Publications

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Chemical crosslinking is an important tool for probing protein structure and protein-protein interactions. The approach usually involves crosslinking of specific amino acids within a folded protein or protein complex, enzymatic digestion of the crosslinked protein(s), and identification of the resulting crosslinked peptides by liquid chromatography/mass spectrometry (LC/MS). In this manner, distance constraints are obtained for residues that must be in close proximity to one another in the native structure or complex. As the complexity of the system under study increases, for example, a large multi-protein complex, simply measuring the mass of a crosslinked species will not always be sufficient to determine the identity of the crosslinked peptides. In such a case, tandem mass spectrometry (MS/MS) could provide the required information if the data can be properly interpreted. In MS/MS, a species of interest is isolated in the gas phase and allowed to undergo collision induced dissociation (CID). Because the gas-phase dissociation pathways of peptides have been well studied, methods are established for determining peptide sequence by MS/MS. However, although crosslinked peptides dissociate through some of the same pathways as isolated peptides, the additional dissociation pathways available to the former have not been studied in detail. Software such as MS2Assign has been written to assist in the interpretation of MS/MS from crosslinked peptide species, but it would be greatly enhanced by a more thorough understanding of how these species dissociate. We are thus systematically investigating the dissociation pathways open to crosslinked peptide species. A series of polyalanine and polyglycine model peptides have been synthesized containing one or two lysine residues to generate defined inter- and intra-molecular crosslinked species, respectively. Each peptide contains 11 total residues, and one arginine residue is present at the carboxy terminus to mimic species generated by tryptic digestion. The peptides have been allowed to react with a series of commonly used crosslinkers such as DSS, DSG, and DST. The tandem mass spectra acquired for these crosslinked species are being examined as a function of crosslinker identity, site(s) of crosslinking, and precursor charge state. Results from these model studies and observations from actual experimental systems are being incorporated into the MS2Assign software to enhance our ability to effectively use chemical crosslinking in protein complex determination.

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The Surface Evolver was used to compute the equilibrium microstructure of random soap foams with bidisperse cell-size distributions and to evaluate topological and geometric properties of the foams and individual cells. The simulations agree with the experimental data of Matzke and Nestler for the probability {rho}(F) of finding cells with F faces and its dependence on the fraction of large cells. The simulations also agree with the theory for isotropic Plateau polyhedra (IPP), which describes the F-dependence of cell geometric properties, such as surface area, edge length, and mean curvature (diffusive growth rate); this is consistent with results for polydisperse foams. Cell surface areas are about 10% greater than spheres of equal volume, which leads to a simple but accurate relation for the surface free energy density of foams. The Aboav-Weaire law is not valid for bidisperse foams.

Bulk migration of particles towards regions of lower shear occurs in suspensions of neutrally buoyant spheres in Newtonian fluids undergoing creeping flow in the annular region between two rotating, coaxial cylinders (a wide-gap Couette). For a monomodal suspension of spheres in a viscous fluid, dimensional analysis indicates that the rate of migration at a given concentration should scale with the square of the sphere radius. However, a previous experimental study showed that the rate of migration of spherical particles at 50% volume concentration actually scaled with the sphere radius to approximately the 2.9 power.

Three nested molybdenum wire arrays with initial outer diameters of 45, 50, and 55 mm were imploded by the - 20 MA, 90 ns rise-time current pulse of Sandia's Z accelerator. The implosions generated Mo plasmas with {approx} 10% of the array's initial mass reaching Ne-like and nearby ionization stages. These ions emitted 2-4 keV L-shell x rays with radiative powers approaching 10 TW. Mo L-shell spectra with axial and temporal resolution were captured and have been analyzed using a collisional-radiative model. The measured spectra indicate significant axial variation in the electron density, which increases from a few times 10{sup 20} cm{sup -3} at the cathode up to - 3 x 10{sup 21} cm{sup -3} near the middle of the 20 mm plasma column (8 mm from the anode). Time-resolved spectra indicate that the peak electron density is reached before the peak of the L-shell emission and decreases with time, while the electron temperature remains within 10% of 1.7 keV over the 20-30 ns L-shell radiation pulse. Finally, while the total yield, peak total power, and peak L-shell power all tended to decrease with increasing initial wire array diameters, the L-shell yield and the average plasma conditions varied little with the initial wire array diameter.

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ODRPAC (TOMS Algorithm 676) has provided a complete package for weighted orthogonal distance regression for many years. The code is complete with user selectable reporting facilities, numerical and analytic derivatives, derivative checking, and many more features. The foundation for the algorithm is a stable and efficient trust region Levenberg-Marquardt minimizer that exploits the structure of the orthogonal distance regression problem. ODRPAC95 is a modification of the original ODRPAC code that adds support for bound constraints, uses the newer Fortran 95 language, and simplifies the interface to the user called subroutine.

We consider the accuracy of predictions made by integer programming (IP) models of sensor placement for water security applications. We have recently shown that IP models can be used to find optimal sensor placements for a variety of different performance criteria (e.g. minimize health impacts and minimize time to detection). However, these models make a variety of simplifying assumptions that might bias the final solution. We show that our IP modeling assumptions are similar to models developed for other sensor placement methodologies, and thus IP models should give similar predictions. However, this discussion highlights that there are significant differences in how temporal effects are modeled for sensor placement. We describe how these modeling assumptions can impact sensor placements.

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A focused ion beam (FIB) is used to accurately sculpt predetermined micron-scale, curved shapes in a number of solids. Using a digitally scanned ion beam system, various features are sputtered including hemispheres and sine waves having dimensions from 1-50 {micro}m. Ion sculpting is accomplished by changing pixel dwell time within individual boustrophedonic scans. The pixel dwell times used to sculpt a given shape are determined prior to milling and account for the material-specific, angle-dependent sputter yield, Y({theta}), as well as the amount of beam overlap in adjacent pixels. A number of target materials, including C, Au and Si, are accurately sculpted using this method. For several target materials, the curved feature shape closely matches the intended shape with milled feature depths within 5% of intended values.

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Ccaffeine is a Common Component Architecture (CCA) framework devoted to high-performance computing. In this note we give an overview of the system features of Ccaffeine and CCA that support component-based HPC application development. Object-oriented, single-threaded and lightweight, Ccaffeine is designed to get completely out of the way of the running application after it has been composed from components. Ccaffeine is one of the few frameworks, CCA or otherwise, that can compose and run applications on a parallel machine interactively and then automatically generate a static, possibly self-tuning, executable for production runs. Users can experiment with and debug applications interactively, improving their productivity. When the application is ready, a script is automatically generated, parsed and turned into a static executable for production runs. Within this static executable, dynamic replacement of components can be performed by self-tuning applications.