Researcher in Computational Biochemistry

Uppsala University Department of Chemistry

Researcher in Computational Biochemistry

Published: 2022-12-19

Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 54,000 students, more than 7,500 employees and a turnover of around SEK 8 billion.

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Department of Chemistry – BMC conducts research and education in analytical chemistry, biochemistry and organic chemistry. More than 100 people work at the department. New employees and students are recruited from all over the world and English is the main working language. The department is located at the Biomedical Centre in Uppsala, which facilitates collaborations with research groups in biology, pharmacy, medicine and SciLifeLab and gives access to advanced infrastructure for experimental and theoretical studies. You can find more information about us here.

We offer a stimulating, friendly, and interdisciplinary work environment, excellent working conditions, frontier research projects in computational biochemistry, and the opportunity to contribute with and develop your ideas.

We are working in international teams and flexible working hours and home office options, adequate remuneration.

Moreover, the candidate will be mainly involved in an EU project, iSenseDNA, funded in the framework of 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 exploiting the activity of engineered topoisomerases. The tailor-made DNA-nanotransducers will be exploited for both detection and conformational analysis of molecular dynamics in one functional unit. iSenseDNA will use bioinformatics approaches to predict the 3D structure of conformational states modeling real-time evolution of interacting DNA-NT and proteins, and machine learning (ML) models to directly link the atomistic structure, conformational state, and dynamics, together with the optical assessment of protein-DNA-NT interaction using linear and “On-chip” non-linear spectroscopies for detecting the vibrational signatures of organic molecular systems, and recognizing the structural changes in the optical signal in real-time. Our group, with the expertise in enzyme evolution, and structure-function-dynamics relationships in biomolecular systems, will focus on the computational modeling of topoisomerases to develop a ‘next-generation class of enzymes’ to produce tailor-made DNA-NT and study the dynamic of interaction proteins-DNA-NT, using a wide range of computational techniques, including molecular dynamics simulations, free energy calculations, and various enhanced sampling approaches. 

More details about the project will be disclosed upon request.

If you want to read more about the group follow this link 

Duties

The position is full-time research. From a scientific perspective, this position will involve 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, and QM/MM simulations, free energy calculations to propose single or multiple point mutations, as well as bioinformatics tools for structural prediction. It will also include travel to conferences, project meetings with collaborators, and participation in outreach project activities. You are encouraged to take responsibility for the execution of your project and to contribute creatively to our team’s research program.

Requirements

To qualify for employment as a researcher you must have a Ph.D. degree or a foreign degree equivalent to a Ph.D. degree in STEM or a foreign degree equivalent to a Ph.D. degree in STEM. The degree must be obtained at the time of the employment decision. Additional working experience in the field of protein engineering and 3D structural prediction is considered essential for the role.

Moreover, we attach great importance to personal qualities such as creativity, enthusiasm, flexibility, and a positive attitude to work in a team. The applicant will be responsible for a part of a large and challenging project, and the ability to work independently and to take responsibility will be required.

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

Additional qualifications

Moreover, either (1) experience in modeling enzyme reaction mechanisms and/or enzyme function-dynamics relationships, in the context of understanding enzyme evolution or for biocatalytic applications, and modeling enzyme-DNA interaction or (2) experience in using enhanced sampling approaches (such as replica exchange or metadynamics) to study biomolecular systems, with particular preference given to studies of the role of conformational dynamics in enzyme engineering or evolution are considered a plus.

Note that attention will be paid to not just overall scientific achievements, but scientific achievements relative to career stage and years of research experience.

All qualifying requirements will be assessed by interview and personal references.

About the employment

The employment is a permanent position (a probationary period of 6 months may be applied).

Scope of employment 100%. Preferable starting date ASAP or as mutually agreed. Placement: Department of Chemistry – BMC, Uppsala University

For further information about the position, please contact:

Antonietta Parracino and Mikeal Widersten
E-mail: antonietta.parracino@kemi.uu.se, Telephone: +4670-01679430, +4618-471 5697.
E-mail: Mikael.Widersten@kemi.uu.se, Telephone: +460736951863 +46018471 4992

Please submit your application by January 30th 2023, UFV-PA 2023/5013

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Submit your application through Uppsala University's recruitment system.

Placement: Department of Chemistry - BMC

Type of employment: Full time , Permanent position

Pay: Individual salary

Number of positions: 1

Working hours: 100%

Town: Uppsala

County: Uppsala län

Country: Sweden

Union representative: Seko Universitetsklubben seko@uadm.uu.se
ST/TCO tco@fackorg.uu.se
Saco-rådet saco@uadm.uu.se

Number of reference: UFV-PA 2022/5013

Last application date: 2023-01-30

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