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To better understand the capture process by a nanopore, we introduce anefficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times andlarge system sizes by mapping the dynamic of a point-like particle in a 3Dspherically symmetric system onto the 1D biased random walk. Our algorithmrecovers the steady-state analytical solution and allows us to studytime-dependent processes such as transients. Simulation results show that thesteady-state depletion zone near pore is barely larger than the pore radius andnarrows at higher field intensities; as a result, the time to reachsteady-state is much smaller than the time required to empty a zone of the sizeof the capture radius $\lambda_e$. When the sample reservoir has a finite size,a second depletion region propagates inward from the outer wall, and thecapture rate starts decreasing when it reaches the capture radius $\lambda_e$.We also note that the flatness of the electric field near the pore, which isoften neglected, induces a traffic jam that can increase the transient time byseveral orders of magnitude. Finally, we propose a new proof-of-concept schemeto separate two analytes of the same mobility but different diffusioncoefficients using time-varying fields.

An efficient Kinetic Monte Carlo to study analyte capture by a nanopore: Transients, boundary conditions and time-dependent fields