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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

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QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Effect of bacteriocin produced by Lactococcus sp. HY 449 on skin-inflammatory bacteria.

Late Transition Metal Doped MXenes Showing Superb Bifunctional Electrocatalytic Activities for Water Splitting via Distinctive Mechanistic Pathways

The low-lying electronic states of Ag3−(1Σg+,3B2), Ag3(2B2,2A1,2B1,4B2,2Σu+,1 2Σg+,2 2Σg+,2Πu,4Σu+), and Ag3+(1A1,1Σg+,3Σu+,3A1) are studied by ab initio calculations with the Stuttgart effective core potentials and corresponding (8s7p6d)/[6s5p3d] and (8s7p5d3f )/[6s5p3d3f] basis sets. The geometries, vibrational frequencies, and energetic splittings are obtained by the coupled-cluster method including singles and doubles (CCSD) and those including up to the noniterative triples [CCSD(T)] correlation methods with additional frozen core molecular orbitals corresponding to 4s and 4p orbitals. The results for well-studied states (Ag3− 1Σg+;Ag3 2B2,2A1,2Σu+;Ag3+ 1A1) are in good agreement with previous experimental results, and therefore our results for other newly studied states are expected to be reliable. The vertical detachment energies of Ag3− are obtained by the electron excitation equation-of-motion coupled-cluster (EE-EOM-CCSD) method and the average deviation from the experimental results is small wi...

Ab initio study of the low-lying electronic states of Ag3−, Ag3, and Ag3+: A coupled-cluster approach

Owing to the utility of redox phenomena of silver in many chemical systems, it is important to understand the coordination chemistry of Ag+ ion and hence the hydration structure. The lowest-energy conformations of Ag+(H2O)1–6 are sensitive to the calculation method employed. The coordination number (Nc) of Ag+(H2O)n is predicted to be 2 for n=2–6 at the density functional theory level, while the Nc for n=3–5 is 3, and that for n=6 is 4 at the second-order Moller–Plesset perturbation level. Further accurate analysis based on coupled-cluster singles and doubles theory with perturbative corrections for triple excitations agrees with the MP2 results except that Nc of 4 is also as competitive as Nc of 3 for n=5. To identify the correct Nc, it would be useful to facilitate the IR experimental characterization. We thus provide the OH spectra for various possible structures. It is interesting to note that the hydration chemistry of Ag+ ion is somewhat different from that of alkali metal ions.

Structures, energies, and spectra of aqua-silver (I) complexes

In an effort to examine the intricacies of electronic nanodevices, we present an atomistic description of the electronic transport properties of an isolated benzene molecule. We have carried out ab initio calculations to understand the modulation of the molecular orbitals (MOs) and their energy spectra under the external electric field, and conducting behavior of the benzene molecule. Our study shows that with an increase in the applied electric field, the energy of the third lowest unoccupied molecular orbital (LUMO) of benzene decreases, while the first and second LUMO energies are not affected. Above a certain threshold of the external electric field, the third LUMO is lowered below the original LUMO and becomes the real LUMO. Since the transport through a molecule is to a large extent mediated by the molecular orbitals, the change in MOs can lead to a dramatic increase in the current passing through the benzene molecule. Thus, in the course of this study, we show that the modulation of the molecular orbitals in the presence of a tuning parameter(s) such as the external electric field can play important roles in the operation of molecular devices. We believe that this understanding would be helpful in the design of electronic nanodevices.

Kwang S. Kim

Papers

Effect of bacteriocin produced by Lactococcus sp. HY 449 on skin-inflammatory bacteria.

Late Transition Metal Doped MXenes Showing Superb Bifunctional Electrocatalytic Activities for Water Splitting via Distinctive Mechanistic Pathways

Ab initio study of the low-lying electronic states of Ag3−, Ag3, and Ag3+: A coupled-cluster approach

Structures, energies, and spectra of aqua-silver (I) complexes

Role of molecular orbitals of the benzene in electronic nanodevices.