Berlin 2012 – scientific programme

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BP: Fachverband Biologische Physik

BP 18: Posters: Statistical Physics in Biological Systems

BP 18.23: Poster

Wednesday, March 28, 2012, 17:30–19:30, Poster A

Identification of Metastable States through dynamical clustering of Free Energy Landscape of Biomolecules — •Abhinav Jain and Gerhard Stock — Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg.

Recent simulation of peptides, proteins and RNA have shown that in many cases the free energy landscape can be well characterized in terms of metastable conformational states. They can be employed to construct transition networks of the system, reveal relevant pathways, and influence the average folding times by means of kinetic traps. We introduce a new approach that consists of (i) initial preprocessing to reduce the dimensionality of the data via principal components analysis, followed by k-means clustering to generate microstates [1], (ii) the most probable path algorithm to identify the metastable states of the system, and (iii) boundary corrections of these states to obtain the correct dynamics. The potential of the method is demonstrated with application to the villin headpiece subdomain.
Jain; Hegger; Stock. J. Phys. Chem. Lett. 2010, 1, 2769 - 2773