Dresden 2017 – scientific programme

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BP: Fachverband Biologische Physik

BP 24: Posters - Protein Structure and Dynamics

BP 24.14: Poster

Tuesday, March 21, 2017, 14:00–16:00, P1A

Global Langevin model of multidimensional biomolecular dynamics — •Benjamin Lickert, Norbert Schaudinnus, Mithun Biswas, and Gerhard Stock — Albert Ludwigs University, 79104 Freiburg, Germany

Biomolecular processes, recorded by molecular dynamics simulations, are often treated as diffusive motions on low-dimensional free energy landscapes F(x^→). A theoretical basis of such an interpretation is provided by Zwanzig’s system-bath Hamiltonian approach which allows to derive a memory-free Langevin equation describing the motion of the system x^→ on the free energy landscape F(x^→).
While the theoretical framework of Zwanzig generally assumes a highly idealised form of the bath Hamiltonian and the system-bath coupling, it would be desirable to apply the approach to realistic data-based biomolecular systems. Here, we propose a practical method to construct an analytically defined global model of structural dynamics. On basis of molecular dynamics simulations and suitable system coordinates our approach uses an "empirical valence bond"-type model to represent the multidimensional free energy and an approximate description of the friction. We show for several systems that the resulting Langevin models reproduce the results of the underlying all-atom simulations. Since the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (e.g., delta-correlated Gaussian noise), the analytically defined model provides a correct realisation of Zwanzig’s formulation.