PhD Position in Computational Chemistry and AI

Faculty/Services:  Faculty of Science
Educational level:  Master
Function type:  PhD position
Closing date:  15 december 2022
Vacancy number:  10814



Do you enjoy working in an interdisciplinary research setting where computational chemistry and AI oriented research are joining forces?  The Van ‘t Hoff Institute for Molecular Sciences , in collaboration with Microsoft Research Amsterdam, is looking for an ambitious PhD student to develop and apply novel computational techniques to answer important chemical/biological/physical questions. Many systems and processes in biology, medicine and material science consist of many interacting molecules that give rise to emergent, complex behaviour. Such complex systems undergo transitions between states, such as the folding of a protein, the association of a ligand, or a phase transition to another state or regime.  These transitions are crucial to understand the systems behaviour, but are often rare and difficult to study. Molecular dynamics simulation is a powerful method to study such systems and processes, but since the events are rare and complex, special simulation methodology in combination with Machine Learning is required, to tack this enormous challenge. 

What are you going to do?


This project focusses on using trajectory sampling to collect path ensembles at an atomistic resolution, in order to compute kinetics and free energy profiles. In addition, using Machine Learning one can extract the most important features, which creates crucial mechanistic insight and allows a grip on the transition of interest, and eventually even allows control and optimization of relevant model parameters in the molecular system.  You will develop and apply such special simulation techniques to both simple catalytic processes, as well as biomolecular processes such as protein conformational changes, and binding/association reactions. 

Tasks and responsibilities: 

•    Perform research in the computational chemistry theme of the van t Hoff Institute for Molecular Sciences 
•    Be and active member of the computational chemistry theme 
•    Take part actively in the collaboration with Microsoft Research Amsterdam 
•    Contribute to the teaching of BSc/MSc students. 
•    Publish and present your work within the project and on international scientific platforms. 
•    Contribute to the teaching activities of the department. 

What do you have to offer?


Your experience and profile:

•    A recent MSc degree in science, preferably chemistry, chemical engineering, physics, materials science,  or computational science with a specialization in natural science.  
•    A strong background in chemistry, physics or computational science. 
•    Affinity and/or experience with molecular simulations is preferred.  
•    Good programming skills preferred
•    Good communication skills in oral and written English. 
•    Strong initiative and good time management skills. 
•    Interest in collaborating with students PhDs and postdoctoral researchers in related projects and research groups within and outside the Netherlands 

Our offer


A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is a soon as possible. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students. 


Based on a full-time contract (38 hours per week) the gross monthly salary will range from €2,541 in the first year to €3,247 (scale P) in the last year. This is exclusive 8% holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable.


Besides the salary and a vibrant and challenging environment at Science Park we offer you multiple fringe benefits:
•    232 holiday hours per year (based on fulltime) and extra holidays between Christmas and 1 January;
•    multiple courses to follow from our Teaching and Learning Centre;
•    a complete educational program for PhD students;
•    multiple courses on topics such as time management, handling stress and an online learning platform with 100+ different courses;
•    7 weeks birth leave (partner leave) with 100% salary;
•    partly paid parental leave;
•    the possibility to set up a workplace at home;
•    a pension at ABP for which UvA pays two third part of the contribution;
•    the possibility to follow courses to learn Dutch;
•    help with housing for a studio or small apartment when you’re moving from abroad. 
Are you curious to read more about our extensive package of secondary employment benefits, take a look here.

About us


The Van 't Hoff Institute for Molecular Sciences (HIMS) is one of eight institutes of the University of Amsterdam (UvA) Faculty of Science. HIMS performs internationally recognized chemistry and molecular research, curiosity driven as well as application driven. This is done in close cooperation with the chemical, flavour & food, medical and high-tech industries. Research is organized into four themes: Analytical Chemistry, Computational Chemistry, Synthesis & Catalysis and Molecular Photonics.


Computational Chemistry is one of the research groups within the Van 't Hoff Institute for Molecular Sciences at the University of Amsterdam. Our research focuses on the development and application of advanced molecular simulation and multiscale modelling methodology to obtain novel and improved understanding of the behaviour of (bio)materials, and of complex (bio)chemical and physical processes that are of technological and scientific importance.


The University of Amsterdam is the Netherlands' largest university, offering the widest range of academic programmes. At the UvA, 30,000 students, 6,000 staff members and 3,000 PhD candidates study and work in a diverse range of fields, connected by a culture of curiosity.


The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain. 

Want to know more about our organisation? Read more about working at the University of Amsterdam.


Any questions?


Do you have any questions or do you require additional information? Please contact:


Job application


If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the button below. We accept applications until and including 15 December 2022


Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

•    a detailed CV including the months (not just years) when referring to your education and work experience;
•    a letter of motivation;
•    the names and email addresses of two references who can provide letters of recommendation.

Only complete applications received within the response period via the link below will be considered.

We will invite potential candidates for interviews shortly after the vacancy is closed. The date and time will be indicated to the selected candidates via email.



The UvA is an equal-opportunity employer. We prioritise diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.


If you encounter Error GBB451, reach out to our HR Department directly. They will gladly help you continue your application. 


No agencies please.