title: How proteins squeeze through polymer networks: a Cartesian lattice study.
abstract: In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamical behavior of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense networks are created by a combined version of the bond fluctuation method and a Metropolis Monte Carlo algorithm. Semidilute behavior of the dense chain networks is shown. By comparing diffusion of particles in a static and a dynamical chain network, we demonstrate that chain diffusion does not alter the diffusion process of small particles. However, we prove that a dynamical network facilitates the transport of large particles. By weighting the mean square displacement trajectories of particles in the static chain, network data from the dynamical network can be reconstructed. Additionally, it is shown that subdiffusive behavior of particles on short time scales results from trapping processes in the crowded environment of the chain network. In the presented model a protein with 30 nm diameter has an effective diffusion coefficient of 1.24 x 10(-11) m2/s in a chromatin fiber network.
authors.affiliation: BIOMS Center for Modeling and Simulation in the Biosciences, D-69120 Heidelberg, Germany. a.wedemeier@googlemail.com
authors.forename: Annika
authors.initials: A
authors.lastname: Wedemeier
authors.forename: Holger
authors.initials: H
authors.lastname: Merlitz
authors.forename: Chen-Xu
authors.initials: CX
authors.lastname: Wu
authors.forename: Jörg
authors.initials: J
authors.lastname: Langowski
mesh_terms: D002467:Cell Nucleus / Q000737:chemistry*; D003198:Computer Simulation; D004058:Diffusion; D008956:Models, Chemical; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins