This report talks about Cathodic Arcs: Fractal Voltage and Cohesive Energy Rule

Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set of ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket …

The concepts of international control over technologies and materials in the proliferation sensitive parts of the nuclear fuel cycle, specifically those related to enrichment and reprocessing, have been the subject of many studies and initiatives over the years. For examples: the International Fissionable Material Storage proposal in President Eisenhower's Speech on Atoms for Peace, and in the Charter of the International Atomic Energy Agency (IAEA) when the organization was formed in 1957; the regional nuclear fuel cycle center centers proposed by INFCE in the 80's; and most recently and notably, proposals by Dr. ElBaradei, the Director General of IAEA to limit production and processing of nuclear weapons usable materials to facilities under multinational control; and by U.S. President George W. Bush, to limit enrichment and reprocessing to States that have already full scale, functioning plants. There are other recent proposals on this subject as well. In this paper, the similarities and differences, as well as the effectiveness and challenges in proliferation prevention of these proposals and concepts will be discussed. The intent is to articulate a ''new nuclear regime'' and to develop concrete steps to implement such regime for future nuclear energy and deployment.

The programmatic, facility and criticality safety support staffs at the LLNL Plutonium Facility worked together to successfully develop and implement a project to process legacy (DNFSB Recommendation 94-1 and non-Environmental, Safety, and Health (ES&H) labeled) materials in storage. Over many years, material had accumulated in storage that lacked information to adequately characterize the material for current criticality safety controls used in the facility. Generally, the fissionable material mass information was well known, but other information such as form, impurities, internal packaging, and presence of internal moderating or reflecting materials were not well documented. In many cases, the material was excess to programmatic need, but such a determination was difficult with the little information given on MC&A labels and in the MC&A database. The material was not packaged as efficiently as possible, so it also occupied much more valuable storage space than was necessary. Although safe as stored, the inadequately characterized material posed a risk for criticality safety noncompliances if moved within the facility under current criticality safety controls. A Legacy Item Implementation Plan was developed and implemented to deal with this problem. Reasonable bounding conditions were determined for the material involved, and criticality safety evaluations were completed. Two appropriately designated …

Electrokinetic (EK) phenomena in sediments arise from relative fluid motion in the pore space, which perturbs the electrostatic equilibrium of the double layer at the grain surface. We have developed EK techniques in the laboratory to monitor acoustic wave propagation in electrolyte-saturated, unconsolidated sediments. Our experimental results indicate that as an acoustic wave travels through electrolyte-saturated sand, it can generate electric potentials greater than 1 mV. A careful study of these potentials was performed using medium-grain sand and loose glass microspheres for a range of pore fluid salinities and ultrasonic frequencies. Experimental results are also shown to compare well with numerical and analytical modeling based on the coupled electrokinetic-Biot theory developed by Pride (1994).

The authors apply the nonlinear WENO (Weighted Essentially Nonoscillatory) scheme to the spatial discretization of the Boltzmann Transport Equation modeling linear particle transport. The method is a finite volume scheme which ensures not only conservation, but also provides for a more natural handling of boundary conditions, material properties and source terms, as well as an easier parallel implementation and post processing. It is nonlinear in the sense that the stencil depends on the solution at each time step or iteration level. By biasing the gradient calculation towards the stencil with smaller derivatives, the scheme eliminates the Gibb's phenomenon with oscillations of size O(1) and reduces them to O(h{sup r}), where h is the mesh size and r is the order of accuracy. The current implementation is three-dimensional, generalized for unequally spaced meshes, fully parallelized, and up to fifth order accurate (WENO5) in space. For unsteady problems, the resulting nonlinear spatial discretization yields a set of ODE's in time, which in turn is solved via high order implicit time-stepping with error control. For the steady-state case, they need to solve the non-linear system, typically by Newton-Krylov iterations. There are several numerical examples presented to demonstrate the accuracy, non-oscillatory nature and efficiency …

For astrophysical applications, as well as modeling laser-produced plasmas, there is a continual need for equation-of-state data over a wide domain of physical conditions. This paper presents algorithmic aspects for computing the Helmholtz free energy of plasma electrons for temperatures spanning from a few Kelvin to several KeV, and densities ranging from essentially isolated ion conditions to such large compressions that most bound orbitals become delocalized. The objective is high precision results in order to compute pressure and other thermodynamic quantities by numerical differentiation. This approach has the advantage that internal thermodynamic self-consistency is ensured, regardless of the specific physical model, but at the cost of very stringent numerical tolerances for each operation. The computational aspects we address in this paper are faced by any model that relies on input from the quantum mechanical spectrum of a spherically symmetric Hamiltonian operator. The particular physical model we employ is that of INFERNO; of a spherically averaged ion embedded in jellium. An overview of PURGATORIO, a new implementation of the INFERNO equation of state model, is presented. The new algorithm emphasizes a novel decimation scheme for automatically resolving the structure of the continuum density of states, circumventing limitations of the pseudo-R matrix …

We investigate the potential for CO2 monitoring in thenear-surface environment as an approach to exploration for hiddengeothermal systems. Numerical simulations of CO2 migration from a modelhidden geothermal system show that CO2 concentrations can reach highlevels in the shallow subsurface even for relatively low CO2 fluxes.Therefore, subsurface measurements offer an advantage over above-groundmeasurements which are affected by winds that rapidly disperse CO2. Tomeet the challenge of detecting geothermal CO2 emissions within thenatural background variability of CO2, we propose an approach thatintegrates available detection and monitoring techniques with statisticalanalysis and modeling.

Measurements of radially resolved L-shell Mo spectra from wire array pinches on Sandia's Z generator are presented and analyzed using a collisional-radiative model. The spectra indicate large radial gradients in density over the {approx}8-mm-diameter plasma column, but only the emission from the {approx}2 mm central region of the pinch appears to be influenced by opacity. Population inversions and significant gain factors for 100-200 {angstrom} transitions in Ne-like Mo are predicted to exist at the diagnosed plasma conditions.

None

Possible deterioration of anode sense wires used in a hydrogen-filled neutron detector is investigated. Wires were loaded with free weights and put into a wire detector environment. Stainless Steel, Tungsten, and Platinum wires did not break after exposure to charge equivalent to many wire lifetimes. Furthermore, exposure to hydrogen gas caused no noticeable surface degradation or change in wire yield strength.

Maintaining a multi-model database over a generation or more of model development provides an important framework for assessing model improvement. Using control integrations, we compare the simulation of the El Nino/Southern Oscillation (ENSO), and its extratropical impact, in models developed for the 2007 Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report with models developed in the late 1990's (the so-called Coupled Model Intercomparison Project-2 [CMIP2] models). The IPCC models tend to be more realistic in representing the frequency with which ENSO occurs, and they are better at locating enhanced temperature variability over the eastern Pacific Ocean. When compared with reanalyses, the IPCC models have larger pattern correlations of tropical surface air temperature than do the CMIP2 models during the boreal winter peak phase of El Nino. However, for sea-level pressure and precipitation rate anomalies, a clear separation in performance between the two vintages of models is not as apparent. The strongest improvement occurs for the modeling groups whose CMIP2 model tended to have the lowest pattern correlations with observations. This has been checked by subsampling the multi-century IPCC simulations in a manner to be consistent with the single 80-year time segment available from CMIP2. Our results suggest that multi-century …

Current, mid-term and long range technologies for detection of pathogens and toxins are briefly described in the context of performance metrics and operational scenarios. Predictive (evolutionary) and speculative (revolutionary) assessments are given with trade-offs identified, where possible, among competing performance goals.

We present results for two-particle transverse momentum correlations, ({Delta}p{sub t,i}{Delta}p{sub t,j}), as a function of event centrality for Au+Au collisions at {radical}s{sub NN} = 20, 62, 130, and 200 GeV at the Relativistic Heavy Ion Collider. We observe correlations decreasing with centrality that are similar at all four incident energies. The correlations multiplied by the multiplicity density increase with incident energy and the centrality dependence may show evidence of processes such as thermalization, jet production, or the saturation of transverse flow. The square root of the correlations divided by the event-wise average transverse momentum per event shows little or no beam energy dependence and generally agrees with previous measurements at the Super Proton Synchrotron.

The Bio-Encyclopedia at the Biodefense Knowledge Center (BKC) is being constructed to allow an early detection of emerging biological threats to homeland security. It requires highly structured information extracted from variety of data sources. However, the quantity of new and vital information available from every day sources cannot be assimilated by hand, and therefore reliable high-throughput information extraction techniques are much anticipated. In support of the BKC, Lawrence Livermore National Laboratory and Oak Ridge National Laboratory, together with the University of Utah, are developing an information extraction system built around the bioterrorism domain. This paper reports two important pieces of our effort integrated in the system: key phrase extraction and semantic tagging. Whereas two key phrase extraction technologies developed during the course of project help identify relevant texts, our state-of-the-art semantic tagging system can pinpoint phrases related to emerging biological threats. Also we are enhancing and tailoring the Bio-Encyclopedia by augmenting semantic dictionaries and extracting details of important events, such as suspected disease outbreaks. Some of these technologies have already been applied to large corpora of free text sources vital to the BKC mission, including ProMED-mail, PubMed abstracts, and the DHS's Information Analysis and Infrastructure Protection (IAIP) news clippings. In …

Using a method originally proposed for describing a continuum-space polymer fluid, a new expression for the Helmholtz energy of mixing is proposed for a binary lattice mixture. Molecular size asymmetry and nonrandomness due to segment-segment interactions are taken into account. An expression proposed by Yan, Liu and Hu for a binary lattice mixture of monomers, based on the Ising model, is used as a reference system. Calculated critical constants and liquid-liquid coexistence curves are in good agreement with Monte Carlo simulations for lattice mixtures with modest size asymmetry. Because lattice spacing rises with increasing temperature, comparison of calculated binary liquid-liquid equilibria with experiment requires that calculations take into account that the interchange energy falls as temperature rises. While the new expression for the Helmholtz energy of mixing provides much improvement over the Flory-Huggins equation, calculated liquid-liquid equilibria for three binary systems are similar to those from Guggenheim's quasi-chemical theory.

There has been a significant progress in ab initio approaches to the structure of light nuclei. Starting from realistic two- and three-nucleon interactions the ab initio no-core shell model (NCSM) can predict low-lying levels in p-shell nuclei. It is a challenging task to extend ab initio methods to describe nuclear reactions. In this contribution, we present a brief overview of the NCSM with examples of recent applications as well as the first steps taken toward nuclear reaction applications. In particular, we discuss cross section calculations of p+{sup 6}Li and {sup 6}He+p scattering as well as a calculation of the astrophysically important {sup 7}Be(p, {gamma}){sup 8}B S-factor.

We report on applications of the ab initio, no-core shell model with the primary goal of achieving an accurate description of nuclear structure and reactions from the fundamental inter-nucleon interactions. We show that realistic two-nucleon interactions are inadequate to describe the low-lying structure of {sup 10}B, and that realistic three-nucleon interactions are essential. We report preliminary attempts to compute astrophysical S-factors

As part of an ongoing project to generate a mitochondrial database for terrestrial tortoises based on museum specimens, the complete mitochondrial genome sequences of 10 species and a {approx}14 kb sequence from an eleventh species are reported. The sampling of the present study emphasizes Mediterranean tortoises (genus Testudo and their close relatives). Our new sequences are aligned, along with those of two testudinoid turtles from GenBank, Chrysemys picta and Mauremys reevesii, yielding an alignment of 14,858 positions, of which 3,238 are parsimony informative. We develop a phylogenetic taxonomy for Testudo and related species based on well-supported, diagnosable clades. Several well-supported nodes are recovered, including the monophyly of a restricted Testudo, T. kleinmanni + T. marginata (the Chersus clade), and the placement of the enigmatic African pancake tortoise (Malacochersustornieri) within the predominantly Palearctic greater Testudo group (Testudona tax. nov.). Despite the large amount of sequence reported, there is low statistical support for some nodes within Testudona and Sowe do not propose names for those groups. A preliminary and conservative estimation of divergence times implies a late Miocene diversification for the testudonan clade (6-12 million years ago), matching their first appearance in the fossil record. The multi-continental distribution of testudonan turtles can …

None

The lateral organization and interactions of lipid and protein components within biological membranes are essential for their functions. Investigations of the lateral organization within membranes hinge upon the ability to differentiate one component of interest from another. Typically, fluorophores are conjugated to specific components, and the organization is probed with fluorescence microscopy. However, bulky fluorophores may change the physical properties of the components they label, only the labeled components can be visualized, and the diffraction limit of light restricts the lateral resolution. Here we present a method to image microdomains within supported lipid membranes using isotopic labels and high-resolution secondary ion mass spectrometry (SIMS) performed with the NanoSIMS 50 (Cameca). Lateral resolution of 100 nm is achieved with high sensitivity. Quantitative information on the lipid composition within each domain was determined using calibration curves constructed from homogeneous lipid bilayer samples that systematically varied in the isotopically labeled lipid content.

Mitochondrial (mt) DNA sequences are used extensively to reconstruct evolutionary relationships among recently diverged animals,and have constituted the most widely used markers for species- and generic-level relationships for the last decade or more. However, most studies to date have employed relatively small portions of the mt-genome. In contrast, complete mt-genomes primarily have been used to investigate deep divergences, including several studies of the amount of mt sequence necessary to recover ancient relationships. We sequenced and analyzed 24 complete mt-genomes from a group of salamander species exhibiting divergences typical of those in many species-level studies. We present the first comprehensive investigation of the amount of mt sequence data necessary to consistently recover the mt-genome tree at this level, using parsimony and Bayesian methods. Both methods of phylogenetic analysis revealed extremely similar results. A surprising number of well supported, yet conflicting, relationships were found in trees based on fragments less than {approx}2000 nucleotides (nt), typical of the vast majority of the thousands of mt-based studies published to date. Large amounts of data (11,500+ nt) were necessary to consistently recover the whole mt-genome tree. Some relationships consistently were recovered with fragments of all sizes, but many nodes required the majority of the mt-genome …

In this paper, we will examine how Russia's military and security forces might react to the detonation of a 10-kiloton nuclear weapon placed next to the walls surrounding the Kremlin. At the time of this 'big bang,' Putin is situated outside Moscow and survives the explosion. No one claims responsibility for the detonation. No other information is known. Numerous variables will determine how events ultimately unfold and how the military and security forces will respond. Prior to examining these variables in greater detail, it is imperative to elucidate first what we mean by Russia's military and security forces.

Data-centric workflow middleware systems are workflow systems that treat data as first class objects alongside programs. These systems improve the usability, responsiveness and efficiency of workflow execution over cluster (and grid) computers. In this work, we explore the scalability of one such system, GridDB, on cluster computers. We measure the performance and scalability of GridDB in executing data-intensive image processing workflows from the SuperMACHO astrophysics survey on a large cluster computer. Our first experimental study concerns the scale-up of GridDB. We make a rather surprising finding, that while the middleware system issues many queries and transactions to a DBMS, file system operations present the first-tier bottleneck. We circumvent this bottleneck and increase the scalability of GridDB by more than 2-fold on our image processing application (up to 128 nodes). In a second study, we demonstrate the sensitivity of GridDB performance (and therefore application performance) to characteristics of the workflows being executed. To manage these sensitivities, we provide guidelines for trading off the costs and benefits of GridDB at a fine-grain.