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.

The invention relates to annulenone compounds with anti-tumor activity, a preparation method and application thereof. The chemical name of the compounds (GIBH022) is 3-Ethyl-4R, 5S-dihydroxy-cyclopent-2-enone, and a structural formula thereof is shown in (I). The annulenone compounds GIBH022 can inhibit the growth of tumor cell strains, can be used for developing anti-tumor medicaments, and have broad application prospect.

Annulenone compounds and application thereof in preparing anti-tumor medicaments

The benefits of Out of Order (OOO) processing are well known, as is the effectiveness of predicated execution for unpredictable control flow. However, as previous research has demonstrated, these techniques are at odds with one another. One common approach to reconciling their differences is to simplify the form of predication supported by the architecture. For instance, the only form of predication supported by modern OOO processors is a simple conditional move. We argue that it is the simplicity of conditional move that has allowed its widespread adoption, but we also show that this simplicity compromises its effectiveness as a compilation target. In this paper, we introduce a generalized form of hammock predication - called predicated mutually exclusive groups - that requires few modifications to an existing processor pipeline, yet presents the compiler with abundant predication opportunities. In comparison to non-predicated code running on an aggressively clocked baseline system, our technique achieves an 8% speedup averaged across three important benchmark suites.

Lightweight predication support for out of order processors

BACKGROUND: At present, much attention has been focused on the development of methane (CH₄) sensors due to a series of explosions and fires caused by CH₄ gas leakage. RESULTS: Here, a CH₄ thermoelectric gas sensor (TGS) was fabricated by fixing 3D porous palladium/cobalt oxide (Pd/Co₃O₄) catalyst on a commercial thermoelectric module. 3D porous Pd/Co₃O₄ catalysts were prepared by a co‐precipitation and gel‐casting method. The pore structure in catalysts could be tailored only by adjusting the gel viscosity during the formation process. The protocol to tune the pore structure is facile and effective for the improvement of the activity of catalysts. By means of various techniques, the catalysts were characterized and then the possible catalytic mechanism was revealed. The CH₄ TGS based on the optimal Pd/Co₃O₄ catalyst began to respond at 200 °C, following an obvious output voltage (ΔV) of 5 mV. Enhancing the operating temperature to 240 °C, the value of ΔV reached to 31 mV and exhibited a linear relationship with CH₄ gas concentration. Meanwhile, the CH₄ TGS showed high sensitivity, repeatability and stability. CONCLUSION: The easy and effective preparation method presented to prepare 3D porous Pd/Co₃O₄ catalyst can provide an unique perspective on the development of 3D porous materials with excellent properties. It can be anticipated that the CH₄ TGS based on the 3D porous Pd/Co₃O₄ catalyst will be a potential candidate for the detection of CH₄ gas in industrial settings. © 2020 Society of Chemical Industry

Fabrication of methane thermoelectric gas sensor based on 3D porous Pd/Co3O4 catalyst

The amount of data that a typical translation lookaside bu er (TLB) can map has not kept pace with the growth in cache sizes and application footprints. As a result, the cost of handling TLB misses limits the performance of an increasing number of applications. The use of superpages, multiple adjacent virtual memory pages that can be mapped with a single TLB entry, extends a TLB's reach without signi cantly increasing its size or cost. The diÆculty of identifying what sets of pages should be promoted to superpages combined with the overhead of performing these promotions restricts superpage use almost exclusively to wired system data structures. Previous studies have shown that simple online policies that decide to create superpages dynamically can be e ective in reducing TLB penalties. In this paper we analyze the performance of online superpage promotion for nine benchmarks on a simulated HP PA-RISC system running a BSD Unix kernel. We extend previous work in two ways. First, we study the impact of creating superpages dynamically by remapping pages at the memory controller instead of copying pages to make them contiguous. The use of such a hardware mechanism a ects the choice between two previously described superpage promotion policies. Previous work has shown that an online approximation to a competitive policy is the best choice. Our results show that having hardware support makes a greedy policy perform equally well. Second, we use execution-driven simulation, whereas previous studies have used trace-driven simulation. Our results show that the di erences in accuracy are signi cant, especially when studying complex interactions between operating systems and modern architectures.

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A comparison of online superpage promotion mechanisms

A helical humidity resistive sensor was fabricated by using solution processed supramolecular self-assembly of viologen substituted perylene diimide (PDI-DV). The nanohelices obtained in iPr2O / MeCN under −20 ℃, as...

Lixin Zhang

Papers

Annulenone compounds and application thereof in preparing anti-tumor medicaments

Lightweight predication support for out of order processors

Fabrication of methane thermoelectric gas sensor based on 3D porous Pd/Co3O4 catalyst

A comparison of online superpage promotion mechanisms

Helical Perylene Diimide Self-Assembly with a Redox Active Molecular Switch Applied to Humidity Sensing