20080516 Spontaneous separation of bi-stable biochemical systems
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2008 Journal Club
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20080516 Spontaneous separation of bi-stable biochemical systems
- 1. Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases Johan Elf and Måns Ehrenberg Presented by Jonathan Blakes Computational Foundations of Nanoscience Journal Club 2008-05-16
- 6. Macrophage and Bacterium 2,000,000X 2002 Watercolor by David S. Goodsell
Hinweis der Redaktion
- lengthy abstract, disguises main point, that the supplementary material (which I will be going into) describes the next subvolume stochastic simulation method, this is implemented in MesoRD...
- blood cells lines ODEs
- David S. Goodsell
- Rate matrix is sum of reactant rates (r) and diffusion rates (s), used to load the dice which is rolled to determine whether reaction or diffusion happens at this step.
- Spontaneous domain separation requires that a localised part of the system jumps from an attractor in phase to an attractor out of phase with the surroundings. For this to happen, the size of the part of the system that jumps out of phase must be big enough so that it is not invaded by neighbouring molecules. At the same time, the size must be small enough so that the local escape from the original attractor does not take too long. It is only when there exists a local volume size for which invasion by diffusion takes a longer time than attractor escape, that spatial domains become sufficiently decoupled from their surroundings to allow for spontaneous domain separation. Accordingly, systems in tube-like or flat geometries display domain separation much more easily than do their spherical or cubic equivalents.
- similar program from Luis Serrano’s laboratory, used Next Reaction Method (Gibson and Bruck) but switched to NSM because of overhead [quoth. MesoRD]