BEMÆRK: Ansøgningsfristen er overskredet
PhD fellowship in Computational Protein Biophysics
PhD Project in molecular simulations of the dynamics of protein-ligand interactions
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 is part of the ERC Synergy project DynaPLIX (Dynamics of Protein–Ligand Interactions) that aims to combine molecular dynamics simulations, NMR spectroscopy and time-resolved crystallography to quantify the dynamical pathways of how ligands bind to proteins. The DynaPLIX project is a collaboration with the groups of Mikael Akke (Lund, Sweden; NMR) and Eike Schulz (Hamburg, Germany; crystallography), and the PhD student is expected to interact with researchers in these groups also.
Start date is (expected to be) 1. October 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
Our knowledge of protein function is primarily based on static structures, which have provided great insights about structure-function relationships. Proteins are, however, not static molecules, but undergo spontaneous transitions between alternative structural states, some of which are rare, transient conformations that are essentially invisible to traditional methods. These dynamical properties are known to be critically important for function, but high-resolution studies of dynamics have so far been conducted merely as an “add-on” following structural studies.
In DynaPLIX, we aim to establish “integrative biomolecular dynamics” by developing methods that integrate time-resolved X-ray crystallography, nuclear magnetic resonance spectroscopy, and molecular simulations to study the motions of proteins while they carry out their function. The PhD students in the Lindorff-Larsen group will work on the computational aspects of DynaPLIX, but will work closely also with researchers performing experiments in the groups in Sweden and Germany.
The project is focused on the challenging problem of molecular recognition, specifically, of how proteins bind ligands by describing with atomic resolution the entire dynamic process to reach a consistent kinetic, thermodynamic, and structural view. From the computational side, this involves performing molecular simulations of protein-ligand binding processes and constructing kinetic models of these. In addition to using molecular dynamics simulations, ideally aided by machine learning methods, a key aspect of the project is to develop and apply theory of how to integrate simulations and time-resolved and time-dependent experiments.
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)
- Analysing molecular simulations using machine learning or Markov state models
- Integrating biophysical experiments and molecular simulations
Our group and research- and what do we offer?
The positions are part of an interdisciplinary research effort called DynaPLIX (Dynamics of Protein–Ligand Interactions) that aims to combine molecular simulations, NMR spectroscopy and time-resolved crystallography to quantify the dynamical pathways of how ligands bind to proteins. The DynaPLIX project is funded by a six-year ERC synergy grant and is a collaboration with the groups of Mikael Akke (Lund, Sweden; NMR) and Eike Schulz (Hamburg, Germany; crystallography). The PhD student is expected to interact with researchers in these groups also.
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. The Ph.D. students will work together with scientists from a number of disciplines, and also have the possibility of spending time in one or more of the partner laboratories within DynaPLIX. 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: lindorff@bio.ku.dk
The PhD programme
The PhD programme consists of a three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.
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. physics, biophysics, 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 aimed at high-impact 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 (SØG STILLINGEN) below. Only applications submitted via this system will be evaluated and you should not submit applications directly via e-mail.
Please include:
- A motivated letter of application (max. one page) explaining your background, key skills and how they are relevant to the research in DynaPLIX
- Curriculum vitae (max. two pages) including information about your education, experience, language skills and other skills relevant for the position
- Publication list (if relevant) including preprints and papers in active preparation. Please do not enclose copies of the papers.
- 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.
- 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
Application deadline:
The deadline for applications is 1 August 2023, 23:59 GMT +2.
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 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 via email.
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.
INFORMATIONER OM STILLINGEN:
- Arbejdspladsen ligger i:
Hvidovre Kommune
-Virksomheden tilbyder:
-Arbejdsgiver:
KU - SCIENCE - BIO, Universitetsparken 13, August Krog Byg., 2100 København Ø
-Ansøgning:
Ansøgningsfrist: 30-07-2023; - ansøgningsfristen er overskredet
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