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場所： 横浜市立大学大学院国際総合科学研究科
情報科学セミナー室(B407)
〒230-0045 横浜市鶴見区末広町1-7-29
http://www.tsurumi.yokohama-cu.ac.jp/access.html
Speaker: Prof. Gerhard Stock,
Institute of Physical and Theoretical Chemistry, J. W. Goethe University Frankfurt, Germany
http://www.theochem.uni-frankfurt.de/
Title: Modeling the free energy landscape of biomolecules
Abstract:
A systematic approach to construct a low-dimensional free energy landscape from a classical molecular dynamics (MD) simulation is presented. The approach is based on the recently proposed dihedral angle principal component analysis, which avoids artifacts due to the mixing of internal and overall motion in Cartesian coordinates and circumvents problems associated with the circularity of angular variables. Requiring that the energy landscape reproduces the correct number, energy, and location of the system's metastable states and barriers, the dimensionality of the free energy landscape (i.e., the number of essential components) is obtained. This dimensionality can be determined from the distribution and autocorrelation of the principal components. Performing an 800 ns MD simulation of the folding of heptaalanine in explicit water and using geometric and kinetic clustering techniques, it is shown that a five-dimensional energy landscape is a suitable and accurate representation of the full-dimensional landscape. In a second step, the energy landscape is employed in a Langevin simulation to facilitate a detailed investigation of biomolecular dynamics in low dimensions.