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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 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

LOKI

LOKI is a simulation code that models weakly-coupled plasma evolution using Eulerian kinetic models in four phase space dimensions. The code is useful to understand basic plasma nonlinear plasma physics phenomena - in particular, wave-particle and wave-wave resonances that occur in laser plasma interactions. LOKI can simulate fundamental physical process in low-density plasmas on a scale of hundreds of light wavelengths. It does so by solving the Vlasov and Valsov-Fokker-Planck differential transport equations describing the collision less and low-collisionality evolution of charged particles in electromagnetic fields in two configuration space and two velocity space dimensions. Two principle electromagnetic models are provided: electrostatic (Poisson's Equation) and electromagnetic (Maxwell's equations).

Banks, Jeffrey↗
DOE OSTI2022

Harmonizing model organism data in the Alliance of Genome Resources

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Inositol Pentakisphosphate Isomers Bind PH Domains with Varying Specificity and Inhibit Phosphoinositide Interactions

PH domains represent one of the most common domains in the human proteome. These domains are recognized as important mediators of protein-phosphoinositide and protein-protein interactions. Phosphoinositides are lipid components of the membrane that function as signaling molecules by targeting proteins to their sites of action. Phosphoinositide based signaling pathways govern a diverse range of important cellular processes including membrane remodeling, differentiation, proliferation and survival. Myo-Inositol phosphates are soluble signaling molecules that are structurally similar to the head groups of phosphoinositides. These molecules have been proposed to function, at least in part, by regulating PH domain-phosphoinositide interactions. Given the structural similarity of inositol phosphates we were interested in examining the specificity of PH domains towards the family of myo-inositol pentakisphosphate isomers. In work reported here we demonstrate that the C-terminal PH domain of pleckstrin possesses the specificity required to discriminate between different myo-inositol pentakisphosphate isomers. The structural basis for this specificity was determined using high-resolution crystal structures. Moreover, we show that while the PH domain of Grp1 does not possess this high degree of specificity, the PH domain of protein kinase B does. These results demonstrate that some PH domains possess enough specificity to discriminate between myo-inositol pentakisphosphate isomers allowing for these molecules to differentially regulate interactions with phosphoinositides. Furthermore, this work contributes to the growing body of evidence supporting myo-inositol phosphates as regulators of important PH domain-phosphoinositide interactions. Finally, in addition to expanding our knowledge of cellular signaling, these results provide a basis for developing tools to probe biological pathway.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

EVA Glove Research Team

The goal of the basic research portion of the extravehicular activity (EVA) glove research program is to gain a greater understanding of the kinematics of the hand, the characteristics of the pressurized EVA glove, and the interaction of the two. Examination of the literature showed that there existed no acceptable, non-invasive method of obtaining accurate biomechanical data on the hand. For this reason a project was initiated to develop magnetic resonance imaging as a tool for biomechanical data acquisition and visualization. Literature reviews also revealed a lack of practical modeling methods for fabric structures, so a basic science research program was also initiated in this area.

Strauss, Alvin M.↗
DOE OSTI2015

Final Scientific/Technical Report – March 2015

The Center for Interface Science: Solar Electric Materials (CISSEM) was funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences (BES) from August 1, 2009 – December 31, 2014 under Award Number DE-SC0001084, as part of a broad set of Energy Frontier Research Centers (EFRCs) designed to underpin the development of economical energy conversion platforms for the 21st century. CISSEM successfully integrated the research groups of 19 principal investigators at The University of Arizona (the lead institution), the Georgia Institute of Technology, Princeton University, the University of Washington, and the National Renewable Energy Laboratory (NREL) into a coordinated and synergistic program, while also building a highly productive collaboration with the SLAC National Accelerator Laboratory. Our mission was to advance the understanding of interface science underlying solar energy conversion technologies based on organic and organic-inorganic hybrid materials – specifically in organic photovoltaic solar cells (OPVs); and to inspire, recruit and train future scientists and leaders in the basic science of solar electric energy conversion. CISSEM researchers focused on establishing a foundational understanding of the electronic properties of interfaces in area-scalable, thin-film photovoltaic platforms. Metal oxide interlayers used in OPVs to improve the efficiency of charge harvesting at electrodes was our central focus. A key feature of CISSEM research has been our ability to develop a comprehensive understanding of interfaces and interfacial processes at the atomic and molecular scales. This is a scientific foundation for thin-film photovoltaic technologies and our nation’s pursuit of lowering the costs of transforming the sun’s energy into electricity. Our efforts combined: i) theoretical modeling; ii) new materials development; iii) developing new measurement science approaches to characterize composition, molecular and supramolecular structure, band edge energies, electrical properties, and charge harvesting or injection; and iv) integrating our use-inspired new materials and enhanced knowledge of interfaces and interfacial processes into OPV platforms. The strengths of the characterization methodologies developed in CISSEM were recognized within the EFRC network, and were a major component of our interactions with other DOE-funded programs including EFRCs. CISSEM research has resulted in a legacy of 120+ peer-reviewed publications describing our basic science. Much of this highly collaborative research will now be built upon at CISSEM member institutions, with other extramural funding sources. Furthermore, the state-of-the-art facilities and expertise created for modern interface science, especially as they pertain to energy conversion and energy storage challenges, will ensure their broadest continued impact. DOE EFRC funding has positively impacted and enhanced the training and development of more than 140 graduate students, postdoctoral researchers and research scientists at the five CISSEM institutions, and students from three Colorado universities associated with NREL. Our legacy also includes these student, postdoctoral researcher and scientist alumni who have taken positions of impact and responsibility in technology industries, government agencies and academia in the U.S., Asia and Europe.

14 SOLAR ENERGY↗
DOE OSTI2023

A rapid assay for assessing bacterial effects on Arabidopsis thermotolerance

Abstract Background The role of beneficial microbes in mitigating plant abiotic stress has received considerable attention. However, the lack of a reproducible and relatively high-throughput screen for microbial contributions to plant thermotolerance has greatly limited progress in this area, this slows the discovery of novel beneficial isolates and the processes by which they operate. Results We designed a rapid phenotyping method to assess the effects of bacteria on plant host thermotolerance. After testing multiple growth conditions, a hydroponic system was selected and used to optimize an Arabidopsis heat shock regime and phenotypic evaluation. Arabidopsis seedlings germinated on a PTFE mesh disc were floated onto a 6-well plate containing liquid MS media, then subjected to heat shock at 45 °C for various duration. To characterize phenotype, plants were harvested after four days of recovery to measure chlorophyll content. The method was extended to include bacterial isolates and to quantify bacterial contributions to host plant thermotolerance. As an exemplar, the method was used to screen 25 strains of the plant growth promoting Variovorax spp. for enhanced plant thermotolerance. A follow-up study demonstrated the reproducibility of this assay and led to the discovery of a novel beneficial interaction. Conclusions This method enables rapid screening of individual bacterial strains for beneficial effects on host plant thermotolerance. The throughput and reproducibility of the system is ideal for testing many genetic variants of Arabidopsis and bacterial strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy: An Emerging Method in Structural Biology for Examining Protein Conformations and Protein Interactions

Circular dichroism (CD) spectroscopy is a well-established technique in structural biology. The use of synchrotron radiation as an intense light source for these measurements extends the applications possible using lab-based instruments. In recent years, there has been a major growth in synchrotron radiation circular dichroism (SRCD) beamlines worldwide, including ones at the NSLS, ISA, SRS, HiSOR, BSRF, NSRRC, SOLEIL, Diamond, TERAS, BESSYII, and ANKA synchrotrons. Through the coordinated efforts of beamline scientists and users at these sites, important proof-of-principle studies have been done enabling the method to be developed for novel and productive studies on biological systems. This paper describes the characteristics of SRCD beamlines and some of the new types of applications that have been undertaken using these beamlines.

43 PARTICLE ACCELERATORS↗
NASA NTRS1992

Receptivity of a laminar boundary layer to the interaction of a three-dimensional roughness element with time-harmonic free-stream disturbances

Receptivity of a laminar boundary layer to the interaction of time-harmonic free-stream disturbances with a 3D roughness element is studied. The 3D nonlinear triple-deck equations are solved numerically to provide the basic steady-state motion. At high Reynolds numbers, the governing equations for the unsteady motion are the unsteady linearized 3D triple-deck equations. These equations can only be solved numerically. In the absence of any roughness element, the free-stream disturbances, to the first order, produce the classical Stokes flow, in the thin Stokes layer near the wall (on the order of our lower deck). However, with the introduction of a small 3D roughness element, the interaction between the hump and the Stokes flow introduces a spectrum of all spatial disturbances inside the boundary layer.

Tadjfar, M.↗
DOE OSTI2019

iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast

Here, we developed a flexible toolkit for combinatorial screening in Saccharomyces cerevisiae , which generates large libraries of cells, each uniquely barcoded to mark a combination of DNA elements. This interaction sequencing platform (iSeq 2.0) includes genomic landing pads that assemble combinations through sequential integration of plasmids or yeast mating, 15 barcoded plasmid libraries containing split selectable markers (URA3 AI , KanMX AI , HphMX AI , and NatMX AI ), and an array of ~24,000 “double-barcoder” strains that can make existing yeast libraries iSeq compatible. Various DNA elements are compatible with iSeq: DNA introduced on integrating plasmids, engineered genomic modifications, or entire genetic backgrounds. DNA element libraries are modular and interchangeable, and any two libraries can be combined, making iSeq capable of performing many new combinatorial screens by short-read sequencing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease

HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions

In eukaryotes, ubiquitination is an important posttranslational process achieved through a cascade of ubiquitin-activating (E1), conjugating (E2), and ligase (E3) enzymes. Many pathogenic bacteria deliver virulence factors into the host cell that function as E3 ligases. How these bacterial 'Trojan horses' integrate into the eukaryotic ubiquitin system has remained a mystery. Here we report crystal structures of two bacterial E3s, Salmonella SopA and Escherichia coli NleL, both in complex with human E2 UbcH7. These structures represent two distinct conformational states of the bacterial E3s, supporting the necessary structural rearrangements associated with ubiquitin transfer. The E2-interacting surface of SopA and NleL has little similarity to those of eukaryotic E3s. However, both bacterial E3s bind to the canonical surface of E2 that normally interacts with eukaryotic E3s. Furthermore, we show that a glutamate residue on E3 is involved in catalyzing ubiquitin transfer from E3 to the substrate, but not from E2 to E3. Together, these results provide mechanistic insights into the ubiquitin pathway and a framework for understanding molecular mimicry in bacterial pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1985

Geocoronal structure - The effects of solar radiation pressure and the plasmasphere interaction

The theory of planetary exospheres is extended to incorporate solar radiation pressure in a rigorous manner, and an evaporative geocoronal prototype (classical, motionless exobase) is constructed using Liouville's theorem. Model calculations for density and kinetic temperature at points along the earth-sun axis (solar and antisolar directions) reveal an extensive satellite component, comprising approximately 2/3 of the total hydrogen density near 10 earth radii, and a temperature profile suggestive of an isotropic quasi-Maxwellian velocity distribution for the bound component. A geotail is also evident as an enhancement of the density at local midnight compared to local noon that increases outward (from approximately 25 percent at 10 earth radii to over 60 percent at 20 earth radii). Additional mechanisms acting upon the geocorona alter the basic evaporative case in notable ways. Solar ionization has been included in a simple fashion; the effect is to partially deplete the density without otherwise altering the structure. Interaction with a simple plasmasphere via the Boltzmann equation results in 'heating' the geocorona and enhancing the escape flux at the expense of the density of the bound component, an effect not appreciated in earlier studies; the geotail survives this interaction.

Bishop, J.↗
DOE OSTI2021

Simultaneous measurement of organic scintillator response to carbon and proton recoils

Organic scintillators are widely used for neutron detection in both basic nuclear physics and applications. While the proton light yield of organic scintillators has been extensively studied, measurements of the light yield from neutron interactions with carbon nuclei are scarce. Demonstrate a new approach for the simultaneous measurement of the proton and carbon light yield of organic scintillators. Provide new carbon light yield data for the EJ-309 liquid and EJ-204 plastic organic scintillators. A 33-MeV 2 H + beam from the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory was impinged upon a 3-mm-thick Be target to produce a high-flux, broad-spectrum neutron beam. The double time-of-flight technique was extended to simultaneously measure the proton and carbon light yields of the organic scintillators, wherein the light output associated with the recoil particle was determined using np and nC elastic scattering kinematics. The proton and carbon light yield relations of the EJ-309 liquid and EJ-204 plastic organic scintillators were measured over a recoil energy range of approximately 0.3 to 1 MeV and 2 to 5 MeV, respectively, for EJ-309, and 0.2 to 0.5 MeV and 1 to 4 MeV, respectively, for EJ-204. Furthermore, these data provide new insight into the ionization quenching effect in organic scintillators and key input for simulation of the response of organic scintillators for both basic science and a broad range of applications.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Toward FAIR Representations of Microbial Interactions

Despite an ever-growing number of data sets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations present a major challenge to microbiome research by hindering the streamlined drawing of inferences across studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead?

Global change is altering species distributions and thus interactions among organisms. Organisms live in concert with thousands of other species, some beneficial, some pathogenic, some which have little to no effect in complex communities. Since natural communities are composed of organisms with very different life history traits and dispersal ability it is unlikely they will all respond to climatic change in a similar way. Disjuncts in plant-pollinator and plant-herbivore interactions under global change have been relatively well described, but plant-soil microorganism and soil microbe-microbe relationships have received less attention. Since soil microorganisms regulate nutrient transformations, provide plants with nutrients, allow co-existence among neighbors, and control plant populations, changes in soil microorganism-plant interactions could have significant ramifications for plant community composition and ecosystem function. Finally, in this paper we explore how climatic change affects soil microbes and soil microbe-plant interactions directly and indirectly, discuss what we see as emerging and exciting questions and areas for future research, and discuss what ramifications changes in these interactions may have on the composition and function of ecosystems.

54 ENVIRONMENTAL SCIENCES↗