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At least 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning

Abstract mRNA degradation is a central process that affects all gene expression levels, though it remains challenging to predict the stability of a mRNA from its sequence, due to the many coupled interactions that control degradation rate. Here, we carried out massively parallel kinetic decay measurements on over 50,000 bacterial mRNAs, using a learn-by-design approach to develop and validate a predictive sequence-to-function model of mRNA stability. mRNAs were designed to systematically vary translation rates, secondary structures, sequence compositions, G-quadruplexes, i-motifs, and RppH activity, resulting in mRNA half-lives from about 20 seconds to 20 minutes. We combined biophysical models and machine learning to develop steady-state and kinetic decay models of mRNA stability with high accuracy and generalizability, utilizing transcription rate models to identify mRNA isoforms and translation rate models to calculate ribosome protection. Overall, the developed model quantifies the key interactions that collectively control mRNA stability in bacterial operons and predicts how changing mRNA sequence alters mRNA stability, which is important when studying and engineering bacterial genetic systems.

Cetnar, Daniel P.↗
DOE OSTI2022

MEITNER Resource Team Modeling and Simulation Support to Holos-Quad Reactor Development (Final CRADA Report)

The main objective of this CRADA is to provide Argonne National Laboratory (ANL)’s modeling and simulation capabilities via ARPA-E's MEITNER (Modeling-Enhanced Innovations Trailblazing Nuclear Energy Reinvigoration) Resource Team (RT) arrangement to support the demonstration of the viability of HolosGen’s Holos-Quad reactor design. The Holos-Quad reactor design is an advanced reactor concept that incorporates many new design features, such as the neutron-coupled Subcritical Power Modules (SPMs) in its core design, elimination of balance of plant (BOP) by direct integration of a helium Brayton cycle power conversion system with each SPM, among many other innovative features. The demonstration of the viability of such an innovative reactor design warrants iterations of modeling and simulation and testing. The purpose of this project is to utilize ANL’s modeling and simulation capabilities in nuclear reactor analysis and power conversion system analysis to inform HolosGen and the Design Team (DT) in the design and optimization of the Holos-Quad concept. The major work scopes of this project include: to investigate conceptual designs and materials for radiation shielding to protect personnel and internal components such as turbomachinery; Assess the the helium Brayton cycle power conversion system performance in both nominal and load following conditions; Investigate power conversion components and overall system performance; Identify control strategies to enable load following; Perform simulations of HolosGen’s subscale simulator and using available test data for code validation/benchmark purpose; Perform core thermal-hydraulics, safety analysis, and structural analysis.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2024

Beyond Conventional Charge Density Wave for Strongly Enhanced 2D Superconductivity in 1H‐TaS 2 Superlattices

Noncentrosymmetric transition metal dichalcogenide (TMD) monolayers offer a fertile platform for exploring unconventional Ising superconductivity (SC) and charge density waves (CDWs). However, the vulnerability of isolated monolayers to structural disorder and environmental oxidation often degrade their electronic coherence. Herein, an alternative approach is reported for fabricating stable and intrinsic monolayers of 1H-TaS2 sandwiched between SnS blocks in a (SnS) 1.15 TaS 2 van der Waals (vdW) superlattice. The SnS block layers not only decouple individual 1H-TaS 2 sublayers to endow them with monolayer-like electronic characteristics, but also protect the 1H-TaS 2 layers from electronic degradation. The results reveal the characteristic 3 × 3 CDW order in 1H-TaS 2 sublayers associated with electronic rearrangement in the low-lying sulfur p band, which uncovers a previously undiscovered CDW mechanism rather than the conventional Fermi surface-related framework. Additionally, the (SnS) 1.15 TaS 2 superlattice exhibits a strongly enhanced Ising-like SC with a layer-independent T c of ≈3.0 K, comparable to that of the isolated monolayer 1H-TaS 2 sample, presumably attributed to their monolayer-like characteristics and retained Fermi states. These results provide new insights into the long-debated CDW order and enhanced SC of monolayer 1H-TaS 2 , establishing bulk vdW superlattices as promising platforms for investigating exotic collective quantum phases in the 2D limit.

2D superconductivity↗
DOE OSTI2022

Electronic Properties of the Weyl Semimetals Co 2 MnX (X=Si, Ge, Sn)

Using first-principles electronic structure calculations, iwe show that ferromagnetic Heusler compounds Co2MnX (X = Si, Ge, Sn) present nontrivial topological characteristics and belong to the category of Weyl semimetals. These materials exhibit two topologically interesting band crossings near the Fermi level. These band crossings have complex 3D geometries in the Brillouin zone and are characterized by nontrivial topology as Hopf links and chain-like nodal lines that are protected by the perpendicular mirror planes. The spin–orbit interaction split these nodal lines into several 0D Weyl band crossings. Unlike previously known topologically nontrivial Heusler materials, these majority spin band crossings lie in or very near to the bandgap of minority spin bands, potentially facilitating experimental observation.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD

Neutralizing antibodies (NAbs) hold great promise for clinical interventions against SARS-CoV-2 variants of concern (VOCs). Understanding NAb epitopedependent antiviral mechanisms is crucial for developing vaccines and therapeutics against VOCs. Here we characterized two potent NAbs, EH3 and EH8, isolated from an unvaccinated pediatric patient with exceptional plasma neutralization activity. EH3 and EH8 cross-neutralize the early VOCsandmediatestrong Fc-dependent effector activity in vitro. Structural analyses of EH3 and EH8 in complex with the receptor-binding domain (RBD) revealed the molecular determinantsoftheepitope-drivenprotectionandVOCevasion.WhileEH3represents the prevalent IGHV3-53 NAb whose epitope substantially overlaps with the ACE2 binding site, EH8 recognizes a narrow epitope exposed in both RBD-up and RBD-down conformations. When tested in vivo, a single-dose prophylactic administration of EH3 fully protected stringent K18-hACE2 micefrom lethal challenge with Delta VOC. Our study demonstrates that protective NAbs responses converge in pediatric and adult SARS-CoV-2 patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Topological ultranodal pair states in iron-based superconductors

Abstract Bogoliubov Fermi surfaces are contours of zero-energy excitations that are protected in the superconducting state. Here we show that multiband superconductors with dominant spin singlet, intraband pairing of spin-1/2 electrons can undergo a transition to a state with Bogoliubov Fermi surfaces if spin-orbit coupling, interband pairing and time reversal symmetry breaking are also present. These latter effects may be small, but drive the transition to the topological state for appropriate nodal structure of the intra-band pair. Such a state should display nonzero zero-bias density of states and corresponding residual Sommerfeld coefficient as for a disordered nodal superconductor, but occurring even in the pure case. We present a model appropriate for iron-based superconductors where the topological transition associated with creation of a Bogoliubov Fermi surface can be studied. The model gives results that strongly resemble experiments on FeSe 1− x S x across the nematic transition, where this ultranodal behavior may already have been observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Inhibitors of Mycobacterium tuberculosis EgtD target both substrate binding sites to limit hercynine production

Ergothioneine (EGT) is a low molecular weight histidine betaine essential in all domains of life but only synthesized by selected few organisms. Synthesis of EGT by Mycobacterium tuberculosis (M. tb) is critical for maintaining bioenergetic homeostasis and protecting the bacterium from alkylating agents, oxidative stress, and anti-tubercular drugs. EgtD, an S-adenosylmethionine-dependent methyltransferase (AdoMet), catalyzes the trimethylation of L-Histidine to initiate EGT biosynthesis and this reaction has been shown to be essential for EGT production in mycobacteria and for long-term infection of murine macrophages by M. tb. In this work, library screening and structure-guided strategies identified multiple classes of M. tb EgtD inhibitors that bind in various regions of the enzyme active site. X-ray crystal structures of EgtD-inhibitor complexes confirm that L-Histidine analogs bind solely to the L-Histidine binding site while drug-like inhibitors, such as TGX-221, and S-Glycyl-H-1152 span both the L-Histidine and AdoMet binding sites. These enzyme-inhibitor complexes provide detailed structural information of compound scaffolds useful for developing more potent inhibitors that could shorten Tuberculosis treatment regimens by weakening important bacterial defenses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

New cyclophilin D inhibitor rescues mitochondrial and cognitive function in Alzheimer’s disease

Abstract Mitochondrial dysfunction is an early pathological feature of Alzheimer disease and plays a crucial role in the development and progression of Alzheimer’s disease. Strategies to rescue mitochondrial function and cognition remain to be explored. Cyclophilin D (CypD), the peptidylprolyl isomerase F (PPIase), is a key component in opening the mitochondrial membrane permeability transition pore, leading to mitochondrial dysfunction and cell death. Blocking membrane permeability transition pore opening by inhibiting CypD activity is a promising therapeutic approach for Alzheimer’s disease. However, there is currently no effective CypD inhibitor for Alzheimer’s disease, with previous candidates demonstrating high toxicity, poor ability to cross the blood–brain barrier, compromised biocompatibility and low selectivity. Here, we report a new class of non-toxic and biocompatible CypD inhibitor, ebselen, using a conventional PPIase assay to screen a library of ∼2000 FDA-approved drugs with crystallographic analysis of the CypD-ebselen crystal structure (PDB code: 8EJX). More importantly, we assessed the effects of genetic and pharmacological blockade of CypD on Alzheimer’s disease mitochondrial and glycolytic bioenergetics in Alzheimer’s disease-derived mitochondrial cybrid cells, an ex vivo human sporadic Alzheimer’s disease mitochondrial model, and on synaptic function, inflammatory response and learning and memory in Alzheimer’s disease mouse models. Inhibition of CypD by ebselen protects against sporadic Alzheimer’s disease- and amyloid-β-induced mitochondrial and glycolytic perturbation, synaptic and cognitive dysfunction, together with suppressing neuroinflammation in the brain of Alzheimer’s disease mouse models, which is linked to CypD-related membrane permeability transition pore formation. Thus, CypD inhibitors have the potential to slow the progression of neurodegenerative diseases, including Alzheimer’s disease, by boosting mitochondrial bioenergetics and improving synaptic and cognitive function.

Neurosciences & Neurology↗
DOE OSTI2021

Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae : Hairpin-Swapped Dimer and Its Conformational Change

VxrA and VxrB are cognate histidine kinase (HK)-response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae, a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the type VI secretion system, biofilm formation, and cell wall homeostasis in V. cholerae, providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. Here, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual β hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK. IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the type six secretion system, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structures of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown; however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Lifetime of Almost Strong Edge-Mode Operators in One-Dimensional, Interacting, Symmetry Protected Topological Phases

Almost strong edge-mode operators arising at the boundaries of certain interacting one-dimensional symmetry protected topological phases with Z 2 symmetry have infinite temperature lifetimes that are nonperturbatively long in the integrability breaking terms, making them promising as bits for quantum information processing. We extract the lifetime of these edge-mode operators for small system sizes as well as in the thermodynamic limit. For the latter, a Lanczos scheme is employed to map the operator dynamics to a one-dimensional tight-binding model of a single particle in Krylov space. We suggest this model to be that of a spatially inhomogeneous Su-Schrieffer-Heeger model with a hopping amplitude that increases away from the boundary, and a dimerization that decreases away from the boundary. We associate this dimerized or staggered structure with the existence of the almost strong mode. Thus, the short time dynamics of the almost strong mode is that of the edge mode of the Su-Schrieffer-Heeger model, while the long time dynamics involves decay due to tunneling out of that mode, followed by chaotic operator spreading. Furthermore, we show that competing scattering processes can lead to interference effects that can significantly enhance the lifetime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

The performance of additively manufactured Haynes 282 in supercritical CO 2

The use of supercritical carbon dioxide (sCO 2 ) as a working fluid is garnering interest in next generation power production systems due to the possibility of increased operational efficiencies and lower associated costs. Its implementation requires alloys with excellent high temperature strength and corrosion resistance, which makes Haynes 282® (H282) a suitable candidate. With increasing adoption of additive manufacturing (AM) in the energy industry, there is a need to investigate long-term sCO2 exposure on AM produced materials. Additively manufactured H282 (AM-H282) samples built using laser powder bed fusion in two different orientations were analyzed through imaging, gravimetric analysis, and room-temperature tensile testing before and after 1000-h exposure to CO 2 at 750 °C and 20 MPa. Performed imaging included observation of the sample surfaces and of the material bulk (cross sections) through means of Scanning Electron Microscopy (SEM) and optical microscopy. In comparison to wrought H282, it was found that the exposed material exhibited a similar Cr 2 O 3 oxide protective layer about 2 μm in thickness with additional top-surface TiO 2 oxide and carbon-rich precipitates. It was also similarly observed that internal oxidation was present but limited to a depth of 20 μm, and a 1–3 μm γ’ denuded region appeared to surround all internal and surface oxidation. Thermal aging effects were noted with the precipitation of needle-like structures in the γ/γ’ matrix and a coarsening of the γ’ precipitates from 28 nm to 73 nm. Mass measurements analyzing oxide precipitation revealed a larger increase compared to wrought, representing an approximate 20% difference. Tensile testing results showed similar behavior to wrought with a slight increase in yield strength and a large reduction in elongation in the exposed samples.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Multiscale dynamic experiments on fiber-reinforced composites with damage assessment using high-speed synchrotron X-ray phase-contrast imaging

We report fiber-reinforced composites (FRCs) have been widely used as protection materials to replace heavier metals. However, predictive capabilities for the impact-induced failure of FRCs have not been well-developed. In this work, we introduced an integrated technique to visualize the dynamic failure of FRCs, with the modified Kolsky bar loading and the high-speed synchrotron X-ray phase-contrast imaging (PCI). We summarize our experimental studies across the FRCs’ structural levels by using this integrated technique, including single-fiber tensile experiments, fiber/matrix debonding experiments, and single-edge notched bending experiments on composite laminates. It is revealed that the high-speed synchrotron X-ray PCI technique possesses sufficient spatial resolution to identify the failure behavior of a single fiber in the 10-μm scale level, as well as temporal resolution to identify the time sequence of internal dynamic damage evolution. The technique can penetrate through the opaque composite sample and provide real-time visualization of small-scale damaging mechanisms such as the embedded fiber’s sliding in the matrix and the fiber’s transverse debonding with the matrix. At an expanding scale, the technique can identify the crack initiation and track the cracking behavior inside a single ply or between different plies of a composite laminate. High-speed visualization inside the material by this integrated technique provides critical deformation and failure information to develop physical understanding of the damage inside composites under impact.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Computational Modeling To Adapt Neutralizing Antibody

Monoclonal antibodies (mAbs) is the leading therapy for viral infections because it provides immediate protection and can be administered at higher levels than in a natural immune response. Finding mAbs that neutralize a broad spectrum of viral targets has proven difficult because many species and strains exist and blanket targeting is a slow and laborious process to experimentally screen 108 variants. A new method is needed to rapidly redesign mAbs for homologous targets. This project speeds up redesign using structure-based computational design to reduce the mAbs search space to a manageable level and screen mutants at a much higher rate than in experiments. Computation will also provide critical knowledge about the fundamental interactions. The project will adapt S230, a human antibody that neutralizes SARS-CoV, to neutralize SARS-COV-2.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Integrity Monitoring, Prediction and Assessment, Corrosion Control, and Repair of the Hanford Storage Tanks – 25213

The Hanford Nuclear Reservation site contains approximately 211 million liters of radioactive and chemically hazardous waste arising from nuclear weapons production, beginning with World War II, and continuing through the Cold War [1]. The waste is stored in 177 carbon-steel underground storage tanks, of which 149 are single-shell tanks (SSTs) and the remaining are double-shell tanks (DSTs). The mission of an ongoing River Protection Project is to retrieve the waste from the underground storage tanks and then treat and immobilize (i.e., vitrify) it for disposal. Waste from the older SSTs is being progressively retrieved into the newer DSTs for storage pending treatment, immobilization, and disposal. Figure 1 depicts a typical DST design [2]. The tank is approximately 23 m in diameter and 9 m high and has a domed structure and has a capacity of 4000 m3. The tank wall and floor vary in thickness between approximately 10 mm and 25 mm depending on location. The thicker wall sections are near the curved transition between the tank wall and the floor, while the thinner sections are located near the top of the tank wall. The tank floor thickness varies from 25 mm at the tank center to 10 mm near the tank wall. The tanks were constructed of either ASTM A516 Grade 65 or ASTM A537 Class 1 carbon steel and were post-weld heat treated to reduce the risk of SCC.

Shukla, Pavan K. [Savannah River National Laborato↗
DOE OSTI2024

Aging of Limestones and Silane–Siloxane-Based Protective Hydrophobics: The Impact of Heating–Cooling and Freeze–Thaw Cycles

Stones are traditionally used in construction and architectural applications as building elements due to their aesthetic and technical/structural performance. Like other environmental factors (rain, humidity, moisture, salt presence, biological activity, etc.), heating–cooling and freeze–thaw cycles significantly threaten the longevity of stone materials. Hence, considering the socio-economic and cultural value of stones, preventive actions such as hydrophobic coatings are applied to prevent or mitigate damage. The scope of this study is the performance assessment of limestones with different characteristics and the efficiency of various commercial silane/siloxane-based hydrophobic coatings when exposed to thermal variation and freeze–thaw. For that purpose, the standards EN 14066:2013 (determination of resistance to aging by thermal shock) and EN 12371:2010 (determination of frost resistance) were followed. Open porosity and static contact angles were estimated to assess the stone durability and water protection capabilities of the hydrophobics. Additionally, sound speed propagation velocity, quality of building material index, elastic modulus and flexural strength were measured to evaluate the variation of mechanical properties. Static contact angle revealed that the coatings maintained an efficient level of hydrophobicity even after thermal-shock and freeze–thaw weathering tests. The study also revealed a critical interaction between freeze–thaw cycles, hydrophobic coatings and structural integrity of the stones, mostly on more porous ones. When they are subjected to harsh environmental conditions, untreated porous limestones keep structural cohesion, allowing for the natural absorption and release of water during freezing and thawing. On the contrary, when limestones are treated, the hydrophobic coatings can moderately obstruct the water release due to the partial saturation of the porous framework by the products. It also probably resulted from the different mechanical behavior between the inner matrix and layer of stone coated, resulting in a premature breakout and mechanical damage of the stone.

Lisci, Carla (ORCID:000000032179130X)↗
DOE OSTI2022

Lignin as a bioactive polymer and heavy metal absorber- an overview

As a pulping and bio-refinery by-product with phenolic chemical structure, lignin indicated high potential as natural antioxidant activity, UV blocker, antibacterial and toxic material absorbent properties. Presence of phenolic hydroxyl groups in lignin structure plays the main role of its antioxidant activity. However, lignin antioxidant power can change depending on its other structural features and functional groups like ortho-methoxy groups, –OCH 3 groups, the α-CH 2 groups, the aliphatic carbonyl groups, and the size of π-conjugated systems. Lignin in mixture with synthetic polymers, improved their thermal stability. Lignin has high UV light absorbing potential in broad-spectrum (UVA, UVB). Adding 1–5% of lignin into hand cream indicated excellent range of sun protection factor (SPF) with more than 95% UV light absorption. Lignin also indicated strong UV light protection when applied in different transparent film and protect paint, oil, and varnish from UV degradation. Further, lignosulfonate and other modified lignin including chemically modification, nano-particles and lignin hydrogel indicated high potential as heavy metal absorber.

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

Free volume manipulation of a 6FDA-HAB polyimide using a solid-state protection/deprotection strategy

We report tert-butoxycarbonyl (t-BOC) is a thermally labile moiety that can be used to protect hydroxyl groups on polymers. In this study, t-BOC was appended onto a polyimide consisting of 2,2'-bis-(3,4-dicarboxyphenyl) hexafluoropropane dianhydride (6FDA) and 3,3'-dihydroxy-4,4'-diamino-biphenyl (HAB), after which the polymer was formed into self-standing films. Solid-state thermal treatments were performed to systematically remove t-BOC moieties to alter the physical packing structure and concomitant gas transport properties of the polymer. Despite performing deprotection reactions well below the glass transition temperature of 6FDA-HAB (~300 °C), this free volume manipulation (FVM) approach produced only subtle differences in polymer density, fractional free volume, average free volume element size, and gas transport properties relative to the unprotected polymer. While these findings suggest that thermally removing covalently bound functional groups from polymer films can be used to manipulate free volume and gas transport performance for glassy polymers, more robust polymer systems than linear polyimides are required to preserve the nascent free volume architecture generated from this approach.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Property space mapping of Pseudomonas aeruginosa permeability to small molecules

Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗