Professors:

In this study, we will show the adaptation of molecular dynamics simulations using CHARMM (Chemistry at HARvard Macromolecular Mechanics) for protein folding research to the environment of widely distributed computing. We will then investigate the performance and efficiency of such a migration. In particular, we will go through some critical issues such as the scheduling, the fault tolerance and the communication problems related to the migration, proposing some interesting solutions. For the proof of feasibility, we aim at a realistic setting using commodity hardware and well-known software components. Since the idea of widely distributed computing is quite well established, we rely on existing middleware to do the distribution of the computation. Therefore, we teamed up with the company United Devices, Inc., and are using their software to investigate the feasibility of widely distributed molecular simulations. Acknowledgements First of all, I would like to thank Prof. Stricker and Prof. Caflisch for giving me the opportunity to do my diploma thesis work on this interesting interdisciplinary project