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At least 307 records · Page 17

Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer

Computationally designing protein-protein interactions with high affinity and desired orientation is a challenging task. Incorporating metal-binding sites at the target interface may be one approach for increasing affinity and specifying the binding mode, thereby improving robustness of designed interactions for use as tools in basic research as well as in applications from biotechnology to medicine. Here we describe a Rosetta-based approach for the rational design of a protein monomer to form a zinc-mediated, symmetric homodimer. Our metal interface design, named MID1 (NESG target ID OR37), forms a tight dimer in the presence of zinc (MID1-zinc) with a dissociation constant <30 nM. Without zinc the dissociation constant is 4 {micro}M. The crystal structure of MID1-zinc shows good overall agreement with the computational model, but only three out of four designed histidines coordinate zinc. However, a histidine-to-glutamate point mutation resulted in four-coordination of zinc, and the resulting metal binding site and dimer orientation closely matches the computational model (C{alpha} rmsd = 1.4 {angstrom}).

Der, Bryan S.↗

t matrix of metallic wire structures

To study the electromagnetic resonance and scattering properties of complex structures of which metallic wire structures are constituents within multiple scattering theory, the t matrix of individual structures is needed. We have recently developed a rigorous and numerically efficient equivalent circuit theory in which retardation effects are taken into account for metallic wire structures. Here, we show how the t matrix can be calculated analytically within this theory. We illustrate our method with the example of split ring resonators. The density of states and cross sections for scattering and absorption are calculated, which are shown to be remarkably enhanced at resonant frequencies. The t matrix serves as the basic building block to evaluate the interaction of wire structures within the framework of multiple scattering theory. This will open the door to efficient design and optimization of assembly of wire structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

EFFECTS OF ALFVEN WAVES ON ELECTRON CYCLOTRON MASER EMISSION IN CORONAL LOOPS AND SOLAR TYPE I RADIO STORMS

Solar type I radio storms are long-lived radio emissions from the solar atmosphere. It is believed that these type I storms are produced by energetic electrons trapped within a closed magnetic structure and are characterized by a high ordinary (O) mode polarization. However, the microphysical nature of these emissions is still an open problem. Recently, Wu et al. found that Alfven waves (AWs) can significantly influence the basic physics of wave-particle interactions by modifying the resonant condition. Taking the effects of AWs into account, this work investigates electron cyclotron maser emission driven by power-law energetic electrons with a low-energy cutoff distribution, which are trapped in coronal loops by closed solar magnetic fields. The results show that the emission is dominated by the O mode. It is proposed that this O mode emission may possibly be responsible for solar type I radio storms.

79 ASTRONOMY AND ASTROPHYSICS↗

Recent progress on tritium technology research and development for a fusion reactor in Japan Atomic Energy Agency

JAEA (Japan Atomic Energy Agency) manages 2 tritium handling laboratories: Tritium Processing Laboratory (TPL) in Tokai and DEMO-RD building in Rokkasho. TPL has been accumulating a gram level tritium safety handling experiences without any accidental tritium release to the environment for more than 25 years. Recently, our activities have focused on 3 categories, as follows. First, the development of a detritiation system for ITER. This task is the demonstration test of a wet Scrubber Column (SC) as a pilot scale (a few hundreds m{sup 3}/h of processing capacity). Secondly, DEMO-RD tasks are focused on investigating the general issues required for DEMO-RD design, such as structural materials like RAFM (Reduced Activity Ferritic/Martensitic steels) and SiC/SiC, functional materials like tritium breeder and neutron multiplier, and tritium. For the last 4 years, we have spent a lot of time and means to the construction of the DEMO-RD facility and to its licensing, so we have just started the actual research program with tritium and other radioisotopes. This tritium task includes tritium accountancy, tritium basic safety research such as tritium interactions with various materials, which will be used for DEMO-RD and durability. The third category is the recovery work from the Great East Japan earthquake (2011 earthquake). It is worth noting that despite the high magnitude of the earthquake, TPL was able to confine tritium properly without any accidental tritium release.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Bogoliubov quasiparticles in superconducting qubits

Extending the qubit coherence times is a crucial task in building quantum information processing devices. In the three-dimensional cavity implementations of circuit QED, the coherence of superconducting qubits was improved dramatically due to cutting the losses associated with the photon emission. Next frontier in improving the coherence includes the mitigation of the adverse effects of superconducting quasiparticles. In these lectures, we review the basics of the quasiparticles dynamics, their interaction with the qubit degree of freedom, their contribution to the qubit relaxation rates, and approaches to control their effect.

Glazman, Leonid↗

Strangeness Production in Jets with ALICE at the LHC

At this laboratory Physicists and Engineers study fundamental particles using the world’s largest and most complex instruments. Here particles are made to collide at close to the speed of light to see how they interact and help to discover the basic laws of nature. One type of instrument used at CERN is a particle accelerator that boosts beams of particles to high energies and make them collide with either stationary particles or each other. Other types of instruments are the detectors which observe and record the collisions. CERN was founded in 1954 and sits by the France-Swiss border near Geneva. It was one of Europe’s first joint ventures and now has 20 member states. The name CERN is an acronym for the French "Conseil Européen pour la Recherche Nucléaire", or European Council for Nuclear Research, a provisional body founded in 1952 with the mandate of establishing a world-class fundamental physics research organization in Europe. At that time, pure physics research concentrated on understanding the inside of the atom. CERN's main area of research is particle physics the study of the fundamental constituents of matter and the forces acting between them. The laboratory operated by CERN is often referred to as the European Laboratory for Particle Physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Advancements in mass spectrometry for biological samples: Protein chemical cross-linking and metabolite analysis of plant tissues

This thesis presents work on advancements and applications of methodology for the analysis of biological samples using mass spectrometry. Included in this work are improvements to chemical cross-linking mass spectrometry (CXMS) for the study of protein structures and mass spectrometry imaging and quantitative analysis to study plant metabolites. Applications include using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) to further explore metabolic heterogeneity in plant tissues and chemical interactions at the interface between plants and pests. Additional work was focused on developing liquid chromatography-mass spectrometry (LC-MS) methods to investigate metabolites associated with plant-pest interactions.

59 BASIC BIOLOGICAL SCIENCES↗

High Energy Physics Network Requirements Review (Final Report, July-October 2020)

Throughout 2020, ESnet and the Office of High Energy Physics (HEP) of the DOE SC organized an ESnet requirements review of HEP-supported activities. Preparation for this event included identification of key stakeholders: program and facility management, research groups, technology providers, and a number of external observers. These individuals were asked to prepare formal case study documents about their relationship to the HEP program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward. A series of pre-planning meetings better prepared case study authors for this task, along with guidance on how the review would proceed in a virtual fashion.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Plant root associated chitinases: structures and functions

Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent K M values of (20-40 µM) for the substrate 4-MU-GlcNAc 3 . They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5–7 and 30–40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50–60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc 3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere.

60 APPLIED LIFE SCIENCES↗

The ISEE-1 and ISEE-2 plasma wave investigation

The ISEE-1 and ISEE-2 plasma wave experiments are designed to provide basic information on wave-particle interactions in the earth's magnetosphere and in the solar wind. The ISEE-1 plasma wave instrument uses three electric dipole antennas with lengths of 215, 73.5 and 0.61 m for electric field measurements, and a triaxial search coil antenna for magnetic field measurements. The ISEE-2 instrument uses two electric dipole antennas with lengths of 30 and 0.61 m for electric field measurements and a single-axis search coil antenna for magnetic field measurements. The primary scientific objectives of the experiments are described, including the resolution of space-time relationships of plasma wave phenomena and VLBI studies. The instrumentation is described, with emphasis on the antennas and the electronics.

Gurnett, D. A.↗

A climate hypothesis describing the solar-terrestrial system as a frequency domain with specific response characteristics

A climatological model of the earth-sun system based on an analogy to Planck's law of quantum mechanics is developed. The role of the diabatically important trace gases O3, H2O, and CO2 in the complex processes by which solar cycles affect tropospheric-stratospheric stability, and the value of the resonance concept in understanding these phenomena are examined. Consideration is given to climate complexity and the Laplace transform of the solar cycle, direct versus indirect solar signals, intense convection in coupled dynamics, the basic mechanisms of solar-terrestrial interaction, and the Planck's-law analog. The quantum approach, taking complexity into account, is shown to be more appropriate for evaluating the effects of anthropogenic modifications of the atmosphere (e.,g., increasing CO2) than the linear bulk-heating approaches usually applied.

Paine, D. A.↗

Metallurgical and tensile property analysis of several silicon carbide/titanium composite systems

Several silicon-carbide fiber reinforced titanium matrix composite systems were investigated to determine composite degradation mechanisms and to develop techniques to minimize loss of mechanical properties during fabrication and in service. Emphasis was on interface control by fiber or matrix coatings. Fibers and matrix materials were sputter coated with various metals to determine the effects of the coatings on basic fiber properties, fiber-matrix interactions, and on composite properties. The effects of limited variations in fabrication temperature on composite properties were determined for composites consolidated by standard press-diffusion-bonding techniques.

Brewer, W. D.↗

Thrust for interorbital propulsion - A question of lifetime

The most promising operational window for the use of magnetoplasmadynamic (MPD) thrusters is identified to be at megawatt power levels for orbital maneuvering. For such applications, the operation of a steady-state MPD thruster system imposes stringent requirements on the lifetime of thruster surfaces which will erode due to interactions with the plasma working fluid. Basic erosion mechanisms are presented and the problems associated with measuring the erosion rates are discussed. An experimental approach that would allow the development of a phenomenological model for erosion is proposed.

Gabriel, S. B.↗

Modeling of dense sprays from LOX/H2 coaxial injectors under supercritical conditions

Assumptions commonly employed in the analytical description of a thin spray become unacceptable as the droplet density and droplet volume displacement become large. Changes in the semiempirical models describing drop-drop or drop-gas interactions as well as in the basic modeling approach itself may be necessary. A number of efforts undertaken to improve such models of the atomization-evaporation process to render them applicable in the dense-spray, supercritical regime are described. The improvements include those for variable drop density, supercritical properties, stripping evaporation and drop reincorporation into the liquid stream. The models are developed for use with the ARICC three-phase finite difference combustion code. Selected results from a sample calculation are presented, demonstrating the enhanced realism achievable with the upgraded models.

Liang, P. Y.↗

Manual for obscuration code with space station applications

The Obscuration Code, referred to as SHADOW, is a user-oriented computer code to determine the case shadow of an antenna in a complex environment onto the far zone sphere. The surrounding structure can be composed of multiple composite cone frustums and multiply sided flat plates. These structural pieces are ideal for modeling space station configurations. The means of describing the geometry input is compatible with the NEC-BASIC Scattering Code. In addition, an interactive mode of operation has been provided for DEC VAX computers. The first part of this document is a user's manual designed to give a description of the method used to obtain the shadow map, to provide an overall view of the operation of the computer code, to instruct a user in how to model structures, and to give examples of inputs and outputs. The second part is a code manual that details how to set up the interactive and non-interactive modes of the code and provides a listing and brief description of each of the subroutines.

Marhefka, R. J.↗

An exact solution to the relativistic equation of motion of a charged particle driven by a linearly polarized electromagnetic wave

An exact analytic solution is found for a basic electromagnetic wave-charged particle interaction by solving the nonlinear equations of motion. The particle position, velocity, and corresponding time are found to be explicit functions of the total phase of the wave. Particle position and velocity are thus implicit functions of time. Applications include describing the motion of a free electron driven by an intense laser beam..

Shebalin, John V.↗

Exercise, exercise training, and the immune system. A compendium of research (1902-1991)

This compendium includes abstracts and synopses of clinical observations and of more basic studies involving physiological mechanisms concerning interaction of physical exercise and the human immune system. If the author's abstract or summary was appropriate, it was included. In other cases, a more detailed synopsis of the paper was prepared under the subheadings 'Purpose,' 'Methods,' 'Results,' and 'Conclusions.' Author and subject indices are provided, plus a selected bibliography of related work or those papers received after the volume was being prepared for publication. This volume includes material published from 1902 through 1991.

Hardesty, A. J.↗

Water Metabolism and Fluid Compartment Volumes in Humans at Altitude. A Compendium of Research (1914 - 1996)

This compendium includes abstracts and synopses of clinical observations and of more basic studies involving physiological mechanisms concerning interaction of water metabolism and fluid compartment volumes in humans during altitude exposure. If the author's abstract or summary was appropriate, it was included. In other cases a more detailed synopsis of the paper was prepared under the subheadings Purpose, Methods, Results, and Conclusions. Author and subject indices are provided, plus an additional selected bibliography of related work of those papers received after the volume was being prepared for publication. This volume includes material published from 1914 through 1995.

Chou, J. L.↗