PhD position in biophysics and molecular modelling

Vrije Universiteit Amsterdam
  • PhD position in biophysics and molecular modelling
  • University Graduate
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.

FTE: 1

Job description

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)

To be eligible for this position, the applicant must satisfy the following requirements conform the Marie Curie admission requirements you:

  • 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.

What are we offering?

A 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

About Vrije Universiteit Amsterdam

The ambition of Vrije Universiteit Amsterdam is clear: to contribute to a better world through outstanding education and ground-breaking research. And to be a university where personal education and societal involvement play a leading role. Where people from different disciplines and backgrounds work together on innovations and on generating new knowledge. Our teaching and research embrace the whole spectrum of science – from the humanities, the social sciences and the pure sciences through to the life sciences and the medical sciences.

Vrije Universiteit Amsterdam is home to more than 26,500 students. We employ more than 4,600 individuals. The VU campus is easily accessible, located in the heart of Amsterdam’s Zuidas district, a truly inspiring environment for teaching and research.

Diversity is one of our university’s core values. We are an inclusive community, and we believe that diversity and international activities enhance the quality of education and research. We are always looking for people who can enhance diversity on our campus thanks to their background and experience.

The Faculty of Science
The Faculty of Science inspires researchers and students to find sustainable solutions for complex societal issues. From forest fires to big data, from obesity to medicines and from molecules to the moon: our teaching and research programmes cover the full spectrum of the natural sciences. We share knowledge and experience with leading research institutes and industries, both here in the Netherlands and abroad.

Working at the Faculty of Science means working with students, PhD candidates and researchers, all with a clear focus on their field and a broad view of the world. We employ more than 1,250 staff members, and we are home to around 6,000 students.

The MIRIADE project
The project is being pursued in the framework of the Marie Skłodowska-Curie Innovative Training Network (Multi‐omics Interdisciplinary Research Integration to Address DEmentia diagnosis). The overarching goal of the MIRIADE project is to train a novel generation of scientists able to accelerate dementia biomarker development.

Dementia is a deterioration in cognitive abilities affecting areas including memory, language skills, perception, reasoning, and problem-solving. It can also be accompanied by an associated decline in behavioural abilities related to emotional control, social behaviour, or motivation. Around 50 million people worldwide suffer from dementia and there are approximately 10 million new cases each year. Despite the widespread prevalence and debilitating effects of dementia, there are currently no reliable tests to detect the underlying pathophysiology years before the symptoms begin. MIRIADE is working on changing that with the help of a new generation of researchers. The focus is on biomarker discovery and clinical validation, including addressing regulatory requirements. Early diagnosis will significantly enhance options for monitoring and modulating progression.

MIRIADE comprises of ten world-leading research organisations, 5 small to large industries and 2 patient organisations, from 12 countries in the EU, South-Korea and USA. A total of 15 Early Stage Researchers (ESRs) will be hosted across the network. The project will leverage existing proteomics datasets to identify the most promising candidate biomarkers for the major forms of dementias.

The primary host of the project is: the Vrije Universiteit Amsterdam, The Netherlands. As an early stage researcher you will be supervised by an Associate Professor in Bioinformatics (Dr Sanne Abeln) and will collaborate with groups at the LGC in London (Dr Milena Quaglia). In addition you will collaborate with the Neurochemistry group at the Amsterdam UMC location VUmc (Prof Charlotte Teunissen). You will be part of a young, multidisciplinary team, with ample experience in structural bioinformatics, assay development and machine learning.


Are 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
Are you interested in this position? Please apply via the application button and upload your curriculum vitae and cover letter until 30 April 2020. The job interviews are planned for mid May, when possible please take them into account when applying for the position. The intended starting date for this position is September 2020.

Applications received by e-mail will not be processed.

Vacancy questions
If you have any questions regarding this vacancy, you may contact:

Name: Caroline Waij

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