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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The collisional particle-in-cell method for the Vlasov–Maxwell–Landau equations

We introduce an extension of the particle-in-cell method that captures the Landau collisional effects in the Vlasov–Maxwell–Landau equations. The method arises from a regularisation of the variational formulation of the Landau equation, leading to a discretisation of the collision operator that conserves mass, charge, momentum and energy, while increasing the (regularised) entropy. The collisional effects appear as a fully deterministic effective force, thus the method does not require any transport–collision splitting. The scheme can be used in arbitrary dimension, and for a general interaction, including the Coulomb case. We validate the scheme on scenarios such as the Landau damping, the two-stream instability and the Weibel instability, demonstrating its effectiveness in the numerical simulation of plasma.

Bailo, Rafael (ORCID:0000000180183799)↗
DOE OSTI2021

Magnetic-Field-Driven Electron Dynamics in Graphene

Graphene exhibits unique optoelectronic properties originating from the band structure at the Dirac points. It is an ideal model structure to study the electronic and optical properties under the influence of the applied magnetic field. In graphene, electric field, laser pulse, and voltage can create electron dynamics which is influenced by momentum dispersion. However, computational modeling of momentum-influenced electron dynamics under the applied magnetic field remains challenging. In this work, we perform computational modeling of the photoexcited electron dynamics achieved in graphene under an applied magnetic field. Our results show that magnetic field leads to local deviation from momentum conservation for charge carriers. With the increasing magnetic field, the delocalization of electron probability distribution increases and forms a cyclotron-like trajectory. Our work facilitates understanding of momentum resolved magnetic field effect on non-equilibrium properties of graphene, which is critical for optoelectronic and photovoltaic applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway

Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Research progress on ionic plasmas generated in an intense hydrogen negative ion source

Characteristics of ionic plasmas, observed in a high-density hydrogen negative ion source, are investigated with a multi-diagnostics system. The ionic plasma, which consists of hydrogen positive- and negative-ions with a significantly low-density of electrons, is generated in the ion extraction region, from which the negative ions are extracted through the plasma grid. The negative ion density, i.e., the ionic plasma density, as high as the order of 1×10{sup 17}m{sup −3}, is measured with cavity ring-down spectroscopy, while the electron density is lower than 1×10{sup 16}m{sup −3}, which is confirmed with millimeter-wave interferometer. Reduction of the negative ion density is observed at the negative ion extraction, and at that time the electron flow into the ionic plasma region is observed to conserve the charge neutrality. Distribution of the plasma potential is measured in the extraction region in the direction normal to the plasma grid surface with a Langmuir probe, and the results suggest that the sheath is formed at the plasma boundary to the plasma grid to which the bias voltage is applied. The beam extraction should drive the negative ion transport in the ionic plasma across the sheath formed on the extraction surface. Larger reduction of the negative ions at the beam extraction is observed in a region above the extraction aperture on the plasma grid, which is confirmed with 2D image measurement of the Hα emission and cavity ring-down spectroscopy. The electron distribution is also measured near the plasma grid surface. These various properties observed in the ionic plasma are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3

CC chemokine ligand 5 (CCL5) and CCL3 are critical for immune surveillance and inflammation. Consequently, they are linked to the pathogenesis of many inflammatory conditions and are therapeutic targets. Oligomerization and glycosaminoglycan (GAG) binding of CCL5 and CCL3 are vital for the functions of these chemokines. Our structural and biophysical analyses of human CCL5 reveal that CCL5 oligomerization is a polymerization process in which CCL5 forms rod-shaped, double-helical oligomers. This CCL5 structure explains mutational data and offers a unified mechanism for CCL3, CCL4, and CCL5 assembly into high-molecular-weight, polydisperse oligomers. Here, a conserved, positively charged BBXB motif is key for the binding of CC chemokines to GAG. However, this motif is partially buried when CCL3, CCL4, and CCL5 are oligomerized; thus, the mechanism by which GAG binds these chemokine oligomers has been elusive. Our structures of GAG-bound CCL5 and CCL3 oligomers reveal that these chemokine oligomers have distinct GAG-binding mechanisms. The CCL5 oligomer uses another positively charged and fully exposed motif, KKWVR, in GAG binding. However, residues from two partially buried BBXB motifs along with other residues combine to form a GAG-binding groove in the CCL3 oligomer. The N termini of CC chemokines are shown to be involved in receptor binding and oligomerization. We also report an alternative CCL3 oligomer structure that reveals how conformational changes in CCL3 N termini profoundly alter its surface properties and dimer–dimer interactions to affect GAG binding and oligomerization. Such complexity in oligomerization and GAG binding enables intricate, physiologically relevant regulation of CC chemokine functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Structural studies of viperin, an antiviral radical SAM enzyme

Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45–362) complexed with S-adenosylhomocysteine (SAH) or 5'-deoxyadenosine (5'-dAdo) and l-methionine (l-Met). Viperin contains a partial (βα)6-barrel fold with a disordered N-terminal extension (residues 45–74) and a partially ordered C-terminal extension (residues 285–362) that bridges the partial barrel to form an overall closed barrel structure. Cys84, Cys88, and Cys91 located after the first β-strand bind a [4Fe-4S] cluster. The active site architecture of viperin with bound SAH (a SAM analog) or 5'-dAdo and l-Met (SAM cleavage products) is consistent with the canonical mechanism of 5'-deoxyadenosyl radical generation. The viperin structure, together with sequence alignments, suggests that vertebrate viperins are highly conserved and that fungi contain a viperin-like ortholog. Many bacteria and archaebacteria also express viperin-like enzymes with conserved active site residues. Structural alignments show that viperin is similar to several other radical SAM enzymes, including the molybdenum cofactor biosynthetic enzyme MoaA and the RNA methyltransferase RlmN, which methylates specific nucleotides in rRNA and tRNA. As a result, the viperin putative active site contains several conserved positively charged residues, and a portion of the active site shows structural similarity to the GTP-binding site of MoaA, suggesting that the viperin substrate may be a nucleoside triphosphate of some type.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular characterization of a fungal gasdermin-like protein

Programmed cell death (PCD) in filamentous fungi prevents cytoplasmic mixing following fusion between conspecific genetically distinct individuals (allorecognition) and serves as a defense mechanism against mycoparasitism, genome exploitation, and deleterious cytoplasmic elements (i.e., senescence plasmids). Recently, we identified regulator of cell death-1 ( rcd-1 ), a gene controlling PCD in germinated asexual spores in the filamentous fungus Neurospora crassa . rcd-1 alleles are highly polymorphic and fall into two haplogroups in N. crassa populations. Coexpression of alleles from the two haplogroups, rcd-1–1 and rcd-1–2 , is necessary and sufficient to trigger a cell death reaction. Here, we investigated the molecular bases of rcd-1 -dependent cell death. Based on in silico analyses, we found that RCD-1 is a remote homolog of the N-terminal pore-forming domain of gasdermin, the executioner protein of a highly inflammatory cell death reaction termed pyroptosis, which plays a key role in mammalian innate immunity. We show that RCD-1 localizes to the cell periphery and that cellular localization of RCD-1 was correlated with conserved positively charged residues on predicted amphipathic α-helices, as shown for murine gasdermin-D. Similar to gasdermin, RCD-1 binds acidic phospholipids in vitro, notably, cardiolipin and phosphatidylserine, and interacts with liposomes containing such lipids. The RCD-1 incompatibility system was reconstituted in human 293T cells, where coexpression of incompatible rcd-1–1/rcd-1–2 alleles triggered pyroptotic-like cell death. Oligomers of RCD-1 were associated with the cell death reaction, further supporting the evolutionary relationship between gasdermin and rcd-1 . This report documents an ancient transkingdom relationship of cell death execution modules involved in organismal defense.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Human sperm TMEM95 binds eggs and facilitates membrane fusion

Tmem95 encodes a sperm acrosomal membrane protein, whose knockout has a male-specific sterility phenotype in mice. Tmem95 knockout murine sperm can bind to, but do not fuse with, eggs. How TMEM95 plays a role in membrane fusion of sperm and eggs has remained elusive. Here, we utilize a sperm penetration assay as a model system to investigate the function of human TMEM95. We show that human TMEM95 binds to hamster egg membranes, providing evidence for a TMEM95 receptor on eggs. Using X-ray crystallography, we reveal an evolutionarily conserved, positively charged region of TMEM95 as a putative receptor-binding surface. Amino acid substitutions within this region of TMEM95 ablate egg-binding activity. We identify monoclonal antibodies against TMEM95 that reduce the number of human sperm fused with hamster eggs in sperm penetration assays. Strikingly, these antibodies do not block binding of sperm to eggs. Taken together, these results provide strong evidence for a specific, receptor-mediated interaction of sperm TMEM95 with eggs and suggest that this interaction may have a role in facilitating membrane fusion during fertilization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Dark halos around neutron stars and gravitational waves

Here, we find that models of MeV-GeV dark matter in which dark matter interacts strongly can be constrained by the observation of gravitational waves from binary neutron star (BNS) mergers. Trace amounts of dark matter, either produced during the supernova or accreted later, can alter the structure of neutron stars (NS) and influence their tidal deformability. We focus on models of dark matter interacting by the exchange of light vector gauge bosons that couple to a conserved dark charge. In these models, dark matter accumulated in neutron stars can extend to large radii. Gravitational waves detected from the first observed BNS merger GW170817 places useful constraints on such not-so compact objects. Dark halos, if present, further predict a greater variability of neutron star tidal deformabilities than expected for ordinary neutron stars.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Understanding Majorana braiding in superconductors with a fixed total number of particles

Mean-field one-dimensional topological superconductors host edge Majorana zero modes (MZMs) that encode a topologically protected ground-state degeneracy and enable robust braiding operations within this subspace. Mean-field states lack definite particle number and thus cannot represent isolated systems. Nevertheless, projecting them onto fixed particle number can yield good approximations to an isolated superconductor ground state. In earlier work [Sajith et al., Phys. Rev. B 109, 184509 (2024)] we showed that the projected Kitaev wave function of a single wire preserves some important mean-field features, such as the zero-energy spectral peaks near the wire edges. However, uniqueness of the fixed-number ground state does not allow for any nontrivial operations in the ground-state subspace. To overcome this limitation, here we consider the case of multiple wires with a conserved total charge, using the same approach. In the limit of vanishing interwire coupling, this system has a macroscopic ground-state degeneracy. We show how this degeneracy is resolved by coherent single-particle tunneling, and identify special many-body states which play the same role as the MZM parity states in the mean field. In this work, we demonstrate how braiding operations can be implemented and discuss both intrinsic and extrinsic limits on their fidelity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Symmetries and anomalies of Hamiltonian staggered fermions

We review the shift (translation) and time reversal symmetries of Hamiltonian staggered fermions and their connection to continuum symmetries concentrating in particular on the case of massless fermions and (3+1) dimensions. We construct operators using the staggered fields that implement these symmetries on finite lattices. We show that shifts composed of an odd multiple of the elementary shift anticommute with time reversal and are related to continuum axial transformations. We argue that the presence of these nontrivial commutation relations implies the existence of lattice ’t Hooft anomalies. From the shifts we also construct a set of conserved, quantized charges that generate continuous symmetries of the lattice theory. In general these do not commute with the vector charge signaling further ’t Hooft anomalies.

Anomalies↗
DOE OSTI2025

Dynamic, symmetry-preserving, and hardware-adaptable circuits for quantum computing many-body states and correlators of the Anderson impurity model

We present a hardware-reconfigurable ansatz on N q -qubits for the variational preparation of many-body states of the Anderson impurity model (AIM) with N imp + N bath = N q /2 sites, which conserves total charge and spin z component within each variational search subspace. The many-body ground state of the AIM is determined as the minimum over all minima of O(N$^2_ q$) distinct charge-spin sectors. Hamiltonian expectation values are shown to require ω(N q ) < N meas. $\leqslant$ O(N imp N bath ) symmetry-preserving, parallelizable measurement circuits, each amenable to postselection. To obtain the one-particle impurity Green’s function we show how initial Krylov vectors can be computed via midcircuit measurement and how Lanczos iterations can be computed using the symmetry-preserving ansatz. For a single-impurity Anderson model with a number of bath sites increasing from one to seven, we show using numerical emulation that the ease of variational ground-state preparation is suggestive of linear scaling in circuit depth and subquartic scaling in optimizer complexity. We therefore expect that, combined with time-dependent methods for Green’s function computation, our ansatz provides a useful tool to account for electronic correlations on early fault-tolerant processors. Finally, with a view towards computing real materials properties of interest like magnetic susceptibilities and electron-hole propagators, we provide a straightforward method to compute many-body, time-dependent correlation functions using a combination of time evolution, midcircuit measurement-conditioned operations, and the Hadamard test.

36 MATERIALS SCIENCE↗
DOE OSTI2012

The ice age ecologist: testing methods for reserve prioritization during the last global warming: Reserve selection and the ice age ecologist

We play the role of an ice age ecologist (IAE) charged with conserving biodiversity during the climate changes accompanying the last deglaciation. We develop reserve-selection strategies for the IAE and check them against rankings based on modern data. Three reserve-selection strategies are developed. (1) Abiotic: the IAE uses no information about species–climate relationships, instead maximizing the climatic and geographic dispersion of reserves. (2) Species distribution models (SDMs): the IAE uses boosted-regression trees calibrated against pollen data and CCSM3 palaeoclimatic simulations from 21 to 15 ka bp to predict modern taxon distributions, then uses these as input to the Zonation reserve-ranking program. (3) Rank-and-regress: regression models are used to identify climatic predictors of zonation rankings. All strategies are assessed against a Zonation ranking based on modern pollen distributions. Analysis units are ecoregions and grid cells. The abiotic strategy has a negative or no correlation between predicted and actual rankings. The SDM-based strategy fares better, with a significantly positive area-corrected correlation (r= 0.474, P < 0.001) between predicted and actual rankings. Predictive ability drops when grid cells are the analysis unit (r= 0.217, P = 0.058). Predictive ability for the rank-and-regress strategy is similar to the SDM results. For the IAE, SDMs improve the predictive ability of reserve-selection strategies. However, predictive ability is limited overall, probably due to shifted realized niches during past no-analogue climates, new species interactions as species responded individually to climate change, and other environmental changes not included in the model. Twenty-first-century conservation planning also faces these challenges, and is further complicated by other anthropogenic impacts. The IAE's limited success does not preclude the use of climate scenarios and niche-based SDMs when developing adaptation strategies, but suggests that such tools offer at best only a rough guide to identifying possible areas of future conservation value.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Analysis of 2D Transport and Performance Characteristics for Lateral Power Devices Based on AlGaN Alloys

In this paper, predicted lateral power device performance as a function of alloy composition is characterized by a standard lateral device figure-of-merit (LFOM) that depends on mobility, critical electric field, and sheet carrier density. The paper presents calculations of AlGaN electron mobility in lateral devices such as HEMTs across the entire alloy composition range. Alloy scattering and optical polar phonon scattering are the dominant mechanisms limiting carrier mobility. Due to the significant degradation of mobility from alloy scattering, at room temperature Al fractions greater than about 85% are required for improved LFOM relative to GaN using a conservative sheet charge density of 1 × 10 13 cm –2 . However, at higher temperatures at which AlGaN power devices are anticipated to operate, this “breakeven” composition decreases to about 65% at 500 K, for example. For high-frequency applications, the Johnson figure-of-merit (JFOM) is the relevant metric to compare potential device performance across materials platforms. At room temperature, the JFOM for AlGaN alloys is predicted to surpass that of GaN for Al fractions greater than about 40%.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Structure of the Intermediate Filament-Binding Region of Desmoplakin

Here, desmoplakin (DP) is a cytoskeletal linker protein that connects the desmosomal cadherin/plakoglobin/plakophilin complex to intermediate filaments (IFs). The C-terminal region of DP (DPCT) mediates IF binding, and contains three plakin repeat domains (PRDs), termed PRD-A, PRD-B and PRD-C. Previous crystal structures of PRDs B and C revealed that each is formed by 4.5 copies of a plakin repeat (PR) and has a conserved positively charged groove on its surface. Although PRDs A and B are linked by just four amino acids, B and C are separated by a 154 residue flexible linker, which has hindered crystallographic analysis of the full DPCT. Here we present the crystal structure of a DPCT fragment spanning PRDs A and B, and elucidate the overall architecture of DPCT by small angle X-ray scattering (SAXS) analysis. The structure of PRD-A is similar to that of PRD-B, and the two domains are arranged in a quasi-linear arrangement, and separated by a 4 amino acid linker. Analysis of the B-C linker region using secondary structure prediction and the crystal structure of a homologous linker from the cytolinker periplakin suggests that the N-terminal ~100 amino acids of the linker form two PR-like motifs. SAXS analysis of DPCT indicates an elongated but non-linear shape with R g = 51.5 Å and D max = 178 Å. These data provide the first structural insights into an IF binding protein containing multiple PRDs and provide a foundation for studying the molecular basis of DP-IF interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Lattice Clifford fractons and their Chern-Simons-like theory

We use Dirac matrix representations of the Clifford algebra to build fracton models on the lattice and their effective Chern-Simons-like theory. As an example, we build lattice fractons in odd D spatial dimensions and their (D+1) spacetime dimensional effective theory. The model possesses an anti-symmetric K matrix resembling that of hierarchical quantum Hall states. The gauge charges are conserved in sub-dimensional manifolds which ensures the fractonic behavior. The construction extends to any lattice fracton model built from commuting projectors and with tensor products of spin-1/2 degrees of freedom at the sites.

Fontana, Weslei↗
DOE OSTI2014

Fundamental Studies of Recombinant Hydrogenases

This research addressed the long term goals of understanding the assembly and organization of hydrogenase enzymes, of reducing them in size and complexity, of determining structure/function relationships, including energy conservation via charge separation across membranes, and in screening for novel H2 catalysts. A key overall goal of the proposed research was to define and characterize minimal hydrogenases that are produced in high yields and are oxygen-resistant. Remarkably, in spite of decades of research carried out on hydrogenases, it is not possible to readily manipulate or design the enzyme using molecular biology approaches since a recombinant form produced in a suitable host is not available. Such resources are essential if we are to understand what constitutes a “minimal” hydrogenase and design such catalysts with certain properties, such as resistance to oxygen, extreme stability and specificity for a given electron donor. The model system for our studies is Pyrococcus furiosus, a hyperthermophile that grows optimally at 100°C, which contains three different nickel-iron [NiFe-] containing hydrogenases. Hydrogenases I and II are cytoplasmic while the other, MBH, is an integral membrane protein that functions to both evolve H2 and pump protons. Three important breakthroughs were made during the funding period with P. furiosus soluble hydrogenase I (SHI). First, we produced an active recombinant form of SHI in E. coli by the co-expression of sixteen genes using anaerobically-induced promoters. Second, we genetically-engineered P. furiosus to overexpress SHI by an order of magnitude compared to the wild type strain. Third, we generated the first ‘minimal’ form of SHI, one that contained two rather than four subunits. This dimeric form was stable and active, and directly interacted with a pyruvate-oxidizing enzyme with any intermediate electron carrier. The research resulted in five peer-reviewed publications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Dark Matter in the Heavens and at Colliders: Models and Constraints

In this dissertation, we investigate various aspects of dark matter detection and model building. Motivated by the cosmic ray positron excess observed by PAMELA, we construct models of decaying dark matter to explain the excess. Specifically we present an explicit, TeV-scale model of decaying dark matter in which the approximate stability of the dark matter candidate is a consequence of a global symmetry that is broken only by instanton-induced operators generated by a non-Abelian dark gauge group. Alternatively, the decaying operator can arise as a Planck suppressed correction in a model with an Abelian discrete symmetry and vector-like states at an intermediate scale that are responsible for generating lepton Yukawa couplings. A flavor-nonconserving dark matter decay is also considered in the case of fermionic dark matter. Assuming a general Dirac structure for the four-fermion contact interactions of interest, the cosmic-ray electron and positron spectra were studied. We show that good fits to the current data can be obtained for both charged-leptonflavor- conserving and flavor-violating decay channels. Motivated by a possible excess of gamma rays in the galactic center, we constructed a supersymmetric leptophilic higgs model to explain the excess. Finally, we consider an improvement on dark matter collider searches using the Razor analysis, which was originally utilized for supersymmetry searches by the CMS collaboration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗