All biological functions, including respiration, digestion and muscle motion, are based upon the intrinsic dynamics of biological macromolecules and their interactions within a cellular architecture. The intrinsic difficulty of these systems lies in the fact that small motions on the molecular scale are closely coupled to the function of the entire cell. Many experimental tools exist for probing such processes, but often have to impose rather artificial conditions and are limited to either resolving spatial or temporal details. Simulation techniques, on the other hand, face the difficulty of choosing appropriate levels of modeling the system and have to solve high performance computing problems on all scales.

Our scientific goals:

• Develop mathematical and computational methods for simulation and modeling of biomolecules

• Develop efficient simulation methods for cellular processes which resolve the diffusional motion and pattern formation of single molecules

• Create a theoretical framework to combine experimental and simulation data, so as to help closing the gap between both worlds

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• Noé, F. and Schütte, Ch. and Vanden-Eijnden, E. and Reich, L. and Weikl, T. (2009) Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations. Proc. Natl. Acad. Sci. USA, 106 (45). pp. 19011-19016.

• Prinz, J.-H. and Wu, H. and Sarich, M. and Keller, B. and Fischbach, M. and Held, M. and Chodera, J. D. and Schütte, Ch. and Noé, F. (2010) Markov models of molecular kinetics: Generation and Validation. J. Chem. Phys. . (Submitted)

• Held, M. and Metzner, Ph. and Prinz, J.-H. and Noé, F. (2010) Mechanisms of Protein-Ligand association and its modulation by protein mutations. Biophys. J. . (In Press)