Berlin 2018 – scientific programme

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BP: Fachverband Biologische Physik

BP 12: Computational Biophysics I

BP 12.2: Talk

Tuesday, March 13, 2018, 09:45–10:00, H 1058

Refolding dynamics of molecular constructs after a force quench — •Ken Schäfer and Gregor Diezemann — Institut fuer Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany

In typical force-probe molecular dynamics simulations (FP-MD) one end of a molecular complex is fixed in space and another end is pulled away with a constant velocity. This allows to gather detailed atomistic information about the mechanical unfolding of the complex and the corresponding free energy landscape.

The folding process can be studied by first mechanically unfolding the system and afterwards releasing the external force either completely or to a finite value. This method allows to study the mechanical folding pathway in a systematic way as a function of the quench force. In FP-MD simulations this is of particular interest because it allows to consider forces much smaller than typically used in the standard protocol with a time-dependent force.[1]

We apply the method to study the refolding transition in a calixarene catenane system investigated earlier[2] and extract the kinetic rates for the transition that are analyzed using stochastic models.
[1] C. Hyeon, G. Morrison, D. Thirumalai, PNAS, 2009, 106, 48.

[2] T. Schlesier et al., 2011 J. Phys. Chem. B, 115, 6445.