Spatial simulations in systems biology: from molecules to cells

M Klann, H Koeppl - International journal of molecular sciences, 2012 - mdpi.com
Cells are highly organized objects containing millions of molecules. Each biomolecule has a
specific shape in order to interact with others in the complex machinery. Spatial dynamics …

Hybrid spatial Gillespie and particle tracking simulation

M Klann, A Ganguly, H Koeppl - Bioinformatics, 2012 - academic.oup.com
Motivation: Cellular signal transduction involves spatial–temporal dynamics and often
stochastic effects due to the low particle abundance of some molecular species. Others can …

Coarse-grained brownian dynamics simulation of rule-based models

M Klann, L Paulevé, T Petrov, H Koeppl - Computational Methods in …, 2013 - Springer
Studying spatial effects in signal transduction, such as co-localization along scaffold
molecules, comes at a cost of complexity. In this paper, we propose a coarse-grained …