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We present results of molecular simulations of a model protein whose hydrophobic collapse proceeds as a cascade of downhill transitions between distinct intermediate states. Different intermediates are stabilized by means of appropriate harmonic constraints, allowing explicit calculation of the equilibrium free energy landscape. Nonequilibrium collapse trajectories are simulated independently and compared to diffusion on the calculated free energy surface. We find that collapse generally adheres to this surface, but quantitative agreement is complicated by nonequilibrium effects and by dependence of the diffusion coefficient on position on the surface.
Using lattice models we explore the factors that determine the tendencies of polypeptide chains to aggregate by exhaustively sampling the sequence and conformational space. The morphologies of the fibril-like structures and the time scales ($tau_{fib
Dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an alignment
We analyse the dynamics of polymer translocation in the strong force regime by recasting the problem into solving a differential equation with a moving absorbing boundary. For the total translocation time, $tau_{rm tr}$, our simple mean-field model p
Biological activity gives rise to non-equilibrium fluctuations in the cytoplasm of cells; however, there are few methods to directly measure these fluctuations. Using a reconstituted actin cytoskeleton, we show that the bending dynamics of embedded m
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a work fluctu