Article discussing research on correlation function and generalized master equation of arbitrary age.

Article discussing a unified cosolvency model for calculating solute solubility in mixed solvents.

Article discussing a general treatment of solubility and principle component analysis (PCA) of the solubilities of diverse solutes in diverse solvents.

Article on a computational study of the thermochemistry of bromine- and iodine-containing methanes and methyl radicals.

The author argues that the physics of the scattering of very high energy strongly interacting particles is controlled by a new, universal form of matter, the Color Glass Condensate. I motivate the existence of this matter and describe some of its properties.

Sparse systems of linear equations and eigen-equations arise at the heart of many large-scale, vital simulations in DOE. Examples include the Accelerator Science and Technology SciDAC (Omega3P code, electromagnetic problem), the Center for Extended Magnetohydrodynamic Modeling SciDAC(NIMROD and M3D-C1 codes, fusion plasma simulation). The Terascale Optimal PDE Simulations (TOPS)is providing high-performance sparse direct solvers, which have had significant impacts on these applications. Over the past several years, we have been working closely with the other SciDAC teams to solve their large, sparse matrix problems arising from discretization of the partial differential equations. Most of these systems are very ill-conditioned, resulting in extremely poor convergence deployed our direct methods techniques in these applications, which achieved significant scientific results as well as performance gains. These successes were made possible through the SciDAC model of computer scientists and application scientists working together to take full advantage of terascale computing systems and new algorithms research.

Significant experimental and theoretical progress has been made in the U.S. heavy ion fusion program on high-current sources, injectors, transport, final focusing, chambers and targets for high energy density physics (HEDP) and inertial fusion energy (IFE) driven by induction linac accelerators. One focus of present research is the beam physics associated with quadrupole focusing of intense, space-charge dominated heavy-ion beams, including gas and electron cloud effects at high currents, and the study of long-distance-propagation effects such as emittance growth due to field errors in scaled experiments. A second area of emphasis in present research is the introduction of background plasma to neutralize the space charge of intense heavy ion beams and assist in focusing the beams to a small spot size. In the near future, research will continue in the above areas, and a new area of emphasis will be to explore the physics of neutralized beam compression and focusing to high intensities required to heat targets to high energy density conditions as well as for inertial fusion energy.

We develop and illustrate a general regional multi-species model that describes the fate and transport of mercury in three forms, elemental, divalent, and methylated, in a generic regional environment including air, soil, vegetation, water and sediment. The objectives of the model are to describe the fate of the three forms of mercury in the environment and determine the dominant physical sinks that remove mercury from the system. Chemical transformations between the three groups of mercury species are modeled by assuming constant ratios of species concentrations in individual environmental media. They illustrate and evaluate the model with an application to describe the fate and transport of mercury in the San Francisco Bay Area of California. The model successfully rationalizes the identified sources with observed concentrations of total mercury and methyl mercury in the San Francisco Bay Estuary. The mass balance provided by the model indicates that continental and global background sources control mercury concentrations in the atmosphere but loadings to water in the San Francisco Bay estuary are dominated by runoff from the Central Valley catchment and re-mobilization of contaminated sediments deposited during past mining activities. The model suggests that the response time of mercury concentrations in the San Francisco Bay …

This paper is the summary of a conceptual study of a Proton Driver for Neutrino Factory based on the use of a Fixed-Field Alternating-Gradient (FFAG) Accelerator. The required proton energy range for an optimum neutrino production is 5 to 12 GeV. This can be accomplished with a group of three concentric rings each with 807 m circumference [1]. FFAG Accelerators [2] have the capability to accelerate charged particles over a large momentum range ({+-}30-50%) and the feature of constant bending and focusing fields. Particles can be accelerated very fast at the rate given by the accelerating field of RF cavities placed in proper locations between magnets. The performance of FFAG accelerators is to be placed between that of Super-Conducting Linear Accelerators (SCL), with which they share the fast acceleration rate, and Rapid-Cycling Synchrotrons (RCS), as they allow the beam to re-circulate over fewer revolutions. Brookhaven National Laboratory is involved in the study of feasibility of FFAG Accelerators to accelerate intense beams of protons in the GeV energy range for a variety of applications the most important of which is the Upgrade of the Alternating Gradient Synchrotron (AGS) with a new FFAG injector [3] accelerating from 400 MeV to 1.5 GeV. …

Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light strand replication and the nearby tRNA genes or the regions flanking the origin of heavy strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and non-tandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mtDNAs, up to 25 percent of the total length is composed of tandem duplications of non-coding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with otherwise unassignable sequences. These data …

The National Fusion Collaboratory project is developing and deploying new distributed computing and remote collaboration technologies with the goal of advancing magnetic fusion energy research. This work has led to the development of the US Fusion Grid (FusionGrid), a computational grid composed of collaborative, compute, and data resources from the three large US fusion research facilities and with users both in the US and in Europe. Critical to the development of FusionGrid was the creation and deployment of technologies to ensure security in a heterogeneous environment. These solutions to the problems of authentication, authorization, data transfer, and secure data storage, as well as the lessons learned during the development of these solutions, may be applied outside of FusionGrid and scale to future computing infrastructures such as those for next-generation devices like ITER.

Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the thermodynamics of folding for a Miyazawa-Jernigan model 64-mer in isolation to results obtained in the presence of additional chains. The melting temperature falls as the chain concentration increases. In multi-chain systems, free-energy landscapes for folding show an increased preference for misfolded states. Misfolding is accompanied by an increase in inter-protein interactions; however, near the folding temperature, the transition from folded chains to misfolded and associated chains isentropically driven. A majority of the most probable inter-protein contacts are also native contacts, suggesting that native topology plays a role in early stages of aggregation.

The National Fusion Collaboratory project is developing and deploying new distributed computing and remote collaboration technologies with the goal of advancing magnetic fusion energy research. This work has led to the development of the US Fusion Grid (FusionGrid), a computational grid composed of collaborative, compute, and data resources from the three large US fusion research facilities and with users both in the US and in Europe. Critical to the development of FusionGrid was the creation and deployment of technologies to ensure security in a heterogeneous environment. These solutions to the problems of authentication, authorization, data transfer, and secure data storage, as well as the lessons learned during the development of these solutions, may be applied outside of FusionGrid and scale to future computing infrastructures such as those for next-generation devices like ITER.

SciDAC has had a major impact on computational beam dynamics and the design of particle accelerators. Particle accelerators--which account for half of the facilities in the DOE Office of Science Facilities for the Future of Science 20 Year Outlook--are crucial for US scientific, industrial, and economic competitiveness. Thanks to SciDAC, accelerator design calculations that were once thought impossible are now carried routinely, and new challenging and important calculations are within reach. SciDAC accelerator modeling codes are being used to get the most science out of existing facilities, to produce optimal designs for future facilities, and to explore advanced accelerator concepts that may hold the key to qualitatively new ways of accelerating charged particle beams. In this poster we present highlights from the SciDAC Accelerator Science and Technology (AST) project Beam Dynamics focus area in regard to algorithm development, software development, and applications.

Large-scale eigenvalue problems arise in a number of DOE applications. This paper provides an overview of the recent development of eigenvalue computation in the context of two SciDAC applications. We emphasize the importance of Krylov subspace methods, and point out its limitations. We discuss the value of alternative approaches that are more amenable to the use of preconditioners, and report the progression using the multi-level algebraic sub-structuring techniques to speed up eigenvalue calculation. In addition to methods for linear eigenvalue problems, we also examine new approaches to solving two types of non-linear eigenvalue problems arising from SciDAC applications.

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Semiconductor tetrapods are three dimensional branched nanostructures, representing a new class of materials for electrical conduction. We employ the single electron transistor approach to investigate how charge carriers migrate through single nanoscale branch points of tetrapods. We find that carriers can delocalize across the branches or localize and hop between arms depending on their coupling strength. In addition, we demonstrate a new single-electron transistor operation scheme enabled by the multiple branched arms of a tetrapod: one arm can be used as a sensitive arm-gate to control the electrical transport through the whole system. Electrical transport through nanocrystals, molecules, nanowires and nanotubes display novel quantum phenomena. These can be studied using the single electron transistor approach to successively change the charge state by one, to reveal charging energies, electronic level spacings, and coupling between electronic, vibrational, and spin degrees of freedom. The advent of colloidal synthesis methods that produce branched nanostructures provides a new class of material which can act as conduits for electrical transport in hybrid organic-inorganic electrical devices such as light emitting diodes and solar cells. Already, the incorporation of branched nanostructures has yielded significant improvements in nanorod/polymer solar cells, where the specific pathways for charge migration can have …

Small-scale (100 kW-5 MW) on-site distributed generation (DG) economically driven by combined heat and power (CHP) applications and, in some cases, reliability concerns will likely emerge as a common feature of commercial building energy systems in developed countries over the next two decades. In the U.S., private and public expectations for this technology are heavily influenced by forecasts published by the Energy Information Administration (EIA), most notably the Annual Energy Outlook (AEO). EIA's forecasts are typically made using the National Energy Modeling System (NEMS), which has a forecasting module that predicts the penetration of several possible commercial building DG technologies over the period 2005-2025. Annual penetration is forecast by estimating the payback period for each technology, for each of a limited number of representative building types, for each of nine regions. This process results in an AEO2004 forecast deployment of about a total 3 GW of DG electrical generating capacity by 2025, which is only 0.25 percent of total forecast U.S. capacity. Analyses conducted using both the AEO2003 and AEO2004 versions of NEMS changes the baseline costs and performance characteristics of DG to reflect a world without U.S. Department of Energy (DOE) research into several thermal DG technologies, which is …

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Conventional organic fluorophores suffer from poor photo stability, narrow absorption spectra and broad emission feature. Semiconductor nanocrystals, on the other hand, are highly photo-stable with broad absorption spectra and narrow size-tunable emission spectra. Recent advances in the synthesis of these materials have resulted in bright, sensitive, extremely photo-stable and biocompatible semiconductor fluorophores. Commercial availability facilitates their application in a variety of unprecedented biological experiments, including multiplexed cellular imaging, long-term in vitro and in vivo labeling, deep tissue structure mapping and single particle investigation of dynamic cellular processes. Semiconductor nanocrystals are one of the first examples of nanotechnology enabling a new class of biomedical applications.

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Successfully attacking underground storage facilities for chemical and biological (C/B) weapons is an important mission area for the Department of Defense. The fate of a C/B agent during an attack depends critically on the pressure and thermal environment that the agent experiences. The initial environment is determined by the blast wave from an explosive device. The byproducts of the detonation provide a fuel source that burn when mixed with oxidizer (after burning). Additional energy can be released by the ignition of the C/B agent as it mixes with the explosion products and the air in the chamber. Hot plumes venting material from any openings in the chamber can provide fuel for additional energy release when mixed with additional oxidizer. Assessment of the effectiveness of current explosives as well as the development of new explosive systems requires a detailed understanding of all of these modes of energy release. Using methodologies based on the use of higher-order Godunov schemes combined with Adaptive Mesh Refinement (AMR), implemented in a parallel adaptive framework suited to the massively parallel computer systems provided by the DOD High-Performance Computing Modernization program, we use a suite of programs to develop predictive models for the simulation of the energetics …

The performance of the Eulerian gyrokinetic-Maxwell solver code GYRO is analyzed on five high performance computing systems. First, a manual approach is taken, using custom scripts to analyze the output of embedded wall clock timers, floating point operation counts collected using hardware performance counters, and traces of user and communication events collected using the profiling interface to Message Passing Interface (MPI) libraries. Parts of the analysis are then repeated or extended using a number of sophisticated performance analysis tools: IPM, KOJAK, SvPablo, TAU, and the PMaC modeling tool suite. The paper briefly discusses what has been discovered via this manual analysis process, what performance analyses are inconvenient or infeasible to attempt manually, and to what extent the tools show promise in accelerating or significantly extending the manual performance analyses.

Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is Large-scale workflows are becoming increasingly important in both the scientific research and business domains. Science and commerce have both experienced an explosion in the sheer amount of data that must be analyzed. An important tool for analyzing these huge datasets is a compute cluster of hundreds or thousands of machines. However, debugging and tuning clusters requires specialized tools. Current cluster performance tools are more oriented towards tightly coupled parallel applications. We describe how the NetLogger Toolkit methodology is more appropriate for this class of cluster computing, and describe our new automatic work flow anomaly detection component. We also describe how this methodology is being used in the Nearby Supernova Factory (SN factory) project at Lawrence Berkeley National Laboratory.