Ratcheted diffusion transport through crowded nanochannels.

Abstract

The problem of transport through nanochannels is one of the major questions in cell biology, with a wide range of applications. Brownian ratchets are fundamental in various biochemical processes, and are roughly divided into two categories: active (usually ATP-powered) molecular motors and passive constructions with a directional bias, where the transport is driven by thermal motion. In this paper we discuss the latter process, of spontaneous translocation of molecules (Brownian particles) by ratcheted diffusion with no external energy input: a problem relevant for protein translocation along bacterial flagella or injectosome complex, or DNA translocation by bacteriophages. We use molecular dynamics simulations and statistical theory to identify two regimes of transport: at low rate of particles injection into the channel the process is controlled by the individual diffusion towards the open end (the first passage problem), while at a higher rate of injection the crowded regime sets in. In this regime the particle density in the channel reaches a constant saturation level and the resistance force increases substantially, due to the osmotic pressure build-up. To achieve a steady-state transport, the apparatus that injects new particles into a crowded channel has to operate with an increasing power consumption, proportional to the length of the channel and the required rate of transport. The analysis of resistance force, and accordingly -- the power required to inject the particles into a crowded channel to oversome its clogging, is also relevant for many microfluidics applications.