PhD Candidate in Materials Science (University of Amsterdam)

Are you a highly motivated MSc graduate with a strong affinity for machine learning and molecular modeling? The Computational Chemistry group is seeking a curious and ambitious PhD candidate to perform fundamental research on molecule and material design and structure-property prediction using state-of-the-art machine learning techniques and generative AI combined with quantum chemical modeling. Research context Designing new molecules and materials is at the core of chemistry, but in practice, creating molecular structures with useful properties is a difficult and time-consuming task, simply because there are so many possibilities of connecting different atoms together to form new molecules, most of which are useless. Optimizing molecules or materials with desired characteristics, such as optimal thermodynamic, electronic, or mechanical properties, usually relies on chemical intuitions combined with trial and error. In the Computational Chemistry group, we develop and combine molecular simulation with 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 with generative AI algorithms to predict molecular properties, sample chemical space, and suggest improved molecules and materials, such as catalyst complexes, to our experimental collaborators. Your work will take place at the Van ‘t Hoff Institute for Molecular Sciences (HIMS), one of the research institutes of the University of Amsterdam. You will also be connected with the FNWI AI4Science Laboratory, which is located in the Institute for Informatics (IvI). What are you going to do? This project focuses on developing and applying a state-of-the-art computational framework for designing improved organic molecules and metal-complex catalyst materials. You will: • develop graph neural network models for structure-property prediction, in particular for so-called safe and sustainable by design optimization of organic molecules; • use quantum chemical calculations to condition generative models, such as denoising diffusion models, for property guided ligand design; • develop a framework for inverse design of catalyst materials; • investigate molecular latent embedding spaces and develop tools to sample, navigate, and interpret such spaces to find molecules with optimal properties. Tasks and responsibilities: • complete a PhD thesis within the official appointment duration of four years; • conduct independent research in the Computational Chemistry group; • be an active member of the research group and take responsibility for shared tasks; discuss your work with the group members and during work discussion meetings, incorporate feedback and give input to others; • collaborate with your colleagues in the Computational Chemistry group at HIMS, the AI4Science Laboratory at IvI, and in experimental groups at HIMS; • take a leading role in writing manuscripts and publish and present your work in peer-reviewed international journals, books and conferences; • participate in the Faculty of Science PhD training program; • contribute to the supervision of BSc/MSc student projects; • contribute to the teaching activities of the department. Your experience and profile • a creative, curious and driven nature; • a Master’s degree in artificial intelligence with a specialization in natural science or in science, preferably in chemistry, chemical engineering, physics, engineering physics, materials science, computational science; • experience with geometric machine learning is preferred; • experience with molecular simulation is preferred; • good programming skills; • excellent 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. You are passionate about science and have a particular interest in modelling. You enjoy close collaboration with domain experts. You have a creative mind and look forward to work at the cutting-edge of computational technology. Finally, you are a team player and a pleasant colleague who enjoys being part of an interdisciplinary team of computational researchers and plant scientists. Our offer 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 is December 2024 to March 2025. 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 € 2.872 in the first year to €3.670 (scale P) in the last year. This does not include 8% holiday allowance and 8,3% year-end allowance. 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; • 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; • 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. Are you curious to read more about our extensive package of secondary employment benefits, take a look here. About us 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. 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 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. Questions Do you have any questions or do you require additional information? Please contact: Dr. B. Ensing, associate professor of Computational Chemistry and director of the AI4Science Laboratory. Email: b.ensing@uva.nl 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 November 1st, 2024. 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 university grades; • Contact details of two academic referees (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 November 2024. We will recruit until the position is filled and close the position when a suitable candidate is found. The UvA is an equal-opportunity employer. We prioritize 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. No agencies please. If you apply for this position please say you saw it on Engineeroxy

Are you a highly motivated MSc graduate with a strong affinity for machine learning and molecular modeling? The Computational Chemistry group is seeking a curious and ambitious PhD candidate to perform fundamental research on molecule and material design and structure-property prediction using state-of-the-art machine learning techniques and generative AI combined with quantum chemical modeling.

Research context

Designing new molecules and materials is at the core of chemistry, but in practice, creating molecular structures with useful properties is a difficult and time-consuming task, simply because there are so many possibilities of connecting different atoms together to form new molecules, most of which are useless. Optimizing molecules or materials with desired characteristics, such as optimal thermodynamic, electronic, or mechanical properties, usually relies on chemical intuitions combined with trial and error. In the Computational Chemistry group, we develop and combine molecular simulation with 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 with generative AI algorithms to predict molecular properties, sample chemical space, and suggest improved molecules and materials, such as catalyst complexes, to our experimental collaborators. Your work will take place at the Van ‘t Hoff Institute for Molecular Sciences (HIMS), one of the research institutes of the University of Amsterdam. You will also be connected with the FNWI AI4Science Laboratory, which is located in the Institute for Informatics (IvI).

What are you going to do?

This project focuses on developing and applying a state-of-the-art computational framework for designing improved organic molecules and metal-complex catalyst materials.

You will:
•   develop graph neural network models for structure-property prediction, in particular for so-called safe and sustainable by design optimization of organic molecules;
•   use quantum chemical calculations to condition generative models, such as denoising diffusion models, for property guided ligand design;
•   develop a framework for inverse design of catalyst materials;
•   investigate molecular latent embedding spaces and develop tools to sample, navigate, and interpret such spaces to find molecules with optimal properties.

Tasks and responsibilities:
•   complete a PhD thesis within the official appointment duration of four years;
•   conduct independent research in the Computational Chemistry group;
•   be an active member of the research group and take responsibility for shared tasks; discuss your work with the group members and during work discussion meetings, incorporate feedback and give input to others;
•   collaborate with your colleagues in the Computational Chemistry group at HIMS, the AI4Science Laboratory at IvI, and in experimental groups at HIMS;
•   take a leading role in writing manuscripts and publish and present your work in peer-reviewed international journals, books and conferences;
•   participate in the Faculty of Science PhD training program;
•   contribute to the supervision of BSc/MSc student projects;
•   contribute to the teaching activities of the department.

Your experience and profile

•   a creative, curious and driven nature;
•   a Master’s degree in artificial intelligence with a specialization in natural science or in science, preferably in chemistry, chemical engineering, physics, engineering physics, materials science, computational science;
•   experience with geometric machine learning is preferred;
•   experience with molecular simulation is preferred;
•   good programming skills;
•   excellent 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.

You are passionate about science and have a particular interest in modelling. You enjoy close collaboration with domain experts. You have a creative mind and look forward to work at the cutting-edge of computational technology. Finally, you are a team player and a pleasant colleague who enjoys being part of an interdisciplinary team of computational researchers and plant scientists.

Our offer

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 is December 2024 to March 2025. 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 € 2.872 in the first year to €3.670 (scale P) in the last year. This does not include 8% holiday allowance and 8,3% year-end allowance. 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;
•   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;
•   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.

Are you curious to read more about our extensive package of secondary employment benefits, take a look here.

About us

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.

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 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.

Questions

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

Dr. B. Ensing, associate professor of Computational Chemistry and director of the AI4Science Laboratory.
Email: b.ensing@uva.nl

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 November 1st, 2024.

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 university grades;
•   Contact details of two academic referees (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 November 2024.

We will recruit until the position is filled and close the position when a suitable candidate is found.

The UvA is an equal-opportunity employer. We prioritize 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.

No agencies please.

If you apply for this position please say you saw it on Engineeroxy

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