CSC

	Tehdyt toimenpiteet University of Oulu The Biocenter and the Dep. of Biochemistry Group leader: Andre Juffer Home page: http://www.biochem.oulu.fi/Biocomputing The Biocomputing group in Oulu is predominantly concerned with computer simulations of biomolecular systems. The general research interests are concerned with (i) the understanding of biomolecular structure, dynamics and function, and (ii) the development and application of computer models and simulation methods for molecular systems. An important simulation tool is molecular dynamics, which relies on the classical equations of motion to simulate the dynamics of for instance a solvated protein in water or even a membrane environment. Also, the technique of Monte Carlo simulation is employed. For instance, in combination with continuum electrostatics and the boundary element method, this simulation technique is used to calculate acid dissociation constants of titrating sites in proteins. More recently, a stochastic event-based model has been developed that is capable of simulating ribosome traffic along mRNA sequences and mimics in fact recombinant protein synthesis as it happens inside the cell. An important challenge for the future is to reach larger length and longer time scales. For this, we follow two strategies. One is concerned with the implementation of Grid aware simulation tools and the second is to develop alternative simulation models that operate at a coarse-grained or mesoscopic level to cover substantially longer time and length scales. Most likely, it is the combination of both that will be successful. For the first strategy, we have successfully build a Linux-based computing cluster that is scheduled to become part of the new national material science Grid in 2005. For the second strategy, we are currently developing, among other, a method that is based upon dissipative particle dynamics (DPD), where special attention is given to long ranged electrostatic interactions. Its application to protein simulation would involve selecting suitable degrees of freedoms, a set of DPD particles and their interactions. Back to the group list