There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award.

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants

The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.

Frame refreshes, that are used to retain frame images from frame buffers for display subsystems in mobile devices, waste energy and memory bandwidth. In this paper, we propose an intelligent frame refresh mechanism to reduce redundant frame refreshes and useless data accesses to frame buffers, which bridges the semantic gap between frame buffers and frame refreshes, and exploits the knowledge of frame buffers to guide frame refreshes. Based on this mechanism, we introduce two detailed schemes to optimize refreshes by utilizing different information. The flipping-aware frame refresh scheme uses the frame buffer switching operations to detect frame image updates and triggers useful refreshes. The row-level frame refresh scheme supports to refresh only modified rows instead of the whole frame, under the guidance of pixel status information of frame buffers. Our evaluation results show that our proposed mechanism can reduce memory requests by nearly 50% and memory power consumption up to 30%, compared to conventional fixed frame refresh mechanism.

Intelligent frame refresh for energy-aware display subsystems in mobile devices

Reversal of meticillin resistance in Staphylococcus aureus by the anthelmintic avermectin.

The ATP-dependent serine protease Lon belongs to the AAA+ superfamily, which is widely distributed in bacteria, archaea, and eukaryotic cells. Lon participates in the regulation of numerous physiological processes and gene expression via degrading various unstable and non-native regulators. In this study, we showed that the Arabidopsis atlon4 mutant is more sensitive to drought stress than wild-type plants. Compared with wild-type plants, atlon4 mutant plants showed increased water loss, decreased water use efficiency, and impaired stomatal closure in drought stress conditions.

Increased sensitivity to drought stress in atlon4 Arabidopsis mutant

In at least one embodiment, a processor includes at least one execution unit and instruction sequencing logic that fetches instructions for execution by the execution unit. The instruction sequencing logic includes branch logic that outputs predicted branch target addresses for use as instruction fetch addresses. The branch logic includes a branch target address cache (BTAC) having at least one direct entry providing storage for a direct branch target address prediction associating a first instruction fetch address with a branch target address to be used as a second instruction fetch address immediately after the first instruction fetch address and at least one indirect entry providing storage for an indirect branch target address prediction associating a third instruction fetch address with a branch target address to be used as a fourth instruction fetch address subsequent to both the third instruction fetch address and an intervening fifth instruction fetch address.

Data processing system, processor and method of data processing having branch target address cache storing direct predictions

A computer, control device and data processing method; the computer comprises a processing unit and a control device; the processing unit is used to add a label to an application request and to transmit to the control device the application request with the label added; and the control device is used to receive the application request with the label added, to determine, according to the label and a pre-stored resource allocation policy, the quantity of resources to be allocated for the application request, and to instruct the components of the computer to process the application request according to the quantity of resources allocated for the application request, the above resource allocation policy comprising a corresponding relationship between the label and the quantity of resources allocated for the application request. The computer, the control device and the data processing method are used to improve the service quality of an application request.

Lixin Zhang

Papers

Intelligent frame refresh for energy-aware display subsystems in mobile devices

Reversal of meticillin resistance in Staphylococcus aureus by the anthelmintic avermectin.

Increased sensitivity to drought stress in atlon4 Arabidopsis mutant

Data processing system, processor and method of data processing having branch target address cache storing direct predictions

Computer, control device and data processing method