1,091 research outputs found
Processor Allocation for Optimistic Parallelization of Irregular Programs
Optimistic parallelization is a promising approach for the parallelization of
irregular algorithms: potentially interfering tasks are launched dynamically,
and the runtime system detects conflicts between concurrent activities,
aborting and rolling back conflicting tasks. However, parallelism in irregular
algorithms is very complex. In a regular algorithm like dense matrix
multiplication, the amount of parallelism can usually be expressed as a
function of the problem size, so it is reasonably straightforward to determine
how many processors should be allocated to execute a regular algorithm of a
certain size (this is called the processor allocation problem). In contrast,
parallelism in irregular algorithms can be a function of input parameters, and
the amount of parallelism can vary dramatically during the execution of the
irregular algorithm. Therefore, the processor allocation problem for irregular
algorithms is very difficult.
In this paper, we describe the first systematic strategy for addressing this
problem. Our approach is based on a construct called the conflict graph, which
(i) provides insight into the amount of parallelism that can be extracted from
an irregular algorithm, and (ii) can be used to address the processor
allocation problem for irregular algorithms. We show that this problem is
related to a generalization of the unfriendly seating problem and, by extending
Tur\'an's theorem, we obtain a worst-case class of problems for optimistic
parallelization, which we use to derive a lower bound on the exploitable
parallelism. Finally, using some theoretically derived properties and some
experimental facts, we design a quick and stable control strategy for solving
the processor allocation problem heuristically.Comment: 12 pages, 3 figures, extended version of SPAA 2011 brief announcemen
STITCH 4: integration of protein-chemical interactions with user data
STITCH is a database of protein-chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions. Available at http://stitch.embl.de, the resulting interaction network includes 390 000 chemicals and 3.6 million proteins from 1133 organisms. Compared with the previous version, the number of high-confidence protein-chemical interactions in human has increased by 45%, to 367 000. In this version, we added features for users to upload their own data to STITCH in the form of internal identifiers, chemical structures or quantitative data. For example, a user can now upload a spreadsheet with screening hits to easily check which interactions are already known. To increase the coverage of STITCH, we expanded the text mining to include full-text articles and added a prediction method based on chemical structures. We further changed our scheme for transferring interactions between species to rely on orthology rather than protein similarity. This improves the performance within protein families, where scores are now transferred only to orthologous proteins, but not to paralogous proteins. STITCH can be accessed with a web-interface, an API and downloadable files
Diffusion of gold nanoclusters on graphite
We present a detailed molecular-dynamics study of the diffusion and
coalescence of large (249-atom) gold clusters on graphite surfaces. The
diffusivity of monoclusters is found to be comparable to that for single
adatoms. Likewise, and even more important, cluster dimers are also found to
diffuse at a rate which is comparable to that for adatoms and monoclusters. As
a consequence, large islands formed by cluster aggregation are also expected to
be mobile. Using kinetic Monte Carlo simulations, and assuming a proper scaling
law for the dependence on size of the diffusivity of large clusters, we find
that islands consisting of as many as 100 monoclusters should exhibit
significant mobility. This result has profound implications for the morphology
of cluster-assembled materials
Economic and Market Analysis of CO2 Utilization Technologies – Focus on CO2 derived from North Dakota lignite
AbstractBased on information obtained about the technical aspects of the technologies, several challenges are expected to be faced by any potential CO2 utilization technologies intended for North Dakota lignite plants. The weather, alkaline content of lignite fly ash, and space limitations in the immediate vicinity of existing power plants are challenging hurdles to overcome. Currently, no CO2 utilization option is ready for implementation or integration with North Dakota power plants. Mineralization technologies suffer from the lack of a well-defined product and insufficient alkalinity in lignite fly ash. Algae and microalgae technologies are not economically feasible and will have weather- related challenges
Nonorientable spacetime tunneling
Misner space is generalized to have the nonorientable topology of a Klein
bottle, and it is shown that in a classical spacetime with multiply connected
space slices having such a topology, closed timelike curves are formed.
Different regions on the Klein bottle surface can be distinguished which are
separated by apparent horizons fixed at particular values of the two angular
variables that eneter the metric. Around the throat of this tunnel (which we
denote a Klein bottlehole), the position of these horizons dictates an ordinary
and exotic matter distribution such that, in addition to the known diverging
lensing action of wormholes, a converging lensing action is also present at the
mouths. Associated with this matter distribution, the accelerating version of
this Klein bottlehole shows four distinct chronology horizons, each with its
own nonchronal region. A calculation of the quantum vacuum fluctuations
performed by using the regularized two-point Hadamard function shows that each
chronology horizon nests a set of polarized hypersurfaces where the
renormalized momentum-energy tensor diverges. This quantum instability can be
prevented if we take the accelerating Klein bottlehole to be a generalization
of a modified Misner space in which the period of the closed spatial direction
is time-dependent. In this case, the nonchronal regions and closed timelike
curves cannot exceed a minimum size of the order the Planck scale.Comment: 11 pages, RevTex, Accepted in Phys. Rev.
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de
STRING v10: protein-protein interaction networks, integrated over the tree of life
The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. The STRING database (http://string-db.org) aims to provide a critical assessment and integration of protein-protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks
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