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PhD position (no. 3) in biological microED and single molecule electron diffraction

Starting on 1 September or as per agreement

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birth place of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

A PhD position funded by the Swiss National Science Foundation is available from September 2021 onwards in the group of Prof Jan Pieter Abrahams at the Biozentrum of the University of Basel.

Cryo-electron microscopy can reveal the atomic structures of biological molecules by focusing the electrons that are scattered by the sample into an image. These electron images have low contrast and are very noisy, because electron beam damages the sample.

The Abrahams group has generated strong evidence that the signal-to-noise ratio of the electron image can be boosted significantly by measuring the scattered electrons directly. This resulted in the development of protein nano-crystallography (micro-ED) and we are extending the method to include non-crystalline samples and single molecule electron diffraction (simED). Novel, dedicated hardware will allow us to develop methods for automatically generating vast amounts of electron diffraction data short periods of time. We aim to develop novel tools based on Artificial Intelligence and Big Data technologies for interpreting these data. An important biological focus of our group is on molecular machines for protein degradation. (I. Mohammed, K. A. Schmitz, N. Schenck, T. Maier, J. P. Abrahams, Catalytic cycling of human mitochondrial Lon protease. Sci. Adv. 7, eabf0156 (2021).

Part of the work will be performed at, and will be supported by the Paul Scherrer Institute (

Your project
Optimal data acquisition for protein simED. A dedicated single molecule diffraction instrument, based on a JEOL F200 with post-column energy filter and hybrid pixel detectors will be commissioned at the PSI (summer 2021), with a data collection capacity of 20 Gbyte/s. Optimizing beam – and scanning parameters, in close collaboration with a PhD student working on optimal data acquisition for microED, is part of your project. Data will be generated by scanning a narrow, parallel electron beam across a sample at liquid N2 temperature of biological macromolecular complexes suspended in a vitrified aqueous buffer. The thickness of the vitreous layer will be in the order of 100 nm and preferably less. The biomolecular complexes can range between 10 nm and 100 nm in diameter. We will pilot data collection with thin hydrated, vitrified protein samples containing nanocrystals (e.g. catalase) or TMV, a 300 nm long, 20 nm diameter cylindrical plant virus with helical symmetry.

Your profile
We are looking for a talented PhD student with the following research profiles:

  • Background in either structural biology, crystallography, and/or electron microscopy.
  • A keen interest in developing break-through technologies.

The project is highly synergistic, and you will work collaboratively as an enthusiastic team towards achieving the common goals. You will have prime responsibility for one particular project, while providing strong support for the other projects.

We offer
We offer an exciting and stimulating work environment with scientific collaborations within the institute and worldwide.

Basel is an international city with people from 150 nations. Located on the border where three countries meet - Switzerland-Germany- France -, it is Europe’s most important life sciences hub. Basel provides a high standard of living and a rich and varied cultural atmosphere.

Application / Contact
Please apply online with a cover letter, CV, reference letters, diplomas and contact information of two referees: Please note that only online applications will be accepted:

For specific questions, feel free to contact Prof. Jan Pieter Abrahams, e-mail: jp.abrahams(at)unibasto make life hard for spam