Denys Biriukov | NCBR (National Centre for Biomolecular Research)

Denys Biriukov, Ph.D.

Research topics

We are the Computational Glycobiology team, and our research focuses on uncovering the complex world of glycans (also known as sugars or carbohydrates) and their roles in various biological processes and related applications. Using cutting-edge multiscale molecular simulations, we study their structure, function, and dynamics in detail. Our computer simulations provide valuable insights into how glycans interact with other biomolecules, influencing key processes such as cell signaling, immune responses, and disease progression. We are also deeply committed to advancing simulation techniques, improving simulation models, and staying at the cutting edge of rapidly emerging methodologies like evolutionary algorithms and artificial intelligence.

Denys Biriukov, Ph.D.

e‑mail:

Member of research group:

Peptide Therapeutics

Current projects

Tailoring polymeric implant coatings against bacteria attachment by studying bacterial glycans' affinity for functionalized polymers
- in collaboration with groups of Prof. Lukasz Cwiklik from the J. Heyrovsky Institute of Physical Chemistry in Prague and Prof. Andrzej Kotarba from the Jagiellonian University in Krakow
- supported by the Czech Science Foundation, project GA24-11274S (01.01.2024–31.12.2026)
Modeling glycosaminoglycans in the context of glycocalyx, extracellular matrix, and the design of biocompatible hydrogels
- in collaboration with the group of Dr. Hector Martinez-Seara from the Institute of Organic Chemistry and Biochemistry in Prague
Developing novel simulation models for glycans within the de novo comprehensive force field for biological systems that accounts for electronic polarisation in a mean-field way via charge scaling
- in collaboration with the group of Prof. Pavel Jungwirth from the Institute of Organic Chemistry and Biochemistry in Prague
- the overall project is funded by an ERC Advanced Grant "Q-SCALING" (01.10.2023–30.09.2028)

Team members

Team leader

Dr. Denys Biriukov, Ph.D.

Master students

Bc. Tereza Tutková

Bachelor students

Tamara Polačková

Selected publications

Riopedre-Fernandez, M.; Biriukov, D.; Dračínský, M.; Martinez-Seara, H. Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity. Carbohydr. Polym. 2024, 325, 121568.

Nencini, R.; Tempra, C.; Biriukov, D.; Riopedre-Fernandez, M.; Chamorro, V. C.; Polák, J.; Mason, P. E.; Ondo, D.; Heyda, J.; Ollila, O. H. S.; Jungwirth, P.; Javanainen, M.; Martinez-Seara, H. О. Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field. J. Chem. Theory Comput. 2024, 20 (17), 7546–7559.

Riopedre-Fernandez, M.; Kostal, V.; Martinek, T.; Martinez-Seara, H.; Biriukov, D. Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations to Accurately Model Glycosaminoglycan Electrostatic Interactions. J. Chem. Inf. Model. 2024, 64 (18), 7122–7134.