Department Bionanoscience
Principal investigator Timon Idema
E-mail address t.idema@tudelft.nl
Website www.idemalab.tudelft.nl
Coarse-grained model of cardiolipin curvature sensing in lipid membranes
Suitable as a BEP? Yes
Suitable as a MEP? Yes
Suitable as an Academic Research Project? Yes
Techniques:
- Molecular dynamics simulations
Lipid membranes exhibit complex curvature-dependent behaviors that play a key role in many biological processes. Cardiolipins, a class of conical-shaped membrane lipids, are typically found in regions of high curvature and are believed to influence membrane shape and dynamics. Understanding their effect on membrane curvature is essential for a deeper insight into the structural organization of biological membranes.
In this project, we will use coarse-grained methods to simulate vesicles with varying cardiolipin concentrations and analyze how these molecules modify membrane curvature and mechanical properties. We will look at various membrane shapes and various models for the cardiolipin molecules. We aim to better understand internal membrane dynamics in living cells and develop ideas for shaping artificial cell membranes.
Further reading (click to link to article)
I. R. Cooke, K. Kremer, and M. Deserno, “Tunable generic model for fluid bilayer membranes” Phys. Rev. E 72, 011506 (2005), doi: 10.1103/PhysRevE.72.011506
Protein–membrane interactions at the mesoscale
Suitable as a BEP? Yes
Suitable as a MEP? Yes
Suitable as an Academic Research Project? No
Techniques:
- Molecular dynamics simulations
Protein interactions with lipid membranes play a crucial role in processes such as membrane remodeling, signaling, and trafficking. Many membrane-associated proteins can sense or induce curvature, leading to large-scale structural reorganization of the membrane. Understanding these effects requires models that bridge the molecular and cellular scales.
This project focuses on studying the emergent behavior of protein–membrane interactions using a mesoscale membrane model. The student will investigate how proteins cluster on membranes and how their presence influences or responds to membrane curvature. As a case study, the student will model a specific curvature-active protein provided by our experimental collaborators, allowing for direct comparison between simulations and experimental data.
Further reading (click to link to article)
H. Yuan, C. Huang, J. Li, G. Lykotrafitis and S. Zhang, “One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes”, Phys. Rev. E 82, 011905 (2010), doi: 10.1103/PhysRevE.82.011905
(Example) projects submitted by lab in past years
(2024-2025) Particle-based membrane model
Supervisor: Timon Idema, t.idema@tudelft.nl
Lipid bilayer membranes can be simulated at the individual lipid level, but this high resolution comes at the price of restricted length and timescales. Alternatively, we can coarse-grain the system, using a single bead to describe multiple lipids. With such a model we can go up to cellular scales, and simulate processes like membrane self-organization and cell deformation. Unfortunately, existing models are highly unstable, making it difficult to draw conclusions. In this project we will implement an alternative model with particle-particle interactions drawn from the theory of liquid crystals, which closely follow the actual deformation modes of the lipid bilayer membrane. We will investigate if this approach yields more stable membranes, and if we can use it to simulate large-scale cellular deformations.
Techniques
- Simulations
- Data analysis
Further reading
Yuan et al., Phys. Rev. E 82, 011905 (2010), doi: 10.1103/PhysRevE.82.011905
(2024-2025) Endocytosis in theory and simulation
Supervisor: Timon Idema, t.idema@tudelft.nl
Endocytosis, the uptake of particles from the environment, is a key process in cellular function. Surprisingly however, a dynamic description of the process, even in the simplest setup where the particle sticks to the cellular membrane, is lacking. In this project, we will combine analytical, numerical and simulation techniques to study this phenomenon, with the aim of arriving at a full dynamic description of the membrane shape and evolution as it wraps around the particle.
Techniques
- Analytical and numerical solutions of differential equations
- Simulations.
Further reading
Spanke et al., Phys. Rev. Research 4, 023080 (2022), doi: 10.1103/PhysRevResearch.4.023080
(2024-2025) Simulating protein-membrane interactions
Supervisor: Pietro Sillano, p.sillano@tudelft.nl
Proteins binding to lipid bilayer membranes can change the structure of the membrane by the very act of binding. Inversely, the binding can also affect the shape of the protein. The simple act of binding can therefore have far-reaching consequences, and is likely involved in many cellular processes. To be able to reproduce such processes in artificial cells, we need a better understanding of what happens at the molecular level. In this project, we will use a combination of alphafold predictions of protein structures and membrane-protein simulations to see how protein binding can lead to membrane fission, a key step in the reproductive cycle of a cell.
Techniques
- Simulation,
- Data analysis
Further reading
De Franceschi et al., Nat. Nanotech. 19, 70 (2024), doi: 10.1038/s41565-023-01510-3
(2024-2025) Bacterial colony growth and shape
Supervisor: Timon Idema, t.idema@tudelft.nl
Bacterial colonies grow through repeated growth-and-division cycles. Rod-shaped bacteria do so by elongating along their long axis, defining a clear local orientation. However, after a couple of division rounds, the global orientation is lost, and orientational defects appear. In this project, we’ll study how the properties of the colony, like the defect density, correlation length, and colony shape, are affected by the bacterial properties, such as their growth protocol (‘adder’ and ‘sizer’ models) and their interactions, to figure out which of these we can induce directly from experimental observations of growing colonies.
Techniques
- Simulations
- Data analysis
Further reading
Los, R., et al. arXiv/2003.10509 (2022), doi: 10.48550/arXiv.2003.10509.