Showing papers in "Lawrence Berkeley National Laboratory in 2009"

Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections

Abstract: Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections Jeng-Da Chai ∗ and Martin Head-Gordon † Department of Chemistry, University of California and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA (Dated: June 14, 2008) We report re-optimization of a recently proposed long-range corrected (LC) hybrid density func- tionals [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)] to include empirical atom-atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent sys- tems, ωB97X-D shows slight improvement over other empirical dispersion-corrected density func- tionals, while for covalent systems and kinetics, it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions. I. INTRODUCTION Due to its favorable cost-to-performance ratio, Kohn- Sham density-functional theory (KS-DFT) [1, 2] has be- come the most popular electronic structure theory for large-scale ground-state systems [3–5]. Its extension for treating excited-state systems [6, 7], time-dependent den- sity functional theory (TDDFT), has also been developed to the stage where it is now very widely used. The essential ingredient of KS-DFT, the exchange- correlation energy functional E xc , remains unknown and needs to be approximated. Semi-local gradient-corrected density functionals, though successful in many applica- tions, lead to qualitative failures in some circumstances, where the accurate treatment of non-locality of exchange- correlation hole becomes crucial. These situations occur mostly in the asymptotic regions of molecular systems, such as spurious self-interaction effects upon dissociation [8, 9] and dramatic failures for long-range charge-transfer excitations [10–12]. Widely used hybrid density function- als, like B3LYP [13, 14], do not qualitatively resolve these problems. These self-interaction errors can be qualitatively re- solved using the long-range corrected (LC) hybrid density functionals [15, 16, 18], which employ 100% Hartree-Fock (HF) exchange for long-range electron-electron interac- tions. This is accomplished by a partition of unity, using erf(ωr)/r for long-range (treated by HF exchange) and erfc(ωr)/r for short-range (treated by an exchange func- tional), with the parameter ω controlling the partition- ing. Over the past five years, the LC hybrid scheme has been attracting increasing attention [15] since its compu- tational cost is comparable with standard hybrid func- tionals [13]. However, LC functionals have tended to be inferior to the best hybrids for properties such as ther- mochemistry. ∗ Electronic † Author address: jdchai@berkeley.edu to whom correspondence should be addressed. Electronic address: mhg@cchem.berkeley.edu Recently we have improved the overall accuracy at- tainable with the LC functionals by using a systematic optimization procedure [18]. One important conclusion is that optimizing LC and hybrid functionals with identical numbers of parameters in their GGA exchange and cor- relation terms leads to noticeably better results for all properties using the LC form. The resulting LC func- tional is called ωB97. Further statistically significant improvement results from re-optimizing the entire func- tional with one extra parameter corresponding to an ad- justable fraction of short-range exact exchange, defining the ωB97X functional. Independent test sets covering thermochemistry and non-covalent interactions support these conclusions. However, problems associated with the lack of non-locality of the correlation hole, such as the lack of dispersion interactions (London forces), still remain, as the semi-local correlation functionals cannot capture long-range correlation effects [19, 20]. There have been significant efforts to develop a frame- work that can account for long-range dispersion effects within DFT. Zaremba and Kohn (ZK) [21] derived an exact expression for the second-order dispersion energy in terms of the exact density-density response functions of the two separate systems. To obtain a tractable non- local dispersion functional, Dobson and Dinite (DD) [22] made local density approximations to the ZK response functions. DD’s non-local correlation functional was ob- tained independently [23] by modifying the effective den- sity defined in the earlier work of Rapcewicz and Ashcroft Starting from the formally exact expression of KS- DFT, the adiabatic connection fluctuation-dissipation theorem (ACFDT), for the ground-state exchange- correlation energy, Langreth and co-workers [25] devel- oped a so-called van der Waals density functional (vdW- DF) by making a series of reasonable approximations to yield a computationally tractable scheme. Recently, Becke and Johnson (BJ) developed a series of post-HF correlation models with a novel treatment for dispersion interactions based on the exchange-hole dipole moment [26]. The origin of dispersion claimed in the BJ models was recently questioned by Alonso, and A.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor

Abstract: PLoS BIOLOGY Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor Jean-Philippe Coppe 1 , Christopher K. Patil 1[ , Francis Rodier 1,2[ , Yu Sun 3 , Denise P. Mun oz 1,2 , Joshua Goldstein 1¤ , Peter S. Nelson 3 , Pierre-Yves Desprez 1,4 , Judith Campisi 1,2* 1 Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, 2 Buck Institute for Age Research, Novato, California, United States of America, 3 Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America, 4 California Pacific Medical Center Research Institute, San Francisco, California, United States of America Cellular senescence suppresses cancer by arresting cell proliferation, essentially permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the use of antibody arrays to provide a quantitative assessment of factors secreted by senescent cells. We show that human cells induced to senesce by genotoxic stress secrete myriad factors associated with inflammation and malignancy. This senescence-associated secretory phenotype (SASP) developed slowly over several days and only after DNA damage of sufficient magnitude to induce senescence. Remarkably similar SASPs developed in normal fibroblasts, normal epithelial cells, and epithelial tumor cells after genotoxic stress in culture, and in epithelial tumor cells in vivo after treatment of prostate cancer patients with DNA- damaging chemotherapy. In cultured premalignant epithelial cells, SASPs induced an epithelial–mesenchyme transition and invasiveness, hallmarks of malignancy, by a paracrine mechanism that depended largely on the SASP factors interleukin (IL)-6 and IL-8. Strikingly, two manipulations markedly amplified, and accelerated development of, the SASPs: oncogenic RAS expression, which causes genotoxic stress and senescence in normal cells, and functional loss of the p53 tumor suppressor protein. Both loss of p53 and gain of oncogenic RAS also exacerbated the promalignant paracrine activities of the SASPs. Our findings define a central feature of genotoxic stress-induced senescence. Moreover, they suggest a cell-nonautonomous mechanism by which p53 can restrain, and oncogenic RAS can promote, the development of age-related cancer by altering the tissue microenvironment. Citation: Coppe JP, Patil CK, Rodier F, Sun Y, Mun oz DP, et al. (2008) Senescence-associated secretory phenotypes reveal cell-nonautonomous functions of oncogenic RAS and the p53 tumor suppressor. PLoS Biol 6(12): e301. doi:10.1371/journal.pbio.0060301 Introduction Cancer is a multistep disease in which cells acquire increasingly malignant phenotypes. These phenotypes are acquired in part by somatic mutations, which derange normal controls over cell proliferation (growth), survival, invasion, and other processes important for malignant tumorigenesis [1]. In addition, there is increasing evidence that the tissue microenvironment is an important determinant of whether and how malignancies develop [2,3]. Normal tissue environ- ments tend to suppress malignant phenotypes, whereas abnormal tissue environments such at those caused by inflammation can promote cancer progression. Cancer development is restrained by a variety of tumor suppressor genes. Some of these genes permanently arrest the growth of cells at risk for neoplastic transformation, a process termed cellular senescence [4–6]. Two tumor suppressor pathways, controlled by the p53 and p16INK4a/pRB proteins, regulate senescence responses. Both pathways integrate multiple aspects of cellular physiology and direct cell fate towards survival, death, proliferation, or growth arrest, depending on the context [7,8]. Several lines of evidence indicate that cellular senescence is a potent tumor-suppressive mechanism [4,9,10]. Many poten- tially oncogenic stimuli (e.g., dysfunctional telomeres, DNA PLoS Biology | www.plosbiology.org damage, and certain oncogenes) induce senescence [6,11]. Moreover, mutations that dampen the p53 or p16INK4a/pRB pathways confer resistance to senescence and greatly increase cancer risk [12,13]. Most cancers harbor mutations in one or both of these pathways [14,15]. Lastly, in mice and humans, a senescence response to strong mitogenic signals, such as those delivered by certain oncogenes, prevents premalignant lesions from progressing to malignant cancers [16–19]. Academic Editor: Julian Downward, Cancer Research UK, United Kingdom Received June 27, 2008; Accepted October 22, 2008; Published December 2, 2008 Copyright: O 2008 Coppe et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abbreviations: CM, conditioned medium; DDR, DNA damage response; ELISA, enzyme-linked immunosorbent assay; EMT, epithelial–mesenchymal transition; GSE, genetic suppressor element; IL, interleukin; MIT, mitoxantrone; PRE, presenescent; PrEC, normal human prostate epithelial cell; REP, replicative exhaustion; SASP, senescence-associated secretory phenotype; SEN, senescent; shRNA, short hairpin RNA; XRA, X-irradiation * To whom correspondence should be addressed. E-mail: jcampisi@lbl.gov [ These authors contributed equally to this work. ¤ Current address: Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America December 2008 | Volume 6 | Issue 12 | e301

Tough, bio-inspired hybrid materials

Abstract: Tough, bio-inspired hybrid materials E. Munch, 1 M. E. Launey, 1 D. H. Alsem, 1,2 E. Saiz, 1 A.P. Tomsia, 1 R. O. Ritchie 1,3∗ The notion of mimicking natural structures in the synthesis of new structural materials has generated enormous interest but has yielded few practical advances. Natural composites achieve strength and toughness through complex hierarchical designs extremely difficult to replicate synthetically. Here we emulate Nature’s toughening mechanisms through the combination of two ordinary compounds, aluminum oxide and polymethylmethacrylate, into ice-templated structures whose toughness can be over 300 times (in energy terms) that of their constituents. The final product is a bulk hybrid ceramic material whose high yield strength and fracture toughness (~200 MPa and ~30 MPa√m) provide specific properties comparable to aluminum alloys. These model materials can be used to identify the key microstructural features that should guide the synthesis of bio-inspired ceramic-based composites with unique strength and toughness. With the quest for more efficient energy-related technologies, there is an imperative to develop lightweight, high-performance structural materials that possess both exceptional strength and toughness. Unfortunately, these two properties tend to be mutually exclusive and the attainment of optimal mechanical performance is invariably a compromise often achieved through the empirical design of microstructures. Nature has long developed the ability to combine brittle minerals and organic molecules into hybrid composites with exceptional fracture resistance and structural capabilities (1-3); indeed, many natural materials like bone, wood and nacre (abalone shell) have highly sophisticated structures with complex hierarchical designs whose properties are far in excess what could be expected from a simple mixture of their components (2,4). Biological mineralized composites, in particular bone, dentin and nacre (5-7), can generate fracture toughness (i.e., resistance to the initiation and growth of a crack) primarily by extrinsic toughening mechanisms (8) that “shield” any crack from the applied loads. These mechanisms, which are quite different to those that toughen metals for Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA Department of Materials Science and Engineering, University of California, Berkeley, California, 94720, USA To whom correspondence should be addressed. E-mail: roritchie@lbl.gov

Nanostructured Cobalt Oxide Clusters in Mesoporous Silica as Efficient Oxygen-Evolving Catalysts

Abstract: Author(s): Jiao, Feng | Abstract: The development of integrated artificial photosynthetic systems for the direct conversion of carbon dioxide and water to fuel depends on the availability of efficient and robust catalysts for the chemical transformations. Catalysts need to exhibit turnover frequency (TOF) and density (hence size) commensurate with the solar flux at ground level (1000Wm2, airmass (AM) 1.5)[1] to avoid wasting of incident solar photons. For example, a catalyst with a TOF of 100 s1 requires a density of one catalytic site per square nanometer. Catalysts with lower rates or taking up a larger space will require a high-surface-area, nanostructured support that affords tens to hundreds of catalytic sites per square nanometer. Furthermore, catalysts need to operate close to the thermodynamic potential of the redox reaction so that a maximum fraction of the solar photon energy is converted to chemical energy. Stability considerations favor all-inorganic oxide materials, as does avoidance of harsh reaction conditions of pH value or temperature.

Pyramidal and Chiral Groupings of Gold Nanocrystals Assembled Using DNA Scaffolds

Abstract: Nanostructures constructed from metal and semiconductor nanocrystals conjugated to, and organized by DNA are an emerging class of material with collective optical properties. We created discrete pyramids of DNA with gold nanocrystals at the tips. By taking small angle X-ray scattering (SAXS) measurments from solutions of these pyramids we confirmed that this pyramidal geometry creates structures which are more rigid in solution than linear DNA. We then took advantage of the tetrahedral symmetry to demonstrate construction of chiral nanostructures.

Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms

Abstract: We are witnessing a dramatic change in computer architecture due to the multicore paradigm shift, as every electronic device from cell phones to supercomputers confronts parallelism of unprecedented scale. To fully unleash the potential of these systems, the HPC community must develop multicore specific-optimization methodologies for important scientific computations. In this work, we examine sparse matrix-vector multiply (SpMV) - one of the most heavily used kernels in scientific computing - across a broad spectrum of multicore designs. Our experimental platform includes the homogeneous AMD quad-core, AMD dual-core, and Intel quad-core designs, the heterogeneous STI Cell, as well as one of the first scientific studies of the highly multithreaded Sun Victoria Falls (a Niagara2 SMP). We present several optimization strategies especially effective for the multicore environment, and demonstrate significant performance improvements compared to existing state-of-the-art serial and parallel SpMV implementations. Additionally, we present key insights into the architectural trade-offs of leading multicore design strategies, in the context of demanding memory-bound numerical algorithms.

The Limits of Quintessence

Abstract: We present evidence that the simplest particle-physics scalar-field models of dynamical dark energy can be separated into distinct behaviors based on the acceleration or deceleration of the field as it evolves down its potential towards a zero minimum. We show that these models occupy narrow regions in the phase-plane of w and w', the dark energy equation-of-state and its time-derivative in units of the Hubble time. Restricting an energy scale of the dark energy microphysics limits how closely a scalar field can resemble a cosmological constant. These results, indicating a desired measurement resolution of order \sigma(w')\approx (1+w), define firm targets for observational tests of the physics of dark energy.

IMG ER: A System for Microbial Genome Annotation Expert Review and Curation

Abstract: IMG ER: A System for Microbial Genome Annotation Expert Review and Curation Victor M. Markowitz 1, *, Konstantinos Mavromatis 2 , Natalia N. Ivanova 2 , I-Min A. Chen 1 , Ken Chu 1 , and Nikos C. Kyrpides 2 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA Genome Biology Program , DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA 94598, USA ABSTRACT A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG’s rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER’s annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG’s comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes. INTRODUCTION A rapidly increasing number of microbial genomes are sequenced by organizations worldwide, undergo similar annotation procedures, and are eventually included into public genome data resources. First, raw (“read”) sequences of microbial genomes are assembled into longer “contigs” (contiguous sequences) in order to produce “draft” genome sequences, with draft genomes sometimes “finished” by closing gaps between contigs. Next, annotation pipelines are used for predicting genes and determining their functional roles in draft or finished genomes. Subsequently, annotated microbial genome sequences are submitted to/collected by primary archival public sequence data repositories, such as Genbank (Benson et al. 2009), which perform data validation on genome datasets in order to ensure consistency of their format and, to a certain degree, their content. Datasets in these resources have different degrees of precision and resolution due to diverse annotation methods employed by individual data providers. Secondary public resources, such as NCBI’s RefSeq (Pruitt et al. 2007), further process microbial genome data from primary resources with the dual goals of providing the most current view on microbial genome sequences and of gradually increasing the quality and completeness of their associated functional annotations via manual curation and computation. In addition to public primary and secondary resources, microbial genome datasets are incorporated into a variety of tertiary resources, such as SEED (Overbeek et al. 2005) and IMG To whom correspondence should be addressed.

Formic Acid Dehydrogenation on Au-Based Catalysts at Near-Ambient Temperatures

Abstract: Accepted for publication in Angewandte Chemie Formic Acid Dehydrogenation on Au-Based Catalysts at Near-Ambient Temperatures Manuel Ojeda and Enrique Iglesia* Department of Chemical Engineering, University of California and Chemical Sciences Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA * corresponding author (iglesia@berkeley.edu)

Colloid Science of Metal Nanoparticle Catalysts in 2D and 3D Structures. Challenges of Nucleation, Growth, Composition, Particle Shape, Size Control and their Influence on Activity and Selectivity

Abstract: Colloid Science of Metal Nanoparticle Catalysts in 2D and 3D Structures. Challenges of Nucleation, Growth, Composition, Particle Shape, Size Control and their Influence on Activity and Selectivity Gabor A. Somorjai 1, 2, * and Jeong Y. Park 1, 2 Department of Chemistry, University of California, Berkeley, CA 94720 Materials Sciences Division and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 To whom correspondence should be addressed. E-mail: somorjai@berkeley.edu. Recent breakthroughs in synthesis in nanosciences have achieved control of size and shapes of nanoparticles that are relevant for catalyst design. In this article, we review the advance of synthesis of nanoparticles, fabrication of two and three dimensional model catalyst system, characterization, and studies of activity and selectivity. The ability to synthesize monodispersed platinum and rhodium nanoparticles in the 1-10 nm range permitted us to study the influence of composition, structure, and dynamic properties of monodispersed metal nanoparticle on chemical reactivity and selectivity. We review the importance of size and shape of nanoparticles to determine the reaction selectivity in multi-path reactions. The influence of metal-support interaction has been studied by probing the hot electron flows through the metal-oxide interface in catalytic nanodiodes. Novel designs of nanoparticle catalytic systems are discussed.

Cooling our Communities. A Guidebook on Tree Planting and Light-Colored Surfacing

Abstract: United States Environmental Agency Protection Policy, Planning And Evaluation (PM-221) 22P.2001 January 1992 EPA __t CoolingOur Communities A Guidebook On Tree Planting And Light-ColoredSurfacing

Voro++: a three-dimensional Voronoi cell library in C++

Abstract: Voro++ is a free software library for the computation of three dimensional Voronoi cells. It is primarily designed for applications in physics and materials science, where the Voronoi tessellation can be a useful tool in the analysis of densely-packed particle systems, such as granular materials or glasses. The software comprises of several C++ classes that can be modified and incorporated into other programs. A command-line utility is also provided that can use most features of the code. Voro++ makes use of a direct cell-by-cell construction, which is particularly suited to handling special boundary conditions and walls. It employs algorithms which are tolerant for numerical precision errors, and it has been successfully employed on very large particle systems.

Structure Sensitivity of Carbon-Nitrogen Ring Opening: Impact of Platinum Particle Size from below 1 to 5 nm upon Pyrrole Hydrogenation Product Selectivity over Monodisperse Platinum Nanoparticles Loaded onto Mesoporous Silica

Abstract: Structure Sensitivity of Carbon-Nitrogen Ring Opening: Impact of Platinum Particle Size from below 1 to 5 nm upon Pyrrole Hydrogenation Product Selectivity over Monodisperse Platinum Nanoparticles Loaded onto Mesoporous Silica John N. Kuhn, Wenyu Huang, Chia-Kuang Tsung, Yawen Zhang, ‡ and Gabor A. Somorjai* Department of Chemistry, University of California, Berkeley, California 94720 and the Chemical and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 ‡ College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. RECEIVED DATE (automatically inserted by publisher); *E-mail: somorjai@berkeley.edu The ability to control fundamental properties (e.g., particle size, surface structure, and metal-oxide interface) in order to design highly selective heterogeneous catalysts would greatly reduce energy intensive separations. Particle size dependence (i.e., structure sensitivity) upon selectivity can now be examined with well defined nanoparticles (NPs) because of advances in synthetic chemistry. Colloidal chemistry has provided means for synthesizing monodisperse Pt NPs as small as ~2 nm. 1,2 Using a dendrimer templated approach, Pt NPs smaller than 1 nm – a new size regime for studying size induced effects in heterogeneous catalysis – can be synthesized (Scheme 1). 3,4 In this contribution, we report that ring opening for pyrrole hydrogenation is distinctly different for Pt NPs smaller than 2 nm. This insight has not been demonstrated for hydrogenation of cyclic heteroatom bonds to the best of our knowledge. This finding adds fundamental insight into hydrodenitrogenation (HDN) chemistry, which is important for fuel processing and involves removal of N-containing organics. Advances in HDN catalysis are needed to meet new fuel quality regulations because N-containing organics inhibit hydrodesulfurization (HDS) through competitive adsorption 5 and poison acid catalysts 6 , which are used for downstream processing and as supports for HDS catalysts. Pyrrole was selected as the reactant because organics with 5-member N-containing rings are the most common components in fuel. 7,8 Scheme 1. Strategy for Pt NP size control. from the Pt ion to dendrimer ratio and is caused by formation of interdendrimer complexes because the number of Pt atoms per dendrimer approached the number (62) of available internal tertiary amine groups. Pt NPs (1.5, 2.9, and 5.0 nm) were synthesized with polyvinylpyrolidone (PVP) by existing procedures 1,2 with a TEM image in Figure 1b for 5.0 nm Pt NPs. Figure 1. TEM images for (a) dendrimer-templated 2.0 nm Pt, (b) PVP capped 5.0 nm Pt, and (c) PVP capped 1.5 nm Pt loaded onto SBA-15. Pt NPs between 0.8 and 5.0 nm were synthesized by two techniques. For ultrasmall NPs, fourth generation hydroxyl terminated polyamidoamine (PAMAM) dendrimers were used as the templating and capping agent. 4 Synthesis and characterization of Pt 20 and Pt 40 NPs (subscripts denote the average number of metal atoms per NP) have been described. 4,9 The average number of metal atoms per NP is controlled by the Pt ion to dendrimer ratio. Due to difficulties in obtaining accurate size distributions from TEM, sizes were calculated from the average number of metal ions added per dendrimer, which was proven as accurate by X-ray absorption studies. 10 Sizes of Pt 20 and Pt 40 NPs were calculated to be 0.8 and 1.0 nm, respectively. 11 A TEM image (Figure 1a) of the Pt 60 NPs showed that the Pt size was 1.95 ± 0.27 nm. This size is larger than that expected Pt NPs were loaded onto SBA-15 silica (TEM image in Figure 1c for 1.5 nm Pt NPs). For PVP capped NPs, H 2 chemisorption indicated that Pt dispersion decreased as the NP size increased (Table S1). However, reliable dispersion measurements could not be obtained by this method for dendrimer encapsulated Pt NPs so ethylene hydrogenation, a structure insensitive reaction 12-15 , was performed to demonstrate an available catalytic surface (Table S1). Although the TOFs of smaller Pt NPs were comparable to results acquired over model Pt surfaces, these values were lower than those of the larger Pt NPs. This effect was attributed to reduction being more difficult for smaller NPs, which led to less metallic character necessary for activity, and may be caused by the dendrimer covering more of the Pt surface than PVP. 16 As shown in Table S2, steady-state TOFs for hydrogenation of pyrrole (Scheme 2) are presented at equal pyrrole conversions (11±2%), which is necessary for selectivity comparisons. TOFs

FastBit: interactively searching massive data

Abstract: As scientific instruments and computer simulations produce more and more data, the task of locating the essential information to gain insight becomes increasingly difficult. FastBit is an efficient software tool to address this challenge. In this article, we present a summary of the key underlying technologies, namely bitmap compression, encoding, and binning. Together these techniques enable FastBit to answer structured (SQL) queries orders of magnitude faster than popular database systems. To illustrate how FastBit is used in applications, we present three examples involving a high-energy physics experiment, a combustion simulation, and an accelerator simulation. In each case, FastBit significantly reduces the response time and enables interactive exploration on terabytes of data.

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

Abstract: We present a new lock-free parallel algorithm for computing betweenness centrality of massive small-world networks. With minor changes to the data structures, our algorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in HPCS SSCA#2, a benchmark extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the Threadstorm processor, and a single-socket Sun multicore server with the UltraSPARC T2 processor. For a small-world network of 134 million vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.

Storage and Turnover of Organic Matter in Soil

Abstract: Historically, attention on soil organic matter (SOM) has focused on the central role that it plays in ecosystem fertility and soil properties, but in the past two decades the role of soil organic carbon in moderating atmospheric CO{sub 2} concentrations has emerged as a critical research area. This chapter will focus on the storage and turnover of natural organic matter in soil (SOM), in the context of the global carbon cycle. Organic matter in soils is the largest carbon reservoir in rapid exchange with atmospheric CO{sub 2}, and is thus important as a potential source and sink of greenhouse gases over time scales of human concern (Fischlin and Gyalistras 1997). SOM is also an important human resource under active management in agricultural and range lands worldwide. Questions driving present research on the soil C cycle include: Are soils now acting as a net source or sink of carbon to the atmosphere? What role will soils play as a natural modulator or amplifier of climatic warming? How is C stabilized and sequestered, and what are effective management techniques to foster these processes? Answering these questions will require a mechanistic understanding of how and where C is stored in soils. The quantitymore » and composition of organic matter in soil reflect the long-term balance between plant carbon inputs and microbial decomposition, as well as other loss processes such as fire, erosion, and leaching. The processes driving soil carbon storage and turnover are complex and involve influences at molecular to global scales. Moreover, the relative importance of these processes varies according to the temporal and spatial scales being considered; a process that is important at the regional scale may not be critical at the pedon scale. At the regional scale, SOM cycling is influenced by factors such as climate and parent material, which affect plant productivity and soil development. More locally, factors such as plant tissue quality and soil mineralogy affect decomposition pathways and stabilization. These factors influence the stability of SOM in part by shaping its molecular characteristics, which play a fundamental role in nearly all processes governing SOM stability but are not the focus of this chapter. We review here the most important controls on the distribution and dynamics of SOM at plot to global scales, and methods used to study them. We also explore the concepts of controls, processes, and mechanisms, and how they operate across scales. The concept of SOM turnover, or mean residence time, is central to this chapter and so it is described in some detail. The Appendix details the use of radiocarbon ({sup 14}C), a powerful isotopic tool for studying SOM dynamics. Much of the material here was originally presented at a NATO Advanced Study Institute on 'Soils and Global Change: Carbon Cycle, Trace Gas Exchange and Hydrology', held June 16-27, 1997, at the Chateau de Bonas, France.« less

Small Neutrino Masses from Supersymmetry Breaking

Abstract: An alternative to the conventional see-saw mechanism is proposed to explain the origin of small neutrino masses in supersymmetric theories. The masses and couplings of the right-handed neutrino field are suppressed by supersymmetry breaking, in a way similar to the suppression of the Higgs doublet mass, $\mu$. New mechanisms for light Majorana, Dirac and sterile neutrinos arise, depending on the degree of suppression. Superpartner phenomenology is greatly altered by the presence of weak scale right-handed sneutrinos, which may have a coupling to a Higgs boson and a left-handed sneutrino. The sneutrino spectrum and couplings are quite unlike the conventional case - the lightest sneutrino can be the dark matter and predictions are given for event rates at upcoming halo dark matter direct detection experiments. Higgs decays and search strategies are changed. Copious Higgs production at hadron colliders can result from cascade decays of squarks and gluinos.

LHC Signals from Warped Extra Dimensions

Abstract: We study production of Kaluza-Klein gluons (KKG) at the Large Hadron Collider (LHC) in the framework of a warped extra dimension with the Standard Model (SM) fields propagating in the bulk. We show that the detection of KK gluon is challenging since its production is suppressed by small couplings to the proton's constituents. Moreover, the KK gluon decaysmostly to top pairs due to an enhanced coupling and hence is broad. Nevertheless, we demonstrate that for MKKG <~;; 4 TeV, 100 fb-1 of data at the LHC can provide discovery of the KK gluon. We utilize a sizeable left-right polarization asymmetry from the KK gluon resonance to maximize the signal significance, and we explore the novel feature of extremely highly energetic top-jets. We briefly discuss how the detection of electroweak gauge KK states (Z/W) faces a similar challenge since their leptonic decays ( golden modes) are suppressed. Our analysis suggests that other frameworks, for example little Higgs, which rely on UV completion via strong dynamics might face similar challenges, namely (1) Suppressed production rates for the new particles (such as Z'), due to their lightfermion-phobic nature, and (2) Difficulties in detection since the new particles are broad and decay predominantly to third generation quarks and longitudinal gauge bosons.

Estimated Value of Service Reliability for Electric Utility Customers in the United States

Abstract: Information on the value of reliable electricity service can be used to assess the economic efficiency of investments in generation, transmission and distribution systems, to strategically target investments to customer segments that receive the most benefit from system improvements, and to numerically quantify the risk associated with different operating, planning and investment strategies. This paper summarizes research designed to provide estimates of the value of service reliability for electricity customers in the US. These estimates were obtained by analyzing the results from 28 customer value of service reliability studies conducted by 10 major US electric utilities over the 16 year period from 1989 to 2005. Because these studies used nearly identical interruption cost estimation or willingness-to-pay/accept methods it was possible to integrate their results into a single meta-database describing the value of electric service reliability observed in all of them. Once the datasets from the various studies were combined, a two-part regression model was used to estimate customer damage functions that can be generally applied to calculate customer interruption costs per event by season, time of day, day of week, and geographical regions within the US for industrial, commercial, and residential customers. Estimated interruption costs for different types of customers and of different duration are provided. Finally, additional research and development designed to expand the usefulness of this powerful database and analysis are suggested.

A bacterial metapopulation adapts locally to phage predation despite global dispersal

Abstract: Bacterial metapopulation dispersal and adaptation Kunin et al A bacterial metapopulation adapts locally to phage predation despite global dispersal Victor Kunin 1 , Shaomei He 2 , Falk Warnecke 1 , S. Brook Peterson 3 , Hector Garcia Martin 1 , Matthew Haynes 4 , Natalia Ivanova 3 , Linda L. Blackall 5 , Mya Breitbart 6 , Forest Rohwer 4 , Katherine D. McMahon 2 and Philip Hugenholtz 1 Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, USA. Department of Civil and Environmental Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, USA. Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, USA. Department of Biology, San Diego State University, CA, USA. Advanced Wastewater Management Centre, University of Queensland, St Lucia, 4072, Queensland, AUSTRALIA. University of South Florida, St. Petersburg, Florida, United States of America Corresponding author: fax 925-296-5720 • email: phugenholtz@lbl.gov

The Minimal Supersymmetric Fat Higgs Model

Abstract: We present a calculable supersymmetric theory of a composite fat' Higgs boson. Electroweak symmetry is broken dynamically through a new gauge interaction that becomes strong at an intermediate scale. The Higgs mass can easily be 200-450 GeV along with the superpartner masses, solving the supersymmetric little hierarchy problem. We explicitly verify that the model is consistent with precision electroweak data without fine-tuning. Gauge coupling unification can be maintained despite the inherently strong dynamics involved in electroweak symmetry breaking. Supersymmetrizing the Standard Model therefore does not imply a light Higgs mass, contrary to the lore in the literature. The Higgs sector of the minimal Fat Higgs model has a mass spectrum that is distinctly different from the Minimal Supersymmetric Standard Model.

Open Automated Demand Response Communications Specification (Version 1.0)

Abstract: The development of the Open Automated Demand Response Communications Specification, also known as OpenADR or Open Auto-DR, began in 2002 following the California electricity crisis. The work has been carried out by the Demand Response Research Center (DRRC), which is managed by Lawrence Berkeley National Laboratory. This specification describes an open standards-based communications data model designed to facilitate sending and receiving demand response price and reliability signals from a utility or Independent System Operator to electric customers. OpenADR is one element of the Smart Grid information and communications technologies that are being developed to improve optimization between electric supply and demand. The intention of the open automated demand response communications data model is to provide interoperable signals to building and industrial control systems that are preprogrammed to take action based on a demand response signal, enabling a demand response event to be fully automated, with no manual intervention. The OpenADR specification is a flexible infrastructure to facilitate common information exchange between the utility or Independent System Operator and end-use participants. The concept of an open specification is intended to allow anyone to implement the signaling systems, the automation server or the automation clients.

Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts

Abstract: We used molecular techniques to analyze basalts of varying ages that were collected from the East Pacific Rise, 9 oN, from the rift axis of the Juan de Fuca Ridge, and from neighboring seamounts. Cluster analysis of 16S rDNA Terminal Restriction Fragment Polymorphism data revealed that basalt endoliths are distinct from seawater and that communities clustered, to some degree, based on the age of the host rock. This age-based clustering suggests that alteration processes may affect community structure. Cloning and sequencing of bacterial and archaeal 16S rRNA genes revealed twelve different phyla and sub-phyla associated with basalts. These include the Gemmatimonadetes, Nitrospirae, the candidate phylum SBR1093 in the c, and in the Archaea Marine Benthic Group B, none of which have been previously reported in basalts. We delineated novel ocean crust clades in the gamma-Proteobacteria, Planctomycetes, and Actinobacteria that are composed entirely of basalt associated microflora, and may represent basalt ecotypes. Finally, microarray analysis of functional genes in basalt revealed that genes coding for previously unreported processes such as carbon fixation, methane-oxidation, methanogenesis, and nitrogen fixation are present, suggesting that basalts harbor previously unrecognized metabolic diversity. These novel processes could exert a profound influence on ocean chemistry.

The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens

Abstract: Background: The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. Results: The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE) regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes. Conclusion: The genomic evidence suggests that metabolism, physiology and regulation of gene expression in G. metallireducens may be dramatically different from other Geobacteraceae.

Evolution of porosity and diffusivity associated with chemical weathering of a basalt clast

Abstract: Evolution of porosity and diffusivity associated with chemical weathering of a basalt clast Alexis Navarre-Sitchler 1,3* Carl Steefel 2,3 , Li Yang 2,3 , Liviu Tomutsa 2 , Susan Brantley 3,4 Corresponding Author: alexis.sitchler@uwyo.edu Department of Geology and Geophysics, The University of Wyoming, Laramie WY 82071 Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA Center for Environmental Kinetics Analysis, The Pennsylvania State University, University Park PA 16802 Earth and Environmental Systems Institute, The Pennsylvania State University, University Park PA 16802

Laboratory Investigations of a Low-Swirl Injector with H2 and CH4 at Gas Turbine Conditions

Abstract: Laboratory Investigations of a Low-swirl Injector with H 2 and CH 4 at Gas Turbine Conditions R. K. Cheng and D. Littlejohn Environmental Energy Technologies Division Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA P.A. Strakey and T. Sidwell National Energy Technology Laboratory Morgantown, WV Abstract Laboratory experiments were conducted at gas turbine and atmospheric conditions (0.101 < P 0 < 0.810 MPa, 298 < T 0 < 580K, 18 < U 0 < 60 m/s) to characterize the overall behaviors and emissions of the turbulent premixed flames produced by a low-swirl injector (LSI) for gas turbines. The objective was to investigate the effects of hydrogen on the combustion processes for the adaptation to gas turbines in an IGCC power plant. The experiments at high pressures and temperatures showed that the LSI can operate with 100% H 2 at up to φ = 0.5 and has a slightly higher flashback tolerance than an idealized high-swirl design. With increasing H 2 fuel concentration, the lifted LSI flame begins to shift closer to the exit and eventually attaches to the nozzle rim and assumes a different shape at 100% H 2 . The STP experiments show the same phenomena. The analysis of velocity data from PIV shows that the stabilization mechanism of the LSI remains unchanged up to 60% H 2 . The change in the flame position with increasing H 2 concentration is attributed to the increase in the turbulent flame speed. The NO x emissions show a log linear dependency on the adiabatic flame temperature and the concentrations are similar to those obtained previously in a LSI prototype developed for natural gas. These results show that the LSI exhibits the same overall behaviors at STP and at gas turbine conditions. Such insight will be useful for scaling the LSI to operate at IGCC conditions.

Substructure of High-pT Jets at the LHC

Abstract: Substructure of high-pT Jets at the LHC Leandro G. Almeida, Seung J. Lee, Gilad Perez, Ilmo Sung & Joseph Virzi This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or The Regents of the University of California.

Change in cell shape is required for matrix metalloproteinase-induced epithelial-mesenchymal transition of mammary epithelial cells

Abstract: Change in cell shape is required for matrix metalloproteinase-induced epithelial- mesenchymal transition of mammary epithelial cells Celeste M. Nelson 1,2,* , Davitte Khauv 3 , Mina J. Bissell 1, & Derek C. Radisky 3,* Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Chemical Engineering, Princeton University, Princeton, NJ 08544 Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, FL 32224 *Correspondence to Celeste M. Nelson (celesten@princeton.edu) and Derek C. Radisky (radisky.derek@mayo.edu). Running head: MMP3-induced EMT requires altered cell shape. Keywords: Cell morphology; cell spreading; matrix metalloproteinase; epithelial- mesenchymal transition; Rac1b; TGFβ; micropatterned substrata; mammary epithelial cells; reactive oxygen species Number of figures: 5 Abbreviations: EMT, epithelial-mesenchymal transition; MMP, matrix metalloproteinase; TGF-β, transforming growth factor-β; NAC, N-acetyl cysteine; ROS, reactive oxygen species.

Holographic Protection of Chronology in Universes of the Godel Type

Abstract: We analyze the structure of supersymmetric Godel-like cosmological solutions of string theory Just as the original four-dimensional Godel universe, these solutions represent rotating, topologically trivial cosmologies with a homogeneous metric and closed timelike curves First we focus on phenomenological aspects of holography, and identify the preferred holographic screens associated with inertial comoving observers in Godel universes We find that holography can serve as a chronology protection agency: The closed timelike curves are either hidden behind the holographic screen, or broken by it into causal pieces In fact, holography in Godel universes has many features in common with de Sitter space, suggesting that Godel universes could represent a supersymmetric laboratory for addressing the conceptual puzzles of de Sitter holography Then we initiate the investigation of microscopic aspects of holography of Godel universes in string theory We show that Godel universes are T-dual to pp-waves, and use this fact to generate new Godel-like solutions of string and M-theory by T-dualizing known supersymmetric pp-wave solutions