Nanomechanics of Biomolecules

Thursday, July 26, 2007 - 9:55am - 10:55am
EE/CS 3-180
Christof Schütte (Freie Universität Berlin)
The talk will demonstrate how to extract nanomechanical properties
like stiffnesses and friction parameters of biomolecules from molecular dynamics
simulations. The aim is to construct optimal sets of parameters from molecular
dynamics time series for all important conformations of a biomolecule under
investigation. Parameter optimality will be measured in a maximal likelihood
estimation sense, i.e., such parameters are optimal for which the probability
that the observed time series is an output of equations of motions with these
parameters is the highest possible. It will be demonstrated how to derive the
equation for the optimal parameter set, how these can be implemented
efficiently, and how the resulting algorithm perform for moderately sized
examples (12-alanine with implicit water and some B-DNA 16mer with explicit