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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 OSTI2024

Confinement and Kink Entanglement Asymmetry on a Quantum Ising Chain

In this work, we explore the interplay of confinement, string breaking and entanglement asymmetry on a 1D quantum Ising chain. We consider the evolution of an initial domain wall and show that, surprisingly, while the introduction of confinement through a longitudinal field typically suppresses entanglement, it can also serve to increase it beyond a bound set for free particles. Our model can be tuned to conserve the number of domain walls, which gives an opportunity to explore entanglement asymmetry associated with link variables. We study two approaches to deal with the non-locality of the link variables, either directly or following a Kramers-Wannier transformation that maps bond variables (kinks) to site variables (spins). We develop a numerical procedure for computing the asymmetry using tensor network methods and use it to demonstrate the different types of entanglement and entanglement asymmetry.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

A Framework for Error-Bounded Approximate Computing, with an Application to Dot Products

Approximate computing techniques, which trade off the computation accuracy of an algorithm for better performance and energy efficiency, have been successful in reducing computation and power costs in several domains. However, error sensitive applications in high-performance computing are unable to benefit from existing approximate computing strategies that are not developed with guaranteed error bounds. While approximate computing techniques can be developed for individual high-performance computing applications by domain specialists, this often requires additional theoretical analysis and potentially extensive software modification. Hence, the development of low-level error-bounded approximate computing strategies that can be introduced into any high-performance computing application without requiring additional analysis or significant software alterations is desirable. In this paper, we provide a contribution in this direction by proposing a general framework for designing error-bounded approximate computing strategies and apply it to the dot product kernel to develop \bf qdot---an error-bounded approximate dot product kernel. Following the introduction of qdot, here we perform a theoretical analysis that yields a deterministic bound on the relative approximation error introduced by qdot. Empirical tests are performed to illustrate the tightness of the derived error bound and to demonstrate the effectiveness of qdot on a synthetic dataset, as well as two scientific benchmarks---the conjugate gradient (CG) and power methods. In some instances, using qdot for the dot products in CG can result in many components being quantized to half precision without increasing the iteration count required for convergence to the same solution as CG using a double precision dot product.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Structure of VanS from vancomycin-resistant enterococci: A sensor kinase with weak ATP binding

The VanRS two-component system regulates the resistance phenotype of vancomycin-resistant enterococci. VanS is a sensor histidine kinase that responds to the presence of vancomycin by autophosphorylating and subsequently transferring the phosphoryl group to the response regulator, VanR. The phosphotransfer activates VanR as a transcription factor, which initiates the expression of resistance genes. Structural information about VanS proteins has remained elusive, hindering the molecular-level understanding of their function. Here, we present X-ray crystal structures for the catalytic and ATP-binding (CA) domains of two VanS proteins, derived from vancomycin-resistant enterococci types A and C. Both proteins adopt the canonical Bergerat fold that has been observed for CA domains of other prokaryotic histidine kinases. We attempted to determine structures for the nucleotide-bound forms of both proteins; however, despite repeated efforts, these forms could not be crystallized, prompting us to measure the proteins' binding affinities for ATP. Unexpectedly, both CA domains displayed low affinities for the nucleotide, with K D values in the low millimolar range. Since these K D values are comparable to intracellular ATP concentrations, this weak substrate binding could reflect a way of regulating expression of the resistance phenotype.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

On the application of a frequency domain controller design methodology to non-minimum phase and unstable systems

A frequency-domain design methodology was developed for controller synthesis maximizing the allowable size of an unknown-but-bounded disturbance while satisfying prespecified control and output constraints. The design technique, which accounts for bandwidth limitations, is based on mapping time-domain constraints into the frequency domain. Application of this technique to non-minimum-phase and/or unstable systems is presented. A non-minimum-phase, unstable SIMO (single-input/multiple-output) system is examined, and the results are compared to those obtained by the set-theoretic (ST) approach. The comparison shows that this methodology can yield controllers that reject step disturbances larger than those obtained by the ST method.

Sobhani, Massoud↗
NASA NTRS2014

Bifurcation Analysis Using Rigorous Branch and Bound Methods

For the study of nonlinear dynamic systems, it is important to locate the equilibria and bifurcations occurring within a specified computational domain. This paper proposes a new approach for solving these problems and compares it to the numerical continuation method. The new approach is based upon branch and bound and utilizes rigorous enclosure techniques to yield outer bounding sets of both the equilibrium and local bifurcation manifolds. These sets, which comprise the union of hyper-rectangles, can be made to be as tight as desired. Sufficient conditions for the existence of equilibrium and bifurcation points taking the form of algebraic inequality constraints in the state-parameter space are used to calculate their enclosures directly. The enclosures for the bifurcation sets can be computed independently of the equilibrium manifold, and are guaranteed to contain all solutions within the computational domain. A further advantage of this method is the ability to compute a near-maximally sized hyper-rectangle of high dimension centered at a fixed parameter-state point whose elements are guaranteed to exclude all bifurcation points. This hyper-rectangle, which requires a global description of the bifurcation manifold within the computational domain, cannot be obtained otherwise. A test case, based on the dynamics of a UAV subject to uncertain center of gravity location, is used to illustrate the efficacy of the method by comparing it with numerical continuation and to evaluate its computational complexity.

Smith, Andrew P.↗
DOE OSTI2024

Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation

Abstract Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA–ssDNA complexes using single-molecule FRET and double electron–electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.

Biochemistry & Molecular Biology↗
NASA NTRS2000

Preparation and Fluorescence Anisotropy Study of a Ribonuclease-Lucifer Yellow Conjugate

We have prepared a chemical derivative of ribonuclease A (RNase) with lucifer yellow (LY). The rotational dynamics of the LY-RNase conjugate were characterized by steady state and time resolved fluorescence techniques. Steady state anisotropy measurements were performed at varying viscosities at 10C and 20C, and the rotational correlation time of both RNase and the covalently linked LY probe were determined by time resolved frequency domain measurements. Our data suggest that the fluorophore is rigidly bound at 10C.

Malone, C. C.↗
DOE OSTI2020

The C‐Terminal Domain of α‐Synuclein Confers Steric Stabilization on Synaptic Vesicle‐Like Surfaces

Abstract While α‐synuclein, an intrinsically disordered protein linked to Parkinson's disease, has been shown to associate with membrane organelles, its overall cellular function remains nebulous. α‐Synuclein binds to membranes through its amino‐terminal domain (first ≈100 residues), but there is no consensus on the biophysical function of the carboxyl‐terminal domain (last ≈40 residues) due, in part, to its lack of strong interaction partners and persisting intrinsic disorder even when membrane bound. Here, by directly applying force on α‐synuclein bound to spherical nanoparticle‐supported lipid bilayers (SSLBs) and tracking higher‐order structural changes through small‐angle X‐ray scattering, strong evidence is presented that α‐synuclein sterically stabilizes membrane surfaces through its carboxyl‐terminal domain. Full‐length α‐synuclein dramatically increases the critical osmotic pressure at which SSLBs cluster ( P C ≈ 1.3 × 10 5 Pa) compared to α‐synuclein without the carboxyl‐terminal domain ( P C ≈ 1.9 × 10 4 Pa) at physiological salt and temperature conditions. This clustering of α‐synuclein‐bound SSLBs is shown to be reversible and sensitive to monovalent/divalent salt, both features of grafted polyelectrolyte‐mediated steric stabilization. In elucidating the biophysical function of α‐synuclein in the framework of polymer science, it is demonstrated that the carboxyl‐terminal domain can potentially utilize its persisting intrinsic disorder to functionalize membrane surfaces.

Chung, Peter J.↗
DOE OSTI2020

Clostridioides difficile Toxin A Remodels Membranes and Mediates DNA Entry Into Cells to Activate Toll-Like Receptor 9 Signaling

Background & Aims: Clostridioides difficile toxin A (TcdA) activates the innate immune response. TcdA co-purifies with DNA. Toll-like receptor 9 (TLR9) recognizes bacterial DNA to initiate inflammation. We investigated whether DNA bound to TcdA activates an inflammatory response in murine models of C difficile infection via activation of TLR9. Methods: We performed studies with human colonocytes and monocytes and macrophages from wild-type and TLR9 knockout mice incubated with TcdA or its antagonist (ODN TTAGGG) or transduced with vectors encoding TLR9 or small-interfering RNAs. Cytokine production was measured with enzyme-linked immunosorbent assay. We studied a transduction domain of TcdA (TcdA 57-80 ), which was predicted by machine learning to have cell-penetrating activity and confirmed by synchrotron small-angle X-ray scattering. Intestines of CD1 mice, C57BL6J mice, and mice that express a form of TLR9 that is not activated by CpG DNA were injected with TcdA, TLR9 antagonist, or both. Enterotoxicity was estimated based on loop weight to length ratios. A TLR9 antagonist was tested in mice infected with C difficile. We incubated human colon explants with an antagonist of TLR9 and measured TcdA-induced production of cytokines. Results: The TcdA 57-80 protein transduction domain had membrane remodeling activity that allowed TcdA to enter endosomes. TcdA-bound DNA entered human colonocytes. TLR9 was required for production of cytokines by cultured cells and in human colon explants incubated with TcdA. TLR9 was required in TcdA-induced mice intestinal secretions and in the survival of mice infected by C difficile. Even in a protease-rich environment, in which only fragments of TcdA exist, the TcdA 57-80 domain organized DNA into a geometrically ordered structure that activated TLR9. Conclusions: TcdA from C difficile can bind and organize bacterial DNA to activate TLR9. TcdA and TcdA fragments remodel membranes, which allows them to access endosomes and present bacterial DNA to and activate TLR9. Rather than inactivating the ability of DNA to bind TLR9, TcdA appears to chaperone and organize DNA into an inflammatory, spatially periodic structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Modeling approaches for addressing unrelaxable bound constraints with unconstrained optimization methods

We explore novel approaches for solving nonlinear optimization problems with unrelaxable bound constraints, which must be satisfied before the objective function can be evaluated. Our method reformulates the unrelaxable bound-constrained problem as an unconstrained optimization problem that is amenable to existing unconstrained optimization methods. The reformulation relies on a domain warping to form a merit function; the choice of the warping determines the level of exactness with which the unconstrained problem can be used to find solutions to the bound-constrained problem, as well as key properties of the unconstrained formulation such as smoothness. We develop theory when the domain warping is a multioutput sigmoidal warping, and we explore the practical elements of applying unconstrained optimization methods to the formulation. Here, we develop an algorithm that exploits the structure of the sigmoidal warping to guarantee that unconstrained optimization algorithms applied to the merit function will find a stationary point to the desired tolerance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System

Recent studies have shown that the stimulator of interferon gene (STING) protein plays a central role in the immune system by facilitating the production of type I interferons in cells. The STING signaling pathway is also a prominent activator of cancer-killing T cells that initiate a powerful adaptive immune response. Since biomolecular signaling pathways are complicated and not easily identified through traditional experiments, molecular dynamics (MD) has often been used to study structural and dynamical responses of biological pathways. In this work, we carried out MD simulations for full-length chicken and human STING (chSTING and hSTING) proteins. Specifically, we investigated ligand-bound closed (holo) and ligand-unbound open (apo) forms of STING in the membrane system by comparing their conformational and dynamical differences. Our research provides clues for understanding the mechanism of the STING signaling pathway by uncovering detailed insights for the examined systems: the residues from each chain in the binding pocket are strongly correlated to one another in the open STING structure compared with those in the closed STING structure. Ligand-bound closed STING displays ~174° rotation of the ligand-binding domain (LBD) relative to the open STING structure. The dynamical analysis of residue Cys148 located in the linker region of hSTING does not support the earlier hypothesis that Cys148 can form disulfide bonds between adjacent STING dimers. We also demonstrate that using the full-length proteins is critical, since the MD simulations of the LBD portion alone cannot properly describe the global conformational properties of STING.

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

Adaptive responses of marine diatoms to zinc scarcity and ecological implications

Scarce dissolved surface ocean concentrations of the essential algal micronutrient zinc suggest that Zn may influence the growth of phytoplankton such as diatoms, which are major contributors to marine primary productivity. However, the specific mechanisms by which diatoms acclimate to Zn deficiency are poorly understood. Using global proteomic analysis, we identified two proteins (ZCRP-A/B, Zn/Co Responsive Protein A/B) among four diatom species that became abundant under Zn/Co limitation. Characterization using reverse genetic techniques and homology data suggests putative Zn/Co chaperone and membrane-bound transport complex component roles for ZCRP-A (a COG0523 domain protein) and ZCRP-B, respectively. Metaproteomic detection of ZCRPs along a Pacific Ocean transect revealed increased abundances at the surface (<200 m) where dZn and dCo were scarcest, implying Zn nutritional stress in marine algae is more prevalent than previously recognized. These results demonstrate multiple adaptive responses to Zn scarcity in marine diatoms that are deployed in low Zn regions of the Pacific Ocean.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Hybrid epoxy–acrylate resins for wavelength-selective multimaterial 3D printing

Structures in nature have evolved to combine hard and soft materials in precise 3D arrangements, which imbues bulk properties and functionality that remain elusive to mimic synthetically. However, the potential for biomimetic analogs to seamlessly interface hard materials with soft surfaces for applications ranging from robotics and sealants to medical devices (e.g., prosthetics and wearable health monitors) has driven the demand for innovative chemistries and manufacturing approaches. Herein, we unveil a liquid resin for rapid, high resolution digital light processing (DLP) 3D printing of multimaterial objects with an unprecedented combination of strength, elasticity, and resistance to aging. Two enabling discoveries are the use of a covalently bound (hybrid) epoxy-acrylate monomer that precludes plasticization of soft domains and a wavelength-selective photosensitizer that accelerates cationic curing for hard domains. Using dual projection for multicolor DLP 3D printing (UV and violet light), several bioinspired metamaterial structures are fabricated, including one with hard springs embedded in a soft cylinder to adjust compressive behavior and a detailed knee joint featuring “bones” and “ligaments” for smooth motion. Lastly, the application of this system to facilitate selective stretching for electronic devices is demonstrated with a proof-of-concept device.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging

Abstract Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several that efficiently label the brain in animals. When bound to a near-infrared dye-ligand, WHaloCaMP shows a 7× increase in fluorescence intensity and a 2.1-ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a to image Ca 2+ responses in vivo in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae and to quantify Ca 2+ concentration using fluorescence lifetime imaging microscopy (FLIM).

Biochemistry & Molecular Biology↗
DOE OSTI2021

Vascular K ATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides

Vascular tone is dependent on smooth muscle K ATP channels comprising pore-forming Kir6.1 and regulatory SUR2B subunits, in which mutations cause Cantú syndrome. Unique among K ATP isoforms, they lack spontaneous activity and require Mg-nucleotides for activation. Structural mechanisms underlying these properties are unknown. Here, we determined cryogenic electron microscopy structures of vascular K ATP channels bound to inhibitory ATP and glibenclamide, which differ informatively from similarly determined pancreatic K ATP channel isoform (Kir6.2/SUR1). Unlike SUR1, SUR2B subunits adopt distinct rotational “propeller” and “quatrefoil” geometries surrounding their Kir6.1 core. The glutamate/aspartate-rich linker connecting the two halves of the SUR-ABC core is observed in a quatrefoil-like conformation. Molecular dynamics simulations reveal MgADP-dependent dynamic tripartite interactions between this linker, SUR2B, and Kir6.1. The structures captured implicate a progression of intermediate states between MgADP-free inactivated, and MgADP-bound activated conformations wherein the glutamate/aspartate-rich linker participates as mobile autoinhibitory domain, suggesting a conformational pathway toward K ATP channel activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria

Abstract Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis , suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis for heparan sulfate co-polymerase action by the EXT1–2 complex

Heparan sulfate (HS) proteoglycans are extended (-GlcAβ1,4GlcNAcα1,4-)n co-polymers containing decorations of sulfation and epimerization that are linked to cell surface and extracellular matrix proteins. In mammals, HS repeat units are extended by an obligate heterocomplex of two exostosin family members, EXT1 and EXT2, where each protein monomer contains distinct GT47 (GT-B fold) and GT64 (GT-A fold) glycosyltransferase domains. In this study, we generated human EXT1–EXT2 (EXT1–2) as a functional heterocomplex and determined its structure in the presence of bound donor and acceptor substrates. Structural data and enzyme activity of catalytic site mutants demonstrate that only two of the four glycosyltransferase domains are major contributors to co-polymer syntheses: the EXT1 GT-B fold β1,4GlcA transferase domain and the EXT2 GT-A fold α1,4GlcNAc transferase domain. Furthermore, the two catalytic sites are over 90 Å apart, indicating that HS is synthesized by a dissociative process that involves a single catalytic site on each monomer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗