Hi Fridolin, I've used FiPy with non-linear boundary conditions before, e.g. (quite like yours) n\cdot\nabla c = c/(c+k) in which k is a constant and c is an independent variable.
You can probably take care of the geometry with Gmsh, which is referenced in the install documentation for FiPy (and also in the comprehensive tutorials). Best of luck, Ray On Tue, Dec 10, 2013 at 7:36 AM, Fridolin Gross <[email protected] > wrote: > Hello, > > I’m looking for a PDE tool for a biological model describing a population > of cells that interact via a diffusive messenger molecule. > Before learning to use fipy, I’d like to know if it is the right tool for > my purposes. > > I have a rectangular domain, intersected with circular regions (=cells). > The interior of the cells is not part of the domain. In the intercellular > region there is diffusion of the messenger molecule, > while reactions take place on the circular boundaries (=cell membranes) > that bind or degrade the molecules. > The model requires a non-trivial Neumann boundary condition on those > circular boundaries, with flux proportional to u/(k+u), where u is the > concentration of messenger at the boundary. > I was disappointed to find out that the matlab pdetoolbox cannot deal with > parabolic problems with boundary conditions that depend non-linearly on the > solution. > Would this be possible in fipy? > > Thanks a lot for any kind of help! > > Fridolin > _______________________________________________ > fipy mailing list > [email protected] > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >
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