PhD position in computational biophysics and biomolecular modeling

The Timr group at the J. Heyrovský Institute of Physical Chemistry in Prague offers a PhD position in computational biophysics and biomolecular modeling.

Are you fascinated by the complexity of the interior of living cells? Do you enjoy constructing models of proteins and other biomolecules in the computer? Would you like to use the tools of physics, chemistry, and mathematics to describe processes in cells?

Our research group focuses on the computer simulation of the cell interior. Using multi-scale computational models, we aim to elucidate the physical and chemical mechanisms governing the organization of metabolic pathways in living cells. Supported by the Lumina Quaeruntur Award and a grant from the Czech Science Foundation, our team is integrated into the interdisciplinary Department of Computational Chemistry. This department bridges the physical chemistry and biophysics of proteins and membranes with theoretical enzymology and spectroscopy.

PhD project: Computational modeling of dynamic enzyme assemblies

In living cells, various enzymes have been found to assemble into transient structures, appearing and disassembling in response to external conditions. Such dynamic enzyme assemblies, identified in processes like glycolysis and purine synthesis, play an important role in regulating cellular metabolism. They potentially act as switches between competing metabolic pathways. However, the mechanisms behind the formation and functionality of these assemblies are yet to be fully elucidated. This project will explore dynamic enzyme assemblies through a combination of atomistic, coarse-grained, and kinetic modeling, closely integrated with experimental data. The student will characterize the molecular interactions that promote assembly formation and investigate how the crowded environment within these assemblies impacts the transfer of substrates between consecutive enzymes in a pathway. The computational methodologies developed in this work will serve as a basis for the prediction of metabolic fluxes from the composition and architecture of a dynamic enzyme assembly. Thus, the project will enhance our understanding of the regulation and control of metabolic pathways in cells, offering insights into their adaptability and efficiency.

Starting date: Summer 2024 (no later than October 1)

Type of contract: Temporary

Job status: Full-time


The candidates are expected to hold an MSc (or an equivalent) in physics, chemistry, or a related field before the start of the position. They should be interested in biomolecules, capable of formulating mathematical models, and motivated to learn new things. Moreover, they should possess good computer skills and be fluent in English. Experience with molecular simulations and programming will be a plus. The successful candidates will enroll at Charles University in Prague, the top-ranking university in the Czech Republic.

We offer:

  • 5 weeks paid leave of absence (holidays) per year + 3 days of paid sick-leave in addition to the statutory insurance
  • Flexible working-time, the possibility of part-time work
  • Lunch vouchers
  • Possibility of attending children groups of the CAS
  • Sports goods rental, free parking, trade union library
  • Language courses
  • Possibility of further education and career development by participating in courses organized by our institute.

Eligibility criteria:

To apply, please send your CV, a motivation letter, transcripts of all courses and grades, and contact information for two references to (recruitment[at]jh-inst[dot]cas[dot]cz) and (stepan[dot]timr[at]jh-inst[dot]cas[dot]cz). In your motivation letter, please explain how the proposed research aligns with your interests and why you believe you are a good fit for the position. Please include SC2024_12 in the email subject line. For any inquiries, contact (stepan[dot]timr[at]jh-inst[dot]cas[dot]cz).

Selection process

By providing us with your personal data in your CV, you have allowed J. Heyrovský Institute of Physical Chemistry to process and file your CV in the HR database. Your personal data will be used for the internal HR needs of the J. Heyrovský Institute of Physical Chemistry only. At the same time, you confirm here that the personal data as stated in the CV you have sent to us is true and accurate.

Application deadline
2. 4. 2024