Mesoscopic-microscopic hybrid algorithm with automatic partitioning

We have developed a multiscale method coupling the mesoscopic and microscopic scales. On the mesoscopic scale, systems are modeled as discrete jump processes on a structured or unstructured grid, while on the microscopic scale, molecules are modeled by hard spheres diffusing in continuous space. Microscopic simulations are accurate but computationally expensive. In this paper we […]

At Isaac Newton Institute

I will be spending Feb 15-March 17 at the Isaac Newton Institute, Cambride, UK, for a program on Stochastic Dynamical Systems in Biology: Numerical Methods and Applications. Big thanks to the organizers,Radek Erban (Oxford), David Holcman (ENS – Paris), Samuel Isaacson (Boston) and Konstantinos Zygalakis (Southampton) for organizing this amazing opportunity to gather many creative people in […]

PhD and Postdoc positions

The Center for Applied Mathematics (CIM) in Uppsala are looking for up to 3 PhD students in applied mathematics. Within this call there is an opportunity to joint the group working on the project From cell-cell interactions to embryo development: Multiscale models and simulation in systems biology. This project is a collaboration with Carolina Wählby. […]

Multiscale and hybrid algorithms for stochastic chemical kinetics

Many biochemical network models display scale separation with respect to reaction rates and/or molecular copy numbers. Depending on the type of question under study, different models are best suited to simulate the system. For some parts of the system, a macroscopic model might be appropriate. For other parts, a mesoscopic model may provide additional insight […]