Berlin 2012 – scientific programme
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BP: Fachverband Biologische Physik
BP 18: Posters: Statistical Physics in Biological Systems
BP 18.30: Poster
Wednesday, March 28, 2012, 17:30–19:30, Poster A
Langevin Modeling of Biomolecular Dynamics — •Norbert Schaudinnus1, Rainer Hegger2, and Gerhard Stock1 — 1Biomolecular Dynamics, Physikalisches Institut, Universität Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg — 2J.W. Goethe University, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt/Main
Principal component analysis is widely used to obtain coordinates that monitor essential dynamics of high-dimensional biomolecular systems. Applying this technique to MD simulations of various peptides allows a separation of slow large-amplitude motions and high-frequency fluctuations [1].
A Langevin simulation on the first few principal components using local estimates of drift and diffusion fields is shown to reproduce the conformational dynamics of those peptides [2]. Particularly, a set of short trajectories can be used instead of one continuous trajectory as input.
We demonstrate thermodynamical characteristics of the studied peptide systems revealed by this method. Furthermore, we present first attempts to construct an analytical model to characterize the free energy landscape.
A. Altis, M. Otten, P.H. Nguyen, R. Hegger and G. Stock, J. Chem. Phys. 128, 245102 (2008)
R. Hegger and G. Stock, J. Chem. Phys. 130, 034106 (2009)