Background: Most bacterial genes were acquired by horizontalgene transfer from other bacteria instead of being inherited bycontinuous vertical descent from an ancient ancestor}. To understand howthe regulation of these {acquired} genes evolved, we examined theevolutionary histories of transcription factors and of regulatoryinteractions from the model bacterium Escherichia coli K12. Results:Although most transcription factors have paralogs, these usually arose byhorizontal gene transfer rather than by duplication within the E. colilineage, as previously believed. In general, most neighbor regulators --regulators that are adjacent to genes that they regulate -- were acquiredby horizontal gene transfer, while most global regulators evolvedvertically within the gamma-Proteobacteria. Neighbor regulators wereoften acquired together with the adjacent operon that they regulate, sothe proximity might be maintained by repeated transfers (like "selfishoperons"). Many of the as-yet-uncharacterized (putative) regulators havealso been acquired together with adjacent genes, so we predict that theseare neighbor regulators as well. When we analyzed the histories ofregulatory interactions, we found that the evolution of regulation byduplication was rare, and surprisingly, many of the regulatoryinteractions that are shared between paralogs result from convergentevolution. Another surprise was that horizontally transferred genes aremore likely than other genes to be regulated by multiple regulators, andmost of this complex regulation probably evolved …

Currently there are three platforms that offer quasi-isentropic compression or ramp-wave compression (RWC): light-gas gun, magnetic flux (Z-pinch), and laser. We focus here on the light-gas gun technique and on some current theoretical insights from experimental data. A gradient impedance through the length of the impactor provides the pressure pulse upon impactor to the subject material. Applications and results are given concerning high-pressure strength and liquid to solid, phase transition of water plus its associated phase fraction history. We also introduce the Korteweg-deVries-Burgers equation as a means to understand the evolution these RWC waves that propagate through the thickness of the subject material. This equation has the necessary competition between non-linear, dispersion, and dissipation processes, which is shown through observed structures that are manifested in the experimental particle velocity histories. Such methodology points towards a possible quantifiable dissipation, through which RWC experiments may be analyzed.

Computational science research components were vital parts of the SciDAC-1 accelerator project and are continuing to play a critical role in newly-funded SciDAC-2 accelerator project, the Community Petascale Project for Accelerator Science and Simulation (ComPASS). Recent advances and achievements in the area of computational science research in support of petascale electromagnetic modeling for accelerator design analysis are presented, which include shape determination of superconducting RF cavities, mesh-based multilevel preconditioner in solving highly-indefinite linear systems, moving window using h- or p- refinement for time-domain short-range wakefield calculations, and improved scalable application I/O.

The influence of epitaxial strain, in the form of tetragonal distortions, on the magnetic and magnetotransport properties of La{sub 0.67}Sr{sub 0.33}MnO{sub 3} thin films was studied. The tetragonal distortion (c/a ratio) was modulated through the choice of the substrate, ranging from c/a=1.007 on (001)-oriented (LaAlO{sub 3}){sub 0.3}(Sr{sub 2}AlTaO{sub 6}){sub 0.7} substrates to 0.952 on (110)-oriented GdScO{sub 3} substrates. In agreement with previous theoretical predictions, these large values of tensile strain cause the Curie temperature and the saturation magnetization to decrease, alter the temperature dependence of the resistivity and magnetoresistance, and increase the resistivity several orders of magnitude.

We used the Near Infrared Camera (NIRC) on Keck I to obtain K{sub s}-band images of four candidate high-redshift radio galaxies selected using optical and radio data in the NOAO Deep Wide-Field Survey in Bootes. Our targets have 1.4 GHz radio flux densities greater than 1 mJy, but are undetected in the optical. Spectral energy distribution fitting suggests that three of these objects are at z > 3, with radio luminosities near the FR-I/FR-II break. The other has photometric redshift z{sub phot} = 1.2, but may in fact be at higher redshift. Two of the four objects exhibit diffuse morphologies in K{sub s}-band, suggesting that they are still in the process of forming.

The market for photovoltaics in the United States remains small relative to the nation's solar resource potential. Nonetheless, annual grid-connected PV installations have grown from just 4 MW in 2000 to over 100 MW in 2006, fast enough to the catch the attention of the global solar industry. The state of California deserves much of the credit for this growth. The State's historical rebate programs resulted in roughly 75% of the nation's grid-connected PV additions from 2000 through 2006 being located in California, and the $3 billion California Solar Initiative will ensure that the State remains a mainstay of the US solar industry for years to come. But California is not the only market for solar in the US; other states have recently developed policies that may rival those of the western state in terms of future growth potential. In particular, 25 states, as well as Washington, D.C., have established renewables portfolio standards (RPS), sometimes called quota systems in Europe, requiring electricity suppliers in those states to source a minimum portion of their need from renewable electricity. (Because a national RPS is not yet in place, my focus here is on state policies). Under many of these state policies, solar …

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We report Raman and infrared absorption spectroscopy alongwith X-ray diffraction for brucite-type beta-Cd(OH)2 to 28 GPa at 300 K.The OH-stretching modes soften with pressure and disappear at 21 GPa withtheir widths increasing rapidly above 5 GPa, consistent with a gradualdisordering of the H sublattice at 5 20 GPa similar to that previouslyobserved for Co(OH)2.Asymmetry in the peak shapes of the OH-stretchingmodes suggests the existence of diverse disordered sitesfor H atoms inCd(OH)2 under pressure. Above 15 GPa, the A1g(T) lattice mode showsnon-linear behavior and softens to 21 GPa, at which pressure significantchanges are observed: new Raman modes appear, two Raman-active latticemodes and the OH-stretching modes of the low-pressure phase disappears,and the positions of some X-ray diffraction lines change abruptly withthe appearance of weak new diffraction features. These observationssuggest that amorphization of the H sublattice is accompanied by acrystalline-to-crystalline transition at 21 GPa in Cd(OH)2, which has notbeen previously observed in the brucite-type hydroxides. The Ramanspectra of the high-pressure phase of Cd(OH)2 is similar to those of thehigh-pressure phase of single-crystal Ca(OH)2 of which structure has beententatively assigned to the Sr(OH)2 type.

The availability of whole-cell level metabolic networks of high quality has made it possible to develop a predictive understanding of bacterial metabolism. Using the optimization framework of flux balance analysis, I investigate metabolic response and activity patterns to variations in the availability of nutrient and chemical factors such as oxygen and ammonia by simulating 30,000 random cellular environments. The distribution of reaction fluxes is heavy-tailed for the bacteria H. pylori and E. coli, and the eukaryote S. cerevisiae. While the majority of flux balance investigations have relied on implementations of the simplex method, it is necessary to use interior-point optimization algorithms to adequately characterize the full range of activity patterns on metabolic networks. The interior-point activity pattern is bimodal for E. coli and S. cerevisiae, suggesting that most metabolic reaction are either in frequent use or are rarely active. The trimodal activity pattern of H. pylori indicates that a group of its metabolic reactions (20%) are active in approximately half of the simulated environments. Constructing the high-flux backbone of the network for every environment, there is a clear trend that the more frequently a reaction is active, the more likely it is a part of the backbone. Finally, I briefly …

The Linac Coherent Light Source (LCLS) is a SASE x-ray Free-Electron Laser (FEL) project under construction at SLAC [1]. The injector section, from drive-laser and RF photocathode gun through the first bunch compressor, was commissioned in the spring and summer of 2007. The second phase of commissioning, including the second bunch compressor and various main linac modifications, was completed in January through August of 2008. We report here on experience gained during this second phase of machine commissioning, including the injector, the first and second bunch compressor stages, the linac up to 14 GeV, and beam stability measurements. The final commissioning phase, including the undulator and the long transport line from the linac, is set to begin in December 2008, with first light expected in July 2009.

Transmission Electron Microscopy (TEM) and opticalmeasurements obtained from InN and In1-xGaxNfilms (0<x<0.54)grown by Molecular Beam Epitaxy are presented. Energy gaps measuredbyabsorption, PR, and PL for InN films grown on c-plane Al2O3 were in therange of 0.7 eV. No In or otherinclusions were observed in these films,ruling out the possibility of a strong Mie scattering mechanism. IntheIn1-xGaxN films the relationship between the structural properties andthe optical properties, inparticular the presence or absence of a Stokesshift between absorption and PL, is discussed. TEM studiesshow that highquality layers do not have a Stokes shift. Some films had compositionalordering; thesefilms also showed a shift between absorption edge andluminescence peak.

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Laser-wakefield accelerators (LWFA) can produce electricfields of order 10-100 GV/m suitable for acceleration of electrons torelativistic energies. The wakefields are excited by a relativisticallyintense laser pulse propagating through a plasma and have a phasevelocity determined by the group velocity of the light pulse. Twoimportant effects that can limit the acceleration distanceand hence thenet energy gain obtained by an electron are diffraction of the drivelaser pulse and particle-wake dephasing. Diffraction of a focusedultra-short laser pulse can be overcome by using preformed plasmachannels. The dephasing limit can be increased by operating at a lowerplasma density, since this results in an increase in the laser groupvelocity. Here we present detailed results on the generation of GeV-classelectron beams using an intense femtosecond laser beamand a 3.3 cm longpreformed discharge-based plasma channel [W.P. Leemans et al., NaturePhysics 2, 696-699 (2006)]. The use of a discharge-based waveguidepermitted operation at an order ofmagnitude lower density and 15 timeslonger distance than in previous experiments that relied on laserpreformed plasma channels. Laser pulses with peak power ranging from10-50 TW were guided over more than 20 Rayleigh ranges and high-qualityelectron beams with energy up to 1 GeV were obtained by channelling a 40TW peak power laser pulse. The dependence of …

The chloroplast genome of Pelargonium e hortorum has beencompletely sequenced. It maps as a circular molecule of 217,942 bp, andis both the largest and most rearranged land plant chloroplast genome yetsequenced. It features two copies of a greatly expanded inverted repeat(IR) of 75,741 bp each, and consequently diminished single copy regionsof 59,710 bp and 6,750 bp. It also contains two different associations ofrepeated elements that contribute about 10 percent to the overall sizeand account for the majority of repeats found in the genome. Theyrepresent hotspots for rearrangements and gene duplications and include alarge number of pseudogenes. We propose simple models that account forthe major rearrangements with a minimum of eight IR boundary changes and12 inversions in addition to a several insertions of duplicated sequence.The major processes at work (duplication, IR expansion, and inversion)have disrupted at least one and possibly two or three transcriptionaloperons, and the genes involved in these disruptions form the core of thetwo major repeat associations. Despite the vast increase in size andcomplexity of the genome, the gene content is similar to that of otherangiosperms, with the exceptions of a large number of pseudogenes as partof the repeat associations, the recognition of two open reading frames(ORF56 and ORF42) …

In the Ge on Si model heteroepitaxial system, metal patterns on the silicon surface provide unprecedented control over the morphology of highly ordered Ge islands. Island shape including nanorods and truncated pyramids is set by the metal species and substrate orientation. Analysis of island faceting elucidates the prominent role of the metal in promoting growth of preferred facet orientations while investigations of island composition and structure reveal the importance of Si-Ge intermixing in island evolution. These effects reflect a remarkable combination of metal-mediated growth phenomena that may be exploited to tailor the functionality of island arrays in heteroepitaxial systems.

Qualification of the ITER conductor is absolutely necessary. Testing large scale conductors is expensive and time consuming. To test straight 3-4m long samples in a bore of a split solenoid is a relatively economical way in comparison with fabrication of a coil to be tested in a bore of a background field solenoid. However, testing short sample may give ambiguous results due to different constraints in current redistribution in the cable or other end effects which are not present in the large magnet. This paper discusses processes taking place in the ITER conductor, conditions when conductor performance could be distorted and possible signal processing to deduce behavior of ITER conductors in ITER magnets from the test data.

The Muon Ionization Cooling Experiment (MICE) willdemonstrate ionization cooling in a short section of a realistic coolingchannel using a muon beam at Rutherford Appleton Laboratory (RAL) in theUK. A five-coil, superconducting spectrometer solenoid magnet at each endof the cooling channel will provide a 4 T uniform field region for thescintillating fiber tracker within the magnet bore tubes. The trackermodules are used to measure the muon beam emittance as it enters andexits the cooling channel. The cold mass for the 400 mm warm bore magnetconsists of two sections: a three-coil spectrometer magnet and a two-coilmatching section that matches the uniform field of the solenoid into theMICE cooling channel. The spectrometer solenoid detailed designandanalysis has been completed, and the fabrication of the magnets is wellunder way. The primary features of the spectrometer solenoid magnet andmechanical designs are presented along with a summary of key fabricationissues and photos of the construction.

The purpose of this study is to design, fabricate and optimize microfluidic mixers to investigate the kinetics of protein secondary structure formation with Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy. The mixers are designed to rapidly initiate protein folding reaction through the dilution of denaturant. The devices are fabricated out of fused silica, so that they are transparent in the UV. We present characterization of mixing in the fabricated devices, as well as the initial SRCD data on proteins inside the mixers.

The advanced tokamak research program at DIII-D relies critically on the measurement of the current density profile. This was made possible by the development of a Motional Stark Effect (MSE) polarimeter that was first installed in 1992. Three major upgrades have since occurred, and improvements in our understanding of critical performance issues and calibration techniques are ongoing. In parallel with these improvements, we have drawn on our DIII-D experience to begin studies and design work for MSE on burning plasmas and ITER. This paper first reviews how Motional Stark Effect polarimetry (MSE) is used to determine the tokamak current profile. It uses the DIII-D MSE system as an example, and shows results from the latest upgrade that incorporates an array of channels from a new counter-Ip injected neutral beam. The various calibration techniques presently used are reviewed. High-leverage or unresolved issues affecting MSE performance and reliability in ITER are discussed. Next, we show a four-mirror collection optics design for the two ITER MSE views. Finally, we discuss measurements of the polarization properties of a few candidate mirrors for the ITER MSE.

Various relations for the detonation energy and velocity as they relate to the inverse radius of the cylinder are explored. The detonation rate-inverse slope relation seen in reactive flow models can be used to derive the familiar Eyring equation. Generalized inverse radii can be shown to fit large quantities of cylinder and sphere results. A rough relation between detonation energy and detonation velocity is found from collected JWL values. Cylinder test data for ammonium nitrate mixes down to 6.35 mm radii are presented, and a size energy effect is shown to exist in the Cylinder test data. The relation that detonation energy is roughly proportional to the square of the detonation velocity is shown by data and calculation.

A detailed chemical kinetic mechanism has been developed and used to study the oxidation of methyl decanoate, a surrogate for biodiesel fuels. This model has been built by following the rules established by Curran et al. for the oxidation of n-heptane and it includes all the reactions known to be pertinent to both low and high temperatures. Computed results have been compared with methyl decanoate experiments in an engine and oxidation of rapeseed oil methyl esters in a jet stirred reactor. An important feature of this mechanism is its ability to reproduce the early formation of carbon dioxide that is unique to biofuels and due to the presence of the ester group in the reactant. The model also predicts ignition delay times and OH profiles very close to observed values in shock tube experiments fueled by n-decane. These model capabilities indicate that large n-alkanes can be good surrogates for large methyl esters and biodiesel fuels to predict overall reactivity, but some kinetic details, including early CO{sub 2} production from biodiesel fuels, can be predicted only by a detailed kinetic mechanism for a true methyl ester fuel. The present methyl decanoate mechanism provides a realistic kinetic tool for simulation of biodiesel …

The Lawrence Berkeley National Laboratory has developed a device that measures the water content of wood chips, pulp and brown stock for the paper industry. This device employs a permanent magnet as the central part of a NMR measurement system. This report describes the magnet and the NMR measurement system. The results of water content measurements in wood chips in a magnetic field of 0.47 T are presented.

This project's goal is to provide a proof of concept for mobile data collection applications, and identify the best ways such applications could be implemented and used. Such an application should decrease the time and resources users now need to devote to redundant data processes, and provide an easy of locating and retrieving data at a later time. The two types of available mobile devices, Personal Digital Assistants and Tablet Personal Computers, each have their particular strengths that suggest themselves for certain types of applications. As such, parallel data collection applications have been developed, with a common web application for uploading information to the database. While these aspects have been developed and proven, it still remains to refine these applications, develop the tables to hold their data, and field-test with users for their feedback.

A Plesset-type treatment [J. Appl. Phys. 25, 96 (1954)] is used to assess the effects of contiguous density gradients at an accelerating spherical classical interface on Rayleigh-Taylor and Bell-Plesset perturbation growth. Analytic expressions are obtained that describe enhanced Rayleigh-Taylor instability growth from contiguous density gradients aligned with the acceleration and which increase the effective Atwood number of the perturbed interface. A new pathway for geometric amplification of surface perturbations on an accelerating interface with contiguous density gradients is identified. A resonance condition between the density-gradient scalelength and the radius of the interface is also predicted based on a linearized analysis of Bernoulli's equation, potentially leading to enhanced perturbation growth. Comparison of the analytic treatment with detailed two-dimensional single-mode growth-factor simulations shows good agreement for low-mode numbers where the effects of spherical geometry are most manifested.