Flow-Induced Ring Polymer Translocation through Nanopores

Abstract

We investigate the flow-induced linear and ring polymer translocation through nanopores using a hybrid simulation method that combines a lattice-Boltzmann approach for the fluid with a molecular dynamics model for the polymer chain. Our results illustrate that the critical velocity flux for the linear and ring chain exhibits characteristic differences: for the linear chain, the critical velocity flux is independent of the chain length, which is in agreement with previous work; whereas, for the ring chain, the critical velocity flux decreases slowly with the increase of the chain length and gets closer to the critical velocity flux of the linear chain. In addition, we find that the ring chain shows much faster translocation compared to the linear chain with the same chain length. Moreover, the ring chain and the folded linear chain display the similar configurational deformation during the translocation. These results above indicate that with the increase of the chain length, the separation between the linear and ring polymers in the flow-induced translocation through nanopores becomes increasingly difficult.

Size-based separation of supercoiled plasmid DNA using ultrafiltration

“…The sieving coefficients for the two plasmids are very similar for all values of the filtrate flux, with differences of less than 8% (except for a single data point at 40 μm/s for the Biomax ® 100 kDa membrane). Thus, the good selectivity for the supercoiled plasmids seen in [22] and experimental studies [23] have confirmed the universal transmission behavior of linear polymers with different chain length.…”

Flow-Induced Translocation and Conformational Transition of Polymer Chains through Nanochannels: Recent Advances and Future Perspectives

“…22,85,97 Yeomans et al and we also found that P(q)−q curve shows the smooth feature in simulation work. 26,86 However, Wu and Neel et al supported the opposite conclusion. 98,100 Note that there exists a similar debate when discussing the conformational transition in free flows.…”

“…In the first mode, the chain end is put at the channel entrance first to form an initial deformation, 86,96 which makes it more popular in the past few decades due to a much shorter simulation time compared with the free capture mode. 26,37 In simulation, the pressure-driven flow can be implemented in the LB algorithm by introducing an external force density (F ext ), which plays the role of a body force. 26,86 For small Reynolds numbers, the velocity flow rate caused by applying external force density obeys a linear dependence (Darcy's law), q = k c F ext .…”

“…26,37 In simulation, the pressure-driven flow can be implemented in the LB algorithm by introducing an external force density (F ext ), which plays the role of a body force. 26,86 For small Reynolds numbers, the velocity flow rate caused by applying external force density obeys a linear dependence (Darcy's law), q = k c F ext . Thus, fitting the linear relationship can get an accurate k c , which is related to the channel size and the dynamic viscosity of the fluid.…”

“…Thus, fitting the linear relationship can get an accurate k c , which is related to the channel size and the dynamic viscosity of the fluid. 26,86 Thus, the translocation probability P(q), as a function of the velocity flux, can be quantified, which is defined as the ratio of the number of successful translocations to the total number of samples. Importantly, the simulation result P(q) can be directly compared with the rejection coefficient (R obs ) obtained in experimental observation by P(q) = 1 − R obs .…”