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At least 73 records · Page 4

A Proposed Model for Protein Crystal Nucleation and Growth

How does one take a molecule, strongly asymmetric in both shape and charge distribution, and assemble it into a crystal? We propose a model for the nucleation and crystal growth process for tetragonal lysozyme, based upon fluorescence, light, neutron, and X-ray scattering data, size exclusion chromatography experiments, dialysis kinetics, AFM, and modeling of growth rate data, from this and other laboratories. The first species formed is postulated to be a 'head to side' dimer. Through repeating associations involving the same intermolecular interactions this grows to a 4(sub 3) helix structure, that in turn serves as the basic unit for nucleation and subsequent crystal growth. High salt attenuates surface charges while promoting hydrophobic interactions. Symmetry facilitates subsequent helix-helix self-association. Assembly stability is enhanced when a four helix structure is obtained, with each bound to two neighbors. Only two unique interactions are required. The first are those for helix formation, where the dominant interaction is the intermolecular bridging anion. The second is the anti-parallel side-by-side helix-helix interaction, guided by alternating pairs of symmetry related salt bridges along each side. At this stage all eight unique positions of the P4(sub3)2(sub 1),2(sub 1) unit cell are filled. The process is one of a) attenuating the most strongly interacting groups, such that b) the molecules begin to self-associate in defined patterns, so that c) symmetry is obtained, which d) propagates as a growing crystal. Simple and conceptually obvious in hindsight, this tells much about what we are empirically doing when we crystallize macromolecules. By adjusting the growth parameters we are empirically balancing the intermolecular interactions, preferentially attenuating the dominant strong (for lysozyme the charged groups) while strengthening the lesser strong (hydrophobic) interactions. In the general case for proteins the lack of a singularly defined association pathway may lead to formation of multiple species, i.e., amorphous precipitation. Weak interactions, such as hydrogen bonds, are promiscuous, serving to strengthen rather than define specific interactions. Participation in an interaction sequesters that surface from subsequent interactions, and we expect the strongest bonds to form first. This model, its basis, how it fits into the currently understood osmotic second virial coefficient approach to crystallization, and what it suggests will be discussed.

Pusey, Marc↗

Diffusion effects on the helium abundance of the solar transition region and corona

The diffusion of helium in the solar transition region is studied by solving the mass and momentum conservation equations for a hydrogen-helium plasma given a representative temperature profile. Steady state solutions show that two distinct atmospheres may result. In cases where the thermal force on alpha-particles is balanced by the partial pressure gradient force, helium is the dominant coronal species. On the other hand, if it is the frictional force between protons and alpha-particles which balances the thermal force on alpha-particles then hydrogen is the major coronal component. In order to explore which of these solutions are attainable within reasonable time scales, the time-dependent equations are solved, starting from an initial state with a uniform helium abundance of 10 percent. The atmosphere as a whole is close to hydrostatic equilibrium, but due the thermal forces the individual elements are not. This force inbalance leads to a differential flow between species. It is found that this differential flow leads to a significant enhancement of the coronal helium abundance. Even for the relatively shallow temperature gradient used the helium abundance in the lower corona increases to 30 percent over a 24 hr period.

Hansteen, Viggo H.↗

Flow and Crystallization in Two-Layer Liquid Systems with and without a Magnetic Field

Flow, heat and mass transfer in a two-layer liquid system is investigated when the layers are subjected to a static magnetic field. The physical system consists of two immiscible liquids in a layer configuration with a free surface and an interfacial layer simulating two crystal growth configurations, namely, floating zone and horizontal zone melting. Mass transfer effects due to crystallization of one of the layers is also considered. The resulting flows are categorized into three types depending on: (a) the dominance of the free surface effect top layer, (b) a balance between the thermocapillary effect on the free surface and the interface effect between the two layers, or (c) the dominance of interfacial effects, in determining the system thermo-fluid characteristics. The use of an additional liquid layer atop the crystallizing layer leads to a reduction of the radial dopant inhomogeneity in comparison to the one-layer case. The effect an externally imposed magnetic field on dopant distribution in this two-layer configuration is rather ambiguous and depends on its direction and intensity resulting in the necessity of optimizing the applied magnetic field for a specific situation. In case of electrically non-conducting melts, the calculations show that some measure of flow control can be achieved by using an electrically conducting encapsulant layer of the desired thickness.

Feonychev, Alexander I.↗

The western redcedar genome reveals low genetic diversity in a self-compatible conifer

We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one of the most complete genome assemblies for a conifer. Population genomic analysis revealed WRC to be one of the most genetically depauperate wild plant species, with an effective population size of approximately 300 and no significant genetic differentiation across its geographic range. Nucleotide diversity, π, is low for a continuous tree species, with many loci showing zero diversity, and the ratio of π at zero- to fourfold degenerate sites is relatively high (approximately 0.33), suggestive of weak purifying selection. Using an array of genetic lines derived from up to five generations of selfing, we explored the relationship between genetic diversity and mating system. Although overall heterozygosity was found to decline faster than expected during selfing, heterozygosity persisted at many loci, and nearly 100 loci were found to deviate from expectations of genetic drift, suggestive of associative overdominance. Nonreference alleles at such loci often harbor deleterious mutations and are rare in natural populations, implying that balanced polymorphisms are maintained by linkage to dominant beneficial alleles. This may account for how WRC remains responsive to natural and artificial selection, despite low genetic diversity.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of workpiece curvature on the tool influence function during hemispherical sub-aperture tool glass polishing

The influence of workpiece curvature on the tool influence function spot during polishing of fused silica glass with cerium oxide slurry, while using a rotating hemispherical pad-foam tool for a wide variety of process conditions (tool displacement, inclination angle, and rotation rate), has been investigated. (Workpiece curvature ranged from 500 mm radius concave to 43 mm radius convex.) The TIF spot decreases in diameter and increases in the peak removal rate on more convex workpieces. In contrast, the TIF spot increases both in diameter and peak removal rate on more concave workpieces. For the range of workpiece curvatures investigated, both the spot size and the peak removal rate changed significantly, as much as 2 times. An elastic sphere–sphere contact mechanics model, which utilizes both a modified displacement (that leads to a change in the applied load) as well as a mismatch factor (that influences the pressure distribution shape), has been developed. Furthermore, the model was validated using both offline load-displacement measurements and finite-element analysis simulations. The model quantitatively describes the measured change in the relative contact diameter and relative pressure distribution, as well as semiquantitively describes the change in the relative volumetric removal rate on a large variety of TIF spots. The change in the volumetric removal rate for convex workpieces is a result of the balance between a decreasing spot size (reducing removal) and an increasing peak pressure (increasing removal), which usually results in relatively small changes in volumetric removal. In the case of concave workpieces, the volumetric removal rate change is also governed by a similar balance, but the spot size increase contribution dominates, resulting in a significant increase in volumetric removal rate. Understanding these trends can enable methods to add greater determinism during the fabrication of freeform optics by adjusting polishing parameters (such as dwell time) while the tool translates along a workpiece surface with different local curvatures.

47 OTHER INSTRUMENTATION↗

Design of inertial fusion implosions reaching the burning plasma regime

One of the last remaining milestones in fusion research before reaching ignition is creating a burning plasma state, where alpha particles from deuterium-tritium (DT) fusion reactions redeposit their energy as the dominant source of heating in the plasma. The indirect-drive inertial confinement fusion approach at the National Ignition Facility (NIF) uses a laser-generated radiation cavity (hohlraum) to spherically implode DT fuel to high temperatures and densities in a central ”hot spot”. Here, we deliver more energy to the hot spot than ever before, while maintaining the extreme pressures required for inertial confinement, by increasing the size of the implosion compared to previous experiments. We develop more efficient hohlraums, to drive these larger implosions within NIF’s current laser energy and power capability and control symmetry by moving energy between laser beams and by changing the shape of the hohlraum. These designs resulted in record fusion powers of 1.5 petawatts, greater than the input power of the laser, and 170 kJ of fusion energy. Radiation hydrodynamics simulations show alpha particle heating as the dominant term in the hot spot energy balance, e.g. a burning plasma state. This work is expected to motivate future studies of burning plasmas and improve predictive capability by providing a benchmark for modeling used to understand the proximity to ignition.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Low-g simulation testing of propellant systems using neutral buoyancy

A two liquid, neutral buoyancy technique is being used to simulate propellant behavior in a weightless environment. By equalizing the density of two immiscible liquids within a container (propellant tank), the effect of gravity at the liquid interface is balanced. Therefore the surface-tension forces dominate to control the liquid/liquid system configuration in a fashion analogous to a liquid/gas system in a zero gravity environment.

Balzer, D. L.↗

The effect of clouds on the earth's solar and infrared radiation budgets

The effect of global cloudiness on the solar and infrared components of the earth's radiation balance is studied in general circulation model experiments. A wintertime simulation is conducted in which the cloud radiative transfer calculations use realistic cloud optical properties and are fully interactive with model-generated cloudiness. This simulation is compared to others in which the clouds are alternatively non-interactive with respect to the solar or thermal radiation calculations. Other cloud processes (formation, latent heat release, precipitation, vertical mixing) were accurately simulated in these experiments. It is concluded that on a global basis clouds increase the global radiation balance by 40 W/sq m by absorbing longwave radiation, but decrease it by 56 W/sq m by reflecting solar radiation to space. The net cloud effect is therefore a reduction of the radiation balance by 16 W/sq m, and is dominated by the cloud albedo effect. Changes in cloud frequency and distribution and in atmospheric and land temperatures are also reported for the control and for the non-interactive simulations. In general, removal of the clouds' infrared absorption cools the atmosphere and causes additional cloudiness to occur, while removal of the clouds' solar radiative properties warms the atmosphere and causes fewer clouds to form. It is suggested that layered clouds and convective clouds over water enter the climate system as positive feedback components, while convective clouds over land enter as negative components.

Herman, G. F.↗

Proceedings for the ICASE Workshop on Heterogeneous Boundary Conditions

Domain Decomposition is a complex problem with many interesting aspects. The choice of decomposition can be made based on many different criteria, and the choice of interface of internal boundary conditions are numerous. The various regions under study may have different dynamical balances, indicating that different physical processes are dominating the flow in these regions. This conference was called in recognition of the need to more clearly define the nature of these complex problems. This proceedings is a collection of the presentations and the discussion groups.

Perkins, A. Louise↗

Suprathermal Ion Pressure in the Local Interstellar Medium

The first published results from IBEX and Cassini, and the earlier termination shock crossings by the Voyagers, are strongly suggestive of geometric relation of the local interstellar magnetic field to the outer boundary region of the heliosphere. The inferred pressure of the magnetic field is not, however, high enough to balance the heliosheath particle pressure computed from the IBEX and Cassini measurements. Since the interstellar ram pressure is also relatively low, and higher energy Ge V cosmic ray ions are not trapped on the local interstellar field lines, the pressure balance at the heliopause is more likely dominated by suprathermal keV-MeV particles on both sides. This should not be surprising in view of the long history of early work by Parker and others on cosmic ray particle pressure in interstellar space but with the new insight that the dominant contribution may be at suprathermal keV-MeV energies. Supporting pressure calculations are reviewed for a model interstellar proton spectrum from earlier work of Cooper et al. (2003, 2006, 2008).

Cooper, John F.↗

Dynamics of CMEs in the LASCO Field of View

A large set (16000) of coronal mass ejections (CMEs) observed during 1996-2011 was selected to study their dynamics in the LASCO field of view (LFOV). These events were selected based on the criterion that at least three height-time measurements were available for each CME. The height-time measurements included in the SOHO/LASCO catalog were used to determine velocities and accelerations of the respective CMEs at successive distances from the Sun. Next, these parameters were sorted into 30 subsamples depending on the distance from the Sun at which they were determined. The mean velocities and accelerations calculated for the successive distance-dependent subsamples of CMEs were used to study their dynamics. We demonstrate that CMEs in the LFOV manifest three distinct phases of propagation: (i) The propelling Lorentz force dominates the dynamics of CMEs in the inner (C2 LASCO) FOV, (ii) a stable propagation occurs as a result of the balance between the propelling and drag forces, (iii) the drag force dominates at the outer edge of the LFOV. When we considered different categories of CME separately, we found different acceleration distance profiles for different categories.

Michalek, G.↗

The application of support vector machines to analysis of global satellite data sets from MlSR

The Multi-angle Imaging Spectro Radiometer (MISR) is one of a suite of five instruments onboard NASA's Terra EOS satellite, launched in December 1999. Typical satellite imagers view the earth from a single direction, but MISR's cameras image the earth simultaneously from nine different directions in four spectral bands. In this way, MISR provides unique multiangle information about solar radiation scattered from clouds, aerosols and other terrestrial surfaces. One of the primary goals of the MISR mission is to improve our understanding of how clouds and aerosols affect the earth's global energy balance.

support vector machines↗

Graphene-polyelectrolyte multilayer membranes with tunable structure and internal charge

One great advantage of graphene-polyelectrolyte multilayer (GPM) membranes is their tunable structure and internal charge for improved separation performance. In this study, we synthesized GO-dominant GPM membrane with internal negatively-charged domains, polyethyleneimine (PEI)-dominant GPM membrane with internal positively-charged domains and charge-balanced dense/loose GPM membranes by simply adjusting the ionic strength and pH of the GO and PEI solutions used in layer-by-layer membrane synthesis. A combined system of quartz crystal microbalance with dissipation (QCM-D) and ellipsometry was used to analyze the mass deposition, film thickness, and layer density of the GPM membranes. The performance of the GPM membranes were compared in terms of both permeability and selectivity to determine the optimal membrane structure and synthesis strategy. One effective strategy to improve the GPM membrane permeability-selectivity tradeoff is to assemble charge-balanced dense membranes under weak electrostatic interactions. This balanced membrane exhibits the highest MgCl 2 selectivity (~86%). Another effective strategy for improved cation removal is to create PEI-dominant membranes that provide internal positively-charged barrier to enhance cation selectivity without sacrificing water permeability. Finally, these findings shine lights on the development of a systematic approach to push the boundary of permeability-selectivity tradeoff for GPM membranes.

42 ENGINEERING↗

Design of inertial fusion implosions reaching the burning plasma regime

Abstract In a burning plasma state 1–7 , alpha particles from deuterium–tritium fusion reactions redeposit their energy and are the dominant source of heating. This state has recently been achieved at the US National Ignition Facility 8 using indirect-drive inertial-confinement fusion. Our experiments use a laser-generated radiation-filled cavity (a hohlraum) to spherically implode capsules containing deuterium and tritium fuel in a central hot spot where the fusion reactions occur. We have developed more efficient hohlraums to implode larger fusion targets compared with previous experiments 9,10 . This delivered more energy to the hot spot, whereas other parameters were optimized to maintain the high pressures required for inertial-confinement fusion. We also report improvements in implosion symmetry control by moving energy between the laser beams 11–16 and designing advanced hohlraum geometry 17 that allows for these larger implosions to be driven at the present laser energy and power capability of the National Ignition Facility. These design changes resulted in fusion powers of 1.5 petawatts, greater than the input power of the laser, and 170 kJ of fusion energy 18,19 . Radiation hydrodynamics simulations 20,21 show energy deposition by alpha particles as the dominant term in the hot-spot energy balance, indicative of a burning plasma state.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The near Earth current sheet: ISEE-1 and -2 case studies

Two crossings of the near Earth current sheet are examined using magnetic field and plasma data from ISEE-1 and 2. The current sheet thickness is measured to be 0.9 Re using a 2 satellite technique which greatly reduces the ambiguity of such measurements. Approximate pressure balance is found to exist between the diamagnetically dominated current sheet and surrounding, already high beta, plasma sheet. The accurate calculation of the sheet normal velocity with the two satellite technique allows the calculation of the current density distribution in the sheet. The crosstail current density is found to peak about an ion-gyroradius on both sides of the center of the sheet. A simple model consistent with these results is discussed.

Mccomas, D. J.↗

The effect of cloud type on Earth's energy balance - Global analysis

The role of fractional area coverage by cloud types in the energy balance of the earth is investigated through joint use of International Satellite Cloud Climatology Project (ISCCP) C1 cloud data and Earth Radiation Budget Experiment (ERBE) broadband energy flux data for the one-year period March 1985 through February 1986. Multiple linear regression is used to relate the radiation budget data to the cloud data. Comparing cloud forcing estimates obtained from the ISCCP-ERBE regression with those derived from the ERBE scene identification shows generally good agreement except over snow, in tropical convective regions, and in regions that are either nearly cloudless or always overcast. It is suggested that a substantial fraction of the disagreement in longwave cloud forcing in tropical convective regions is associated with the fact that the ERBE scene identification does not take into account variations in upper-tropospheric water vapor. On a global average basis, low clouds make the largest contribution to the net energy balance of the Earth, because they cover such a large area and because their albedo effect dominates their effect on emitted thermal radiation. High, optically thick clouds can also very effectively reduce the energy balance, however, because their very high albedos overcome their low emission temperatures.

Hartmann, Dennis L.↗

Characterizing W sources in the all-W wall, all-RF WEST tokamak environment

In this work, experimental data, together with interpretive modeling tools, are examined to study trends in the tungsten (W) source in the all-W environment of the WEST tokamak, both from the divertor and from the main chamber. In particular, a poloidal limiter protecting an ion cyclotron resonance heating (ICRH) antenna is used as proxy for main chamber sourcing. The key study is carried out by stepping up lower hybrid current drive (LHCD) power, as the only auxiliary power source. Limiter and divertor W sources exhibit a qualitatively similar proportionality to the total power crossing the separatrix, P SEP , although the main chamber source remains substantially lower than the divertor source, for the range of P SEP accessible in the experiments. Intepretive modeling of the limiter source is carried out with a particle-in-cell (PIC) sheath model coupled to a surface sputtering model. Oxygen is used as a proxy for all light impurity species allowing for characterization of the critical W erosion regions. To get a good quantitative match to the data, it is necessary to assume that the oxygen arrives at the surface mostly at high ionization stages (4+ and above). A separate simulation with SOLEDGE-EIRENE, constrained to measured upstream scrape-off-layer plasma profiles, gives oxygen fractional abundances that are compatible with the PIC simulation result. This is understood to arise from transport processes that dominate over recombination. Substituting the LHCD by ICRH, in an equivalent experiment, the local W source exhibits a 3× enhancement. This can be matched by the simulation, by assuming local RF electric field rectification, based on ~100 eV peak-to-peak, near-antennna electric field. This work has highlighted the particular importance of understanding the ion charge state balance of light impurities as these are most likely the dominant sputtering species in fusion devices with high-Z walls.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

On the role of ion temperature gradient turbulence in driving ion thermal transport in neutral beam injection-heated L-mode plasmas in a superconducting tokamak

In this paper, we report a detailed experimental study of the role of ion-temperature-gradient driven turbulence in driving ion thermal transport in neutral beam injection (NBI)-heated L-mode plasmas in Experimental Advanced Superconducting Tokamak (EAST) (Wan et al 2000 Nucl. Fusion 40 1057) coupled with linear and nonlinear gyrokinetic simulations. Significant ion-scale turbulence k ⟂ < cm −1 (k ⟂ < 1.5, where k ⟂ where is the perpendicular wavenumber and ρ s is the ion gyroradius calculated using local electron temperature T e ), measured with a microwave reflectometer, is observed in the plasma core at for r/a ≈ 0.265 and 0.5 (where r is half the diameter of the closed flux surface at a given radial position, and a is half the diameter of the last closed flux surface). Local linear stability analysis with experimental equilibrium quantities at these two radial locations using the GS2 gyrokinetic code shows that the most unstable ion-scale micro-instability is the ion temperature gradient (ITG) mode. Since the computed maximum ion-scale linear growth rates are larger than the local Waltz-Miller E × B shearing rate (Waltz and Miller 1999 Phys. Plasmas 6 4265), the E × B shear is unable to suppress ion-scale turbulence, consistent with the experimental observation of ion-scale turbulence. Experimental ion and electron thermal transports, calculated with power balance analysis, are both anomalous with ion thermal transport being the dominant channel. Nonlinear gyrokinetic simulations using the electrostatic global particle-in-cell gyrokinetic tokamak simulation (GTS) code (Weixing Wang et al 2010 Phys. Plasmas 17 072511) show good quantitative agreement between predicted ion thermal transport and that from the power balance analysis. These results demonstrate for the first time the important role of ITG turbulence in driving thermal transport in NBI-heated L-mode plasmas in EAST, showing the effectiveness of GTS code in simulating electrostatic turbulence in EAST and the need of suppressing ITG turbulence to improve energy confinement in EAST.

Sun, P. J. [Chinese Academy of Sciences (CAS), Hef↗