Realizing the autonomous division of synthetic cells is a key step toward creating life-like systems. In natural cells, this process is driven by a large protein network, the translation of which from genome, involves more than 150 proteins. Here, we take a fundamentally different approach: using RNA origami to construct an RNA-based divisome capable of constricting the cell, bypassing the protein translation step in the central dogma.

Our lab, experienced in biomimetic DNA nanostructures [1], is developing RNA tile–based filaments [2] with integrated actuation mechanisms to constrict synthetic cell membranes. We aim to encode these RNA divisome modules as an RNA circuit on a synthetic DNA template, encapsulated in giant unilamellar vesicles (GUVs), where the expressed RNA filaments will anchor to the membrane, form a division ring, and drive membrane constriction and division.

In this multidisciplinary project, you will gain insights into the biophysical mechanisms underlying cell division and force generation in cells,exploring them creatively by designing dynamic RNA nanostructures. In the wet lab, you will contribute to the biochemical and structural characterization of new RNA nanostructure designs and assess the effects of force generation mechanisms on supported lipid bilayers and GUVs. You may also take part in structural design, simulation, and data analysis using specialized software and basic programming tools (Python, MATLAB).

We welcome students from diverse levels and backgrounds to join our efforts in building an RNA-based synthetic cell divisome. If you are interested in this exciting project, please contact Yunshi Yang at y.yang–18[REMOVETHIS]tudelft.nl.

Reading the amino-acid sequence of a single protein — and the chemical modifications written on top of it — would transform how we study biology and diagnose disease. It also remains a major unsolved challenge. We are developing nanopore technology to do exactly this, and there are student projects available throughout the year on every part of the problem, including but are not limited to:

– Engineering the pore — design and test nanopore variants that let proteins translocate efficiently
– Driving the protein through — use different motor proteins to translocate peptide
– Reading modifications — detect phosphorylation, sulfation or glycosylation on single peptides
– Modeling the physics — simulate the forces and polymer conformations that shape the sequencing signal
– Building the electronics — develop hardware for real-time sequencing control and readout
– Decoding the signal — write computational and statistical methods that turn current traces into sequence
– Preparing the samples — establish biochemical workflows for protein and PTM identification
– Making pores from DNA — build synthetic nanopores using DNA origami

We are looking for BEP/MEP and international students eager to help develop the future of nanopore-based proteomics. These projects are multidisciplinary, at the intersection of physics, biology, biochemistry, electronics and data science. You can work at the bench, on data analysis in Python, or both — whichever suits you, there is a place for you here.

Interested? Contact the PhD students or postdocs working on nanopore sequencing for details. We look forward to hearing from you!

Accurate DNA segregation is essential for all living cells. In nature, this process is usually controlled by complex protein machinery. In this project, we ask a more fundamental question: Can physical confinement and entropy alone drive DNA molecules to separate?

We are developing a nanofluidic platform in which fluorescently labelled DNA molecules are confined inside narrow channels and connected compartments. Under strong confinement, overlapping DNA molecules lose conformational freedom, which may cause them to spontaneously segregate. By changing the channel dimensions and compartment geometry, we aim to determine when segregation occurs, how long it takes, and which device geometries promote efficient separation.

The student will perform experiments using nanofluidic devices developed in our lab, including DNA preparation and fluorescent labelling, sample loading, fluorescence and confocal microscopy, FRAP measurements, and quantitative image analysis. The results will be compared with theoretical predictions and simulations to understand DNA motion and segregation under confinement and to further optimize the device geometry and experimental parameters.

Through this experimental and multidisciplinary project, you will gain experience in wet-lab work, micro- and nanofluidic setups, fluorescence microscopy, and time-lapse image analysis. If you are interested in this project, please contact Xiliang Yang (X.Yang-3@[REMOVE THIS]tudelft.nl) for more information. Previous experience in biology, physics, microfluidics, microscopy, or image analysis is helpful but not required.