Chloroplast genome structure, gene order and content arehighly conserved in land plants. We sequenced the complete chloroplastgenome sequence of Trachelium caeruleum (Campanulaceae) a member of anangiosperm family known for highly rearranged chloroplast genomes. Thetotal genome size is 162,321 bp with an IR of 27,273 bp, LSC of 100,113bp and SSC of 7,661 bp. The genome encodes 115 unique genes, with 19duplicated in the IR, a tRNA (trnI-CAU) duplicated once in the LSC and aprotein coding gene (psbJ) duplicated twice, for a total of 137 genes.Four genes (ycf15, rpl23, infA and accD) are truncated and likelynonfunctional; three others (clpP, ycf1 and ycf2) are so highly divergedthat they may now be pseudogenes. The most conspicuous feature of theTrachelium genome is the presence of eighteen internally unrearrangedblocks of genes that have been inverted or relocated within the genome,relative to the typical gene order of most angiosperm chloroplastgenomes. Recombination between repeats or tRNAs has been suggested as twomeans of chloroplast genome rearrangements. We compared the relativenumber of repeats in Trachelium to eight other angiosperm chloroplastgenomes, and evaluated the location of repeats and tRNAs in relation torearrangements. Trachelium has the highest number and largest repeats,which are concentrated near inversion endpoints or other rearrangements.tRNAs occur at …

We present the results of ab initio calculations for elasticelectron scattering by tetrahydrofuran (THF) using the complex Kohnvariational method. We carried out fixed-nuclei calculations at theequilibrium geometry of the target molecule for incident electronenergies up to 20 eV. The calculated momentum transfer cross sectionsclearly reveal the presence of broad shape resonance behavior in the 8-10eV energy range, in agreement with recent experiments. The calculateddifferential cross sections at 20 eV, which include the effects of thelong-range electron-dipole interaction, are alsofound to be in agreementwith the most recent experimental findings.

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.

Mitochondria and plastids (collectively called organelles)descended from prokaryotes that adopted an intracellular, endosymbioticlifestyle within early eukaryotes. Comparisons of their remnant genomesaddress a wide variety of biological questions, especially when includingthe genomes of their prokaryotic relatives and the many genes transferredto the eukaryotic nucleus during the transitions from endosymbiont toorganelle. The pace of producing complete organellar genome sequences nowmakes it unfeasible to do broad comparisons using the primary literatureand, even if it were feasible, it is now becoming uncommon for journalsto accept detailed descriptions of genome-level features. Unfortunatelyno database is currently useful for this task, since they have littlestandardization and are riddled with error. Here I outline what iscurrently wrong and what must be done to make this data useful to thescientific community.

The point spread function (PSF) is an important measure of spatial resolution in CCDs for point-like objects, since it affects image quality and spectroscopic resolution. We present new data and theoretical developments for lateral charge diffusion in thick, fully-depleted charge-coupled devices (CCDs) developed at Lawrence Berkeley National Laboratory (LBNL). Because they can be over-depleted, the LBNL devices have no field-free region and diffusion is controlled through the application of an external bias voltage. We give results for a 3512 x 3512 format, 10.5 {micro}m pixel back-illuminated p-channel CCD developed for the SuperNova/Acceleration Probe (SNAP), a proposed satellite-based experiment designed to study dark energy. The PSF was measured at substrate bias voltages between 3 V and 115 V. At a bias voltage of 115 V, we measure an rms diffusion of 3.7 {+-} 0.2 {micro}m. Lateral charge diffusion in LBNL CCDs will meet the SNAP requirements.

Cathepsin B (CTSB) and cathepsin L (CTSL) are two widelyexpressed cysteine proteases thought to predominantly reside withinlysosomes. Functional analysis of CTSL in humans is complicated by theexistence of two CTSL-like homologues (CTSL and CTSL2), in contrast tomice which contain only one CTSL enzyme. Thus transgenic expression ofhuman CTSL in CTSL deficient mice provides an opportunity to study the invivo functions of this human protease without interference by its highlyrelated homologue. While mice with single gene deficiencies for murineCTSB or CTSL survive without apparent neuromuscular impairment, murineCTSB/CTSL double deficient mice display degeneration of cerebellarPurkinje cells and neurons of the cerebral cortex, resulting in severehypotrophy, motility defects, and lethality during their third to fourthweek of life. Here we show that expression of human CTSL through agenomic transgene results in widespread expression of human CTSL in themouse which is capable of rescuing the lethality found in CTSB/CTSLdouble-deficient animals. Human CTSL is expressed in the brain of thesecompound mutants predominantly in neurons of the cerebral cortex and inPurkinje cells of the cerebellum, where it appears to prevent neuronalcell death.

A micromechanical model is developed for grain bridging inmonolithic ceramics. Specifically, bridge formation of a single,non-equiaxed grain spanning adjacent grains is addressed. A cohesive zoneframework enables crack initiation and propagation along grainboundaries. The evolution of the bridge is investigated through avariance in both grain angle and aspect ratio. We propose that thebridging process can be partitioned into five distinct regimes ofresistance: propagate, kink, arrest, stall, and bridge. Although crackpropagation and kinking are well understood, crack arrest and subsequent"stall" have been largely overlooked. Resistance during the stall regimeexposes large volumes of microstructure to stresses well in excess of thegrain boundary strength. Bridging can occur through continued propagationor reinitiation ahead of the stalled crack tip. The driving forcerequired to reinitiate is substantially greater than the driving forcerequired to kink. In addition, the critical driving force to reinitiateis sensitive to grain aspect ratio but relatively insensitive to grainangle. The marked increase in crack resistance occurs prior to bridgeformation and provides an interpretation for the rapidly risingresistance curves which govern the strength of many brittle materials atrealistically small flaw sizes.

Atomic scale surface structure plays an important roleindescribing many properties of materials, especially in the case ofnanomaterials. One of the most effective techniques for surface structuredetermination is low-energy electron diffraction (LEED), which can beused in conjunction with optimization to fit simulated LEED intensitiesto experimental data. This optimization problem has a number ofcharacteristics that make it challenging: it has many local minima, theoptimization variables can be either continuous or categorical, theobjective function can be discontinuous, there are no exact analyticderivatives (and no derivatives at all for categorical variables), andfunction evaluations are expensive. In this study, we show how to apply aparticular class of optimization methods known as pattern search methodsto address these challenges. These methods donot explicitly usederivatives, and are particularly appropriate when categorical variablesare present, an important feature that has not been addressed in previousLEED studies. We have found that pattern search methods can produceexcellent results, compared to previously used methods, both in terms ofperformance and locating optimal results.

In the first part of the talk, I explain what empirical evidence points to the need for having an effective grand unification-like symmetry possessing the symmetry SU(4)-color in 4D. If one assumes the premises of a future predictive theory including gravity--be it string/M theory or a reincarnation--this evidence then suggests that such a theory should lead to an effective grand unification-like symmetry as above in 4D, near the string-GUT-scale, rather than the standard model symmetry. Advantages of an effective supersymmetric G(224) = SU(2){sub L} x SU(2){sub R} x SU(4){sup c} or SO(10) symmetry in 4D in explaining (1) observed neutrino oscillations, (2) baryogenesis via leptogenesis, and (3) certain fermion mass-relations are noted. And certain distinguishing tests of a SUSY G(224) or SO(10)-framework involving CP and flavor violations (as in {mu} {yields} e{gamma}, {tau} {yields} {mu}{gamma}, edm's of the neutron and the electron) as well as proton decay are briefly mentioned. Recalling some of the successes we have had in our understanding of nature so far, and the current difficulties of string/M theory as regards the large multiplicity of string vacua, some comments are made on the traditional goal of understanding vis a vis the recently evolved view of landscape and …

A combination of cyclic polarization tests, electrochemical impedance spectroscopy, and electrochemical quartz crystal microbalance (EQCM) measurements indicate a film is formed when aluminum is polarized above 4.5V in 1:1 EC+DMC with 1M LiBOB. The quantity of film that is formed increases with increasing applied potential. Results of EQCM tests suggest the film is AlBO{sub 3}. The film is very protective against corrosion and inhibits pitting corrosion of aluminum in normally corrosive 1M LiTFSI.

The bonding of hexanethiols to gold nanoparticles of 1.5, 2.0 and 3 nm was studied using X-ray Absorption Near Edge Spectroscopy (XANES) and Extended X-ray Absorption Fine Structure (EXAFS). The XANES spectra revealed that a substantial fraction of hexanethiol molecules were weakly bound, in addition to the molecules forming covalent bonds with Au surface atoms. The weakly bound molecules could be easily removed by washing in dichloromethane. After removal of the weakly bound molecules the S K-edge XANES spectrum reveals peaks due to S-Au and S-C bonds with intensities that change as a function of particle size. We explain this as the result of distortions occurring in the molecules adsorbed on the smaller particles. The distortions arise from the poor packing due to the high curvature of the particles. In addition, EXAFS results show that the smaller particles bind more molecules per Au atom than the larger ones, which is again interpreted as a result of the curved nature of the surface.

There are divergent results in the literature on the(in)dependence of the ion velocity distribution functions on the ioncharge states. Apparently, most time-of-flight methods of measurementsindicate independence whereas most measurements with electrostaticanalyzers state the opposite. It is shown here that this grouping iscoincidental with investigations of pulsed and continuous arcs. Allresults can be consolidated by taking ion-neutral interaction intoaccount, especially charge exchange collisions with the metal neutralsproduced by the arc itself. The velocity distribution functions areindependent of charge state when produced at cathode spots but becomecharge-state dependent when the plasma interacts withneutrals.

This paper reports on the efforts to enable fully scalable simulations of Dislocation Line Dynamics (DLD) for direct calculations of strength of crystalline materials. DLD simulations are challenging and do not lend themselves naturally to parallel computing. Through a combinations of novel physical approaches, mathematical algorithms and computational science developments, a new DLD code ParaDiS is shown to take meaningful advantage of BG/L and, by doing so, to enable discovery class science by computation.

The band gap bowing and the electron localization ofGaxIn1-xN are calculated using both the local density approximation (LDA)and screened-exchange local density functional (sX-LDA) methods. Thecalculated sX-LDA band gaps are in good agreement with the experimentallyobserved values, with errors of -0.26 and 0.09 eV for bulk GaN and InN,respectively. The LDA band gap errors are 1.33 and 0.81 eV for GaN andInN, in order. In contrast to the gap itself, the band gap bowingparameter is found to be very similar in sX-LDA and LDA. We identify thelocalization of hole states in GaxIn1-xN alloys along In-N-In chains. Thepredicted localizationis stronger in sX-LDA.

Technetium-99 is an abundant, long-lived (t1/2 = 213,000 yr)fission product that creates challenges for the safe, long-term disposalof nuclear waste. While 99Tc receives attention largely due to its highenvironmental mobility, it also causes problems during its incorporationinto nuclear waste glass due to the volatility of Tc(VII) compounds. Thisvolatility decreases the amount of 99Tc stabilized in the waste glass andcauses contamination of the waste glass melter and off-gas system. Theapproach to decrease the volatility of 99Tc that has received the mostattention is reduction of the volatile Tc(VII) species to less volatileTc(IV) species in the glass melt. On engineering scale experiments,rhenium is often used as a non-radioactive surrogate for 99Tc to avoidthe radioactive contamination problems caused by volatile 99Tc compounds.However, Re(VII) is more stable towards reduction than Tc(VII), so morereducing conditions would be required in the glass melt to produceRe(IV). To better understand the redox behavior of Tc and Re in nuclearwaste glass, a series of glasses were prepared under different redoxconditions. The speciation of Tc and Re in the resulting glasses wasdetermined by X-ray absorption fine structure spectroscopy. Surprisingly,Re and Tc do not behave similarly in the glass melt. Although Tc(0),Tc(IV), and Tc(VII) were observed in these samples, only Re(0) andRe(VII) …

In recent years, the search to develop large-area solar cells at low cost has led to research on photovoltaic (PV) systems based on nanocomposites containing conjugated polymers. These composite films can be synthesized and processed at lower costs and with greater versatility than the solid state inorganic semiconductors that comprise today's solar cells. However, the best nanocomposite solar cells are based on a complex architecture, consisting of a fine blend of interpenetrating and percolating donor and acceptor materials. Cell performance is strongly dependent on blend morphology, and solution-based fabrication techniques often result in uncontrolled and irreproducible blends, whose composite morphologies are difficult to characterize accurately. Here we incorporate 3-dimensional hyper-branched colloidal semiconductor nanocrystals in solution-processed hybrid organic-inorganic solar cells, yielding reproducible and controlled nanoscale morphology.

We discuss the temperature-dependence of S-wave quarkonium spectral functions in a nonrelativistic Green's function approach and compare these to lattice QCD results.

The Heavy Ion Fusion Science Virtual National Laboratory (HIFS-VNL) is a collaboration of Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and Princeton Plasma Physics Laboratory. These laboratories, in cooperation with researchers at other institutions, are carrying out a coordinated effort to apply intense ion beams as drivers for studies of the physics of matter at extreme conditions, and ultimately for inertial fusion energy. Progress on this endeavor depends upon coordinated application of experiments, theory, and simulations. This paper describes the state of the art, with an emphasis on the coordination of modeling and experiment; developments in the simulation tools, and in the methods that underly them, are also treated.

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We examine procedures for detecting the point-group symmetryof macromolecular datasets and propose enhancements. To validate apoint-group, it is sufficient to compare pairs of Bragg reflections thatare related by each of the group's component symmetry operators.Correlation is commonly expressed in the form of a single statisticalquantity (such as Rmerge) that incorporates information from all of theobserved reflections. However, the usual practice of weighting all pairsof symmetry-related intensities equally can obscure the fact that thevarious symmetry operators of the point-group contribute differingfractions of the total set. In some cases where particular symmetryelements are significantly under-represented, statistics calculatedglobally over all observations do not permit conclusions about thepoint-group and Patterson symmetry. The problem can be avoided byrepartitioning the data in a way that explicitly takes note of individualoperators. The new analysis methods, incorporated into the programLABELIT (cci.lbl.gov/labelit), can be performed early enough during dataacquisition, and are quick enough, that it is feasible to pause tooptimize the data collection strategy.

Historically, large items of TRU Waste, which were too large to be packaged in drums for disposal have been packaged in various sizes of custom made plywood boxes at the Savannah River Site (SRS), for many years. These boxes were subsequently packaged into large steel ''Black Boxes'' for storage at SRS, pending availability of Characterization and Certification capability, to facilitate disposal of larger items of TRU Waste. There are approximately 107 Black Boxes in inventory at SRS, each measuring some 18' x 12' x 7', and weighing up to 45,000 lbs. These Black Boxes have been stored since the early 1980s. The project to repackage this waste into Standard Large Boxes (SLBs), Standard Waste Boxes (SWB) and Ten Drum Overpacks (TDOP), for subsequent characterization and WIPP disposal, commenced in FY04. To date, 10 Black Boxes have been repackaged, resulting in 40 SLB-2's, and 37 B25 overpack boxes, these B25's will be overpacked in SLB-2's prior to shipping to WIPP. This paper will describe experience to date from this project.

This study developed novel hydrides for hydrogen storage through a novel synthesis technique utilizing high hydrogen overpressure at elevated temperatures denoted as Molten State Processing, MSP. The ultimate goal is to produce materials that have high hydrogen capacity, are stable after cycling and possess favorable thermodynamic and kinetic characteristics compatible with onboard hydrogen storage for automotive applications. In order to achieve these goals the MSP Process was developed and used to modify and form new complex hydride compounds with desired characteristics. This synthesis technique holds the potential of fusing different known complex hydrides at elevated temperatures and pressures to form new complexes having different sorption and thermodynamic properties. The new complex hydrides produced by this method were identified through structural determination and thermodynamic characterization in order to achieve a more fundamental understanding of their formation and dissociation mechanisms.

The Purgatorio code [Wilson et al., JQSRT 99, 658-679 (2006)] is a new implementation of the Inferno model describing a spherically symmetric average atom embedded in a uniform plasma. Bound and continuum electrons are treated using a fully relativistic quantum mechanical description, giving the electron-thermal contribution to the equation of state (EOS). The free-electron density of states can also be used to calculate scattering cross sections for electron transport. Using the extended Ziman formulation, electrical conductivities are then obtained by convolving these transport cross sections with externally-imposed ion-ion structure factors.

The Image Content Engine (ICE) is a framework of software and underlying mathematical and physical models that enable scientists and analysts to extract features from Terabytes of imagery and search the extracted features for content relevant to their problem domain. The ICE team has developed a set of tools for feature extraction and analysis of image data, primarily based on the image content. The scale and volume of imagery that must be searched presents a formidable computation and data bandwidth challenge, and a search of moderate to large scale imagery quickly becomes intractable without exploiting high degrees of data parallelism in the feature extraction engine. In this paper we describe the software and hardware architecture developed to build a data parallel processing engine for ICE. We discuss our highly tunable parallel process and job scheduling subsystem, remote procedure invocation, parallel I/O strategy, and our experience in running ICE on a 16 node, 32 processing element (CPU) Linux Cluster. We present performance and benchmark results, and describe how we obtain excellent speedup for the imagery searches in our test-bed prototype.