  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 non-uniform charge distributions. We also use currents
in the non-equilibrium 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.
