Doctoral Student in Theoretical Chemistry (MSCA COFUND project PRISMAS) (PA2023/599)

PRISMAS - PhD Research and Innovation in Synchrotron Methods and Applications in Sweden – is a new doctoral network training the next generation of 40 leading synchrotron experts, co-funded by the Horizon Europe MSCA COFUND Programme.

As a PRISMAS PhD student, you will have the chance to conduct cutting-edge research in your field, taking advantage of state of the art tools that will bring to attractive future job opportunities in academia or industry. Moreover, you are part of designing the future of synchrotron technology and instrumentation and using these to tackle some of the most significant global challenges the world faces today while acquiring interdisciplinary and intersectoral knowledge. Being part of the PRISMAS programme gives you the one-of-a-kind experience in form of a secondment at the world´s first 4th generation synchrotron, MAX IV in Lund, Sweden. Complemented with a tailored training programme, including courses to build scientific and technical competence as well as strengthen transferrable skills, PRISMAS provides you with the skills, knowledge and competence needed to successfully achieve your doctoral degree.

Description of the workplace

At the Division of Theoretical Chemistry (Department of Chemistry at the Science Faculty), we study chemical processes with the help of computational methods, including quantum chemical calculations and statistical mechanics simulations. The aim is to understand chemical systems and processes at the molecular level, including interactions, structure and dynamics. The work is often done in connection with experimental studies. The division currently consists of nine senior scientist, five postdoctoral scientists and eleven PhD students.

The group of theoretical biochemistry is currently comprised of five PhD students and two postdocs. It aims at studying proteins using all available computational methods, from advanced quantum chemical methods and density-functional theory to molecular-mechanics methods, molecular dynamics simulations and free-energy calculations. The group has three focus areas: mechanisms of enzymes (mostly metalloenzymes), e.g. nitrogenase, lytic polysaccharide monooxygenase and particulate methane monooxygenase, ligand-binding calculations (drug development) and the combination of computational chemistry and experimental structure methods like X-ray or neutron crystallography, NMR and cryogenic electron microscopy (cryo-EM). The flagship for the latter project has been quantum refinement, a combination of X-ray crystallography and quantum mechanical calculations, which allows us to improve and interpret crystal structures. The group is led by Prof. Ulf Ryde (https://www.teokem.lu.se/people/seniors/ryde), who received his PhD in 1991 and became a professor in theoretical chemistry in 2004. He has published 297 articles and has 19 900 citations and a h-index of 76.

References

• J. Bergmann, E. Oksanen, U. Ryde (2022) "Combining crystallography with quantum mechanics", Curr. Opin. Struct. Biol., 72 18-26; http://dx.doi.org/10.1021/acs.jctc.1c00374.
• J. Bergmann, E. Oksanen & U. Ryde (2021) "Critical evaluation of a crystal structure of nitrogenase with bound N₂ ligands", J. Biol. Inorg. Chem., 26, 341-353; http://dx.doi.org/10.1007/s00775-021-01858-8.
• L. Cao & U. Ryde (2020) "Quantum refinement with multiple conformations; applications to the P-cluster in nitrogenase", Acta Crystal. D, 76, 1145-1156; http://dx.doi.org/10.1107/S2059798320012917.

What we offer

Lund University is a public authority which means that employees get particular benefits, generous annual leave and an advantageous occupational pension scheme. Read more on the University website about being a Lund University employee Benefits for employees | Lund University

The MSCA COFUND project PRISMAS offers you outstanding opportunities as well as a stimulating and inspiring surrounding for performing cutting-edge research. Supporting your mobility, it creates perfect conditions for strengthening your international network.

Work duties and responsibilities

You will develop and apply methods to combine quantum mechanical calculations with time-resolved X-ray crystallography of proteins. 

X-ray crystallography has traditionally been the prime source of structural information of biological macromolecules. Such information is essential for the understanding of biomacromolecules and it is mandatory for any rational modification of these molecules, e.g. by mutagenesis or drug development. Recently, the development of powerful X-ray sources has opened the opportunity to collect series of structures during dynamic events or during reactions using time-resolved crystallography methods. A challenge for these methods is to interpret the data. Since synchronisation of the dynamic event is never perfect, the collected data typically reflect a mixture of structures, e.g. the reactant, product and intermediate states of a reaction, and it is a challenge to sort out what is really seen for the relatively poor resolution of biomacromolecules. Normally, the structures are interpreted as a mixture of states with non-unity occupancies, using empirical restraints to ensure that the structures make chemical sense. In practice, the results are often biased by what the crystallographer hope to see. Therefore, there is a need for more strict procedures for the refinement of time-resolved crystallographic structures. You will employ the quantum-refinement procedure developed in our group, which provides an ideal solution for mixtures of several states and provides an optimal compromise between the experimental data and the quantum mechanical calculations. When the electron density is ambiguous, the quantum mechanical calculations will give an unbiased and accurate interpretation of the density. The method will be combined with kinetic modelling of the reaction to provide an unbiased interpretation of the structure. An important part is to make the methods available for any crystallography user at MAX IV.

The training implies a secondment of 3-12 months at MAX IV laboratory  in Lund, Sweden. Additional secondments and/or short stays may be arranged in agreement with the supervisor of the research project. Moreover, you will attend international conferences, participate in periodical project meetings and training schools as well as in specialised courses at different universities to complement your knowledge.  A certain amount of travelling is foreseen in relation to these activities.

Qualifications

You must have MSc, civil engineer or an equivalent education in chemistry, physics, bioinformatics or similar.
Practical experience of theoretical chemistry methods (quantum chemistry, molecular dynamics, free energy perturbations, etc.) and practical experience with crystallography are qualifying, as are programming skills and courses in quantum mechanics, statistical mechanics, physical chemistry, mathematics, and crystallography.

Eligibility

Students with basic eligibility for third-cycle studies are those who have completed a

• second-cycle degree have completed courses of at least 240 credits, of which at least 60 credits are from second-cycle courses,
• have acquired largely equivalent knowledge in some other way, in Sweden or abroad.

The employment of doctoral students is regulated in the Swedish Code of Statues 1998: 80. Only those who are or have been admitted to PhD-studies may be appointed to doctoral studentships. When an appointment to a doctoral studentship is made, the ability of the student to benefit from PhD-studies shall primarily be taken into account. In addition to devoting themselves to their studies, those appointed to doctoral studentships may be required to work with educational tasks, research and administration, in accordance with specific regulations in the ordinance.

To comply with the mobility rule of the MSCA COFUND programme, you are eligible if you have not resided in Sweden for more than 12 months during the period 2020-05-01 to 2023-05-02 for your main work or studies.

By the employment date (before 01/09/2023) you must have completed courses of at least 240 credits, of which at least 60 credits are from second-cycle courses, have been awarded a Master´s degree or have acquired largely equivalent knowledge in some other way, in Sweden or abroad.

In addition to the criteria abovementioned, you must have fulfilled a second cycle education in a relevant field, such as chemistry, physics, bioinformatics.

You are eligible for the PRISMAS programme, if you are a doctoral candidate, i.e., are not already in possession of a doctoral degree.

Type of employment

Limit of tenure, four years according to HF 5 kap 7§.

The position is a fixed term position for four years at 100% of full time and foreseen to start on 01/09/2023.

The holders of these positions have a primary obligation to successfully fulfil their postgraduate (third cycle) education ending with a doctoral degree (PhD). A position as doctoral student can contain some limited teaching or other departmental work at the Department of Theoretical Chemistry. The maximum amount of such work is 20%.

How to apply

Applications are to be submitted via Varbi and must include the following documents:

• CV in Europass format
• A two-page cover letter, justifying your interest in the position and how it matches your qualifications as well as the prioritization in case of applying to several PRISMAS positions.
• at least one reference letter
• an evidence of English 3 proficiency (minimum B2 level)
• Copy of academic records (including marks for all coursework) with a transcript of diploma in English,
• and any other document to which you would like to draw attention (details of referees, letters of recommendation, etc.)

These documents should be uploaded (pdf) in the job application portal. Exam certificates and other documents on paper should be scanned or photographed before being uploaded.

The application will be evaluated based on scientific excellence, the adequacy of your career plan and your thesis project as well as your research experience, communication and collaborative skills.

Details on the novel, unique and common selection process for all the PRISMAS positions can be found here: How to apply – MAX IV (lu.se)

Contact

For more detailed information on the position or the research project, please contact:
Prof. Ulf Ryde, [email protected]

If you have questions on the selection process, please contact:

[email protected]

For questions on the employment conditions and the university, please contact:
Mia Hedin, Human Resources Administrator, [email protected]