A “Tug-of-War” in a three dimensional Double-Nanopore system

In an experimental “Tug-of-War” (X. Liu et al., Small 2019, 1901704), a DNA segment co-captured in both the pores in a Double-Nanopore system is subject to two equal and opposite biases at two pore locations for better control and repeated measurements of the same segment. We simulate a model system in three dimensions and use Brownian dynamics to reveal the details of the single file translocation. Specifically, we study the consequence of increased persistence length of the segment in between the pores due to the tug-of-war forces. We characterize the diffusive motion of the chain either for exact “Tug-of-War” with zero bias, or subject to a small net bias, and provide error estimates of the length translocated through the Double- nanopore from the velocity measurements. Furthermore, we compare the velocities of the individual monomers with the average velocity of the entire chain and explore measures to reduce the fluctuation in velocity along the chain.