Short report of our meeting today:

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Present: Frank, Jaap, Jan, Jordi, Klaas, Maciek, Joke

- Presentation of Maciek: Modeling biochemical networks, what can go 
wrong?
Overview of some litterature on the (im)possibilities of biochemical
modeling with ODEs/PDEs. Factors: continuum hypothesis (number of 
molecules), stochastic nature of reactions
Q: # molecules in cell. processes?
A: enzymes 1000-5000
    transcription factors 10-100
    RNA 100-1000
    (numbers in Goodsell, The Machinery of Life)

- Presentation of Jordi: Mesoscopic stochastic spatial simulations of 
biochemical networks
Report on experiments done with multiparticle lattice gas approach for
reaction-diffusion. Case-study PTS. Experiments with high densities
which should in principle converge to PDE results. Experiments until now
show a different behaviour near the membrane.

Klaas suggested to look also into the boundary layer behaviour near the
membrane (different pH, electric charges; resulting in space dependent
reaction rates). Klaas will look for available data.

Case-studies:
------------
- e-coli division / Min system (papers of Howard e.a. and Margolin e.a.)
Nice problem but difficult/impossible to do experiments on. First Q:
Give a model that finds the long axis

- scaffolds / signal separation.
Doable. Q: number of scaffolds in a cell (concentration of scaffolds?)

- endosome formation / lipid rafts
Not directly clear how to model, but certainly interesting problem.

- stochastic effects
Q: are there experiments which show (at the macroscopic experiment-level)
the necessity to include stochastic effects
A: Leibner: Bi-stable state / stochastic fluctuations (ref?)

-- introductory material for PhD students
List has been provided with suggestions from Jan (systems and control 
theory), Jaap (lattice methods, developmental biology), Joke (mathematical 
modelling and computation). Klaas and Frank will give a list of chapters
from Alberts e.a.. Other biological introduction: Goodsell's Machinery of 
Life)

-- Jan offered to give a 1-2hr  introduction on stochastic ODEs and PDEs.
Will be after 6/12. Date list follows.

-- Mail-adresses of CellMath group: see adressees of this mail. I propose 
to use always "CLS-CellMath" in the Subject to allow for automatic 
foldering
(see also http://www.siliconcell.net/sica/NWO-CLS/CellMath/participants.html)

-- NWO-CLS programme day 25/2/05: CellMath should be there with 
presentation (Mark/Joke?) and posters

-- weekend 26-27/2/05: Jan can only be there on Saturday. More 
info/questions will follow.

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Please comment. I am not sure that my report is not coloured/blurred by 
the beers and the discussion in de Stelling :-)

Final report + presentations + reading suggestions on the sica website
(www.siliconcell.net/sica/NWO-CLS/CellMath)? Or should we create a 
different place for communication purposes?

Joke