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BP: Fachverband Biologische Physik

BP 45: Systems biology

BP 45.2: Vortrag

Donnerstag, 19. März 2015, 15:15–15:30, H 1028

Reaction-diffusion processes and molecular crowding — •David Gomez and Stefan Klumpp — Max Planck Institute of Colloids and Interfaces, Potsdam, Germany

The interior of a living cell is a highly crowded environment, with macromolecules occupying up to 20-40% of the total cell volume. Molecular crowding affects both the thermodynamics and the kinetics of molecular binding, via their equilibrium constant and the diffusion coefficients, respectively. Using random walk on a lattice as well as off- lattice simulations with the simulation software ReaDDy, we consider reactions that uncouple the effects of molecular crowding on binding equilibria and the effects on molecular diffusion. As an application of our method, we combine the two uncoupled reactions into a Michaelis-Menten-like reaction and study the effects of molecular crowding on the overall product synthesis rate. The conditions to obtain the maximal product synthesis rate depend on crowding levels and other parameters intrinsic to the reaction.