Abstract

Describing particle transport at the macroscopic or mesoscopic level in non-ideal environments poses fundamental theoretical challenges in domains ranging from inter and intra-cellular transport in biology to diffusion in porous media. Yet, often the nature of the constraints coming from many-body interactions or reflecting a complex and confining environment are better understood and modeled at the microscopic level. In this paper we review the subtle link between microscopic exclusion processes and the mean-field equations that ensue from them in the continuum limit. We show that in an inhomogeneous medium, i.e. when jumps are controlled by site-dependent hopping rates, one can obtain three different nonlinear advection-diffusion equations in the continuum limit, suitable for describing transport in the presence of quenched disorder and external fields, depending on the particular rule embodying site inequivalence at the microscopic level. In a situation that might be termed point-like scenario, when particles are treated as point-like objects, the effect of crowding as imposed at the microscopic level manifests in the mean-field equations only if some degree of inhomogeneity is enforced into the model. Conversely, when interacting agents are assigned a finite size, under the more realistic extended crowding framework, exclusion constraints persist in the unbiased macroscopic representation.

Highlights

  • Diffusive transport is central in many areas of physics, chemistry, biology, and soft matter [1,2,3,4]

  • In this paper we review the subtle link between macroscopic transport equations, such as the diffusion equation, and microscopic processes, modeling the stochastic dynamics of some agents

  • The cytoplasm is quite densely packed, different molecular species competing for the available spatial resources

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Summary

INTRODUCTION

Diffusive transport is central in many areas of physics, chemistry, biology, and soft matter [1,2,3,4]. As shown in Galanti et al [34], the effect of crowding can result in crossovers between normal and anomalous diffusion, leading to different descriptive scenarios which appear to depend on the selected initial conditions and on the specific time scale of observation Another related issue is that of diffusion-limited reactions [35], which are ubiquitous in many domains in biology and chemistry, touching upon problems such as association, folding and stability of proteins [13, 36] and bimolecular reactions in solution [37,38,39,40,41], including enzyme kinetics [42], and the dynamics of active agents [43, 44]. In the last section we draw the conclusions and we summarize the different extent to which the crowding fine-tunes deviation from the classical picture

FROM MICROSCOPIC PROCESSES TO MACROSCOPIC EQUATIONS
Mean-Field Equations
Site-Dependent Rates
EXTENDED CROWDING
Findings
SUMMARY AND DISCUSSION
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