Diffusive spreading of a polydisperse polymer solution in a channel

TL;DR

This study uses Monte Carlo simulations to analyze how polydisperse DNA fragments diffuse in a narrow channel, revealing key factors affecting the time needed for fragments to be distinguishable for mapping purposes.

Contribution

It introduces a stochastic model for polydisperse polymer diffusion in channels, highlighting the impact of molecular size distribution and randomness on spreading times.

Findings

Spreading time depends on molecular size distribution and stochastic effects.

The final spatial distribution correlates with a new sequence randomness parameter, Z.

Spreading time distribution follows a known first-passage time form, with variance decreasing linearly with fragment number.

Abstract

Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it takes for these fragments to travel distances large enough for an experimental device to distinguish them and (possibly) estimate their size. In essence, this is a single-file diffusion process in which molecules of different sizes and hence different diffusion coefficients spread out from an initially dense configuration. We use Monte Carlo methods to investigate this class of problems and define the time taken to reach the required final state as a first-passage \textit{spreading time}. Our results demonstrate that the stochastic nature of the diffusion process is as significant as the specifics of the molecular size distribution in determining the spreading time. We examine the relationship between the spreading time and the final space occupied by the fragments as a function of the experimental parameters and determine the fundamental length scale governing this process. We introduce a molecular sequence randomness parameter, $Z$, which is linearly correlated with the final spreading time. Finally, we show that the distribution function of spreading times follows a well-known form for first-passage time problems, and that its variance decreases linearly with the number of fragments.