The cyclotide MCoTI-II is a powerful trypsin inhibitor recently isolated from the seeds of Momordica cochinchinensis, a plant member of cucurbitaceae family. We report for the first time the in vivo biosynthesis of natively-folded MCoTI-II inside live E. coli cells. Our biomimetic approach involves the intracellular backbone cyclization of a linear cyclotide-intein fusion precursor mediated by a modified protein splicing domain. The cyclized peptide then spontaneously folds into its native conformation. The use of genetically engineered E. coli cells containing mutations in the glutathione and thioredoxin reductase genes considerably improves the production of folded MCoTI-II in vivo. Biochemical and structural characterization of the recombinant MCoTI-II confirmed its identity. Biosynthetic access to correctly-folded cyclotides allows the possibility of generating cell-based combinatorial libraries that can be screened inside living cells for their ability to modulate or inhibit cellular processes.

Many experimental approaches in biology and biophysics, as well as applications in diagnosis and drug discovery, require proteins to be immobilized on solid supports. Protein microarrays, for example, provide a high-throughput format to study biomolecular interactions. The technique employed for protein immobilization is a key to the success of these applications. Recent biochemical developments are allowing, for the first time, the selective and traceless immobilization of proteins generated by cell-free systems without the need for purification and/or reconcentration prior to the immobilization step.

The quadratic function approaching method (QFAM) is introduced for magnetotelluric sounding (MT) data inversion. The method takes the advantage of that quadratic function has single extreme value, which avoids leading to an inversion solution for local minimum and ensures the solution for global minimization of an objective function. The method does not need calculation of sensitivity matrix and not require a strict initial earth model. Examples for synthetic data and field measurement data indicate that the proposed inversion method is effective.

In this talk I discuss what we can learn about quarkonium dissociation from lattice-potential based models, and summarize the current understanding of lattice data on quarkonium.

An overview of the Lawrence Discrete Element Code (LDEC) is presented, and results from a study investigating the effect of explosive and impact loading on geologic materials using the Livermore Distinct Element Code (LDEC) are detailed. LDEC was initially developed to simulate tunnels and other structures in jointed rock masses using large numbers of polyhedral blocks. Many geophysical applications, such as projectile penetration into rock, concrete targets, and boulder fields, require a combination of continuum and discrete methods in order to predict the formation and interaction of the fragments produced. In an effort to model this class of problems, LDEC now includes implementations of Cosserat point theory and cohesive elements. This approach directly simulates the transition from continuum to discontinuum behavior, thereby allowing for dynamic fracture within a combined finite element/discrete element framework. In addition, a Smooth Particle Hydrodynamics (SPH) capability has been incorporated into LDEC, permitting the simulation of fluid-structure interaction. We will present results from a study of detonation-induced fracture and fragmentation of geologic media surrounding a tunnel using LDEC.

Soft x-ray microscopy has now achieved 15 nm spatial resolution with new zone plates and bending magnet radiation. Combined with elemental sensitivity and flexible sample environment (applied magnetic or electric fields, wet samples, windows, overcoatings) this emerges as a valuable tool for nanoscience and nanotechnology, complimenting common electron and scanning tip microscopies. In this presentation we describe recent advances in spatial resolution, expectations for the near future, and applications to magnetic materials, bio-tomography, etc.

Samarium-neodymium isotopic analyses of unleached and acid-leached mineral fractions from the recently identified olivine-bearing shergottite Northwest Africa 1195 yield a crystallization age of 348 {+-} 19 Ma and an {var_epsilon}{sub Nd}{sup 143} value of +40.1 {+-} 1.3. Maskelynite fractions do not lie on the Sm-Nd isochron and appear to contain a martian surface component with low {sup 147}Sm/{sup 144}Nd and {sup 143}Nd/{sup 144}Nd ratios that was added during shock. The Rb-Sr system is disturbed and does not yield an isochron. Terrestrial Sr appears to have affected all of the mineral fractions, although a maximum initial {sup 87}Sr/{sup 86}Sr ratio of 0.701614 {+-} 16 is estimated by passing a 348 Ma reference isochron through the maskelynite fraction that is least affected by contamination. The high initial {var_epsilon}{sub Nd}{sup 143} value and the low initial {sup 87}Sr/{sup 86}Sr ratio, combined with the geologically young crystallization age, indicate that Northwest Africa 1195 is derived from a source region characterized by a long-term incompatible element depletion. The age and initial Sr and Nd isotopic compositions of Northwest Africa 1195 are very similar to those of Queen Alexandra Range 94201, indicating these samples were derived from source regions with nearly identical Sr-Nd isotopic systematics. These …

An important problem in porous media involves the ability of micron and submicron-sized biological particles such as viruses or bacteria to move in groundwater systems through geologic media characterized by rock or mixed gravel, clay and sand materials. Current simulation capabilities require properly upscaled (continuum) models of colloidal filtration and adsorption to augment existing theories of fluid flow and chemical transport. Practical models typically address flow and transport behavior in aquifers over distances of 1 to 10 km where, for example, fluid momentum balance is governed by the simple Darcy's Law as a function of a pressure gradient, elevation gradient and a medium-dependent permeability parameter. In addition to fluid advection, there are multiple transport processes occurring in these systems including diffusion, dispersion and chemical interactions with solids or other aqueous chemical species. Particle transport is typically modeled in the same way as dissolved species, except that additional loss terms are incorporated to model particle filtration (physical interception), adsorption (chemical interception) and inactivation. Proper resolution of these processes at the porous medium continuum scale constitutes an important closure problem in subsurface science. We present a new simulation capability based on enabling technologies developed for microfluidics applications to model transport of colloidal-sized …

Understanding the effects of cold nuclear matter on J/psi production is a key requirement in order to interpret the J/psi suppression reported in heavy-ion collisions. Based on a Glauber model, the J/psi-nucleon inelastic cross section is determined from a statistical analysis of J/psi world data on nuclear targets. The global fit of all data gives sigmaJ/psiN = 3.4 +/- 0.2 mb, significantly smaller than previous estimates, yet the chi2 of the fit is pretty large, chi2/ndf = 1.5. A similar value, sigmaJ/psiN = 3.5 +/- 0.2 +/- 1.7 mb, is obtained when the De Florian-Sassot modifications of the nuclear parton densities are included in the analysis, although we emphasize that the present uncertainties on gluon (anti)shadowing do not allow for a precise determination of sigmaJ/psiN. Finally, the possible energy dependence of the J/psi-nucleon inelastic cross section is investigated within this framework. No significant energy dependence of the J/psi-N interaction is observed.

Research on a large-area, cost-effective Muon Telescope Detector (MTD) has been carried out for RHIC and for next generation detectors at future QCD Lab. We utilize state-of-the-art multi-gap resistive plate chambers with large modules and long readout strips in detector design. The results from cosmic ray and beam test will be presented to address intrinsic timing and spatial resolution for a Long-MRPC. The prototype performance of a novel muon telescope detector at STAR will be reported, including muon identification capability, timing and spatial resolution.

A proof-of-principle electron electric dipole moment (e-EDM)experiment using slow cesium atoms, nulled magnetic fields, and electricfield quantization has been performed. With the ambient magnetic fieldsseen by the atoms reduced to less than 200 pT, an electric field of 6MV/m lifts the degeneracy between states of unequal lbar mF rbar and,along with the low (approximately 3 m/s) velocity, suppresses thesystematic effect from the motional magnetic field. The low velocity andsmall residual magnetic field have made it possible to induce transitionsbetween states and to perform state preparation, analysis, and detectionin regions free of applied static magnetic and electric fields. Thisexperiment demonstrates techniques that may be used to improve the e-EDMlimit by two orders of magnitude, but it is not in itself a sensitivee-EDM search, mostly due to limitations of the laser system.

A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.

The phase diagrams of Ce, Th, and Pu metals have been studied by means of density-functional theory (DFT). In addition to these metals, the phase stability of Ce-Th and Pu-Am alloys has been also investigated from first-principles calculations. Equation-of-state (EOS) for Ce, Th, and the Ce-Th alloys has been calculated up to 1 Mbar pressure in good comparison to experimental data. Present calculations shows that the Ce-Th alloys adopt a body-centeredtetragonal (bct) structure upon hydrostatic compression that is in excellent agreement with measurements. The ambient pressure phase diagram of Pu is shown to be very poorly described by traditional DFT but rather well modeled when including magnetic interactions. In particular, the anomalous {var_sigma} phase of Pu is shown to be stabilized by magnetic disorder at elevated temperatures. The Pu-Am system has also been studied in a similar fashion and it is shown that this system, for about 25% Am content, becomes antiferromagnetic below about 400 K that corroborate the recent discovery of a Curie-Weiss behavior in this system.

Model systems for studying molecular surface chemistry have evolved from single crystal surfaces at low pressure to colloidal nanoparticles at high pressure. Low pressure surface structure studies of platinum single crystals using molecular beam surface scattering and low energy electron diffraction techniques probe the unique activity of defects, steps and kinks at the surface for dissociation reactions (H-H, C-H, C-C, O{double_bond}O bonds). High-pressure investigations of platinum single crystals using sum frequency generation vibrational spectroscopy have revealed the presence and the nature of reaction intermediates. High pressure scanning tunneling microscopy of platinum single crystal surfaces showed adsorbate mobility during a catalytic reaction. Nanoparticle systems are used to determine the role of metal-oxide interfaces, site blocking and the role of surface structures in reactive surface chemistry. The size, shape and composition of nanoparticles play important roles in determining reaction activity and selectivity.

The deep-sea gorgonian octocoral Primnoa resedaeformis is distributed throughout the Atlantic and Pacific Oceans at depths of 65-3200 m. It has a two-part skeleton of calcite and gorgonin. Towards the inside of the axial skeleton gorgonin and calcite are deposited in concentric growth rings, similar to tree rings. Colonies were collected from the Northeast Channel (northwest Atlantic Ocean, southwest of Nova Scotia, Canada) from depths of 250-475 m. Radiocarbon was measured in individual rings isolated from sections of each colony, after dissolution of calcite. Each {Delta}{sup 14}C measurement was paired with a ring age determined by three amateur ring counters. The precision of ring counts averaged better than {+-} 2 years. Accurate reconstruction of 20th century bomb-radiocarbon shows that (1) the growth rings are formed annually, (2) the gorgonin is derived from surface particulate organic matter (POM) and (3) useful environmental data are recorded in the organic endoskeletons of deep-sea octocorals. These results support the use of Primnoa resedaeformis as a long-term, high resolution monitor of surface ocean conditions, particularly in temperate and boreal environments where proxy data are lacking.

Biodetection instrumentation that is capable of functioning effectively outside the controlled laboratory environment is critical for the detection of health threats, and is a crucial technology for Health Security. Experience in bringing technologies from the basic research laboratory to integrated fieldable instruments suggests lessons for the engineering of these systems. This overview will cover several classes of such devices, with examples from systems developed for homeland security missions by Lawrence Livermore National Laboratory (LLNL). Recent trends suggest that front-end sample processing is becoming a critical performance-determining factor for many classes of fieldable biodetection devices. This paper introduces some results of a recent study that was undertaken to assess the requirements and potential technologies for next-generation integrated sample processing.

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Fracture mechanics methodologies for flaw stability analysis of a storage tank were compared in terms of the maximum stable through-wall flaw sizes or ''instability lengths.'' The comparison was made at a full range of stress loading at a specific set of mechanical properties of A285 carbon steel and with the actual tank configuration. The two general methodologies, the J-integral-tearing modulus (J-T) and the failure assessment diagram (FAD), and their specific estimation schemes were evaluated. A finite element analysis of a flawed tank was also performed for validating the J estimation scheme with curvature correction and for constructing the finite element-based FAD. The calculated instability crack lengths show that the J-T methodology that uses an estimated scheme, and the material-specific FAD, most closely approximate the result calculated with finite element analysis for the stress range that bounds those expected at the highest fill levels in the storage tanks. The results from the other FAD methods show instability lengths less than the J-T results over this range.

Typically, large scientific datasets (order of terabytes) are generated at large computational centers, and stored on mass storage systems. However, large subsets of the data need to be moved to facilities available to application scientists for analysis. File replication of thousands of files is a tedious, error prone, but extremely important task in scientific applications. The automation of the file replication task requires automatic space acquisition and reuse, and monitoring the progress of staging thousands of files from the source mass storage system, transferring them over the network, archiving them at the target mass storage system or disk systems, and recovering from transient system failures. We have developed a robust replication system, called DataMover, which is now in regular use in High-Energy-Physics and Climate modeling experiments. Only a single command is necessary to request multi-file replication or the replication of an entire directory. A web-based tool was developed to dynamically monitor the progress of the multi-file replication process.

We provide a framework for preconditioning nonlinear 3D electromagnetic inverse scattering problems using nonlinear conjugate gradient (NLCG) and limited memory (LM) quasi-Newton methods. Key to our approach is the use of an approximate adjoint method that allows for an economical approximation of the Hessian that is updated at each inversion iteration. Using this approximate Hessian as a preconditoner, we show that the preconditioned NLCG iteration converges significantly faster than the non-preconditioned iteration, as well as converging to a data misfit level below that observed for the non-preconditioned method. Similar conclusions are also observed for the LM iteration; preconditioned with the approximate Hessian, the LM iteration converges faster than the non-preconditioned version. At this time, however, we see little difference between the convergence performance of the preconditioned LM scheme and the preconditioned NLCG scheme. A possible reason for this outcome is the behavior of the line search within the LM iteration. It was anticipated that, near convergence, a step size of one would be approached, but what was observed, instead, were step lengths that were nowhere near one. We provide some insights into the reasons for this behavior and suggest further research that may improve the performance of the LM methods.

Conventional and high resolution electron microscopy havebeen applied for studying lattice defects in nonpolar a-plane GaN grownon a 4H-SiC substrate with an AlN buffer layer. Samples in plan-view andcross-section configurations have been investigated. Basal and prismaticstacking faults together with Frank and Shockley partial dislocationswere found to be the main defects in the GaN layers. High resolutionelectron microscopy in combination with image simulation supported Drum smodel for the prismatic stacking faults. The density of basal stackingfaults was measured to be ~;1.6_106cm-1. The densities of partialdislocations terminating I1 and I2 types of intrinsic basal stackingfaults were ~;4.0_1010cm-2 and ~;0.4_1010cm-2, respectively. The energyof the I2 stacking fault in GaN was estimated to be (40+-4) erg/cm2 basedon the separation of Shockley partial dislocations. To the best of ourknowledge, the theoretically predicted I3 basal stacking fault in GaN wasobserved experimentally for the first time.

The effect of Cl on the activity of Pt/Al{sub 2}O{sub 3} catalysts for methane oxidation has been studied by H{sub 2} and CO chemisorption, O{sub 2} isotopic exchange, kinetic studies and EXAFS spectroscopy. Catalysts containing 1.5% pt/Al{sub 2}O{sub 3} were prepared by incipient wetness from H{sub 2}PtCl{sub 6} and Pt(NH{sub 3}){sub 4}(NO{sub 3}){sub 2} precursors. Both reduced catalysts have similar dispersion (0.8) as determined by H{sub 2} chemisorption. At low methane concentration (0.3 vol.% CH{sub 4}, 16 vol.% O{sub 2}) the Cl-free catalyst was about 20 times more active during complete methane oxidation than the Cl-containing catalyst. Both CO chemisorption and oxygen exchange were observed on the Cl-free catalyst, whereas they were not detected on the Cl-containing catalyst. On the Cl-free catalyst, only Pt-Pt and Pt-O bonds were detected from the EXAFS results, while on the Cl-containing catalyst additional Pt-Cl bonds were present. The effect of chlorine on activity strongly depended on the reactant concentration. Exposure of the Cl-free catalyst to higher concentrations of methane (3 vol.% CH{sub 4}) reduced the activity to a level similar to that of the Cl-containing catalyst. Addition of HCl to the Cl-free catalyst rendered the activity identical to the catalyst prepared from Cl-containing precursors. …

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We summarize four of our group's high-risk/high-payoff research projects funded by the Intelligence Technology Innovation Center (ITIC) in conjunction with our DHS-funded pathogen informatics activities. These are (1) quantitative assessment of genomic sequencing needs to predict high quality DNA and protein signatures for detection, and comparison of draft versus finished sequences for diagnostic signature prediction; (2) development of forensic software to identify SNP and PCR-RFLP variations from a large number of viral pathogen sequences and optimization of the selection of markers for maximum discrimination of those sequences; (3) prediction of signatures for the detection of virulence, antibiotic resistance, and toxin genes and genetic engineering markers in bacteria; (4) bioinformatic characterization of virulence factors to rapidly screen genomic data for potential genes with similar functions and to elucidate potential health threats in novel organisms. The results of (1) are being used by policy makers to set national sequencing priorities. Analyses from (2) are being used in collaborations with the CDC to genotype and characterize many variola strains, and reports from these collaborations have been made to the President. We also determined SNPs for serotype and strain discrimination of 126 foot and mouth disease virus (FMDV) genomes. For (3), currently >1000 probes …