Abstract
We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer-obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer-obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer-crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids.
Highlights
The trapping times spent by the tracer on the obstacle surface are analysed in Section IIIB, and in Section IIIC we investigate the time averaged mean squared displacement (MSD) based on single trajectory time series
The local scaling exponent b(t) is computed as discretised logarithmic derivative from the MSD traces obtained from the simulations (i.e., we compute the local derivative of log(MSD) with respect to the logarithmically sampled time, see eqn (3) of ref. 57)
We studied the passive motion of a tracer particle in an ordered, stationary array of attractive spherical crowders
Summary
Macromolecular crowding (MMC) abounds in living biological cells, with up to f E 30–35% of the volume of the cytoplasmic fluid being occupied by large biopolymers such as proteins, nucleic acids, ribosomes, as well as membranous structures, and other complexes.[1,2,3,4,5] These volume-excluding and often non-inert obstacles alter the diffusion behaviour of cellular components and the rates of biochemical reactions taking place in this highly complex liquid.[6,7,8,9,10,11] These changes occur both due to an enhanced solution viscosity[12] and the sheer physical obstruction imposed on particle diffusion due to the presence of the obstacles. Diffusion is more localised and the value of b(t) smaller.[53] Remarkably, the transient subdiffusion regime was shown to disappear at higher obstacle mobility.[52,53] the distribution of particle trapping times in dynamical cages formed between the crowders observed in simulations for mobile, confined, and static obstacles was shown to be inconsistent with CTRW models[52,54] Recent experimental advances in the field of obstructed obstacle-mediated tracer diffusion, including the regimes of transient anomalous diffusion, are presented in ref. We perform extensive Monte-Carlo simulations of tracer diffusion on 3D lattices of sticky spherical obstacles of varying radius R In this obstruction-and-binding diffusion model we examine the trapping time distributions of the tracers, the time averaged MSD—which is a more relevant observable when compared to experimental situations than the ensemble averaged MSD (1)—and the effective tracer diffusivity D.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
