Date
Thu, 07 Jun 2012
Time
13:00 - 14:00
Location
DH 1st floor SR
Speaker
Radek Erban

I will discuss methods for spatio-temporal modelling in cellular and molecular biology. Three classes of models will be considered: (i) microscopic (molecular-based, individual-based) models which are based on the simulation of trajectories of individual molecules and their localized interactions (for example, reactions); (ii) mesoscopic (lattice-based) models which divide the computational

domain into a finite number of compartments and simulate the time evolution of the numbers of molecules in each compartment; and (iii) macroscopic (deterministic) models which are written in terms of reaction-diffusion-advection PDEs for spatially varying concentrations. In the first part of my talk, I will discuss connections between the modelling frameworks (i)-(iii). I will consider chemical reactions both at a surface and in the bulk. In the second part of my talk, I will present hybrid (multiscale) algorithms which use models with a different level of detail in different parts of the computational domain. The main goal of this multiscale methodology is to use a detailed modelling approach in localized regions of particular interest (in which accuracy and microscopic detail is important) and a less detailed model in other regions in which accuracy may be traded for simulation efficiency. I will also discuss hybrid modelling of chemotaxis where an individual-based model of cells is coupled with PDEs for extracellular chemical signals.

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