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

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

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“Bioinformatics” 특집을 내면서

日本物理学会誌及びJournal of the Physical Society of Japanの月刊について

We study numerically the thermal conductivity in several different one-dimensional chains. We show that the phonon-lattice interaction is the main ingredient of the Fourier heat law. Our argument provides a rather satisfactory explanation to all existing numerical results concerning this problem.

Heat conduction in one-dimensional chains

Two classes of one-dimensional nonintegrable systems represented by the Fermi-Pasta-Ulam (FPU) model and the discrete ${\ensuremath{\varphi}}^{4}$ model are studied to seek a generic mechanism of energy transport on a microscopic level sustaining macroscopic behaviors. The results enable us to understand why the class represented by the ${\ensuremath{\varphi}}^{4}$ model has a normal thermal conductivity and the class represented by the FPU model does not even though the temperature gradient can be established.

Heat conduction in one-dimensional nonintegrable systems

In this Letter, I propose that a properly rescaled spatiotemporal correlation function of the energy density fluctuations may be applied to characterize the equilibrium diffusion processes in lattice systems with finite temperature. Applying this function, the diffusion processes in three one-dimensional nonlinear lattices are studied. The diffusion exponent is shown to be related to the diverging exponent of the thermal conductivity of a lattice through the relation , as has been proved based on the Levy walk assumption. The diffusion behavior is explained in terms of solitons and phonons.

Identifying diffusion processes in one-dimensional lattices in thermal equilibrium.

We study heat conduction behavior of one-dimensional lattices with asymmetric, momentum conserving interparticle interactions. We find that with a certain degree of interaction asymmetry, the heat conductivity measured in nonequilibrium stationary states converges in the thermodynamical limit. Our analysis suggests that the mass gradient resulting from asymmetric interactions may provide a phonon scattering mechanism in addition to that caused by nonlinear interactions.

Normal heat conduction in one-dimensional momentum conserving lattices with asymmetric interactions

We study heat conduction in one-dimensional mass-disordered harmonic and anharmonic lattices. It is found that the thermal conductivity $\ensuremath{\kappa}$ of the disordered anharmonic lattice is finite at low temperature, whereas it diverges as $\ensuremath{\kappa}\ensuremath{\sim}{N}^{0.43}$ at high temperature. Moreover, we demonstrate that a unique nonequilibrium stationary state in the disordered harmonic lattice does not exist at all.

Hong Zhao

Papers

Heat conduction in one-dimensional chains

Heat conduction in one-dimensional nonintegrable systems

Identifying diffusion processes in one-dimensional lattices in thermal equilibrium.

Normal heat conduction in one-dimensional momentum conserving lattices with asymmetric interactions

Can disorder induce a finite thermal conductivity in 1D lattices