Diffusion Dynamics Of Macromolecule In Crowded Environments

Diffusion is a ubiquitous phenomenon in the nature and it is key to a lot of phisical and chemical processes. As the development of macromolecular science, the effects of macromolecular crowding on a lot of phisical and chemical processesin macromolecular systems, such as the protein-DNA recognition and target searching on surface, have been discovered. The investigation on diffusion processes in macromolecular crowded systems is beneficial to the understanding of the nature of many phisical and chemical processes in macromolecular systems. Here we show our investigations on three kinds of diffusion-controlled processes in crowded environments:First, in gas or liquid consists of small molecules such as water, the relationship between the mean squared displacement of the molecules and diffusion time is <r2(t)>～t, but in macromolecular crowded systems such as biosystems, subdiffusional behavior of the marcromolecules is found,i.e., <r2 (t)>～tα,α<1. We use Langevin dynamics simulation to investigate how the density and size of the crowders affect the subdiffusion exponent of the tracer.Second, the search process of the protein to specific sites on DNA plays an imprtant role of the trascription and replication of the DNA, and facilitated diffusion model was proposed to describe this process. We use Langevin dynamics simulation to study the effect of macromolecular crowding and non-specific protein-DNA attraction on the protein’s search process to its target on DNA.Third, a lot of physical and chemical processes on the surface, such as immune reactions on cell membrans. are controlled by the diffusion characteristcs of the reactants. Here we use Langevin dynamics simulation to investigate the relationship between the search rate of the reactants and the density of the crowders in the system, and the non-specific attraction between the reactant and the surface.