PhD/Post-doc positions on Building a Synthetic Cell & Membrane Biology (7.0 FTE)

Prof. Bert Poolman, Membrane Enzymology (b.poolman@rug.nl)
Prof. Dirk-Jan Slotboom, Structural Membrane Biology (d.j.slotboom@rug.nl)
We aim to design and construct minimal cells from molecular building blocks that are capable of accumulating amino acids for protein synthesis from peptide precursors via a single peptide transport system in conjunction with encapsulated aminopeptidases. Similarly, we aim to obtain nucleotides for DNA and RNA synthesis and cofactor regeneration by developing minimal metabolic networks in vesicle based systems. Example and founding work: doi: 10.1021/jacsau.1c00406
Application link: https://bit.ly/3Wrntej

Prof. Siewert-Jan Marrink, Molecular Dynamics (s.j.marrink@rug.nl)
Based on the Martini force field and associated tools, we are currently at a stage where we can simulate the dynamics of entire cells and cellular organelles at near-atomic resolution. We aim to construct realistic models of minimal cells as well as mitochondria in order to obtain insight in their molecular level organization. Alongside, we will develop improved Martini models for the constituents, as well as efficient tools to facilitate the workflow of simulating such complex systems.
Example and founding work: doi:10.1002/wcms.1620
Application link: https://bit.ly/3UQrCar

Prof. Siewert-Jan Marrink, Molecular Dynamics (s.j.marrink@rug.nl)
Prof. Timon Idema, TU Delft (t.idema@tudelft.nl)
To aid in the rational design of synthetic cells we use a multiscale modeling framework, coupling mesoscale simulation approaches to detailed molecular dynamics simulations. We aim to understand what is needed to drive the cell to successful fission, an essential step during cell division. Improving the coupling between the different levels of resolutions will be one of the associated challenges.
Example and founding work: doi:10.3389/fmolb.2019.00059
Application link: https://bit.ly/3UNA9dV

Prof. Matthias Heinemann, Molecular Systems Biology (m.heinemann@rug.nl)
Prof. Bert Poolman, Membrane Enzymology (b.poolman@rug.nl)
The challenges of developing functional synthetic systems increase exponentially with the number of components. We aim to tackle the integration of metabolic networks by merging of reconstituted vesicles, carrying different synthetic modules, by membrane fusion as well the separation of modules over different synthetic cells and allow cross feeding. Second, by model-based experimental analysis of reconstituted systems we will debug the networks and obtain insight for further engineering.
Example and founding work: doi: 10.1038/s41467-019-12287-2
Application link: https://bit.ly/3Y8VxNT

Prof. Giovanni Maglia, Chemical Biology (giovanni.maglia@rug.nl)
Biological nanopores are protein-based sensors that have been used in single-molecule DNA and protein sequencing, and to identify molecules in complex biological samples. In our group and startup company, we use synthetic biochemistry techniques to designing and engineer nanopores for a variety of applications, with the aim of replace standard techniques such as microarrays and mass spectrometry for the analysis and sequencing of proteins.
Example and founding work: DOI: 10.1038/s41557-021-00824-w
Application link: https://bit.ly/3uJHYGY

Prof. Bert Poolman, Membrane Enzymology (b.poolman@rug.nl)
Prof. Cristina Paulino Electron Microscopy (c.paulino@rug.nl)
Physicochemical homeostasis is the ability of a system to maintain steady internal physical and chemical conditions such as pH, ionic strength, osmotic pressure and (macro)molecular crowding. The 2nd messenger cyclic-di-AMP plays a crucial regulatory role in physicochemical homeostasis of bacterial cells. We aim to elucidate the structural basis of cyclic-di-AMP sensing and control of the internal pools using biochemical and biophysical approaches, among which high-resolution electron microscopy and activity assays.
Example and founding work: doi: 10.1126/sciadv.abd7697
Application link: https://bit.ly/3Bu6DmG

Prof. Dirk Slotboom, Membrane Enzymology (d.j.slotboom@rug.nl)
Uptake of vitamins by Gram-positive bacteria is often carried out by essential Energy-Coupling Factor transporters, which are powered by ATP hydrolysis. These proteins use a unique mechanism of transport that includes conformation-specific modulation of the lipid bilayer morphology changes to steer substrate translocation. We aim to elucidate the structural basis of this unique mechanism using biochemical and biophysical approaches, among which high-resolution electron microscopy and activity assays, and molecular dynamics simulations.
Example and founding work: doi: 10.1073/pnas.2105014118
Application link: https://bit.ly/3Hx9z5U

• the most important criteria are enthusiasm, excellence, commitment to research and team spirit. Educational background preferably in the area of bioengineering, biochemistry, biophysics, multiscale modeling, systems biology or synthetic biology (see Job descriptions)
• candidates for a PhD position need to have completed a European Master’s degree or equivalent prior to the application deadline. Post doc candidates need to have completed their PhD
• excellent proficiency in English language.

We offer you in accordance with the Collective Labour Agreement for Dutch Universities:

• for the PhD position: a salary of € 2,541 gross per month in the first year, up to a maximum of € 3,247 gross per month (based on fulltime employment) in the fourth and final year. The successful candidate will first be offered a temporary position of one year with the option of renewal for another three years. Prolongation of the contract is contingent on sufficient progress in the first year to indicate that successful completion of the PhD thesis within the next three years is to be expected. A PhD training program is part of the agreement and the successful candidate will be enrolled in the Graduate School of Science and Engineering
• for the postdoc position: a temporary appointment of three years and a salary from a minimum of € 3,557 gross per month up to a maximum of € 4,670 gross per month (salary scale 10) based on a full-time position and dependent on qualification and work experience
• a full-time position (1.0 FTE)
• a holiday allowance of 8% gross annual income
• an 8.3% end-of-year bonus and participation in a pension scheme for employees.

Starting date: early 2023

The University of G