| Project Detail |
An agent-based simulation will help explain the behaviour of biomolecular condensates
Organisms are largely water with many interspersed biomolecules, compounds and ions. Within cells, these constituents form different compartments to fulfill functions. While large compartments are often surrounded by a membrane, most smaller compartments form spontaneously from the interactions among dispersed molecules. Consequently, these biomolecular condensates behave similarly to liquid droplets. Their malfunction is involved in diseases, including Alzheimer’s, Parkinson’s and cancer. The EU-funded EmulSim project will investigate how healthy cells control their condensates on all length scales to elucidate how they become malfunctioning in diseased states. The insight will lead to a novel agent-based simulation framework to support the development of new therapeutics.
Biological cells consist of a myriad of interacting biomolecules that collectively arrange in stable structures. For example, molecules undergo phase separation to form so-called biomolecular condensates. We now know that malfunctioning condensates can cause diseases like Alzheimer’s, Parkinson’s, and cancer. Yet, we do not understand how condensates become malfunctioning and how healthy cells control them. Some challenges in understanding condensate dynamics are that cells are heterogeneous, have complex material properties, and exhibit significant thermal fluctuations. Biological cells are also alive and use fuel molecules to control processes actively. I recently showed that active chemical reactions could generally affect the dynamics of droplets. However, it is unclear how such active droplets behave in the complex environments inside cells.
EmulSim will study how cells control biomolecular condensates and provide a novel integrated simulation method incorporating relevant processes on all length scales. On the scale of individual droplets, I will investigate the influence of driven reactions and elastic material properties of droplets. On the cellular scale, I will study the effect of the elastic cytoskeleton and the presence of multiple compartments. For each of these processes, I will derive experimentally verified models using examples of relevant biological processes, including cell division, chromatin organization, and signaling. Combining the physical theories for these critical processes will culminate in an agent-based model describing a collection of droplets, ultimately also including number fluctuations. This novel simulation framework will model biomolecular condensates in their cellular environment. Taken together, EmulSim will propel our understanding of biomolecular condensates and lay the ground for the development of novel therapies in medicine. |
