Langevin dynamics for the transport of flexible biological macromolecules in confined geometries

The transport of flexible biological macromolecules in confined geometries is found in a variety of important biophysical systems including biomolecular movements through pores in cell walls, vesicle walls, and synthetic nanopores for sequencing methods. In this study, we extend our previous analysis of the Fokker–Planck and Langevin dynamics for describing the coupled translational and rotational motions of single structuredmacromolecules near structured external surfaces or walls [M. H. Peters, J. Chem. Phys. 110, 528 (1999); 112, 5488 (2000)] to the problem of many interacting macromolecules in the presence of structured external surfaces representing the confining geometry. Overall macromolecular flexibility is modeled through specified interaction potentials between the structured Brownian subunits (B-particles), as already demonstrated for protein and DNA molecules briefly reviewed here. We derive the Fokker–Planck equation using a formal multiple time scale perturbation expansion of the Liouville equation for the entire system, i.e., solvent,macromolecules, and external surface. A configurational–orientational Langevin displacement equation is also obtained for use in Brownian dynamics applications. We demonstrate important effects of the external surface on implicit solvent forces through formal descriptions of the grand frictiontensor and equilibrium average force of the solvent on the B-particles. The formal analysis provides both transparency of all terms of the Langevin displacement equation as well as a prescription for their determination. As an example, application of the methods developed, the real-time movement of an α-helix protein through a carbon nanotube is simulated