Molecular dynamics machining

Beazley D M and Lomdahl P S 1993 Message-passing multi-cell molecular dynamics on the Connection Machine 5 Parallel Comput. 20 173-95... 

D. Brown, J. H. R. Clarke, M. Okuda and T. Yamazaki, A domain decomposition strategy for molecular dynamics simulations on distributed memory machines . Comp. Phys. Comm., Vol 74, 67-80, 1993. 

Y. Hwang, R. Das, F. H. Saltz, M. Hadoscek and B. R. Brooks, Parallelizing molecular dynamics programs for distributed-memory machines , IEEE Computational Science and Engineering, Vol 2, no 2, 18-29, 1995. 

V. E. Taylor, R. L. Stevens and K. E. Arnold, Parallel molecular dynamics Communication requirements for massively parallel machines , Proc. Frontiers... 

B. Murray, P. Bash, and M. Katplus, Molecular Dynamics on the Connection Machine, Thinking Machines Cotp., Cambridge, Mass., 1989. 

GROMOS A general-purpose molecular dynamics computer simulation package for the study of biomolecules http //igc.ethz.ch/gromos/weicome.htmi GROMACS (GROningen MAchine for Chemical Simulations) http //rugmdO. chem. rug.ni/ gmx/... 

Methods. In using molecular dynamics for conformational analysis, there are many possible approaches. Assume that one is able to dedicate a machine for two weeks for this task. For this octapeptide, 70 energy evaluations can be performed each second. This implies that in two weeks, roughly 100 million iterations can be performed. Three distinct approaches could be ... 

To the disappointment of Lilly s guest relations department, Lilly s Cray-2 was later replaced with a Cray J90, a mundane-looking machine. But the J90 was more economical, especially because it was leased. The supercomputers were almost always busy with molecular dynamics and quantum mechanical calculations [100]. Of the personnel at the company, the computational chemists were the main beneficiaries of supercomputing. 

The assembly of the p- and y-amino-acid building blocks to peptidic chains was achieved by simply using the established methods of peptide synthesis - in solution [6], on solid phase [11], or in a synthesizer machine [39] also, the so-called native ligation can be applied with p-peptides [54]. Furthermore, the methods of analyzing and studying the structures of a-peptides and natural proteins can mostiy be applied to P-peptides as well (the same is true for y-peptides [51,55-60]). These methods are CD [35,37] and NMR [6, 49] spectroscopy, mass spectrometry [27,35], X-ray analysis [6,21,24,25,36], molecular dynamics (MD) calculations [9,13,18,31,38] and biological investigations [6, 15,20,26,30,41-43,45,46,48]. All of this sounds like routine, but the results are rather spectacular. 

As part of their efforts to employ parallel computers for molecular dynamics simulations, Schulten and co-workers generated a series of MD benchmarks based on their own program on a wide range of machines, including an Apple Macintosh II, a Silicon Graphics 320 VGX, a 32K-processor Conneaion Machine CM-200, a 60-node INMOS Transputer system, and a network of Sun workstations (using Linda).2 8 j e benchmarks demonstrated that the program runs very efficiently on many platforms (e.g., at sevenfold Cray 2 processor speed on the CM-200 and at Cray 2 processor speed on the Transputer system). 

A. Melcuk, R. Giles, and H. Gould, Comput. Phys., 5, 311 (1991). Molecular Dynamics Simulation of Liquids on the Connection Machine. 

D. M. Beazley and P. S. Lomdahl, Technical Report LA-UR-92-3158, Los Alamos National Laboratories, Los Alamos, NM, 1992. Message-Passing Multi-Cell Molecular Dynamics on the Connection Machine 5. 

S. Y. Liem, D. Brown, and J. H. R. Clarke, Comput. Phys. Commun., 67, 261 (1991). Molecular Dynamics Simulations on Distributed Memory Machines. 

R. K, Kalia, S. De Leeuw, A., Nakano, and P. Vashishta, Comput. Phys. Commun., 74, 316 (1993). Molecular-Dynamics Simulations of Coulombic Systems on Distributed-Memory MIMD Machines. 

B. Boltjes and S. W. De Leeuw, Mol. Simulation, 7, 1 (1991). Molecular Dynamics on the Connection Machine Using Fortran. 

Crossed molecular beam machines count among the experimental arrangements which allowed a significant breakthrough in reaction dynamics. A recent review by Casavecchia et al. shows how improvements in the crossed molecular beam technique made possible recent progresses in the understanding of gas-phase reaction dynamics [14]. 

With the current growing appreciation of cellular processes as molecular chemical machines, it is clear that more ample understanding, beyond lesion processing by polymerases, is needed. In the cell, there is a dynamic interplay between replication, transcription, and various repair mechanisms [105-108]. How these various processes are called into play in the face of DNA lesions is currently the focus of research in areas that span structural, molecular, cellular, and systems biology, with computational approaches playing increasingly vital roles [109]. Recent advances in these areas promise exciting future developments. 

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