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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 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Population-based heteropolymer design to mimic protein mixtures

Biological fluids, the most complex blends, have compositions that constantly vary and cannot be molecularly defined. Despite these uncertainties, proteins fluctuate, fold, function and evolve as programmed. We propose that in addition to the known monomeric sequence requirements, protein sequences encode multi-pair interactions at the segmental level to navigate random encounters; synthetic heteropolymers capable of emulating such interactions can replicate how proteins behave in biological fluids individually and collectively. Here, we extracted the chemical characteristics and sequential arrangement along a protein chain at the segmental level from natural protein libraries and used the information to design heteropolymer ensembles as mixtures of disordered, partially folded and folded proteins. For each heteropolymer ensemble, the level of segmental similarity to that of natural proteins determines its ability to replicate many functions of biological fluids including assisting protein folding during translation, preserving the viability of fetal bovine serum without refrigeration, enhancing the thermal stability of proteins and behaving like synthetic cytosol under biologically relevant conditions. Molecular studies further translated protein sequence information at the segmental level into intermolecular interactions with a defined range, degree of diversity and temporal and spatial availability. This framework provides valuable guiding principles to synthetically realize protein properties, engineer bio/abiotic hybrid materials and, ultimately, realize matter-to-life transformations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Random heteropolymers as enzyme mimics

Despite successes in replicating the primary–secondary–tertiary structure hierarchy of protein, it remains elusive to synthetically materialize protein functions that are deeply rooted in their chemical, structural and dynamic heterogeneities. We propose that for polymers with backbone chemistries different from that of proteins, programming spatial and temporal projections of sidechains at the segmental level can be effective in replicating protein behaviours; and leveraging the rotational freedom of polymer can mitigate deficiencies in monomeric sequence specificity and achieve behaviour uniformity at the ensemble level. Here, guided by the active site analysis of about 1,300 metalloproteins, we design random heteropolymers (RHPs) as enzyme mimics based on one-pot synthesis. We introduce key monomers as the equivalents of the functional residues of protein and statistically modulate the chemical characteristics of key monomer-containing segments, such as segmental hydrophobicity. The resultant RHPs form pseudo-active sites that provide key monomers with protein-like microenvironments, co-localize substrates with catalytic or cofactor-binding sidechains and catalyse reactions such as oxidation and cyclization of citronellal with isopulegol/menthoglycol selectivity. This RHP design led to enzyme-like materials that can retain catalytic activity under non-biological conditions, are compatible with scalable processing and have expanded substrate scope, including environmentally long-lasting antibiotic tetracycline.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Binary vector copy number engineering improves Agrobacterium -mediated transformation

The copy number of a plasmid is linked to its functionality, yet there have been few attempts to optimize higher-copy-number mutants for use across diverse origins of replication in different hosts. We use a high-throughput growth-coupled selection assay and a directed evolution approach to rapidly identify origin of replication mutations that influence copy number and screen for mutants that improve Agrobacterium-mediated transformation (AMT) efficiency. By introducing these mutations into binary vectors within the plasmid backbone used for AMT, we observe improved transient transformation of Nicotiana benthamiana in four diverse tested origins (pVS1, RK2, pSa and BBR1). For the best-performing origin, pVS1, we isolate higher-copy-number variants that increase stable transformation efficiencies by 60–100% in Arabidopsis thaliana and 390% in the oleaginous yeast Rhodosporidium toruloides. Our work provides an easily deployable framework to generate plasmid copy number variants that will enable greater precision in prokaryotic genetic engineering, in addition to improving AMT efficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

AZD5582 plus SIV-specific antibodies reduce lymph node viral reservoirs in antiretroviral therapy-suppressed macaques

The main barrier to HIV cure is a persistent reservoir of latently infected CD4 + T cells harboring replication-competent provirus that fuels rebound viremia upon antiretroviral therapy (ART) interruption. A leading approach to target this reservoir involves agents that reactivate latent HIV proviruses followed by direct clearance of cells expressing induced viral antigens by immune effector cells and immunotherapeutics. We previously showed that AZD5582, an antagonist of inhibitor of apoptosis proteins and mimetic of the second mitochondrial-derived activator of caspases (IAPi/SMACm), induces systemic reversal of HIV/SIV latency but with no reduction in size of the viral reservoir. In this study, we investigated the effects of AZD5582 in combination with four SIV Env-specific Rhesus monoclonal antibodies (RhmAbs) ± N-803 (an IL-15 superagonist) in SIV-infected, ART-suppressed rhesus macaques. Here we confirm the efficacy of AZD5582 in inducing SIV reactivation, demonstrate enhancement of latency reversal when AZD5582 is used in combination with N-803 and show a reduction in total and replication-competent SIV-DNA in lymph-node-derived CD4 + T cells in macaques treated with AZD5582 + RhmAbs. Further exploration of this therapeutic approach may contribute to the goal of achieving an HIV cure.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Chromatin organization regulates viral egress dynamics

Various types of DNA viruses are known to elicit the formation of a large nuclear viral replication compartment and marginalization of the cell chromatin. We used three-dimensional soft x-ray tomography, confocal and electron microscopy, combined with numerical modelling of capsid diffusion to analyse the molecular organization of chromatin in herpes simplex virus 1 infection and its effect on the transport of progeny viral capsids to the nuclear envelope. Our data showed that the formation of the viral replication compartment at late infection resulted in the enrichment of heterochromatin in the nuclear periphery accompanied by the compaction of chromatin. Random walk modelling of herpes simplex virus 1–sized particles in a three-dimensional soft x-ray tomography reconstruction of an infected cell nucleus demonstrated that the peripheral, compacted chromatin restricts viral capsid diffusion, but due to interchromatin channels capsids are able to reach the nuclear envelope, the site of their nuclear egress.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Predicting structural material degradation in advanced nuclear reactors with ion irradiation

Swelling associated with the formation and growth of cavities is among the most damaging of radiation-induced degradation modes for structural materials in advanced nuclear reactor concepts. Ion irradiation has emerged as the only practical option to rapidly assess swelling in candidate materials. For decades, researchers have tried to simulate the harsh environment in a nuclear reactor in the laboratory at an accelerated rate. Here we present the first case in which swelling in a candidate alloy irradiated ~ 2 years in a nuclear reactor was replicated using dual ion irradiation in ~ 1 day with precise control over damage rate, helium injection rate, and temperature and utilize physical models to predict the effects of radiation in reactors. The capability to predict and replicate the complex processes surrounding cavity nucleation and growth across many decades of radiation dose rate highlights the potential of accelerated radiation damage experiments. More importantly, it demonstrates the capability to predict the swelling evolution and the possibility to predict other features of the irradiated microstructure evolution that control material property degradation required to accelerate the development of new, radiation-tolerant materials.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Fusion and fission events regulate endosome maturation and viral escape

Endosomes are intracellular vesicles that mediate the communication of the cell with its extracellular environment. They are an essential part of the cell’s machinery regulating intracellular trafficking via the endocytic pathway. Many viruses, which in order to replicate require a host cell, attach themselves to the cellular membrane; an event which usually initiates uptake of a viral particle through the endocytic pathway. In this way viruses hijack endosomes for their journey towards intracellular sites of replication and avoid degradation without host detection by escaping the endosomal compartment. Recent experimental techniques have defined the role of endosomal maturation in the ability of enveloped viruses to release their genetic material into the cytoplasm. Endosome maturation depends on a family of small hydrolase enzymes (or GTPases) called Rab proteins, arranged on the cytoplasmic surface of its membrane. Here, we model endosomes as intracellular compartments described by two variables (its levels of active Rab5 and Rab7 proteins) and which can undergo coagulation (or fusion) and fragmentation (or fission). The key element in our approach is the “per-cell endosomal distribution” and its dynamical (Boltzmann) equation. The Boltzmann equation allows us to derive the dynamics of the total number of endosomes in a cell, as well as the mean and the standard deviation of its active Rab5 and Rab7 levels. We compare our mathematical results with experiments of Dengue viral escape from endosomes. The relationship between endosomal active Rab levels and pH suggests a mechanism that can account for the observed variability in viral escape times, which in turn regulate the viability of a viral intracellular infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A study of degradation mechanisms in PVDF-based photovoltaic backsheets

Abstract Commercial backsheets based on polyvinylidene fluoride (PVDF) can experience premature field failures in the form of outer layer cracking. This work seeks to provide a better understanding of the changes in material properties that lead to crack formation and find appropriate accelerated tests to replicate them. The PVDF-based backsheet outer layer can have a different structure and composition, and is often blended with a poly(methyl methacrylate) (PMMA) polymer. We observed depletion of PMMA upon aging with sequential (MAST) and combined (C-AST) accelerated stress testing. In field-aged samples from Arizona and India, where PVDF crystallizes in its predominant α-phase, the degree of crystallinity greatly increased. MAST and C-AST protocols were, to some extent, able to replicate the increase in crystallinity seen in PVDF after ~ 7 years in the field, but no single-stress test condition (UV, damp heat, thermal cycling) resulted in significant changes in the material properties. The MAST regimen used here was too extreme to produce realistic degradation, but the test was useful in discovering weaknesses of the particular PVDF-based outer layer structure studied. No excessive β-phase formation was observed after aging with any test condition; however, the presence of β-phase was identified locally by Fourier transform infrared spectroscopy (FTIR). We conclude that both MAST and C-AST are relevant tests for screening outdoor failure mechanisms in PVDF backsheets, as they were successful in producing material degradation that led to cracking.

14 SOLAR ENERGY↗
DOE OSTI2018

Atomic imprinting into metallic glasses

Abstract Nanoimprinting by thermoplastic forming has attracted significant attention due to its promise of low-cost fabrication of functionalized surfaces and nanostructured devices, and metallic glasses have been identified as a material class ideally suited for nanoimprinting. In particular, their featureless atomic structure suggests that there may not be an intrinsic size limit to the material’s ability to replicate a mould. Here we demonstrate atomic-scale imprinting into a platinum-based metallic glass alloy under ambient conditions using atomic step edges of a strontium titanate single crystal as a mould. The moulded metallic glass replicates the ‘atomic smoothness’ of the strontium titanate, with identical roughness to the one measured on the mould even after multiple usages and with replicas exhibiting an exceptional long-term stability of years. By providing a practical, reusable, and potentially high-throughput approach for atomic imprinting, our findings may open novel applications in surface functionalization through topographical structuring.

Li, Rui↗
DOE OSTI2013

Methane dissociative chemisorption and detailed balance on Pt(111): Dynamical constraints and the modest influence of tunneling

A dynamically biased (d-) precursor mediated microcanonical trapping (PMMT) model of the activated dissociative chemisorption of methane on Pt(111) is applied to a wide range of dissociative sticking experiments, and, by detailed balance, to the methane product state distributions from the thermal associative desorption of adsorbed hydrogen with coadsorbed methyl radicals. Tunneling pathways were incorporated into the d-PMMT model to better replicate the translational energy distribution of the desorbing methane product from the laser induced thermal reaction of coadsorbed hydrogen and methyl radicals occurring near T{sub s} = 395 K. Although tunneling is predicted to be inconsequential to the thermal dissociative chemisorption of CH{sub 4} on Pt(111) at the high temperatures of catalytic interest, once the temperature drops to 395 K the tunneling fraction of the reactive thermal flux reaches 15%, and as temperatures drop below 275 K the tunneling fraction exceeds 50%. The d-PMMT model parameters of (E{sub 0} = 58.9 kJ/mol, s = 2, η{sub v} = 0.40) describe the apparent threshold energy for CH{sub 4}/Pt(111) dissociative chemisorption, the number of surface oscillators involved in the precursor complex, and the efficacy of molecular vibrational energy to promote reaction, relative to translational energy directed along the surface normal. Molecular translations parallel to the surface and rotations are treated as spectator degrees of freedom. Transition state vibrational frequencies are derived from generalized gradient approximation-density functional theory electronic structure calculations. The d-PMMT model replicates the diverse range of experimental data available with good fidelity, including some new effusive molecular beam and ambient gas dissociative sticking measurements. Nevertheless, there are some indications that closer agreement between theory and experiments could be achieved if a surface efficacy less than one was introduced into the modeling as an additional dynamical constraint.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Sequential data assimilation for single-molecule FRET photon-counting data

Data assimilation is a statistical method designed to improve the quality of numerical simulations in combination with real observations. Here, we develop a sequential data assimilation method that incorporates one-dimensional time-series data of smFRET (single-molecule Förster resonance energy transfer) photon-counting into conformational ensembles of biomolecules derived from “replicated” molecular dynamics (MD) simulations. A particle filter using a large number of “replicated” MD simulations with a likelihood function for smFRET photon-counting data is employed to screen the conformational ensembles that match the experimental data. We examine the performance of the method using emulated smFRET data and coarse-grained (CG) MD simulations of a dye-labeled polyproline-20. The method estimates the dynamics of the end-to-end distance from smFRET data as well as revealing that of latent conformational variables. The particle filter is also able to correct model parameter dependence in CG MD simulations. We discuss the applicability of the method to real experimental data for conformational dynamics of biomolecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Characterization of laser-induced plasmas as a complement to high-explosive large-scale detonations

Experimental investigations into the characteristics of laser-induced plasmas indicate that LIBS provides a relatively inexpensive and easily replicable laboratory technique to isolate and measure reactions germane to understanding aspects of high-explosive detonations under controlled conditions. Furthermore, we examine spectral signatures and derived physical parameters following laser ablation of aluminum, graphite and laser-sparked air as they relate to those observed following detonation of high explosives and as they relate to shocked air. Laser-induced breakdown spectroscopy (LIBS) reliably correlates reactions involving atomic Al and aluminum monoxide (AlO) with respect to both emission spectra and temperatures, as compared to small- and large-scale high-explosive detonations. Atomic Al and AlO resulting from laser ablation and a cited small-scale study, decay within ~10 -5 s, roughly 100 times faster than the Al and AlO decay rates (~10 -3 s) observed following the large-scale detonation of an Al-encased explosive. Temperatures and species produced in laser-sparked air are compared to those produced with laser ablated graphite in air. With graphite present, CN is dominant relative to N 2 + . Thus, in studies where the height of the ablating laser's focus was altered relative to the surface of the graphite substrate, CN concentration was found to decrease with laser focus below the graphite surface, indicating that laser intensity is a critical factor in the production of CN, via reactive nitrogen.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Charge carrier motion and effect of fixed oxide charge in a microstructured silicon radiation detector

Signal formation in a microstructured semiconductor neutron detector is more complex than in planar diode geometry. Three-dimensional microstructures are laterally smaller than the ionization cloud length, and the electric fields may be weak enough to exhibit plasma time effects. This work is the first detailed treatment of charge carrier motion in these complex semiconductor devices to replicate the time profile and signal magnitude. Simulations were performed using COMSOL Multiphysics to investigate various parameters that affect the propagation of the charge cloud. It was observed that the size of the simulated three-dimensional structure had an impact on the induced current pulse, indicating the importance of simulation geometry optimization to accurately simulate charge cloud expansion. COMSOL Multiphysics was used to replicate accurate charge creation profiles using energy deposition information imported from radiation transport codes. A detailed simulation methodology is presented to benchmark preamplifier event pulses along with complexities in modeling the charge carrier motion along the etched microstructured trenches with Si–SiO 2 boundary conditions, including fixed oxide charge and interface trapping.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Shock state distributions in porous tantalum and characterization with multipoint velocimetry

Heterogenous materials under shock compression can be expected to reach different shock states throughout the material according to local differences in microstructure and the history of wave propagation. Here, in this work, a compact, multiple-beam focusing optic assembly is used with high-speed velocimetry to interrogate the shock response of porous tantalum films prepared through thermal-spray deposition. The distribution of particle velocities across a shocked interface is compared to results obtained using a set of defocused interferometric beams that sampled the shock response over larger areas. The two methods produced velocity distributions along the shock plateau with the same mean, while a larger variance was measured with narrower beams. The finding was replicated using three-dimensional, mesoscopically resolved hydrodynamics simulations of solid tantalum with a pore structure mimicking statistical attributes of the material and accounting for radial divergence of the beams, with agreement across several impact velocities. Accounting for pore morphology in the simulations was found to be necessary for replicating the rise time of the shock plateau. The validated simulations were then used to show that while the average velocity along the shock plateau could be determined accurately with only a few interferometric beams, accurately determining the width of the velocity distribution, which here was approximately Gaussian, required a beam dimension much smaller than the spatial correlation lengthscale of the velocity field, here by a factor of ∼30×, with implications for the study of other porous materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity

Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli ( Ec )-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec- dGTPase, including an X-ray free-electron laser structure of the free Ec- -dGTPase enzyme to 3.2 Å. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec- dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec- dGTPase residues at the end of the substrate-binding pocket mimic Watson–Crick interactions providing guanine base specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 Å) of single-stranded DNA in an allosteric site primes the active site by conformationally “opening” a tyrosine gate allowing enhanced substrate binding.

Barnes, Christopher O.↗
DOE OSTI2019

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae , which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN

High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3'-to-5' exoribonuclease (ExoN) in nonstructural protein 14 (nsp14), which excises nucleotides including antiviral drugs misincorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here, we determined a 1.6-Å resolution crystal structure of severe acute respiratory syndrome CoV 2 (SARS-CoV-2) ExoN in complex with its essential cofactor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3' end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. We also show that the ExoN activity can rescue a stalled RNA primer poisoned with sofosbuvir and allow RdRp to continue its extension in the presence of the chain-terminating drug, biochemically recapitulating proofreading in SARS-CoV-2 replication. Molecular dynamics simulations further show remarkable flexibility of multidomain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA binding to support its exonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN–nsp10 complex serves as a platform for future development of anticoronaviral drugs or strategies to attenuate the viral virulence.

60 APPLIED LIFE SCIENCES↗