317 research outputs found

    Seventh Biennial Report : June 2003 - March 2005

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    Sixth Biennial Report : August 2001 - May 2003

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    Data-Driven Rational Drug Design

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    Vast amount of experimental data in structural biology has been generated, collected and accumulated in the last few decades. This rich dataset is an invaluable mine of knowledge, from which deep insights can be obtained and practical applications can be developed. To achieve that goal, we must be able to manage such Big Data\u27\u27 in science and investigate them expertly. Molecular docking is a field that can prominently make use of the large structural biology dataset. As an important component of rational drug design, molecular docking is used to perform large-scale screening of putative associations between small organic molecules and their pharmacologically relevant protein targets. Given a small molecule (ligand), a molecular docking program simulates its interaction with the target protein, and reports the probable conformation of the protein-ligand complex, and the relative binding affinity compared against other candidate ligands. This dissertation collects my contributions in several aspects of molecular docking. My early contribution focused on developing a novel metric to quantify the structural similarity between two protein-ligand complexes. Benchmarks show that my metric addressed several issues associated with the conventional metric. Furthermore, I extended the functionality of this metric to cross different systems, effectively utilizing the data at the proteome level. After developing the novel metric, I formulated a scoring function that can extract the biological information of the complex, integrate it with the physics components, and finally enhance the performance. Through collaboration, I implemented my model into an ultra-fast, adaptive program, which can take advantage of a range of modern parallel architectures and handle the demanding data processing tasks in large scale molecular docking applications

    Physiological and genomic characterization of thermophilic methanotrophic archaea and their partner-bacteria

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    Methane is a potent greenhouse gas and its atmospheric concentration is strongly influenced by microbial processes. In anoxic marine environments 80% of the methane is oxidized by anaerobic microorganisms leading to reduced oceanic methane emissions. This anaerobic oxidation of methane (AOM) is coupled to sulfate reduction and is mediated by microbial consortia of anaerobic methane-oxidizing archaea and partner bacteria. The physiology of the consortia is incompletely understood but is thought to base on a metabolic interdependency of the partners, a syntrophy. The research presented in this PhD thesis focused on the physiology and genomic profile of AOM consortia, in particular on the microorganisms that are active at elevated temperatures (thermophiles). The thermophilic AOM is performed by a unique consortium of ANME-1 archaea and HotSeep-1 bacteria. In Chapter II we describe physiological studies and gene expression experiments with thermophilic AOM consortia and propose a syntrophy of AOM via direct exchange of reducing equivalents. In support of this hypothesis we visualized cell-to-cell connections in these consortia that we suggest to function as conductive nanowires in interspecies electron transfer. For the thermophilic bacterial partner, HotSeep-1 we obtained an ANME-1-free enrichment culture using hydrogen as alternative energy source, and by physiological and genomic investigation we show in Chapter III that this bacterial partner grows as chemolithoautotrophic sulfate reducer. Based on phylogenetic analysis we propose that HotSeep-1 presents a novel species, Candidatus Desulfofervidus auxilii. ANME-1, the archaeon participating in thermophilic AOM, belongs to a large group of uncultured organisms, which are known to have reversed the methanogenesis pathway to metabolize methane. The metabolic diversity among members of the ANME-1 group is still widely unexplored. In a comparative genome analysis of different ANME-1 in Chapter IV we show central aspects of their metabolism including a modified reverse methanogenesis pathway and abundant cytochromes possibly relevant for electron transfer. Environments of AOM activity and in vitro AOM enrichments are dominated by AOM consortia, but other microorganisms sustain as low abundant community whose function is not well understood. In Chapter V we show the cultivation of methanogens and sulfur-disproportionating bacteria from AOM enrichments. In conclusion the work of this PhD thesis has advanced our understanding of the functioning of thermophilic AOM, while further detailed comparative approaches are necessary to comprehend AOM syntrophy in all its detail and diversity

    Performance analysis for parallel programs from multicore to petascale

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    Cutting-edge science and engineering applications require petascale computing. Petascale computing platforms are characterized by both extreme parallelism (systems of hundreds of thousands to millions of cores) and hybrid parallelism (nodes with multicore chips). Consequently, to effectively use petascale resources, applications must exploit concurrency at both the node and system level --- a difficult problem. The challenge of developing scalable petascale applications is only partially aided by existing languages and compilers. As a result, manual performance tuning is often necessary to identify and resolve poor parallel and serial efficiency. Our thesis is that it is possible to achieve unique, accurate, and actionable insight into the performance of fully optimized parallel programs by measuring them with asynchronous-sampling-based call path profiles; attributing the resulting binary-level measurements to source code structure; analyzing measurements on-the-fly and postmortem to highlight performance inefficiencies; and presenting the resulting context- sensitive metrics in three complementary views. To support this thesis, we have developed several techniques for identifying performance problems in fully optimized serial, multithreaded and petascale programs. First, we describe how to attribute very precise (instruction-level) measurements to source-level static and dynamic contexts in fully optimized applications --- all for an average run-time overhead of a few percent. We then generalize this work with the development of logical call path profiling and apply it to work-stealing-based applications. Second, we describe techniques for pinpointing and quantifying parallel inefficiencies such as parallel idleness, parallel overhead and lock contention in multithreaded executions. Third, we show how to diagnose scalability bottlenecks in petascale applications by scaling our our measurement, analysis and presentation tools to support large-scale executions. Finally, we provide a coherent framework for these techniques by sketching a unique and comprehensive performance analysis methodology. This work forms the basis of Rice University's HPCTOOLKIT performance tools

    First International Conference on Laboratory Research for Planetary Atmospheres

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    Proceedings of the First International Conference on Laboratory Research for Planetary Atmospheres are presented. The covered areas of research include: photon spectroscopy, chemical kinetics, thermodynamics, and charged particle interactions. This report contains the 12 invited papers, 27 contributed poster papers, and 5 plenary review papers presented at the conference. A list of attendees and a reprint of the Report of the Subgroup on Strategies for Planetary Atmospheres Exploration (SPASE) are provided in two appendices

    Evolutionary genomics : statistical and computational methods

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    This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

    Articles indexats publicats per investigadors del Campus de Terrassa: 2013

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    Aquest informe recull els 228 treballs publicats per 177 investigadors/es del Campus de Terrassa en revistes indexades al Journal Citation Report durant el 2013Preprin

    41st Rocky Mountain Conference on Analytical Chemistry

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    Final program, abstracts, and information about the 41st annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-sponsored by the Colorado Section of the American Chemical Society and the Rocky Mountain Section of the Society for Applied Spectroscopy. Held in Denver, Colorado, August 1-5, 1999

    Report 2011

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