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

/pdf/first-principles-study-of-the-adsorption-of-c-2-h-2-and-c-2-3u270k7el1.pdf

First-principles study of the adsorption of C 2 H 2 and C 2 H 4 on Si(100)

The nature of the interaction of paramagnetic atoms A (=4N,4P,3O,3S) with π systems and C60 in the A⋅⋅⋅C6H6 complexes and endohedral fullerenes (A@C60) has been investigated employing second-order Moller–Plesset perturbation level of theory and density functional theory calculations. The coupled cluster theory with single and double excitations, and with perturbed triplet excitations have also been carried out for the A⋅⋅⋅C6H6 complexes. The calculated geometries indicate that the paramagnetic N and P atoms lie on the C6 axis of benzene in the A⋅⋅⋅C6H6 complex and at the center of the C60 cage in A@C60. On the other hand, the O and S atoms are slightly shifted towards the C–C bond of benzene in the A⋅⋅⋅C6H6 complex. A comparison of the calculated binding energies (BEs) of these paramagnetic complexes and the corresponding rare gas complexes like He⋅⋅⋅C6H6 and He@C60 indicate that the BEs of the former are much larger than those of the latter. For both the rare gas and paramagnetic atom complexes dispersiv...

Nature of the interaction of paramagnetic atoms (A=4N,4P,3O,3S) with π systems and C60: A theoretical investigation of A⋅⋅⋅C6H6 and endohedral fullerenes A@C60

/pdf/interaction-of-na-ion-with-the-solvated-gramicidin-a-oo05nsis73.pdf

Interaction of Na + Ion With the Solvated Gramicidin A Transmembrane Channel

Influence of intermolecular hydrogen bonding on water dissociation at the MgO(001) surface

The relative stabilities of the lowest energy structures are calculated for the gold octamer, Au8, employing highly correlated ab initio methods. The question of dimensionality of these clusters is addressed, and a guideline for future structural studies of such systems is provided. In particular, the importance of geometry relaxation beyond the MP2 level of theory as well as the need for basis sets toward the complete limit (CBS) are discussed. The planar D(4h) symmetric structure of Au8 is the lowest energy structure. At the CCSD(T)/CBS limit, it is separated by 16 kJ mol(-1) from the next higher Td symmetric isomer.

Kwang S. Kim

Papers

First-principles study of the adsorption of C 2 H 2 and C 2 H 4 on Si(100)

Nature of the interaction of paramagnetic atoms (A=4N,4P,3O,3S) with π systems and C60: A theoretical investigation of A⋅⋅⋅C6H6 and endohedral fullerenes A@C60

Interaction of Na + Ion With the Solvated Gramicidin A Transmembrane Channel

Influence of intermolecular hydrogen bonding on water dissociation at the MgO(001) surface

Spatial Structure of Au8: Importance of Basis Set Completeness and Geometry Relaxation