Quantifying transport in crowded biochemical environments

Abstract

Transport of cells and biochemical molecules often takes place in crowded, heterogeneous environments. As such, it is important we understand how to quantify crowded transport phenomena, and the possibilities of extracting transport coefficients from limited observations. We employ a volume-excluding random walk model on a square lattice where different fractions of lattice sites are filled with inert, immobile obstacles to investigate whether it is possible to estimate parameters associated with transport when crowding is present. By collecting and analysing data obtained on multiple spatial scales we demonstrate that commonly used models of motility within crowded environments can be used to reliably predict our random walk data. However, infeasibly large amounts of data are needed to estimate transport parameters, and quantitative estimates may differ depending on the spatial scale on which they are collected. We also demonstrate that in models of crowded environments there is a relatively large region of the parameter space within which it is difficult to distinguish between the “best fit” parameter values. This suggests commonly used descriptions of transport within crowded systems may not be appropriate, and that we should be careful in choosing models to represent the effects of crowding upon motility within biochemical systems.