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.

/pdf/quantum-espresso-a-modular-and-open-source-software-project-4t6vlupbeh.pdf

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

Behavior of nitrogen and sulfur compounds in the rice husk pellet bioscrubber and its circulation water.

A ternary Mn-Zn-Fe oxide nanocomposite was fabricated by a one-step coprecipitation method for the remotion of H2S and SO2 gases at room temperature. The nanocomposite has ZnO, MnO2, and ferrites with a surface area of 21.03 m2 g-1. The adsorbent was effective in mineralizing acidic sulfurous gases better in wet conditions. The material exhibited a maximum H2S and SO2 removal capacity of 1.31 and 0.49 mmol g-1, respectively, in the optimized experimental conditions. The spectroscopic analyses confirmed the formation of sulfide, sulfur, and sulfite as the mineralized products of H2S. Additionally, the nanocomposite could convert SO2 to sulfate as the sole oxidation by-product. The oxidation of these toxic gases was driven by the dissolution and dissociation of gas molecules in surface adsorbed water, followed by the redox behaviour of transition metal ions in the presence of molecular oxygen and water. Thus, the study presented a potential nanocomposite adsorbent for deep desulfurization applications. 

/pdf/ternary-metal-oxide-nanocomposite-for-room-temperature-h2s-f3z7ebt5.pdf

Ternary metal oxide nanocomposite for room temperature H2S and SO2 gas removal in wet conditions

Copper is considered to be the most promising substrate for the growth of high-quality and large area graphene by chemical vapor deposition (CVD), in particular, on the (111) facet. Because the interactions between graphene and Cu substrates influence the orientation, quality, and properties of the synthesized graphene, we studied the interactions using angle-resolved photoemission spectroscopy. The evolution of both the Shockley surface state of the Cu(111) and the π band of the graphene was measured from the initial stage of CVD growth to the formation of a monolayer. Graphene growth was initiated along the Cu(111) lattice, where the Dirac band crossed the Fermi energy (EF) at the K point without hybridization with the d-band of Cu. Then two rotated domains were additionally grown as the area covered with graphene became wider. The Dirac energy was about -0.4 eV and the energy of the Shockley surface state of Cu(111) shifted toward the EF by ~0.15 eV upon graphene formation. These results indicate weak interactions between graphene and Cu, and that the electron transfer is limited to that between the Shockley surface state of Cu(111) and the π band of graphene. This weak interaction and slight lattice mismatch between graphene and Cu resulted in the growth of rotated graphene domains (9.6° and 8.4°), which showed no significant differences in the Dirac band with respect to different orientations. These rotated graphene domains resulted in grain boundaries which would hinder a large-sized single monolayer growth on Cu substrates.

Rotated Domains in Chemical Vapor Deposition-grown Monolayer Graphene on Cu(111)

Trifluoroethanol Increases the Stability of Δ5-3-Ketosteroid Isomerase 15N NMR RELAXATION STUDIES

A hydroiodic acid molecule is dissociated by more than four water molecules. Here, the effect of an excess electron on the hexahydated hydroiodic acid where the dissociated structure [H3O+(H2O)5I−] is much more stable than the undissociated one [(H2O)6HI], is investigated. Upon binding an excess electron (e−), the cluster releases a hydrogen radical and forms the stable hexahydrated iodide [(H2O)6I−] when the initial kinetic energy is above ∼200 K, due to the small transition barrier (∼0.5 eV). The system with the hydrogen radical released, [(H2O)6I− + H·], is much more stable than the systems with an excess electron, [(H3O)+{e−(H2O)5}I−] or [e−(H2O)2(H3O)+(H2O)3I−].

Kwang S. Kim

Papers

Behavior of nitrogen and sulfur compounds in the rice husk pellet bioscrubber and its circulation water.

Ternary metal oxide nanocomposite for room temperature H2S and SO2 gas removal in wet conditions

Rotated Domains in Chemical Vapor Deposition-grown Monolayer Graphene on Cu(111)

Trifluoroethanol Increases the Stability of Δ5-3-Ketosteroid Isomerase 15N NMR RELAXATION STUDIES

Hydrogen detachment of the hexahydrated hydroiodic acid upon attaching an excess electron