211-1976/24-2H PhD fellowship in Computational Protein Biophysics

PhD fellowship in Computational Protein Biophysics
PhD Project in computational methods for protein biophysics and structure
Department of Biology
Faculty of SCIENCE
University of Copenhagen

The Lindorff-Larsen group at the Linderstrøm-Lang Centre for Protein Science, Department of Biology, Faculty of Science, University of Copenhagen, Denmark invites applicants for one or more PhD fellowships in computational protein biophysics. The project aims to combine research in (i) the PRISM (Protein Interactions and Stability in Medicine and Genomics) centre that bridges protein biophysics and genomics and (ii) the ERC Synergy project DynaPLIX (Dynamics of Protein–Ligand Interactions) that aims to combine molecular modelling to quantify the dynamical pathways of how ligands bind to proteins.

Start date is expected to be 1. March 2025 or as soon as possible thereafter. Details about the project, what we are looking for and how to apply can be found below.

The project

The PhD students will work on one or more of the subprojects within PRISM and DynaPLIX. We have recently developed predictive models for how genomic variation in protein-coding regions (protein variants) affect the stability and function of proteins, and are in particular interested in developing predictive models that can be interpreted in terms of specific biological mechanisms. We aim to expand this work to go beyond modelling proteins via static structures as dynamical properties are known to be critically important for function.

Research topics for the PhD projects include:

• Development and application of machine learning and biophysical methods to interpret genomic variation for dynamic proteins and protein interactions
• Interpreting sequence variation in disordered regions through machine learning and simulations
• Developing computational models to study protein dynamics and heterogeneity using for example cryoEM

Who are we looking for?
We are seeking motivated applicants with an MSc degree in physics, biophysics, chemistry or biochemistry or similar fields, ideally with some prior research experience (e.g. through MSc projects) within one or more of these areas:

• Advanced molecular dynamics methods (ideally beyond standard molecular simulations)
• Integrating biophysical experiments and molecular simulations
• Structural bioinformatics and related machine learning methods
• Computational methods for analysing cryoEM data

Our group and research- and what do we offer?
The positions are part of an interdisciplinary research efforts called PRISM and DynaPLIX. The Ph.D. students will work in the group of Kresten Lindorff-Larsen, located at the Department of Biology in central Copenhagen. The group is also part of an interdisciplinary and collaborative research environment at the Linderstrøm-Lang Centre for Protein Science, and the Ph.D. students will work together with scientists from a number of disciplines. The group is highly international and a good level of spoken and written English is required. We offer creative working conditions in dynamic and international research environment. Current members of the research group come from a broad range of scientific and personal backgrounds, and we value collaborations and interdisciplinary work.

Principal supervisor is Professor Kresten Lindorff-Larsen, Department of Biology, E-mail: [email protected]

Qualifications needed for the regular programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. , e.g. bioinformatics, computational biophysics, physics, chemistry or biochemistry. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in both PhD programmes

• Carry through an independent research project under supervision
• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers for publication as preprints and in scientific journals
• Write and defend a PhD thesis on the basis of your project

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Application and Assessment Procedure

Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include:

1. Motivated letter of application (max. one page) explaining your background, key skills and how they are relevant to the research in Lindorff-Larsen group
2. Curriculum vitae (max. 2 pages) including information about your education, experience, language skills and other skills relevant for the position (incl. relevant programming experience)
3. Publication list (if relevant) including preprints and papers in active preparation. Do not enclose copies of the papers.
4. Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
5. If you do not yet hold your MSc and would like to apply, please submit a letter from your supervisor regarding your expected graduation date
6. Reference letters (If available)

Application deadline:
The deadline for applications is Sunday 10 November 2024, 23:59 GMT +1.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/.

Interviews with selected candidates are expected Interviews with selected candidates are expected initially to be held online followed by in-house interviews on dates agreed upon with the candidate.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.