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?
FiPy has no particular sophisticated ways to handle this above and beyond what a regular FV sheme can do. However, mostly anything to do with boundary conditions can be programmed to work iteratively (explicitly and sometimes implicitly) and of course everything is available for you to tinker with. Whether the iterations converge is a whole other question of course. -- Daniel Wheeler _______________________________________________ fipy mailing list [email protected] http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
