385081 Modeling Polymer Translocation through Biological and Solid-State Nanopores

Monday, November 17, 2014
Galleria Exhibit Hall (Hilton Atlanta)
Harshwardhan Katkar, Department of Chemical Engineering, University of Massachusetts, AMHERST, MA and Murugappan Muthukumar, Polymer Science and Engineering, University of Massachusetts, Amherst, MA

We have investigated the ubiquitous phenomenon of electrophoretically-driven transport of single macromolecules through single biological and solid-state nanopores, by using a combination of Langevin Dynamics simulations and Fokker-Planck formalism. In our theoretical/modeling work, we have explicitly accounted for geometry and charge decoration of the nanopores and the chemical sequences of the macromolecules which are transported by the single-file motion. Specifically, we will present results for the following three related issues: (1) Translocation of a uniformly charged flexible polyelectrolyte, such as ss-DNA, through a narrow cylindrical pore bearing charge patterns under an externally applied electric field. We find unexpected nonmonotonic dependence of the kinetics of transport on the period of patterning. An explanation of this novel phenomenon is derived by performing statistical mechanics calculation, based on polymer statistics and the Fokker-Planck representation of polymer transport. The role of sequences on the polyelectrolyte is also addressed. In addition, we report the consequences of the stochastic resonance between an oscillatory driving field and the ratcheting mechanism of a translocating polymer along a patterned pore. (2) In the interest of composing suitable strategies to optimize translocation speed of DNA in the context of DNA-sequencing, we have modeled the diffusion and mobility of DNA through a nanopore under a ratcheting force from a polymerase. Our work offers a quantitative measure of the signal-to-noise ratio for the readability of base calling in the electrophoresis- based DNA sequencing. (3) Translocation of branched polyelectrolyte molecules through nanopores. We find that the transport kinetics of branched polymers depends crucially on the architecture of the polymer and the dimensions of the nanopore, suggesting a new analytical technique to characterize such polymers in aqueous media, as an alternative to gel permeation chromatography.

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