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

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

Permeation through nanometer pores is important in the design of materials for filtration and separation techniques and because of unusual fundamental behavior arising at the molecular scale. We found that submicrometer-thick membranes made from graphene oxide can be completely impermeable to liquids, vapors, and gases, including helium, but these membranes allow unimpeded permeation of water (H 2 O permeates through the membranes at least 10 10 times faster than He). We attribute these seemingly incompatible observations to a low-friction flow of a monolayer of water through two-dimensional capillaries formed by closely spaced graphene sheets. Diffusion of other molecules is blocked by reversible narrowing of the capillaries in low humidity and/or by their clogging with water.

/pdf/unimpeded-permeation-of-water-through-helium-leak-tight-50chaotsy2.pdf

Unimpeded permeation of water through helium-leak-tight graphene-based membranes.

: 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

A review is presented of the mechanics of microscale adhesion in microelectromechanical systems (MEMS). Some governing dimensionless numbers such as Tabor number, adhesion parameter and peel number for microscale elastic adhesion contact are discussed in detail. The peel number is modified for the elastic contact between a rough surface in contact with a smooth plane. Roughness ratio is introduced to characterize the relative importance of surface roughness for microscale adhesion contact, and three kinds of asperity height distributions are discussed: Gaussian, fractal, and exponential distributions. Both Gaussian and exponential distributions are found to be special cases of fractal distribution. Casimir force induced adhesion in MEMS, and adhesion of carbon nanotubes to a substrate are also discussed. Finally, microscale plastic adhesion contact theory is briefly reviewed, and it is found that the dimensionless number, plasticity index of various forms, can be expressed by the roughness ratio.

Mechanics of adhesion in MEMS - a review

We present an approach for measuring the water flow rate through individual ultralong carbon nanotubes (CNTs) using field effect transistors array defined on individual tubes. Our work exhibits a rate enhancement of 882-51 and a slip length of 53-8 nm for CNTs with diameters of 0.81-1.59 nm. We also found that the enhancement factor does not increase monotonically with shrinking tube diameter and there exists a discontinuous region around 0.98-1.10 nm. We believe that these single-tube level results would help understand the intrinsic nanofluidics of water in CNTs.

Measurement of the Rate of Water Translocation through Carbon Nanotubes

An analysis based on the energy conservation is presented for the self-propelled droplet during coalescence of two droplets of the same size over a superhydrophobic rough surface. The self-propelled behavior occurs only for the coalescence of droplets with a certain range of radius. An analytical relation is established among the coalescence-induced velocity, surface energy, viscous dissipation, and droplet size if gravity is negligible. The coalescence-induced velocity increases with increasing droplet size to a maximum and then decreases with the size, which is in good accord with the experimental observation reported in the literature. (C) 2011 American Institute of Physics. [doi:10.1063/1.3553782]

Size effect on the coalescence-induced self-propelled droplet

Adsorption of formaldehyde molecule on the intrinsic and Al-doped graphene: A first principle study

The influence of Casimir force on the nonlinear behavior of nanoscale electrostatic actuators is studied in this paper. A one degree of freedom mass-spring model is adopted and the bifurcation properties of the actuators are obtained. With the change of the geometrical dimensions, the number of equilibrium point varies from zero to two. Stability analysis shows that one equilibrium point is Hopf point and the other is unstable saddle point when there are two equilibrium points. We also obtain the phase portraits, in which the periodic orbits exist around the Hopf point, and a homoclinic orbit passes through the unstable saddle point.

/pdf/nonlinear-behavior-for-nanoscale-electrostatic-actuators-3ymsmeqv3u.pdf

Ya-Pu Zhao

Papers

Mechanics of adhesion in MEMS - a review

Measurement of the Rate of Water Translocation through Carbon Nanotubes

Size effect on the coalescence-induced self-propelled droplet

Adsorption of formaldehyde molecule on the intrinsic and Al-doped graphene: A first principle study

Nonlinear behavior for nanoscale electrostatic actuators with Casimir force