Polymer deformation in Brownian ratchets: Theory and molecular dynamics simulations

We examine polymers in the presence of an applied asymmetric sawtooth (ratchet) potential which is periodically switched on and off, using molecular dynamics (MD) simulations with an explicit Lennard-Jones solvent. We show that the distribution of the center of mass for a polymer in a ratchet is relatively wide for potential well depths U-0 on the order of several k(B)T. The application of the ratchet potential also deforms the polymer chains. With increasing U-0 the Flory exponent varies from that for a free three-dimensional (3D) chain, nu=3/5 (U-0=0), to that corresponding to a 2D compressed (pancake-shaped) polymer with a value of nu=3/4 for moderate U-0. This has the added effect of decreasing a polymer's diffusion coefficient from its 3D value D-3D to that of a pancaked-shaped polymer moving parallel to its minor axis D-2D. The result is that a polymer then has a time-dependent diffusion coefficient D(t) during the ratchet off time. We further show that this suggests a different method to operate a ratchet, where the off time of the ratchet, t(off), is defined in terms of the relaxation time of the polymer, tau(R). We also derive a modified version of the Bader ratchet model [Bader , Proc. Natl. Acad. Sci. U.S.A. 96, 13165 (1999)] which accounts for this deformation and we present a simple expression to describe the time dependent diffusion coefficient D(t). Using this model we then illustrate that polymer deformation can be used to modulate polymer migration in a ratchet potential.