Theoretical analysis of selectivity mechanisms in molecular transport through channels and nanopores

Abstract

Selectivity is one of the most fundamental concepts in natural sciences, and it is also critically important in various technological, industrial and medical applications. Although there are many experimental methods that allow to separate molecules, frequently they are expensive and not efficient. Recently, a new method of separation of chemical mixtures based on utilization of channels and nanopores has been proposed and successfully tested in several systems. However, mechanisms of selectivity in the molecular transport during the translocation are still not well understood. Here we develop a simple theoretical approach to explain the origin of selectivity in molecular fluxes through channels. Our method utilizes discrete-state stochastic models that take into account all relevant chemical transitions and can be solved analytically. More specifically, we analyze channels with one and two binding sites employed for separating mixtures of two types of molecules. The effects of the symmetry and the strength of the molecular-pore interactions are examined. It is found that for one-site binding channels the differences in the strength of interactions for two species drive the separation. At the same time, in more realistic two-site systems the symmetry of interaction potential becomes also important. The most efficient separation is predicted when the specific binding site is located near the entrance to the nanopore. In addition, the selectivity is higher for large entrance rates into the the channel. It is also found that the molecular transport is more selective for repulsive interactions than for attractive interactions. The physical-chemical origin of the observed phenomena are discussed.

The role of fluid-wall interactions on confined liquid diffusion using Mori theory

“…5,6 Diffusion of the fluid in various nanogeometries is of great interest because of various applications, such as molecular sensing, 7-11 controlled drug delivery, 12,13 and nanofiltration. [14][15][16][17] Recent studies suggest that the transport properties of fluid in confined nanogeometries show anisotropic behavior. [18][19][20][21][22] The self-diffusivity of fluids confined in various nanogeometries, such as slit shaped nano-pores, [23][24][25][26] cylindrical nanotube, 27,28 and carbon nanotube [29][30][31][32][33] have been widely investigated using molecular dynamics simulation.…”

Theoretical insights into mechanisms of channel-facilitated molecular transport in the presence of stochastic gating

“…A comprehensive theoretical framework for investigation of chemical mechanisms of translocation and selectivity under stationary-state conditions was recently developed based on this discrete-state kinetic approach. 6,8,10 Importantly, it was also shown that both theoretical methods are mathematically equivalent. 6,8 Recently, stochastic gating has been investigated theoretically using the continuum diffusion description.…”

“…2,3 The importance of translocation through pores stimulated extensive theoretical studies to uncover the underlying molecular mechanisms. [3][4][5][6][7][8][9][10][11][12] But many questions remain open. Specifically, most of existing theoretical studies of channel-facilitated molecular transport concentrate on investigating systems, where interactions between particles and the channel are constant over the time.…”

“…An alternative approach employs a discrete chemical-kinetic description, where the molecular transport is represented as a sequence of chemical transitions between different states that correspond to minima in the interaction potential (free-energy) profile. 6,8,10 The advantage of this approach is that some of these transition rates can be measured in experiments on channel transport. A comprehensive theoretical framework for investigation of chemical mechanisms of translocation and selectivity under stationary-state conditions was recently developed based on this discrete-state kinetic approach.…”

Direct detection of molecular intermediates from first-passage times

“…In chemical kinetics, reaction profiles have long been used to qualitatively rationalise the outcomes of chemical reactions, casting light upon preferred mechanisms and the effects of catalysis [1,2]. In biology, energy landscapes are central to understanding the microscopic origins of processes, including protein folding [3,4,5,6,7,8] and selective transport through membrane channels [9,10,11,12,13,14]. Elucidating the factors governing the dynamics of stochastic processes may be central to even more diverse problems, such as understanding electron transport [15] or the changing stock prices in financial markets [16,17,18].…”