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

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

Note: Times Cited: 875 Reference EPFL-ARTICLE-206025doi:10.1021/cr0501846View record in Web of Science URL: ://WOS:000249839900009 Record created on 2015-03-03, modified on 2017-05-12

Complex Hydrides for Hydrogen Storage

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Triggered by the resounding success of cisplatin, the past decades have seen tremendous efforts to produce clinically beneficial analogues. The recent achievement of oxaliplatin for the treatment of colon cancer should, however, not belie the imbalance between a plethora of investigated complexes and a very small number of clinically approved platinum drugs. Strategies opening up new avenues are increasingly being sought using complexes of metals other than platinum such as ruthenium or gallium. Based on the chemical differences between these metals, the spectrum of molecular mechanisms of action and potential indications can be broadened substantially. Other approaches focus on complexes with tumour-targeting properties, thereby maximizing the impact on cancer cells and minimizing the problem of adverse side effects, and complexes with biologically active ligands.

Antitumour metal compounds: more than theme and variations

The focus of this review is the presentation of the most important aspects of chemical bonding in molecules of the main group atoms according to the current state of knowledge. Special attention is...

Chemical Bonding and Bonding Models of Main-Group Compounds

The alkaline earth metals calcium (Ca), strontium (Sr), and barium (Ba) typically engage in chemical bonding as classical main-group elements through their n s and n p valence orbitals, where n is the principal quantum number. Here we report the isolation and spectroscopic characterization of eight-coordinate carbonyl complexes M(CO) 8 (where M = Ca, Sr, or Ba) in a low-temperature neon matrix. Analysis of the electronic structure of these cubic O h -symmetric complexes reveals that the metal–carbon monoxide (CO) bonds arise mainly from [M(d π )] → (CO) 8 π backdonation, which explains the strong observed red shift of the C-O stretching frequencies. The corresponding radical cation complexes were also prepared in gas phase and characterized by mass-selected infrared photodissociation spectroscopy, confirming adherence to the 18-electron rule more conventionally associated with transition metal chemistry.

http://science.sciencemag.org/content/sci/361/6405/912.full.pdf

Observation of alkaline earth complexes M(CO)8 (M = Ca, Sr, or Ba) that mimic transition metals

Hardness and electrophilicity values for several molecules involved in different chemical reactions are calculated at various levels of theory and by using different basis sets. Effects of these aspects as well as different approximations to the calculation of those values vis-a-vis the validity of the maximum hardness and minimum electrophilicity principles are analyzed in the cases of some representative reactions. Among 101 studied exothermic reactions, 61.4% and 69.3% of the reactions are found to obey the maximum hardness and minimum electrophilicity principles, respectively, when hardness of products and reactants is expressed in terms of their geometric means. However, when we use arithmetic mean, the percentage reduces to some extent. When we express the hardness in terms of scaled hardness, the percentage obeying maximum hardness principle improves. We have observed that maximum hardness principle is more likely to fail in the cases of very hard species like F–, H2, CH4, N2, and OH appearing in t...

Sudip Pan

Papers

Chemical Bonding and Bonding Models of Main-Group Compounds

Observation of alkaline earth complexes M(CO)8 (M = Ca, Sr, or Ba) that mimic transition metals

On the Validity of the Maximum Hardness Principle and the Minimum Electrophilicity Principle during Chemical Reactions

Eyringpy: A program for computing rate constants in the gas phase and in solution

B182−: a quasi-planar bowl member of the Wankel motor family