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.

Based on dynamic microlayer evaporation model. Heat transfer mechanism of nuclear boiling and microlayer thickness under single bubble on heated surface. It has a lot to do with the temperature of the wall. Therefore, this paper studies the mechanism of bubble microlayer and makes comparative analysis with its experiments. It is helpful to master nuclear boiling heat transfer more comprehensively. In the study of individual bubble microlayer thickness. The effects of time and radius on wall temperature are considered in this paper. The theoretical formula of initial thickness of microlayer is deduced. The theoretical formula is compared with the experimental data of microlayer evaporation under the nucleation bubble. It was found that the experimental data fell within ±25% of the formula range. It is consistent with the previous experimental research.

https://iopscience.iop.org/article/10.1088/1742-6596/2280/1/012034/pdf

Study on boiling heat transfer mechanism based on microlayer evaporation theory

This paper presents the Impulse adaptable memory system, which allows applications to make efficient use of cache space and bus bandwidth. Impulse has a configurable memory controller that allows applications to remap data in the memory system. As a result, applications can control how their data is accessed, organized, and cached. We describe the current design of the Impulse architecture, describe the software transformations that will be necessary to make full use of Impulse, and examine in detail the optimizations that Impulse enables: scatter/gather access to sparse data, no-copy page coloring, and no-copy tile remapping. Results of a simulation study show that Impulse can improve the performance of conjugate gradient by 30%.

Impulse : An Adaptable Memory System

The invention discloses a data copying method, equipment and system, relates to the field of the computer and can improve data copying efficiency. The data copying method comprises the following steps: receiving a copying request message sent from a memory controller, wherein the copying request message is characterized in that a data block in a first memory module is written into a second memory module; and according to the copying request message, generating a read request and a write request, sending the read request to the first memory module to request to read data from the first memory module, and sending a write request to the second memory module to request to write data read from the first memory module into the second memory module. The data copying method, equipment and system provided by the embodiment of the invention can be used for copying the data.

Data copying method, equipment and system

PROBLEM TO BE SOLVED: To provide a processor with a branch target address cache and a data processing method. SOLUTION: An instruction sequencing logic 13 for fetching instructions from a memory system 12 comprises a branch logic 36 for outputting predicted branch target addresses for use as instruction fetch addresses. The branch logic 36 comprises a level one branch target address cache (BTAC) and a level two BTAC, and each BTAC entry associates at least a tag with a predicted branch target address. The branch logic evaluates the level one and level two BTACs in parallel with a tag portion of a first instruction fetch address to obtain a first predicted branch target address from the level one BTAC for use as a second instruction fetch address in a first clock cycle and a second predicted branch target address from the level two BTAC for use as a third instruction fetch address in a second clock cycle. COPYRIGHT: (C)2009,JPO&INPIT

Lixin Zhang

Papers

Study on boiling heat transfer mechanism based on microlayer evaporation theory

Impulse : An Adaptable Memory System

Data copying method, equipment and system

Processor with branch target address cache and data processing method

Au–Ag Nanoparticles with Controllable Morphologies for the Surface-Enhanced Raman Scattering Detection of Trace Thiram