Experimental results are reported from two measurementtechniques (semiconductor switching and electro-optic sampling) thatallow temporal characterization of electron bunches produced by alaser-driven plasma-based accelerator. As femtosecond electron bunchesexit the plasma-vacuum interface, coherent transition radiation (at THzfrequencies) is emitted. Measuring the properties of this radiationallows characterization of the electron bunches. Theoretical work on theemission mechanism is represented, including a model that calculates theTHz waveform from a given bunch profile. It is found that the spectrum ofthe THz pulse is coherent up to the 200 mu m thick crystal (ZnTe)detection limit of 4 THz, which corresponds to the production of sub-50fs (root-mean-square) electron bunch structure. The measurementsdemonstrate both the shot-to-shot stability of bunch parameters that arecritical to THz emission (such as total charge and bunch length), as wellas femtosecond synchrotron between bunch, THz pulse, and laserbeam.

What is the best description that we can construct of athermodynamic system that is not in equilibrium, given only one, or afew, extra parameters over and above those needed for a description ofthe same system at equilibrium? Here, we argue the most appropriateadditional parameter is the non-equilibrium entropy of the system, andthat we should not attempt to estimate the probability distribution ofthe system, but rather the metaprobability (or hyperensemble) that thesystem is described by a particular probability distribution. The resultis an entropic distribution with two parameters, one a non-equilibriumtemperature, and the other a measure of distance from equilibrium. Thisdispersion parameter smoothly interpolates between certainty of acanonical distribution at equilibrium and great uncertainty as to theprobability distribution as we move away from equilibrium. We deducethat, in general, large, rare fluctuations become far more common as wemove away from equilibrium.

The identification of enhancers with predicted specificitiesin vertebrate genomes remains a significant challenge that is hampered bya lack of experimentally validated training sets. In this study, weleveraged extreme evolutionary sequence conservation as a filter toidentify putative gene regulatory elements and characterized the in vivoenhancer activity of human-fish conserved and ultraconserved1 noncodingelements on human chromosome 16 as well as such elements from elsewherein the genome. We initially tested 165 of these extremely conservedsequences in a transgenic mouse enhancer assay and observed that 48percent (79/165) functioned reproducibly as tissue-specific enhancers ofgene expression at embryonic day 11.5. While driving expression in abroad range of anatomical structures in the embryo, the majority of the79 enhancers drove expression in various regions of the developingnervous system. Studying a set of DNA elements that specifically droveforebrain expression, we identified DNA signatures specifically enrichedin these elements and used these parameters to rank all ~;3,400human-fugu conserved noncoding elements in the human genome. The testingof the top predictions in transgenic mice resulted in a three-foldenrichment for sequences with forebrain enhancer activity. These datadramatically expand the catalogue of in vivo-characterized human geneenhancers and illustrate the future utility of such training sets for avariety of iological applications including decoding the regulatoryvocabulary of …

The complexes [Ce(tmtaa)2], [Ce(tmtaa)(tmtaaH)]and[Ce2(tmtaa)3(thf)2]are obtained from Ce[N(SiMe3)2]3 and tmtaaH2, themacrocyclic ligand 6,8,15,17-tetramethyldibenzotetraaza[14]-annulene,depending on the stoichiometry, solvent and temperature. The crystalstructure of Ce(tmtaa)2 is isostructural with Zr(tmtaa)2, howevermagnetic susceptibility measurements in the range 5-300 K show thatCe(tmtaa)2 is not diamagnetic, but is a temperature-independentparamagnet (TIP), similar to Ce(cot)2, cerocene.

It is shown that the transient expansion of plutonium-gallium alloys observed both in the lattice parameter as well as in the dimension of a sample held at ambient temperature can be explained by assuming incipient precipitation of Pu{sub 3}Ga. However, this ordered {zeta}-phase is also subject to radiation-induced disordering. As a result, the gallium-stabilized {delta}-phase, being metastable at ambient temperature, is driven towards thermodynamic equilibrium by radiation-enhanced diffusion of gallium and at the same time reverted back to its metastable state by radiation-induced disordering. A steady state is reached in which only a modest fraction of the gallium present is arranged in ordered {zeta}-phase regions.

Since the earliest days of ultra-relativistic heavy ion physics, there has been interest in strange particle production. Originally, an anomalously large strangeness production was believed to be a signature of the Quark Gluon Plasma. Now the flavor composition of the plasma as reflected in the ratios of abundances of strange and non-strange particles is believed by advocates to tell us the temperature and baryon number density of the Quark Gluon Plasma at decoupling. In addition, there are arguments that suggest that the abundances of strange particles might at intermediate energy or at non-central rapidity, signal the existence of a critical end point of phase transitions in the baryon number chemical potential temperature plane. The purpose of this workshop is to assess the current theoretical and experimental understanding of strangeness production for ultra-relativistic heavy ion collisions.

Monte Carlo simulations are used to establish the potential of mean force between two globular proteins in an aqueous electrolyte solution. This potential includes nonelectrostatic contributions arising from dispersion forces first, between the globular proteins, and second, between ions in solution and between each ion and the globular protein. These latter contributions are missing from standard models. The potential of mean force, obtained from simulation, is fitted to an analytic equation. Using our analytic potential of mean force and Barker-Henderson perturbation theory, we obtain phase diagrams for lysozyme solutions that include stable and metastable fluid-fluid and solid-fluid phases when the electrolyte is 0.2 M NaSCN or NaI or NaCl. The nature of the electrolyte has a significant effect on the phase diagram.

The acceleration of the expansion of the universe, and theneed for Dark Energy, were inferred from the observations of Type Iasupernovae (SNe Ia) 1;2. There is consensus that SNeIa are thermonuclearexplosions that destroy carbon-oxygen white dwarf stars that accretematter from a companion star3, although the nature of this companionremains uncertain. SNe Ia are thought to be reliable distance indicatorsbecause they have a standard amount of fuel and a uniform trigger theyare predicted to explode when the mass of the white dwarf nears theChandrasekhar mass 4 - 1.4 solar masses. Here we show that the highredshift supernova SNLS-03D3bb has an exceptionally high luminosity andlow kinetic energy that both imply a super-Chandrasekhar mass progenitor.Super-Chandrasekhar mass SNeIa shouldpreferentially occur in a youngstellar population, so this may provide an explanation for the observedtrend that overluminous SNe Ia only occur in young environments5;6. Sincethis supernova does not obey the relations that allow them to becalibrated as standard candles, and since no counterparts have been foundat low redshift, future cosmology studies will have to considercontamination from such events.

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We consider the adiabatic and quasi-static compression of adilute classical gas, confined in a piston and initially equilibratedwith a heat bath. We find that the work performed during this process isdescribed statistically by a gamma distribution. We use this result toshow that the model satisfies the non-equilibrium work and fluctuationtheorems, but not the fluctation-dissipation relation. We discuss therare but dominant realizations that contribute most to the exponentialaverage of the work, and relate our results to potentially universal workdistributions.

Multilayer coatings for the 7 EUV channels of the AIA have been developed and completed successfully on all AIA flight mirrors. Mo/Si coatings (131, 171, 193.5, 211 {angstrom}) were deposited at Lawrence Livermore National Laboratory (LLNL). Mg/SiC (304, 335 {angstrom}) and Mo/Y (94 {angstrom}) coatings were deposited at Columbia University. EUV reflectance of the 131/335 {angstrom}, 171 {angstrom}, 193.5/211 {angstrom} primary and secondary flight mirrors and the 94/304 {angstrom} secondary flight mirror was measured at beamline 6.3.2. of the Advanced Light Source (ALS) at LBNL. EUV reflectance of the 94/304 {angstrom} primary and secondary flight mirrors was measured at beamline X24C of the National Synchrotron Light Source (NSLS) at Brookhaven National Lab. Preliminary EUV reflectance measurements of the 94, 304 and 335 {angstrom} coatings were performed with a laser plasma source reflectometer located at Columbia University. Prior to multilayer coating, Atomic Force Microscopy (AFM) characterization and cleaning of all flight substrates was performed at LLNL.

Time-resolved FT-IR spectra of carbon monoxide hydrogenation over alumina-supported ruthenium were recorded on the millisecond timescale at 703 K using various H{sub 2} concentrations (1 atm total pressure). Adsorbed carbon monoxide was detected along with gas phase products methane (3016 and 1306 cm{sup -1}), water (sharp bands from 1900 - 1300 cm{sup -1}), and carbon dioxide (2348 cm{sup -1}). No other surface species were detected other than adsorbed carbon monoxide. The rate of formation of methane (2.5 {+-} 0.4 s{sup -1}) coincides with the rate of formation of carbon dioxide (3.4 {+-} 0.6 s{sup -1}), and bands due to water are observed to grow in over time. These results establish that methane and carbon dioxide originate from the same intermediate. The adsorbed carbon monoxide band is broad and unsymmetrical with a maximum at 2010 cm{sup -1} in spectra observed at 36 ms that shifts over 3000 ms to 1960 cm{sup -1} due to decreasing amounts of adsorbed carbon monoxide. Kinetic analysis of the adsorbed carbon monoxide band reveals that only a portion of the band can be temporally linked to gas phase products that we observe over the first 1000 ms of catalysis. This result suggests that we are observing …

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Seismic wave propagation through the earth is often strongly affected by the presence of fractures. When these fractures are filled with fluids (oil, gas, water, CO{sub 2}, etc.), the type and state of the fluid (liquid or gas) can make a large difference in the response of the seismic waves. This paper will summarize some early work of the author on methods of deconstructing the effects of fractures, and any fluids within these fractures, on seismic wave propagation as observed in reflection seismic data. Methods to be explored here include Thomsen's anisotropy parameters for wave moveout (since fractures often induce elastic anisotropy), and some very convenient fracture parameters introduced by Sayers and Kachanov that permit a relatively simple deconstruction of the elastic behavior in terms of fracture parameters (whenever this is appropriate).

Density modulation of charged particle beams may occur as a consequence of deliberate action, or may occur inadvertently because of imperfections in the particle source or acceleration method. In the case of intense beams, where space charge and external focusing govern the beam dynamics, density modulation may under some circumstances be converted to velocity modulation, with a corresponding conversion of potential energy to kinetic energy. Whether this will occur depends on the properties of the beam and the initial modulation. This paper describes the evolution of discrete and continuous density modulations on intense beams, and discusses three recent experiments related to the dynamics of density-modulated electron beams.

WRN is unique among the five human RecQ DNA helicases by having a functional exonuclease domain (WRN-exo) and being defective in the premature aging and cancer-related disorder Werner syndrome. Here, we characterize WRN-exo crystal structures, biochemical activity and participation in DNA end-joining. Metal ion complex structures, active site mutations and activity assays reveal a two-metal-ion mediated nuclease mechanism. The DNA end-binding Ku70/80 complex specifically stimulates WRN-exo activity, and structure-based mutational inactivation of WRN-exo alters DNA end-joining in human cells. We furthermore establish structural and biochemical similarities of WRN-exo to DnaQ family replicative proofreading exonucleases, with WRN-specific adaptations consistent with dsDNA specificity and functionally important conformational changes. These results indicate WRN-exo is a human DnaQ family member and support analogous proof-reading activities that are stimulated by Ku70/80 with implications for WRN functions in age related pathologies and maintenance of genomic integrity.

Filamentous actinobacteria from the genus Frankia anddiverse woody trees and shrubs together form N2-fixing actinorhizal rootnodule symbioses that are a major source of new soil nitrogen in widelydiverse biomes 1. Three major clades of Frankia sp. strains are defined;each clade is associated with a defined subset of plants from among theeight actinorhizal plant families 2,3. The evolution arytrajectoriesfollowed by the ancestors of both symbionts leading to current patternsof symbiont compatibility are unknown. Here we show that the competingprocesses of genome expansion and contraction have operated in differentgroups of Frankia strains in a manner that can be related to thespeciation of the plant hosts and their geographic distribution. Wesequenced and compared the genomes from three Frankia sp. strains havingdifferent host plant specificities. The sizes of their genomes variedfrom 5.38 Mbp for a narrow host range strain (HFPCcI3) to 7.50Mbp for amedium host range strain (ACN14a) to 9.08 Mbp for a broad host rangestrain (EAN1pec.) This size divergence is the largest yet reported forsuch closely related bacteria. Since the order of divergence of thestrains is known, the extent of gene deletion, duplication andacquisition could be estimated and was found to be inconcert with thebiogeographic history of the symbioses. Host plant isolation favoredgenome …

A new stabilized nodal integration scheme is proposed and implemented. In this work, focus is on the natural neighbor meshless interpolation schemes. The approach is a modification of the stabilized conforming nodal integration (SCNI) scheme and is shown to perform well in several benchmark problems.

Technologically important nanomaterials come in all shapes and sizes. They can range from small molecules to complex composites and mixtures. Depending upon the spatial dimensions of the system and properties under investigation computer modeling of such materials can range from equilibrium and nonequilibrium Quantum Mechanics, to force-field-based Molecular Mechanics and kinetic Monte Carlo, to Mesoscale simulation of evolving morphology, to Finite-Element computation of physical properties. This brief review illustrates some of the above modeling techniques through a number of recent applications with carbon nanotubes: nano electromechanical sensors (NEMS), chemical sensors, metal-nanotube contacts, and polymer-nanotube composites.

We describe an efficient implementation and present aperformance study of an algebraic multilevel sub-structuring (AMLS)method for sparse eigenvalue problems. We assess the time and memoryrequirements associated with the key steps of the algorithm, and compareitwith the shift-and-invert Lanczos algorithm in computational cost. Oureigenvalue problems come from two very different application areas: theaccelerator cavity design and the normal mode vibrational analysis of thepolyethylene particles. We show that the AMLS method, when implementedcarefully, is very competitive with the traditional method in broadapplication areas, especially when large numbers of eigenvalues aresought.

This paper investigates the impact of proposed repositorythermal-loading on mountain-scale flow and heat transfer in theunsaturated fractured rock of Yucca Mountain, Nevada. In this context, amodel has been developed to study the coupled thermal-hydrological (TH)processes at the scale of the entire Yucca Mountain. This mountain-scaleTH model implements the current geological framework and hydrogeologicalconceptual models, and incorporates the latest rock thermal andhydrological properties. The TH model consists of a two-dimensionalnorth-south vertical cross section across the entire unsaturated zonemodel domain and uses refined meshes near and around the proposedrepository block, based on the current repository design, drift layout,thermal loading scenario, and estimated current and future climaticconditions. The model simulations provide insights into thermallyaffected liquid saturation, gas- and liquid-phase fluxes, and elevatedwater and rock temperature, which in turn allow modelers to predict thechanges in water flux driven by evaporation/condensation processes, anddrainage between drifts.

The objective of this paper is to set down the rationale for a separate Science & Technology (S&T) Program within every national deep-geological-isolation program. The fundamental rationale for such a Program is to provide a dedicated focus for longer-term science and technology activities that ultimately will benefit the whole repository mission. Such a Program, separately funded and with a dedicated staff (separate from the ''mainline'' activities to develop the repository, the surface facilities, and the transportation system), can devote itself exclusively to the development and management of a long-term science and technology program. Broad experience in governments worldwide has demonstrated that line offices are unlikely to be able to develop and sustain both the appropriate longer-term philosophy and the specialized skills associated with managing longer-term science and technology projects. Accomplishing both of these requires a separate dedicated program office with its own staff.

In this paper, we present a three-dimensional model forself-consistently modeling ion beam formation from plasma ion sources andtransporting in low energy beam transport systems. A multi-sectionoverlapped computational domain has been used to break the originaltransport system into a number of weakly coupled subsystems. Within eachsubsystem, macro-particle tracking is used to obtain the charge densitydistribution in this subdomain. The three-dimensional Poisson equation issolved within the subdomain after each particle tracking to obtain theself-consistent space-charge forces and the particle tracking is repeateduntil the solution converges. Two new Poisson solvers based on acombination of the spectral method and the finite difference multigridmethod have been developed to solve the Poisson equation in cylindricalcoordinates for the straight beam transport section and in Frenet-Serretcoordinates for the bending magnet section. This model can have importantapplication in design and optimization of the low energy beam line opticsof the proposed Rare Isotope Accelerator (RIA) front end.

Cadmium (Cd{sup 2+}), nickel (Ni{sup 2+}) and cobalt (Co{sup 2+}) are human and/or animal carcinogens. Zinc (Zn{sup 2+}) is not categorized as a carcinogen, and rather an essential element to humans. Metals were recently shown to inhibit DNA repair proteins that use metals for their function and/or structure. Here we report that the divalent ions Cd{sup 2+}, Ni{sup 2+}, and Zn{sup 2+} can inhibit the activity of a recombinant human N-methylpurine-DNA glycosylase (MPG) toward a deoxyoligonucleotide with ethenoadenine (var epsilonA). MPG removes a variety of toxic/mutagenic alkylated bases and does not require metal for its catalytic activity or structural integrity. At concentrations starting from 50 to 1000 {micro}M, both Cd{sup 2+} and Zn{sup 2+} showed metal-dependent inhibition of the MPG catalytic activity. Ni{sup 2+} also inhibited MPG, but to a lesser extent. Such an effect can be reversed with EDTA addition. In contrast, Co{sup 2+} and Mg{sup 2+} did not inhibit the MPG activity in the same dose range. Experiments using HeLa cell-free extracts demonstrated similar patterns of inactivation of the var epsilonA excision activity by the same metals. Binding of MPG to the substrate was not significantly affected by Cd{sup 2+}, Zn{sup 2+}, and Ni{sup 2+} at concentrations that …