BMC Biophys 2014 24;7:11. Epub 2014 Oct 24.
Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany.
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PLoS One 2013 11;8(9):e74261. Epub 2013 Sep 11.
Department of Mathematics, Free University of Berlin, Berlin, Germany.
We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. Read More
J Mol Graph Model 2013 Sep 28;45:144-56. Epub 2013 Aug 28.
Department of Biochemistry & Molecular Biology and Department of Chemistry, Michigan State University, 603 Wilson Road, BCH 218, East Lansing, MI 48824, United States; RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address:
An increasing number of studies are aimed at modeling cellular environments in a comprehensive and realistic fashion. A major challenge in these efforts is how to bridge spatial and temporal scales over many orders of magnitude. Furthermore, there are additional challenges in integrating different aspects ranging from questions about biomolecular stability in crowded environments to the description of reactive processes on cellular scales. Read More
BMC Syst Biol 2011 May 14;5:71. Epub 2011 May 14.
Automatic Control Laboratory, ETH Zurich, Physikstrasse 3 8092 Zurich, Switzerland.
Background: In this paper we apply a novel agent-based simulation method in order to model intracellular reactions in detail. The simulations are performed within a virtual cytoskeleton enriched with further crowding elements, which allows the analysis of molecular crowding effects on intracellular diffusion and reaction rates. The cytoskeleton network leads to a reduction in the mobility of molecules. Read More
J Comput Biol 2012 Jun;19(6):606-18
Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.
Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Read More