Department of Information Technology
Department of Information Technology
Uppsala UniversityInformation TechnologyResearchScientific Computing
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Computational Systems Biology

Participants

The CSB project group currently consists of

Group Photo from Spring 2016

group_photo_2016.jpg

From left to right: Sonja Mathias, Andreas Hellander, Stefan Engblom, Adrien Coulier, Per Lötstedt, Pavol Bauer, Lina Meinecke

Research

Modern molecular biology has discovered and examined a vast number of cellular components. The mechanisms of regulation and functionality of the different molecules is still largely unknown. To understand the principles for cellular regulation mathematical models are now constructed and there is a need to simulate these models in silico. In some biological systems, the dynamics is given by partial differential equations. In other systems, a trajectory of the system is generated by discrete stochastic simulation. The randomness is due to the small number of molecules involved in the reaction networks and probabilistic models for chemical reactions. There is a need to develop numerical multiscale algorithms for simulation from single molecules to concentrations of chemical species and from single cells to agglomeration of cells in tissues.

Past research endeavours can be found here.

Modelling Cell Populations

In a colony, biological cells are able to exhibit emergent behaviour. However, the internal mechanisms enabling communication between cells remain poorly understood. To tackle this problem, we are interested in developing efficient ways to simulate these biological systems. The challenges consist both of the modelling itself - the exact underlying biological processes are usually unknown - and the multi-scale aspects of the processes which can take place on a wide range of spatial and temporal scales.

Molecular Crowding

Up to 35% of the volume inside living cells are occupied by macromolecules. This leads to diffusion behaving differently in vivo and in vitro.

Publications

A full list of all publications including theses can be found here.

2016

2015

Doctoral theses

Updated  2017-02-04 14:34:26 by Kurt Otto.