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.
CURRENTLY AVAILABLE POSITIONS
Postdoctoral position in computational biochemistry and mesoscale modeling
We are looking for a postdoctoral associate with a strong background in the mesoscale simulation and kinetic modeling of biochemical processes.
The successful candidate will create mesoscopic computational models of dynamic enzyme assemblies to understand how metabolic pathways can be controlled by the spatial organization of enzymes in the cytoplasm. To build the models, available experimental data will be integrated with insights from detailed molecular simulations. The initial contract period will be for 1 year with a possible extension to up to 4 years.
Requirements: The ideal candidate has obtained their PhD in Computational Biochemistry/Biology, Biophysics, Chemical Engineering, Applied Mathematics, or a related field. Strong skills in developing and implementing mathematical models, preferably with a focus on enzyme kinetics, are essential, together with proficiency in programming and scripting (e.g., Python, C++, Fortran) for model development and data analysis. Solid experience with classical MD simulations, Markov state models, and reaction-diffusion modeling will be a plus. In addition, excellent communication and collaboration skills are highly desirable.
Application deadline: November 12
If you are interested, please send us your CV together with a list of publications, your motivation letter, and two contacts as a reference to firstname.lastname@example.org and email@example.com. Please write in the subject line of your email CS2023_24. For any questions, contact firstname.lastname@example.org.
Starting date: January 2024 (can be negotiated)
Fully funded 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 that can appear and disassemble as a function of external conditions. Among other examples, such dynamic assemblies have been identified in glycolysis or in the purine synthesis pathway. Recent experimental evidence points to a key role of dynamic enzyme assemblies in the regulation and adaptation of cellular metabolism, including their possible role as a switch between two or more competing pathways. However, the mechanisms underlying the formation and function of these assemblies are yet to be elucidated. By using a combination of atomistic, coarse-grained and ultra-coarse-grained molecular modeling and working in tight connection with experimental data, the PhD student will characterize molecular interactions promoting assembly formation and quantify the diffusivities of enzymes and reactants inside dynamic enzyme assemblies. In particular, he/she will evaluate the potential for substrate channeling, that is, passing the intermediate products efficiently between consecutive enzymes of a pathway. The computational methodology developed in this work will serve as a basis for the prediction of metabolic fluxes given a composition and architecture of an enzyme assembly.
The candidates are expected to hold a MSc (or an equivalent) in physics, chemistry, or related fields before the start of the position. They should be interested in biomolecules and motivated to learn new things. Moreover, they should possess good computer skills and be fluent in English. Experience with molecular simulations and programming would be a plus. The successful candidate will enroll at Charles University in Prague, the top-ranking university in the Czech Republic.