Simulation of Molecular Transport in Systems Containing Mobile Obstacles

Crowding and confinement act in concert to slow DNA diffusion within cell-sized droplets

Dynamics of biological macromolecules, such as DNA, in crowded and confined environments are critical to understanding cellular processes such as transcription, infection, and replication. However, the combined effects of cellular confinement and crowding on macromolecular dynamics remain poorly understood. Here, we use differential dynamic microscopy to investigate the diffusion of large DNA molecules confined in cell-sized droplets and crowded by dextran polymers. We show that confined and crowded DNA molecules exhibit universal anomalous subdiffusion with scaling that is insensitive to the degree of confinement and crowding. However, effective DNA diffusion coefficients Deff decrease up to 2 orders of magnitude as droplet size decreases—an effect that is enhanced by increased crowding. We mathematically model the coupling of crowding and confinement by combining polymer scaling theories with confinement-induced depletion effects. The generality and tunability of our system and models render them applicable to elucidating wide-ranging crowded and confined systems.

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DNA diffusion measured in cell-sized droplets with differential dynamic microscopy

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Combination of crowding and confinement leads to subdiffusion and slowing

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Diffusion coefficients of DNA decrease strongly with decreasing droplet size

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Polymer scaling theories and depletion effects predict observed dynamics

Molecular transport in systems containing binding obstacles

We studied the movement of particles in crowded environments by means of extensive Monte Carlo simulations. The dynamic lattice liquid model was employed for this purpose. It is based on the cooperative movement concept and allows the study of systems at high densities. The cooperative model of molecular transport is assumed: the motion of all moving particles is highly correlated. The model is supposed to mimic lateral motion in a membrane and therefore the system is two-dimensional with moving objects and traps placed on a triangular lattice. In our study the interaction (binding) of traps with moving particles was assumed. The conditions in which subdiffusive motion appeared in the system were analysed. The influence of the strength of binding on the dynamic percolation threshold was also shown. The differences in the dynamics compared to systems with impenetrable obstacles and with systems without correlation in motion were presented and discussed. It was shown that in the case of correlated motion the influence of deep traps is similar to that of impenetrable obstacles. If the traps are shallow a recovery to normal diffusion was observed for longer time periods.

Diffusion of small particles in polymer films

The motion of small probe molecules in a two-dimensional system containing frozen polymer chains was studied by means of Monte Carlo simulations. The model macromolecules were coarse-grained and restricted to vertices of a triangular lattice. The cooperative motion algorithm was used to generate representative configurations of macromolecular systems of different polymer concentrations. The remaining unoccupied lattice sites of the system were filled with small molecules. The structure of the polymer film, especially near the percolation threshold, was determined. The dynamic lattice liquid algorithm was then employed for studies of the dynamics of small objects in the polymer matrix. The influence of chain length and polymer concentration on the mobility and the character of motion of small molecules were studied. Short- and long-time dynamic behaviors of solvent molecules were also described. Conditions of anomalous diffusions' appearance in such systems are discussed. The influence of the structure of the matrix of obstacles on the molecular transport was discussed.