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.

This year (2008) deuterons and gold ions were collided in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory (BNL) for the first time since 2003. The setup and performance of the collider for the 2008 run is reviewed with a focus on improvements that have led to an order of magnitude increase in luminosity over that achieved in the 2003 run.

We are developing cryogenic bolometers to measure the total energy of the Linac Coherent Light Source (LCLS) free electron X-ray laser that is currently being built at the Stanford Linear Accelerator Center. LCLS will produce ultrashort {approx}200 fs X-ray laser pulses with {approx}10{sup 13} photons at 0.8 keV up to {approx}10{sup 12} photons at 8 keV per pulse at a repeat interval as short as 8 ms, and will be accompanied by a halo of spontaneous undulator radiation. Our bolometer consists of a 375 {micro}m thick Si absorber and a Nd{sub 0.67}Sr{sub 0.33}MnO{sub 3} sensor operated at its metal-insulator transition. It will measure the total energy of each pulse with a precision of <1%, and is designed to meet the conflicting requirements of radiation hardness, sensitivity, linearity over a dynamic range of three orders of magnitude, and readout speed compatible with the LCLS pulse rate. Here we discuss bolometer design and fabrication, and the photoresponse of prototype devices to pulsed optical lasers.

Dual partial snake scheme has been used for the Brookhaven AGS (Alternating Gradient Synchrotron) polarized proton operation for several years. It has provided polarized proton beams with 1.5 x 10{sup 11} intensity and 65% polarization for RHIC spin program. There is still residual polarization loss. Several schemes such as putting horizontal tune into the spin tune gap, and injection-on-the-fly were tested in the AGS to mitigate the loss. This paper presents the experiment results and analysis.

Injection and acceleration of ions in a lower charge state reduces space charge effects, and, if further elcctron stripping is needed, may allow elimination of a stripping stage and the associated beam losses. The former is of interest to the accelerators in the GSI FAIR complex, the latter for BNL RHIC collider operation at energies lower than the current injection energy. Lower charge state ions, however, have a higher likelihood of electron stripping which can lead to dynamic pressures rises and subsequent beam losses. We report on experiments in the AGS where Au{sup 31+} ions were injected and accelerated instead of the normally used Au{sup 77+} ions. Beam intensities and the average pressure in the AGS ring are recorded, and compared with calculations for dynamic pressures and beam losses. The experimental results will be used to benchmark the StrahlSim dynamic vacuum code and will be incorporated in the GSI FAIR SIS100 design.

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.

A central question addressed by the VERTIGO (VERtical Transport In the Global Ocean) study was 'What controls the efficiency of particle export between the surface and subsurface ocean'? Here, we present data from sites at ALOHA (N Central Pacific Gyre) and K2 (NW subarctic Pacific) on phytoplankton processes, and relate them via a simple planktonic foodweb model, to subsurface particle export (150-500 m). Three key factors enable quantification of the surface-subsurface coupling: a sampling design to overcome the temporal lag and spatial displacement between surface and subsurface processes; data on the size-partitioning of Net Primary Production (NPP) and subsequent transformations prior to export; estimates of the ratio of algal- to faecal-mediated vertical export flux. At ALOHA, phytoplankton were characterized by low stocks, NPP, F{sub v}/F{sub m} (N-limited), and were dominated by picoplankton. The HNLC waters at K2 were characterized by both two-fold changes in NPP and floristic shifts (high to low proportion of diatoms) between deployment 1 and 2. Prediction of export exiting the euphotic zone was based on size-partitioning of NPP, a copepod-dominated foodweb and a ratio of 0.2 (ALOHA) and 0.1 (K2) for algal:faecal particle flux. Predicted export was 20-22 mg POC m{sup -2} d{sup -1} at ALOHA …

We have studied the evolution of the structural properties as well as the static and dynamic spin correlations of spin ice Ho2Ti2O7, where Ho was partially replaced by non-magnetic La. The crystal structure of diluted samples Ho2-xLaxTi2O7 was characterized by x-ray and neutron diffraction and by Ho L-III-edge and Ti K-edge extended x-ray absorption fine structure (EXAFS) measurements. It is found that the pyrochlore structure remains intact until about x = 0.3, but a systematic increase in local disorder with increasing La concentration is observed in the EXAFS data, especially from the Ti K edge.Quasi-elastic neutron scattering and ac susceptibility measurements show that, in x<= 0.4 samples at temperatures above macroscopic freezing, the spin -spin correlations are short ranged and dynamic in nature. The main difference with pure spin ice in the dynamics is the appearance of a second, faster, relaxation process.

We report scanning Hall probe microscopy of highly underdoped superconducting YBa{sub 2}Cu{sub 3}O{sub 6+z} with T{sub c} ranging from 5 to 15 K which showed distinct flux bundles with less than one superconducting flux quantum ({Phi}{sub 0}) through the sample surface. The sub-{Phi}{sub 0} features occurred more frequently for lower T{sub c}, were more mobile than conventional vortices, and occurred more readily when the sample was cooled with an in-plane field component. We show that these features are consistent with kinked stacks of pancake vortices.

Initial- and final-state rescattering, neglected in the parton model, have a profound effect in QCD hard-scattering reactions, predicting single-spin asymmetries, diffractive deep inelastic scattering, diffractive hard hadronic reactions, the breakdown of the Lam Tung relation in Drell-Yan reactions, and nuclear shadowing and non-universal antishadowing--leading-twist physics not incorporated in the light-front wavefunctions of the target computed in isolation. I also discuss the use of diffraction to materialize the Fock states of a hadronic projectile and test QCD color transparency, and anomalous heavy quark effects. The presence of direct higher-twist processes where a proton is produced in the hard subprocess can explain the large proton-to-pion ratio seen in high centrality heavy ion collisions. I emphasize the importance of distinguishing between static observables such as the probability distributions computed from the square of the light-front wavefunctions versus dynamical observables which include the effects of rescattering.

The VERtical Transport In the Global Ocean (VERTIGO) study examined particle sources and fluxes through the ocean's 'twilight zone' (defined here as depths below the euphotic zone to 1000 m). Interdisciplinary process studies were conducted at contrasting sites off Hawaii (ALOHA) and in the NW Pacific (K2) during 3 week occupations in 2004 and 2005, respectively. We examine in this overview paper the contrasting physical, chemical and biological settings and how these conditions impact the source characteristics of the sinking material and the transport efficiency through the twilight zone. A major finding in VERTIGO is the considerably lower transfer efficiency (T{sub eff}) of particulate organic carbon (POC), POC flux 500/150 m, at ALOHA (20%) vs. K2 (50%). This efficiency is higher in the diatom-dominated setting at K2 where silica-rich particles dominate the flux at the end of a diatom bloom, and where zooplankton and their pellets are larger. At K2, the drawdown of macronutrients is used to assess export and suggests that shallow remineralization above our 150 m trap is significant, especially for N relative to Si. We explore here also surface export ratios (POC flux/primary production) and possible reasons why this ratio is higher at K2, especially during the …

Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERTIGO (VERtical Transformations In the Global Ocean) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by {approx}100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting three weeks, contrasted oligotrophic station ALOHA (22.75{sup o}N 158{sup o}W), sampled in June-July 2004, with a biologically productive location (47{sup o}N 161{sup o}E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C{sub org}, N, P, Ca, Si, Sr, Ba, Mn) in <1, 1-51, and >51 {micro}m size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C{sub org} and C-Star particle beam attenuation coefficient (C{sub P}) were consistently related at both sites with a 27 {micro}M m{sup -1} conversion factor. 26 At K2, C{sub P} profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed {approx}40% and 10%, …

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 …

I discuss several novel phenomenological features of QCD which are observable in deep inelastic lepton-nucleon and lepton-nucleus scattering. Initial- and final-state interactions from gluon exchange, normally neglected in the parton model, have a profound effect on QCD hard-scattering reactions, leading to leading-twist single-spin asymmetries, the diffractive contribution to deep inelastic scattering, and the breakdown of the pQCD Lam-Tung relation in Drell-Yan reactions. Leading-twist diffractive processes in turn lead to nuclear shadowing and non-universal antishadowing--physics not incorporated in the light-front wavefunctions of the nucleus computed in isolation.

Mammary gland development, functional differentiation, and homeostasis are orchestrated and sustained by a balance of biochemical and biophysical cues from the organ's microenvironment. The three-dimensional microenvironment of the mammary gland, predominantly 'encoded' by a collaboration between the extracellular matrix (ECM), hormones, and growth factors, sends signals from ECM receptors through the cytoskeletal intracellular matrix to nuclear and chromatin structures resulting in gene expression; the ECM in turn is regulated and remodeled by signals from the nucleus. In this chapter, we discuss how coordinated ECM deposition and remodeling is necessary for mammary gland development, how the ECM provides structural and biochemical cues necessary for tissue-specific function, and the role of the cytoskeleton in mediating the extra - to intracellular dialogue occurring between the nucleus and the microenvironment. When operating normally, the cytoskeletal-mediated dynamic and reciprocal integration of tissue architecture and function directs mammary gland development, tissue polarity, and ultimately, tissue-specific gene expression. Cancer occurs when these dynamic interactions go awry for an extended time.

Here we describe a simple micromolding method to construct three-dimensional arrays of organotypic epithelial tissue structures that approximate in vivo histology. An elastomeric stamp containing an array of posts of defined geometry and spacing is used to mold microscale cavities into the surface of type I collagen gels. Epithelial cells are seeded into the cavities and covered with a second layer of collagen. The cells reorganize into hollow tissues corresponding to the geometry of the cavities. Patterned tissue arrays can be produced in 3-4 h and will undergo morphogenesis over the following one to three days. The protocol can easily be adapted to study a variety of tissues and aspects of normal and neoplastic development.

The beam intensity of ion beams in RHIC is limited by a fast transverse instability at transition, driven by the machine impedance and electron clouds. For gold and deuteron beams we analyze the dependence of the instability threshold on beam and machine parameters from recent operational data and dedicated experiments. We fit the machine impedance to the experimental data.

Supermassive black holes (SMBHs) are a ubiquitous component of the nuclei of galaxies. It is normally assumed that, following the merger of two massive galaxies, a SMBH binary will form, shrink due to stellar or gas dynamical processes and ultimately coalesce by emitting a burst of gravitational waves. However, so far it has not been possible to show how two SMBHs bind during a galaxy merger with gas due to the difficulty of modeling a wide range of spatial scales. Here we report hydrodynamical simulations that track the formation of a SMBH binary down to scales of a few light years following the collision between two spiral galaxies. A massive, turbulent nuclear gaseous disk arises as a result of the galaxy merger. The black holes form an eccentric binary in the disk in less than a million years as a result of the gravitational drag from the gas rather than from the stars.

To better understand the role of groundwater-level changes on rock-slope deformation and damage, a carbonate rock slope (30 m x 30 m x 15 m) was extensively instrumented for mesoscale hydraulic and mechanical measurements during water-level changes. The slope is naturally drained by a spring that can be artificially closed or opened by a water gate. In this study, a 2-hour slope-dewatering experiment was analyzed. Changes in fluid pressure and deformation were simultaneously monitored, both at discontinuities and in the intact rock, using short-base extensometers and pressure gauges as well as tiltmeters fixed at the slope surface. Field data were analyzed with different coupled hydromechanical (HM) codes (ROCMAS, FLAC{sup 3D}, and UDEC). Field data indicate that in the faults, a 40 kPa pressure fall occurs in 2 minutes and induces a 0.5 to 31 x 10{sup -6} m normal closure. Pressure fall is slower in the bedding-planes, lasting 120 minutes with no normal deformation. No pressure change or deformation is observed in the intact rock. The slope surface displays a complex tilt towards the interior of the slope, with magnitudes ranging from 0.6 to 15 x 10{sup -6} rad. Close agreement with model for both slope surface and internal measurements …

We report the discovery of a giant Ly{alpha} emitter (LAE) with a Spitzer/IRAC counterpart near the reionization epoch at z = 6.595. The giant LAE is found from the extensive 1 deg{sup 2} Subaru narrow-band survey for z = 6.6 LAEs in the Subaru/XMM-Newton Deep Survey (SXDS) field, and subsequently identified by deep spectroscopy of Keck/DEIMOS and Magellan/IMACS. Among our 207 LAE candidates, this LAE is not only the brightest narrow-band object with L(Ly{alpha}) = 3.9 {+-} 0.2 x 10{sup 43} erg s{sup -1} in our survey volume of 10{sup 6} Mpc{sup 3}, but also a spatially extended Ly{alpha} nebula with the largest isophotal area whose major axis is at least {approx_equal} 3-inches. This object is more likely to be a large Ly{alpha} nebula with a size of {approx}> 17-kpc than to be a strongly-lensed galaxy by a foreground object. Our Keck spectrum with medium-high spectral and spatial resolutions suggests that the velocity width is v{sub FWHM} = 251 {+-} 21 km s{sup -1}, and that the line-center velocity changes by {approx_equal} 60 km s{sup -1} in a 10-kpc range. The stellar mass and star-formation rate are estimated to be 0.9-5.0 x 10{sup 10}M{sub {circle_dot}} and > 34 M{sub {circle_dot}}yr{sup …

Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications(PTMs). Although PTMs are a critical aspectof cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this …

The authors present measurements of branching fractions for five B-meson decays to two-body charmless final states. The data, collected with the BABAR detector at the Stanford Linear Accelerator Center, represent 459 million B{bar B} pairs. The results for branching fractions are, in units of 10{sup -6} (upper limits at 90% C.L.): {Beta}(B{sup +} {yields} {eta}{rho}{sup +}) = 9.9 {+-} 1.2 {+-} 0.8, {Beta}(B{sup 0} {yields} {eta}{prime}{eta}) = 0.5 {+-} 0.4 {+-} 0.1 (< 1.2), {Beta}(B{sup 0} {yields} {eta}{pi}{sup 0}) = 0.9 {+-} 0.4 {+-} 0.1 (< 1.5), {Beta}(B{sup 0} {yields} {eta}{prime}{pi}{sup 0}) = 0.9 {+-} 0.4 {+-} 0.1 (< 1.5), and {Beta}(B{sup 0}{sup 0} {yields} {omega}{pi}{sup 0}) = {eta}{rho}{sup +} mode, they measure the charge asymmetry {Alpha}{sub ch} (B{sup +} {yields} {eta}{rho}{sup +}) = 0.13 {+-} 0.11 {+-} 0.02.

During Run-8, the Relativistic Heavy Ion Collider (RHIC) provided collisions of spin-polarized proton beams at two interaction regions. Helical spin rotators at these two interaction regions were used to control the spin orientation of both beams at the collision points. Physics data were taken with different orientations of the beam polarization. We present recent developments and improvements as well as the luminosity and polarization performance achieved during Run-8.

The connection between macro-particle shape functions and non-physical phase-space"heating" in the particle-in-cell (PIC) algorithm is examined. The development of fine-scale phasespace structures starting from a cold initial condition is shown to be related to spatial correlations in the interpolated fields used in the Lorentz force. It is shown that the plasma evolution via the PIC algorithm from a cold initial condition leads to a state that is not consistent with that of a thermal plasma.