Integrated simulations of active emulsions in complex environments
EmulSim aims to develop an integrated simulation framework to understand biomolecular condensate dynamics in cells, enhancing insights for potential medical therapies.
Projectdetails
Introduction
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.
Challenges in Understanding Condensate Dynamics
Some challenges in understanding condensate dynamics are that:
- Cells are heterogeneous
- Cells have complex material properties
- Cells 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.
Project Overview
EmulSim will study how cells control biomolecular condensates and provide a novel integrated simulation method incorporating relevant processes on all length scales.
Scale of Individual Droplets
On the scale of individual droplets, I will investigate the influence of:
- Driven reactions
- Elastic material properties of droplets
Cellular Scale
On the cellular scale, I will study the effect of:
- The elastic cytoskeleton
- The presence of multiple compartments
Model Development
For each of these processes, I will derive experimentally verified models using examples of relevant biological processes, including:
- Cell division
- Chromatin organization
- 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.
Conclusion
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.
Financiële details & Tijdlijn
Financiële details
Subsidiebedrag | € 1.998.334 |
Totale projectbegroting | € 1.998.334 |
Tijdlijn
Startdatum | 1-10-2022 |
Einddatum | 30-9-2027 |
Subsidiejaar | 2022 |
Partners & Locaties
Projectpartners
- MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EVpenvoerder
Land(en)
Vergelijkbare projecten binnen European Research Council
Project | Regeling | Bedrag | Jaar | Actie |
---|---|---|---|---|
Interface between Membraneless Organelles and MembranesThis project aims to uncover the molecular mechanisms of interactions between liquid biomolecular condensates and membrane-bound organelles, enhancing our understanding of cellular organization and disease. | ERC Starting... | € 1.499.648 | 2024 | Details |
Cell-free synthesis and assembly of biomolecular condensates: Engineering properties, functions and regulationThis project aims to engineer and characterize biomolecular condensates using a microfluidic cell-free system to enhance synthetic compartmentalization in biotechnology and synthetic biology applications. | ERC Starting... | € 1.500.000 | 2023 | Details |
Designer Condensates for Regulation of Catalytic ProcessesDevelop synthetic biomolecular condensates with tunable properties from peptide libraries to enhance reaction regulation and sustainable drug synthesis in aqueous environments. | ERC Starting... | € 1.498.750 | 2024 | Details |
Computational Microscopy of CellsThe project aims to develop advanced computational microscopy methods to simulate and study cell membranes and organelles in their natural cellular environment at molecular resolution. | ERC Advanced... | € 2.498.148 | 2022 | Details |
The geometrical and physical basis of cell-like functionalityThe project aims to uncover mechanistic principles for building life-like systems from minimal components using theoretical modeling and in-silico evolution to explore protein patterns and membrane dynamics. | ERC Advanced... | € 2.498.813 | 2024 | Details |
Interface between Membraneless Organelles and Membranes
This project aims to uncover the molecular mechanisms of interactions between liquid biomolecular condensates and membrane-bound organelles, enhancing our understanding of cellular organization and disease.
Cell-free synthesis and assembly of biomolecular condensates: Engineering properties, functions and regulation
This project aims to engineer and characterize biomolecular condensates using a microfluidic cell-free system to enhance synthetic compartmentalization in biotechnology and synthetic biology applications.
Designer Condensates for Regulation of Catalytic Processes
Develop synthetic biomolecular condensates with tunable properties from peptide libraries to enhance reaction regulation and sustainable drug synthesis in aqueous environments.
Computational Microscopy of Cells
The project aims to develop advanced computational microscopy methods to simulate and study cell membranes and organelles in their natural cellular environment at molecular resolution.
The geometrical and physical basis of cell-like functionality
The project aims to uncover mechanistic principles for building life-like systems from minimal components using theoretical modeling and in-silico evolution to explore protein patterns and membrane dynamics.