PhD position in biophysics and molecular modelling
Are you about to graduate from a MSc degree, do you have an interest in combining simulations and experimental work to understand conformational changes in proteins? Are you interested to figure out which antibodies are good binders for biomarkers in Alzheimer's disease? Please apply to the Vrije Universiteit Amsterdam.
- De Boelelaan, Amsterdam, Noord-Holland
- Tijdelijk contract / Tijdelijke opdracht
- Uren per week:
- 40 - 40 uur
- € 2325 - € 2972 per maand
We seek a new colleague who will work on a collaborative PhD project within the MIRIADE consortium (see below) in the Bioinformatics group at the Vrije Universiteit Amsterdam. The aim is to develop novel approaches in biomarker development for dementias. Crucial is here to develop models to rationalise the prediction how biomarkers, in a specific medium, will be able to bind specific antibodies for detection. Biophysical experiments (HD exchange mass-spectrometry) and biophysical simulations will play an important role in this research. The specific goal of the PhD project is to investigate the change in solvent accessibility for proteins binding to antibodies in different biological matrices.
Your main tasks and responsibilities in this project are:
- Develop an algorithm for surface matrix specific surface accessibility prediction
- Experimentally study protein folding states in different biological matrices by quantifying surface accessibility in biological matrices using HDX-MS for bound and unbound states of the protein (LGC).
- Model the resulting protein structure ensembles
- Communicate your work with both biomedical researchers, bioinformaticians and physicists
- Supervise computer practicals to MSc students (<5% fte)
- We look for excellent candidates with an M.Sc. degree in Biophysics. Chemistry, Biotechnology or related fields.
- Have knowledge of and a keen interest in protein structures
- Be familiar in vitro experiments handling proteins; having experience with proteomics (MS), would be a pre
- Some programming skills (and an interest to develop this further)
- must not already hold a PhD;
- must be within the first four years (full-time equivalent) of their research career;
- must not have resided or carried out their main activity (work, studies, etc.) within the Netherlands for more than 12 months in the three years immediately prior to their recruitment.
ConditionsA challenging position in a socially involved organisation. The salary will be in accordance with university regulations for academic personnel and amounts €2,325 (PhD) per month during the first year and increases to €2,972 (PhD) per month during the fourth year, based on a full-time employment.
The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a total duration of 4 years.
Additionally, Vrije Universiteit Amsterdam offers excellent fringe benefits and various schemes and regulations to promote a good work/life balance, such as:
- a maximum of 41 days of annual leave based on full-time employment
- 8% holiday allowance and 8.3% end-of-year bonus
- contribution to commuting expenses
- good paid parental leave scheme
- child daycare facilities available on campus
Additional informationAre you interested in this position? Please apply via the application button and upload your:
- curriculum vitae (CV)
- highlighting research experience
- including two references we may contact
- cover letter (CL)
- including a motivation for this PhD position
- explaining how you fulfill the requirements for this position
- BSc and MSc academic transcripts
- containing all your grades at university level
Applications received by e-mail will not be processed.
If you have any questions regarding this vacancy, you may contact:
Name: Caroline Waij