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Simulating the Capture and Translocation of Rigid fd Viruses though a Nanopore

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The passage of long biological molecules from one side of a membrane to the other through a nanoscale hole has been the subject of intense research in recent years. Motivated by the possibility of new sequencing technologies the focus of this work has been studying the translocation of DNA across biological and synthetic membranes. In this talk I will present results from a joint experimental-simulation study examining the translocation of rod-like fd viruses through a nanopore. While DNA is relatively flexible the fd virus has a persistence length that is over twice that of its contour length and is thus stiff. In principle translocation in this rod-like limit is much easier to model. However I will show that experimental results for the distribution of translocation times exhibit significant deviations from the expected result. I will present a model for fd translocation that was developed to probe these results. Simulations based on this model yield insight into previously unclear experimental results including i) details of how the polymer is capture by the pore at different external fields ii) a correlation between the translocation time and the conformation at capture and iii) sources for the increased dispersion in the translocation time distributions.