Simulation​ ​platform​ ​for​ ​cell​ ​biology

People involved: Francois Nedelec

KeywordsCellular processes, Cytoskeleton, Simulations, Realistic animations,

Computer games

Project Description


One of the fundamental questions of biology is to understand how stochastic interactions between proteins and other molecules lead to order at much larger scales. This question is essential because the spatial organization of the components in any system is directly linked to its ability to perform the function for which it exists. The form is inseparable from function, at all scales of biological matter. Importantly, an organization often arises from the interaction of the components in a non-intuitive manner, and in that case theory is essential to understand how order emerges from seemingly random interactions. A theory is however abstract and difficult to explain, but it helps to be able to visualize the dynamics of the system. This is however seldom made at the cellular scale because of the lack of tools dedicated to visualizing processes inside the living cell.


Our research focuses on the cytoskeleton, which consists of filaments, such as microtubules and actin filaments, together with their associated proteins. It is a conserved machinery of eukaryotic cells responsible for many essential processes, including motility, division, polarization, cell shape changes, etc. In model organisms such as yeast, the properties of the elements are known, as well as the system components for some processes. We know precisely the physical properties of microtubules, their number in different cellular configurations, the speed of kinesins and other molecular motors that can move on them. To analyze how these components work collectively, we simulate their interactions in a computer.


At the CRI, I will further develop our simulation platform Cytosim to make it more accessible. We will improve the graphical output using photo-realistic raytracing engines, and produce realistic movies of mitotic spindle assembly, nuclear migration, endocytosis, cytokinesis, contraction of cortical actomyosin networks and cilia beating. We will also conceive a game based on the core engine of Cytosim, to appeal to an even wider public. This engine is sufficiently fast to support an interactive experience, and I feel that dynamic filaments are material for a game, but we need to find a scenario. Finally, we can develop Cytosim as a tool to explore the dynamics of cytoskeletal systems for students, at the undergraduate and at more advanced levels.