Role of the potential landscape on the single-file diffusion through channels.

Transport of colloid particles through narrow channels is ubiquitous in cell biology as well as becoming increasingly important for microfluidic applications or targeted drug delivery. Membrane channels in cells are useful models for artificial designs because of their high efficiency, selectivity, and robustness to external fluctuations. Here, we model the passive channels that let cargo simply diffuse through them, affected by a potential profile along the way. Passive transporters achieve high levels of efficiency and specificity from binding interactions with the cargo inside the channel. This however leads to a paradox: why should channels which are so narrow that they are blocked by their cargo evolve to have binding regions for their cargo if that will effectively block them? Using Brownian dynamics simulations, we show that different potentials, notably symmetric, increase the flux through narrow passive channels - and investigate how shape and depth of potentials influence the flux. We find that there exist optimal depths for certain potential shapes and that it is most efficient to apply a small force over an extended region of the channel. On the other hand, having several spatially discrete binding pockets will not alter the flux significantly. We also explore the role of many-particle effects arising from pairwise particle interactions with their neighbours and demonstrate that the relative changes in flux can be accounted for by the kinetics of the absorption reaction at the end of the channel.Simulations were funded by the Cavendish Laboratory teaching committee and per- formed using the Darwin Supercomputer of the Univer- sity of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/), provided by Dell Inc. us- ing Strategic Research Infrastructure Funding from the Higher Education Funding Council for England.This is the accepted manuscript. The final version is available from AIP at http://scitation.aip.org/content/aip/journal/jcp/141/22/10.1063/1.490317