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.

There has long been interest in the use of oxygenated hydrocarbon additives to conventional fuels. These oxygenates have been shown to reduce soot emissions in diesel engines and CO emissions in spark-ignition engines; and often allow diesel operation with decreased NO{sub x}. The current widely used additive, MTBE is targeted for elimination as a gasoline additive due to its damaging effects on the environment. This creates a need for alternative oxygenated additives; and more importantly, amplifies the importance to fully understand the thermochemical and kinetic properties on these oxyhydrocarbons fuels and for their intermediate and radical breakdown products. We use CBS-Q and density-functional methods with isodesmic reactions (with group balance when possible) to compute thermodynamic quantities for these species. We have studied hydrocarbons with multiple substituted methoxy groups. In several cases, multioxygenated species are evaluated that may have potential use as new oxygenated fuel additives. Thermodynamic quantities (H{sub 298}{sup 0}, S{sub 298}{sup 0}, C{sub p}(T)) as well as group additivity contributions for the new oxygenated groups are reported. We also report trends in bond-energies with increasing methoxy substitution.

In this article the authors concisely present several modern strategies that are applicable to drift-dominated carrier transport in higher-order deterministic models such as the drift-diffusion, hydrodynamic, and quantum hydrodynamic systems. The approaches include extensions of upwind and artificial dissipation schemes, generalization of the traditional Scharfetter-Gummel approach, Petrov-Galerkin and streamline-upwind Petrov Galerkin (SUPG), entropy variables, transformations, least-squares mixed methods and other stabilized Galerkin schemes such as Galerkin least squares and discontinuous Galerkin schemes. The treatment is representative rather than an exhaustive review and several schemes are mentioned only briefly with appropriate reference to the literature. Some of the methods have been applied to the semiconductor device problem while others are still in the early stages of development for this class of applications. They have included numerical examples from the recent research tests with some of the methods. A second aspect of the work deals with algorithms that employ unstructured grids in conjunction with adaptive refinement strategies. The full benefits of such approaches have not yet been developed in this application area and they emphasize the need for further work on analysis, data structures and software to support adaptivity. Finally, they briefly consider some aspects of software frameworks. These include dial-an-operator approaches …

This paper describes the design, fabrication and testing of the Anti-Coincidence Detector (ACD) for the Gamma-ray Large Area Space Telescope (GLAST) Large Area Telescope (LAT). The ACD is LAT's first-level defense against the charged cosmic ray background that outnumbers the gamma rays by 3-5 orders of magnitude. The ACD covers the top and 4 sides of the LAT tracking detector, requiring a total active area of {approx}8.3 square meters. The ACD detector utilizes plastic scintillator tiles with wave-length shifting fiber readout. In order to suppress self-veto by shower particles at high gamma-ray energies, the ACD is segmented into 89 tiles of different sizes. The overall ACD efficiency for detection of singly charged relativistic particles entering the tracking detector from the top or sides of the LAT exceeds the required 0.9997.

The properties of pentaamine (5-cyano-2H-tetrazolato-N2) cobalt (III) perchlorate (CP), which was first synthesized in 1968, continues to be of interest for predicting behavior in handling, shipping, aging, and thermal cook-off situations. We report coefficient of thermal expansion (CTE) values over four specific temperature ranges, decomposition kinetics using linear heating rates, and the reaction to three different types of stimuli: impact, spark, and friction. The CTE was measured using a Thermal Mechanical Analyzer (TMA) for samples that were uniaxially compressed at 10,000 psi and analyzed over a dynamic temperature range of -20 C to 70 C. Using differential scanning calorimetry, DSC, CP was decomposed at linear heating rates of 1, 3, and 7 C/min and the kinetic triplet calculated using the LLNL code Kinetics05. Values are also reported for spark, friction, and impact sensitivity.

Point defects induced in high quality optical-grade based silica by high power (>30 J/cm{sup 2}) 355 nm laser pulses have been investigated to elucidate the nature of laser damage in transparent optics designed for use at the National Ignition Facility (NIF). Six defects have been identified: the NBOHC (non-bridging oxygen hole center), a STE (self-trapped exciton), an ODC (oxygen-deficient center), interstitial oxygen, the E'{sub {gamma}}, and E'{sub 74}. The former four defects were identified and spatially resolved in the damage craters using cathodoluminescence (CL) microanalysis (spectroscopy and microscopy). The latter two defects were identified using ESR spectroscopy at cryogenic temperatures. These defects are unlikely to be a prime factor in damage growth by subsequent laser pulses. Their concentration is too low to effect a high enough temperature rise by a volume absorption mechanism.

This paper demonstrates the use of appropriate consequence evaluation criteria in conjunction with generic likelihood of occurrence data to produce consistent hazard analysis results for nonreactor nuclear facility Safety Analysis Reports (SAR). An additional objective is to demonstrate the use of generic likelihood of occurrence data as a means for deriving defendable accident sequence frequencies, thereby enabling the screening of potentially incredible events (<10{sup {minus}6} per year) from the design basis accident envelope. Generic likelihood of occurrence data has been used successfully in performing SAR hazard and accident analyses for two nonreactor nuclear facilities at Sandia National Laboratories. DOE-STD-3009-94 addresses and even encourages use of a qualitative binning technique for deriving and ranking nonreactor nuclear facility risks. However, qualitative techniques invariably lead to reviewer requests for more details associated with consequence or likelihood of occurrence bin assignments in the test of the SAR. Hazard analysis data displayed in simple worksheet format generally elicits questions about not only the assumptions behind the data, but also the quantitative bases for the assumptions themselves (engineering judgment may not be considered sufficient by some reviewers). This is especially true where the criteria for qualitative binning of likelihood of occurrence involves numerical ranges. Oftentimes reviewers …

Steady-state dissolution rates of diopside are measured as a function of solution saturation state using a titanium flow-through reactor at pH 7.5 and temperature ranging from 125 to 175 C. Diopside dissolved stoichiometrically under all experimental conditions and rates were not dependent on sample history. At each temperature, rates continuously decreased by two orders of magnitude as equilibrium was approached and did not exhibit a dissolution plateau of constant rates at high degrees of undersaturation. The variation of diopside dissolution rates with solution saturation can be described equally well with a ion exchange model based on transition state theory or pit nucleation model based on crystal growth/dissolution theory from 125 to 175 C. At 175 C, both models over predict dissolution rates by two orders of magnitude indicating that a secondary phase precipitated in the experiments. The ion exchange model assumes the formation of a Si-rich, Mg-deficient precursor complex. Lack of dependence of rates on steady-state aqueous calcium concentration supports the formation of such a complex, which is formed by exchange of protons for magnesium ions at the surface.

Growth of InAs/AlAs short-period superlattices on appropriately miscut (001) InP substrates is shown to alter the microstructure of composition modulation from a 2D organization of short compositionally enriched wires to a single dominant modulation direction and wire lengths up to {approximately}1 {micro}m. The effects of miscut are interpreted in terms of surface step orientation and character. The material is strongly modulated and exhibits intense optical emission. The 1D modulations appear potentially useful for new devices that take advantage of the preferred direction formed in the growth plane.

Remediation by soil-vapor extraction has been used for over a decade at Lawrence Livermore National Laboratory (LLNL). We have found that natural changes in environmental conditions affect the rate of soil-vapor extraction. Data on flow rate observations collected over this time are compared to in-situ measurements of several different environmental parameters (soil-gas pressure, soil-temperature, soil-moisture, Electrical Resistance Tomography (ERT), rainfall and barometric pressure). Environmental changes that lead to increased soil-moisture are associated with reduced soil-vapor extraction flow rates. We have found that the use of higher extraction vacuums combined with dual-phase extraction can help to increase pneumatic conductivity when vadose zone saturation is a problem. Daily changes in barometric pressure and soil-gas temperature were found to change flow rate measurements by as much as 10% over the course of a day.

The role of orbital magnetism in the laser-induced demagnetization of Fe/Gd multilayers was investigated using time-resolved X-ray magnetic circular dichroism at 2-ps time resolution given by an x-ray streak camera. An ultrafast transfer of angular momentum from the spin via the orbital momentum to the lattice was observed which was characterized by rapidly thermalizing spin and orbital momenta. Strong interlayer exchange coupling between Fe and Gd led to a simultaneous demagnetization of both layers.

Curved lipid membranes are ubiquitous in living systems and play an important role in many biological processes. To understand how curvature and lipid composition affect membrane formation and fluidity we have assembled and studied mixed 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (DOPC) and 1,2-Dioleoyl-sn-Glycero-3-Phosphoethanolamine (DOPE) supported lipid bilayers on amorphous silicon nanowires with controlled diameters ranging from 20 nm to 200 nm. Addition of cone-shaped DOPE molecules to cylindrical DOPC molecules promotes vesicle fusion and bilayer formation on smaller diameter nanowires. Our experiments demonstrate that nanowire-supported bilayers are mobile, exhibit fast recovery after photobleaching, and have low concentration of defects. Lipid diffusion coefficients in these high-curvature tubular membranes are comparable to the values reported for flat supported bilayers and increase with decreasing nanowire diameter.

The Savannah River Site (SRS) Burial Ground had a container labeled as Box 33 for which they had no reliable solid waste stream designation. The container consisted of an outer box of dimensions 48-inch x 46-inch x 66-inch and an inner box that contained high density and high radiation dose material. From the outer box Radiation Control measured an extremity dose rate of 22 mrem/h. With the lid removed from the outer box, the maximum dose rate measured from the inner box was 100 mrem/h extremity and 80 mrem/h whole body. From the outer box the material was sufficiently high in density that the Solid Waste Management operators were unable to obtain a Co-60 radiograph of the contents. Solid Waste Management requested that the Analytical Development Section of Savannah River National Laboratory perform a {gamma}-ray assay of the item to evaluate the radioactive content and possibly to designate a solid waste stream. This paper contains the results of three models used to analyze the measured {gamma}-ray data acquired in an unusual configuration.

A novel X-ray technique was used, exploiting synchrotron radiation at the Advanced Photon Source at Argonne National Laboratory, to investigate the growth stresses in {alpha}-Al{sub 2}O{sub 3}. In-situ measurements of Debye-Scherrer diffraction patterns from the scale were recorded during oxidation and cooling, and the elliptical distortion of the diffraction rings was analyzed to yield the in-plane strain. Fe-28Al, Fe-40Al, Fe-40Al-0.2Hf, Fe-20Cr-10Al and Ni-50Al (at. %) were studied. Data were acquired in air at temperatures between 950-1100 C and during cool down. In all cases, the steady stage growth strain was relatively low (<0.1%) and was either tensile or compressive depending on the alloy. A higher tensile strain often existed during the initial oxidation period when transition alumina was present. Thermal stresses imposed on NiAl by reducing the sample temperature to 950 C for a period of time showed noticeable stress relaxation by creep. Different degrees of relaxation were also found during cooling depending on alloy composition and scale microstructure. On all Fe-based alloys, the first formed {alpha}-Al{sub 2}O{sub 3} was highly textured with the degree of texture decreasing with further oxidation. The relationships between stress development, scale wrinkling, oxide phase changes, and the effect of reactive element addition on growth …

Magnetization reversal in patterned ferromagnetic nanowires usually occurs via domain wall (DW) nucleation and propagation from one end (or both ends) of the wire which can be significantly reduced by a large, magnetically soft pad on one of the wire ends. These 'nucleation pads' reverse at lower fields than an isolated nanowire and introduce a DW to the wire from the wire end attached to the pad. Once a critical 'injection' field is reached, the DW sweeps through the wire, reversing its magnetization. Nucleation pads are frequently used as part of nanowire devices and experimental structures. Magnetic-field-driven shift register memory can include an injection pad to write data while those attached to nanowire spiral turn sensors act as both a source and sink of domain walls. Both of these devices use two-dimensional wire circuits and therefore require the use of orthogonal in-plane magnetic fields to drive domain walls through wires of different orientations. These bi-axial fields can significantly alter the fields at which DW injection occurs and control the number of different injection modes. We have used magnetic transmission soft X-ray microscopy (M-TXM) [6] providing 25nm spatial resolution to image the evolution of magnetization configurations in patterned 24nm thick Ni{sub …

The charge-state-resolved ion energy distributions (IEDs) in filtered aluminum vacuum arc plasmas were measured and analyzed at different oxygen and argon pressures in the range 0.5 8.0 mTorr. A significant reduction of the ion energy was detected as the pressure was increased, most pronounced in an argon environment and for the higher charge states. The corresponding average charge state decreased from 1.87 to 1.0 with increasing pressure. The IEDs of all metal ions in oxygen were fitted with shifted Maxwellian distributions. The results show that it is possible to obtain a plasma composition with a narrow charge-state distribution as well as a narrow IED. These data may enable tailoring thin-film properties through selecting growth conditions that are characterized by predefined charge state and energy distributions.

The authors introduce a class of damage models on regular lattices with isotropic interactions between the broken cells of the lattice. Quasistatic fiber bundles are an example. The interactions are assumed to be weak, in the sense that the stress perturbation from a broken cell is much smaller than the mean stress in the system. The system starts intact with a surface-energy threshold required to break any cell sampled from an uncorrelated quenched-disorder distribution. The evolution of this heterogeneous system is ruled by Griffith's principle which states that a cell breaks when the release in potential (elastic) energy in the system exceeds the surface-energy barrier necessary to break the cell. By direct integration over all possible realizations of the quenched disorder, they obtain the probability distribution of each damage configuration at any level of the imposed external deformation. They demonstrate an isomorphism between the distributions so obtained and standard generalized Ising models, in which the coupling constants and effective temperature in the Ising model are functions of the nature of the quenched-disorder distribution and the extent of accumulated damage. In particular, they show that damage models with global load sharing are isomorphic to standard percolation theory, that damage models with …

For highly crosslinked, polymer networks bonded to a solid surface, the effect of interfacial bond density as well as system size on interfacial fracture is studied molecular dynamics simulations. The correspondence between the stress-strain curve and the sequence of molecular deformations is obtained. The failure strain for a fully bonded surface is equal to the strain necessary to make taut the average minimal path through the network from the bottom solid surface to the top surface. At bond coverages less than full, nanometer scale cavities form at the surface yielding an inhomogeneous strain profile. The failure strain and stress are linearly proportional to the number of bonds at the interface unless the number of bonds is so few that van der Waals interactions dominate. The failure is always interfacial due to fewer bonds at the interface than in the bulk.

We present a simple superfield Lagrangian for massive supergravity. It comprises the minimal supergravity Lagrangian with interactions as well as mass terms for the metric superfield and the chiral compensator. This is the natural generalization of the Fierz-Pauli Lagrangian for massive gravity which comprises mass terms for the metric and its trace. We show that the on-shell bosonic and fermionic fields are degenerate and have the appropriate spins: 2, 3/2, 3/2 and 1. We then study this interacting Lagrangian using goldstone superfields. We find that achiral multiplet of goldstones gets a kinetic term through mixing, just as the scalar goldstone does in the non-supersymmetric case. This produces Planck scale (Mpl) interactions with matter and all the discontinuities and unitarity bounds associated with massive gravity. In particular, the scale of strong coupling is (Mpl m^4)^1/5, where m is the multiplet's mass. Next, we consider applications of massive supergravity to deconstruction. We estimate various quantum effects which generate non-local operators in theory space. As an example, we show that the single massive supergravity multiplet in a 2-site model can serve the function of an extra dimension in anomaly mediation.

The atomic process, kinetics, and equilibrium thermodynamics underlying the gettering of transition-metal impurities in Si are reviewed from a mechanistic perspective. Methods for mathematical modeling of gettering are reviewed and illustrated. Needs for further research are discussed.

Experiments are conducted on the JET tokamak to assess the diagnostic potential of MHD active and passive spectroscopy, for the plasma bulk and its suprathermal components, using Alfv{acute e}n Eigenmodes (AEs) excited by external antennas and by energetic particles. The measurements of AE frequencies and mode numbers give information on the bulk plasma. Improved equilibrium reconstruction, in particular in terms of radial profiles of density and safety factor, is possible from the comparison between the antenna driven spectrum and that calculated theoretically. Details of the time evolution of the non-monotonic safety factor profile in advanced scenarios can be reconstructed from the frequency of ICRH-driven energetic particle modes. The plasma effective mass can be inferred from the resonant frequency of externally driven AEs in discharges with similar equilibrium profiles. The stability thresholds and the nonlinear development of the instabilities can give clues on energy and spatial distribution of the fast particle population. The presence of unstable AEs provides lower limits in the energy of ICRH generated fast ion tails. Fast ion pressure gradients and their evolution can be inferred from the stability of AEs at different plasma radial positions. Finally, the details of the AE spectrum in the nonlinear stage can …

The strength and deformation behavior of ball-milled, iron-base materials containing nano-scale subgrains have been evaluated. As reported by several authors, nanosubgrains form during the early stages of ball milling as a result of severe plastic deformation inherent in the ball milling process. The strength for these nano-scale subgrains are compared with the strength of larger-scale subgrains in iron and iron-base alloys produced by traditional mechanical working. The data covers over 2 orders of magnitude in subgrain size (from 30 nm to 6 {micro}m) and shows a continuous pattern of behavior. For all materials studied, the strength varied as {lambda}{sup -1}, where {lambda} is the subgrain size. Strengthening from subgrains was found to breakdown at a much smaller subgrain size than strengthening from grains. In addition, the ball-milled materials showed significant strengthening contributions from nano-scale oxide particles. Shear bands are developed during testing of ball-milled materials containing ultra-fine subgrains. A model for shear band development in nano-scale subgrains during deformation has also been developed. The model predicts a strain state of uniaxial compression in the shear band with a strain of -1.24. Subgrains are shown to offer the opportunity for high strength and good work hardening with the absence of yield …

The new class of diode-pumped alkali vapor lasers (DPALs) offers high efficiency cw laser radiation at near-infrared wavelengths: cesium 895 nm, rubidium 795 nm, and potassium 770 nm. The working physical principles of DPALs will be presented. Initial 795 nm Rb and 895 nm Cs laser experiments performed using a titanium sapphire laser as a surrogate pump source demonstrated DPAL slope power conversion efficiencies in the 50-70% range, in excellent agreement with device models utilizing only literature spectroscopic and kinetic data. Using these benchmarked models for Rb and Cs, optimized DPALs with optical-optical efficiencies >60%, and electrical efficiencies of 25-30% are projected. DPAL device architectures for near-diffraction-limited power scaling into the high kilowatt power regime from a single aperture will be described. DPAL wavelengths of operation offer ideal matches to silicon and gallium arsenide based photovoltaic power conversion cells for efficient power beaming.