title: Dynamics of a polymer in a Brownian ratchet.
abstract: We have used Brownian dynamics simulations to study the dynamics of a bead-and-spring polymer subject to a flashing ratchet potential. To elucidate the role of hydrodynamic (HD) interactions, simulations were carried out for the cases where HD interactions are present and when they are absent. The average speed of the polymer and its conformational properties were examined upon variation in the polymer length, N, and the ratchet spatial period, L. Two distinct dynamical regimes were evident. In the low-N/high-L regime, the velocity decreases with increasing N, and center-of-mass diffusion is a key part of the motional mechanism. By contrast, in the high-N /low-L regime, the velocity is insensitive to variation in N, and motion is achieved via the coupling of internal modes to the cycling of the ratchet potential. The location of the regimes is correlated with the average conformational state of the polymer. Incorporating HD interactions increases the average polymer velocity for all polymer lengths and ratchet spatial periods considered. The dynamical behavior of polymers in the low-N/high-L regime can be understood using simple a theoretical model that yields quantitatively reasonable predictions of the polymer velocity.
authors.affiliation: Department of Physics, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada C1A 4P3.
authors.forename: James M
authors.initials: JM
authors.lastname: Polson
authors.forename: Brian
authors.initials: B
authors.lastname: Bylhouwer
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Zuckermann
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Horton
authors.forename: William M
authors.initials: WM
authors.lastname: Scott
mesh_terms: D004058:Diffusion; D055595:Mechanical Phenomena; D008962:Models, Theoretical; D009038:Motion; D011108:Polymers / Q000737:chemistry*; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D011108:Polymers