Article discussing molecules, mechanisms, and materials and current applications of computational chemistry in the Journal of the American Chemical Society (JACS).

Article on yeast lipin orthologue Pah1p and its importance for biogenesis of lipid droplets.

As high-performance computing approaches exascale, the existing I/O system design is having trouble keeping pace in both performance and scalability. We propose to address this challenge by adopting database principles and techniques in parallel I/O systems. First, we propose to adopt an array data model because many scientific applications represent their data in arrays. This strategy follows a cardinal principle from database research, which separates the logical view from the physical layout of data. This high-level data model gives the underlying implementation more freedom to optimize the physical layout and to choose the most effective way of accessing the data. For example, knowing that a set of write operations is working on a single multi-dimensional array makes it possible to keep the subarrays in a log structure during the write operations and reassemble them later into another physical layout as resources permit. While maintaining the high-level view, the storage system could compress the user data to reduce the physical storage requirement, collocate data records that are frequently used together, or replicate data to increase availability and fault-tolerance. Additionally, the system could generate secondary data structures such as database indexes and summary statistics. We expect the proposed Scientific Data Services approach …

The thermal stability of formohydroxamic acid (FHA) was evaluated to address the potential for exothermic decomposition during storage and its use in the uranium extraction process. Accelerating rate calorimetry showed rapid decomposition at a temperature above 65 {degree}C; although, the rate of pressure rise was greater than two orders of magnitude less than the lower bound for materials which have no explosive properties with respect to transportation. FHA solutions in water and nitric acid did not reach runaway conditions until 150 {degree}C. Analysis by differential scanning calorimetry showed that FHA melted at 67 {degree}C and thermally decomposed at 90 {degree}C with an enthalpy of -1924 J/g. The energics of the FHA thermal decomposition are comparable to those measured for aqueous solutions of hydroxylamine nitrate. Solid FHA should be stored in a location where the temperature does not exceed 20-25 {degree}C. As a best practice, the solid material should be stored in a climate-controlled environment such as a refrigerator or freezer. FHA solutions in water are not susceptible to degradation by acid hydrolysis and are the preferred way to handle FHA prior to use.

Realizing the experimental potential of high-brightness, next generation synchrotron and free-electron laser light sources requires the development of reflecting x-ray optics capable of wavefront preservation and high-resolution nano-focusing. At the Advanced Light Source (ALS) beamline 5.3.1, we are developing broadly applicable, high-accuracy, in situ, at-wavelength wavefront measurement techniques to surpass 100-nrad slope measurement accuracy for diffraction-limited Kirkpatrick-Baez (KB) mirrors. The at-wavelength methodology we are developing relies on a series of wavefront-sensing tests with increasing accuracy and sensitivity, including scanning-slit Hartmann tests, grating-based lateral shearing interferometry, and quantitative knife-edge testing. We describe the original experimental techniques and alignment methodology that have enabled us to optimally set a bendable KB mirror to achieve a focused, FWHM spot size of 150 nm, with 1 nm (1.24 keV) photons at 3.7 mrad numerical aperture. The predictions of wavefront measurement are confirmed by the knife-edge testing.The side-profiled elliptically bent mirror used in these one-dimensional focusing experiments was originally designed for a much different glancing angle and conjugate distances. This work demonstrates that high-accuracy, at-wavelength wavefront-slope feedback can be used to optimize the pitch, roll, and mirror-bending forces in situ, using procedures that are deterministic and repeatable.

Previous experiments at the Rifle, Colorado Integrated Field Research Challenge (IFRC) site demonstrated that field-scale addition of acetate to groundwater reduced the ambient soluble uranium concentration. In this report, sediment samples collected before and after acetate field addition were used to assess the active microbes via {sup 13}C acetate stable isotope probing on 3 phases [coarse sand, fines (8-approximately 150 {micro}m), groundwater (0.2-8 {micro}m)] over a 24-day time frame. TRFLP results generally indicated a stronger signal in {sup 13}C-DNA in the 'fines' fraction compared to the sand and groundwater. Before the field-scale acetate addition, a Geobacter-like group primarily synthesized {sup 13}C-DNA in the groundwater phase, an alpha Proteobacterium primarily grew on the fines/sands, and an Acinetobacter sp. and Decholoromonas-like OTU utilized much of the {sup 13}C acetate in both groundwater and particle-associated phases. At the termination of the field-scale acetate addition, the Geobacter-like species was active on the solid phases rather than the groundwater, while the other bacterial groups had very reduced newly synthesized DNA signal. These findings will help to delineate the acetate utilization patterns of bacteria in the field and can lead to improved methods for stimulating distinct microbial populations in situ.

Epitaxial films along the Fe{sub 3-x}Ti{sub x}O{sub 4} (titanomagnetite) compositional series from pure end-members magnetite (Fe{sub 3}O{sub 4}) to ulvöspinel (Fe{sub 2}TiO{sub 4}) were successfully grown by pulsed laser deposition on MgO(100) substrates. Spectroscopic characterization including high resolution x-ray diffraction, x-ray photoelectron spectroscopy, and synchrotron-based x-ray absorption and magnetic circular dichroism consistently shows that Ti(IV) substitutes for Fe(III) in the inverse spinel lattice with a proportional increase in lattice Fe(II) concentration. No evidence of Ti interstitials, spinodal decomposition, or secondary phases was found in the bulk of the grown films. At the uppermost few nanometers of the Ti-bearing film surfaces, evidence suggests that Fe(II) is susceptible to facile oxidation, and that an associated lower Fe/Ti ratio in this region is consistent with surface compositional incompleteness or alteration to a titanomaghemite-like composition and structure. The surface of these films nonetheless appear to remain highly ordered and commensurate with the underlying structure despite facile oxidation, a surface condition that is found to be reversible to some extent by heating in low oxygen environments.

Manual library construction is a limiting factor in Illumina sequencing. Constructing libraries by hand is costly, time-consuming, low-throughput, and ergonomically hazardous, and constructing multiple libraries introduces risk of library failure due to pipetting errors. The ability to construct multiple libraries simultaneously in automated fashion represents significant cost and time savings. Here we present a strategy to construct up to 96 unamplified indexed libraries using Illumina TruSeq reagents and a Biomek FX robotic platform. We also present data to indicate that this library construction method has little or no risk of cross-contamination between samples.

Compliance with National and State environmental regulations (e.g. Resource Conservation and Recovery Act (RCRA) and Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) aka SuperFund) requires Savannah River Site (SRS) to extensively collect and report groundwater monitoring data, with potential fines for missed reporting deadlines. Several utilities have been developed at SRS to facilitate production of the regulatory reports which include maps, data tables, charts and statistics. Components of each report are generated in accordance with complex sets of regulatory requirements specific to each site monitored. SRS developed a relational database to incorporate the detailed reporting rules with the groundwater data, and created a set of automation tools to interface with the information and generate the report components. These process improvements enhanced quality and consistency by centralizing the information, and have reduced manpower and production time through automated efficiencies.

Using four genomes: Chamydomonas reinhardtii, Agaricus bisporus, Aspergillus carbonarius, and Sporotricum thermophile with EST coverage of 2.9x, 8.9x, 29.5x, and 46.3x respectively, we identified 11 alternative splicing (AS) types that were dominated by intron retention (RI; biased toward short introns) and found 15, 35, 52, and 63percent AS of multiexon genes respectively. Genes with AS were more ancient, and number of AS correlated with number of exons, expression level, and maximum intron length of the gene. Introns with tendency to be retained had either stop codons or length of 3n+1 or 3n+2 presumably triggering nonsense-mediated mRNA decay (NMD), but introns retained in major isoforms (0.2-6percent of all introns) were biased toward 3n length and stop codon free. Stopless introns were biased toward phase 0, but 3n introns favored phase 1 that introduced more flexible and hydrophilic amino acids on both ends of introns which would be less disruptive to protein structure. We proposed a model in which minor RI intron could evolve into major RI that could facilitate intron loss through exonization.

In the second half of 2007 a major upgrade has been implemented on the Frascati DA{Phi}NE collider in order to test the novel idea of Crab-Waist collisions. New vacuum chambers and permanent quadrupole magnets have been designed, built and installed to realize the new configuration. At the same time the performances of relevant hardware components, such as fast injection kickers and shielded bellows have been improved relying on new design concepts. The collider has been successfully commissioned in this new configuration. The paper describes several experimental results about linear and non-linear optics setup and optimization, damping of beam-beam instabilities and discusses the obtained luminosity performances. DA{Phi}NE [1] is the Frascati lepton collider working at the c m. energy of the {Phi} meson resonance (1020). It came in operation in 2001 and till summer 2007 provided luminosity, in sequence, to three different experiments which logged a total integrated luminosity of {approx} 4.4 fb{sup -1}. During these years the collider reached its best performances in terms of luminosity and background (L{sub peak} = 1.6 x 10{sup 32} cm{sup -2}s{sup -1} L{sub day} {approx} 10 pb{sup -1}) by means of several successive upgrades, relying on the experience gathered during the collider operations and …

The conference will present and discuss current science that underlies solar fuels production, and will focus on direct production pathways for production. Thus, recent advances in design and understanding of molecular systems and materials for light capture and conversion of relevance for solar fuels will be discussed. An important set of topics will be homogeneous, heterogeneous and biological catalysts for the multi-electron processes of water oxidation, hydrogen production and carbon dioxide reduction to useful fuels. Also, progress towards integrated and scalable systems will be presented. Attached is a copy of the formal schedule and speaker program and the poster program.

The ITRS requires < 1.2nm line-edge roughness (LER) for the 22nm half-pitch node. Currently, we can consistently achieve only about 3nm LER. Further progress requires understanding the principle causes of LER. Much work has already been done on how both the resist and LER on the mask effect the final printed LER. What is poorly understood, however, is the extent to which system-level effects such as mask surface roughness, illumination conditions, and defocus couple to speckle at the image plane, and factor into LER limits. Presently, mask-roughness induced LER is studied via full 2D aerial image modeling and subsequent analysis of the resulting image. This method is time consuming and cumbersome. It is, therefore, the goal of this research to develop a useful 'rule-of-thumb' analytic model for mask roughness induced LER to expedite learning and understanding.

The objective of this project is to detect and locate more microearthquakes using the empirical matched field processing (MFP) method than can be detected using only conventional earthquake detection techniques. We propose that empirical MFP can complement existing catalogs and techniques. We test our method on continuous seismic data collected at the Salton Sea Geothermal Field during November 2009 and January 2010. In the Southern California Earthquake Data Center (SCEDC) earthquake catalog, 619 events were identified in our study area during this time frame and our MFP technique identified 1094 events. Therefore, we believe that the empirical MFP method combined with conventional methods significantly improves the network detection ability in an efficient matter.

Mask defects inspection and imaging is one of the most important issues for any pattern transfer lithography technology. This is especially true for EUV lithography where the wavelength-specific properties of masks and defects necessitate actinic inspection for a faithful prediction of defect printability and repair performance. In this paper we will present a technique to obtain a quantitative characterization of mask phase defects from EUV aerial images. We apply this technique to measure the aerial image phase of native defects on a blank mask, measured with the SEMATECH Berkeley Actinic Inspection Tool (AIT) an EUV zoneplate microscope that operates at Lawrence Berkeley National Laboratory. The measured phase is compared with predictions made from AFM top-surface measurements of those defects. While amplitude defects are usually easy to recognize and quantify with standard inspection techniques like scanning electron microscopy (SEM), defects or structures that have a phase component can be much more challenging to inspect. A phase defect can originate from the substrate or from any level of the multilayer. In both cases its effect on the reflected field is not directly related to the local topography of the mask surface, but depends on the deformation of the multilayer structure. Using the …

As extreme-ultraviolet lithography (EUVL) approaches introduction at the 22-nm half-pitch node, several key aspects of absorber height effects remain unexplored. In particular, sidewall angle (SWA) restrictions based on the height of the mask absorber has not yet been clearly defined. In addition, the effects of absorber height on line-edge roughness (LER) from shadowing has not been examined. We make an initial investigation into how tight SWA constraints are and the extent to which shadow LER alters basic LER. Our approach to SWA aims to find SWA restrictions based on 10% of the total CD error budget (10% of CD). Thus, we allot the SWA budget a {+-}0.2nm tolerance for 22nm half-pitch. New with EUVL is the off-axis illumination system. One potential pitfall that must be carefully monitored is the effect of mask absorber height blocking light from reaching, and therefore, correctly detecting, the base edge position of a feature. While mask features can correctly compensate sizing to target at the wafer, the effects of this shadowing on LER have not yet been investigated. Specifically, shadow LER may exacerbate or mitigate the inherent LER on the mask. Shadowing may also cause a difference in the observed LER on the right and …

The authors present time-resolved synchrotron x-ray diffraction to probe the {var_epsilon}-{delta} phase transition of iron during pulse-laser heating in a diamond anvil cell. The system utilizes a monochromatic synchrotron x-ray beam, a two-dimensional pixel array x-ray detector and a dual beam, double side laser-heating system. Multiple frames of the diffraction images are obtained in real-time every 22 ms over 500 ms of the entire pulse heating period. The results show the structural evolution of iron phases at 17 GPa, resulting in thermal expansion coefficient 1/V({Delta}V/{Delta}T){sub p} = 7.1 * 10{sup -6}/K for {var_epsilon}-Fe and 2.4 * 10{sup -5}/K for {gamma}-Fe, as well as the evidence for metastability of {gamma}-Fe at low temperatures below the {var_epsilon}-{gamma} phase boundary.

We describe a lattice simulation of the masses and decay constants of the lowest-lying vector and axial resonances, and the electroweak S parameter, in an SU(3) gauge theory with N{sub f} = 2 and 6 fermions in the fundamental representation. The spectrum becomes more parity doubled and the S parameter per electroweak doublet decreases when N{sub f} is increased from 2 to 6, motivating study of these trends as N{sub f} is increased further, toward the critical value for transition from confinement to infrared conformality.

This review summarizes exemplary secondary education and outreach programs of the particle physics community. We examine programs from the following areas: research experiences, high-energy physics data for students, informal learning for students, instructional resources, and professional development. We report findings about these programs' impact on students and teachers and provide suggestions for practices that create effective programs from those findings. We also include some methods for assessing programs.

Lattice-Boltzmann methods are versatile numerical modeling techniques capable of reproducing a wide variety of fluid-mechanical behavior. These methods are well suited to parallel implementation, particularly on the single-instruction multiple data (SIMD) parallel processing environments found in computer graphics processing units (GPUs). Although more recent programming tools dramatically improve the ease with which GPU programs can be written, the programming environment still lacks the flexibility available to more traditional CPU programs. In particular, it may be difficult to develop modular and extensible programs that require variable on-device functionality with current GPU architectures. This paper describes a process of automatic code generation that overcomes these difficulties for lattice-Boltzmann simulations. It details the development of GPU-based modules for an extensible lattice-Boltzmann simulation package - LBHydra. The performance of the automatically generated code is compared to equivalent purpose written codes for both single-phase, multiple-phase, and multiple-component flows. The flexibility of the new method is demonstrated by simulating a rising, dissolving droplet in a porous medium with user generated lattice-Boltzmann models and subroutines.

Detonation waves in insensitive, TATB based explosives are believed to have multi-time scale regimes. The initial burn rate of such explosives has a sub-microsecond time scale. However, significant late-time slow release in energy is believed to occur due to diffusion limited growth of carbon. In the intermediate time scale concentrations of product species likely change from being in equilibrium to being kinetic rate controlled. They use the thermo-chemical code CHEETAH linked to an ALE hydrodynamics code to model detonations. They term their model chemistry resolved kinetic flow as CHEETAH tracks the time dependent concentrations of individual species in the detonation wave and calculates EOS values based on the concentrations. A HE-validation suite of model simulations compared to experiments at ambient, hot, and cold temperatures has been developed. They present here a new rate model and comparison with experimental data.

The Neutralized Drift Compression Experiment (NDCX-II) is an 11 M$ induction accelerator project currently in construction at Lawrence Berkeley National Laboratory for warm dense matter (WDM) experiments investigating the interaction of ion beams with matter at elevated temperature and pressure. The machine consists of a lithium injector, induction accelerator cells, diagnostic cells, a neutralized drift compression line, a final focus solenoid, and a target chamber. The induction cells and some of the pulsed power systems have been reused from the decommissioned Advanced Test Accelerator at Lawrence Livermore National Laboratory after refurbishment and modification. The machine relies on a sequence of acceleration waveforms to longitudinally compress the initial ion pulse from 600 ns to less than 1 ns in {approx} 12 m. Radial confinement of the beam is achieved with 2.5 T pulsed solenoids. In the initial hardware configuration, 50 nC of Li{sup +} will be accelerated to 1.25 MeV and allowed to drift-compress to a peak current of {approx}40 A. The project started in the summer of 2009. Construction of the accelerator will be completed in the fall of 2011 and will provide a worldwide unique opportunity for ion-driven warm dense matter experiments as well as research related to novel …

CdZnTe (CZT) continues to be a major thrust interest mainly due to its potential application as a room temperature radiation detector. The performance of CZT detectors is directly related to the charge collection ability which can be affected by the configuration of the electrical contact. The charge collection efficiency is determined in part by the specific geometry of the anode contact which serves as the readout electrode. In this report, contact geometries including single pixel, planar, coplanar, and dual anode will be systematically explored by comparing the performance efficiencies of the detector using both low and high energy gamma rays. To help eliminate the effect of crystal quality variations, the contact geometries were fabricated on the same crystal detector with minimal polishing between contact placements.

The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessary accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors.