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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 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

U-splines: Splines over unstructured meshes

U-splines are a novel approach to the construction of a spline basis for representing smooth objects in Computer-Aided Design (CAD) and Computer-Aided Engineering (CAE). A spline is a piecewise-defined function that satisfies continuity constraints between adjacent cells in a mesh. U-splines differ from existing spline constructions, such as Non-Uniform Rational B-splines (NURBS), subdivision surfaces, T-splines, and hierarchical B-splines, in that they can accommodate local variation in cell size, polynomial degree, and smoothness simultaneously over more varied mesh configurations. Mixed cell types (e.g., triangle and quadrilateral cells in the same mesh) and T-junctions are also supported, although the continuity of interfaces with triangle and tetrahedral cells is limited in the present work. The U-spline algorithm introduces a new technique for using local null space solutions to construct basis functions for the global spline null space problem. The U-spline construction is presented for curves, surfaces, and volumes with higher dimensional generalizations possible. Lastly, a set of requirements are given to ensure that the U-spline basis is positive, forms a partition of unity, is complete, and is locally linearly independent.

42 ENGINEERING↗
DOE OSTI2019

Cardiac myosin activation with 2-deoxy-ATP via increased electrostatic interactions with actin

The naturally occurring nucleotide 2-deoxy-adenosine 5'-triphosphate (dATP) can be used by cardiac muscle as an alternative energy substrate for myosin chemomechanical activity. We and others have previously shown that dATP increases contractile force in normal hearts and models of depressed systolic function, but the structural basis of these effects has remained unresolved. In this work, we combine multiple techniques to provide structural and functional information at the angstrom-nanometer and millisecond time scales, demonstrating the ability to make both structural measurements and quantitative kinetic estimates of weak actin–myosin interactions that underpin sarcomere dynamics. Exploiting dATP as a molecular probe, we assess how small changes in myosin structure translate to electrostatic-based changes in sarcomere function to augment contractility in cardiac muscle. Through Brownian dynamics simulation and computational structural analysis, we found that deoxy-hydrolysis products [2-deoxy-adenosine 5′-diphosphate (dADP) and inorganic phosphate (Pi)] bound to prepowerstroke myosin induce an allosteric restructuring of the actin-binding surface on myosin to increase the rate of cross-bridge formation. We then show experimentally that this predicted effect translates into increased electrostatic interactions between actin and cardiac myosin in vitro. Finally, using small-angle X-ray diffraction analysis of sarcomere structure, we demonstrate that the proposed increased electrostatic affinity of myosin for actin causes a disruption of the resting conformation of myosin motors, resulting in their repositioning toward the thin filament before activation. The dATP-mediated structural alterations in myosin reported here may provide insight into an improved criterion for the design or selection of small molecules to be developed as therapeutic agents to treat systolic dysfunction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail

Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each RNP incorporates multiple copies of nucleoprotein (NP), a fragment of the viral genome (vRNA), and a viral RNA-dependent RNA polymerase (POL), and is responsible for packaging the viral genome and performing critical functions including replication and transcription. A complete model of an Influenza RNP in atomic detail can elucidate the structural basis for viral genome functions, and identify potential targets for viral therapeutics. In this work we construct a model of a complete Influenza A RNP complex in atomic detail using multiple sources of structural and sequence information and a series of homology-modeling techniques, including a motif-matching fragment assembly method. Our final model provides a rationale for experimentally-observed changes to viral polymerase activity in numerous mutational assays. Further, our model reveals specific interactions between the three primary structural components of the RNP, including potential targets for blocking POL-binding to the NP-vRNA complex. The methods developed in this work open the possibility of elucidating other functionally-relevant atomic-scale interactions in additional RNP structures and other biomolecular complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Galilei invariant technique for quantum system description

Problems with quantum systems models, violating Galilei invariance are examined. The method for arbitrary non-relativistic quantum system Galilei invariant wave function construction, applying a modified basis where center-of-mass excitations have been removed before Hamiltonian matrix diagonalization, is developed. For identical fermion system, the Galilei invariant wave function can be obtained while applying conventional antisymmetrization methods of wave functions, dependent on single particle spatial variables.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

On the Depth of k-Valued Logic Functions Over Arbitrary Bases

The behavior of the Shannon function of the depth of k-valued logic functions realized by circuits over an arbitrary complete basis is examined. For all k, k ≥ 3, for an arbitrary basis of k-valued logic functions, the existence of the asymptotic behavior of the Shannon function of the depth is established. The asymptotic behavior is linear for finite bases and it is constant or logarithmic for infinite bases. Thus, the complete picture of asymptotic behavior of the Shannon function of the depth is obtained for all k, k ≥ 2.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

The effect of hydrogen-bonding on flavin’s infrared absorption spectrum

Cluster and continuum solvation computational models are employed to model the effect of hydrogen bonding interactions on the vibrational modes of lumiflavin. Calculated spectra were compared to experimental Fourier-transform infrared (FTIR) spectra in the diagnostic 1450–1800 cm –1 range, where intense V C=C , V C=N , V C 2 =O , and V C 4 =O stretching modes of flavin’s isoalloxazine ring are found. Local mode analysis is used to describe the strength of hydrogen-bonding in cluster models. The computations indicate that V C=C and V C=N mode frequencies are relatively insensitive to intermolecular interactions while the V C 2 =O and V C 4 =O modes are sensitive to direct (and also indirect for V C 2 =O ) hydrogen-bonding interactions. Although flavin is neutral, basis sets without the diffuse functions provide incorrect relative frequencies and intensities. The 6-31+G* basis set is found to be adequate for this system, and there is limited benefit to considering larger basis sets. Calculated vibrational mode frequencies agree with experimentally determined frequencies in solution when cluster models with multiple water molecules are used. Accurate simulation of relative FTIR band intensities, on the other hand, requires a continuum (or possibly quantum mechanical/molecular mechanical) model that accounts for long-range electrostatic effects. Lastly, an experimental peak at ca. 1624 cm –1 that is typically assigned to the V C 2 =O vibrational stretching mode has a complicated shape that suggests multiple underlying contributions. Our calculations show that this band has contributions from both the C 6 –C 7 and C 2 = O stretching vibrations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Physiological Effect of XoxG(4) on Lanthanide-Dependent Methanotrophy

ABSTRACT A recent surprising discovery of the activity of rare earth metals (lanthanides) as enzyme cofactors as well as transcriptional regulators has overturned the traditional assumption of biological inertia of these metals. However, so far, examples of such activities have been limited to alcohol dehydrogenases. Here we describe the physiological effects of a mutation in xoxG , a gene encoding a novel cytochrome, XoxG(4), and compare these to the effects of mutation in XoxF, a lanthanide-dependent methanol dehydrogenase, at the enzyme activity level and also at the community function level, using Methylomonas sp. strain LW13 as a model organism. Through comparative phenotypic characterization, we establish XoxG as the second protein directly involved in lanthanide-dependent metabolism, likely as a dedicated electron acceptor from XoxF. However, mutation in XoxG caused a phenotype that was dramatically different from the phenotype of the mutant in XoxF, suggesting a secondary function for this cytochrome, in metabolism of methane. We also purify XoxG(4) and demonstrate that this protein is a true cytochrome c , based on the typical absorption spectra, and we demonstrate that XoxG can be directly reduced by a purified XoxF, supporting one of its proposed physiological functions. Overall, our data continue to suggest the complex nature of the interplay between the calcium-dependent and lanthanide-dependent alcohol oxidation systems, while they also suggest that addressing the roles of these alternative systems is essential at the enzyme and community function level, in addition to the gene transcription level. IMPORTANCE The lanthanide-dependent biochemistry of living organisms remains a barely tapped area of knowledge. So far, only a handful of lanthanide-dependent alcohol dehydrogenases have been described, and their regulation by lanthanides has been demonstrated at the transcription level. Little information is available regarding the concentrations of lanthanides that could support sufficient enzymatic activities to support specific metabolisms, and so far, no other redox proteins involved in lanthanide-dependent methanotrophy have been demonstrated. The research presented here provides enzyme activity-level data on lanthanide-dependent methanotrophy in a model methanotroph. Additionally, we identify a second protein important for lanthanide-dependent metabolism in this organism, XoxG(4), a novel cytochrome. XoxG(4) appears to have multiple functions in methanotrophy, one function as an electron acceptor from XoxF and another function remaining unknown. On the basis of the dramatic phenotype of the XoxG(4) mutant, this function must be crucial for methanotrophy.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Structural basis for type VI secreted peptidoglycan dl-endopeptidase function, specificity and neutralization in Serratia marcescens

Crystal structures of type VI secretion system-associated immunity proteins, a peptidoglycan endopeptidase and a complex of the endopeptidase and its cognate immunity protein are reported together with assays of endopeptidase activity and functional assessment. Some Gram-negative bacteria target their competitors by exploiting the type VI secretion system to extrude toxic effector proteins. To prevent self-harm, these bacteria also produce highly specific immunity proteins that neutralize these antagonistic effectors. Here, the peptidoglycan endopeptidase specificity of two type VI secretion-system-associated effectors from Serratia marcescens is characterized. These small secreted proteins, Ssp1 and Ssp2, cleave between γ-d-glutamic acid and l-meso-diaminopimelic acid with different specificities. Ssp2 degrades the acceptor part of cross-linked tetratetrapeptides. Ssp1 displays greater promiscuity and cleaves monomeric tripeptides, tetrapeptides and pentapeptides and dimeric tetratetra and tetrapenta muropeptides on both the acceptor and donor strands. Functional assays confirm the identity of a catalytic cysteine in these endopeptidases and crystal structures provide information on the structure–activity relationships of Ssp1 and, by comparison, of related effectors. Functional assays also reveal that neutralization of these effectors by their cognate immunity proteins, which are called resistance-associated proteins (Raps), contributes an essential role to cell fitness. The structures of two immunity proteins, Rap1a and Rap2a, responsible for the neutralization of Ssp1 and Ssp2-like endopeptidases, respectively, revealed two distinct folds, with that of Rap1a not having previously been observed. The structure of the Ssp1–Rap1a complex revealed a tightly bound heteromeric assembly with two effector molecules flanking a Rap1a dimer. A highly effective steric block of the Ssp1 active site forms the basis of effector neutralization. Comparisons with Ssp2–Rap2a orthologues suggest that the specificity of these immunity proteins for neutralizing effectors is fold-dependent and that in cases where the fold is conserved sequence differences contribute to the specificity of effector–immunity protein interactions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Communication: The description of strong correlation within self-consistent Green's function second-order perturbation theory

We report an implementation of self-consistent Green's function many-body theory within a second-order approximation (GF2) for application with molecular systems. This is done by iterative solution of the Dyson equation expressed in matrix form in an atomic orbital basis, where the Green's function and self-energy are built on the imaginary frequency and imaginary time domain, respectively, and fast Fourier transform is used to efficiently transform these quantities as needed. We apply this method to several archetypical examples of strong correlation, such as a H{sub 32} finite lattice that displays a highly multireference electronic ground state even at equilibrium lattice spacing. In all cases, GF2 gives a physically meaningful description of the metal to insulator transition in these systems, without resorting to spin-symmetry breaking. Our results show that self-consistent Green's function many-body theory offers a viable route to describing strong correlations while remaining within a computationally tractable single-particle formalism.

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

Modeling L 2,3 -edge X-ray absorption spectroscopy with linear response exact two-component relativistic time-dependent density functional theory

X-ray absorption spectroscopy (XAS) is a powerful tool that can provide physical insights into element-specific chemical processes and reactivities. Although relativistic time-dependent density functional theory (TDDFT) has been previously applied to model the L-edge region in XAS, there has not been a more comprehensive study of the choices of basis sets and density functional kernels available for variational relativistic excited state methods. In this work, we introduce the implementation of the generalized preconditioned locally harmonic residual algorithm to solve the complex-valued relativistic TDDFT for modeling the L-edge X-ray absorption spectra. Further, we investigate the L 2,3 -edge spectra of a series of molecular complexes using relativistic linear response TDDFT with a hybrid iterative diagonalization algorithm. A systematic error analysis was carried out with a focus on the energetics, intensities, and magnitude of L 2 –L 3 splitting compared to experiments. Additionally, the results from relativistic TDDFT calculations are compared to those computed using other theoretical methods, and the multideterminantal effects on the L-edge XAS were investigated.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Anisotropy of the Surface Energy and Work Function of IIB Metals

On the basis of electron-statistical method of calculation of the surface energy of metals, a technique for estimating the electron work function of hexagonal and rhombohedral metallic crystals has been developed. This technique relates surface energy to work function and can thus be applied to estimate the surface energy of crystal faces from experimental data for a work function. Computations have been made for cadmium, zinc, and mercury macrocrystals. The temperature and orientation dependences of both quantities have been constructed. Our results are in good agreement with literature experimental data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Determination of L-AP4-bound human mGlu8 receptor amino terminal domain structure and the molecular basis for L-AP4’s group III mGlu receptor functional potency and selectivity

Here, L-2-Amino-4-phosphonobutyric acid (L-AP4) is a known potent and selective agonist for the Group III mGlu receptors. However, it does not show any selectivity among the individual group III mGlu subtypes. In order to understand the molecular basis for this group selectivity, we solved the first human mGlu8 amino terminal domain (ATD) crystal structures in complex with L-glu and L-AP4. In comparison with other published L-glu-bound mGlu ATD structures, we have observed L-glu binds in a significantly different manner in mGlu1. Furthermore, these new structures provided evidence that both the electronic and steric nature of the distal phosphate of L-AP4 contribute to its exquisite Group III functional agonist potency and selectivity.

Schkeryantz, Jeffery M.↗
DOE OSTI2016

An approach to develop chemical intuition for atomistic electron transport calculations using basis set rotations

Single molecule conductance measurements are often interpreted through computational modeling, but the complexity of these calculations makes it difficult to directly link them to simpler concepts and models. Previous work has attempted to make this connection using maximally localized Wannier functions and symmetry adapted basis sets, but their use can be ambiguous and non-trivial. Starting from a Hamiltonian and overlap matrix written in a hydrogen-like basis set, we demonstrate a simple approach to obtain a new basis set that is chemically more intuitive and allows interpretation in terms of simple concepts and models. By diagonalizing the Hamiltonians corresponding to each atom in the molecule, we obtain a basis set that can be partitioned into pseudo-σ and −π and allows partitioning of the Landuaer-Büttiker transmission as well as create simple Hückel models that reproduce the key features of the full calculation. This method provides a link between complex calculations and simple concepts and models to provide intuition or extract parameters for more complex model systems.

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

Gravitational form factors and mechanical properties of quarks in protons: A basis light-front quantization approach

We compute the gravitational form factors (GFFs) and study their applications for the description of the mechanical properties such as the pressure, shear force distributions, and the mechanical radius of the proton from its light-front wave functions (LFWFs) based on basis light-front quantization (BLFQ). The LFWFs of the proton are given by the lowest eigenvector of a light-front effective Hamiltonian that incorporates a three-dimensional confining potential and a one-gluon exchange interaction with fixed coupling between the constituent quarks solved in the valence Fock sector. We find acceptable agreement between our BLFQ computations and the lattice QCD for the GFFs. Our D -term form factor also agrees well with the extracted data from the deeply virtual Compton scattering experiments at Jefferson Lab, and the results of different phenomenological models. The distributions of pressures and shear forces are similar to those from different models. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2016

Rigorous Ab Initio Quantum Embedding for Quantum Chemistry Using Green’s Function Theory: Screened Interaction, Nonlocal Self-Energy Relaxation, Orbital Basis, and Chemical Accuracy

We present a detailed discussion of the self-energy embedding theory (SEET), which is a quantum embedding scheme allowing us to describe a chosen subsystem very accurately while keeping the description of the environment at a lower level. We apply SEET to molecular examples where our chosen subsystem is made out of a set of strongly correlated orbitals while the weakly correlated orbitals constitute an environment. Consequently, a highly accurate method is used to calculate the self-energy for the system, while a lower-level method is employed to find the self-energy for the environment. Such a self-energy separation is very general, and to make the SEET procedure applicable to multiple systems, a detailed and practical procedure for the evaluation of the system and environment self-energy is necessary. We list all of the intricacies for one of the possible procedures while focusing our discussion on many practical implementation aspects such as the choice of best orbital basis, impurity solver, and many steps necessary to reach chemical accuracy. Finally, on a set of carefully chosen molecular examples, we demonstrate that SEET, which is a controlled, systematically improvable Green’s function method, can be as accurate as established wave function quantum chemistry methods.

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

Fast HARDI Uncertainty Quantification and Visualization with Spherical Sampling

In this paper, we study uncertainty quantification and visualization of orientation distribution functions (ODF), which corresponds to the diffusion profile of high angular resolution diffusion imaging (HARDI) data. The shape inclusion probability (SIP) function is the state‐of‐the‐art method for capturing the uncertainty of ODF ensembles. The current method of computing the SIP function with a volumetric basis exhibits high computational and memory costs, which can be a bottleneck to integrating uncertainty into HARDI visualization techniques and tools. We propose a novel spherical sampling framework for faster computation of the SIP function with lower memory usage and increased accuracy. In particular, we propose direct extraction of SIP isosurfaces, which represent confidence intervals indicating spatial uncertainty of HARDI glyphs, by performing spherical sampling of ODFs. Our spherical sampling approach requires much less sampling than the state‐of‐the‐art volume sampling method, thus providing significantly enhanced performance, scalability, and the ability to perform implicit ray tracing. Our experiments demonstrate that the SIP isosurfaces extracted with our spherical sampling approach can achieve up to 8164× speedup, 37282× memory reduction, and 50.2% less SIP isosurface error compared to the classical volume sampling approach. We demonstrate the efficacy of our methods through experiments on synthetic and human‐brain HARDI datasets.

97 MATHEMATICS AND COMPUTING↗