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Other IDs

ResearcherID: Q-4898-2018
Scopus Author ID: 57204029881

Keywords

molecular simulations, sugar-protein interactions, solid/liquid interfaces, aqueous solutions, ion pairing

Countries

Ukraine, Czech Republic

Activities

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Employment (4)

Masaryk University: Brno, CZ

2024-01-01 to present | Project Investigator (National Centre for Biomolecular Research)
Employment
Source: Self-asserted source
Denys Biriukov

Masaryk University: Brno, CZ

2023-01-01 to present | Postdoctoral Researcher (CEITEC - Central European Institute of Technology)
Employment
Source: Self-asserted source
Denys Biriukov

Institute of Organic Chemistry and Biochemistry: Prague, CZ

2020-07-01 to present | Postdoctoral Researcher (Group of Molecular Modeling)
Employment
Source: Self-asserted source
Denys Biriukov

University of South Bohemia in České Budějovice: České Budějovice, CZ

2016-03-07 to 2022-12-31 | Research Assistant (Department of Physics)
Employment
Source: Self-asserted source
Denys Biriukov

Education and qualifications (3)

University of South Bohemia in České Budějovice: České Budějovice, CZ

2016-03-07 to 2020-06-18 | Doctor of Philosophy (Institute of Physics)
Education
Source: Self-asserted source
Denys Biriukov

V. N. Karazin Kharkiv National University: Kharkiv, UA

2014-09-01 to 2015-06-30 | Master of Science (School of Radiophysics, Biomedical Electronics and Computer Systems)
Education
Source: Self-asserted source
Denys Biriukov

V. N. Karazin Kharkiv National University: Kharkiv, UA

2010-09-01 to 2014-06-30 | Bachelor of Science (School of Radiophysics, Biomedical Electronics and Computer Systems)
Education
Source: Self-asserted source
Denys Biriukov

Works (29)

Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations

Journal of Chemical Information and Modeling
2025-01-27 | Journal article
DOI: 10.1021/acs.jcim.4c01960
Contributors: Timothée Rivel; Denys Biriukov; Ivo Kabelka; Robert Vácha
Source: check_circle
Crossref

Testing the hypothesis that solvent exchange limits the rates of calcite growth and dissolution

RSC Advances
2024 | Journal article
DOI: 10.1039/D4RA00565A
Contributors: Nikhil Rampal; Hsiu-Wen Wang; Alexander B. Brady; Jose M. Borreguero; Denys Biriukov; Eugene Mamontov; Andrew G. Stack
Source: check_circle
Crossref

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
2024-09-23 | Journal article
DOI: 10.1021/acs.jcim.4c00981
Contributors: Miguel Riopedre-Fernandez; Vojtech Kostal; Tomas Martinek; Hector Martinez-Seara; Denys Biriukov
Source: check_circle
Crossref

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field

Journal of Chemical Theory and Computation
2024-09-10 | Journal article
DOI: 10.1021/acs.jctc.4c00743
Contributors: Ricky Nencini; Carmelo Tempra; Denys Biriukov; Miguel Riopedre-Fernandez; Victor Cruces Chamorro; Jakub Polák; Philip E. Mason; Daniel Ondo; Jan Heyda; O. H. Samuli Ollila et al.
Source: check_circle
Crossref

The Origins of Arginine “Magic”: Guanidinium Like-Charge Ion Pairing and Oligoarginine Aggregation in Water by NMR, Cryoelectron Microscopy, and Molecular Dynamics Simulations

2024-08-05 | Preprint
DOI: 10.1101/2024.08.04.606526
Contributors: Denys Biriukov; Zuzana Osifová; Man Nguyen Thi Hong; Philip E. Mason; Martin Dračínský; Pavel Jungwirth; Jan Heyda; Mattia I. Morandi; Mario Vazdar
Source: check_circle
Crossref

Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050

ACS Physical Chemistry Au
2024-07-24 | Journal article
DOI: 10.1021/acsphyschemau.4c00003
Contributors: Denys Biriukov; Robert Vácha
Source: check_circle
Crossref

Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters for Glycosaminoglycans via Ab Initio Molecular Dynamics Simulations

2024-06-03 | Preprint
DOI: 10.1101/2024.05.31.596767
Contributors: Miguel Riopedre-Fernandez; Vojtech Kostal; Tomas Martinek; Hector Martinez-Seara; Denys Biriukov
Source: check_circle
Crossref

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field

2024-06-03 | Preprint
DOI: 10.1101/2024.05.31.596781
Contributors: Ricky Nencini; Carmelo Tempra; Denys Biriukov; Miguel Riopedre-Fernandez; Victor Cruces Chamorro; Jakub Polak; Philip E. Mason; Daniel Ondo; Jan Heyda; O. H. Samuli Ollila et al.
Source: check_circle
Crossref

Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity

Carbohydrate Polymers
2024-02 | Journal article
DOI: 10.1016/j.carbpol.2023.121568
Part of ISSN: 0144-8617
Contributors: Miguel Riopedre-Fernandez; Denys Biriukov; Martin Dračínský; Hector Martinez-Seara
Source: Self-asserted source
Denys Biriukov

Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin

Physical Chemistry Chemical Physics
2023 | Journal article
DOI: 10.1039/D3CP00197K
Contributors: Outi Vilhelmiina Kontkanen; Denys Biriukov; Zdenek Futera
Source: check_circle
Crossref

Evolution of the electrical double layer with electrolyte concentration probed by second harmonic scattering

Faraday Discussions
2023 | Journal article
DOI: 10.1039/D3FD00036B
Contributors: Bingxin Chu; Denys Biriukov; Marie Bischoff; Milan Předota; Sylvie Roke; Arianna Marchioro
Source: check_circle
Crossref

The Sec61/TRAP Translocon Scrambles Lipids

2023-11-23 | Preprint
DOI: 10.1101/2023.11.23.568215
Contributors: Matti Javanainen; Sudeep Karki; Dale Tranter; Denys Biriukov; Ville O. Paavilainen
Source: check_circle
Crossref

Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints

Journal of Chemical Theory and Computation
2023-09-26 | Journal article
DOI: 10.1021/acs.jctc.3c00614
Contributors: Denys Biriukov; Matti Javanainen
Source: check_circle
Crossref

Stealthy Player in Lipid Experiments? EDTA Binding to Phosphatidylcholine Membranes Probed by Simulations and Monolayer Experiments

The Journal of Physical Chemistry B
2023-06-22 | Journal article
DOI: 10.1021/acs.jpcb.3c03207
Contributors: Katarina Vazdar; Carmelo Tempra; Agnieszka Olżyńska; Denys Biriukov; Lukasz Cwiklik; Mario Vazdar
Source: check_circle
Crossref

Efficient Simulations of Membrane and Solvent Asymmetry With Flat-Bottom Restraints

2023-05-28 | Preprint
DOI: 10.1101/2023.05.26.542460
Contributors: Denys Biriukov; Matti Javanainen
Source: check_circle
Crossref

A Stealthy Player in Lipid Experiments? EDTA Binding to Phosphatidylcholine Membranes Probed by Simulations and Monolayer Experiments

2023-03-13 | Preprint
DOI: 10.1101/2023.03.12.532294
Contributors: Katarina Vazdar; Carmelo Tempra; Agnieszka Olzynska; Denys Biriukov; Lukasz Cwiklik; Mario Vazdar
Source: check_circle
Crossref

Ionic Strength and Solution Composition Dictate the Adsorption of Cell-Penetrating Peptides onto Phosphatidylcholine Membranes

Langmuir
2022-09-20 | Journal article
DOI: 10.1021/acs.langmuir.2c01435
Contributors: Man Thi Hong Nguyen; Denys Biriukov; Carmelo Tempra; Katarina Baxova; Hector Martinez-Seara; Hüseyin Evci; Vandana Singh; Radek Šachl; Martin Hof; Pavel Jungwirth et al.
Source: check_circle
Crossref

The “good,” the “bad,” and the “hidden” in neutron scattering and molecular dynamics of ionic aqueous solutions

The Journal of Chemical Physics
2022-05-21 | Journal article
DOI: 10.1063/5.0093643
Contributors: Denys Biriukov; Hsiu-Wen Wang; Nikhil Rampal; Carmelo Tempra; Patrik Kula; Joerg C. Neuefeind; Andrew G. Stack; Milan Předota
Source: check_circle
Crossref

Reorganization free energy of copper proteins in solution, in vacuum, and on metal surfaces

The Journal of Chemical Physics
2022-05-07 | Journal article
DOI: 10.1063/5.0085141
Contributors: Outi Vilhelmiina Kontkanen; Denys Biriukov; Zdenek Futera
Source: check_circle
Crossref

Second Harmonic Scattering Reveals Ion-Specific Effects at the SiO2 and TiO2 Nanoparticle/Aqueous Interface

The Journal of Physical Chemistry C
2021-11-18 | Journal article
DOI: 10.1021/acs.jpcc.1c07191
Contributors: Marie Bischoff; Denys Biriukov; Milan Předota; Arianna Marchioro
Source: check_circle
Crossref

Local molecular environment drives speciation and reactivity of ion complexes in concentrated salt solution

Journal of Molecular Liquids
2021-10 | Journal article
DOI: 10.1016/j.molliq.2021.116898
Part of ISSN: 0167-7322
Source: Self-asserted source
Denys Biriukov

Adsorption of Amino Acids at the Gold/Aqueous Interface: Effect of an External Electric Field

The Journal of Physical Chemistry C
2021-04-15 | Journal article
DOI: 10.1021/acs.jpcc.0c11248
Contributors: Denys Biriukov; Zdenek Futera
Source: check_circle
Crossref

Electronic continuum correction without scaled charges

Journal of Molecular Liquids
2020-09 | Journal article
DOI: 10.1016/j.molliq.2020.113571
Part of ISSN: 0167-7322
Source: Self-asserted source
Denys Biriukov

Surface Potential and Interfacial Water Order at the Amorphous TiO2 Nanoparticle/Aqueous Interface

The Journal of Physical Chemistry C
2020-05-21 | Journal article
DOI: 10.1021/acs.jpcc.0c01158
Contributors: Marie Bischoff; Denys Biriukov; Milan Předota; Sylvie Roke; Arianna Marchioro
Source: check_circle
Crossref

Zeta Potential Determination from Molecular Simulations

The Journal of Physical Chemistry C
2020-02-06 | Journal article
DOI: 10.1021/acs.jpcc.9b11371
Contributors: Denys Biriukov; Pavel Fibich; Milan Předota
Source: check_circle
Crossref

Surface Characterization of Colloidal Silica Nanoparticles by Second Harmonic Scattering: Quantifying the Surface Potential and Interfacial Water Order

The Journal of Physical Chemistry C
2019-08-22 | Journal article
DOI: 10.1021/acs.jpcc.9b05482
Contributors: Arianna Marchioro; Marie Bischoff; Cornelis Lütgebaucks; Denys Biriukov; Milan Předota; Sylvie Roke
Source: check_circle
Crossref

Oxalic Acid Adsorption on Rutile: Experiments and Surface Complexation Modeling to 150 °C

Langmuir
2019-06-18 | Journal article
DOI: 10.1021/acs.langmuir.8b03982
Contributors: Michael L. Machesky; Moira K. Ridley; Denys Biriukov; Ondřej Kroutil; Milan Předota
Source: check_circle
Crossref

Oxalic Acid Adsorption on Rutile: Molecular Dynamics and ab Initio Calculations

Langmuir
2019-06-18 | Journal article
DOI: 10.1021/acs.langmuir.8b03984
Contributors: Denys Biriukov; Ondřej Kroutil; Martin Kabeláč; Moira K. Ridley; Michael L. Machesky; Milan Předota
Source: check_circle
Crossref

Modeling of solid–liquid interfaces using scaled charges: rutile (110) surfaces

Physical Chemistry Chemical Physics
2018 | Journal article
DOI: 10.1039/C8CP04535F
Contributors: Denys Biriukov; Ondřej Kroutil; Milan Předota
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Peer review (11 reviews for 10 publications/grants)

Review activity for Advanced materials interfaces. (1)
Review activity for Chem. (1)
Review activity for Journal of chemical information and modeling. (1)
Review activity for Journal of chemical physics. (2)
Review activity for Journal of chemical theory and computation : (1)
Review activity for Journal of physical chemistry. (1)
Review activity for PLoS biology. (1)
Review activity for Review Commons (1)
Review activity for Small structures. (1)
Review activity for The journal of physical chemistry. (1)
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