Abstract
In this review we compiled recent advances concerning the cooperative motion in crowded soft matter systems. We tried to answer the question how to perform dynamic Monte Carlo simulations of dense macromolecular systems effectively. This problem is not simple due to the fact that the movement in such systems is strictly correlated which leads to cooperative phenomena. The influence of crowding was found interesting especially for two-dimensional cases, e.g., in membranes where the presence of macromolecules, proteins and cytoskeleton often changed the mean-square displacement as a function of the lag time and anomalous diffusion appeared. Simple models are frequently used to shed a light on molecular transport in biological systems. The emphasis was given to the Dynamic Lattice Liquid model. The latter model became a basis for a parallel algorithm that takes into account coincidences of elementary molecular motion attempts resulting in local cooperative structural transformations. The emphasis is put on influence of the model of molecular transport on the diffusion. The comparison to alternative approaches like single agent model was carried out.
Highlights
Molecular transport in crowded environments plays a key role in a variety of areas [1,2,3,4] while dynamic behavior in such systems is not fully recognized and even its origin is debatable [5,6,7,8,9,10].Major experimental techniques used for studies of transport in disordered systems are mainly fluorescence correlation spectroscopy [11] and single particle tracking [12, 13]
Real experiments showed exponent α between 0.2 and 0.9 [5, 14] while computer simulations for matrices of obstacles revealed that at the percolation threshold the exponent α approached the value 0.697 [10, 14,15,16,17,18,19] An anomalous diffusion was found in several models but we are interested in the case of obstructive motion where it is caused by the presence of other objects [5, 15, 16]
This work reviews the problem of dynamics in a soft matter model employing the Dynamic lattice liquid (DLL) [37, 38] where the correlations in motion between mobile objects were introduced into the system
Summary
Received: 17 September 2020 Accepted: 10 November 2020 Published: 27 November 2020. Citation: Polanowski P and Sikorski A (2020) The Concept of Cooperative Dynamics in Simulations of Soft Matter. We tried to answer the question how to perform dynamic Monte Carlo simulations of dense macromolecular systems effectively. This problem is not simple due to the fact that the movement in such systems is strictly correlated which leads to cooperative phenomena. Simple models are frequently used to shed a light on molecular transport in biological systems. The emphasis was given to the Dynamic Lattice Liquid model. The latter model became a basis for a parallel algorithm that takes into account coincidences of elementary molecular motion attempts resulting in local cooperative structural transformations. The emphasis is put on influence of the model of molecular transport on the diffusion.
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