Hybrid Molecular Dynamics simulations of living filaments

Jean-Paul Ryckaert

Physique des Polymères, Université Libre de Bruxelles,

Campus Plaine, CP 223, B-1050 Brussels, Belgium

After a general introduction on the phenomenology and statistical mechanics treatments of living filaments (cytoskeleton), we stress the relevance of developping a wormlike chain “living filament “model. Hence, based on such a model, we adopt a hybrid Molecular Dynamics/Multi-particle Collision Dynamics technique to simulate a set of self-assembled semiflexible filaments and free monomers to which we add a Monte-Carlo scheme dealing with single monomer addition (polymerization) or removal (depolymerization), satisfying the detailed balance. Preliminary results concern “equilibrium polymers” with distinct reaction rates at both ends, such as self-assembled ADP-actin filaments in the absence of ATP hydrolysis and other proteins. We report the static distribution of filament lengths and the corresponding dynamical fluctuations on an equilibrium trajectory. Potential generalizations of this method to include irreversible steps like ATP-actin hydrolysis are discussed.