Procedure is presented for preparation of diffraction-quality crystals of a vertebrate mitochondrial respiratory Complex II. The crystals have the potential to diffract to at least 2.0 Angstrom with optimization of post-crystal-growth treatment and cryoprotection. This should allow determination of the structure of this important and medically relevant membrane protein complex at near-atomic resolution and provide great detail of the mode of binding of substrates and inhibitors at the two substrate-binding sites.

Non-biological factors give rise to unwanted variations in cDNA microarray data. There are many normalization methods designed to remove such variations. However, to date there have been few published systematic evaluations of these techniques for removing variations arising from dye biases in the context of downstream, higher-order analytical tasks such as classification. Ten location normalization methods that adjust spatial- and/or intensity-dependent dye biases, and three scale methods that adjust scale differences were applied, individually and in combination, to five distinct, published, cancer biology-related cDNA microarray data sets. Leave-one-out cross-validation (LOOCV) classification error was employed as the quantitative end-point for assessing the effectiveness of a normalization method. In particular, a known classifier, k-nearest neighbor (k-NN), was estimated from data normalized using a given technique, and the LOOCV error rate of the ensuing model was computed. We found that k-NN classifiers are sensitive to dye biases in the data. Using NONRM and GMEDIAN as baseline methods, our results show that single-bias-removal techniques which remove either spatial-dependent dye bias (referred later as spatial effect) or intensity-dependent dye bias (referred later as intensity effect) moderately reduce LOOCV classification errors; whereas double-bias-removal techniques which remove both spatial- and intensity effect reduce LOOCV classification errors even …

A non-invasive, wide-band electromagnetic (EM) impedance difference system for shallow subsurface electrical structure characterization in environmental and engineering problems has been developed at the Lawrence Berkeley National Laboratory (LBNL). Electrical parameters of interest are electrical conductivity and dielectric permittivity that are deduced from the impedance difference data. The prototype system includes a magnetic loop transmitter, which operates between 0.1 MHz and 100 MHz, an electrical dipole antenna for observing the electric field, and a loop antenna for measuring the magnetic field.All antennas are mounted on a cart made of non-metallic material for easy movement of the whole array for profiling. Surface EM impedance difference is obtained by taking the difference of the ratios of the electric fields to the magnetic fields at selected frequencies at two different levels. Numerical simulations will be presented to verify this new approach. A set of the impedance difference data acquired at the University of California's Richmond Field Station compares reasonably well with simulation results based on a model obtained with the resistivity method and in situ TDR (time domain reflectometry)measurements.

Nearly a century ago, Edgar Buckingham (1907) published a seminal work on the movement of soil moisture which is part of the foundation of modern soil physics. It also constitutes a pioneering contribution in the study of multi-phase flow in porous media. A physicist, Buckingham took on an earth science issue of importance to society, and produced superb basic science as a byproduct. Buckingham impresses us with his ability to combine experiment and theory, and his capacity to intuitively explain difficult ideas to a wide audience. Science progresses both by gradual accretion of knowledge, and by sudden influx of ideas. Buckingham's contribution belongs in the latter category. After a brief, four-year rendezvous with soil science, he went on to pursue a long and distinguished career in physics with the National Bureau of Standards. This paper is an appreciation of Buckingham's contribution on soil moisture in the context of contemporary developments in diffusion theory, and the rapid growth of science in America at the turn of the twentieth century.

Monosodium titanate (MST) is an inorganic adsorbent powder that effectively removes strontium, plutonium, neptunium, and other trace elements from alkaline high-level waste (HLW) supernate. This work tested one commercial titanate and four general methods to engineer MST into particles large enough to use in adsorption columns. The most successful of the engineered products selected from batch contact and chemical stability testing succeeded in treating 2900 bed volumes (BV) of simulated salt waste containing dissolved plutonium and strontium. There was no detectable strontium breakthrough and only 6 per cent plutonium breakthrough--well within the processing goal--at the end of the demonstration which operated at 5.3 BV/hour. Additional column tests at nominally 15 BV/hr demonstrated similar removal performance. Batch testing of adsorbents used both actual Savannah River Site (SRS) tank supernate as well as simulated salt solutions spiked with strontium, neptunium, and plutonium. In tank waste tests, internal gelation beads produced by the Oak Ridge National Laboratory (ORNL) demonstrated a batch distribution coefficient of 35,000 +/- 4,000 mL/g for plutonium at a phase ratio of 1970 mL/g. In the same batch the sorbent demonstrated a batch distribution coefficient of 99,000 +/- 7,500 mL/g for strontium. These results indicate that this material should be …

The synthesis and characterization of dislocation-free, undoped, single crystals of Si enriched in all 3 stable isotopes is reported: {sup 28}Si (99.92%), {sup 29}Si (91.37%), and {sup 30}Si (89.8%). A silane-based process compatible with the relatively small amounts of isotopically enriched precursors that are practically available was used. The silane is decomposed to silicon on a graphite starter rod heated to 700-750 C in a recirculating flow reactor. A typical run produces 35 gm of polycrystalline Si at a growth rates of 5 {micro}m/min and conversion efficiency >95%. Single crystals are grown by the floating zone method and characterized by electrical and optical measurements. Concentrations of shallow dopants (P and B) are as low as mid-10{sup 13} cm{sup -3}. Concentrations of C and O lie below 10{sup 16} and 10{sup 15} cm{sup -3}, respectively.

Demonstration of association between common genetic variants and chronic human diseases such as obesity could have profound implications for the prediction, prevention and treatment of these conditions. Unequivocal proof of such an association, however, requires adherence to established methodological guidelines, which include independent replication of initial positive findings. Recently, single nucleotide polymorphisms (SNPs) within GAD2 were found to be associated with class III obesity (BMI > 40 kg/m2) in 188 families (612 individuals) segregating the condition and a case-control study of 575 cases and 646 lean controls. Functional data supporting a pathophysiological role for one of the SNPs (-243A>G) were also presented. In the present study, we attempted to replicate this association in larger groups of subjects, and to extend the functional studies of the -243A>G SNP. In 2,327 subjects comprising 692 German nuclear families with severe, early-onset obesity, we found no evidence for a relationship between the three GAD2 SNPs and obesity, whether SNPs were studied individually or as haplotypes. In two independent case-control studies (a total of 680 class III obesity cases and 1,186 lean controls), there was no significant relationship between the -243A>G SNP and obesity (odds ratio (OR) = 0.99, 95% CI 0.83 - 1.18,in the …

We describe a new damage testing approach and instrumentation that provides quantitative measurements of bulk damage performance versus fluence for several frequencies. A major advantage of this method is that it can simultaneously provide direct information on pinpoint density and size, and beam obscuration. This allows for more accurate evaluation of material performance under operational conditions. Protocols for laser conditioning to improve damage performance can also be easily and rapidly evaluated.This damage testing approach has enabled us to perform complex experiments toward probing the fundamental mechanisms of damage initiation and conditioning.

New results of the jet driven ignition target are presented, both with direct and indirect drive. This target is based on the conical guided target used in fast ignition, but use only one laser pulse. The ignition of the target is started by the impact of a jet produced in the guiding cone, instead of using charged particles generated by a other high power laser. We have shown that a laser or X-ray pulse could be used to produce a high velocity jet of several hundred of km/s by an accumulative effect, and we use these ideas to design this new kind of targets. In order to increase the efficiency of the process, we scan in the simulations different materials, cone profiles and laser intensities. ANALOP is a code developed to calculate opacities for hot plasmas, using analytical potentials including density and temperature effects. It has been recently updated to include the radiative transport into the rate equations by mean of the escape factors, and in parallel a line transport code which solve self-consistently the rate equation and radiative transfer equation in 1D planar geometry has been also developed. We have developed a comprehensive methodology to compute uncertainties on activation …

A two laser technique is used to study laser-particle interactions and the disintegration of soot by high power UV light. Two separate 20 ns laser pulses irradiate combustion generated soot nanoparticles with 193 nm photons. The first laser pulse, from 0 to 14.7 J/cm{sup 2}, photofragments the soot particles and electronically excites the liberated carbon atoms. The second laser pulse, held constant at 13 J/cm{sup 2}, irradiates the remaining particle fragments and other products of the first laser pulse. The atomic carbon fluorescence at 248 nm produced by the first laser pulse increases linearly with laser fluence from 1 to 6 J/cm{sup 2}. At higher fluences, the signal from atomic carbon signal saturates. The carbon fluorescence from the second laser pulse decreases as the fluence from the first laser increases, ultimately approaching zero as first laser fluence approaches 10 J/cm{sup 2}, suggesting that the particles fully disintegrate at high laser fluences. We use an energy balance parameter, called the photon-atom ratio (PAR), to aid in understanding laser-particle interactions. These results help define the regimes where photofragmentation fluorescence methods quantitatively measure total soot concentrations.

Indirectly-driven double-shell implosions are being investigated as a possible noncryogenic path to ignition on the National Ignition Facility (NIF). In recent double-shell implosions, the inner shell trajectory was shown to exhibit a strong sensitivity to the temporal history of the M-band (2-5 keV) radiation emitted from the Au hohlraum wall. A large time-dependent discrepancy was observed between measurement and simulation of the x-ray flux in this range. In order to better characterize the radiation environment seen in these implosions, an experimental campaign was conducted on the Omega Laser. A number of diagnostics were used to measure both the temporal and spectral nature of the M-band flux. Results were obtained from an absolutely calibrated 12 channel filtered x-ray diode array (Dante) as well as two streaked crystal spectrometers and an absolutely calibrated time-integrated spectrometer (Henway). X-ray backlighting was also used to directly measure the effect of M-band radiation on the trajectory of the inner shell. The data from all diagnostics are shown to be in excellent agreement and provide a consistent picture of the M-band flux. These results are being used to improve the simulation of hohlraum-generated M-band radiation that will be necessary for the design of future double-shell implosions employing …

We use the High Current Experiment (HCX) to study three mitigation measures: a rough surface to reduce electron emission and gas desorption from ions striking walls near grazing incidence, a suppressor electrode after the magnets to block beam-induced electrons off the end structures from drifting upstream, and clearing electrodes to remove electrons from drift regions between magnets. We find that each technique performs as intended.

The vadose zone is an extremely important zone that recharges our subsurface water resources and also serves as the repository for municipal, industrial and government waste. It acts as a buffer and filter for contaminants introduced by agricultural activities, and also serves as a reservoir for many agricultural crops. As safe and effective use of the vadose zone environment is a major challenge facing our society, there is a great need to improve our understanding of processes, their dynamics and their spatial and temporal patterns. With an increasing demand for investigation methods that have both high accuracy and high resolution across a variety of spatial scales, a new discipline ''hydrogeophysics'' has evolved, which aims at combining knowledge from various disciplines such as hydrogeology, soil physics, biogeochemistry, and geophysics to improve subsurface hydrogeological characterization and monitoring. Geophysical methods offer the advantage of being able to measure subsurface structures and to estimate flow and transport properties in a minimally or non-invasive manner. The discipline of hydrogeophysics is expanding rapidly, and studies are being performed using a wide range of standard geophysical methods as well as new methods that have been developed specifically for hydrologic applications. Time-lapse imaging has illustrated the potential of …

We report on an ongoing study on modular Heavy Ion Fusion drivers. The modular driver is characterized by 10 to 20 nearly identical induction linacs, each carrying a single high current beam. In this scheme, the Integrated Research Experiment (IRE) can be one of the full size induction linacs. Hence, this approach offers significant advantages in terms of driver development path. For beam transport, these modules use solenoids which are capable of carrying high line charge densities, even at low energies. A new injector concept allows compression of the beam to high line densities right at the source. The final drift compression is performed in a plasma, in which the large repulsive space charge effects are neutralized. Finally, the beam is transversely compressed onto the target, using either external solenoids or current-carrying channels (in the Assisted Pinch Mode of beam propagation). We will report on progress towards a self-consistent point design from injector to target. Considerations of driver architecture, chamber environment as well as the methodology for meeting target requirements of spot size, pulse shape and symmetry will also be described. Finally, some near-term experiments to address the key scientific issues will be discussed.

We have developed NADS (Nuclear and Atomic Data System), a web-based graphical interface for viewing pointwise and grouped cross-sections and distributions. Our implementation is a client / server model. The client is a Java applet that displays the graphical interface, which has interactive 2-D, 3-D, and 4-D plots and tables. The server, which can serve and perform computations the data, has been implemented in Python using the FUDGE package developed by Bret Beck at LLNL. Computational capabilities include algebraic manipulation of nuclear evaluated data in databases such as LLNL's ENDL-99, ENDF/B-V and ENDF/B-VI as well as user data. Processed data used in LLNL's transport codes are accessible as well. NADS is available from http://nuclear.llnl.gov/

The National Ignition Facility (NIF) at Lawrence Livermore National Laboratory, when completed in 2008, will contain a 192-beam, 1.8-Megajoule, 500-Terawatt, ultraviolet laser system together with a 10-meter-diameter target chamber and room for 100 diagnostics. NIF is housed in a 26,000 square meter environmentally controlled building and is the world's largest and most energetic laser experimental system. NIF provides a scientific center for the study of inertial confinement fusion and the physics of matter at extreme energy densities and pressures. NIF's energetic laser beams will compress fusion targets to conditions required for thermonuclear burn, liberating more energy than required to initiate the fusion reactions. Other NIF experiments will study physical processes at temperatures approaching 10{sup 8} K and 10{sup 11} bar; conditions that exist naturally only in the interior of stars and planets. NIF is currently configured with four laser beams activated in late 2002. These beams are being regularly used for laser performance and physics experiments and to date nearly 250 system shots have been conducted. NIF's laser beams have generated 106 kilojoules in 23-ns pulses of infrared light and over 16 kJ in 3.5-ns pulses at the third harmonic (351 nm). A number of target experimental systems are being …

Although the concept of the photon as a quantum particle is sharpened by the quantization of the energy of the classical radiation field in a cavity, the photon's spin has remained a classical degree of freedom. The photon is considered a spin-1 particle, although only two classical polarization states transverse to its direction of propagation are allowed. Effectively therefore the photon is a spin-1/2 particle, although it still obeys Bose-Einstein statistics because the photon-photon interaction is zero. Here they show that the two polarization states of the photon can be quantized using Pauli's spin vector, such that a suitable equation of motion for the photon is Dirac's relativistic wave equation for zero mass and zero charge. Maxwell's equations for a free photon are inferred from the Dirac-field formalism and thus provide proof of this claim. For photons in the presence of electronic sources for electromagnetic fields we posit Lorentz-invariant inhomogeneous photonic equations of motion. Electro-dynamic operator equations are inferred from this modified Dirac-field formalism which reduce to Maxwell's equations if spin-dependent terms in the radiation-matter interaction are dropped.

Habitat use has been shown to be an important factor in the bioaccumulation of contaminants in striped bass. This study examines migration in striped bass as part of a larger study investigating bioaccumulation and maternal transfer of xenobiotics to progeny in the San Francisco Estuary system. Habitat use, residence time and spawning migration over the life of females (n = 23) was studied. Female striped bass were collected between Knights Landing and Colusa on the Sacramento River during the spawning runs of 1999 and 2001. Otoliths were removed, processed and aged via otolith microstructure. Subsequently, otoliths were analyzed for strontium/calcium (Sr/Ca) ratio using an electron-microprobe to measure salinity exposure and to distinguish freshwater, estuary, and marine habitat use. Salinity exposure during the last year before capture was examined more closely for comparison of habitat use by the maternal parent to contaminant burden transferred to progeny. Results were selectively confirmed by ion microprobe analyses for habitat use. The Sr/Ca data demonstrate a wide range of migratory patterns. Age of initial ocean entry differs among individuals before returning to freshwater, presumably to spawn. Some fish reside in freshwater year-round, while others return to more saline habitats and make periodic migrations to freshwater. …

A new continuum model for directional tensile failure has been developed that can simulate weakening and void formation due to directional tensile failure. The model is developed within the context of a properly invariant nonlinear thermomechanical theory. A second order damage tensor is introduced which allows simulation of weakening to tension applied in one direction, without weakening to subsequent tension applied in perpendicular directions. This damage tensor can be advected using standard methods in computer codes. Porosity is used as an isotropic measure of volumetric void strain and its evolution is influenced by tensile failure. The rate of dissipation due to directional tensile failure takes a particularly simple form, which can be analyzed easily. Specifically, the model can be combined with general constitutive equations for porous compaction and dilation, as well as viscoplasticity. A robust non-iterative numerical scheme for integrating these evolution equations is proposed. This constitutive model has been implemented into an Eulerian shock wave code with adaptive mesh refinement. A comparison of experimental results and computational simulations of spherical wave propagation in Danby marble was made. The experiment consisted of a 2-cm-diameter explosive charge detonated in the center of a cylindrical rock sample. Radial particle velocity histories were …

The effective stress model is used to model the stress-strain, volumetric, and strength behavior in saturated materials under shock loading. The effective stress concept provides a predictive model of the behavior of wet porous materials based on the dry material properties. An effective stress model that allows for arbitrary fluid and solid equations of state and varying levels of saturation is incorporated into an adaptive mesh refinement (AMR) Eulerian shock physics hydrocode. Good agreement is found between simulation results and experimental data for saturated materials, even at moderately high pressures.

A new thermodynamically consistent material model for large deformation has been developed. It describes quasistatic loading of limestone as well as high-rate phenomena. This constitutive model has been implemented into an Eulerian shock wave code with adaptive mesh refinement. This approach was successfully used to reproduce static triaxial compression tests and to simulate experiments of blast loading and damage of limestone. Results compare favorably with experimentally available wave profiles from spherically-symmetric explosion in rock samples.

High-power Free-Electron Lasers were made possible by advances in superconducting linac operated in an energy-recovery mode. In order to get to much higher power levels, say a fraction of a megawatt average power, many technological barriers are yet to be broken. We describe work on CW, high-current and high-brightness electron beams. This will include a description of a superconducting, laser-photocathode RF gun employing a new secondary-emission multiplying cathode, an accelerator cavity, both capable of producing of the order of one ampere average current and plans for an ERL based on these units.

This article investigates the use of a multi-conjugate adaptive optics system to improve the field-of-view for the system. The emphasis of this research is to develop techniques to improve the performance of optical systems with applications to horizontal imaging. The design and wave optics simulations of the proposed system are given. Preliminary results from the multi-conjugate adaptive optics system are also presented. The experimental system utilizes a liquid-crystal spatial light modulator and an interferometric wave-front sensor for correction and sensing of the phase aberrations, respectively.

The chemical inertness typically observed for Au does not imply a general inability to form stable bonds with non-metals but is rather a consequence of high reaction barriers. The Au-S interaction is probably the most intensively studied interaction of Au surfaces with non-metals as, for example, it plays an important role in Au ore formation, and controls the structure and dynamics of thiol-based self-assembled-monolayers (SAMs). In recent years a quite complex picture of the interaction of sulfur with Au(111) surfaces emerged, and a variety of S-induced surface structures was reported under different conditions. The majority of these structures were interpreted in terms of a static Au surface, where the positions of the Au atoms remain essentially unperturbed. Here we demonstrate that the Au(111) surface exhibits a very dynamic character upon interaction with adsorbed sulfur: low sulfur coverages modify the surface stress of the Au surface leading to lateral expansion of the surface layer; large-scale surface restructuring and incorporation of Au atoms into a growing two-dimensional AuS phase were observed with increasing sulfur coverage. These results provide new insight into the Au-S surface chemistry, and reveal the dynamic character of the Au(111) surface.