparum proteins for generating anti-Plasmodium specific compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

DyFe 2 O 4 : A new trigonal rare-earth ferrite grown by molecular-beam epitaxy

Using epitaxial stabilization, we synthesized single-phase (001)-oriented thin films of DyFe 2 O 4+x on (111) MgAl 2 O 4 substrates by molecular-beam epitaxy. The metastable DyFe 2 O 4 polymorph formed is isostructural to known trigonal ferrimagnetic RFe 2 O 4 phases with space group $R\bar{3}m$, where R = Ho to Lu. The epitaxial DyFe 2 O 4 thin films have two in-plane orientation relationships: [100] DyFe 2 O 4 || [$2\bar{1}1$] MgAl 2 O 4 plus a twin variant related by a 60° in-plane rotation. DyFe 2 O 4 is not bulk stable and has never been synthesized before. Indeed, it has been predicted to be on the edge energetically of what may be possible to stabilize. The fact that the RFe 2 O 4 phase is stable for all elements leading up to dysprosium (Ho–Lu) leads us to believe that DyFe 2 O 4 could be a “remnant metastable phase,” one which, given the right thermodynamic conditions, could become the lowest free energy phase. We find that although we are able to get structurally very close to $R\bar{3}m$ DyFe 2 O 4 , the films are not stoichiometric as they have an increased c lattice parameter, indicative of extra oxygen as is sometimes seen in other RFe2O4 phases. The unintended surplus oxygen opens questions regarding what may be achievable using such tricks as epitaxial stabilization to access metastable phases and whether this indeed constitutes “remnant metastability.”

36 MATERIALS SCIENCE↗
DOE OSTI2022

SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Beta variant of concern (VOC) resists neutralization by major classes of antibodies from COVID-19 patients and vaccinated individuals. In this study, serum of Beta-infected patients revealed reduced cross-neutralization of wild-type virus. From these patients, we isolated Beta-specific and cross-reactive receptor-binding domain (RBD) antibodies. The Beta-specificity results from recruitment of VOC-specific clonotypes and accommodation of mutations present in Beta and Omicron into a major antibody class that is normally sensitive to these mutations. The Beta-elicited cross-reactive antibodies share genetic and structural features with wild type–elicited antibodies, including a public VH1-58 clonotype that targets the RBD ridge. These findings advance our understanding of the antibody response to SARS-CoV-2 shaped by antigenic drift, with implications for design of next-generation vaccines and therapeutics.

60 APPLIED LIFE SCIENCES↗