Regensburg 2022 – scientific programme

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BP: Fachverband Biologische Physik

BP 7: Poster 1

BP 7.9: Poster

Monday, September 5, 2022, 18:00–20:00, P1

Hierarchical dynamics as result of log-periodic oscillations in proteins — •Emanuel Dorbath, Gerhard Stock, and Steffen Wolf — Albert-Ludwigs-Universität, Freiburg, Germany

Logarithmic oscillations were observed in earthquakes, financial crashes and several biomolecular systems such as proteins. In many protein systems it is generally assumed, that the time scales, ranging from femtoseconds up to microseconds and longer, are in fact not independent but structured hierarchical in the sense that the fast time scales are a prerequisite for the slower ones.

This hierarchy can be well described via the free energy landscape which then gives rise to the logarithmic oscillations and a power-law. From the logarithmic oscillations, multiple relaxation times can be derived extending over several orders of magnitude [Metzler 1999].

Here, an analysis is presented to derive the respective time scales using logarithmic oscillations in non-equilibrium simulations. For this three systems are studied: A 1-dimensional model with an inherent hierarchical energy landscape is used as proof of principle and demonstration of the method. The second one is the simple hierarchical peptide Aib9 with two helical states which has been researched already in the past [Buchenberg 2015]. Finally, the widely studied PDZ2 domain is studied which shows complex conformational folding and restructure mechanisms.