An efficient kinetic Monte Carlo to study analyte capture by a nanopore: transients, boundary conditions and time-dependent fields. Issue 2 (5th January 2021)

• Record Type: Journal Article
• Authors: Qiao, Le; Ignacio, Maxime; Slater, Gary W.
• Is Part Of: Physical chemistry chemical physics. Volume 23:Issue 2(2020)
• Page Start: 1489
• Page End: 1499
• Publication Date: 2021-01-05
• Subjects: Chemistry, Physical and theoretical -- Periodicals; 541.3
• DOI: 10.1039/d0cp03638b
• Languages: English
• ISSNs: 1463-9076

Abstract

Abstract : We introduce an efficient KMC algorithm to simulate voltage-driven translocation, as well as a new pulsed-field method to selectively translocate molecules. Abstract : To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically symmetric system onto the 1D biased random walk. Our algorithm recovers the steady-state analytical solution and allows us to study time-dependent processes such as transients. Simulation results show that the steady-state depletion zone near pore is barely larger than the pore radius and narrows at higher field intensities; as a result, the time to reach steady-state is much smaller than the time required to empty a zone of the size of the capture radius λ e . When the sample reservoir has a finite size, a second depletion region propagates inward from the outer wall, and the capture rate starts decreasing when it reaches the capture radius λ e . We also note that the flatness of the electric field near the pore, which is often neglected, induces a traffic jam that can increase the transient time by several orders of magnitude. Finally, we propose a new proof-of-concept scheme to separate two analytes of the same mobility but different diffusion coefficients using time-varying fields.