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Research Project: DBSIM

  Brownian Dynamics Simulation

Abstract: The goal of the project is to develop and combine suitable algorithms to support an effective and efficient simulation of Brownian dynamics Simulations. The results of the micro-scale simulations shall provide additional insights into biological phenomena that cannot be treated at higher levels of abstraction (e.g. molecular crowding).

  Research Project Information
Runtime: Aug 01, 2009 until Jul 31, 2012
Project coordination: Prof. Dr. rer. nat. habil. Adelinde M. Uhrmacher ; Prof. Dr. Ronald Redmer

The last years have seen an increase of interest in micro-scale approaches to cell biological and molecular simulations, as some biological phenomena like molecular crowding cannot be adequately treated at higher levels of abstraction. Among those methods Brownian dynamics plays a central role. Despite improvements in existing algorithms they remain computationally expensive which hampers simulating long periods in time and large scale systems. Therefore, parallel approaches appear as a promising solution. Other approaches trade accuracy for speed to address the problem of efficiency. The suitability of these methods, however, depends on the model, the questions to be answered, and the available infrastructure. It is the aim of this project to exploit the flexibility of James II in order to develop and combine suitable algorithms to support an effective and efficient simulation of Brownian dynamics. Thereby, the role of Brownian dynamics in Computational Biology and its potential application for cell biological simulations shall be explored.