Numerical simulation of conformational variability in biopolymer translocation through wide nanopores

Details Numerical simulation of conformational variability in biopolymer translocation through wide nanopores Numerical simulation of conformational variability in biopolymer translocation through wide nanopores

2009-01-16

arxiv.org/abs/0901.2497v1

Physics

Biological Physics

10 pages, 6 figures, to appear in J. Stat. (2009)

Scientific paper

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 multi-folded 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 it 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 to the number of resident beads in the pore. Finally, analysis of the statistics over the translocation work unravels the importance of the hydrodynamic interactions in the process.

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