The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

Magnetic Resonance Imaging (MRI) techniques have been used to detect areas of low crosslink density in damaged silicone parts in an effort to develop a QA/QC protocol to be used in the development of new parts. Model materials of varying crosslink density first demonstrated the applicability of the method. Analysis of damaged pads has been shown to be clearly distinguishable by MRI. It is our belief that both the T{sub 2} weighted SPI NMR and the T{sub 2} weighted water/fat suppression MRI experiments can be used to map out the location of different cross-linking densities, ultimately determining the quality or homogeneity in polymers.

Ice clouds play a major role in the radiative energy budget of the Earth-atmosphere system (Liou 1986). Their radiative effect is governed primarily by the equilibrium between their albedo and greenhouse effects. Both macrophysical and microphysical properties of ice clouds regulate this equilibrium. For quantifying the effect of these clouds onto climate and weather systems, they must be properly characterized in atmospheric models. In this paper we use remote-sensing measurements from the SIRTA ground based atmospheric observatory (Site Instrumental de Recherche par Teledetection Atmospherique, http://sirta.lmd.polytechnique.fr). Lidar and radar observations taken over 18 months are used, in order to gain statistical confidence in the model evaluation. Along this period of time, 62 days are selected for study because they contain parts of ice clouds. We use the ''model to observations'' approach by simulating lidar and radar signals from MM5 outputs. Other more classical variables such as shortwave and longwave radiative fluxes are also used. Four microphysical schemes, among which that proposed by Reisner et al. (1998) with original or modified parameterizations of particle terminal fall velocities (Zurovac-Jevtic and Zhang 2003, Heymsfield and Donner 1990), and the simplified Dudhia (1989) scheme are evaluated in this study.

Matlab is a matrix manipulation language originally developed to be a convenient language for using the LINPACK and EISPACK libraries. What makes Matlab so appealing for accelerator physics is the combination of a matrix oriented programming language, an active workspace for system variables, powerful graphics capability, built-in math libraries, and platform independence. A number of software toolboxes for accelerators have been written in Matlab--the Accelerator Toolbox (AT) for machine simulations, LOCO for accelerator calibration, Matlab Channel Access Toolbox (MCA) for EPICS connections, and the Middle Layer. This paper will describe the ''middle layer'' software toolbox that resides between the high-level control applications and the low-level accelerator control system. This software was a collaborative effort between ALS (LBNL) and SPEAR3 (SSRL) but easily ports to other machines. Five accelerators presently use this software. The high-level Middle Layer functionality includes energy ramp, configuration control (save/restore), global orbit correction, local photon beam steering, insertion device compensation, beam-based alignment, tune correction, response matrix measurement, and script-based programs for machine physics studies.

The equations of radiation transport for thermal photons are notoriously difficult to solve in thick media without resorting to asymptotic approximations such as the diffusion limit. One source of this difficulty is that in thick, absorbing media thermal emission is almost completely balanced by strong absorption. In a previous publication [SB03], the photon transport equation was written in terms of the deviation of the specific intensity from the local equilibrium field. We called the new form of the equations the difference formulation. The difference formulation is rigorously equivalent to the original transport equation. It is particularly advantageous in thick media, where the radiation field approaches local equilibrium and the deviations from the Planck distribution are small. The difference formulation for photon transport also clarifies the diffusion limit. In this paper, the transport equation is solved by the Symbolic Implicit Monte Carlo (SIMC) method and a comparison is made between the standard formulation and the difference formulation. The SIMC method is easily adapted to the derivative source terms of the difference formulation, and a remarkable reduction in noise is obtained when the difference formulation is applied to problems involving thick media.

A finite-difference method for computing the first arrival traveltimes by solving the Eikonal equation in the celerity domain has been developed. This algorithm incorporates the head and diffraction wave. We also adapt a fast sweeping method, which is extremely simple to implement in any number of dimensions, to obtain accurate first arrival times in complex velocity models. The method, which is stable and computationally efficient, can handle instabilities due to caustics and provide head waves traveltimes. Numerical examples demonstrate that the celerity-domain Eikonal solver provides accurate first arrival traveltimes. This new method is three times accurate more than the 2nd-order fast marching method in a linear velocity model with the same spacing.

The production of defect-free mask blanks, and the development of techniques for inspecting and qualifying EUV mask blanks, remains a key challenge for EUV lithography. In order to ensure a reliable supply of defect-free mask blanks, it is necessary to develop techniques to reliably and accurately detect defects on un-patterned mask blanks. These inspection tools must be able to accurately detect all critical defects whilst simultaneously having the minimum possible false-positive detection rate. There continues to be improvement in high-speed non-actinic mask blank inspection tools, and it is anticipated that these tools can and will be used by industry to qualify EUV mask blanks. However, the outstanding question remains one of validating that non-actinic inspection techniques are capable of detecting all printable EUV defects. To qualify the performance of non-actinic inspection tools, a unique dual-mode EUV mask inspection system has been installed at the Advanced Light Source (ALS) synchrotron at Lawrence Berkeley National Laboratory. In high-speed inspection mode, whole mask blanks are scanned for defects using 13.5-nm wavelength light to identify and map all locations on the mask that scatter a significant amount of EUV light. In imaging, or defect review mode, a zone plate is placed in the reflected …

The morphology of Si{sub 1-Y} Ge{sub Y}:H films in the range of Y=0.23 to 0.9 has been studied by AFM. The films were deposited by Low Frequency (LF) PE CVD at substrate temperature T{sub s}=300 C and discharge frequency f=110 kHz from silane+germane mixture with and without, Ar and H{sub 2} dilution. The films were deposited on silicon and glass substrates. AFM images were taken and analyzed for 2 x 2 mm{sup 2} area. All the images demonstrated ''grain'' like structure, which was characterized by the height distribution function F(H) average roughness <H>, standard height deviation Rq, lateral correlation length L{sub c} area distribution function F(s), mean grain area <s>, diameter distribution function F(d), and mean grain diameter <d>. The roughness <H> of the films monotonically increases with Y for all dilutions, but more significantly in the films deposited without dilution. L{sub c} continuously grows with Y in the films deposited without dilution, while more complex behavior L{sub c}(Y) is observed in the films deposited with H- or Ar dilution. The sharpness of F(H) characterized by curtosis {gamma} depends on dilution and the sharpest F(H) are for the films deposited with Ar ({gamma}=5.30,Y=0.23) and without dilution ({gamma}=4.3, Y=0.45). Isothermal annealing …

This paper for the 2005 National Hydrogen Association conference analyzes the hydrogen infrastructure needed to accommodate a transitional hydrogen fuel cell vehicle demand.

The transport of chemicals or heat in fractured reservoirs is strongly affected by the fracture-matrix interfacial area. In a vapor-dominated geothermal reservoir, this area can be estimated by inert gas tracer tests, where gas diffusion between the fracture and matrix causes the tracer breakthrough curve (BTC) to have a long tail determined by the interfacial area. For water-saturated conditions, recent studies suggest that sorbing solute tracers can also generate strong tails in BTCs that may allow a determination of the fracture-matrix interfacial area. To theoretically explore such a useful phenomenon, this paper develops an analytical solution for BTCs in slug-tracer tests in a water-saturated fractured reservoir. The solution shows that increased sorption should have the same effect on BTCs as an increase of the diffusion coefficient. The solution is useful for understanding transport mechanisms, verifying numerical codes, and for identifying appropriate chemicals as tracers for the characterization of fractured reservoirs.

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Silver and platinum were incorporated within diamondlike carbon (DLC) thin films using a multicomponent target pulsed laser deposition process. Transmission electron microscopy of the DLC-silver and DLC-platinum composite films reveals that the metals self-assemble into particulate nanocomposite structures. Nanoindentation testing has shown that diamondlike carbon-silver films exhibit hardness and Young's modulus values of approximately 37 GPa and 333 GPa, respectively. DLC-silver-platinum films exhibited antimicrobial properties against Staphylococcus bacteria. Diamondlike carbon-biofunctional metal nanocomposite films have a variety of potential medical and antimicrobial applications.

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Nonequilibrium molecular dynamics (MD) simulations show that shock-induced void collapse in copper occurs by emission of shear loops. These loops carry away the vacancies which comprise the void. The growth of the loops continues even after they collide and form sessile junctions, creating a hardened region around the collapsing void. The scenario seen in our simulations differs from current models that assume that prismatic loop emission is responsible for void collapse. We propose a new dislocation-based model that gives excellent agreement with the stress threshold found in the MD simulations for void collapse as a function of void radius.

An attempt to confirm production of superheavy elements in the reaction of 48Ca beams with actinide targets has been performed using the 238U(48Ca,3n)283112 reaction. Two 48Ca projectile energies were used, that spanned the energy range where the largest cross sections have been reported for this reaction. No spontaneous fission events were observed. No alpha decay chains consistent with either reported or theoretically predicted element 112 decay properties were observed. The cross section limits reached are significantly smaller than the recently reported cross sections.

Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps and provide useful resources for sequencing entire genomes. Drosophilabuzzatii is a representative species of the repleta group in the Drosophila subgenus, which is being widely used as a model in studies of genome evolution, ecological adaptation and speciation. We constructed a Bacterial Artificial Chromosome (BAC) genomic library of D. buzzatii using the shuttle vector pTARBAC2.1. The library comprises 18,353 clones with an average insert size of 152 kb and a {approx}18X expected representation of the D. buzzatii euchromatic genome. We screened the entire library with six euchromatic gene probes and estimated the actual genome representation to be {approx}23X. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9,555 clones, and assembled them using Finger Printed Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670singletons. Finally, we anchored 181 large contigs (containing 7,788clones) to the D. buzzatii salivary gland polytene chromosomes by in situ hybridization of 427 representative clones. The BAC library and a database with all the information regarding the high coverage BAC-based physical map described in this paper are available …

Studies of beam halo became unavoidable feature of high-intensity machines where uncontrolled beam loss should be kept to extremely small level. For a well controlled stable beam such a loss is typically associated with the low density halo surrounding beam core. In order to minimize uncontrolled beam loss or improve performance of an accelerator, it is very important to understand what are the sources of halo formation in a specific machine of interest. The dominant mechanisms are, in fact, different in linear accelerators, circular machines or Energy Recovering Linacs (ERL). In this paper, we summarize basic mechanisms of halo formation in high-intensity beams and discuss their application to various types of accelerators of interest, such as linacs, rings and ERL.

Presently the CDMS-II collaboration's Weakly Interacting Massive Particle (WIMP) search at the Soudan Underground Laboratory sets the most stringent exclusion limits of any WIMP cold dark matter direct-detection experiment. To extend our reach further, to WIMP-nucleon cross sections in the range 10{sup -46}-10{sup -44} cm{sup 2}, we propose SuperCDMS, which would take advantage of a very deep site. One promising site is the recently approved SNOLab facility in Canada. In this paper we will present our overall plan, identify primary issues, and set the goals that need to be met prior to embarking upon each phase of SuperCDMS.

The lack of understanding of the mechanical characteristics of cellulosic feedstocks is a limiting factor in economically collecting and processing crop residues, primarily wheat and barley stems and corn stover. Several testing methods, including compression, tension, and bend have been investigated to increase our understanding of the biomechanical behavior of cellulosic feedstocks. Biomechanical data from these tests can provide required input to numerical models and help advance harvesting, handling, and processing techniques. In addition, integrating the models with the complete data set from this study can identify potential tools for manipulating the biomechanical properties of plant varieties in such a manner as to optimize their physical characteristics to produce higher value biomass and more energy efficient harvesting practices.

An analytical formulation of conductivity bounds by Bergman and Milton is used in a different way to obtain rigorous bounds on the real transport coefficients (electrical conductivity, thermal conductivity, and/or fluid permeability) of a fluid-saturated porous medium. These bounds do not depend explicitly on the porosity, but rather on two formation factors--one associated with the pore space and the other with the solid frame. Hashin-Shtrikman bounds for transport in random polycrystals of porous-material laminates will also be discussed.

We present the ''C4 Cluster Catalog'', a new sample of 748 clusters of galaxies identified in the spectroscopic sample of the Second Data Release (DR2) of the Sloan Digital Sky Survey (SDSS). The C4 cluster-finding algorithm identifies clusters as overdensities in a seven-dimensional position and color space, thus minimizing projection effects that have plagued previous optical cluster selection. The present C4 catalog covers {approx}2600 square degrees of sky and ranges in redshift from z = 0.02 to z = 0.17. The mean cluster membership is 36 galaxies (with redshifts) brighter than r = 17.7, but the catalog includes a range of systems, from groups containing 10 members to massive clusters with over 200 cluster members with redshifts. The catalog provides a large number of measured cluster properties including sky location, mean redshift, galaxy membership, summed r-band optical luminosity (L{sub r}), velocity dispersion, as well as quantitative measures of substructure and the surrounding large-scale environment. We use new, multi-color mock SDSS galaxy catalogs, empirically constructed from the {Lambda}CDM Hubble Volume (HV) Sky Survey output, to investigate the sensitivity of the C4 catalog to the various algorithm parameters (detection threshold, choice of passbands and search aperture), as well as to quantify the …

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The authors present results of a study of 12 dust-reddened quasars with 0.4 < z < 2.65 and reddenings in the range 0.15 < E(B-V) < 1.7. They obtained ACIS-S X-ray spectra of these quasars, estimated the column densities towards them, and hence obtained the gas:dust ratios in the material obscuring the quasar. They detect all but one of the red quasars in the X-rays. Even though there is no obvious correlation between the X-ray determined column densities of the sources and their optical color or reddening, all of the sources show absorbed X-ray spectra. When they correct the luminosity for absorption, they can be placed among luminous quasars; therefore their objects belong to the group of high luminosity analogues of the sources contributing to the X-ray background seen in deep X-ray observations. Such sources are also found in serendipitous shallow X-ray surveys. There is a hint that the mean spectral slope of the red quasar is higher than that of normal, unobscured quasars, which could be an indication for higher accretion rates and/or an evolutionary effect. They investigate the number density of these sources compared to type 2 AGN based on the X-ray background and estimate how many moderate …