This site hosts code investigating the role of spatial heterogeneity in biochemical signaling. Motivated by several biological examples, we study the behavior of covalent modification networks when the activating component is localized to a planar membrane in either a random or clustered configuration. Reactions and diffusion are implemented on a three-dimensional lattice.
The application of the code is described in the published manuscript "Membrane clustering and the role of rebinding in biochemical signaling". A preprint is also freely available here. If used in your scientific work, please cite as:
Andrew Mugler, Aimee Gotway Bailey, Koichi Takahashi, and Pieter Rein ten Wolde, "Membrane clustering and the role of rebinding in biochemical signaling", Biophysical Journal, 102(5):1069-1078, 2012.
The code is implemented in Perl, C++, and MATLAB, and can be downloaded here. We encourage the use ofthis code in further scientific applications; if you choose to use this software, please contact us so we can learn about your research.
This work was performed at AMOLF in the Netherlands. It is part of the research program of the “Stichting voor Fundamenteel Onderzoek der Materie (FOM)”, which is financially supported by the “Nederlandse organisatie voor Wetenschappelijk Onderzoek (NWO)”.