Doctoral student in Computational Biophysical chemistry

Description of the workplace

The research at the division for Biophysical Chemistry is dedicated to the study of biomolecular interactions, structure and dynamics, with the aim of understanding biological systems and processes at the molecular level. The emphasis is on experimental and theoretical studies of the physical properties of proteins in solution.

The division of Biophysical Chemistry is part of the Center for Molecular Protein Science (CMPS), which offers a highly creative environment conducive to excellent research. CMPS is the proud home of several research groups that have received prestigious research grants, currently including 1 ERC-Consolidator, 1 ERC-Advanced, 1 ERC-Synergy, and 3 project grants awarded by the Knut and Alice Wallenberg Foundation. CMPS comprises research groups with competence in a range of biochemical and biophysical methods (please see: https://www.cmps.lu.se), thereby offering an excellent learning environment for PhD students and postdocs.

The current position is tied to the research groups of Prof. Mikael Akke and Assoc. Prof. Pär Söderhjelm and is funded by a project grant awarded by the Knut and Alice Wallenberg Foundation. The project involves a collaboration between research groups representing complementary expertise in biophysical methods: Mikael Akke (NMR spectroscopy), Pär Söderhjelm (molecular dynamics simulations and computational chemistry) and Sara Linse (surface plasmon resonance) at Lund University and Erik Lindahl (molecular dynamics simulations and computational chemistry) at Stockholm University. The project addresses the relationship between conformational dynamics, energetics, and allostery in proteins.

Subject description

In this PhD project, you will learn to use advanced simulation methods to map out the conformational energy landscape of a protein bound to various ligands. You will investigate the dynamics and make computational predictions that can be tested experimentally to advance our understanding of allosteric regulation and thereby lay the foundation for new types of rational drug development.

Work duties

PhD student in Biophysical Chemistry.

The work involves setting up simulation models of protein systems, designing strategies for large-scale conformational sampling of the systems, implementing these strategies at high-performance computer clusters, developing new analysis methods and finally using these methods to obtain a better understanding of the specific system as well as allosteric regulation in general.

The main duties of doctoral students are to devote themselves to their research studies which includes participating in research projects and third cycle courses. The work duties will also include teaching and other departmental duties (no more than 20%). The division is responsible for courses in physical chemistry, NMR spectroscopy and biophysical chemistry.

The work also involves participating in workshops and conferences to present your research and learn from others.

Admission requirements

A person meets the general admission requirements for third-cycle courses and study programmes if the applicant:

• has been awarded a second-cycle qualification, or
• has satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second cycle, or
• has acquired substantially equivalent knowledge in some other way in Sweden or abroad.

A person meets the specific admission requirements for third cycle studies in biophysical chemistry if the applicant has:

• an MSc in Engineering or other comparable degree with significant components of mathematics, molecular sciences and life sciences. Depending on the student’s research project, second-cycle (MSc) courses in physical chemistry, biophysical chemistry, computational chemistry, protein science and/or molecular spectroscopy may be required. Finally, the student must be judged to have the potential to complete the program.
   

Additional requirements:

• Very good oral and written proficiency in English.
• Very good written and oral communication skills. 

Assessment criteria

Selection for third-cycle studies is based on the student’s potential to profit from such studies. The assessment of potential is made primarily on the basis of academic results from the first and second cycle. Special attention is paid to the following:

1. Knowledge and skills relevant to the thesis project and the subject of study.
2. An assessment of ability to work independently and to formulate and tackle research problems.
3. Written and oral communication skills.
4. Other experience relevant to the third-cycle studies, e.g. professional experience.

Other assessment criteria:

• Experience in computational chemistry, in particular molecular dynamics simulations of biomolecular systems. 
• Knowledge of statistical mechanics and/or biophysical chemistry 
• Good molecular understanding. 
• Experience of advanced computational methods, such as Markov state modelling and Transition path sampling
• Understanding of experimental techniques such as protein NMR spectroscopy.

Consideration will also be given to good collaborative skills, drive and independence, and how the applicant, through experience and skills, is deemed to have the abilities necessary for successfully completing the third cycle programme.

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 Work at Lund University. https://www.lunduniversity.lu.se/about-university/work-lund-university

Terms of employment

Only those admitted to third cycle studies may be appointed to a doctoral studentship. Third cycle studies at LTH consist of full-time studies for 4 years. A doctoral studentship is a fixed-term employment of a maximum of 5 years (including 20% departmental duties). Doctoral studentships are regulated in the Higher Education Ordinance (1993:100), chapter 5, 1-7 §§.

How to apply

Applications shall be written in English and include a one page cover letter stating the reasons why you are interested in the position and in what way the research project corresponds to your interests and educational background. The application must also contain a CV, degree certificate or equivalent including grade transcripts, a copy of the applicant’s master’s thesis or diploma thesis (pdf) and other documents you wish to be considered (contact information for your references, letters of recommendation, etc.).

Welcome to apply!