Current students



Reinier de Bruin

Applied Physics student

I am Reinier de Bruin, a second year MSc Applied Physics student, enrolled in the Health and Life track. After doing a few extracurricular computer science courses, I got excited about doing a MSc thesis project that lies at the junction of biophysics and computer science.

At the Jakobi lab, I will try to develop new algorithms to improve interpretation of three-dimensional (3D) volumes of protein complexes obtained by cryo-EM imaging. This will consist of coming up with suitable 3D map metrics, designing and training a deep neural network and benchmarking this network against a phyiscs-based contrast restoration procedure. By doing this, we hope to improve the reliability of interpretation for cryo-EM maps.

Outside the lab, I like following societal developments, while having the tendency to let myself believe that I would do a better job than the currently employed politicians at solving them. Given the very low chances of me being a rare undiscovered political talent, we can safely assume that that’s not true. While being fed up about that rather undisputable conclusion, I enjoy going out for a run or do other sports. Like most, I like hanging out with people I find interesting and fun, because in the end, people are amazing: that’s where it’s all about.

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Alumni



Rhodé van den Dool

Nanobiology student

I am a Nanobiology bachelor student, doing my BEP at the Jakobi lab. I will look at algorithms from small angle x-ray scattering as a potential new way to produce initial models that are usable for cryo-EM structure determination.






Anna Daamen

Nanobiology student (February 2020 - February 2021)

My name is Anna Daamen and I am a Nanobiology master student. The High Resolution Imaging course during my first year as a master student is what got me excited about electron microscopy, so in February I started my Master End Project in the Jakobi lab. During my project I will try to reconstitute the lipid modification of proteins in intracellular immunity in vitro and in vivo. The lipid modification of these proteins is what enables them to interact with the membrane and assemble in large molecular machineries. I will study their assemblies on liposomes and the interactions with the membrane using Cryo-EM.





Eva van Oosten

Nanobiology student (February 2020 - February 2021)

As a Nanobiology master student, I am doing my academic internship in the [Jakobi Lab]http://cryoem.tudelft.nl(). The group focuses on cellular auto-immunity, but the mechanisms the key proteins carry out are still quite unknown. Therefore I will look into the interactions between these proteins as this could give more insight in their different functions. I am curious to see what we will find out!





Marre Niessen

Nanobiology student (September 2019 - November 2020)

As part of my masters Nanobiology, I am doing my final project in the Jakobi lab. I will be working on the development of a new correlative imaging and nanomanipulation setup for cryo-EM sample preparation. With this setup, we will be able to investigate processes of cell-autonomous immunity in an entirely new way.

Marre is now an experimental physicist at Delmic.





Arent Kievits

Nanobiology student (September 2019 - August 2020)

I am a Nanobiology student doing my MEP project in the Jakobi lab. I am interested in high-resolution imaging, image processing and data science. Therefore I took on the challenge to develop new methods that aim to utilize machine learning tools to automate data collection and analysis of electron diffraction data from macromolecular crystals. These tools will hopefully contribute to accelerating structural analysis of biomacromolecules using electron diffraction. When I am not analyzing data I like to play songs on my guitar or swim some lanes in the pool.

Arent went on for a PhD student with our friends in the lab of Jacob Hoogenboom.





Angelique Biemans

Applied Physics student (September 2019 - November 2019)

I am a 3rd year bachelor student in Applied Physics and currently doing my final BEP project in the Jakobi lab. I am working on the data processing of electron diffraction patterns from crystals. From these patterns the orientation and structure of a crystal can be determined. In my project I try making data analysis of these patterns easier and more automated.





Amanda van der Sijs

Nanobiology student September 2018 - July 2019)

I am a Nanobiology student doing my master thesis at Jakobi lab and Brouns lab. I will study recombinant phages with using cryo-EM and (hopefully!) resolve a high-resolution 3D structure of the phages to gain more insight into phage evolution. My project will consist of the optimization of the sample preparation, finding the best imaging technique and the image analysis of the microscopy data.

Amanda went on for a PhD in the Physical & Colloid Chemistry lab at Utrecht University.





Lars van Roemburg

Nanobiology student (April 2019 - July 2019)

I’m a third year Nanobiology student and I’m doing my BEP at Jakobi Lab. I will be working on the contrast enhancement in the image analysis of the electron microscopy. The current program needs an initial atomic model for contrast enhancement and I will try to get rid of this. With this we could get a better look at proteins we don’t know anything of yet.

Lars went on to follow the Master program in Nanobiology at TU Delft.





Floor Dolsma

Nanobiology student (April 2019 - July 2019)

I am a bachelor student in the Nanobiology programme working on my BEP in the Jakobi Lab. I am trying to develop co-expression systems for lipid modification of intracellular immune effectors.

Floor went on to follow the Master program in Nanobiology at TU Delft.





Danilo Remmers

Nanobiology student (April 2019 - July 2019)

As a Nanobiology Bachelor’s student, I am working on my Bachelor End Project in the Jakobi Lab. I will be working on in vivo biotinylation of intracellular immune effectors. This will eventually enable me to study the interactions between these effectors in higher-order assemblies and to visualize these interactions using cryo-EM.

Danilo went on to follow the Master program in Nanobiology at TU Delft.





Albert Wieland

Nanobiology student (April 2018 - August 2018)

I am third year student in the Nanobiology program and I am currently doing my BEP in the Electron Nanoscopy group at the Bionanoscience department. In this project I will be working on faciltiating the interpretability of single particle cryo-EM maps by further developing local sharpening as implemented in the LocScale method.

Albert went on to follow the Master program in Applied Physics at TU Delft.





Cheng Jin

Life Science and Technology student (April 2018 - August 2018)

I am currently in my third year of the Life Science & Technology program. For my BEP, I joined the Electron Nanoscopy group at the Kavli Institute in Delft. For this project, I will focus on the isolation and characterization of proteins involved in the cellular response against viral or bacterial attacks.