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 a data processing system capable of concurrently executing multiple hardware threads of execution, an intermediate address translation unit in a processing unit translates an effective address for a memory access into an intermediate address. A cache memory is accessed utilizing the intermediate address. In response to a miss in cache memory, the intermediate address is translated into a real address by a real address translation unit that performs address translation for multiple hardware threads of execution. The system memory is accessed with the real address.

Address translation through an intermediate address space

Two-dimensional van der Waals heterostructures (vdWHs) with tunable band alignment have the potential to be benignant in the development of minimal multi-functional and controllable electronics, but they have received little attention thus far. It is crucial to characterize and control the band alignment in semiconducting vdWHs, which determines the electronic and optoelectronic properties. The future success of optoelectronic devices will require improved electronic property control techniques, such as using an external electric field or strain engineering, to change the electronic structures directly. Herein, we review heterostructures fabricated as transition metal dichalcogenides (TMDCs) as one of their constituent monolayers with other notable 2D materials that can transfer from type-II to type-III (type-III > type-II) band alignment when a biaxial strain or electric field is applied.

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Two-dimensional van der Waals heterostructures (vdWHs) with band alignment transformation in multi-functional devices

Structural strength analysis and optimization of portable hydrogen storage vessel made of fiberglass tube

A method for fast remote communication and computation between processors is provided in the illustrative embodiments. A direct core to core communication unit (DCC) is configured to operate with a first processor, the first processor being a remote processor. A memory associated with the DCC receives a set of bytes, the set of bytes being sent from a second processor. An operation specified in the set of bytes is executed at the remote processor such that the operation is invoked without causing a software thread to execute.

Lixin Zhang

Papers

Address translation through an intermediate address space

Two-dimensional van der Waals heterostructures (vdWHs) with band alignment transformation in multi-functional devices

Structural strength analysis and optimization of portable hydrogen storage vessel made of fiberglass tube

Fast remote communication and computation between processors using store and load operations on direct core-to-core memory

Study on Heat and Mass Transfer Distance of Water-Film Evaporation in Limited Space Using Dual-Wavelength Digital Holographic Interference