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At least 865 records · Page 48

Inherent dynamics within the Crimean-Congo Hemorrhagic fever virus protease are localized to the same region as substrate interactions

Crimean-Congo Hemorrhagic fever virus (CCHFV) is one of several lethal viruses that encodes for a viral ovarian tumor domain (vOTU), which serves to cleave and remove multiple proteins involved in cellular signaling such as ubiquitin (Ub) and interferon stimulated gene produce 15 (ISG15). Such manipulation of the host cell machinery serves to downregulate the host response and, therefore, complete characterization of these proteases is important. While several structures of the CCHFV vOTU protease have been solved, both free and bound to Ub and ISG15, few structural differences have been found and little insight has been gained as to the dynamic plasticity of this protease. Therefore, we have used NMR relaxation experiments to probe the dynamics of CCHV vOTU, both alone and in complex with Ub, thereby discovering a highly dynamic protease that exhibits conformational exchange within the same regions found to engage its Ub substrate. These experiments reveal a structural plasticity around the N-terminal regions of CCHV vOTU, which are unique to vOTUs, and provide a rationale for engaging multiple substrates with the same binding site.

Environmental Molecular Sciences Laboratory↗

Two-Way Integration of WRF and CCSM for Regional Climate Simulations

Under the support of the DOE award DE-SC0004670, we have successfully developed an integrated climate modeling system by nesting Weather Research and Forecasting (WRF) model within the Community Climate System Model (CCSM) and the ensuing new generation Community Earth System Model (CESM). The integrated WRF/CESM system is intended as one method of global climate modeling with regional simulation capabilities. It allows interactive dynamical regional downscaling in the computational flow of present or future global climate simulations. This capability substantially simplifies the process of dynamical downscaling by avoiding massive intermediate model outputs at high frequency that are typically required for offline regional downscaling. The inline coupling also has the advantage of higher temporal resolution for the interaction between regional and global model components. With the aid of the inline coupling, a capability has also been developed to ingest other global climate simulations (by CESM or other models), which otherwise may not have necessary intermediate outputs for regional downscaling, to realize their embedded regional details. It is accomplished by relaxing the global atmospheric state of the integrated model to that of the source simulations with an appropriate time scale. This capability has the potential to open a new venue for ensemble regional climate simulations using a single modeling system. Furthermore, this new modeling system provides an effective modeling framework for the studies of physical and dynamical feedbacks of regional weather phenomena to the large scale circulation. The projected uses of this capability include the research of up-scaling effect of regional weather system, and its use as an alternative physical representation of sub-scale processes in coarser-resolution climate models.

54 ENVIRONMENTAL SCIENCES↗

Alternative trajectories of electron density to plot the atomic connectivity graph in the region of nondirectional interactions

Model supramolecular associates possessing nondirectional intermolecular interactions were investigated in order to demonstrate the opportunity of plotting of an atomic connectivity graph based on trajectories of Hessian eigenvector of electron density corresponding to the largest eigenvalue. Such trajectories are a reasonable alternative to the gradient bond paths in the case of proximity of the latter to the T-shaped form upon the presence of parallel surface of the zero-flux of electron density in the neighborhood of gradient-based trajectory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Monte Carlo Perturbation Analysis of Fuel Temperature Variations in the MCNP Model of the Annular Core Research Reactor

The Annular Core Research Reactor (ACRR) Monte Carlo N-Particle (MCNP) model is used by ACRR reactor operators and experiment designers at Sandia National Laboratories for a variety of computational calculations ranging from reactor kinetics parameter estimates and safety analyses to experimental planning. To understand the dominant source of uncertainty within the MCNP model, perturbations in temperature were applied to individual ACRR MCNP fuel rods. Fuel rod temperatures were randomly sampled from a uniform distribution from operational temperatures to quantify temperature-related uncertainty effects. Stochastic mixing was used to blend the cross sections of the desired temperatures using the MCNP continuous and Thermal Neutron Scattering Treatment [S(α,β)] libraries in ENDF/B-VII.1. Furthermore, this uncertainty analysis produced a 640 row × 640 column correlation and covariance matrix of the neutron energy spectra. Positive covariance was produced around the 1-MeV region and the 0.2-eV region. Correlation was found in the thermal and fast energy regions, but no correlation was observed in the slowing-down energy region because interactions in this region are not dominated by fuel.

ACRR↗

Use of operational analyses to study the dynamics of troposphere-stratosphere interactions in polar regions

Operational analyses produced by large weather centers have been used in the past to monitor various aspects of the general circulation as well as address dynamical questions. For a number years researchers have been monitoring National Meteorological Center (NMC) analyses at 100 millibars because it is the level from which stratospheric analyses are built. In particular, they closely examined the pressure-work term at that level which is an important parameter related to the forcing of the stratosphere by the troposphere. Rapid fluctuations typically seen in this quanity during the months of July-November, and similarly noted by Randel et al., (1987) may raise some concern about the quality of the analyses. Researchers investigated the behavior of the term mainly responsible for these variations, namely the eddy flux of heat, and furthermore have corroborated the presence of these variations in contemporaneous analyses produced by the European Centre for Medium Range Forecasts (ECMWF). Researchers demonstrated that fluctuations in standing eddy heat fluxes, related to the forcing of the stratosphere by the troposphere, agree in two largely independent meteorological analyses. Researchers believe, that these fluctuations are mostly real.

Salstein, David A.↗

Nongray radiative interactions in entry region flows with variable properties

The entrance region flow between parallel plates is investigated numerically and the variation of fluid properties with temperature is considered. The effect of variable properties for both laminar and turbulent flows is presented. Laminar flows are found to be affected to a larger extent than turbulent flows, as far as the effect of variable properties are concerned.

Krishnamurthy, R.↗

The spatial distribution of p-mode absorption in active regions

The interaction of solar p-mode waves and active regions has been the subject of recent observational and theoretical investigations. Observations show that up to one-half of the power of incident high-degree acoustic may be absorbed in and around sunspots. In this paper the horizontal spatial distribution of high-degree p-mode absorption in solar active regions is explored. An appropriate Fourier-Hankel transform can be used to detect the mean absorption of waves passing through any given point on the solar surface. By repeating the analysis at multiple positions a map of the absorption can be constructed. A technique for optimal computation of absorption maps is developed and applied to observations of several active regions and an area of quiet sun near disk center. By comparing the distribution of p-mode absorption with magnetograms and line-wing intensity images, it is directly observed that the absorption is not limited to the location of the visible sunspots but is also associated with magnetic fields in the surrounding plage. It is estimated that the absorption efficiency scales roughly with the magnetic flux density, although the absorption appears to saturate inside the strongest fields.

Braun, D. C.↗

HIV-1 Nef binds with human GCC185 protein and regulates mannose 6 phosphate receptor recycling

HIV-1 Nef modulates cellular function that enhances viral replication in vivo which culminate into AIDS pathogenesis. With no enzymatic activity, Nef regulates cellular function through host protein interaction. Interestingly, trans-cellular introduction of recombinant Nef protein in Caenorhabditis elegans results in AIDS like pathogenesis which might share common pathophysiology because the gene sequence of C. elegans and humans share considerable homology. Therefore employing C. elegans based initial screen complemented with sequence based homology search we identified GCC185 as novel host protein interacting with HIV-1 Nef. The detailed molecular characterization revealed N-terminal EEEE{sub 65} acidic domain of Nef as key region for interaction. GCC185 is a tethering protein that binds with Rab9 transport vesicles. Our results show that Nef-GCC185 interaction disrupts Rab9 interaction resulting in delocalization of CI-MPR (cation independent Mannose 6 phosphate receptor) resulting in elevated secretion of hexosaminidase. In agreement with this, our studies identified novel host GCC185 protein that interacts with Nef EEEE65 acidic domain interfering GCC185-Rab9 vesicle membrane fusion responsible for retrograde vesicular transport of CI-MPR from late endosomes to TGN. In light of existing report suggesting critical role of Nef-GCC185 interaction reveals valuable mechanistic insights affecting specific protein transport pathway in docking of late endosome derived Rab9 bearing transport vesicle at TGN elucidating role of Nef during viral pathogenesis. -- Highlights: •Nef, an accessory protein of HIV-1 interacts with host factor and culminates into AIDS pathogenesis. •Using Caenorhabditis elegans based screen system, novel Nef interacting cellular protein GCC185 was identified. •Molecular characterization of Nef and human protein GCC185 revealed Nef EEEE{sub 65} key region interacted with full length GCC185. •Nef impeded the GCC185-Rab 9 interaction and perturb the mannose 6 phosphate receptor recycling. •Our study identified novel Nef interacting human GCC185 protein and their role regulation of M6P receptor recycling.

60 APPLIED LIFE SCIENCES↗

A numerical solution of the flow field over a transonic airfoil including strong-shock-induced flow separation

An approximate numerical method has been developed for computing the entire transonic flow field over an airfoil, including the boundary layer, the shock-wave/boundary-layer interaction, and the shock-induced-separation. The inviscid flow, the turbulent boundary layer in the weak interaction zone, and the strong interaction elliptic region are solved separately. The inviscid flow is represented by the solution of the transonic small-disturbance equation, while the boundary layer is solved by the generalized Galerkin method, and the strong interaction region (including the wake) is computed from the time-averaged Navier-Stokes equations. A second-order interaction is computed iteratively using the inviscid pressure distribution as a boundary condition for the boundary layer and Navier-Stokes codes, and the viscous displacement thickness to modify the airfoil geometry for the inviscid computation. The computed pressure distributions and shock-wave profiles are compared with experimental data. Agreement is very good except that the pressure recovery on the trailing edge is greater than the experimental data.

Seginer, A.↗

Effect of plasma inhomogeneity on plasma wakefield acceleration driven by long bunches

Effects of plasma inhomogeneity on self-modulating proton bunches and accelerated electrons were studied numerically. The main effect is the change of the wakefield wavelength which results in phase shifts and loss of accelerated particles. This effect imposes severe constraints on density uniformity in plasma wakefield accelerators driven by long particle bunches. The transverse two stream instability that transforms the long bunch into a train of micro-bunches is less sensitive to density inhomogeneity than are the accelerated particles. The bunch freely passes through increased density regions and interacts with reduced density regions.

43 PARTICLE ACCELERATORS↗

CORONAL HEATING BY THE INTERACTION BETWEEN EMERGING ACTIVE REGIONS AND THE QUIET SUN OBSERVED BY THE SOLAR DYNAMICS OBSERVATORY

The question of what heats the solar corona remains one of the most important puzzles in solar physics and astrophysics. Here we report Solar Dynamics Observatory Atmospheric Imaging Assembly observations of coronal heating by the interaction between emerging active regions (EARs) and the surrounding quiet Sun (QS). The EARs continuously interact with the surrounding QS, resulting in dark ribbons which appear at the boundary of the EARs and the QS. The dark ribbons visible in extreme-ultraviolet wavelengths propagate away from the EARs with speeds of a few km s{sup −1}. The regions swept by the dark ribbons are brightening afterward, with the mean temperature increasing by one quarter. The observational findings demonstrate that uninterrupted magnetic reconnection between EARs and the QS occurs. When the EARs develop, the reconnection continues. The dark ribbons may be the track of the interface between the reconnected magnetic fields and the undisturbed QS’s fields. The propagating speed of the dark ribbons reflects the reconnection rate and is consistent with our numerical simulation. A long-term coronal heating which occurs in turn from nearby the EARs to far away from the EARs is proposed.

79 ASTRONOMY AND ASTROPHYSICS↗

On the length of the drift region in the Ramsey cavity

The interaction of atoms in a beam with the microwave field in a separated field geometry such as a Ramsey cavity is generally described in terms of the three regions traversed successively by the atoms, namely two interaction regions of length (l) separated by a drift, or free precession, region of length L. For a monokinetic beam of velocity v, the linewidth of the central fringe in the Ramsey resonance pattern is usually expressed as delta omega equals pi v/L. A more detailed calculation shows, however, that the linewidth is equal to pi v/L asterisk, where the equivalent drift L asterisk is larger than L by an amount of the order of l/L. The correction depends on the field distribution in the interaction regions. Its origin lies in the fact that atomic precession is not limited to the field-free regions but also occurs in the interaction regions, where atomic coherence builds up or decreases continuously. Although the correction to the equivalent length of the drift region is small, it may be relevant to the evaluation of the second-order Doppler effect bias in primary cesium-beam standards to the extent that the atomic velocity is deduced from the lineshape and from the geometrical parameters of the cavity. It is shown that in current and projected standards with atoms of average thermal velocity, use of corrected dimensions may lead to a change of the calculated bias of the order of 10(exp -14), which is significant at the levels of accuracy considered nowadays.

Thomann, Pierre↗

Studies of shock/shock interaction on smooth and transpiration-cooled hemispherical nosetips in hypersonic flow

A program of experimental research and analysis was conducted to examine the heat transfer and pressure distributions in regions of shock/shock interaction over smooth and transpiration-cooled hemispherical noseshapes. The objective of this investigation was to determine whether the large heat transfer generated in regions of shock/shock interaction can be reduced by transpiration cooling. The experimental program was conducted at Mach numbers of 12 to 16 in the Calspan 48-Inch Shock Tunnel. Type 3 and type 4 interaction regions were generated for a range of freestream unit Reynolds numbers to provide shear layer Reynolds numbers from 10 exp 4 to 10 exp 6 to enable laminar and turbulent interaction regions to be studied. Shock/shock interactions were investigated on a smooth hemispherical nosetip and a similar transpiration-cooled nosetip, with the latter configuration being examined for a range of surface blowing rates up to one-third of the freestream mass flux. While the heat transfer measurements on the smooth hemisphere without shock/shock interaction were in good agreement with Fay-Riddell predictions, those on the transpiration-cooled nosetip indicated that its intrinsic roughness caused heating-enhancement factors of over 1.5. In the shock/shock interaction studies on the smooth nosetip, detailed heat transfer and pressure measurements were obtained to map the variation of the distributions with shock-impingement position for a range of type 3 and type 4 interactions. Such sets of measurements were obtained for a range of unit Reynolds numbers and Mach numbers to obtain both laminar and turbulent interactions. The measurements indicated that shear layer transition has a significant influence on the heating rates for the type 4 interaction as well as the anticipated large effects on type 3 interaction heating. In the absence of blowing, the peak heating in the type 3 and type 4 interaction regions, over the transpiration-cooled model, did not appear to be influenced by the model's rough surface characteristics. The studies of the effects of the transpiration cooling on type 3 and type 4 shock/shock interaction regions demonstrated that large surface blowing rates had significant effect on the structure of the flowfield, enlarging the shock layer and moving the region of peak-heating interaction around the body.

Holden, Michael S.↗

DIFFRACTION, REFRACTION, AND REFLECTION OF AN EXTREME-ULTRAVIOLET WAVE OBSERVED DURING ITS INTERACTIONS WITH REMOTE ACTIVE REGIONS

We present observations of the diffraction, refraction, and reflection of a global extreme-ultraviolet (EUV) wave propagating in the solar corona. These intriguing phenomena are observed when the wave interacts with two remote active regions, and together they exhibit properties of an EUV wave. When the wave approached AR11465, it became weaker and finally disappeared in the active region, but a few minutes later a new wavefront appeared behind the active region, and it was not concentric with the incoming wave. In addition, a reflected wave was also simultaneously observed on the wave incoming side. When the wave approached AR11459, it transmitted through the active region directly and without reflection. The formation of the new wavefront and the transmission could be explained with diffraction and refraction effects, respectively. We propose that the different behaviors observed during the interactions may be caused by different speed gradients at the boundaries of the two active regions. We find that the EUV wave formed ahead of a group of expanding loops a few minutes after the start of the loops' expansion, which represents the initiation of the associated coronal mass ejection (CME). Based on these results, we conclude that the EUV wave should be a nonlinear magnetosonic wave or shock driven by the associated CME, which propagated faster than the ambient fast mode speed and gradually slowed down to an ordinary linear wave. Our observations support the hybrid model that includes both fast wave and slow non-wave components.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Localization and implication of oblique whistler wave in the magnetopause region

Nonlinear interaction between highly oblique whistler wave and ion acoustic wave pertinent to magnetopause has been investigated. The density perturbation in whistler wave is supposed to be originated due to the presence of ion acoustic wave in the background. The ponderomotive force components arising due to the high amplitude pump wave, viz., whistler wave are constituted in the nonlinear dynamics of low frequency ion acoustic wave. The coupled nonlinear dynamical equations are then modelled in the form of modified nonlinear Schrödinger equation by considering adiabatic response of low frequency ion acoustic wave. The numerical simulation of this coupled nonlinear equation is performed to study the temporal evolution of nonlinear whistler wave. The obtained simulation results show that the temporal evolution also leads to the cascade of broadband turbulence spectrum at smaller wavelengths. The relevance of the obtained results with the observations of THEMIS spacecraft in the magnetopause region has been pointed out.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dynamical Modulation of Solar Flare Electron Acceleration due to Plasmoid-shock Interactions in the Looptop Region

A fast-mode shock can form in the front of reconnection outflows and has been suggested as a promising site for particle acceleration in solar flares. Recent developments in the study of magnetic reconnection have shown that numerous plasmoids can be produced in a large-scale current layer. Here we investigate the dynamical modulation of electron acceleration in the looptop region when plasmoids intermittently arrive at the shock by combining magnetohydrodynamics simulations with a particle kinetic model. As plasmoids interact with the shock, the looptop region exhibits various compressible structures that modulate the production of energetic electrons. The energetic electron population varies rapidly in both time and space. The number of 5–10 keV electrons correlates well with the compression area, while that of >50 keV electrons shows good correlation with the strong compression area but only moderate correlation with shock parameters. We further examine the impacts of the first plasmoid, which marks the transition from a quasi-steady shock front to a distorted and dynamical shock. The number of energetic electrons is reduced by ~20% at 15–25 keV and nearly 40% for 25–50 keV, while the number of 5–10 keV electrons increases. In addition, the electron energy spectrum above 10 keV evolves softer with time. We also find that double or even multiple distinct sources can develop in the looptop region when the plasmoids move across the shock. Our simulations have strong implications to the interpretation of nonthermal looptop sources, as well as the commonly observed fast temporal variations in flare emissions, including the quasi-periodic pulsations.

79 ASTRONOMY AND ASTROPHYSICS↗