Polanowski, Piotr

Sikorski, Andrzej

English

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The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and ApplicationSimulation of diffusion in a crowded environment: The application of theDynamic Lattice Liquid Model (DLL)Piotr Polanowski1∗, Andrzej Sikorski21Department of Molecular Physics, Technical University of Łódź, Łódź, Poland2Department of Chemistry, University of Warsaw, Warsaw, Poland∗piotr.polanowski@p.lodz.plExtensive and systematic simulation studies of two-dimensional fluid motion in a complex crowdedenvironment were performed. In contrast to other works we focused on cooperative phenomena thatoccurred where the motion of particles takes place in a dense crowded system. Our main goal was toanswer the question how do fluid molecules move in an environment which has a complex structureand taking into consideration the fact that motion of fluid molecules is highly correlated. The DynamicLattice Liquid (DLL) model, which can work at the highest fluid density, was employed. It becamethe basis for a parallel algorithm, which took into account coincidences of attempts of elementarymolecular motion resulting in local cooperative structural transformations. Within the frame of theDLL model we considered cooperative motions of fluid particles in an environment that containedstatic obstacles. We studied the dynamic properties of the system, like the mean square displacementand the relaxation time of the position as a function of the concentration of obstacles. The changesof hydrodynamic interactions were also investigated by studies of the distribution of cooperative looplength. The subdiffusive motion of particles was found in the crowded system. It was also shown that thepercolation threshold determined from the dynamic behavior of the mobile particles was considerablylower than that determined from the cluster analysis.The authors gratefully acknowledge the financial support from NCN grant nr 2011/01/B/ST5/06319.References[1] H.-X. Zhou, G. Rivas, A.P. Minton: Macromolecular crowding and confinement: Biochemical,biophysical, and potential physiological consequences. Annu. Rev. Biophys. 37, 375–397 (2008)[2] D. Ben-Avraham, S. Havlin: Diffusion and reactions in fractals and disordered systems. Cam-bridge University Press, Cambridge (2000)[3] P. Polanowski, T. Pakula: Studies of mobility, interdiffusion, and self-diffusion in two-componentmixtures using the dynamic lattice liquid model. J. Chem. Phys. 118, 11139–11146 (2003)

Simulation of diffusion in a crowded environment: the application of the Dynamic Lattice Liquid Model (DLL)

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Simulation of diffusion in a crowded environment: the application of the Dynamic Lattice Liquid Model (DLL)

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