1-2 PhD students in Machine Learning of Physics-Based Force Fields

1-2 PhD students in Machine Learning of Physics-Based Force Fields

Are you interested in working with machine learning in biochemistry, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favourable working conditions? We welcome you to apply for a Ph.D. position at Uppsala University.  

The Department of Cell and Molecular Biology is divided into seven research programs, each focusing on different areas within cell and molecular biology: computational biology and bioinformatics, microbiology and immunology, molecular biology, molecular biophysics, molecular evolution, molecular systems biology, and structural biology. The scientific foundation of what we do lies in biology, but our research overlaps with other fields such as medicine, computer science, mathematics, chemistry, engineering, and physics. The department has over 200 employees, including around 50 doctoral students. Please read more about our work at https://icm.uu.se

The research program for Computational Biology and Bioinformatics hosts research in both applied and theoretical computational biochemistry. Important topics include fundamental methodological developments as well as applications to enzyme function and drug design. We now have two open Ph.D. position in Machine Learning of Physics-Based Force Fields in the group of Prof. David van der Spoel and we are looking for highly motivated individuals to join the team. You will be trained in performing state-of-the-art research in computational chemistry and machine learning, in software development and management, as well as in presenting academic research in writing as well as orally.

Duties
You will work on building new physical models for organic molecules including biomolecules from scratch. To do so, you will use the locally developed open-source Alexandria Chemistry Toolkit to perform machine-learning of force fields, based on existing as well as new quantum chemistry data. Code development in Python and C++ are an integral part of the position, that are necessary to introduce new physical models to the code and evaluate and validate those models. The new force fields will be applied to problems ranging from ecotoxicology to studies of crowding inside cells. Other duties include work as teaching assistant up to 20% of your working time. 

Requirements
To meet the entry requirements for doctoral studies, you must

• - hold a Master’s (second-cycle) degree in X, or
• - have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• - have acquired substantially equivalent knowledge in some other way.

Although the doctoral education is individual, development and maintenance of software is a team effort. Therefore, we are looking for new team members that have good interpersonal and collaboration skills. In addition, you have to be fluent in English and have excellent working knowledge of at least one of the Python or C++ programming languages.

Additional qualifications
The qualifications below are considered to strengthen your application
-    good working knowledge of both Python and C++
-    documented skills in data science including machine learning and / or artificial intelligence
-    good working knowledge of organic chemistry, physical chemistry or molecular physics
-    documented experience working with Linux / command-line based computing 
-    documented experience with high-performance computing
-    documented experience of software development (preferably in a team)

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date 2025-09-01 or as agreed. Placement: Uppsala.

For further information about the position, please contact: Prof. David van der Spoel, tel: +46184714205, email: david.vanderspoel@icm.uu.se.

Please submit your application by May 15th 2025, UFV-PA 2025/963.

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