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

Do you want to work with machine learning in biochemistry, supported by competent and friendly colleagues in an international environment? Do you want an employer that invests in sustainable employment and offers secure, favorable working conditions? Welcome to apply for a PhD 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 for what we do lies within 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 500 PhD students. Please read more about our work at https://icm.uu.se (https://icm.uu.se).

The Computational Biology and Bioinformatics program hosts research (https://www.uu.se/institution/cell-och-molekylarbiologi/forskning/berakningsbiologi-och-bioinformatik) in both applied and theoretical biochemistry. Some key topics include the development of fundamental methods and applications in enzyme function and drug development. There are currently two open PhD positions in the research group led by Prof. David van der Spoel, and we welcome motivated individuals to apply for the position to strengthen the group. As a PhD student, you will be trained in cutting-edge research in computational chemistry and machine learning, software development and management, as well as scientific presentation, both written and oral.

Job Responsibilities

You will work on developing new physical models for organic molecules, including biomolecules from scratch. For this purpose, you will use our own code, Alexandria Chemistry Toolkit, https://github.com/AlexandriaChemistry (https://github.com/AlexandriaChemistry), which is a machine learning code for generating force fields based on quantum chemical data. The code is distributed as open source. Code development in C++ and Python is a natural part of the project and is necessary both to introduce new physics into the code and to handle large amounts of data to evaluate and validate the code and models. The new force fields will be applied to problems from ecotoxicology to studies of crowding inside cells. An additional task will be to serve as a lab assistant in teaching courses for up to 20% of the working time.

Qualifications

Eligible for doctoral education is someone who has:

• completed a master's degree in X, or
• completed at least 240 higher education credits, of which at least 60 higher education credits at an advanced level including an independent project of at least 15 higher education credits, or
• acquired equivalent knowledge in some other way.

Although doctoral education is individual, software development and management require teamwork. For this reason, we are looking for new group members with good collaboration and communication skills. You need to be proficient in English and have excellent skills in at least one of the programming languages C++ or Python.

Desirable/meritorious qualifications

Meritorious qualifications include:

• good skills in both C++ and Python
• documented skills in data science, including machine learning and artificial intelligence
• good knowledge of organic chemistry, physical chemistry, or molecular physics
• documented experience working with Linux or command-line based computer usage
• documented experience using high-performance computing clusters
• documented experience in software development (preferably in a team)

Regulations for doctoral students can be found in the Higher Education Ordinance Chapter 5 §§ 1-7 and in the university's rules and guidelines. https://regler.uu.se/?languageId=3 (https://regler.uu.se/?languageId=3)

About the Position

The position is temporary, according to HF Chapter 5 § 7. The extent is full-time. Start date is 2025-09-01 or by agreement. Location: Uppsala

For inquiries about the position, please contact: Prof. David van der Spoel, +4618 471 4205, email: david.vanderspoel@icm.uu.se (mailto:david.vanderspoel@icm.uu.se)

Welcome with your application by May 15, 2025, UFV-PA 2025/963.

Uppsala University is a broad research university with a strong international standing. The ultimate goal is to conduct education and research of the highest quality and relevance to make a difference in society. Our most important asset is all 7,600 employees and 53,000 students who, with curiosity and commitment, make Uppsala University one of the country's most exciting workplaces.

Read more about our benefits and what it is like to work at Uppsala University https://uu.se/om-uu/jobba-hos-oss/ (https://uu.se/om-uu/jobba-hos-oss/)

The position may be subject to security clearance. In the case of security clearance, a prerequisite for employment is that the applicant is approved.

We kindly decline offers of recruitment and advertising assistance.

Applications are received in Uppsala University's recruitment system.