Numerical simulation of conformational variability in biopolymer translocation through wide nanopores

Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of long polymers (up to 8000 monomers) are monitored as they pass through nanopores. Comparison between the different pore sizes shows that wide pores can host a larger number of multiple biopolymer segments, as compared to smaller pores. The simulations provide clear evidence of folding quantization in the translocation process as the biopolymers undertake multifolded configurations, characterized by a well-defined integer number of folds. Accordingly, the translocation time is no longer represented by a single-exponent power-law dependence on the length, as is the case for single-file translocation through narrow pores. The folding quantization increases with the biopolymer length, while the rate of translocated beads at each time step is linearly correlated with the number of resident beads in the pore. Finally, analysis 6 Present address: Department Physik, Technische Universität München, Garching, 85747, Germany. c ©2009 IOP Publishing Ltd and SISSA 1742-5468/09/P06009+10$30.00 .S tt.M ech. (209) P 0009 Numerical simulation of long biopolymer translocation of the statistics over the translocation work unravels the importance of the hydrodynamic interactions in the process.