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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 …
specific shape in order to interact with others in the complex machinery. Spatial dynamics …
Hybrid spatial Gillespie and particle tracking simulation
Motivation: Cellular signal transduction involves spatial–temporal dynamics and often
stochastic effects due to the low particle abundance of some molecular species. Others can …
stochastic effects due to the low particle abundance of some molecular species. Others can …
Coarse-grained brownian dynamics simulation of rule-based models
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 …
molecules, comes at a cost of complexity. In this paper, we propose a coarse-grained …