title: Characteristics of the polymer transport in ratchet systems.
abstract: Molecules with complex internal structure in time-dependent periodic potentials are studied by using short Rubinstein-Duke model polymers as an example. We extend our earlier work on transport in stochastically varying potentials to cover also deterministic potential switching mechanisms, energetic efficiency, and nonuniform charge distributions. We also use currents in the nonequilibrium steady state to identify the dominating mechanisms that lead to polymer transportation and analyze the evolution of the macroscopic state (e.g., total and head-to-head lengths) of the polymers. Several numerical methods are used to solve the master equations and nonlinear optimization problems. The dominating transport mechanisms are found via graph optimization methods. The results show that small changes in the molecule structure and the environment variables can lead to large increases of the drift. The drift and the coherence can be amplified by using deterministic flashing potentials and customized polymer charge distributions. Identifying the dominating transport mechanism by graph analysis tools is found to give insight in how the molecule is transported by the ratchet effect.
authors.affiliation: Department of Physics, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland. janne.kauttonen@jyu.fi
authors.forename: Janne
authors.initials: J
authors.lastname: Kauttonen
authors.forename: Juha
authors.initials: J
authors.lastname: Merikoski
mesh_terms: D000465:Algorithms; D004058:Diffusion; D007700:Kinetics; D008962:Models, Theoretical; D008968:Molecular Conformation; D020409:Molecular Motor Proteins / Q000378:metabolism; D009038:Motion; D011108:Polymers / Q000737:chemistry; D013269:Stochastic Processes
chemical_list: D020409:Molecular Motor Proteins; D011108:Polymers