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
Qualifications
• 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.
Organisation
The University of Groningen provides an excellent environment for top-notch research in the field of biomolecular sciences. In the framework of a national program on the construction of a synthetic cell, seven PhD/Post-doc positions are available at the Groningen Biomolecular Sciences and Biotechnology Institute of the University of Groningen in The Netherlands.
The building of a synthetic cell is a great scientific and intellectual challenge for biophysicists, biochemists, and biologists. We aim to take on this challenge in the context of the NWO Gravitation Program BaSyC (https://goo.gl/CMRpEZ) and personal funding programs (ERC). We will combine biomolecular building blocks to create an autonomous self-reproducing cell - a synthetic cell that can sustain itself, grow, replicate and divide.
Seven PhD and Post-doc positions are available for both computational and experimental research: (i) to develop computational models at different levels of complexity with the aim to generate a feasible design of the synthetic cell; (ii) to experimentally reconstruct metabolism for cell fuelling and biosynthesis, with the ability to produce energy carriers and molecular building blocks; (iii) to build pathways that are responsible for the biosynthesis of lipids and macromolecules and integrate these pathways into a synthetic cell, (iv) to design proteins de novo that control the molecular transport across protocell membranes, also including the development of nanopores for diverse applications.
Conditions of employment
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
Application
Please send us a complete application with the below-mentioned supporting documents:
• a cover letter with background and motivation to apply for this position (1-2 pages)
• a curriculum vitae including a brief description of your research interests and accomplishments
• two letters of recommendation from former advisors/professors.
You may apply for this position until 30 January 11:59pm / before 31 January 2023 Dutch local time (CET) by means of the application form (click on "Apply" below on the advertisement on the university website).
The University of Groningen strives to be a university in which students and staff are respected and feel at home, regardless of differences in background, experiences, perspectives, and identities. We believe that working on our core values of inclusion and equality are a joint responsibility and we are constructively working on creating a socially safe environment. Diversity among students and staff members enriches academic debate and contributes to the quality of our teaching and research. We therefore invite applicants from underrepresented groups in particular to apply. For more information, see also our diversity policy webpage: https://www.rug.nl/(...)rsity-and-inclusion/
Our selection procedure follows the guidelines of the Recruitment code (NVP): https://www.nvp-hrnetwerk.nl/nl/sollicitatiecode and European Commission's European Code of Conduct for recruitment of researchers: https://euraxess.ec.europa.eu/jobs/charter/code
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Information
For information you can contact:
Please do not use the e-mail address(es) above for applications.
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