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Student projects

We welcome students from a variety of backgrounds to participate in our research. Our group currently has the following opportunities for carrying out a bachelors or masters research project.

1. Genome-in-a-box: DNA organization and dynamics driven by nucleoid associated proteins (NAPs)

The bacterial chromosome is circular an highly compacted (by factor of over 1000!). The compaction and organization of the chromosome is partially governed by the action of so called nucleoid associated proteins (NAPs) [1]. Despite being very abundant, the individual and combined roles of these on the architecture and dynamics of chromosome are mostly poorly understood. Our Genome-in-a-box project, a basic-science, bottom-up approach gives us a unique opportunity to study the effect of isolated NAPs on mega-base scale DNA organization and dynamics. If successful, this will implications on our ability to tackle antibiotic resistance, engineer bacteria on cell and colony level, and control conformations of synthetic genomes in-vitro.

The project has interdisciplinary nature and can be adapted to your interest. You will be closely involved in the design of experiments and learn a lot about chromosome organization and polymer physics. You will the chance to pick up range of skills including cell culture, genetic engineering, genome isolation and transplantation, DNA labeling, gel-based protein and DNA assays, microfluidics, fluorescent microscopy and image and data analysis.

Does this make you curious? Or even excited? Then we will be happy to hear from you! Contact Details: Martin Holub, m.holub@tudelft.nl; please include a statement of motivation, description of your previous lab & research experience and the timeframe for which you are available. Students from any university (incl. mobility, exchange, internship …) are welcome to apply!

[1] Dame, R. T. et al.; Nat Rev Genet 2019. https://doi.org/10.1038/s41576-019-0185-4.


Figure: project1.gif: A time-lapse of chromosome during compaction by a DNA-binding protein

2. Genome-in-a-Box: Microfluidics for studying isolated genomic DNA

Microfluidics allows precise control and manipulation of fluids that are confined to a small scale. It has proven particularly useful for analysis and manipulation of samples in biology and chemistry and offers multiple examples of how tool development can lead to novel applications as well as enable fundamental science. In the framework of our Genome-in-a-box project, where we adopt bottom-up approach for studying the conformations and dynamics of genomes, we seek to design, fabricate, test and implement a novel flow-based microfluidic system for studies of isolated bacterial chromosomes. The nature of our application requires that the device is particularly gentle to the sample and allows for unobstructed observation and precise control of concentrations. Options to achieve this could include multi-layered devices based on PDMS and glass chips [1].

This project is particularly suited for someone with microfabrication/physics/engineering/nanoscience background with interest in biological applications. You will be closely involved in the design of experiments and learn a lot about soft-lithography, imaging and molecular biology. You will the chance to pick up range of skills including numerical modeling, clean room fabrication, genome isolation and transplantation, DNA labeling, gel-based protein and DNA assays, fluorescent microscopy and image and data analysis. You will also have access to fully equipped state of the art cleanroom at TU Delft.

Does this make you curious? Or even excited? Then we will be happy to hear from you! Contact Details: Martin Holub, m.holub@tudelft.nl; please include a statement of motivation, description of your previous lab & research experience and the timeframe for which you are available. Students from any university (incl. mobility, exchange, internship …) are welcome to apply!

[1]: Carlborg, C. F. et al.; J. Microelectromech. Syst. 2010, 19 (5), 1050–1057. https://doi.org/10.1109/JMEMS.2010.2067203. [2]: https://www.synbio.cam.ac.uk/synbiofund/Green_Mother_project_folder/GMM_full


Isolated chromosomes can be observed individually in microfluidic wells


Microfluidics device for controlled supply of nutrients to bacteria [2]

3. Shining Light on the Nuclear Pore Complex using a Zero-Mode Waveguide

Selective transport of the Nuclear Pore Complex (NPC) can be reconstituted in minimalistic systems that consist of a solid-state nanopore functionalized with FG-nucleoporins. However, such systems present limitations in terms of biological relevance (due to applied electric field), and scalability to investigate more complex scenarios.

In this project, we tackle all these issues by with a method based on Zero-Mode waveguides (ZMW), sub-wavelength apertures in metal films (Fig.1), which we engineer with FG-nucleoporins. Even though light can not pass through the metal layer, molecules can still diffuse through the small aperture. As they reach the other side, fluorescent molecules are illuminated by the laser, one by one, resulting in single spikes in the detected signal.

With this technique we can for the first time study:
–       Selective transport at the single-molecule level in free diffusion (no applied electric field)
–       Parallel detection and discrimination of two, or more, proteins that translocate simultaneously
This approach will yield new mechanistic insights about transport through the real nuclear pore complex.

During this inter-disciplinary project you will learn how to work with ZMWs and operating a high end microscope, in order to do single molecule fluorescence experiments. Additionally, you will gather experience in
handling biological samples, functionalizing  ZMWs with purified proteins, protein labelling, and learn about the nuclear pore complex.

If this triggers you, please contact Nils Klughammer (n.klughammer@[REMOVE THIS]tudelft.nl).


Figure 1: Zero-Mode Waveguide

4. Understanding Fluorescence Burst Timetraces

After fluorescent molecules travel through optical nanopores, they light up in a burst of fluorescence, when entering the laser illuminated side. These little flashes of light are recorded on a photodetector and need to be separated in the time-trace from the background light. The real time trace, however, is more complex than just single spikes:
Fluorophores bleach over time, they reenter and emit a different number of photons. The task in this BEP would be to understand and assess these effects. Therefore at first several algorithms to separate fluorescence burst events from background photons should be compared and their performance should be assessed with real and simulated data. In a next step we want to understand the physics underlying the real time traces such as influence of flow and bleaching. During this BEP you will learn basic concepts of statistical analysis, programming and data handling as well as simulating diffusion systems. This project is mainly computer based, but has the possibility to perform own experiments if circumstances permit.

If you find this interesting, please send an email to n.klughammer@[remove-this]tudelft.nl


5. Building nanomachines

In Eukaryotes, cell division is accomplished by constriction of the actomyosin ring. In this wonderful biological machine, the concerted action of molecular motors, actin filaments and cross-linkers is able to achieve membrane constriction at a scale that is several orders of magnitude larger than the proteins themselves. Inspired by the architecture of the actomyosin ring, this project aims at engineering a synthetic constriction machinery by using DNA and RNA origami nanotechnology. This machine will be able to assemble on the surface of giant vesicles and induce membrane constriction, thus matching the complexity of its biological counterpart. This will constitute an invaluable a tool to study the molecular mechanism of constriction with an unprecedented level of control;  it will also provide new engineering principles to develop future origami nanorobots.

We are looking for enthusiastic students who are interested in bottom-up synthetic biology. During this project you will learn how to design and assemble DNA/RNA origami and how to work with biological membranes, in particular Giant Unilamellar Vesicles and Supported Lipid Bilayers. You will image the constriction machinery in action by using a combination of fluorescence microscopy, Atomic Force Microscopy (AFM), High-Speed AFM and Electron Microscopy.


Starry Night & RNA origami Filaments
Vincent van Gogh & Nicola De Franceschi, 1889-2019
Oil on Canvas & Atomic Force Microscopy


Compartimentalization of DNA in the nucleus is one of the central features that distinguishes eukaryotic cells from simpler organisms. Like a door connecting two rooms, a huge multiprotein complex, the nuclear pore complex (NPC), enables communication and controlled passage of molecules between the nucleus and the cytoplasm. Fundamental cellular functions, like protein production, require the messenger molecule RNA to exit the nucleus through the NPC door; yet, how this transport actually occurs is still unclear.
The final goal of the mRNA NEXT project is to recreate a minimal nuclear export system that is able to drive transport of RNA in a functional mimicking of NPC. Recreating the functionality of the NPC de novo will allow us to unravel the nature of the minimal transport complex.

We use a current-base reading that enables us to distinguish single transport events of proteins and RNA through the biomimetic NPC. Since the proteins involved perform other tasks in the cell, our unique bottom-up approach is vital to address these questions. By joining this project, you will contribute to the first-ever successful reconstruction of mRNA export in a completely in vitro system!

You will be directly involved in experimental design, trained on protein production, molecular biology techniques, single molecule nanopore technology and QCM-D, in a unique combination of interdisciplinary methods at the merge of cell biology, biochemistry and bioengineering.

We are looking for independent and enthusiast Master/Bachelor students with Physics, Biology, or interdisciplinary background. International students are especially encouraged to apply.

For more info, contact Paola De Magistris (P.Demagistris@[REMOVE THIS]tudelft.nl) or visit our labs in Applied Sciences (office 58.F0.150).


7. DNA-origami scaffold for NPC mimics

With the help of DNA-origami nanotechnology, we built a minimalistic version of the NPC, where FG-Nups are anchored to the inner walls of a ~30 nm large DNA-origami pore, with predefined stoichiometry and positioning. We employ this platform to study the arrangement of FG-Nups within the pore volume using AFM and TEM imaging techniques.

We are looking for an enthusiastic Master/Bachelor student with an interest in synthetic bottom-up biology. Depending on the duration of your project, you will get trained on building NPC mimics using DNA-origami and FG-Nups, imaging them with TEM and AFM, and processing the data (Matlab/Image J/Gwyddion). 

If interested, please contact Alessio at A.fragasso@[REMOVE THIS]tudelft.nl or drop by office (F0.170).


8. Mimicking selectivity of the Nuclear Pore Complex with Designer FG-Nups

In this project, we attempt at reconstituting NPC selective transport in biomimetic nanopores using bottom-up designed artificial FG-Nups. By testing the impact of systematic variations of artificial FG-Nups on selectivity, we aim at unraveling what are the minimal features for having an efficient and selective transport. We believe this novel approach will finally shed light on some fundamental physical principles that govern the NPC behavior. 

We are looking for an enthusiastic Master/Bachelor student with a multidisciplinary background or interest. Depending on the duration of your project, you will get trained on engineering nanopores with FG-Nups, testing selective behavior of biomimetic NPCs and processing data (Matlab). Besides, you will get hands-on experience in using a TEM machine and detecting protein binding with a QCM-D.

If you feel thrilled, please contact Alessio at A.fragasso@[REMOVE THIS]tudelft.nl or drop by office (F0.170).


9. Characterisation of Zero-mode waveguides for Protein Sequencing

The possibility to measure a protein’s abundance in a very accurate way, will have giant impact on fields such as, cell biology cancer research and proteomics. However, the identification of proteins on a single molecule basis is still a great challenge. In this project we are setting up a system for the identification of individual proteins by protein fingerprinting. With this technique only the sequence of few aminoacids needs to be detected, in order to identify a protein. Our approach is based on Zero-mode waveguides, which are sub-wavelength pores drilled in a metal film.

Zero-mode waveguides have the property to block light, that shines on them. Still molecules can traverse through, either by pure diffusion or driven by a force. Whereas the analyte is not excited by the laser light on one side, it starts fluorescing and gets detected, when it has travelled through. If fluorophores travel through the pore with a spatial separation, this should be visible in a temporal sequence of fluorescence intensity bursts, the signal needed for the protein fingerprinting.

In the current state, we are able to detect fluorophores that are freely diffusing through our Zero-mode waveguides, but the system is not well characterised yet. The aim of this project is to use single fluorophores bound to DNA to find out about temporal and spatial resolution of our setup. The project is extremely interdisciplinary on the interface between Biology and Physics. During the project you will learn how to work with nanopores and how to operate a high end microscope, in order to do single molecule fluorescence experiments. Additionally you will get trained in handling biological samples and how to analyse fluorescence data.

If you find this interesting, please contact Nils Klughammer (n.klughammer@[REMOVE THIS]tudelft.nl


10. BEP/MEP: single-molecule investigation of RNA-polymerase interaction with supercoiled DNA

Cells store their genetic information in DNA. Typical length of the genomic DNA lies in a range of several millimeters to meters which needs to be well-organized for reading genes of demand. Consequently, it is not an easy task to put this long polymer inside the micron sized cell in a very organized fashion. Inter-winding and twisting of the DNA play a key role in packing the DNA into the cell, yet the perpetual access by the proteins, which reads the genetic information from the DNA and convert it into the vital chemical processes, makes the structural status of DNA dynamic and challenging. One such vital process is RNA-transcription where the DNA is read by a protein called RNA-polymerase (RNAP).

It is known that the activity of RNA-polymerase greatly depends on the supercoiled state of the DNA. For instance, while RNA is transcribed by RNAP, plectonemes are generated both downstream and upstream of RNAP/RNA/DNA complex (see figure). This in turn slows down RNA transcription by RNAP. However, most in vitro experiments were performed on linear DNA which does not represent the conditions that RNAP encounters in vivo. Thus, we are interested in studying the interaction of RNAP with supercoiled DNA using our newly developed high-throughput single-molecule technique (see Ganji and Kim et al, Nano Let. 2016). The outcome of this project will improve our understanding of mechanism of RNA transcription by providing detailed mechanism of how RNAP interacts with transiently generated plectonemes. A student with background in physics and/or biology will explore this interdisciplinary project and study how the supercoiled state of the DNA modulates the activity of RNA-polymerase.

For more information, please contact Eugene Kim (e.kim@[REMOVE THIS]tudelft.nl).


11. Single-molecule study of condensin-induced loop extrusion dynamics

It has been hypothesized that Structural Maintenance of Chromosomes (SMC) protein complexes such as condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. We have recently provided experimental evidence for loop extrusion by directly visualizing the formation and progressive extension of DNA loops by yeast condensin in real-time (See Ganji et. al. Science 2018). We aim to further extend this study to investigate loop extrusion mechanism in supercoiled DNA (i.e. over- or under-wound DNA strands) as well as in the presence of RNA polymerase. This project is highly interdisciplinary and the student will be able to gain in-depth knowledge on single-molecule biophysics and experimental skills on HiLO/TIRF/wide-field microscopy and flow cell preparation.

For more information, please contact Eugene Kim (e.kim@[REMOVE THIS]tudelft.nl).


12. Protein sequencing using nanopore technology

Proteins are the molecular machines in the human body. Therefore, understanding protein function is key to understand, detect, and cure diverse diseases. This function is tightly linked to the proteins’s 3D structure and ultimately its specific amino acid sequence.
Electric detection using single molecule nanopore technology has emerged as one of the most promising techniques to sequence proteins in a cheap and fast way: upon translocation through the pore, the protein of interest partially blocks the pore, thus changing the pore’s electric conductance. However, the higher complexity of proteins as compared to DNA (20 amino acids vs. 4 nucleotides) has remained a challenge.

In project 1, we address this complexity by attaching artificial marker molecules to specific amino acids, enabling their reliable recognition. The design and characterization of such chemical tags covers interdisciplinary concepts, such as the physics of nanopore technology, the chemistry of nanopore-tag interactions, and protein biochemisty.
Project 2, aims at controlling the notoriously fast translocation time of molecules through the pore that limits the observation time. Specifically, we exploit a motor protein to control translocation in an ATP-dependent manner. In this innovative approach, we combine the best of two worlds, namely physical single-molecule detection with the function of protein nano-machines. Experience in protein chemistry techniques is favourable for project 2.

Both projects are suitable for BEP and MEP. We look for highly motivated and independent students who seek to pursue interdisciplinary research at the nanoscale.

Sonja Schmid
s.schmid@[REMOVE THIS]tudelft.nl
015-278 7915