1,977 research outputs found

    Constructing workflows from script applications

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    Constructing workflows from script applications

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    Prospects for Observing an Invisibly Decaying Higgs Boson in the t anti-t H Production at the LHC

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    The prospects for observing an invisibly decaying Higgs boson in the t anti-t H production at LHC are discussed. An isolated lepton, reconstructed hadronic top-quark decay, two identified b-jets and large missing transverse energy are proposed as the final state signature for event selection. Only the Standard Model backgrounds are taken into account. It is shown that the t anti-t Z, t anti-t W, b anti-b Z and b anti-b W backgrounds can individually be suppressed below the signal expectation. The dominant source of background remains the t anti-t production. The key for observability will be an experimental selection which allows further suppression of the contributions from the t anti-t events with one of the top-quarks decaying into a tau lepton. Depending on the details of the final analysis, an excess of the signal events above the Standard Model background of about 10% to 100% can be achieved in the mass range m_H= 100-200 GeV.Comment: Final version as accepted by EPJ

    GridSpace Engine of the ViroLab Virtual Laboratory

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    funcX: A Federated Function Serving Fabric for Science

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    Exploding data volumes and velocities, new computational methods and platforms, and ubiquitous connectivity demand new approaches to computation in the sciences. These new approaches must enable computation to be mobile, so that, for example, it can occur near data, be triggered by events (e.g., arrival of new data), be offloaded to specialized accelerators, or run remotely where resources are available. They also require new design approaches in which monolithic applications can be decomposed into smaller components, that may in turn be executed separately and on the most suitable resources. To address these needs we present funcX---a distributed function as a service (FaaS) platform that enables flexible, scalable, and high performance remote function execution. funcX's endpoint software can transform existing clouds, clusters, and supercomputers into function serving systems, while funcX's cloud-hosted service provides transparent, secure, and reliable function execution across a federated ecosystem of endpoints. We motivate the need for funcX with several scientific case studies, present our prototype design and implementation, show optimizations that deliver throughput in excess of 1 million functions per second, and demonstrate, via experiments on two supercomputers, that funcX can scale to more than more than 130000 concurrent workers.Comment: Accepted to ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC 2020). arXiv admin note: substantial text overlap with arXiv:1908.0490

    Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

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    We apply the hit-to-lead ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and lead-optimization TIES (thermodynamic integration with enhanced sampling) methods to compute the binding free energies of a series of ligands at the A1 and A2A adenosine receptors, members of a subclass of the GPCR (G protein-coupled receptor) superfamily. Our predicted binding free energies, calculated using ESMACS, show a good correlation with previously reported experimental values of the ligands studied. Relative binding free energies, calculated using TIES, accurately predict experimentally determined values within a mean absolute error of approximately 1 kcal mol−1. Our methodology may be applied widely within the GPCR superfamily and to other small molecule–receptor protein systems

    In Situ Proteolysis to Generate Crystals for Structure Determination: An Update

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    For every 100 purified proteins that enter crystallization trials, an average of 30 form crystals, and among these only 13–15 crystallize in a form that enables structure determination. In 2007, Dong et al reported that the addition of trace amounts of protease to crystallization trials—in situ proteolysis—significantly increased the number of proteins in a given set that produce diffraction quality crystals. 69 proteins that had previously resisted structure determination were subjected to crystallization with in situ proteolysis and ten crystallized in a form that led to structure determination (14.5% success rate). Here we apply in situ proteolysis to over 270 new soluble proteins that had failed in the past to produce crystals suitable for structure determination. These proteins had produced no crystals, crystals that diffracted poorly, or produced twinned and/or unmanageable diffraction data. The new set includes yeast and prokaryotic proteins, enzymes essential to protozoan parasites, and human proteins such as GTPases, chromatin remodeling proteins, and tyrosine kinases. 34 proteins yielded deposited crystal structures of 2.8 Å resolution or better, for an overall 12.6% success rate, and at least ten more yielded well-diffracting crystals presently in refinement. The success rate among proteins that had previously crystallized was double that of those that had never before yielded crystals. The overall success rate is similar to that observed in the smaller study, and appears to be higher than any other method reported to rescue stalled protein crystallography projects
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