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

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

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Point of care testing for hepatitis C in the priority settings of mental health, prisons and drug and alcohol facilities

A computer-implemented method for determining computational units for computing interactions among sets of bodies located in a computation region includes, for each computation associated with one of the sets of bodies, determining, according to an assignment rule that provides a mapping from a location of each of the bodies to a determined computation unit from the plurality of computation units, a computation unit from a plurality of computation units for performing the computation.

Determining computational units for computing multiple body interactions

TRAMPLE: maximum likelihood estimation of protein unfolding rates from all-atom temperature ramp simulations

ABs!rRAcT DAD3 is a parallel tree-structured machine designed to provide highly significant performance improvements in the execution of large Production systems. The DAD0 machine comprises a large (on the order of a hundred thousand) set of processing elements (PE's), each containing its awn processor, a small amount (2K bytes, in the current design) of local random access memory, and a specialized I/O switch. The PE's are interconnected to form a complete binary tree. This paper describes a general procedure for the parallel execution of production systems on the DAD0 machine, and outlines in general terms how this procedure can be extended to include conmutative and multiple, independent production systems.

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DADO: ATREE-STRUCXUREDMACRINE ARCRITECTURE FoRERODUcTIONSYSTEMS*

The Primary Processing Subsystem of the NON-VON supercomputer potentially may comprise thousands of custom nHOS integrated circuits. It is vital that faulty components be detected and located. This paper provides a collection of algorithms to exercise the Primary Processing Subsystem so that the manifestation of latent faults may be observed.

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David E. Shaw

Papers

Point of care testing for hepatitis C in the priority settings of mental health, prisons and drug and alcohol facilities

Determining computational units for computing multiple body interactions

TRAMPLE: maximum likelihood estimation of protein unfolding rates from all-atom temperature ramp simulations

DADO: ATREE-STRUCXUREDMACRINE ARCRITECTURE FoRERODUcTIONSYSTEMS*

Exercising the NON-VON Primary Processing Subsystem