This presentation on the future of biofuels, hydrogen, and hybrid vehicles was presented at NREL's 21st Industry Growth Forum in Denver, Colorado, on October 28, 2008.

Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors, or NNs) to sequence. We use SAP to assess whether draft data is sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high quality draft with error rates of 10{sup -3}-10{sup -5} ({approx} 8x coverage) of target organisms is suitable for DNA signature prediction. Low quality draft with error rates of {approx} 1% (3x to 6x coverage) of target isolates is inadequate for DNA signature prediction, although low quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high quality draft of target and low quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation …

During Run-8, the Relativistic Heavy Ion Collider (RHIC) provided collisions of spin-polarized proton beams at two interaction regions. Physics data were taken with vertical orientation of the beam polarization, which in the 'Yellow' RHIC ring was significantly lower than in previous years. We present recent developments and improvements as well as the luminosity and polarization performance achieved during Run-8, and we discuss possible causes of the not as high as previously achieved polarization performance of the 'Yellow' ring.

The US Department of Energy’s transuranic (TRU) waste inventory includes about 4,500 m3 of remote-handled TRU (RH-TRU) wastes composed of a variety of containerized waste forms having a contact surface dose rate that exceeds 2 mSv/hr (200 mrem/hr) containing waste materials with a total TRU concentration greater than 3700 Bq/g (100 nCi/g). As part of a research project to investigate the use of active Compton-suppressed room-temperature gamma-ray detectors for direct non-destructive quantification of the TRU content of these RH-TRU wastes, we have designed and purchased a unique detector system using a LaBr3(Ce) primary detector and a NaI(Tl) suppression mantle. The LaBr3(Ce) primary detector is a cylindrical unit ~25 mm in diameter by 76 mm long viewed by a 38 mm diameter photomultiplier. The NaI(Tl) suppression mantle (secondary detector) is 175 mm by 175 mm with a center well that accommodates the primary detector. An important feature of this arrangement is the lack of any “can” between the primary and secondary detectors. These primary and secondary detectors are optically isolated by a thin layer (.003") of aluminized kapton, but the hermetic seal and thus the aluminum can surrounds the outer boundary of the detector system envelope. The hermetic seal at the …

Article on the transcriptional regulator AlgR controlling cyanide production in Pseudomonas aeruginosa.

The pixel purity index (PPI) algorithm proposed by Boardman, et al.1 identifies potential endmember pixels in multispectral imagery. The algorithm generates a large number of skewers (unit vectors in random directions), and then computes the dot product of each skewer with each pixel. The PPI is incremented for those pixels associated with the extreme values of the dot products. A small number of pixels (a subset of those with the largest PPI values) are selected as pure and the rest of the pixels in the image are expressed as linear mixtures of these pure endmembers. This provides a convenient and physically-motivated decomposition of the image in terms of a relatively few components. We report on a variant of the PPI algorithm in which blocks of B skewers are considered at a time. From the computation of B dot products, one can produce a much larger set of derived dot products that are associated with skewers that are linear combinations of the original B skewers. Since the derived dot products involve only scalar operations, instead of full vector dot products, they can be very cheaply computed. We will also discuss a hardware implementation on a field programmable gate array (FPGA) processor …

More than a decade after the explosion of SN 1987A, unresolved discrepancies still remain in attempts to numerically simulate the mixing processes initiated by the passage of a very strong shock through the layered structure of the progenitor star. Numerically computed velocities of the radioactive {sup 56}Ni and {sup 56}CO, produced by shock-induced explosive burning within the silicon layer for example, are still more than 50% too low as compared with the measured velocities. In order to resolve such discrepancies between observation and simulation, an experimental testbed has been designed on the Omega Laser for the study of hydrodynamic issues of importance to supernovae (SNe). In this paper, we present results from a series of scaled laboratory experiments designed to isolate and explore several issues in the hydrodynamics of SN explosions. The results of the experiments are compared with numerical simulations and are generally found to be in reasonable agreement.

A novel sample preparation technique is reported to fabricate electron transparent samples from devices utilizing a FIB process with a successive wet etching step. The high quality of the obtained samples allows for band gap--and chemical composition measurements of In{sub x}Ga{sub 1-x}N quantum wells where electron beam induced damage can be controlled and shown to be negligible. The results reveal indium enrichment in nanoclusters and defects that cause fluctuations of the band gap energy and can be measured by low loss Electron Energy Spectroscopy with nm resolution. Comparing our time, energy, and spatially resolved measurements of band gap energies, chemical composition, and their related fluctuations with literature data, we find quantitative agreement if the band gap energy of InN is 1.5-2 eV.

The large-x behavior of the transverse-momentum dependent quark distributions is analyzed in the factorization-inspired perturbative QCD framework, particularly for the naive time-reversal-odd quark Sivers function which is responsible for the single transverse-spin asymmetries in various semi-inclusive hard processes. By examining the dominant hard gluon exchange Feynman diagrams, and using the resulting power counting rule, we find that the Sivers function has power behavior (1-x){sup 4} at x {yields} 1, which is one power of (1-x) suppressed relative to the unpolarized quark distribution. These power-counting results provide important guidelines for the parameterization of quark distributions and quark-gluon correlations.

None

The biological activity on continents and the oxygen content of the atmosphere determine the chemical pathways through which Fe is processed at the Earth's surface. Experiments have shown that the relevant chemical pathways fractionate Fe isotopes. Measurements of soils, streams, and deep-sea clay indicate that the {sup 56}Fe/{sup 54}Fe ratio ({delta}{sup 56}Fe relative to igneous rocks) varies from +1{per_thousand} for weathering residues like soils and clays, to -3{per_thousand} for dissolved Fe in streams. These measurements confirm that weathering processes produce substantial fractionation of Fe isotopes in the modern oxidizing Earth surface environment. The results imply that biologically-mediated processes, which preferentially mobilize light Fe isotopes, are critical to Fe chemistry in weathering environments, and that the {delta}{sup 56}Fe of marine dissolved Fe should be variable and negative. Diagenetic reduction of Fe in marine sediments may also be a significant component of the global Fe isotope cycle. Iron isotopes provide a tracer for the influence of biological activity and oxygen in weathering processes through Earth history. Iron isotopic fractionation during weathering may have been smaller or absent in an oxygen-poor environment such as that of the early Precambrian Earth.

The extracellular matrix (ECM), once thought to solely provide physical support to a tissue, is a key component of a cell's microenvironment responsible for directing cell fate and maintaining tissue specificity. It stands to reason, then, that changes in the ECM itself or in how signals from the ECM are presented to or interpreted by cells can disrupt tissue organization; the latter is a necessary step for malignant progression. In this review, we elaborate on this concept using the mammary gland as an example. We describe how the ECM directs mammary gland formation and function, and discuss how a cell's inability to interpret these signals - whether as a result of genetic insults or physicochemical alterations in the ECM - disorganizes the gland and promotes malignancy. By restoring context and forcing cells to properly interpret these native signals, aberrant behavior can be quelled and organization re-established. Traditional imaging approaches have been a key complement to the standard biochemical, molecular, and cell biology approaches used in these studies. Utilizing imaging modalities with enhanced spatial resolution in live tissues may uncover additional means by which the ECM regulates tissue structure, on different length scales, through its pericellular organization (short-scale) and by biasing …

The Relativistic Heavy Ion Collider (RHIC) is designed to provide collisions of high energy polarized protons for the quest of understanding the proton spin structure. Polarized proton collisions at a beam energy of 100 GeV have been achieved in RHIC since 2001. Recently, polarized proton beam was accelerated to 250 GeV in RHIC for the first time. Unlike accelerating unpolarized protons, the challenge for achieving high energy polarized protons is to fight the various mechanisms in an accelerator that can lead to partial or total polarization loss due to the interaction of the spin vector with the magnetic fields. We report on the progress of the RHIC polarized proton program. We also present the strategies of how to preserve the polarization through the entire acceleration chain, i.e. a 200 MeV linear accelerator, the Booster, the AGS and RHIC.

Numerous cosmological hydrodynamic studies have addressed the formation of galaxies. Here we choose to study the first stages of galaxy formation, including non-equilibrium atomic primordial gas cooling, gravity and hydrodynamics. Using initial conditions appropriate for the concordance cosmological model of structure formation, we perform two adaptive mesh refinement simulations of {approx} 10{sup 8} M{sub {circle_dot}} galaxies at high redshift. The calculations resolve the Jeans length at all times with more than 16 cells and capture over 14 orders of magnitude in length scales. In both cases, the dense, 10{sup 5} solar mass, one parsec central regions are found to contract rapidly and have turbulent Mach numbers up to 4. Despite the ever decreasing Jeans length of the isothermal gas, we only find one site of fragmentation during the collapse. However, rotational secular bar instabilities transport angular momentum outwards in the central parsec as the gas continues to collapse and lead to multiple nested unstable fragments with decreasing masses down to sub-Jupiter mass scales. Although these numerical experiments neglect star formation and feedback, they clearly highlight the physics of turbulence in gravitationally collapsing gas. The angular momentum segregation seen in our calculations plays an important role in theories that form supermassive …

The AdS/CFT correspondence has led to important insights into the properties of quantum chromodynamics even though QCD is a broken conformal theory. We have recently shown how a holographic model based on a truncated AdS space can be used to obtain the hadronic spectrum of light q{bar q}, qqq and gg bound states. Specific hadrons are identified by the correspondence of string modes with the dimension of the interpolating operator of the hadron's valence Fock state, including orbital angular momentum excitations. The predicted mass spectrum is linear M {proportional_to} L at high orbital angular momentum, in contrast to the quadratic dependence M{sup 2} {proportional_to} L found in the description of spinning strings. Since only one parameter, the QCD scale LQCD, is introduced, the agreement with the pattern of physical states is remarkable. In particular, the ratio of D to nucleon trajectories is determined by the ratio of zeros of Bessel functions. The light-front quantization of gauge theories in light-cone gauge provides a frame-independent wavefunction representation of relativistic bound states, simple forms for current matrix elements, explicit unitarity, and a trivial vacuum. The light-front Fock-state wavefunctions encode the bound state properties of hadrons in terms of their quark and gluon degrees …

The performance of NIF target designs is simulated in three dimensions using the HYDRA multiphysics radiation hydrodynamics code. In simulations of a cylindrical NIF hohlraum that include an imploding capsule, all relevant hohlraum features and the detailed laser illumination pattern, the motion of the wall material inside the hohlraum shows a high degree of axisymmetry. Laser light is able to propagate through the entrance hole for the required duration of the pulse. Gross hohlraum energetics mirror the results from an axisymmetric simulation. A NIF capsule simulation resolved the full spectrum of the most dangerous modes that grow from surface roughness. Hydrodynamic instabilities evolve into the weakly nonlinear regime. There is no evidence of anomalous low mode growth driven by nonlinear mode coupling.

None

None

We have developed and tested a fully autonomous pathogen detection system (APDS) capable of continuously monitoring the environment for airborne biological threat agents. The system was developed to provide early warning to civilians in the event of a bioterrorism incident and can be used at high profile events for short-term, intensive monitoring or in major public buildings or transportation nodes for long-term monitoring. The APDS is completely automated, offering continuous aerosol sampling, in-line sample preparation fluidics, multiplexed detection and identification immunoassays, and nucleic-acid based polymerase chain reaction (PCR) amplification and detection. Highly multiplexed antibody-based and duplex nucleic acid-based assays are combined to reduce false positives to a very low level, lower reagent costs, and significantly expand the detection capabilities of this biosensor. This article provides an overview of the current design and operation of the APDS. Certain sub-components of the ADPS are described in detail, including the aerosol collector, the automated sample preparation module that performs multiplexed immunoassays with confirmatory PCR, and the data monitoring and communications system. Data obtained from an APDS that operated continuously for seven days in a major U.S. transportation hub is reported.

The United States continues to maintain its leadership in ICF as it moves toward the goal of ignition. The flagship of the program is the National Ignition Facility (NIF) presently under construction at LLNL. Experiments had begun on the first four beams of the National Ignition Facility just at the time of the last IFSA Conference. Several new successful campaigns have been conducted since then in planar hydrodynamics and hohlraums as well as activating the VISAR diagnostic for equation of state experiments. Highlights of these results will be reviewed. Presently, the four beam experimental capability has been suspended while the first eight beams are being installed as the first step in building out the project. Meanwhile, much progress has been made in developing ignition designs for using NIF. An array of designs having several ablator materials have been shown computationally to ignite with energies ranging from the design energy to as low as 1 MJ of laser energy. Alternative direct drive designs in the NIF indirect drive configuration have been developed by LLE. This wide array of design choices has increased the chance of achieving ignition sooner on the facility. Plans are now being developed to begin an ignition experimental …

We examine the mechanics of the send and receive mechanism of MPI and in particular how we can implement message passing in a robust way so that our performance is not significantly affected by changes to the MPI system. This leads us to using the Isend/Irecv protocol which will entail sometimes significant algorithmic changes. We discuss this within the context of two different algorithms for sparse Gaussian elimination that we have parallelized. One is a multifrontal solver called MUMPS, the other is a supernodal solver called SuperLU. Both algorithms are difficult to parallelize on distributed memory machines. Our initial strategies were based on simple MPI point-to-point communication primitives. With such approaches, the parallel performance of both codes are very sensitive to the MPI implementation, the way MPI internal buffers are used in particular. We then modified our codes to use more sophisticated nonblocking versions of MPI communication. This significantly improved the performance robustness (independent of the MPI buffering mechanism) and scalability, but at the cost of increased code complexity.

This article discusses electron localization in a two-channel tight-binding model with correlated disorder.

None

The first stars form in dark matter halos of masses {approx}10{sup 6}M{sub {circle_dot}} as suggested by an increasing number of numerical simulations. Radiation feedback from these stars expels most of the gas from their shallow potential well of their surrounding dark matter halos. We use cosmological adaptive mesh refinement simulations that include self-consistent Population III star formation and feedback to examine the properties of assembling early dwarf galaxies. Accurate radiative transport is modeled with adaptive ray tracing. We include supernova explosions and follow the metal enrichment of the intergalactic medium. The calculations focus on the formation of several dwarf galaxies and their progenitors. In these halos, baryon fractions in 10{sup 8} M{sub {circle_dot}} halos decrease by a factor of 2 with stellar feedback and by a factor of 3 with supernova explosions. We find that radiation feedback and supernova explosions increase gaseous spin parameters up to a factor of 4 and vary with time. Stellar feedback, supernova explosions, and H{sub 2} cooling create a complex, multi-phase interstellar medium whose densities and temperatures can span up to 6 orders of magnitude at a given radius. The pair-instability supernovae of Population III stars alone enrich the halos with virial temperatures of 10{sup …