Researcher in Computational Biochemistry

The Department of Chemistry – BMC conducts research and education in analytical chemistry, biochemistry, and organic chemistry.

More than 100 people, including about 45 PhD students, work at the department. New staff and students are recruited from all over the world, and English is the primary working language. The department is located at the Biomedical Center in Uppsala, where there are excellent opportunities for collaboration with research groups in biology, pharmacy, medicine, and SciLifeLab, as well as access to advanced infrastructure for experimental and theoretical studies. The international environment and opportunities for interdisciplinary collaborations provide PhD students at the department the chance to participate in relevant research projects and prepare for an international research career.

Read more about the research at the Department of Chemistry in the life sciences on our website (https://www.uu.se/institution/kemi-for-livsvetenskaperna).

We offer a stimulating, friendly, and interdisciplinary working environment, with excellent working conditions and cutting-edge research projects in computational biochemistry, as well as the opportunity to contribute and develop your ideas. We work in international teams with flexible working hours and options for remote work.

Additionally, the candidate will be involved in an EU project, iSenseDNA, funded under the EIC-pathfinder Open of Horizon Europe.

Project Description

Together with the international and multidisciplinary team of researchers, iSenseDNA aims to develop DNA nanotransducers by harnessing the activity of engineered topoisomerases. The customized DNA nanotransducers will be used for both detection and conformational analysis of molecular dynamics in a functional unit. iSenseDNA will employ computational methods to predict the 3D structure of conformational states and model the real-time development of interacting DNA-NT and proteins, and machine learning models (ML) to link the atomic structures, conformational states, and molecular dynamics, along with optical readout of protein-DNA-NT interactions using linear and "On-chip" nonlinear spectroscopies in real-time. The group at Uppsala University, with expertise in enzyme evolution and the relationship between biomolecules' structure-function-dynamics, focuses on computational modeling of topoisomerases to develop a "next-generation class of enzymes" aimed at producing a customized DNA-NT and studying the dynamics of interaction proteins-DNA-NT.

The research is conducted using a wide range of computational techniques, such as molecular dynamics simulations and free energy calculations.

More information about the project will be provided upon request.

Job Responsibilities

The work within the position involves computational integration of simulation and experimental data using a range of molecular simulation tools, including both conventional and enhanced molecular dynamics simulations, empirical valence bond methods, and QM/MM simulations, free energy calculations to propose one or more point mutations, as well as bioinformatics tools for structural prediction. It will also include travel to conferences and project meetings with partners and participation in outreach project activities. You are expected to take responsibility for the execution of your project and to contribute creatively to our team's research program.

Qualifications

To qualify for a position as a researcher, you must have a PhD or a foreign degree equivalent to a PhD in STEM or a foreign degree equivalent to a PhD in STEM. The degree must be obtained at the time of the employment decision. Additional work experience in the field of protein engineering and prediction of biomolecules' 3D structures is considered crucial for the role.

Furthermore, we place great emphasis on personal qualities such as creativity, enthusiasm, and flexibility, as well as a positive attitude towards working in teams. The applicant will be responsible for part of a large and challenging project, and the ability to work independently and take responsibility is required.

Candidates must be able to express themselves very well in spoken and written English.

Meritorious

Experience in (1) modeling enzyme reaction mechanisms and/or enzyme function-dynamic relationships, in relation to understanding enzyme evolution or for biocatalytic applications, and modeling protein-DNA interactions (2) using enhanced sampling methods (such as replica exchange or metadynamics) in studies of biomolecular systems, particularly for studies of the role of conformational dynamics in enzyme technology or its evolution.

Please note that weight will not only be placed on overall scientific achievements but also on scientific achievements in relation to the career stage and years of research experience.

All qualification requirements will be assessed through interviews and personal references.

About the Position

The position is fixed-term for 12 months. The scope is 100%. Start date as soon as possible or by agreement. Location: Uppsala

For inquiries about the position, please contact: Prof. Mikael Widersten and Dr. Antonietta Parracino Email: [email protected], Phone: +4670-01679430, +4618-471 5697. Email: [email protected], Phone: +460736951863 +46018471 4992

We welcome your application by January 7, 2026, UFV-PA 2025/4050.

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 here (https://uu.se/om-uu/jobba-hos-oss/).

The position may be subject to security clearance. A prerequisite for employment in the case of security clearance is that the applicant is approved.

We kindly decline offers of recruitment and advertising assistance.

Applications are received in Uppsala University's recruitment system.

Union representatives: Saco-S - [email protected], Seko - [email protected], ST (OFR/S) - [email protected]