We propose a method for the theoretical investigation of polymer translocation through composite pore structures possessing arbitrarily specified geometries. The proposed method accounts for possible reverse chain motions at the interface between the constituent parts of a composite pore. As an illustration of our method, we study polymer translocation between two spherical compartments connected by a cylindrical pore and by a composite pore consisting of two connected cylinders of different diameters, which is structurally similar to the α -hemolysin membrane channel. We demonstrate that reverse chain motions between the pore constituents may contribute significantly to the total translocation time. Our results further establish that translocation through a two-cylinder composite pore is faster when the chain is introduced into the pore on the cis (wide) side of the channel rather than the trans (narrow) side.
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