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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

SciDAC Advances in Beam Dynamics Simulation: From Light Sources to Colliders

In this paper, we report on progress that has been made in beam dynamics simulation, from light sources to colliders, during the first year of the SciDAC-2 accelerator project 'Community Petascale Project for Accelerator Science and Simulation (ComPASS).' Several parallel computational tools for beam dynamics simulation are described. Also presented are number of applications in current and future accelerator facilities (e.g., LCLS, RHIC, Tevatron, LHC, and ELIC). Particle accelerators are some of most important tools of scientific discovery. They are widely used in high-energy physics, nuclear physics, and other basic and applied sciences to study the interaction of elementary particles, to probe the internal structure of matter, and to generate high-brightness radiation for research in materials science, chemistry, biology, and other fields. Modern accelerators are complex and expensive devices that may be several kilometers long and may consist of thousands of beamline elements. An accelerator may transport trillions of charged particles that interact electromagnetically among themselves, that interact with fields produced by the accelerator components, and that interact with beam-induced fields. Large-scale beam dynamics simulations on massively parallel computers can help provide understanding of these complex physical phenomena, help minimize design cost, and help optimize machine operation. In this paper, we report on beam dynamics simulations in a variety of accelerators ranging from next generation light sources to high-energy ring colliders that have been studied during the first year of the SciDAC-2 accelerator project.

43 PARTICLE ACCELERATORS↗
DOE OSTI2014

Foundation of Hydrodynamics of Strongly Interacting Systems

Hydrodynamics and quantum mechanics have many elements in common, as the density field and velocity fields are common variables that can be constructed in both descriptions. Starting with the Schroedinger equation and the Klein-Gordon for a single particle in hydrodynamical form, we examine the basic assumptions under which a quantum system of particles interacting through their mean fields can be described by hydrodynamics.

Wong, Cheuk-Yin↗
DOE OSTI2018

High Temperature Superconductivity - Unifying Themes in Diverse Materials

Understanding high temperature superconductivity is a grand challenge of current-day condensed matter physics. Superconductivity describes a coherent macroscopic quantum state of electron pairs. Conventional superconductivity arises in simple metals, where the electrons form pairs from an effective attractive interaction produced by their coupling with the ionic vibrations. In high-temperature and related unconventional superconductors, the electron pairing is believed to be primarily driven by the interactions among the electron correlations themselves. How the repulsive electron-electron interactions can lead to superconductivity is a key open question that is pertinent to a variety of electronic materials. Time is ripe to address this basic question and search for the organizing principles of the interacting electrons in a diverse array of materials with high temperature or otherwise unconventional superconductivity. Recent developments in the study of the iron-based superconductors have renewed hope of reaching even higher superconducting transition temperature, and led to considerable progresses in their understanding. Meanwhile, the study of the copper-based superconductors has undergone a drastic resurgence. The conference will aim to take an especially holistic view about diverse superconducting materials and, in so doing, search for and synthesize the unifying themes of their microscopic physics. The conference will compare and contrast the superconductivity of the iron- and copper-based systems with that of heavy fermion and organic superconductors, as well as superconductivity above 200K that has been reported under extreme pressure in the past three years. In addition, the conference will highlight the recent progresses on quantum criticality and spin liquid physics, which may underlie the unconventional superconductivity in the variety of material s. Funding for the conference would primarily be used to support early career researchers, including those from under-represented groups.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Defining a Two-pronged Structural Model for PB1 (Phox/Bem1p) Domain Interaction in Plant Auxin Responses

Phox/Bem1p (PB1) domains are universal structural modules that use surfaces of different charge for protein-protein association. In plants, PB1-mediated interactions of auxin response factors (ARF) and auxin/indole 3-acetic acid inducible proteins regulate transcriptional events modulated by the phytohormone auxin. Here we investigate the thermodynamic and structural basis for Arabidopsis thaliana ARF7 PB1 domain self-interaction. Isothermal titration calorimetry and NMR experiments indicate that key residues on both the basic and acidic faces of the PB1 domain contribute to and organize coordinately to stabilize protein-protein interactions. Calorimetric analysis of ARF7PB1 site-directed mutants defines a two-pronged electrostatic interaction. Furthermore, the canonical PB1 interaction between a lysine and a cluster of acidic residues provides one prong with an arginine and a second cluster of acidic residues defining the other prong. Evolutionary conservation of this core recognition feature and other co-varying interface sequences allows for versatile PB1-mediated interactions in auxin signaling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Peppytides: Interactive Models of Polypeptide Chains

Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

3D PRINTING↗
DOE OSTI2015

Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex

Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region of the HDAC interaction domain (HID) of the scaffolding protein Sin3A through a bipartite motif comprising a helix and an adjacent extended segment. Sds3 dimerizes through not only one of the predicted coiled-coil motifs but also, the segment preceding it, forming an ~150-Å-long antiparallel dimer. Contrary to previous findings in yeast, Sin3A rather than Sds3 functions in recruiting HDAC1 into the complex by engaging the latter through a highly conserved segment adjacent to the helical HID subdomain. In the resulting model for the ternary complex, the two copies of the HDACs are situated distally and dynamically because of a natively unstructured linker connecting the dimerization domain and the Sin3A interaction domain of Sds3; these features contrast with the static organization described previously for the NuRD (nucleosome remodeling and deacetylase) complex. Finally, the Sds3 linker features several conserved basic residues that could potentially maintain the complex on chromatin by nonspecific interactions with DNA after initial recruitment by sequence-specific DNA-binding repressors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Composite nonlinear structure within the magnetosonic soliton interactions in a spin-1/2 degenerate quantum plasma

We study the basic physical properties of composite nonlinear structure induced by the head-on collision of magnetosonic solitons. Solitary waves are assumed to propagate in a quantum electron-ion magnetoplasma with spin-1/2 degenerate electrons. The main interest of the present work is to investigate the time evolution of the merged composite structure during a specific time interval of the wave interaction process. We consider three cases of colliding-situation, namely, compressive-rarefactive solitons interaction, compressive-compressive solitons interaction, and rarefactive-rarefactive solitons interaction, respectively. Compared with the last two colliding cases, the changing process of the composite structure is more complex for the first situation. Moreover, it is found that they are obviously different for the last two colliding cases.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Manipulation of polystyrene nanoparticles on a silicon wafer in the peak force tapping mode in water: pH-dependent friction and adhesion force

The friction force between nanoparticles and a silicon wafer is a crucial parameter for cleaning processes in the semiconductor industry. However, little is known about the pH-dependency of the friction forces and the shear strength at the interface. Here, we push polystyrene nanoparticles, 100 nm in diameter, with the tip of an atomic force microscope and measure the pH-dependency of the friction, adhesion, and normal forces on a silicon substrate covered with a native silicon dioxide layer. The peak force tapping mode was applied to control the vertical force on these particles. We successively increased the applied load until the particles started to move. The main advantage of this technique over single manipulation processes is the achievement of a large number of manipulation events in short time and in a straightforward manner. Geometrical considerations of the interaction forces at the tip-particle interface allowed us to calculate the friction force and shear strength from the applied normal force depending on the pH of an aqueous solution. The results clearly demonstrated that particle removal should be performed with a basic solution at pH 9 because of the low interaction forces between particle and substrate.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

X-Ray Laser Gets First Real-Time Snapshots of a Chemical Flipping a Biological Switch

Scientists have used the powerful X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory to make the first snapshots of a chemical interaction between two biomolecules – one that flips an RNA “switch” that regulates production of proteins, the workhorse molecules of life. The results, published in Nature, show the game-changing potential of X-ray free-electron lasers, or XFELs, for studying RNA, which guides protein manufacturing in the cell, serves as the primary genetic material in retroviruses such as HIV and also plays a role in most forms of cancer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Quantile-specific heritability of sibling leptin concentrations and its implications for gene-environment interactions

“Quantile-dependent expressivity” occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g., leptin) is high or low relative to its distribution. Leptin concentrations are strongly related to adiposity, whose heritability is quantile dependent. Whether inheritance of leptin concentrations is quantile dependent, and whether this explains the greater heritability in women than men in accordance with their greater adiposity, and explains other gene-environment interactions, remains to be determined. Therefore, leptin and leptin receptor concentrations from 3068 siblings in 1133 sibships from the Framingham Heart Study Third Generation Cohort were analyzed. Free leptin index (FLI) was calculated as the ratio of leptin to soluble leptin receptor concentrations. Full-sib (β FS ) regression slopes were robustly estimated by quantile regression with nonparametric significance assigned from 1000 bootstrap samples. The analyses showed β FS increased significantly with increasing percentiles of the offspring’s age- and sex-adjusted leptin distribution (P linear = 0.0001), which was accelerated at the higher concentrations (P quadratic = 0.0003). β FS at the 90th percentile (0.418 ± 0.066) was 4.7-fold greater than at the 10th percentile (0.089 ± 0.032, P difference = 3.6 × 10 –6 ). Consistent with quantile-dependent expressivity, the β FS was greater in female sibs, which was attributable to their higher leptin concentrations. Reported gene-environment interactions involving adiposity and LEP , LEPR , MnSOD , PPARγ , PPARγ2 , and IRS-1 polymorphisms were consistent with quantile-dependent expressivity of leptin concentrations. β FS for leptin receptor concentrations and free leptin index also increased significantly with increasing percentiles of their distributions (P linear = 0.04 and P linear = 8.5 × 10 –6 , respectively). In conclusion, inherited genetic and shared environmental effects on leptin concentrations were quantile dependent, which likely explains male–female differences in heritability and some gene-environment interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

DHS Internship Final Report

This summer I worked on projects that involved RNA sequencing of pathogens after an infection of host cells. The goal of these projects was to continue developing pathogen enrichment strategies for transcriptomic analysis, and also to perform hostpathogen interaction studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Corrinoids as model nutrients to probe microbial interactions in a soil ecosystem

Earth’s soils are habitats for microbial communities that drive biogeochemical cycling, plant growth, and carbon storage and persistence. The thousands of microbial species living in soil form an intricate web of interactions involving the exchange of molecules produced by different microbes. Understanding in detail how these molecular exchanges occur and how they shape microbial communities may lead to new methods to improve soil health, bioremediation efforts, and better understanding of biogeochemical processes. The overall goal of this research is to gain a deeper knowledge of the microbial interactions that drive soil community structure. However, the high functional and genomic diversity in soil microbiomes has posed a challenge for current microbiology methods to achieve this goal. This research leverages a model group of key metabolites related to cobalamin (vitamin B 12 ), known as corrinoids, to investigate microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

The Development of A Human Systems Simulation Laboratory: Strategic Direction

The Human System Simulation Laboratory (HSSL) at the Idaho National Laboratory is one of few facilities of its kind that allows human factors researchers to evaluate various aspects of human performance and human system interaction for proposed reactor designs and upgrades. A basic system architecture, physical configuration and simulation capability were established to enable human factors researchers to support multiple, simultaneous simulations and also different power plant technologies. Although still evolving in terms of its technical and functional architecture, the HSSL is already proving its worth in supporting current and future nuclear industry needs for light water reactor sustainability and small modular reactors. The evolution of the HSSL is focused on continual physical and functional refinement to make it a fully equipped, reconfigurable facility where advanced research, testing and validation studies can be conducted on a wider range of reactor technologies. This requires the implementation of additional plant models to produce empirical research data on human performance with emerging human-system interaction technologies. Additional beneficiaries of this information include system designers and HRA practitioners. To ensure that results of control room crew studies will be generalizable to the existing and evolving fleet of US reactors, future expansion of the HSSL may also include other SMR plant models, plant-specific simulators and a generic plant model aligned to the current generation of pressurized water reactors (PWRs) and future advanced reactor designs. Collaboration with industry partners is also proving to be a vital component of the facility as this helps to establish a formal basis for current and future human performance experiments to support nuclear industry objectives. A long-range Program Plan has been developed for the HSSL to ensure that the facility will support not only the Department of Energy’s Light Water Reactor Sustainability Program, but also to provide human factors guidance for all future developments of the nuclear industry.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delighted to announce the launch of the Metaproteomics Initiative (www.metaproteomics.org), the goal of which is to promote dissemination of metaproteomics fundamentals, advancements, and applications through collaborative networking in microbiome research. The Initiative aims to be the central information hub and open meeting place where newcomers and experts interact to communicate, standardize, and accelerate experimental and bioinformatic methodologies in this field. We invite the entire microbiome community to join and discuss potential synergies at the interfaces with other disciplines, and to collectively promote innovative approaches to gain deeper insights into microbiome functions and dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma

The oncogenic transcription factor MYC and its binding partner MAX regulate gene expression by binding to DNA at enhancer-box (E-box) elements 5'-CACGTG-3'. In mammalian genomes, the central E-box CpG has the potential to be methylated at the 5-position of cytosine (5mC), or to undergo further oxidation to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), or 5-carboxyl (5caC) forms. We find that MAX exhibits the greatest affinity for a 5caC or unmodified C-containing E-box, and much reduced affinities for the corresponding 5mC, 5hmC or 5fC forms. Crystallization of MAX with a 5caC modified E-box oligonucleotide revealed that MAX Arg36 recognizes 5caC using a 5caC–Arg–Guanine triad, with the next nearest residue to the carboxylate group being Arg60. In an analysis of >800 primary multiple myelomas, MAX alterations occurred at a frequency of ~3%, more than half of which were single nucleotide substitutions affecting a basic clamp-like interface important for DNA interaction. Among these, arginines 35, 36 and 60 were the most frequently altered. In vitro binding studies showed that whereas mutation of Arg36 (R36W) or Arg35 (R35H/L) completely abolished DNA binding, mutation of Arg60 (R60Q) significantly reduced DNA binding, but retained a preference for the 5caC modified E-box. Interestingly, MAX alterations define a subset of myeloma patients with lower MYC expression and a better overall prognosis. Together these data indicate that MAX can act as a direct epigenetic sensor of E-box cytosine modification states and that local CpG modification and MAX variants converge to modulate the MAX-MYC transcriptional network.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Design Function and Structure of a Monomeric CLC Transporter

Channels and transporters of the ClC family cause the transmembrane movement of inorganic anions in service of a variety of biological tasks, from the unusual - the generation of the kilowatt pulses with which electric fish stun their prey - to the quotidian - the acidification of endosomes, vacuoles and lysosomes. The homodimeric architecture of ClC proteins, initially inferred from single-molecule studies of an elasmobranch Cl{sup -} channel and later confirmed by crystal structures of bacterial Cl{sup -}/H{sup +} antiporters, is apparently universal. Moreover, the basic machinery that enables ion movement through these proteins - the aqueous pores for anion diffusion in the channels and the ion-coupling chambers that coordinate Cl{sup -} and H{sup +} antiport in the transporters - are contained wholly within each subunit of the homodimer. The near-normal function of a bacterial ClC transporter straitjacketed by covalent crosslinks across the dimer interface and the behaviour of a concatemeric human homologue argue that the transport cycle resides within each subunit and does not require rigid-body rearrangements between subunits. However, this evidence is only inferential, and because examples are known in which quaternary rearrangements of extramembrane ClC domains that contribute to dimerization modulate transport activity, we cannot declare as definitive a 'parallel-pathways picture in which the homodimer consists of two single-subunit transporters operating independently. A strong prediction of such a view is that it should in principle be possible to obtain a monomeric ClC. Here we exploit the known structure of a ClC Cl{sup -}/H{sup +} exchanger, ClC-ec1 from Escherichia coli, to design mutants that destabilize the dimer interface while preserving both the structure and the transport function of individual subunits. The results demonstrate that the ClC subunit alone is the basic functional unit for transport and that cross-subunit interaction is not required for Cl{sup -}/H{sup +} exchange in ClC transporters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Zanamivir immobilized magnetic beads for voltammetric measurement of neuraminidase at gold-modified boron doped diamond electrode

Biomolecule modified magnetic beads has been widely used in separation and sensing process. This study used streptavidin modified magnetic beads to immobilize biotin modified zanamivir. Biotin-streptavidin affinity facilitates immobilization of zanamivir on magnetic beads. Then interaction of zanamivir and neuraminidase was adopted as basic for enzyme detection. Detection of neuraminidase was performed at gold modified BDD using cyclic voltammetry technique. The measurement was carried out based on alteration of electrochemical signals of working electrode as neuraminidase response. The result showed that zanamivir was successfully immobilized on magnetic beads. The optimum amount of magnetic beads for zanamivir immobilization was 120 ug. Linear responses of neuraminidase were detected in concentration range of 0-15 mU. Detection limit (LOD) of measurement was 2.32 mU (R2 = 0.959) with precision as % RSD of 1.41%. Measurement of neuraminidase on magnetic beads could be also performed in the presence of mucin matrix. The linearity range was 0-8 mU with LOD of 0.64 mU (R2 = 0.950) and % RSD of 7.25%.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗