About Us

We are a group of scientists and students working together to investigate various molecular systems and processes using computer simulation methods. We work at Deparment of Physics, Faculty of Science, University of South Bohemia in České Budějovice and our mission is to conduct cutting-edge research, promote collaboration, and contribute to the scientific community.

Research Areas

Our group focuses mainly on the investigation of charge transfer phenomena in biomolecular systems. Besides, we are interested in the electric field effects on heterogeneous interafces between biomolecules at solid surfaces and behavior of other redox molecular systems.

• Electron transport in protein junctions

  Although electrons in biomolecules are typically transferred by a hopping mechanism, "jumping" through the sequence of available redox sites, when peptides or proteins are incorporated between two metal contacts and form a junction, the transport mechanism changes to coherent tunneling. This drastic change is caused by interactions between metallic and biomolecular electronic states and their mutual positions.

  We investigate these phenomena by a combination of classical molecular dynamics (MD) simulations, hybrid quantum-mechanical/molecular-mechanical (QM/MM) methods, and density functional theory (DFT) calculations.

  Small Tetraheme Cytochrome (STC) junction	Coherent tunneling description	Azurin junction

  	Futera, Z., Ide, I., Kayser, B., Garg, K., Jiang, X., van Wonderen, J. H., Butt, J. N., Ishii, H., Pecht, I., Sheves, M., Cahen, D., Blumberger, J.: Coherent Electron Transport across a 3 nm Bioelectronic Junction Made of Multi-Heme Proteins. J. Phys. Chem. Lett. 11, 9766 (2020) DOI: 10.1021/acs.jpclett.0c02686
  	Futera, Z.: Amino-Acid Interactions with the Au(111) Surface: Adsorption, Band Alignment, and Interfacial Electronic Coupling. Phys. Chem. Chem. Phys. 23, 10257 (2021) DOI: 10.1039/d1cp00218j
  	Kontkanen, O. V., Biriukov, D., Futera, Z.: Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces. J. Chem. Phys. 156, 175101 (2022) DOI: 10.1063/5.0085141
  	Kontkanen, O. V., Biriukov, D., Futera, Z.: Applicability of Perturbed Matrix Method for Charge Transfer Studies at Bio/Metallic Interfaces: A Case of Azurin Phys. Chem. Chem. Phys. 25, 12479 (2023) DOI: 10.1039/d3cp00197k
  	Futera, Z., Wu, X., Blumberger, J.: Tunneling-to-Hopping Transition in Multiheme Cytochrome Bioelectronic Junctions. J. Phys. Chem. Lett. 14, 445-452 (2023) DOI: 10.1021/acs.jpclett.2c03361
  	Jonnalagadda, G. N., Wu, X., Hronek, L., Futera, Z.: Structural, Solvent, and Temperature Effects on Protein Junction Conductance. J. Phys. Chem. Lett. 15, 11608-11614 (2024) DOI: 10.1021/acs.jpclett.4c02230

• Electric field effects on heterogeneous interfaces

  Bio/metallic interfaces, when studied by electrochemical methods like protein film voltammetry (PFV) or electrochemical scanning tunneling microscopy (EC-STM), are affected by the applied potentials and electric fields, which are always present in these measurements. However, such fields can distort the studied biomolecular structures on the interfaces with the electrodes, perturb their electronic properties, and, consequently, affect the probed potential-current (I-V) curves.

  Stronger electric fields or catalytic activity of the electrode surfaces can induce chemical reactions, for example, water splitting. We investigate these effects by non-equilibrium molecular dynamics (NEMD) techniques either at the classical or quantum level of theory using force fields (FF) or density functional theory (DFT), respectively.

  Hematite/water electrochemical cell	Field response of adsorbed amino acids	Aqueous titania/water interfaces

  	Futera, Z., English, N. J.: Electric-Field Effects on Adsorbed-Water Structural and Dynamical Properties of Rutile- and Anatase-TiO2 Surfaces. J. Phys. Chem. C 120, 19603 (2016) DOI: 10.1021/acs.jpcc.0b01907
  	Futera, Z., English, N. J.: Oscillating Electric-Fiel Effects on Adsorbed-Water at Rutile- and Anatase-TiO2 Surfaces. J. Chem. Phys. 145, 204706 (2016) DOI: 10.1063/1.4967520
  	Biriukov, D., Futera, Z.: Adsorption of Amino Acids at the Gold/Aqueous Interface: Effect of an External Electric Field. J. Phys. Chem. C 125, 7856 (2021) DOI: 10.1021/acs.jpcc.0c11248
  	Futera, Z., English, N. J.: Water Breakup at Fe2O3 - Hematite/Water Interfaces: Influence of External Electric Fields from Nonequilibrium Ab Initio Molecular Dynamics J. Phys. Chem. Lett. 12, 6818 (2021) DOI: 10.1021/acs.jpclett.1c01479

Members

• Zdeněk Futera - Group leader
• Gowtham Nirmal Jonnalagadda - Ph.D. student
• Lukáš Hronek - Master student
• Jitka Vysloužilová - Master student

Former members:

• Matyáš Suchý - Bachelor (2022 - 2023)
• Outi Vilhelmiina Kontkanen - Postdoc (2021 - 2022)
• Denys Biriukov - Postdoc (2020 - 2022)

Funding

• Czech Grant Agency (Project 25-16698S, 2025-2027, PI: Z. Futera)
  Mechanisms and dynamics of charge transport in biomolecular junctions
• Czech Grant Agency (Project 20-02067Y, 2020-2022, PI: Z. Futera)
  Electron transfer on electrified heterogeneous interfaces with redox metalloproteins

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