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20080516 Spontaneous separation of bi-stable biochemical systems

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Jonathan Blakes
Jonathan Blakes

2008 Journal Club

Tecnología
1 de 18
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
 
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bi-stable chemical systems ,[object Object],[object Object],[object Object],[object Object]
Assumptions violated ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Macrophage and Bacterium 2,000,000X 2002 Watercolor by David S. Goodsell
Next Subvolume Method (NSM) ,[object Object],[object Object],[object Object],[object Object],The authors tool MesoRD has been used to model the stochastic contribution to different mutant phenotypes in the Min-system in E. coli . Visualisation of a stochastic simulation of a wild type E. coli cell: MinD on the cell membrane and MinE in complex with MinD.
Implementation ,[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],Implementation
Multi-Compartmental Gillespie
Influence of Diffusion ,[object Object],[object Object],[object Object],[object Object]
Specifying Geometries ,[object Object],[object Object],[object Object]
Influence of Geometry ,[object Object],[object Object]
Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
References ,[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
 

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20080516 Spontaneous separation of bi-stable biochemical systems

Notas del editor

  1. 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...
  2. blood cells lines ODEs
  3. David S. Goodsell
  4. 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.
  5. 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.
  6. similar program from Luis Serrano’s laboratory, used Next Reaction Method (Gibson and Bruck) but switched to NSM because of overhead [quoth. MesoRD]