Trapping of single diffusing particles by a circular disk on a reflecting flat surface. Absorbing hemisphere approximation

Dagdug, Leonardo; Berezhkovskii, Alexander M.; Bezrukov, Sergey M.

doi:10.1039/d2cp04357b

Cited by 1 publication

(3 citation statements)

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“…Specifically, the predictions for the particle translocation probability vs. simulation experiments were compared in Refs. [20,39] and those for the particle residence and capture times in Refs. [21,39].…”

Section: Resultsmentioning

confidence: 99%

“…Importantly, the validity of expressions in Equations ( 2), (3) and ( 5) was verified by comparing them with the results of three-dimensional Brownian dynamic simulations [20,21,39].…”

Section: Translocation Probability and Steady-state Fluxmentioning

confidence: 93%

“…Recently, we have studied, both analytically and in Brownian dynamic simulations, trapping the kinetics of single particles diffusing in a half-space bounded by a reflecting flat surface containing an absorbing circular disk [39]. We have shown that within the accuracy of several percent, the probability P dics trap of particle trapping by the disk of radius R can be described by an absorbing hemisphere approximation wherein the probability depends only on the distance r 0 between the particle starting point and the disc center and not on the starting point angle.…”

Section: Translocation Probability and Steady-state Fluxmentioning

confidence: 99%

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Counter-Intuitive Features of Particle Dynamics in Nanopores

Berezhkovskii,

Bezrukov

2023

IJMS

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Using the framework of a continuous diffusion model based on the Smoluchowski equation, we analyze particle dynamics in the confinement of a transmembrane nanopore. We briefly review existing analytical results to highlight consequences of interactions between the channel nanopore and the translocating particles. These interactions are described within a minimalistic approach by lumping together multiple physical forces acting on the particle in the pore into a one-dimensional potential of mean force. Such radical simplification allows us to obtain transparent analytical results, often in a simple algebraic form. While most of our findings are quite intuitive, some of them may seem unexpected and even surprising at first glance. The focus is on five examples: (i) attractive interactions between the particles and the nanopore create a potential well and thus cause the particles to spend more time in the pore but, nevertheless, increase their net flux; (ii) if the potential well-describing particle-pore interaction occupies only a part of the pore length, the mean translocation time is a non-monotonic function of the well length, first increasing and then decreasing with the length; (iii) when a rectangular potential well occupies the entire nanopore, the mean particle residence time in the pore is independent of the particle diffusivity inside the pore and depends only on its diffusivity in the bulk; (iv) although in the presence of a potential bias applied to the nanopore the “downhill” particle flux is higher than the “uphill” one, the mean translocation times and their distributions are identical, i.e., independent of the translocation direction; and (v) fast spontaneous gating affects nanopore selectivity when its characteristic time is comparable to that of the particle transport through the pore.

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Section: Resultsmentioning

confidence: 99%

“…Importantly, the validity of expressions in Equations ( 2), (3) and ( 5) was verified by comparing them with the results of three-dimensional Brownian dynamic simulations [20,21,39].…”

Section: Translocation Probability and Steady-state Fluxmentioning

confidence: 93%

Section: Translocation Probability and Steady-state Fluxmentioning

confidence: 99%

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