Are you fascinated by the complexity of living cells’ interior? Do you enjoy playing with 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?

We are a recently founded research group focusing on the multi-scale computer simulation of the cell interior. In particular, we look into how the local structure and dynamics of the intracellular environment can control metabolic processes. Our research is supported by the prestigious Lumina Quaeruntur Award as well as by a grant from the Czech Science Foundation.

Our group is based at J. Heyrovský Institute of Physical Chemistry in Prague, Czech Republic. The group is integrated into the young and interdisciplinary Department of Computational Chemistry, connecting the physical chemistry and biophysics of proteins and membranes with theoretical enzymology and spectroscopy. 

Interested in joining our team? See below for currently available positions. Don’t hesitate to contact us for more information.

Postdoctoral Position in Mathematical and Computational Biology/Biophysics

We are seeking a highly motivated postdoctoral associate to work on multi-scale modeling of dynamic enzyme assemblies.

The postdoctoral associate will develop mesoscopic computational models to understand the roles of dynamic enzyme assemblies in metabolic regulation. The goal is to develop and implement a novel framework that will integrate detailed insights from all-atom and coarse-grained MD simulations with larger-scale reaction-diffusion models of dynamic enzyme assemblies. This work will be an important contribution to our mechanistic understanding of metabolic pathway organization in cells.

The initial contract period is for one year, possibly extending up to four years. The position will remain open until a suitable candidate is found.


  • PhD in a quantitative field, such as Mathematical/Computational Biology, Biophysics, Chemical Engineering, or Applied Mathematics.
  • Strong skills in developing and implementing mathematical models.
  • Proficiency in programming and scripting languages (e.g., Python, C++) for model development and data analysis.
  • Excellent communication and collaboration skills.

Experience in kinetic modeling of enzymes and metabolic pathways, reaction-diffusion modeling, classical MD simulations, and Markov models will be considered an asset.

To apply, please send your CV, a list of publications, a motivation letter, and contact information for two references to and Please include SC2024_15 in the email subject line. For any inquiries, contact

Starting date

The position is available immediately.

Link to the official job advertisement at Heyrovský Institute’s website

PhD position in computational biophysics and biomolecular modeling

We are looking for a highly motivated PhD student in computational biophysics / physical chemistry / biomolecular modeling to work on the project described below.

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.


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.

To apply, please send your CV, a motivation letter, transcripts of all courses and grades, and contact information for two references to and 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

Starting date

Summer 2024 (no later than October 1)

Link to the official job advertisement at Heyrovský Institute’s website