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.

In at least one embodiment, a processor includes at least one execution unit that executes instructions and instruction sequencing logic, coupled to the at least one execution unit, that fetches instructions from a memory system for execution by the at least one execution unit. The instruction sequencing logic including branch target address prediction circuitry that stores a branch target address prediction associating a first instruction fetch address with a branch target address to be used as a second instruction fetch address. The branch target address prediction circuitry includes delay logic that, in response to at least a tag portion of a third instruction fetch address matching the first instruction fetch address, delays access to the memory system utilizing the second instruction fetch address if no branch target address prediction was made in an immediately previous cycle of operation.

Data processing system, processor and method of data processing having branch target address cache selectively applying a delayed hit

In a previous study, we characterized a high chlorophyll fluorescence Ipa1 mutant of Arabidopsis thaliana, in which approximately 20% photosystem (PS) II protein is accumulated. In the present study, analysis of fluorescence decay kinetics and thermoluminescence profiles demonstrated that the electron transfer reaction on either the donor or acceptor side of PSII remained largely unaffected in the Ipa1 mutant. In the mutant, maximal photochemical efficiency (Fv/Fm, where Fm is the maximum fluorescence yield and Fv is variable fluorescence) decreased with increasing light intensity and remained almost unchanged in wild-type plants under different light conditions. The Fv/Fm values also increased when mutant plants were transferred from standard growth light to low light conditions. Analysis of PSII protein accumulation further confirmed that the amount of PSII reaction center protein is correlated with changes in Fv/Fm in Ipa1 plants. Thus, the assembled PSII in the mutant was functional and also showed increased photosensitivity compared with wild-type plants.



(Managing editor: Ping He)

Photosynthetic Properties of Photosystem II in Arabidopsis thaliana Ipa1 Mutant

Growing MgO(1?1?1) polar ultrathin films (PUFs) on heterogeneous substrates is technologically challenging. By using first-principles calculations, we show that while the O-termination of the supported PUF can be perfectly passivated by H adatoms, the compensation of the Mg-termination at the interface is the key to the stabilization. Proper charge transfer across the interface is highly required, which is dominated by the work function difference between the two surfaces that form the interface. Taking Ag(1?1?1) as an example, we propose that a thin Pt buffer layer can increase the work function of the substrate, and improve the PUF quality significantly.

Substrate engineering in stabilizing epitaxial MgO(1 1 1) polar ultrathin films: first-principles calculations.

The microlayer present at the bottom of the bubble plays a very important role in heat transfer during nucleation boiling. In this paper, the dynamic characteristics of microlayer at the bottom of boiling bubble in a small channel were studied by laser interferometry method and high speed camera, and the results were compared with pool boiling experiments. The results show that the bubbles have an obvious tendency to slip in the flow boiling. The microlayer interference fringe is deformed and no longer a complete Newtonian ring. By analyzing the thickness distribution of microlayer in different directions in flow boiling and the change of micro-contact angle in the flow direction, it was found that the micro-contact angle in the flow direction became larger with the growth of bubbles.

Comparative experimental study on dynamic characteristics of bubble microlayers in small channel flow boiling and pool boiling

The degradation of nitro and azo compounds has attracted wide attention due to their high toxicity and stability in water. Here, we reported the fast degradation of nitro and azo compounds by the direct injection of high-concentration noble-metal ions (Au3+, Ag+, Pd2+, or Pt4+) and discussed the degradation mechanism. The rate constants of the nitro and azo compounds degradation followed the order: K4-NP > K2-NP > K3-NP > K2-NR > KMR > KMO, explained by the substituent effect. The maximum of the degradation rate constant could reach up to 16 min−1, which can be attributed to the atom-nano catalysis motivated by the direct injection of high-concentration ions. Furthermore, based on the method, the highlighted conflicts shown in the nitro and azo compounds degradation could be resolved. Meanwhile, the recovery method (centrifugation, dissolution, and purification) of noble-metal ions was proposed by means of various characterization techniques, and then noble-metal ions were recovered and recycled for five cycles. Obviously, the above degradation technology can have great potential for applications in water pollutant removal and environmental remediation.

Lixin Zhang

Papers

Data processing system, processor and method of data processing having branch target address cache selectively applying a delayed hit

Photosynthetic Properties of Photosystem II in Arabidopsis thaliana Ipa1 Mutant

Substrate engineering in stabilizing epitaxial MgO(1 1 1) polar ultrathin films: first-principles calculations.

Comparative experimental study on dynamic characteristics of bubble microlayers in small channel flow boiling and pool boiling

Fast degradation of nitro and azo compounds in recyclable noble-metal ions systems