Výpis publikací

RIVEL, Timothée Emmanuel Jonathan; Denys BIRIUKOV; Ivo KABELKA a Robert VÁCHA. Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. WASHINGTON: AMER CHEMICAL SOC, 2025, roč. 65, č. 2, s. 908-920. ISSN 1549-9596. Dostupné z: https://doi.org/10.1021/acs.jcim.4c01960.

JAVANAINEN, Matti; Jan ŠIMEK; Dale TRANTER; Sarah O´KEEFE; Sudeep KARKI; Denys BIRIUKOV; Radek ŠACHL a Ville O. PAAVILAINEN. Lipid Scrambling Pathways in the Sec61 Translocon Complex. Journal of the American Chemical Society. American Chemical Society, 2025, roč. 147, č. 19, s. 15970-15984. ISSN 0002-7863. Dostupné z: https://doi.org/10.1021/jacs.4c11142.

HABAJEC, Antun; Marco VITEK; Denys BIRIUKOV a Igor RONCEVIC. Porphyrins as a Platform for Lithium-Selective Two-Dimensional Membranes. Journal of Physical Chemistry Letters. Washington DC: American Chemical Society, 2025, roč. 16, č. 36, s. 9408-9413. ISSN 1948-7185. Dostupné z: https://doi.org/10.1021/acs.jpclett.5c01874.

RIOPEDRE-FERNANDEZ, Miguel; Vojtech KOSTAL; Tomas MARTINEK; Hector MARTINEZ-SEARA a Denys BIRIUKOV. Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions. Journal of Chemical Information and Modeling. American Chemical Society, 2024, roč. 64, č. 18, s. 7122-7134. ISSN 1549-9596. Dostupné z: https://doi.org/10.1021/acs.jcim.4c00981.

NENCINI, Ricky; Carmelo TEMPRA; Denys BIRIUKOV; Miguel RIOPEDRE-FERNANDEZ; Victor Cruces CHAMORRO; Jakub POLÁK; Philip E. MASON; Daniel ONDO; Jan HEYDA; O. H. Samuli OLLILA; Pavel JUNGWIRTH; Matti JAVANAINEN a Hector MARTINEZ-SEARA. Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field. Journal of Chemical Theory and Computation. American Chemical Society, 2024, roč. 20, č. 17, s. 7546-7559. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.4c00743.

BIRIUKOV, Denys a Robert VÁCHA. Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050. ACS PHYSICAL CHEMISTRY AU. WASHINGTON: AMER CHEMICAL SOC, 2024, roč. 4, č. 4, s. 302-313. ISSN 2694-2445. Dostupné z: https://doi.org/10.1021/acsphyschemau.4c00003.

NIKHIL, Rampal; Wang HSIU-WEN; Brady ALEXANDER; Borreguero JOSE; Denys BIRIUKOV; Mamontov EUGENE a Stack ANDREW. Testing the hypothesis that solvent exchange limits the rates of calcite growth and dissolution. RSC Advances. Cambridge: Royal Society of Chemistry, 2024, roč. 14, č. 22, s. 15743-15754. ISSN 2046-2069. Dostupné z: https://doi.org/10.1039/d4ra00565a.

BIRIUKOV, Denys a Matti JAVANAINEN. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2023, roč. 19, č. 18, s. 6332-6341. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.3c00614.

BIRIUKOV, Denys; Riopedre Fernández MIGUEL a Martinez-Seara HECTOR. Model Sugars Right: Improved Interactions of Glycans in All-Atom Molecular Dynamics Simulations. In GGMM 2023 – Young Modellers Conference. 2023.

BIRIUKOV, Denys; Timothée Emmanuel J. RIVEL a Robert VÁCHA. Multiple factors modulating the formation of toroidal membrane pores. In NIVB MEETING 2023. 2023. ISSN 2336-7202.

VAZDAR, K.; C. TEMPRA; A. OLŻYŃSKA; Denys BIRIUKOV; L. CWIKLIK a M. VAZDAR. Stealthy Player in Lipid Experiments? EDTA Binding to Phosphatidylcholine Membranes Probed by Simulations and Monolayer Experiments. Journal of Physical Chemistry B. WASHINGTON: American Chemical Society, 2023, roč. 127, č. 24, s. 5462-5469. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/acs.jpcb.3c03207.