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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

The high-field tokamak physics basis for the ARC fusion power plant

This editorial summarizes the physics basis underlying the ARC high-field tokamak fusion power plant, including recent advances in tokamak plasma understanding, the role of the SPARC device, and key remaining physics questions. It describes how these results guide the ARC Version 3A design and outlines opportunities for the broader fusion community to contribute to the development of first-generation fusion power plants.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Narrow operator models of stellarator equilibria in Fourier Zernike basis

Numerical computation of the ideal magnetohydrodynamic (MHD) equilibrium magnetic field is at the base of stellarator optimisation and provides the starting point for solving more sophisticated partial differential equations like transport or turbulence models. Conventional approaches solve for a single stationary point of the ideal MHD equations, which is fully defined by three invariants and the numerical scheme employed by the solver. We present the first numerical approach that can solve for a continuous distribution of equilibria with fixed boundary and rotational transform, varying only the pressure invariant. This approach minimises the force residual by optimising parameters of multilayer perceptrons that map from a scalar pressure multiplier to the Fourier Zernike basis as implemented in the modern stellarator equilibrium solver DESC.

fusion plasma↗
DOE OSTI2026

Overview of the physics basis for the ARC fusion power plant

Commonwealth Fusion Systems plans to build ARC as the first fusion power plant at a site in Chesterfield County, Virginia, USA by the early 2030s. We present an overview of analysis comprising the physics basis of the ARC V3A design, a high-magnetic-field tokamak with 𝐵 0 =11.4 T, 𝐼 𝑝 =12.0 MA, 𝑅 0 =4.62 m, 𝑎 =1.18 m. ARC V3A is designed to produce 𝑃 𝑓⁡𝑢⁢𝑠 ≈1.13 GW DT fusion power and deliver ⩾400 MW net electric power to the grid. This overview includes quantitative analysis of fundamental issues for design of and operational plasma scenarios for a tokamak power plant, and lays out the design targets and strategic choices for ARC, including empirical fusion performance projections, assessment of H-mode access, ion cyclotron resonance heating simulations, alpha particle physics and time-dependent full-pulse simulations. This is complemented by topical papers on fusion performance and transport, disruption physics, boundary physics and magnetohydrodynamic stability. Critically, these studies identify key model uncertainties and physics risks to be retired through SPARC operation. Due to the modular nature of ARC, early results from SPARC can be incorporated into the design of the first ARC as well as subsequent replacements of the ARC vacuum vessel.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Volatility Basis Set Distributions and Viscosity of Organic Aerosol Mixtures: Insights from Chemical Characterization Using Temperature-Programmed Desorption–Direct Analysis in Real-Time High-Resolution Mass Spectrometry

Quantitative assessment of gas-particle partitioning of individual components within complex atmospheric organic aerosols (OA) mixtures is critical for predicting and comprehending the formation and evolution of OA particles in the atmosphere. This investigation leverages previously documented data obtained through a temperature programmed desorption - direct analysis in real time – high resolution mass spectrometry (TPD-DART-HRMS) platform. This methodology facilitates the bottom-up construction of volatility basis set (VBS) distributions for constituents found in three biogenic secondary organic aerosol (SOA) mixtures produced through the ozonolysis of a-pinene, limonene, and ocimene. The apparent enthalpies (ΔH*, kJ mol -1 ) and saturated vapor mass concentrations (C T *, µg∙m -3 ) of individual SOA components, determined as a function of temperature (T, K), facilitated an assessment of changes in VBS distributions and gas-particle partitioning with respect to T and atmospheric total organic mass loadings (tOM, µg∙m -3 ). Further, the VBS distributions reveal distinct differences in volatilities among monomers, dimers, and trimers, enabling their categorization into separate volatility bins. At the ambient temperature of T = 298 K, only monomers efficiently partition between gas and particle phases across a broad range of atmospherically relevant total organic mass loadings (tOM) values of 1–100 µg∙m -3 . Partitioning of dimers and trimers becomes notable only at T > 360 K and T > 420 K, respectively. The viscosity of SOA mixtures is assessed using a bottom-up calculation approach, incorporating the input of elemental formulas, ΔH*, C T *, and particle-phase mass fractions of the SOA components. Through this approach, we are able to accurately estimate the variations in SOA viscosity that result from the evaporation of its components. These variations are, in turn, influenced by atmospherically relevant changes in tOM and T. Comparison of the calculated SOA viscosity and diffusivity values with literature reported experimental results shows close agreement, thereby validating the employed calculation approach. These findings underscore the significant potential for TPD-DART-HRMS measurements in enabling the untargeted analysis of organic molecules within OA mixtures. This approach facilitates quantitative assessment of their gas-particle partitioning and allows for the estimation of their viscosity and condensed-phase diffusion, thereby contributing valuable insights to atmospheric models.

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

Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization

Enhancing the thermostability of enzymes without impacting their catalytic function represents an important yet challenging goal in protein engineering and biocatalysis. We recently introduced a novel method for enzyme thermostabilization that relies on the computationally guided installation of genetically encoded thioether “staples” into a protein via cysteine alkylation with the noncanonical amino acid O-2-bromoethyl tyrosine (O2beY). Here, we demonstrate the functionality of an expanded set of electrophilic amino acids featuring chloroacetamido, acrylamido, and vinylsulfonamido side-chain groups for protein stapling using this strategy. Using a myoglobin-based cyclopropanase as a model enzyme, our studies show that covalent stapling with pchloroacetamido-phenylalanine (pCaaF) provides higher stapling efficiency and enhanced stability (thermodynamic and kinetic) compared to the other stapled variants and the parent protein. Interestingly, molecular simulations of conformational flexibility of the cross-links show that the pCaaF staple allows fewer energetically feasible conformers than the other staples, and this property may be a broader indicator of stability enhancement. Using this strategy, pCaaF-stapled variants with significantly enhanced stability against thermal denaturation (ΔT m ' = +27 °C) and temperature-induced heme loss (ΔT 50 = +30 °C) were obtained while maintaining high levels of catalytic activity and stereoselectivity. Crystallographic analyses of singly and doubly stapled variants provide key insights into the structural basis for stabilization, which includes both direct interactions of the staples with protein residues and indirect interactions through adjacent residues involved in heme binding. This work expands the toolbox of protein stapling strategies available for protein stabilization.

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

Forces from Stochastic Density Functional Theory under Nonorthogonal Atom-Centered Basis Sets

We develop a formalism for calculating forces on the nuclei within the linear-scaling stochastic density functional theory (sDFT) in a nonorthogonal atom-centered basis set representation (Fabian et al. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2019, 9, e1412, 10.1002/wcms.1412) and apply it to the Tryptophan Zipper 2 (Trp-zip2) peptide solvated in water. We use an embedded-fragment approach to reduce the statistical errors (fluctuation and systematic bias), where the entire peptide is the main fragment and the remaining 425 water molecules are grouped into small fragments. We analyze the magnitude of the statistical errors in the forces and find that the systematic bias is of the order of 0.065 eV/Å (~1.2 × 10 -3 E h / a 0 ) when 120 stochastic orbitals are used, independently of system size. This magnitude of bias is sufficiently small to ensure that the bond lengths estimated by stochastic DFT (within a Langevin molecular dynamics simulation) will deviate by less than 1% from those predicted by a deterministic calculation.

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

Fermi’s Golden Rule Rate Expression for Transitions Due to Nonadiabatic Derivative Couplings in the Adiabatic Basis

Starting from a general molecular Hamiltonian expressed in the basis of adiabatic electronic and nuclear position states, where a compact and complete expression for the nonadiabatic derivative coupling (NDC) Hamiltonian term is obtained, we provide a general analysis of the Fermi’s golden rule (FGR) rate expression for nonadiabatic transitions between adiabatic states. We then consider a quasi-adiabatic approximation that uses crude adiabatic states and NDC couplings, both evaluated at the minimum potential energy configuration of the initial adiabatic state, for the definition of the zeroth and first-order terms of the Hamiltonian. Although the application of this approximation is rather limited, it allows deriving a general FGR rate expression without further approximation while accounting for non-Condon contribution to the FGR rate arising from momentum operators of NDC terms and its coupling with vibronic displacements. For a generic and widely used model where all nuclear degrees of freedom and environmental effects are represented as linearly coupled harmonic oscillators, we derive a closed-form FGR rate expression that requires only Fourier transform. The resulting rate expression includes quadratic contributions of NDC terms and their couplings to Franck–Condon modes, which require evaluation of two additional bath spectral densities in addition to the conventional one that appears in a typical FGR rate theory based on the Condon approximation. Model calculations for the case where nuclear vibrations consist of both a sharp high-frequency mode and an Ohmic bath spectral density illustrate new features and implications of the rate expression. We then apply our theoretical expression to the nonradiative decay from the first excited singlet state of azulene, which illustrates the utility and implications of our theoretical results.

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

Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme

We report the past decades have witnessed an explosion of de novo protein designs with a remarkable range of scaffolds. It remains challenging, however, to design catalytic functions that are competitive with naturally occurring counterparts as well as biomimetic or nonbiological catalysts. Although directed evolution often offers efficient solutions, the fitness landscape remains opaque. Green fluorescent protein (GFP), which has revolutionized biological imaging and assays, is one of the most redesigned proteins. While not an enzyme in the conventional sense, GFPs feature competing excited-state decay pathways with the same steric and electrostatic origins as conventional ground-state catalysts, and they exert exquisite control over multiple reaction outcomes through the same principles. Thus, GFP is an “excited-state enzyme”. Herein we show that rationally designed mutants and hybrids that contain environmental mutations and substituted chromophores provide the basis for a quantitative model and prediction that describes the influence of sterics and electrostatics on excited-state catalysis of GFPs. As both perturbations can selectively bias photoisomerization pathways, GFPs with fluorescence quantum yields (FQYs) and photoswitching characteristics tailored for specific applications could be predicted and then demonstrated. The underlying energetic landscape, readily accessible via spectroscopy for GFPs, offers an important missing link in the design of protein function that is generalizable to catalyst design.

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

Capturing the Relative‐Humidity‐Sensitive Gas–Particle Partitioning of Organic Aerosols in a 2D Volatility Basis Set

Abstract Aerosol water affects the physicochemical properties and mass concentration of organic aerosols (OA), but it is typically omitted by air quality, weather, and climate models. We compare two classes of simplified models to estimate the OA water uptake and gas–particle partitioning of organic compounds. One class uses a single‐hygroscopicity‐parameter (κ) approach while the other is based on the reduced‐complexity Binary Activity Thermodynamics (BAT) model. We show that a BAT‐based two‐dimensional volatility basis set (VBS) model always predicts a higher OA mass concentration at elevated relative humidity (RH), for example, ∼16% at 80% RH, than any variation of theκ‐based method considered—even when BAT‐VBS predicts a lower water uptake. The main reason being that the BAT‐VBS model captures variations in effective saturation mass concentration of organics (C*) with RH, a feature that other VBS methods lack. The BAT‐VBS framework offers an efficient, RH‐sensitive treatment for reduced‐complexity OA modeling.

Geology↗
DOE OSTI2020

Structural basis for Ca2+-dependent activation of a plant metacaspase

Abstract Plant metacaspases mediate programmed cell death in development, biotic and abiotic stresses, damage-induced immune response, and resistance to pathogen attack. Most metacaspases require Ca 2+ for their activation and substrate processing. However, the Ca 2+ -dependent activation mechanism remains elusive. Here we report the crystal structures of Metacaspase 4 from Arabidopsis thaliana ( At MC4) that modulates Ca 2+ -dependent, damage-induced plant immune defense. The At MC4 structure exhibits an inhibitory conformation in which a large linker domain blocks activation and substrate access. In addition, the side chain of Lys225 in the linker domain blocks the active site by sitting directly between two catalytic residues. We show that the activation of At MC4 and cleavage of its physiological substrate involve multiple cleavages in the linker domain upon activation by Ca 2+ . Our analysis provides insight into the Ca 2+ -dependent activation of At MC4 and lays the basis for tuning its activity in response to stresses for engineering of more sustainable crops for food and biofuels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural basis for substrate recognition and chemical inhibition of oncogenic MAGE ubiquitin ligases

Testis-restricted melanoma antigen (MAGE) proteins are frequently hijacked in cancer and play a critical role in tumorigenesis. MAGEs assemble with E3 ubiquitin ligases and function as substrate adaptors that direct the ubiquitination of novel targets, including key tumor suppressors. However, how MAGEs recognize their targets is unknown and has impeded the development of MAGE-directed therapeutics. Here, we report the structural basis for substrate recognition by MAGE ubiquitin ligases. Biochemical analysis of the degron motif recognized by MAGE-A11 and the crystal structure of MAGE-A11 bound to the PCF11 substrate uncovered a conserved substrate binding cleft (SBC) in MAGEs. Mutation of the SBC disrupted substrate recognition by MAGEs and blocked MAGE-A11 oncogenic activity. A chemical screen for inhibitors of MAGE-A11:substrate interaction identified 4-Aminoquinolines as potent inhibitors of MAGE-A11 that show selective cytotoxicity. These findings provide important insights into the large family of MAGE ubiquitin ligases and identify approaches for developing cancer-specific therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation

SARS-CoV-2 is a betacoronavirus virus responsible for the COVID-19 pandemic. Here, we determine the X-ray crystal structure of a potent neutralizing monoclonal antibody, CV30, isolated from a patient infected with SARS-CoV-2, in complex with the receptor binding domain. The structure reveals that CV30 binds to an epitope that overlaps with the human ACE2 receptor binding motif providing a structural basis for its neutralization. CV30 also induces shedding of the S1 subunit, indicating an additional mechanism of neutralization. A germline reversion of CV30 results in a substantial reduction in both binding affinity and neutralization potential indicating the minimal somatic mutation is needed for potently neutralizing antibodies against SARS-CoV-2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The structural basis of promiscuity in small multidrug resistance transporters

By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process. Using solid-supported membrane electrophysiology, we find that promiscuous transport of hydrophobic substituted cations is a general feature of SMR transporters. To understand the molecular basis for promiscuity, we solved X-ray crystal structures of a SMR transporter Gdx-Clo in complex with substrates to a maximum resolution of 2.3 Å. These structures confirm the family’s extremely rare dual topology architecture and reveal a cleft between two helices that provides accommodation in the membrane for the hydrophobic substituents of transported drug-like cations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis for SARS-CoV-2 envelope protein recognition of human cell junction protein PALS1

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has created global health and economic emergencies. SARS-CoV-2 viruses promote their own spread and virulence by hijacking human proteins, which occurs through viral protein recognition of human targets. To understand the structural basis for SARS-CoV-2 viral-host protein recognition, here we use cryo-electron microscopy (cryo-EM) to determine a complex structure of the human cell junction protein PALS1 and SARS-CoV-2 viral envelope (E) protein. Our reported structure shows that the E protein C-terminal DLLV motif recognizes a pocket formed exclusively by hydrophobic residues from the PDZ and SH3 domains of PALS1. Our structural analysis provides an explanation for the observation that the viral E protein recruits PALS1 from lung epithelial cell junctions. In addition, our structure provides novel targets for peptide- and small-molecule inhibitors that could block the PALS1-E interactions to reduce E-mediated virulence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair

Reactive oxygen species (ROS) oxidize cellular nucleotide pools and cause double strand breaks (DSBs). Non-homologous end-joining (NHEJ) attaches broken chromosomal ends together in mammalian cells. Ribonucleotide insertion by DNA polymerase (pol) μ prepares breaks for end-joining and this is required for successful NHEJ in vivo. We previously showed that pol μ lacks discrimination against oxidized dGTP (8-oxo-dGTP), that can lead to mutagenesis, cancer, aging and human disease. Here we reveal the structural basis for proficient oxidized ribonucleotide (8-oxo-rGTP) incorporation during DSB repair by pol μ. Time-lapse crystallography snapshots of structural intermediates during nucleotide insertion along with computational simulations reveal substrate, metal and side chain dynamics, that allow oxidized ribonucleotides to escape polymerase discrimination checkpoints. Abundant nucleotide pools, combined with inefficient sanitization and repair, implicate pol μ mediated oxidized ribonucleotide insertion as an emerging source of widespread persistent mutagenesis and genomic instability.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Structural basis of R-loop recognition by the S9.6 monoclonal antibody

R-loops are ubiquitous, dynamic nucleic-acid structures that play fundamental roles in DNA replication and repair, chromatin and transcription regulation, as well as telomere maintenance. The DNA-RNA hybrid–specific S9.6 monoclonal antibody is widely used to map R-loops. Here, we report crystal structures of a S9.6 antigen-binding fragment (Fab) free and bound to a 13-bp hybrid duplex. We demonstrate that S9.6 exhibits robust selectivity in binding hybrids over double-stranded (ds) RNA and in categorically rejecting dsDNA. S9.6 asymmetrically recognizes a compact epitope of two consecutive RNA nucleotides via their 2'-hydroxyl groups and six consecutive DNA nucleotides via their backbone phosphate and deoxyribose groups. Recognition is mediated principally by aromatic and basic residues of the S9.6 heavy chain, which closely track the curvature of the hybrid minor groove. These findings reveal the molecular basis for S9.6 recognition of R-loops, detail its binding specificity, identify a new hybrid-recognition strategy, and provide a framework for S9.6 protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase

Bacteriophage T7 RNA polymerase (T7 RNAP) is widely used for synthesizing RNA molecules with synthetic modifications and unnatural base pairs (UBPs) for a variety of biotechnical and therapeutic applications. However, the molecular basis of transcription recognition of UBPs by T7 RNAP remains poorly understood. Here we focused on a representative UBP, 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole 2-carbaldehyde (Pa), and investigated how the hydrophobic Ds–Pa pair is recognized by T7 RNAP. Our kinetic assays revealed that T7 RNAP selectively recognizes the Ds or Pa base in the templates and preferentially incorporates their cognate unnatural base nucleotide substrate (PaTP or DsTP) over natural NTPs. Our structural studies reveal that T7 RNAP recognizes the unnatural substrates at the pre-insertion state in a distinct manner compared to natural substrates. These results provide mechanistic insights into transcription recognition of UBP by T7 RNAP and provide valuable information for designing the next generation of UBPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies

Laminin polymerization is the major step in basement membranes assembly. Its failures cause laminin N-terminal domain lamininopathies including Pierson syndrome. We have employed cryo-electron microscopy to determine a 3.7 Å structure of the trimeric laminin polymer node containing α1, β1 and γ1 subunits. The structure reveals the molecular basis of calcium-dependent formation of laminin lattice, and provides insights into polymerization defects manifesting in human disease.

59 BASIC BIOLOGICAL SCIENCES↗