Article on transcriptional networks for lignin biosynthesis.

Elucidating the in situ metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of dsrAB sequences prior to the addition of acetate indicated that Desulfobacteraceae, Desulfobulbaceae, and Syntrophaceae-related sulfate reducers were the most abundant. Quantifying dsrB transcripts of the individual populations suggested that Desulfobacteraceae initially had higher dsrB transcripts per cell than Desulfobulbaceae or Syntrophaceae populations, and that the activity of Desulfobacteraceae increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast, dsrB transcript abundance in Desulfobulbaceae and Syntrophaceae remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the Desulfobacteraceae was consistent with the finding that Desulfobacteraceae became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a …

A unique application of the pulsed-wire measurement method has been implemented for alignment of 2.5 T pulsed solenoid magnets. The magnetic axis measurement has been shown to have a resolution of better than 25 {micro}m. The accuracy of the technique allows for the identification of inherent field errors due to, for example, the winding layer transitions and the current leads. The alignment system is developed for the induction accelerator NDCX-II under construction at LBNL, an upgraded Neutralized Drift Compression experiment for research on warm dense matter and heavy ion fusion. Precise alignment is essential for NDCX-II, since the ion beam has a large energy spread associated with the rapid pulse compression such that misalignments lead to corkscrew deformation of the beam and reduced intensity at focus. The ability to align the magnetic axis of the pulsed solenoids to within 100 pm of the induction cell axis has been demonstrated.

This paper presents a new idea to produce matter in the high energy density physics (HEDP) regime in the laboratory using an intense ion beam. A gas bubble created inside a solid metal may collapse by driving it with an intense ion beam. The melted metal will compress the gas bubble and supply extra energy to it. Simulations show that the spherical implosion ratio can be about 5 and at the stagnation point, the maximum density, temperature and pressure inside the gas bubble can go up to nearly 2 times solid density, 10 eV and a few megabar (Mbar) respectively. The proposed experiment is the first to permit access into the Mbar regime with existing or near-term ion facilities, and opens up possibilities for new physics gained through careful comparisons of simulations with measurements of quantities like stagnation radius, peak temperature and peak pressure at the metal wall.

The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compels additional exploration. We therefore undertook whole genome sequencing of the acidogenic A. niger wild type strain (ATCC 1015), and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was utilized to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 megabase of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome …

Residual impurities in manganese (Mn) are a big obstacle to obtaining high-performance CdMnTe (CMT) X-ray and gamma-ray detectors. Generally, the zone-refining method is an effective way to improve the material's purity. In this work, we purified the MnTe compounds combining the zone-refining method with molten Te, which has a very high solubility for most impurities. We confirmed the improved purity of the material by glow-discharge mass spectrometry (GDMS). We also found that CMT crystals from a multiply-refined MnTe source, grown by the vertical Bridgman method, yielded better performing detectors.

We have used a heated 2 cm x 1 mm SiC microtubular (mu tubular) reactor to decompose acetaldehyde: CH3CHO + DELTA --> products. Thermal decomposition is followed at pressures of 75 - 150 Torr and at temperatures up to 1700 K, conditions that correspond to residence times of roughly 50 - 100 mu sec in the mu tubular reactor. The acetaldehyde decomposition products are identified by two independent techniques: VUV photoionization mass spectroscopy (PIMS) and infrared (IR) absorption spectroscopy after isolation in a cryogenic matrix. Besides CH3CHO, we have studied three isotopologues, CH3CDO, CD3CHO, and CD3CDO. We have identified the thermal decomposition products CH3(PIMS), CO (IR, PIMS), H (PIMS), H2 (PIMS), CH2CO (IR, PIMS), CH2=CHOH (IR, PIMS), H2O (IR, PIMS), and HC=CH (IR, PIMS). Plausible evidence has been found to support the idea that there are at least three different thermal decomposition pathways for CH3CHO: Radical decomposition: CH3CHO + DELTA --> CH3 + [HCO] --> CH3 + H + CO Elimination: CH3CHO + DELTA --> H2 + CH2=C=O. Isomerization/elimination: CH3CHO + DELTA --> [CH2=CH-OH] --> HC=CH + H2O. Both PIMS and IR spectroscopy show compelling evidence for the participation of vinylidene, CH2=C:, as an intermediate in the decomposition of vinyl …

To heat targets to electron-volt temperatures for the study of warm dense matter with intense ion beams, low mass ions, such as lithium, have an energy loss peak (dE/dx) at a suitable kinetic energy. The Heavy Ion Fusion Sciences (HIFS) program at Lawrence Berkeley National Laboratory will carry out warm dense matter experiments using Li{sup +} ion beam with energy 1.2-4 MeV in order to achieve uniform heating up to 0.1-1 eV. The accelerator physics design of Neutralized Drift Compression Experiment (NDCX-II) has a pulse length at the ion source of about 0.5 {micro}s. Thus for producing 50 nC of beam charge, the required beam current is about 100 mA. Focusability requires a normalized (edge) emittance {approx}2 {pi}-mm-mrad. Here, lithium aluminosilicate ion sources, of {beta}-eucryptite, are being studied within the scope of NDCX-II construction. Several small (0.64 cm diameter) lithium aluminosilicate ion sources, on 70%-80% porous tungsten substrate, were operated in a pulsed mode. The distance between the source surface and the mid-plane of the extraction electrode (1 cm diameter aperture) was 1.48 cm. The source surface temperature was at 1220 C to 1300 C. A 5-6 {micro}s long beam pulsed was recorded by a Faraday cup (+300 V on …

Oxide dispersion strengthened (ODS) Ni-based alloys show promise for future energy applications that require high-temperature and oxidation resistant properties. Gas atomization reaction synthesis (GARS), with a mixed (Ar/O{sub 2}) atomization gas, is being developed as a simplified route for producing ODS precursor powders. Internal oxidation studies determined Ni-Cr-Y-(Hf or Ti) containing systems are suitable for production of ODS alloys via hot consolidation, which is used to encourage oxygen exchange between the less stable surface oxide phase and reactive alloying elements, resulting in highly stable nano-metric dispersoid formation. Size control of powders is key to optimizing microstructural and strengthening features. Aspiration and, previously, water modeling experiments were used to develop atomization process parameters that encourage controlled powder production while maintaining reduced operating costs when implemented on an industrial scale. For an increase in pour tube extension: aspiration base pressure at any given operating pressure was found to decrease while wake closure pressure was found to increase. Aspiration hysteresis was observed as recorded previously in the literature. Light emission was observed above wake closure pressures.

Effective solar radiation measurements for research and economic analyses require a strict protocol for maintenance, calibration, and documentation to minimize station downtime and data corruption. The National Renewable Energy Laboratory's Concentrating Solar Power: Best Practices Handbook for the Collection and Use of Solar Resource Data includes guidelines for operating a solar measurement station. This paper describes a suite of automated and semi-automated routines based on the best practices handbook as developed for the National Renewable Energy Laboratory Solar Resource and Meteorological Assessment Project. These routines allow efficient inspection and data flagging to alert operators of conditions that require immediate attention. Although the handbook is targeted for concentrating solar power applications, the quality-assessment procedures described are generic and should benefit many solar measurement applications. The routines use data in one-minute measurement resolution, as suggested by the handbook, but they could be modified for other time scales.

The detonation of a 10 Kiloton Improvised Nuclear Device (IND) is a serious scenario that the United States must be prepared to address. The likelihood of a single nuclear bomb exploding in a single city is greater today than at the height of the Cold War. Layered defenses against domestic nuclear terrorism indicate that our government continues to view the threat as credible. The risk of such an event is further evidenced by terrorists desire to acquire nuclear weapons. The act of nuclear terrorism, particularly an act directed against a large population center in the United States, will overwhelm the capabilities of many local and state governments to respond, and will seriously challenge existing federal response capabilities. A 10 Kiloton IND detonation would cause total infrastructure damage in a 3-mile radius and levels of radiation spanning out 3,000 square miles. In a densely populated urban area, the anticipated casualties would be in excess of several hundred thousand. Although there would be enormous loss of life, housing and infrastructure, an IND detonation is a recoverable event. We can reduce the risk of these high-consequence, nontraditional threats by enhancing our nuclear detection architecture and establishing well planned and rehearsed plans for coordinated …

The Heavy Ion Fusion Science Virtual National Laboratory in the USA is constructing a new Neutralized Drift Compression eXperiment (NDCX-II) at LBNL. This facility is being developed for high energy density physics and inertial fusion energy research. The 12 m long induction linac in NDCX-II will produce a Li{sup +} beam pulse, at energies of 1.2-3 MeV, to heat target material to the warm dense matter regime ({approx} 1 eV). By making use of special acceleration voltage waveforms, 2.5T solenoid focusing, and neutralized drift compression, 20 - 50 nC of beam charge from the ion source will be compressed longitudinally and radially to achieve a subnanosecond pulse length and mm-scale target spot size. The original Neutralized Drift Compression Experiment (NDCX-I) has successfully demonstrated simultaneous radial and longitudinal compression by imparting a velocity ramp to the ion beam, which then drifts in a neutralizing plasma to and through the final focussing solenoid and onto the target. At higher kinetic energy and current, NDCX-II will offer more than 100 times the peak energy fluence on target of NDCX-I. NDCX-II makes use of many parts from the decommissioned Advanced Test Accelerator (ATA) at LLNL. It includes 27 lattice periods between the injector and …

Accelerators are playing increasingly important roles in basic science, technology, and medicine including nuclear power, industrial irradiation, material science, and neutrino production. Proton and light-ion accelerators in particular have many research, energy and medical applications, providing one of the most effective treatments for many types of cancer. Ultra high-intensity and high-energy (GeV) proton drivers are a critical technology for accelerator-driven sub-critical reactors (ADS) and many HEP programs (Muon Collider). These high-intensity GeV-range proton drivers are particularly challenging, encountering duty cycle and space-charge limits in the synchrotron and machine size concerns in the weaker-focusing cyclotrons; a 10-20 MW proton driver is not presently considered technically achievable with conventional re-circulating accelerators. One, as-yet, unexplored re-circulating accelerator, the Fixed-field Alternating Gradient, or FFAG, is an attractive alternative to the cyclotron. Its strong focusing optics are expected to mitigate space charge effects, and a recent innovation in design has coupled stable tunes with isochronous orbits, making the FFAG capable of fixed-frequency, CW acceleration, as in the classical cyclotron. This paper reports on these new advances in FFAG accelerator technology and references advanced modeling tools for fixed-field accelerators developed for and unique to the code COSY INFINITY.

On behalf of the Subsurface Biogeochemical Research (SBR) program managers in the Climate and Environmental Sciences Division (CESD), Office of Biological and Environmental Research (BER), welcome to the 2011 SBR Principal Investigators meeting. Thank you in advance for your attendance and your presentations at this year's meeting. As the events in Japan continue to unfold, we are all reminded that the research we perform on radionuclide behavior in the environment has implications beyond legacy waste cleanup and in fact has its place in the discussion on the expanded use of nuclear power. As in the past, there are three broad objectives to the Principal Investigators meeting: (1) to provide opportunities to share research results and promote interactions among the SBR scientists and other invited guests; (2) to evaluate the progress of each project within the program; and (3) to showcase the scientific expertise and research progress over the past year to senior managers within the DOE Office of Science, the technology offices within DOE, and other invited attendees from other Federal Agencies. This past year has seen a few significant changes within BER and within the SBR program. In November, our Associate Director for BER, Anna Palmisano, retired from Federal …

FACET, the Facility for Advanced Accelerator and Experimental Tests, is a new facility being constructed in sector 20 of the SLAC linac primarily to study beam driven plasma wakefield acceleration. The FACET beamline consists of a chicane and final focus system to compress the 23 GeV, 3.2 nC electron bunches to {approx}20 {micro}m long and {approx}10 {micro}m wide. Simulations of the FACET beamline indicate the short-duration and large, 1.5% rms energy spread beams may suffer a factor of four emittance growth from a combination of chromaticity, incoherent synchrotron radiation (ISR), and coherent synchrotron radiation (CSR). Emittance growth is directly correlated to head erosion in plasma wakefield acceleration and is a limiting factor in single stage performance. Studies of the geometric, CSR, and ISR components are presented. Numerical calculation of the rms emittance can be overwhelmed by long tails in the simulated phase space distributions; more useful definitions of emittance are given. A complete simulation of the beamline is presented as well, which agrees with design specifications.

Sum frequency vibrational spectroscopy was used to study the protonated R-plane (1{bar 1}02 ) sapphire surface. The OH stretch vibrational spectra show that the surface is terminated with three hydroxyl moieties, two from AlOH{sub 2} and one from Al{sub 2}OH functional groups. The observed polarization dependence allows determination of the orientations of the three OH species. The results suggest that the protonated sapphire (1{bar 1}02 ) surface differs from an ideal stoichimetric termination in a manner consistent with previous X-ray surface diffraction (crystal truncation rod) studies. However, in order to best explain the observed hydrogenbonding arrangement, surface oxygen spacing determined from the X-ray diffraction study requires modification.

Despite the closure of the HERA accelerator in the past few years, much physics still remains to be understood, from the quark and gluon content of the nucleon/nucleus across all x to the still unknown spin structure of the proton. The 'Future of DIS' working group was dedicated to discussions on these and many other subjects. This paper represents a brief overview of the discussions. For further details, please refer to individual contributions.

Energy Recovery Linacs are being considered for applications in present and future light sources. ERLs take advantage of the continuous operation of superconducting rf cavities to accelerate high average current beams with low losses. The electrons can be directed through bends, undulators, and wigglers for high brightness x ray production. They are then decelerated to low energy, recovering power so as to minimize the required rf drive and electrical draw. When this approach is coupled with advanced continuous wave injectors, very high power, ultra-short electron pulse trains of very high brightness can be achieved. This paper will review the status of worldwide programs and discuss the technology challenges to provide such beams for photon production.

The object of this work was to identify correlations between performance losses of Pt electrocatalysts on carbon support materials and the chemical and morphological parameters that describe them. Accelerated stress testing, with an upper potential of 1.2 V, was used to monitor changes to cathode properties, including kinetic performance and effective platinum surface area losses. The structure and chemical compositions were studied using X-ray Photoelectron Spectroscopy and Scanning Electron Microscopy coupled with Digital Image Processing. As this is an ongoing study, it is difficult to draw firm conclusions, though a trend between support surface area overall performance loss was found to exist.

We study the effect of filter zero-point uncertainties on future supernova dark energy missions. Fitting for calibration parameters using simultaneous analysis of all Type Ia supernova standard candles achieves a significant improvement over more traditional fit methods. This conclusion is robust under diverse experimental configurations (number of observed supernovae, maximum survey redshift, inclusion of additional systematics). This approach to supernova fitting considerably eases otherwise stringent mission cali- bration requirements. As an example we simulate a space-based mission based on the proposed JDEM satellite; however the method and conclusions are general and valid for any future supernova dark energy mission, ground or space-based.

In this paper, we report the precise control of the size, shape and surface morphology of Au-Pt nanocatalysts (cubes, blocks, octahedrons and dogbones) synthesized via a seed-mediated approach. Gold 'seeds' of different aspect ratios (1 to 4.2), grown by a silver-assisted approach, were used as templates for high-yield production of novel Au-Pt nanocatalysts at a low temperature (40 C). Characterization by electron microscopy (SEM, TEM, HRTEM), energy dispersive X-ray analysis (EDX), UV-Vis spectroscopy, zeta-potential (surface charge), atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and inductively coupled plasma mass spectrometry (ICP-MS) were used to better understand their physico-chemical properties, preferred reactivities and underlying nanoparticle growth mechanism. A rotating disk electrode was used to evaluate the Au-Pt nanocatalysts electrochemical performance in the oxygen reduction reaction (ORR) and the methanol oxidation reaction (MOR) of direct methanol fuel cells. The results indicate the Au-Pt dogbones are partially and in some cases completely unaffected by methanol poisoning during the evaluation of the ORR. The ORR performance of the octahedron particles in the absence of MeOH is superior to that of the Au-Pt dogbones and Pt-black, however its performance is affected by the presence of MeOH.

Future nuclear physics facilities such as the proposed electron ion collider (MEIC) will need to achieve record high luminosities in order to maximize discovery potential. Among the necessary ingredients is the ability to generate, accumulate , accelerate, and store high current ion beams from protons to lead ions. One of the main components of this ion accelerator complex for MEIC chain is the accumulator that also doubles as a pre-booster, which takes 200 MeV protons from a superconducting linear accelerator, accumulates on the order of 1A beam, and boosts its energy to 3GeV, before extraction to the next accelerator in the chain, the large booster. This paper describes its design concepts, and summarizes some preliminary results, including linear optics, space charge dynamics, and spin polarization resonance analysis.

We report on the mineralogy, petrology, chemistry, oxygen isotopes, {sup 26}Al-{sup 26}Mg and {sup 36}Cl-{sup 36}S isotope systematics of the Allende chondrule Al3509 discovered and described by [1] and [2]. This spherical object ({approx}1cm {phi}) contains {approx}10% Na and 1% Cl, and nearly pure {sup 129}Xe [({sup 129}Xe/{sup 127}I) = 1.1 x 10{sup -4} (3)]. This high enrichment in halogens makes it of interest in searching for radiogenic {sup 36}S from {sup 36}Cl (t{sub 1/2} {approx} 0.3 Ma) decay. While there is strong evidence for the presence of {sup 36}Cl in sodalite and wadalite in CV CAIs [4,5], some sodalites show no evidence for excesses of {sup 36}S ({sup 36}S*). In contrast, high inferred initial {sup 36}Cl/{sup 35}Cl = 2 x 10{sup -5} has been found in wadalite from the Allende CAI AJEF [5]. The observed {sup 36}S excesses in sodalite are not correlated with radiogenic {sup 26}Mg, decay product of {sup 26}Al (t{sub 1/2} {approx} 0.72 Ma) [4]. From the inferred initial {sup 36}Cl/{sup 35}Cl ratios and consideration of both AGB and SNe stellar sources, {sup 36}Cl must be the product of charged particle irradiation within the early solar system. However, neither the specific nuclear production mechanism nor the …

Plasma accelerators may be driven by the ponderomotive force of an intense laser or the space-charge force of a charged particle beam. Plasma wake excitation driven by lasers or particle beams is examined, and the implications of the different physical excitation mechanisms for accelerator design are discussed. Plasma-based accelerators have attracted considerable attention owing to the ultrahigh field gradients sustainable in a plasma wave, enabling compact accelerators. These relativistic plasma waves are excited by displacing electrons in a neutral plasma. Two basic mechanisms for excitation of plasma waves are actively being researched: (i) excitation by the nonlinear ponderomotive force (radiation pressure) of an intense laser or (ii) excitation by the space-charge force of a dense charged particle beam. There has been significant recent experimental success using lasers and particle beam drivers for plasma acceleration. In particular, for laser-plasma accelerators (LPAs), the demonstration at LBNL in 2006 of high-quality, 1 GeV electron beams produced in approximately 3 cm plasma using a 40 TW laser. In 2007, for beam-driven plasma accelerators, or plasma-wakefield accelerators (PWFAs), the energy doubling over a meter to 42 GeV of a fraction of beam electrons on the tail of an electron beam by the plasma wave excited …