Short report of the meeting of 05/01/25
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Present: Mark, Jan, Maciek, Jordi, Jaap, Joke. Klaas na 11 uur.

Jan: Good news from the VU/CWI subproject. The PhD position will be occupied by
Hanna Hardin, MSc in biotechnology at Uppsala University in Sweden. She did
an extra year on mathematics/stochastic models and a project on regulatory
networks in Grenoble under the supervision of Hidde de Jong.
A postdoc offer for 3 years (paid by a European programme) has been accepted
by Frank Bruggeman (no intro needed :-))

Progress reports:
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- Maciek is currently looking at hybrid methods and more specifically at
coupling a Monte Carlo method with a continuum PDE system (full, compressible
Navier-Stokes; Finite Volume method). In collaboration with TUe/BMT, where a
Molecular Dynamics code has been coupled to a Monte Carlo code for
micro-channel simulations, this should lead to a comparison between MD, MC and
PDE for micro-channel simulations and a proof-of-concept code for the coupling
of the 3 approaches for advection-diffusion problems.
Jaap suggests that it might be interesting to use a coupled MC/PDE approach
also for the calcium-homeostasis problem that Jiangjun Cui is working on
(Mesoscale project)

- Jordi has developed a stochastic particle-based code (Gillespie +
multiparticle method of Chopard) for the PTS-problem on a circle (sphere?).
Preliminary experiments show no or very small gradients of the concentrations.
Suggestions are made to reduce the diffusion rate, to reduce the lattice
size and/or to use an adaptive lattice (finer near the membrane).
It is not clear whether the latter is possible (intrinsically or just too
expensive/complex?).
Plans for the future are to look at different lattice sizes for different
species (lattice size dependent on ratio reaction/diffusion rates) and to
look at a combination with an MD approach (Brownian motion + reactions) near
the wall.
The work will be submitted to the ECCB/05 conference in Madrid.

NWO-CLS programme day: Programme is not yet known, CellMath will at least
contribute 2 posters. Joke will make a concept-text for the overall project-
description on the posters.

CLS-weekend: From TUe Matthias Roeger (PD) and Yves van Gennip (PhD) will
participate (and Mark of course). Both are working on membrane modelling.
Hanna Hardin has also been asked to join in [and has accepted in the mean time].
Roel van Driel [and maybe also Klaas Hellingwerf] is interested to come part
of the weekend (afternoon + dinner).
Ideas for the programme of the weekend has been discussed. Outcome will be
mailed separately.

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As always: comments are welcome! The final report will be on the sica website
www.siliconcell.net/sica/NWO-CLS/CellMath/meetings.html

Joke