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

Jump relaxation in solid electrolytes

Conformational constraints for amyloid fibrillation: the importance of being unfolded.

https://www.cell.com/trends/biochemical-sciences/pdf/S0968-0004(07)00059-X.pdf

Functional amyloid--from bacteria to humans.

The infrared reflectance spectra of lithium borate glasses (0–73 mol% Li 2 O) have been measured over a broad and continuous spectral range (30–4000 cm −1 ) in an attempt to study systematically their structure. The reflectance data have been analyzed by Kramers-Kronig inversion to obtain the optical and dielectric properties of the materials. The study of the deconvoluted mid-infrared spectra has revealed a glass network built up of various boron-oxygen groups, with structure and concentration strongly dependent on the Li 2 O content. Of particular interest was the far-infrared asymmetric absorption profile, which could be well simulated by two broad bands attributed to vibrations of lithium cations in two distinct network environments. The presence of these two Li + -host site distributions was found to be independent of the details of the borate network structure and has been taken to imply a more general characteristics of ionic conducting oxide glasses.

Infrared reflectance spectra of lithium borate glasses

Vibrational spectra of magnesium-sodium-borate glasses. 2. Raman and mid-infrared investigation of the network structure

Total reflection methods and instrumentation for their use are described for measurements of dielectric permittivity and loss at frequencies to 10 GHz or more. Several cell designs are shown, together with analyses of their performance. Procedures are given for correcting effects of wave propagation in the cells and residual reflections in the cells by bilinear analysis with calibrations using dielectrics of known permittivity. Representative results are presented for highly polar liquids, dilute solutions of polar molecules in nonpolar solvents, electrolyte solutions, and ionic glasses with appreciable ohmic conduction.

Time domain reflection methods for dielectric measurements to 10 GHz

The study of mid infrared and Raman spectra of alkaline earth borate glasses xMO.(1-x)B 2 O 3 (0.15≤x≤0.55) has shown that for M=Ca, Sr and Ba the network is composed of borate arrangements containing charged BO - 4 tetrahedra (O=bridging oxygen atom) and BO 2 O - triangles as well as neutral BO 3 units. The fraction of four coordinated boron atoms, N 4 , was obtained from analysis of the mid infrared spectra and found to exhibit a maximum at compositions depending on the type of alkaline earth ion. For fixed metal oxide contents, N 4 increases with increasing metal ion size, a trend opposite to that exhibited by alkali borate glasses. Mg borate glasses were found to have the lowest N 4 values and this was associated with the coordination requirements of the Mg ion for highly charged oxygen sites. Evidence for this was provided by the spectroscopic signatures of the neutral boroxol rings and the highly charged pyroborate species, B 2 OO 4- 4 in Mg borates with x0.5 while such units are absent from the corresponding structures of Ca, Sr and Ba borates. Analysis of the far infrared profiles suggests the presence of two types of site hosting alkaline earth ions while the average strength of the metal ion site interactions was found to scale linearly with the glass transition temperature in glass series of constant metal oxide content.

Georgios D. Chryssikos

Papers

Infrared reflectance spectra of lithium borate glasses

Vibrational spectra of magnesium-sodium-borate glasses. 2. Raman and mid-infrared investigation of the network structure

Time domain reflection methods for dielectric measurements to 10 GHz

Structure and properties of alkaline earth borate glasses

Borate glass structure by Raman and infrared spectroscopies