Are you a highly motivated MSc graduate with a strong affinity for machine learning and molecular modeling of drug discovery? The AI for Chemistry group, headed by Associate Professor Bernd Ensing, is looking for a curious and ambitious PhD candidate to work on the development of machine learning methodology for drug discovery in a collaborative project within a consortium led by the Vascular Cell Biology group of Prof. Jaap van Buul and connected to the Molecular and Material Design Technology Hub of the Faculty of Science.
PhD Candidate in Machine Learning and Molecular Modelling of Drug Design
- Faculty of Science
- 14298
- Master's
- €2.901 - €3.707
- 38 hours
- Closes on22-08-2025
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Are you a highly motivated MSc graduate with a strong affinity for machine learning and molecular modeling of drug discovery? The AI for Chemistry group, headed by Associate Professor Bernd Ensing, is looking for a curious and ambitious PhD candidate to work on the development of machine learning methodology for drug discovery in a collaborative project within a consortium led by the Vascular Cell Biology group of Prof. Jaap van Buul and connected to the Molecular and Material Design Technology Hub of the Faculty of Science.
PhD Candidate in Machine Learning and Molecular Modelling of Drug Design
- Faculty of Science
- 14298
- Master's
- €2.901 - €3.707
- 38 hours
- Closes on22-08-2025
Working at the UvA
Join us!
Endothelial cell dysfunction, a key factor in cardiovascular diseases, disrupts vascular immunity and leads to severe health issues, including atherosclerosis, rheumatoid arthritis, and complications from infections such as Covid-19. This project is focused on generating and optimizing drug candidates to activate proteins that regulate endothelial barrier function. The aim is to apply and further develop the latest geometric learning technologies in combination with molecular simulations for recognizing and predicting functionalization possibilities to discover new potential drugs for vascular diseases. The Ensing group develops molecular simulation and machine learning techniques to understand molecular behavior and design molecules and materials with desired properties. In this research project, you will develop and apply geometric learning, generative AI, and reinforcement learning algorithms as well as biomolecular simulations to predict molecular properties such as binding energies and synthetic accessibility, sample chemical space, and suggest improved drug molecules to our experimental collaborators.
The project is part of the Vascular Immunology Consortium, an ambitious interdisciplinary research initiative supported by the University of Amsterdam. This consortium bridges the Faculties of Life Sciences and Medicine, fostering a highly collaborative and integrative research environment. The overarching objective of the consortium is to elucidate the complex mechanisms by which the vascular system regulates the human immune response, with a particular focus on how vascular integrity and function are modulated under inflammatory conditions, including leukocyte extravasation and the biophysical stresses imposed by hypertension and blood flow. This consortium offers three PhD positions at the UvA Faculty of Science. For more information about the other two PhD positions, check here and here.
Working at the UvA
Join us!
Endothelial cell dysfunction, a key factor in cardiovascular diseases, disrupts vascular immunity and leads to severe health issues, including atherosclerosis, rheumatoid arthritis, and complications from infections such as Covid-19. This project is focused on generating and optimizing drug candidates to activate proteins that regulate endothelial barrier function. The aim is to apply and further develop the latest geometric learning technologies in combination with molecular simulations for recognizing and predicting functionalization possibilities to discover new potential drugs for vascular diseases. The Ensing group develops molecular simulation and machine learning techniques to understand molecular behavior and design molecules and materials with desired properties. In this research project, you will develop and apply geometric learning, generative AI, and reinforcement learning algorithms as well as biomolecular simulations to predict molecular properties such as binding energies and synthetic accessibility, sample chemical space, and suggest improved drug molecules to our experimental collaborators.
The project is part of the Vascular Immunology Consortium, an ambitious interdisciplinary research initiative supported by the University of Amsterdam. This consortium bridges the Faculties of Life Sciences and Medicine, fostering a highly collaborative and integrative research environment. The overarching objective of the consortium is to elucidate the complex mechanisms by which the vascular system regulates the human immune response, with a particular focus on how vascular integrity and function are modulated under inflammatory conditions, including leukocyte extravasation and the biophysical stresses imposed by hypertension and blood flow. This consortium offers three PhD positions at the UvA Faculty of Science. For more information about the other two PhD positions, check here and here.
All about this vacancy
This is what you will do
- You will develop graph neural network models for structure-property prediction, in particular for predicting binding sites and synthetic accessibility of organic (drug) molecules;
- You will work with generative AI, such as denoising diffusion and flow matching to generate modifications on existing drug scaffolds;
- You will develop a computational framework to optimize drug-binding of molecules from docking calculations and/or enhanced molecular simulations in a closed-loop fashion using Bayesian optimization or reinforcement learning techniques;
- You will work in close collaboration with colleagues in the Computational Chemistry group at HIMS, the AI4Science Laboratory at IvI, and in experimental groups at HIMS and the Medical Center.
This is what we ask of you
You have/are:
- You have a creative, curious and driven nature;
- You have a recent master degree in artificial intelligence with a specialisation in natural science or a master degree in science, such as pharmaceutical science, chemistry, chemical engineering, or physics, with a specialization in machine learning;
- Experience with geometric machine learning and/or molecular simulation is preferred;
- Experience with (bio-) molecular modeling is preferred;
- You have good programming skills;
- You have excellent communication skills in oral and written English;
- You have strong initiative and good time management skills.
This is what we offer you
We 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 between September to February (2026). 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 appointment (38 hours per week) the gross monthly salary will range from € 2,901.- in the first year to €3,707.- (scale P) in the last year. This does not include 8% holiday allowance and 8,3% year-end allowance. The Collective Labour Agreement of Universities of the Netherlands 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;
- a complete educational program for PhD students;
- multiple courses on topics such as leadership for academic staff;
- 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;
- a pension at ABP for which UvA pays two third part of the contribution;
- the possibility to follow courses to learn Dutch.
Are you curious to read more about our extensive package of secondary employment benefits, take a look here.
All about this vacancy
This is what you will do
- You will develop graph neural network models for structure-property prediction, in particular for predicting binding sites and synthetic accessibility of organic (drug) molecules;
- You will work with generative AI, such as denoising diffusion and flow matching to generate modifications on existing drug scaffolds;
- You will develop a computational framework to optimize drug-binding of molecules from docking calculations and/or enhanced molecular simulations in a closed-loop fashion using Bayesian optimization or reinforcement learning techniques;
- You will work in close collaboration with colleagues in the Computational Chemistry group at HIMS, the AI4Science Laboratory at IvI, and in experimental groups at HIMS and the Medical Center.
This is what we ask of you
You have/are:
- You have a creative, curious and driven nature;
- You have a recent master degree in artificial intelligence with a specialisation in natural science or a master degree in science, such as pharmaceutical science, chemistry, chemical engineering, or physics, with a specialization in machine learning;
- Experience with geometric machine learning and/or molecular simulation is preferred;
- Experience with (bio-) molecular modeling is preferred;
- You have good programming skills;
- You have excellent communication skills in oral and written English;
- You have strong initiative and good time management skills.
This is what we offer you
We 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 between September to February (2026). 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 appointment (38 hours per week) the gross monthly salary will range from € 2,901.- in the first year to €3,707.- (scale P) in the last year. This does not include 8% holiday allowance and 8,3% year-end allowance. The Collective Labour Agreement of Universities of the Netherlands 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;
- a complete educational program for PhD students;
- multiple courses on topics such as leadership for academic staff;
- 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;
- a pension at ABP for which UvA pays two third part of the contribution;
- the possibility to follow courses to learn Dutch.
Are you curious to read more about our extensive package of secondary employment benefits, take a look here.
Your place at the UvA
This is where you will work
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.
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, flavor & food, medical and high-tech industries. Research is organized into four themes: Analytical Chemistry, Computational Chemistry, Synthesis & Catalysis and Molecular Photonics.
The Computational Chemistry Group 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 mission of the Informatics Institute (IvI) is to perform curiosity-driven and use-inspired fundamental research in Computer Science. The main research themes are Artificial Intelligence, Computational Science and Systems and Network Engineering. Our research involves complex information systems at large, with a focus on collaborative, data driven, computational and intelligent systems, all with a strong interactive component.
More about the UvA
The University of Amsterdam is ambitious, creative and committed. An inspiration to students since 1632, a vanguard player in international science and a partner in innovation.
The University of Amsterdam is the largest university in the Netherlands, with the broadest range of courses on offer. An intellectual hub with 42,000 students, 6,000 staff and 3,000 PhD students. Connected by a culture of curiosity.
Your place at the UvA
This is where you will be working
This is where you will work
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.
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, flavor & food, medical and high-tech industries. Research is organized into four themes: Analytical Chemistry, Computational Chemistry, Synthesis & Catalysis and Molecular Photonics.
The Computational Chemistry Group 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 mission of the Informatics Institute (IvI) is to perform curiosity-driven and use-inspired fundamental research in Computer Science. The main research themes are Artificial Intelligence, Computational Science and Systems and Network Engineering. Our research involves complex information systems at large, with a focus on collaborative, data driven, computational and intelligent systems, all with a strong interactive component.
More about the UvA
The University of Amsterdam is ambitious, creative and committed. An inspiration to students since 1632, a vanguard player in international science and a partner in innovation.
The University of Amsterdam is the largest university in the Netherlands, with the broadest range of courses on offer. An intellectual hub with 42,000 students, 6,000 staff and 3,000 PhD students. Connected by a culture of curiosity.
Important to know
Your application & contact
If you recognize yourself in the profile and are interested in the position, we look forward to receiving your motivation letter and CV. You can respond via the red button up to and including August 22, 2025.
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 1-page letter of motivation;
- a list of publications;
- the names and email addresses of two references who can provide letters of recommendation (who will be contacted when shortlisted).
Only complete applications received within the response period via the link below will be considered. The interviews will be held in August and September 2025.
Do you have any questions or do you require additional information? Please contact:
- Dr. Bernd Ensing, associate professor of Computational Chemistry and director of the AI4Science Laboratory, [email protected]
A knowledge security check can be part of the selection procedure (for details: national knowledge security guidelines). If you receive an error message while applying from abroad, please try again later or contact us for assistance.
Diversity, Equity & Inclusion
As an employer, the UvA maintains an equal opportunities policy. We value diversity and are fully committed to being a place where everyone feels at home. We nurture inquisitive minds and perseverance and allow room for persistent questioning. With us, curiosity and creativity are the prevailing culture.
Important to know
Your application & contact
If you recognize yourself in the profile and are interested in the position, we look forward to receiving your motivation letter and CV. You can respond via the red button up to and including August 22, 2025.
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 1-page letter of motivation;
- a list of publications;
- the names and email addresses of two references who can provide letters of recommendation (who will be contacted when shortlisted).
Only complete applications received within the response period via the link below will be considered. The interviews will be held in August and September 2025.
Do you have any questions or do you require additional information? Please contact:
- Dr. Bernd Ensing, associate professor of Computational Chemistry and director of the AI4Science Laboratory, [email protected]
A knowledge security check can be part of the selection procedure (for details: national knowledge security guidelines). If you receive an error message while applying from abroad, please try again later or contact us for assistance.
As an employer, the UvA maintains an equal opportunities policy. We value diversity and are fully committed to being a place where everyone feels at home. We nurture inquisitive minds and perseverance and allow room for persistent questioning. With us, curiosity and creativity are the prevailing culture.
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