Coarse-grained molecular dynamics and continuum models for the transport of protein molecules

We describe protein transport across nanopores in a coarse-grained modeling. Numerical results reproduce a rich phenomenology, from fast transport to long blockades. Main translocation features are maintained in a 1D description of the process in an appropriate potential of the mean force. A second-rank tensor is selected as descriptor of the molecular shape. Its dynamics is identified by a power-equivalence procedure and Cauchy-Born rule. The modeling is supplemented by heuristic approaches that appear adequate also in unconstrained dynamics.