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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Enhanced multiscale restriction-smoothed basis (MsRSB) preconditioning with applications to porous media flow and geomechanics

A novel method to enable application of the Multiscale Restricted Smoothed Basis (MsRSB) method to non M-matrices is presented. The original MsRSB method is enhanced with a filtering strategy enforcing M-matrix properties to enable the robust application of MsRSB as a preconditioner. Through applications to porous media flow and linear elastic geomechanics, the method is proven to be effective for scalar and vector problems with multipoint finite volume (FV) and finite element (FE) discretization schemes, respectively. Realistic complex (un)structured two- and three-dimensional test cases are considered to illustrate the method's performance.

58 GEOSCIENCES↗
DOE OSTI2020

The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition

Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, the lethal function of T can be blocked by an antiholin (RI) during lysis inhibition (LIN). LIN sets if the infected cell undergoes superinfection, then the lysis is delayed until host/phage ratio becomes more favorable for the release of progeny. It has been thought that a signal derived from the superinfection is required to activate RI. Here we report structures that suggest a radically different model in which RI binds to T irrespective of superinfection, causing it to accumulate in a membrane as heterotetrameric 2RI–2T complex. Moreover, we show the complex binds non-specifically to DNA, suggesting that the gDNA from the superinfecting phage serves as the LIN signal and that stabilization of the complex by DNA binding is what defines LIN. Finally, we show that soluble domain of free RI crystallizes in a domain-swapped homotetramer, which likely works as a sink for RI molecules released from the RI–T complex to ensure efficient lysis. These results constitute the first structural basis and a new model not only for the historic LIN phenomenon but also for the temporal regulation of phage lysis in general.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. Here, we have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site ‘unwinds’ in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis for inhibition of coagulation factor VIII reveals a shared antigenic hotspot on the C1 domain

Hemophilia A arises from dysfunctional or deficient coagulation factor (F)VIII and leads to inefficient fibrin clot formation and uncontrolled bleeding events. The development of antibody inhibitors is a clinical complication in hemophilia A patients receiving FVIII replacement therapy. LE2E9 is an anti-C1 domain inhibitor previously isolated from a mild/moderate hemophilia A patient and disrupts FVIII interactions with von Willebrand factor and FIXa, though the intermolecular contacts that underpin LE2E9-mediated FVIII neutralization are undefined. To determine the structure of the complex between FVIII and LE2E9 and characterize its mechanism of inhibition. FVIII was bound to the antigen binding fragment (Fab) of NB2E9, a recombinant construct of LE2E9, and its structure was determined by cryogenic electron microscopy. Here, this report communicates the 3.46 Å structure of FVIII bound to NB2E9, with its epitope comprising FVIII residues S2040 to Y2043, K2065 to W2070, and R2150 to H2155. Structural analysis reveals that the LE2E9 epitope overlaps with portions of the epitope for 2A9, a murine-derived inhibitor, suggesting that these residues represent a shared antigenic region on the C1 domain between FVIII –/– mice and hemophilia A patients. Furthermore, the FVIII:NB2E9 structure elucidates the orientation of the LE2E9 glycan, illustrating how the glycan sterically blocks interactions between the FVIII C1 domain and the von Willebrand factor D' domain. A putative model of the FVIIIa:FIXa complex suggests potential clashing between the NB2E9 glycan and FIXa light chain. These results describe an antigenic “hotspot” on the FVIII C1 domain and provide a structural basis for engineering FVIII replacement therapeutics with reduced antigenicity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Higher-order SPOP assembly reveals a basis for cancer mutant dysregulation

The speckle-type POZ protein (SPOP) functions in the Cullin3-RING ubiquitin ligase (CRL3) as a receptor for the recognition of substrates involved in cell growth, survival, and signaling. SPOP mutations have been attributed to the development of many types of cancers, including prostate and endometrial cancers. Prostate cancer mutations localize in the substrate-binding site of the substrate recognition (MATH) domain and reduce or prevent binding. However, most endometrial cancer mutations are dispersed in seemingly inconspicuous solvent-exposed regions of SPOP, offering no clear basis for their cancer-causing and peculiar gain-of-function properties. Herein, we present the first structure of SPOP in its oligomeric form, uncovering several new interfaces important for SPOP self-assembly and normal function. Given that many previously unaccounted-for cancer mutations are localized in these newly identified interfaces, we uncover molecular mechanisms underlying dysregulation of SPOP function, with effects ranging from gross structural changes to enhanced self-association, and heightened stability and activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Achieving performance portability in Gaussian basis set density functional theory on accelerator based architectures in NWChemEx

The numerical integration of the exchange–correlation (XC) potential is one of the primary computational bottlenecks in Gaussian basis set Kohn–Sham density functional theory (KS-DFT). To achieve optimal performance and accuracy, care must be taken in this numerical integration to preserve local sparsity as to allow for near linear weak scaling with system size. This leads to an integration scheme with several performance critical kernels which must be hand optimized for each architecture of interest. As the set of available accelerator hardware goes more diverse, a key challenge for developers of KS-DFT software is to maintain performance portability across a wide range of computational architectures. In this article, we examine a modular software design pattern which decouples the implementation details of performance critical kernels from the expression of high-level algorithmic workflows in a device-agnostic language such as C++; thus allowing for developers to target existing and emerging accelerator hardware within a single code base. We consider the efficacy of such a design pattern in the numerical integration of the XC potential by demonstrating its ability to achieve performance portability across a set of accelerator architectures which are representative of those on current and future U.S. Department of Energy Leadership Computing Facilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Transverse momentum structure of proton within the basis light-front quantization framework

We obtain the leading-twist valence quark transverse-momentum-dependent parton distribution functions (TMD PDFs) for the proton within the basis light-front quantization (BLFQ) framework. Our results are consistent with lattice QCD calculations and our previous results for the collinear limit. We also obtain consistency with the Soffer-type bounds. Within our approach, we find that six T-even TMDs in the leading twist are all independent of each other, and previously found model-dependent relations do not hold. This is a promising sign that our results are representative of future, more extensive treatments of QCD. Furthermore, we obtain a non-trivial x-dependence of the <(p ⊥ ) 2 > and some consistency with the Gaussian ansatz but only in the small <(p ⊥ ) 2 > region. Those features suggest our results may be a useful alternative in future experimental extractions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Molecular basis of functional exchangeability between ezrin and other actin-membrane associated proteins during cytokinesis

Highlights: • Anillin or supervillin depletion affects localization of different domains of ezrin. • Actin binding domains are compatible between ezrin and anillin for furrow ingression. • All ezrin and anillin domains are incompatible for polar cortical control. The mechanism that mediates the interaction between the contractile ring and the plasma membrane during cytokinesis remains elusive. We previously found that ERM (Ezrin/Radixin/Moesin) proteins, which usually mediate cellular pole contraction, become over-accumulated at the cell equator and support furrow ingression upon the loss of other actin-membrane associated proteins, anillin and supervillin. In this study, we addressed the molecular basis of the exchangeability between ezrin and other actin-membrane associated proteins in mediating cortical contraction during cytokinesis. We found that depletion of anillin and supervillin caused over-accumulation of the membrane-associated FERM domain and actin-binding C-terminal domain (C-term) of ezrin at the cleavage furrow, respectively. This finding suggests that ezrin differentially shares its binding sites with these proteins on the actin cytoskeleton or inner membrane surface. Using chimeric mutants, we found that ezrin C-term, but not the FERM domain, can substitute for the corresponding anillin domains in cytokinesis and cell proliferation. On the other hand, either the membrane-associated or the actin/myosin-binding domains of anillin could not substitute for the corresponding ezrin domains in controlling cortical blebbing at the cell poles. Our results highlight specific designs of actin- or membrane-associated moieties of different actin-membrane associated proteins with limited exchangeability, which enables them to support diverse cortical activities on the shared actin-membrane interface during cytokinesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structural response reconstruction using a system-equivalent singular vector basis

Here, this paper develops a novel method for reconstructing the full-field response of structural dynamic systems using sparse measurements. The singular value decomposition is applied to a frequency response matrix relating the structural response to physical loads, base motion, or modal loads. The left singular vectors form a non-physical reduced basis that can be used for response reconstruction with far fewer sensors than existing methods. The contributions of the singular vectors to measured response are termed singular-vector loads (SVLs) and are used in a regularized Bayesian framework to generate full-field response estimates and confidence intervals. The reconstruction framework is applicable to the estimation of single data records and power spectral densities from multiple records. Reconstruction is successfully performed in configurations where the number of SVLs to identify is less than, equal to, and greater than the number of sensors used for reconstruction. In a simulation featuring a seismically excited shear structure, SVL reconstruction significantly outperforms modal FRF-based reconstruction and successfully estimates full-field responses with as few as two uniaxial accelerometers. SVL reconstruction is further verified in a simulation featuring an acoustically excited cylinder. Finally, response reconstruction and uncertainty quantification are performed on an experimental structure with three shaker inputs and 27 triaxial accelerometer outputs.

42 ENGINEERING↗
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↗