Project description
In a healthy cell, proteins fold into compact structures with regions containing regular alpha-helical and beta-strand configurations. In diseases such as Alzheimer’s, proteins misfold and bind to each other using this same beta-stranded structure. The underlying physics, particularly the configurational entropy that explains how favourable this beta-strand state is, is yet to be properly understood.
 
In this project, you will tackle this problem by incorporating information extracted from unfolding experiments and from structural big data in large-scale computer simulations together with a team of local and international researchers..
 
Our approach to obtain these entropic contributions is multidisciplinary and involves mining big experimental data sets, performing focused experiments and simulating models with different levels of detail. We consider two physical systems to extract these contributions: 1) the elongation of amyloid fibrils and 2) the force unfolding of an auto-transporter protein.

To fill the PhD position for this project, we will be looking for a, highly motivated, enthusiastic candidate with the ability to proactively tackle the project’s research questions. The candidate should have a background (master degree or equivalent) in either Bioinformatics or Biophysics; the candidate should also have programming experience, and an outspoken interest in protein biophysics. Lab experience in handling proteins is considered an advantage.

The initial appointment will be for a period of 1 year. After a satisfactory evaluation of the initial appointment this will be extended for a total duration of 4 years. You may find information about our excellent fringe benefits at http://www.workingatvu.nl.
 
• You are expected to travel extensively to our international collaborators; a travel budget is available;
• Remuneration of 8.3% end-of-year bonus and 8% holiday allowance;
• Participation in a solid pension scheme (ABP);
• A minimum of 29 holidays in case of full-time employment. 
   
The salary will be in accordance with university regulations for academic personnel, and range from a minimum of € 2,222 gross per month in the first year up to a maximum of € 2,840 gross per month (salary scale 85.0-3) based on a full-time employment. 

Research at the Faculty of Sciences focuses on the areas of Life & Health, Networked World, Fundamentals of Science, and Energy & Sustainability. The faculty’s teaching activities are directly linked to this excellent research. Cooperation with other faculties on the Vrije Universiteit Amsterdam campus generates attractive, high-quality Bachelor’s and Master’s programmes.  At international level, the faculty cooperates closely with leading scientific institutes and other partners.
 
The VU Department of Computer Science has approximately 170 members, including 35 tenured staff members and 40-50 PhD students. The tenured staff members form the essential basis for the functioning of the department. A tenured staff member is required to make significant contributions to the research and education programmes, and to spend effort on specific tasks at the department level.