Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations. (open access)

Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.

The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
Date: July 18, 2007
Creator: Lau, E Y & Krishnan, V V
System: The UNT Digital Library
Simulation of Comet Impact and Survivability of Organic Compounds (open access)

Simulation of Comet Impact and Survivability of Organic Compounds

Comets have long been proposed as a potential means for the transport of complex organic compounds to early Earth. For this to be a viable mechanism, a significant fraction of organic compounds must survive the high temperatures due to impact. We have undertaken three-dimensional numerical simulations to track the thermodynamic state of a comet during oblique impacts. The comet was modeled as a 1-km water-ice sphere impacting a basalt plane at 11.2 km/s; impact angles of 15{sup o} (from horizontal), 30{sup o}, 45{sup o}, 65{sup o}, and 90{sup o} (normal impact) were examined. The survival of organic cometary material, modeled as water ice for simplicity, was calculated using three criteria: (1) peak temperatures, (2) the thermodynamic phase of H{sub 2}O, and (3) final temperature upon isentropic unloading. For impact angles greater than or equal to 30{sup o}, no organic material is expected to survive the impact. For the 15{sup o} impact, most of the material survives the initial impact and significant fractions (55%, 25%, and 44%, respectively) satisfy each survival criterion at 1 second. Heating due to deceleration, in addition to shock heating, plays a role in the heating of the cometary material for nonnormal impacts. This effect is more …
Date: July 18, 2007
Creator: Liu, B T; Lomov, I N; Blank, J G & Antoun, T H
System: The UNT Digital Library
STATUS OF THE INTERNATIONAL MUON IONIZATION COOLING EXPERIMENT(MICE) (open access)

STATUS OF THE INTERNATIONAL MUON IONIZATION COOLING EXPERIMENT(MICE)

An international experiment to demonstrate muon ionization cooling is scheduled for beam at Rutherford Appleton Laboratory (RAL) in 2007. The experiment comprises one cell of the Study II cooling channel [1], along with upstream and downstream detectors to identify individual muons and measure their initial and final 6D phase-space parameters to a precision of 0.1%. Magnetic design of the beam line and cooling channel are complete and portions are under construction. The experiment will be described, including cooling channel hardware designs, fabrication status, and running plans. Phase 1 of the experiment will prepare the beam line and provide detector systems, including time-of-flight, Cherenkov, scintillating-fiber trackers and their spectrometer solenoids, and an electromagnetic calorimeter. The Phase 2 system will add the cooling channel components, including liquid-hydrogen absorbers embedded in superconducting Focus Coil solenoids, 201-MHz normal-conducting RF cavities, and their surrounding Coupling Coil solenoids. The MICE Collaboration goal is to complete the experiment by 2010; progress toward this is discussed.
Date: July 18, 2007
Creator: Zisman, Michael S.
System: The UNT Digital Library
Rh(I)-Catalyzed Arylation of Heterocycles via C-H Bond Activation: Expanded Scope Through Mechanistic Insight (open access)

Rh(I)-Catalyzed Arylation of Heterocycles via C-H Bond Activation: Expanded Scope Through Mechanistic Insight

A practical, functional group tolerant method for the Rh-catalyzed direct arylation of a variety of pharmaceutically important azoles with aryl bromides is described. Many of the successful azole and aryl bromide coupling partners are not compatible with methods for the direct arylation of heterocycles using Pd(0) or Cu(I) catalysts. The readily prepared, low molecular weight ligand, Z-1-tert-butyl-2,3,6,7-tetrahydrophosphepine, which coordinates to Rh in a bidentate P-olefin fashion to provide a highly active yet thermally stable arylation catalyst, is essential to the success of this method. By using the tetrafluoroborate salt of the corresponding phosphonium, the reactions can be assembled outside of a glove box without purification of reagents or solvent. The reactions are also conducted in THF or dioxane, which greatly simplifies product isolation relative to most other methods for direct arylation of azoles employing high-boiling amide solvents. The reactions are performed with heating in a microwave reactor to obtain excellent product yields in two hours.
Date: July 18, 2007
Creator: Lewis, Jared; Berman, Ashley; Bergman, Robert & Ellman, Jonathan
System: The UNT Digital Library
Porting Inition and Failure to Linked Cheetah (open access)

Porting Inition and Failure to Linked Cheetah

Linked CHEETAH is a thermo-chemical code coupled to a 2-D hydrocode. Initially, a quadratic-pressure dependent kinetic rate was used, which worked well in modeling prompt detonation of explosives of large size, but does not work on other aspects of explosive behavior. The variable-pressure Tarantula reactive flow rate model was developed with JWL++ in order to also describe failure and initiation, and we have moved this model into Linked CHEETAH. The model works by turning on only above a pressure threshold, where a slow turn-on creates initiation. At a higher pressure, the rate suddenly leaps to a large value over a small pressure range. A slowly failing cylinder will see a rapidly declining rate, which pushes it quickly into failure. At a high pressure, the detonation rate is constant. A sequential validation procedure is used, which includes metal-confined cylinders, rate-sticks, corner-turning, initiation and threshold, gap tests and air gaps. The size (diameter) effect is central to the calibration.
Date: July 18, 2007
Creator: Vitello, P & Souers, P C
System: The UNT Digital Library
Physics Design of the National High-power Advanced Torus Experiment (open access)

Physics Design of the National High-power Advanced Torus Experiment

Moving beyond ITER toward a demonstration power reactor (Demo) will require the integration of stable high fusion gain in steady-state, advanced methods for dissipating very high divertor heat-fluxes, and adherence to strict limits on in-vessel tritium retention. While ITER will clearly address the issue of high fusion gain, and new and planned long-pulse experiments (EAST, JT60-SA, KSTAR, SST-1) will collectively address stable steady-state highperformance operation, none of these devices will adequately address the integrated heat-flux, tritium retention, and plasma performance requirements needed for extrapolation to Demo. Expressing power exhaust requirements in terms of Pheat/R, future ARIES reactors are projected to operate with 60-200MW/m, a Component Test Facility (CTF) or Fusion Development Facility (FDF) for nuclear component testing (NCT) with 40-50MW/m, and ITER 20-25MW/m. However, new and planned long-pulse experiments are currently projected to operate at values of Pheat/R no more than 16MW/m. Furthermore, none of the existing or planned experiments are capable of operating with very high temperature first-wall (Twall = 600-1000C) which may be critical for understanding and ultimately minimizing tritium retention with a reactor-relevant metallic first-wall. The considerable gap between present and near-term experiments and the performance needed for NCT and Demo motivates the development of the concept …
Date: July 18, 2007
Creator: Menard, J. E.; Fu, G. Y.; Gorelenkov, N.; Kaye, S. M.; Kramer, G.; Maingi, R. et al.
System: The UNT Digital Library
Neutron capture and (n,2n) measurements on 241Am (open access)

Neutron capture and (n,2n) measurements on 241Am

We report on a set of neutron-induced reaction measurements on {sup 241}Am which are important for nuclear forensics and advanced nuclear reactor design. Neutron capture measurements have been performed on the DANCE detector array at the Los Alamos Neutron Scattering CEnter (LANSCE). In general, good agreement is found with the most recent data evaluations up to an incident neutron energy of {approx} 300 keV where background limits the measurement. Using mono-energetic neutrons produced in the {sup 2}H(d,n){sup 3}He reaction at Triangle University Nuclear Laboratory (TUNL), we have measured the {sup 241}Am(n,2n) excitation function from threshold (6.7 MeV) to 14.5 MeV using the activation method. Good agreement is found with previous measurements, with the exception of the three data points reported by Perdikakis et al. around 11 MeV, where we obtain a much lower cross section that is more consistent with theoretical estimates.
Date: July 18, 2007
Creator: Vieira, D.; Jandel, M.; Bredeweg, T.; Bond, E.; Clement, R.; Couture, A. et al.
System: The UNT Digital Library