Diffusion in crowded biological environments: applications of Brownian dynamics
Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
BMC Biophysics 2011, 4:3 doi:10.1186/2046-1682-4-3Published: 2 March 2011
Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 . Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and signaling. Also, the crowded media can alter, both qualitatively and quantitatively, the reactions in vivo in comparison with their in vitro counterparts. This review focuses on recent developments in particle-based Brownian dynamics algorithms, their applications to model diffusive transport in crowded systems, and their abilities to reproduce and predict the behavior of macromolecules under in vivo conditions.