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Vortrag von Prof. Dr. Martin Zacharias im Rahmen unserer ZBI "Distinguished Speaker Series"

Am Mittwoch, 19. Oktober 2011 wird Prof. Dr. Martin Zacharias (Physik-Department T38, TU München) im Rahmen der ZBI "Distinguished Speaker Series" einen Vortrag zum Thema "Studying nucleic acid flexibility using molecular dynamics and advanced sampling methods" halten (Raum 001, ZBI (Gebäude E 2.1); Beginn: Punkt 17:00 Uhr).



Understanding the dynamics of biomolecules is of critical importance to better understand its biological function. We employ molecular dynamics (MD) simulations to study the dynamics of proteins and nucleic acids during structure formation and binding processes. This includes approaches to extract free energy changes associated with global conformational changes in nucleic acids such as bending and twisting that play a decisive role upon association with proteins. MD simulations can also be used to study double strand formation of DNA or the folding process of structural motifs in nucleic acids. However, for many applications the currently accessible time scales are too short to sufficiently sample relevant conformational states. Replica exchange (REMD) simulations that allow exchanges between MD simulations performed at different temperatures are frequently used to sample conformational states of peptides and proteins. A drawback of the standard REMD method is the rapid increase of the number of replicas with increasing system size to cover a desired temperature range. In an effort to limit the number of replicas we have developed new Hamiltonian-REMD methods that employ various biasing potential levels associated with soft degrees of freedom of the biomolecule for each replica run. The method requires only a very modest number of replicas and was successfully tested on several protein and nucleic acid systems. Applications of the REMD approach to simulate folding and structural transitions in nucleic acids will be presented.