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partitioning.sourceforge.net

This site hosts code investigating the role of spatial partitioning in biochemical signaling. We consider a network motif that is ubiquitous in membrane signaling. We numerically implement the exact solution to a stochastic model of the motif. We also simulate diffusion and reactions of molecules explicitly on a two-dimensional lattice.


The application of the code is described in the manuscript "Spatial partitioning improves the reliability of biochemical signaling," which will soon be published in PNAS. A preprint is also freely available here. If used in your scientific work, please cite as:


Andrew Mugler, Filipe Tostevin, and Pieter Rein ten Wolde, "Spatial partitioning improves the reliability of biochemical signaling", Proceedings of the National Academy of Sciences USA, to appear, 2013.

fig2.m: Partitioning (magenta) linearizes the reponse (A) and reduces noise (B) compared to a well-mixed system (green).

The code is implemented in MATLAB, Mathematica, C++, and Perl, and can be downloaded here. We encourage the use of this 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)”.


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