Publications

1. B. S. Babu, P. Kayshap, S. C. Tripathi, P. Jelínek, B.N. Dwivedi, Spectroscopic Diagnostic of the Footpoints of the Cool Loops, MNRAS, 528, 2474, 2024. https://doi.org/10.1093/mnras/stae166
2. R. Akbarzadeh, M. Předota, ReaxFF Molecular Dynamics of Graphene Oxide/NaCl Aqueous Solution Interfaces, Phys. Chem. Chem. Phys. 26, 2603-2612 (2024). https://doi.org/10.1039/D3CP04735K
3. E. Rezlerová, F. Moučka, M. Předota, and M. Lísal, Structure and self-diffusivity of mixed-cation electrolytes between neutral and charged graphene sheets. J. Chem. Phys., 160, 094701, 2024. https://doi.org/10.1063/5.0188104
4. Milan Novak, Petr Doležal, Ondřej Budík, Ladislav Ptáček, Jakub Geyer, Markéta Davídková, Miloš Prokýšek, Intelligent inspection probe for monitoring bark beetle activities using embedded IoT real-time object detection, Engineering Science and Technology, an International Journal, Volume 51, 2024, 101637, ISSN 2215-0986, https://doi.org/10.1016/j.jestch.2024.101637
5. Özcan, E., Šímová, I., Bína, D., Litvín, R., Polívka, T., Ultrafast spectroscopy of the hydrophilic carotenoid crocin at various pH. Phys. Chem. Chem. Phys. 26, 10225-10233, 2024. https://doi.org/10.1039/D4CP00665H
   
6. Sauer, P. V., Cupellini, L., Sutter, M., Bondanza, M., Dominguez-Martin, M. A., Kirst, H., Bína, D., Fujiet Koh, A., Kotecha, A., Greber, B. J., Nogales, E., Polívka, T., Mennucci, B., Kerfeld, C. A., Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. Sci. Adv. 10, eadk7535, 2024. https://doi.org/10.1126/sciadv.adk7535
7. Chrupková, P., van Stokkum, I., Budisa, N., Tseng, H-W., Moldenhauer, M., Friedrich, T., Cherepanov, D.A., Polívka, T., Maksimov, E.G., Kloz, M. Raman vibration signatures of excited states of echinenone in the orange carotenoid protein (OCP) and implications for its photoactivation mechganism. J. Mol. Biol. 436, 168625, 2024. https://doi.org/10.1016/j.jmb.2024.168625
8. Šímová, I., Chrupková, P., Gardiner, A.T., Koblížek, M., Kloz, M., Polívka, T. Femtosecond stimulated Raman spectroscopy of linear carotenoids. J. Phys. Chem. Lett. 15, 7466–7472, 2024. https://doi.org/10.1021/acs.jpclett.4c01272
9. Özcan, E., Keşan, G., Chábera, P., Litvín, R., Polívka, T. Synthesis and spectroscopic properties of carotenoid bis-phenylhydrazone astaxanthin: Extending conjugation to a C=N group. New J. Chem. 48, 12919-12928, 2024. https://doi.org/10.1039/D4NJ02282C
10. W. Chen, O. Kroutil, M. Předota, S. Pezzotti, and M.-P. Gaigeot, Wetting of a Dynamically Patterned Surface Is a Time-Dependent Matter. J. Phys. Chem. B 128, 11914−11923, 2024. https://doi.org/10.1021/acs.jpcb.4c05163
11. P. Jelínek, M. Karlický, Turbulent plasma flow, its energies and structures: velocity vortices, magnetic field cocoons and plasmoids, Astronomy and Astrophysics,  692, A116, 2024. https://doi.org/10.1051/0004-6361/202449558

1. S. K. Mishra, K. Sangal, P. Kayshap, P. Jelínek, A. K. Srivastava, S. P. Rajaguru, Origin of Quasi-Periodic Pulsation at the Base of Kink Unstable Jet, The Astrophysical Journal, 945, 2, 2023. https://doi.org/10.3847/1538-4357/acb058
2. O. V. Kontkanen, D. Biriukov, Z. Futera: Applicability of Perturbed Matrix Method for Charge Transfer Studies at Bio/Metallic Interfaces: A Case of Azurin. Phys. Chem. Chem. Phys. 25, 12479–12489 (2023) https://doi.org/10.1039/d3cp00197
3. Z. Futera, X. Wu, J. Blumberger: Tunneling-to-Hopping Transition in Multiheme Cytochrome Bioelectronic Junctions. J. Phys. Chem. Lett. 14, 445–452 (2023) https://doi.org/10.1021/acs.jpclett.2c03361
4. Özcan, E., Kuznetsova, V., Keşan, G., Fuciman, M., Litvín, R., Polívka, T.: Ultrafast excited states dynamics of metal ion complexes of the carotenoid astaxanthin. J. Photochem. Photobiol. A. 441, 114737, 2023. https://doi.org/10.1016/j.jphotochem.2023.114737
5. Kuznetsova, V., Fuciman, M., Polívka, T.: Relaxation dynamics of high-energy excited states of carotenoids studied by UV excitation and pump-repump-probe transient absorption spectroscopy. Phys. Chem. Chem. Phys. 25, 22336-22344, 2023. https://doi.org/10.1039/D3CP02485G
6. Keşan, G., Özcan, E., Chábera, P., Polívka, T., Fuciman, M.: Time-resolved spectro-electrochemical dynamics of carotenoid 8’-apo-β-carotenal. ChemPlusChem, e202300404, 2023. https://doi.org/10.1002/cplu.202300404
7. E. Pitula, M. Janik, P. Sezemsky, K. P. Szymanska, M. Olszewski, V. Stranak, M. Koba, M. Smietana: Smartphone-based dynamic measurements of electro-optically modulated lossy-mode resonance and its biosensing applications, Measurement 206, (2023). https://doi.org/10.1016/j.measurement.2022.112349
8. P. Sezemsky, M. Koba, P. Curda, R. Bogdanowicz, V. Stranak, M. Smietana: Electro-optical transducer based on indium-tin-oxide-coated optical fiber for analysis of ionized media, Measurement 212, (2023). https://doi.org/10.1016/j.measurement.2023.112695
9. I. Dominguez, J.M. Corres, I. Del Villar, J.D. Mozo, R. Simerova, P. Sezemsky, V. Stranak, M. Śmietana, I. R. Matias, Electrochemical lossy mode resonance for detection of manganese ions, Sensors and Actuators B: Chemical 394, (2023). http://dx.doi.org/10.1016/j.snb.2023.134446
10. P. Curda, D. Kaftan, T. Kozak, S. Kumar, P. Sezemsky, V. Stranak, High-defined and size-selective deposition of nanoparticles by their manipulation in an electrostatic field, Appl. Surf. Sci. 640, (2023). https://doi.org/10.1016/j.apsusc.2023.158307
11. P. Curda, R. Hippler, M. Cada, O. Kylian, V. Stranak, Z. Hubicka, The role of dimers in the efficient growth of nanoparticles, Surf. Coat. Technol. 473, (2023). https://doi.org/10.1016/j.surfcoat.2023.130045
12. D-S. Kouao, J. Hanus, O. Kylian, R. Simerova, P. Sezemsky, V. Stranak, K. Grochowska, K. Siuzdak, Photoelectrochemical and Electrochemical Activity of Anodic Semitransparent Aligned and Spaced Titania Nanotubes Formed out of Titanium−Silver Alloys, ACS Appl. Nano Mat. XX, (XXX), http://dx.doi.org/10.1021/acsanm
13. B. Chu, D. Biriukov, M. Bischoff, M. Předota, S. Roke and A. Marchioro, Evolution of the Electrical Double Layer with Electrolyte Concentration Probed by Second Harmonic Scattering, Faraday Discuss. 246, 407-425 (2023). https://doi.org/10.1039/D3FD00036B
14. E. Rezlerová, F. Moučka, M. Předota, and M. Lísal, Structure and self-diffusivity of alkali-halide electrolytes in neutral and charged graphene nanochannels, Phys. Chem. Chem. Phys. 25, 21579-21594 (2023). https://doi.org/10.1039/D3CP03027J

1. S. Kumar, J. Kratochvil, Y. Al-Muhkhrabi, E. Kratochvilova, D. Kahoun, D. Kaftan, J. Hanus, J. Sterba, V. Stranak, Surface anchored Ag nanoparticles prepared by gas aggregation source: Antibacterial effect and the role of surface free energy, Surfaces and Interfaces 30, (2022), 101818
2. S. Kumar, J. Kratochvíl, Y. Al-Muhkhrabi, O. Kylián, D. Nikitin, V. Straňák, Ag nanoparticles immobilized on C:H:N:O plasma polymer film by elevated temperature for LSPR sensing, Plasma Processes Polym. 2022, e2100144
3. D. Burnat, P. Sezemsky, K. Lechowicz, M. Koba, M. Janczuk-Richter, M. Janik, V. Stranak, J. Niedziolka-Jonson, R. Bogdanowicz, M. Smietana, Functional fluorine-doped tin oxide coating for opto-electrochemical label-free biosensors, Sensors and Actuators B – Chemical 367, (2022), 132145
4. E. Pituła, M. Janik, P. Sezemsky, K. P. Szymańska, M. Olszewski, V. Stranak, M. Koba, M. Śmietana, Smartphone-Based Dynamic Analysis of Electro-Optically Modulated Lossy-Mode Resonance for Label-Free Biosensing, SSRN Electronic Journal, (2022), http://dx.doi.org/10.2139/ssrn.4129006
5. V. V. Smirnova, Y. Tsap., P. Jelínek, M. Karlický, Transverse oscillations of quiet solar filament observed at the 304 Å EUV passband, Advances in Space Research, 70, 3257, 2022. https://doi.org/10.1016/j.asr.2022.08.064
6. A. Hankova, A. Kuzminova, J. Hanus, P. Sezemsky, R. Simerova, V. Stranak, K. Grochowska, D.-S. Kouao, K. Siuzdak, M. Prochazka, T. Kosutova, O. Kylian, TiO2/Ag nanostructured coatings as recyclable platforms for surface-enhanced Raman scattering detection, Surfaces and Interfaces 35, (2022), http://dx.doi.org/10.1016/j.surfin.2022.102441
7. M. Smietana, B. Janasek, K. Lechowicz, P. Sezemsky, M. Koba, D. Burnat, M. Kieliszczyk, V. Stranak, P. Szczepanski, Electro-optically modulated lossy-mode-resonance, Nanophotonics 11(3), (2022), 593
8. D. Biriukov, H.-W. Wang, N. Rampal, C. Tempra, P. Kula, J. C. Neuefeind, A. G. Stack, and M. Předota: “The “Good,” the “bad,” and the “hidden” in neutron scattering and molecular dynamics of ionic aqueous solutions”, J. Chem. Phys. 156, 194505 (2022). https://doi.org/10.1063/5.0093643
9. Qian, P., Gardiner, A.T., Šímová, I., Naydenova, K., Croll, T., Jackson, P.J., Nupur, Kloz, M., Čubáková, P., Kuzma, M., Zeng, Y., Castro-Hartmann, P., van Knippenberg, B., Goldie, K.N., Kaftan, D., Hrouzek, P., Hájek, J., Agirre, J., Siebert, C.A., Bína, D., Sader, K., Stahlberg, H., Sobotka, R., Russo, C.J., Polívka, T., Hunter, C.N., Koblížek, M. 2.4 Å structure of the double ring Gemmatimonas phototrophica photosystem. Sci. Adv. 8, eabk3139, 2022. https://doi.org/10.1126/sciadv.abk3139
10. Khan, T., Kuznetsova, V., Dominguez-Martin, M.A., Kerfeld, C.A., Polívka, T. UV excitation of carotenoid binding proteins OCP and HCP: Excited-state dynamics and product formation. ChemPhotoChem, 6, e202100194, 2022. https://doi.org/10.1002/cptc.202100194
11. Gray, C., Wei, T., Polívka, T., Daskalakis, V., Duffy, C.D.P. Trivial excitation energy transfer to carotenoids is an unlikely mechanism for non-photochemical quenching in LHCII. Front. Plant Sci., 12, 797373, 2022. https://doi.org/10.3389/fpls.2021.797373
12. Šebelík, V., Duffy, C.D.P., Keil, E., Polívka, T., Hauer, J. Understanding ultrafast energy relaxation in carotenoids. J. Phys. Chem. B, 126, 3985-3994, 2022. https://doi.org/10.1021/acs.jpcb.2c00996
13. Dominguez-Martin, M.A., Sauer, P.V., Kirst, H., Sutter, M., Bína, D., Greber, B.J., Nogales, E., Polívka, T., Kerfeld, C.A. Structures of a phycobilisome in light-harvesting and photoprotected states. Nature, 609, 835-845, 2022. https://doi.org/10.1038/s41586-022-05156-4
14. Šímová, I., Kuznetsova, V., Gardiner, A.T., Šebelík, V., Koblížek, M., Fuciman, M., Polívka, T. Carotenoid as a sensor of excess energy dissipation in the LH2 complex from Rhodoblastus acidophilus. Photosynth. Res. 154, 75-87, 2022. https://doi.org/10.1007/s11120-022-00952-5
15. Zigmantas, D., Polívka, T., Persson, P., Sundström, V. Ultrafast laser spectroscopy uncovers mechanisms of light energy conversion in photosynthesis and sustainable energy materials. Chem. Phys. Rev. In press.
16. P. Jelínek, S. Belov, M. Karlický, Numerical simulations of oscillations in solar corona excited by vortex shedding, The Astrophysical Journal, 941, 124, 2022. https://doi.org/10.3847/1538-4357/aca40d
17. Y. Alvarez-Galvan, B. Minofar, Z. Futera, M. Francoeur, C. Jean-Marius, N. Brehm, Ch. Yacou, U. J. Jauregui-Haza, S. Gaspard: Adsorption of Hexavalent Chromium Using Activated Carbon Produced from Sargassum ssp.: Comparison between Lab Experiments and Molecular Dynamics Simulations. Molecules 27, 6040 (2022) https://doi.org/10.3390/molecules27186040
18. J. P. Hill, P. A. Karr, R. A. Z. Uy, N. K. Subbaiyan , Z. Futera, K. Ariga, S. Ishihara, J. Labuta, F. D’Souza: Analyte Interactions with Oxoporphyrinogen Derivatives: Computational Aspects. Curr. Org. Chem. 26, 580–595 (2022) https://doi.org/10.2174/1385272826666220208101325
19. O. V. Kontkanen, D. Biriukov, Z. Futera: Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces. J. Chem. Phys. 156, 175101 (2022) https://doi.org/10.1063/5.0085141
20. Y. Tateyama, Z. Futera, Y. Ootani, S. Iizuka, L. T. Anh: ”Computational Aspects of Surface and Interface of BDD Electrode” in: Einaga Y. (eds) Diamond Electrodes. Springer, Singapore (2022) https://doi.org/10.1007/978-981-16-7834-9_5
21. H. Wu, M. R. Ghaani, Z. Futera, N. J. English: Effects of Externally Applied Electric Fields on the Manipulation of Solvated-Chignolin Folding: Static- versus Alternating-Field Dichotomy at Play. J. Phys. Chem. B 126, 376-386 (2022) https://doi.org/10.1021/acs.jpcb.1c06857
22. Z. Futera, N. J. English: Dielectric Properties of Ice VII under the Influence of Time-Alternating External Electric Fields. Phys. Chem. Chem. Phys. 24, 56-62 (2022) https://doi.org/10.1039/d1cp04165g
23. D. T. Payne, J. Labuta, Z. Futera, V. Brezina, L. Hanykova, M. K. Chahal, J. P. Hill: Molecular Rotor Based on an Oxidized Resorcinarene. Org. Chem. Front. 9, 39 (2022) https://doi.org/10.1039/d1qo01479j

1. P. Kayshap, D. Tripathi, P. Jelínek, Dynamics of Sunspot Shock Waves in the Chromosphere and Transition Region, The Astrophysical Journal, 906, 121, 2021. https://doi.org/10.3847/1538-4357/abcc6f
2. Khan, T., Litvín, R., Šebelík, V., Polívka, T. Excited state evolution of keto-carotenoids after excess energy excitation in the UV region. ChemPhysChem. 22, 471-480, 2021. https://doi.org/10.1002/cphc.202000982
3. Šebelík, V., Kuznetsova, V., Lokstein, H., Polívka, T. Transient absorption of chlorophylls and carotenoids after two-photon excitation of LHCII. J. Phys. Chem. Lett. 12, 3176-3181, 2021. https://doi.org/10.1021/acs.jpclett.1c00122
4. Biriukov, D., Futera, Z. Adsorption of Amino Acids at the Gold/Aqueous Interface: Effect of an External Electric Field. J. Phys. Chem. C 125, 7856-7867, 2021. https://doi.org/10.1021/acs.jpcc.0c11248
5. Futera, Z. Amino-acid interactions with the Au(111) surface: adsorption, band alignment, and interfacial electronic coupling. Phys. Chem. Chem. Phys. 23, 10257-10266, 2021. https://doi.org/10.1039/d1cp00218j
6. Mrkyvkova, N., Cernescu, A., Futera, Z., Nebojsa, A., Dubroka, A., Sojkova, M., Hulman, M., Majkova, E., Jergel, M., Siffalovic, P., Schreiber, F. Nanoimaging of Orientational Defects in Semiconducting Organic Films. J. Phys. Chem. C 125, 9229-9235, 2021. https://doi.org/10.1021/acs.jpcc.1c00059
7. Kartha, K. K., Takai, A., Futera, Z., Labuta, J., Takeuchi, M. Dynamics of Meso-Chiral Interconversion in a Butterfly-Shape Overcrowded Alkene Rotor Tunable by Solvent Properties. Angew. Chem. Int. Ed. 60, 2-8, 2021. https://doi.org/10.1002/anie.202102719
8. 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, 6818-6826, 2021. https://doi.org/10.1021/acs.jpclett.1c01479
9. N. Rampal, H.-W. Wang, D. Biriukov, A. B. Brady, J. C. Neuefeind, M. Předota, A.G. Stack: Local molecular environment drives speciation and reactivity of ion complexes in concentrated salt solution. J. Mol. Liq. 340, 116898, 2021. https://doi.org/10.1016/j.molliq.2021.116898
10. O. Kroutil, V. D. Nguyen, J. Volánek, A. Kučera, M. Předota, V. Vranová: Clinoptilolite/electrolyte Interface Probed by a Classical Molecular Dynamics Simulations and Batch Adsorption experiments, Microporous and Mesoporous Materials 328, 111406, 2021. https://doi.org/10.1016/j.micromeso.2021.111406
11. A. K. Srivastava, S. K. Mishra, P. Jelínek, The Prominence Driven Forced Reconnection in the Solar Corona and Associated Plasma Dynamics, The Astrophysical Journal, 920, 18, 2021. https://doi.org/10.3847/1538-4357/ac1519
12. M. Bischoff, D. Biriukov, M. Předota, and A. Marchioro: “Second Harmonic Scattering Reveals Ion-Specific Effects at the SiO₂ and TiO₂ Nanoparticle/Aqueous Interface”, J. Phys. Chem. C 125, 25261−25274, 2021. https://doi.org/10.1021/acs.jpcc.1c07191
13. I. Yaroshevich, E. Maksimov, N. Sluchanko, D. Zlenko, A. Stepanov, E. Slutskaya, Y. Slonimskiy, V. Botnarevskii, A. Remeeva, I. Gushchin, K. Kovalev, V. Gordeliy, I. Shelaev, F. Gostev, D. Khakhulin, V. Poddubnyy, T. Gostev, D. Cherepanov, T. Polívka, M. Kloz, T. Friedrich, V. Paschenko, V. Nadtochenko, A. Rubin, M. Kirpichnikov, Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein. Communications Biology, 539, 2021. https://doi.org/10.1038/s42003-021-02022-3
14. T. Khan, V. Kuznetsova, M.A. Dominguez-Martin, C.A. Kerfeld, T. Polívka, UV excitation of carotenoid binding proteins OCP and HCP: Excited-state dynamics and product formation. ChemPhotoChem, 5, 2021. https://doi.org/10.1002/cptc.202100194
15. P. Skotnicová, H. Staleva-Musto, V. Kuznetsova, D. Bína, M.M. Konert, S. Lu, T. Polívka, R. Sobotka, Plant LHC-like proteins show robust folding and static non-photochemical quenching. Nature Communications, 12, 6890, 2021. https://doi.org/10.1038/s41467-021-27155-1
16. J. Kratochvil, V. Prysiazhnyi, F. Dycka, O. Kylian, P. Kus, P. Sezemsky, J. Sterba, V. Stranak, Gas aggregated Ag nanoparticles as the inorganic matrix for laser desorption/ionization mass spectrometry, Appl. Surf. Sci. 541, (2021), 148469. https://doi.org/10.1016/j.apsusc.2020.148469
17. A. Dettlaff, M. Brodowski, M. Kowalski, V. Stranak, V. Prysiazhnyi, E. Klugmann-Radziemska, J. Ryl, R. Bogdanowicz, Highly Oriented Zirconium Nitride and Oxynitride Coatings Deposited via High-Power Impulse Magnetron Sputtering: Crystal-Facet-Driven Corrosion Behavior in Domestic Wastewater, Advanced Engineering Materials (2021), 2001349. https://doi.org/10.1002/adem.202001349
18. P. Sezemsky, D. Burnat, J. Kratochvil, H. Wulff, A. Kruth, K. Lechowicz, M. Janik, R. Bogdanowicz, M. Cada, Z. Hubicka, P. Niedziałkowski, W. Białobrzeska, V. Stranak, M. Smietana, Tailoring properties of indium tin oxide thin films for their work in both electrochemical and optical label-free sensing systems, Sensors and Actuators: B. Chemical 343, (2021), 130173. https://doi.org/10.1016/j.snb.2021.130173
19. V. Prysiazhyi, J. Kratochvil, D. Kaftan, R. Ctvrtlik, V. Stranak, Growth of hard nanostructured ZrN surface induced by copper nanoparticles, Appl. Surf. Sci 562, (2021), 150230. https://www.doi.org/10.1016/j.apsusc.2021.150230
20. A. Azinfar, S. Neuber, M. Vancova, J. Sterba, V. Stranak, C.A. Helm, Influence of deposition Steps and Drying in a Vacuum, Langmuir, Vol. 37, (2021). https://www.doi.org/10.1021/acs.langmuir.1c01409
21. S. Kumar, J. Kratochvíl, Y. Al-Muhkhrabi, O. Kylián, D. Nikitin, V. Stranak, Ag nanoparticles immobilized on C:H:N:O plasma polymer film by elevated temperature for LSPR sensing, Plasma Processes Polym. 2021, e2100144. https://www.doi.org/10.1002/ppap.202100144
22. Ziogos, O. G., Kubas, A., Futera, Z., Xie, W., Elstner, M., Blumberger, J.: HAB79: A New Molecular Dataset for Benchmarking DFT and DFTB Electronic Couplings Against High-Level Ab Initio Calculations. J. Chem. Phys. 155, 234115, 2021. https://doi.org/10.1063/5.0076010
23. M. Śmietana, B. Janaszek, K. Lechowicz, P. Sezemsky, M. Koba, D. Burnat, M. Kieliszczyk, V. Stranak, P. Szczepański, Electro-optically modulated lossy-mode resonance, Nanophotonics, 2021. https://doi.org/10.1515/nanoph-2021-0687

1. Kuznetsova, V., Dominguez-Martin, M.A., Bao, H., Gupta, S., Sutter, M., Kloz, M., Rebarz, M., Přeček, M., Chen, Y., Petzold, C.J., Ralston, C.Y., Kerfeld, C.A., Polívka, T. Comparative ultrafast spectroscopy and structural analysis of OCP1 and OCP2 from Tolypothrix. BBA-Bioenergetics, 1861, 148120, 2020. https://doi.org/10.1016/j.bbabio.2019.148120
2. P. Kayshap, A. K. Srivastava, S. K. Tiwari, P. Jelínek, M. Mathioudakis, Propagation of waves above a plage as observed by IRIS and SDO, Astronomy and Astrophysics 634, A63, 2020. https://doi.org/10.1051/0004-6361/201936070
3. D. Biriukov, P. Fibich, M. Předota, Zeta Potential Determination from Molecular Simulations, J. Phys. Chem. C 124, 3159, 2020. https://doi.org/10.1021/acs.jpcc.9b11371
4. Futera, Z., Jiang, X., Blumberger, J. Ergodicity breaking in thermal biological electron transfer? Cytochrome c revisited II., J. Phys. Chem. B 124, 3336, 2020. https://doi.org/10.1021/acs.jpcb.0c01414
5. Staleva-Musto, H., Kuznetsova, V., Bína, D., Litvín, R., Polívka, T. Intramolecular charge transfer state of carotenoids siphonaxanthin and siphonein: Function of non-conjugated acyl-oxy group. Photosynth. Res. 144, 127-135, 2020. https://doi.org/10.1007/s11120-019-00694-x
6. M. Rycewicz, L. Macewicz, J. Kratochvil, A. Stanisławska, M. Ficek, M. Sawczak, V. Stranak, M. Szkodo, R. Bogdanowicz, Physicochemical and Mechanical Performance of Freestanding Boron-Doped Diamond Nanosheets Coated with C:H:N:O Plasma Polymer, Materials, 13, (2020), 1861. https://doi.org/10.3390/ma13081861
7. M. Bischoff, D. Biriukov, M. Předota, S. Roke, A. Marchioro, Surface Potential and Interfacial Water Order at the Amorphous TiO₂ Nanoparticle/Aqueous Interface, J. Phys. Chem. C 124, 10961, 2020. https://doi.org/10.1021/acs.jpcc.0c01158
8. P. Jelínek, M. Karlický, V. Smirnova, A. Solov'ev, Transverse oscillations of the double-structured solar filament, Astronomy and Astrophysics, 637, A42, 2020. https://doi.org/10.1051/0004-6361/201936836
   
9. J. Kratochvíl, V. Stranak, J. Kousal, P. Kúš, O. Kylián, Theoretical and experimental analysis of defined 2D-graded two-metal nanoparticle-build surfaces, Applied Surface Science, 551, (2020), 145530. https://doi.org/10.1016/j.apsusc.2020.145530
10. M. Vaidulych, P. Pleskunov, J. Kratochvíl, H. Mašková, P. Kočová, D. Nikitin, J. Hanuš, O. Kylián, J. Štěrba, H. Biederman, A. Choukourov, Convex vs concave surface nano-curvature of Ta2O5 thin films for tailoring the osteoblast adhesion, Surface and Coatings Technology, in press, 2020, 125805 https://doi.org/10.1016/j.surfcoat.2020.125805
11. M. Předota, D. Biriukov, Electronic Continuum Correction without Scaled Charges, J. Mol. Liq. 314, 113571 , 2020. https://doi.org/10.1016/j.molliq.2020.113571
12. O. Kroutil, S. Pezzotti, M.-P. Gaigeot, M. Předota, Phase-Sensitive Vibrational SFG Spectra from Simple Classical Force Fields Molecular Dynamics Simulations, J. Phys. Chem. C 124, 15253, 2020. https://doi.org/10.1021/acs.jpcc.0c03576
13. Adamec, F., Farci, D., Bína, D., Litvín, R., Khan, T., Fuciman, M., Piano, D., Polívka, T. Photophysics of deinoxanthin, the keto-carotenoid bound to the main S-layer unit of Deinococcus radiodurans. Photobiol. Sci. 19, 495-503, 2020. https://doi.org/10.1039/d0pp00031k
14. Futera, Z., Tse, J. S., English, N. J. Possibility of realizing superionic ice VII in external electric fields of planetary bodies. Sci. Adv. 6, eaaz2915, 2020. https://doi.org/10.1126/sciadv.aaz2915
15. Khan, T., Dominguez-Martin, M.A., Šímová, , Fuciman, M., Kerfeld, C.A., Polívka, T. Excited state properties of canthaxanthin in cyanobacterial carotenoid-binding proteins HCP2 and HCP3. J. Phys. Chem. B, 124, 4896-4905, 2020. https://doi.org/10.1021/acs.jpcb.0c03137
16. Saccon, F., Durchan, M., Bína, D., Duffy, C.D.P., Ruban, A.V., Polívka, T. A protein environment-modulated energy dissipation channel in LHCII antenna complex. iScience, 23, 101430, 2020. https://doi.org/10.1016/j.isci.2020.101430
17. Šebelík, V., Kloz, M., Rebarz, M., Přeček, M., Kang, E-H., Choi, T-L., Christensen, R.L., Polívka, T. Spectroscopy and excited state dynamics of nearly infinite polyenes. Chem. Chem. Phys. 22, 17867-17879, 2020. https://doi.org/10.1039/d0cp02465a
18. Šebelík, V., West, R.G., Kuthanová Trsková, E., Kaňa, R., Polívka, T. Energy Transfer Pathways in the CAC Light-Harvesting Complex of Rhodomonas salina. BBA-Bioenergetics, 1861, 148280, 2020.https://doi.org/10.1016/j.bbabio.2020.148280/
19. Dominguez-Martin, M.A., Hammel, M., Gupta, S., Lechno-Yossef, S., Sutter, M., Rosenberg, D.J., Chen, Y., Petzold, C.J., Ralston, C., Polívka, T., Kerfeld, C.A. Structural analysis of a new carotenoid-binding protein: The C-terminal domain homolog of the OCP. Scientific Reports, 10, 15564, 2020. https://doi.org/10.1038/s41598-020-72383-y
20. Saccon, F., Durchan, M., Polívka, T., Ruban, A.V. The robustness of the terminal emitter site in major LHCII complexes controls xanthophyll function during photoprotection. Photobiol. Sci. 19, 1308-1318, 2020. https://doi.org/10.1039/d0pp00174k
21. Burnham, Ch. J., Futera, Z., Bacic, Z., English, N. J. Hydrogen intramolecular stretch redshift in the electrostatic environment of type II clathrate hydrates from Schrodinger equation treatment. Appl. Sci. 10, 8504, 2020. https://doi.org/10.3390/app10238504
22. 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. https://doi.org/10.1021/acs.jpclett.0c02686
23. Bould, J., Lang, , Kirakci, K., Cerdán, L., Roca-Sanjuan, D., Frances, A., Clegg, W., Waddell, P.G., Fuciman, M., Polívka, T., Londesborough, M.G.S. A Series of ultra-efficient blue borane fluorophores. Inorg. Chem., in press. https://doi.org/10.1021/acs.inorgchem.0c02277
24. V. Prysiazhnyi, F. Dycka, J. Kratochvil, J. Sterba, V. Stranak, Gas-aggregated Ag nanoparticles for detection of small molecules using LDI MS, Analytical and Bioanalytical Chemistry, 2020 https://doi.org/10.1007/s00216-019-02329-5
25. M. Smietana, M. Koba, P. Sezemsky, K. Szot-Karpinska, D. Burnat, V. Stranak, J. Niedziołka-Jonsson, R. Bogdanowicz, Simultaneous optical and electrochemical label-free biosensing with ITO-coated lossy-mode resonance sensor, Biosensors and Bioelectronics 154 (2020) 112050. https://doi.org/10.1016/j.bios.2020.112050
26. V. Prysiaznyi, F. Dycka, J. Kratochvil, V. Stranak, V. Popok, Effect of Ag Nanoparticle Size on Ion Formation in Nanoparticle Assisted LDI MS, Appl. Nano 1, (2020), 3–13; https://doi.org/10.3390/applnano1010002
27. Janik, P. Niedzialkowski, K. Lechowicz, M. Koba, P. Sezemsky, T. Ossowski, M. Smietana, Electrochemically directed biofunctionalization of a lossy-mode resonance optical fiber sensor, Optical Express 28, (2020), 15934-15942. https://doi.org/10.1364/OE.390780
28. B. Michalak, P. Sezemsky, V. Stranak, M. Smietana, Effect of thermal annealing on sensing properties of optical fiber sensors coated with indium tin oxide nano-overlays, Photonics Letters of Poland 12, (2020), 58-60. http://photonics.pl/PLP/index.php/letters/article/view/12-20
29. V. Prysiaznyi, F. Dycka, J. Kratochvil, V. Stranak, Gas aggregated Ag nanoparticles as the inorganic matrix for laser desorption/ionization mass spectrometry, J. Nanoparticle Res. 22, (2020) 351. https://doi.org/10.1007/s11051-020-05082-4

1. P. Niedziałkowski, W. Białobrzeska, D. Burnat, P. Sezemsky, V. Stranak, H. Wulff, T. Ossowski, R. Bogdanowicz, M. Koba, M. Smietana, Electrochemical performance of indium-tin-oxide-coated lossy-mode resonance optical fiber sensor, Sensors and Actuators B, (2019), 127043 https://doi.org/10.1016/j.snb.2019.127043
2. P. Sezemsky, V. Stranak, J. Kratochvil, M. Čada, R. Hippler, M. Hrabovsky, Z. Hubicka, Modified high frequency probe approach for diagnostics of highly reactive plasma, Plasma Sources Science and Technology, 28 (2019), 115009 https://doi.org/10.1088/1361-6595/ab506c
3. Dominguez-Martin, M.A., Polívka, T., Sutter, M., Ferlez, B. Lechno-Yossef, S., Montgomery, B., Kerfeld, C. Structural and spectroscopic characterization of HCP2. BBA-Bioenergetics, 1860, 414-424, 2019.
4. M. Smietana, P. Niedziałkowski, W. Białobrzeska, D. Burnat, P. Sezemsky, M. Koba, V. Stranak, K. Siuzdak, T. Ossowski, R. Bogdanowicz, Study on Combined Optical and Electrochemical Analysis Using Indium-tin-oxide-coated Optical Fiber Sensor, Electroanalysis, 31, 1 –8 (2019) https://doi.org/10.1002/elan.201800638
5. R. Hippler , M. Cada , V. Stranak, C. A. Helm , Z. Hubicka, Pressure dependence of singly and doubly charged ion formation in a HiPIMS discharge, J. Appl. Phys. 125, 013301 (2019) https://doi.org/10.1063/1.5055356
6. V. Prysiazhnyi, F. Dycka, J. Kratochvil, V. Stranak, P. Ksirova, Z. Hubicka, Silver nanoparticles for solvent-free detection of small molecules and mass-to-charge calibration of laser desorption/ionization mass spectrometry, Journal of Vacuum Science & Technology B, 37, 012906, (2019) https://doi.org/10.1116/1.5050878
7. Bína, D., Durchan, M., Kuznetsova, V., Vácha, F., Litvín, R., Polívka, T. Energy transfer dynamics in a red-shifted violaxanthin-chlorophyll a light harvesting complex. BBA-Bioenergetics, 1860, 111-120, 2019.
8. M. L. Machesky, M. K. Ridley, D. Biriukov, O. Kroutil, M. Předota: “Oxalic Acid Adsorption on Rutile: Experiments and Surface Complexation Modeling to 150 °C”, Langmuir 35, 7631-7640 (2019), https://doi.org/10.1021/acs.langmuir.8b03982
9. Balevičius, V., Wei, T., Di Tommaso, D., Abramavicius, D., Hauer, J., Polívka, T., Duffy, C. The full dynamics of energy relaxation in large organic molecules: from photo-excitation to solvent heating. Chemical Science, 10, 4792-4804, 2019.
10. P. Jelínek, M. Karlický, Pulse-beam heating of deep atmospheric layers, their oscillations and shocks modulating the flare reconnection, Astronomy and Astrophysics 625, A3, 2019. https://doi.org/10.1051/0004-6361/201935188
11. V. Prysiazhnyi, J. Kratochvíl, O. Kylián, V. Stranak, Reactive sputtering deposition of plasma polymerized nylon films with embedded NHx groups, Surface & Coatings Technology, 363, 120-127 (2019) https://doi.org/10.1016/j.surfcoat.2019.02.046
12. D. Biriukov, O. Kroutil, M. Kabeláč, M. K. Ridley, M. L. Machesky, M. Předota: “Oxalic Acid Adsorption on Rutile: Molecular Dynamics and ab Initio Calculations”, Langmuir 35, 7617-7630 (2019), https://doi.org/10.1021/acs.langmuir.8b03984
13. R. Hippler, M. Čada, V. Stranak, Z. Hubička, Ion formation in an argon and argon-oxygen gas mixture of a magnetron sputtering discharge, J. Phys. Commun., 3, 055011 (2019) https://doi.org/10.1088/2399-6528/ab1e82
14. M. Sobaszek, D. Burnat, P. Sezemsky, V. Stranak, R. Bogdanowicz, M. Koba, K. Siuzdak, M. Śmietana, Enhancing electrochemical properties of an ITO-coated lossy-mode resonance optical fiber sensor by electrodeposition of PEDOT:PSS, Optical Materials Express, 9, 3069-3078 (2019) https://doi.org/10.1364/OME.9.003069
15. Šebelík, V., Fuciman, M., West, R., Polívka, T. Time-resolved two-photon spectroscopy of carotenoids. Chem. Phys. 522, 171-177, 2019.
16. J. Kratochvíl, D. Kahoun, O. Kylián, J. Štěrba, T. Kretková, J. Kousal, J. Hanuš, J. Vaclová, V. Prysiazhnyi, P. Sezemský, P. Fojtíková, J. Lieskovská, H. Langhansová, I. Krakovský, V. Straňák, Nitrogen enriched C:H:N:O thin films for improved antibiotics doping, Applied Surface Science, (2019) https://doi.org/10.1016/j.apsusc.2019.07.135
17. Koliada I. , Balk H., Tušer M., Ptáček L., Kubečka J. (2019) Limitations of target detection in horizontal acoustic surveys of extremely shallow water bodies, Fisheries Research 218: 94-104. DOI: 10.1016/j.fishres.2019.05.005
18. Prysiazhnyi, V., Kratochvíl, J., Straňák, V., Tailored wettability of plasma polymers made of C-F, C-H, and N-H, Plasma processes and Polymers (2019) e1900076, DOI: 10.1002/ppap.201900076
19. Janczuk-Richter, M., Piestrzynska, M., Burnat, D., Sezemsky, P., Stranak, V., Bock, W.J., Bogdanowicz, R., Niedziolka-Jonsson, J., Smietana, M., Optical investigations of electrochemical processes using a long-period fiber grating functionalized by indium tin oxide, Sensors and actuators B-chemical (2019), DOI: 10.1016/j.snb.2018.10.001
    
20. A. K. Srivastava, S. K. Mishra, P. Jelínek, T. Samanta, H. Tian, V. Pant, P. Kayshap, D. Banerjee, J. G. Doyle, B. N. Dwivedi, On the Observations of Rapid Forced Reconnection in the Solar Corona, The Astrophysical Journal 887, 2, 2019. https://doi.org/10.3847/1538-4357/ab4a0c5
21. A. Marchioro, M. Bischoff, C. Lütgebaucks, D. Biriukov, M. Předota and S. Roke, Surface Characterization of Colloidal Silica Nanoparticles by Second Harmonic Scattering: Quantifying the Surface Potential and Interfacial Water Order, J. Phys. Chem. C 123, 20393−20404 (2019), DOI: 10.1021/acs.jpcc.9b05482
22. Staleva-Musto, H., West, R.G., Trathnigg, M., Bína, D., Litvín, R., Polívka, T. Carotenoid-chlorophyll energy transfer in the fucoxanthin-chlorophyll complex binding a fucoxanthin acyloxy derivative. Faraday Discussions, 216, 460-475, 2019.
23. Wei, T., Balevičius, V., Polívka, T. Ruban, A.V., Duffy, C.D.P. How carotenoid distortions determine optical properties: Lessons from the Orange Carotenoid Protein. Phys. Chem. Chem. Phys. 21 23187-23197, 2019.
24. Saccon, F., Durchan, M., Kaňa, R., Prášil, O., Ruban, A.V., Polívka, T. Spectroscopic properties of carotenoid triplet states in LHCII are independent of carotenoid composition. J. Phys. Chem. B, 123, 9312-9320, 2019.
25. Yamini K. Rao, Abhishek K. Srivastava, Pradeep Kayshap, and Bhola N. Dwivedi, Signatures of red-shifted foot points in the quiescent coronal loop system, Ann. Geophys., 2019, 765, 35
    
26. Yamini K. Rao, Abhishek K. Srivastava, Pradeep Kayshap, Klaus Wilhelm, and Bhola N. Dwivedi, Plasma Flows in the Cool Loop Systems, 2019, ApJ, 874,56 http://dx.doi.org/10.48550/arXiv.1902.05237
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1. Abhishek Kumar Srivastava, Krzysztof Murawski, Blażej Kuźma, Dariusz Patryk Wójcik, Teimuraz V. Zaqarashvili , Marco Stangalini , Zdzislaw E. Musielak, John Gerard Doyle, Pradeep Kayshap, and Bhola, N. Dwivedi, Confined pseudo-shocks as an energy source for the active solar corona, Nature Astronomy, 2018, 2, 951
2. Pech J., Novak M., Ptacek L., Kalova J.: Construction of Vertical Scanner for Laser Analysis of Gel Samples. IV International Conference on Information Technologies in Engineering Education (Inforino). 2018. DOI: 10.1109/INFORINO.2018.8581832
3. Hurbanova K., Nebesarova J., Ruzicka F., Krzyzanek V. 2018: The innovation of cryo-SEM freeze-fracturing methodology demonstrated on high pressure frozen biofilm. Micron, 110, 28-35.
4. Kučera D., Pernicová I., Kovalčík A., Koller M., Mullerova I., Sedláček P., Mravec F., Nebesářová J., Kalina M., Marová I., Krzyzanek V., Obruča S. 2018: Characterization of the promising poly(3-hydroxybutyrate) producing halophilic bacterium Halomonas halophila. Bioresour Technol, 256, 552-556
5. Ptáček, L.: Automatické rozpoznávání a identifikace ptáků, Automatic bird identification and verification. Skripta. Jihočeská Univerzita v Č. Budějovicích, Přírodovědecká fakulta. 2018, ISBN 978-80-7394-722-4.
6. Ptáček, L., Dolejší, M.: Měření a práce s audio analyzátorem Audio Precision. Technická příručka. Jihočeská Univerzita v Č. Budějovicích, Přírodovědecká fakulta. 2018, ISBN 978-80-7394-723-1.
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8. Kratochvíl, J. Štěrba, J. Lieskovská, H. Langhansová, A. Kuzminova, I. Khalakhan, O. Kylián,V. Straňák. Antibacterial effect of Cu/C:F nanocomposites deposited on PEEK substrates, Materials Letters, 230 (2018) 96-99
9. Stranak, R. Bogdanowicz,P. Sezemsky, H. Wulff, A. Kruth, M. Smietana,J. Kratochvil, M. Cada, Z. Hubicka. Towards high quality ITO coatings: The impact of nitrogen admixture in HiPIMS discharges, Surface & Coatings Technology 335 (2018) 126-133
10. Biriukov, O. Kroutil, M. Předota. Modeling of the Solid-Liquid Interface using Scaled Charges: Rutile (110), Physical Chemistry Chemical Physics 20, 23954 - 23966 (2018).https://doi.org/10.1039/C8CP04535F
11. McLaughlin, V. M. Nakariakov, M. Dominique, P. Jelínek, S. Takasao, Modelling Quasi-periodic Pulsations in Solar and Stellar Flares, Space Sci. Rev. 214, 45, 2018. https://doi.org/10.1007/s11214-018-0478-5
12. Murawski , P. Kayshap, A. K. Srivastava, D. J. Pascoe, P. Jelínek, B. Kuźma, V. Fedun, Magnetic swirls and associated kink waves in a solar chromospheric flux tube, Monthly Notices of the Royal Astronomical Society 474 (1), 77, 2018. https://doi.org/10.1093/mnras/stx2763
13. Šlouf, V., Keşan, G., Litvín, R., Swainsbury, D.J.K., Martin, E.C., Hunter, C.N., Polívka, T. Carotenoid to bacteriochlorophyll energy transfer in the RC-LH1-PufX complex from Rhodobacter sphaeroides containing the extended conjugation keto-carotenoid diketospirilloxanthin. Photosynth. Res. 135, 33-43, 2018.
14. West, R.G., Bína, D., Fuciman, M., Kuznetsova, V., Litvín, R., Polívka, T. Ultrafast multi-pulse transient absorption spectroscopy of fucoxanthin chlorophyll a protein from Phaeodactylum tricornutum. BBA-Bioenergetics, 1859, 357-365, 2018.
15. Staleva-Musto, H., Kuznetsova, V., West, R.G., Keşan, G., Minofar, B., Fuciman, M., Bína, D., Litvín, R., Polívka, T. Non-conjugated acyloxy group deactivates the intramolecular charge transfer state in the carotenoid fucoxanthin. J. Phys. Chem. B. 122, 2922-2930, 2018.
16. Hontani, Y., Kloz, M., Polívka, T., Shukla, M.K., Sobotka, R., Kennis, J.T.M. Molecular origin of photoprotection in oxygenic photosynthesis probed by femtosecond Raman spectroscopy. J. Phys. Chem. Lett. 9, 1788-1792, 2018.
17. West, R,G., Fuciman, M., Staleva-Musto, H., Šebelík, V., Bína, D., Durchan, M., Kuznetsova, V., Polívka, T. Equilibration dependence of fucoxanthin S1 and ICT signatures on polarity, proticity, and temperature by multi-pulse femtosecond absorption spectroscopy. J. Phys. Chem. B, 122, 7264-7276, 2018.
18. Brkljača, D. Namjesnik, J. Lützenkirchen,M. Předota, and T. Preočanin. Quartz/Aqueous Electrolyte Solution Interface: Molecular Dynamic Simulation and Interfacial Potential Measurements, J. Phys. Chem. C 122, 24025-24036 (2018). https://dx.doi.org/10.1021/acs.jpcc.8b04035

1. Kratochvíl, D. Kahoun, J. Štěrba, H. Langhansová, J. Lieskovská, P. Fojtíková, J. Hanuš, J. Kousal, O. Kylián,V. Straňák. Plasma polymerized C:H:N:O thin films for controlled release of antibiotic substances, Plasma processes and Polymers 15 (2018) e1700160
2. Dachev, M., Bína, D., Sobotka, R., Moravcová, L., Gardian, Z., Kaftan, D., Šlouf, V., Fuciman, M., Polívka, T., Koblížek, M. Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica. PloS Biol 15 (12), e2003943, 2017.
3. Stranak, V., Kratochvil, J., Olejnicek, J., Ksirova, P., Sezemsky, P., Cada, M., Hubicka, Z., Enhanced oxidation of TiO2 films prepared by high power impulse magnetron sputtering running in metallic mode, Journal of Applied Physics 121, 17, 2017.
4. P. Jelínek, M. Karlický, T. Van Doorsselaere, M. Bárta, Oscillations excited by plasmoids formed during magnetic reconnection in vertical gravitationally stratified current-sheet, The Astrophysical Journal847, 98, 2017. https://doi.org/10.3847/1538-4357/aa88a6
5. O. Kroutil, M. Předota, M. Kabeláč: “Force Field Parametrization of Hydrogenoxalate and Oxalate Anions with Scaled Charges”, J. Mol. Model.23:327, 2017. https://dx.doi.org/10.1007/s00894-017-3490-x
6. Šlouf, V., Kuznetsova, V., Fuciman, M., Bourcier de Carbon, C., Wilson, A., Kirilovsky, D., Polívka, T. Ultrafast spectroscopy tracks carotenoid configurations in the Orange and Red Carotenoid Proteins from cyanobacteria. Photosynth. Res. 131, 105, 2017.
7. Dvorakova, V., Ptacek, L., Hrouzkova, E., Muller, L., Sumbera, R.:  Mashona Mole-Rat Automatic Individual Identification Based on the Mating Calls, 2017, bioRxiv /2017/129452; doi: https://doi.org/10.1101/ 129452
8. Ptacek, L., Vanek, J., Eisner, J., Pruchova, A., Linhart, P., Muller, L., Jirotkova, D.: Bird-Adapted Filter for Avian Species and Individual Identification Systems Improvement. International Journal of Physical and Mathematical Sciences, Vol:4, No:6, 2017.
9. Llansola-Portoles, M.J., Sobotka, R., Kish, E., Shukla, M.K., Pascal, A.A., Polívka, T., Robert, B. Twisting a β-carotene, an adaptive trick from nature for dissipating energy during photoprotection. J. Biol. Chem. 292, 1396, 2017.
10. Kuznetsova, V., Southall, J., Cogdell, R.J., Fuciman, M., Polívka, T. Spectroscopic properties of the S1 state of linear carotenoids after excess energy excitation. Chem. Phys. Lett. 683, 448, 2017.
11. Kuznetsova, V., Chábera, P., Litvín, R., Polívka, T., Fuciman, M. Effect of isomerization on excited-state dynamics of the carotenoid fucoxanthin. J. Phys. Chem. B 121, 4438, 2017.
12. Šlouf, V., Keşan, G., Litvín, R., Swainsbury, D.J.K., Martin, E.C., Hunter, C.N., Polívka, T. Carotenoid to bacteriochlorophyll energy transfer in the RC-LH1-PufX complex from Rhodobacter sphaeroides containing the extended conjugation keto-carotenoid diketospirilloxanthin. Photosynth. Res. In press.

M. Předota, M. L. Machesky, D. J. Wesolowski, Molecular Origins of the Zeta Potential, Langmuir 32, 10189–10198, 2016.

M. Karlický, P. Jelínek, Quasi-periodic processes in the flare loop generated by sudden temperature enhancements at loop footpoints, Astronomy and Astrophysics, 590, A4, 2016. https://doi.org/10.1051/0004-6361/201527306

V. M. Nakariakov,
V. Pilipenko,
B. Heilig, P. Jelínek,
M. Karlický,
D. Y. Klimushkin, D. Y. Kolotkov,
D.-H. Lee,
G. Nisticò,
T. Van Doorsselaere,
G. Verth,
I.V. Zimovets, Magnetohydrodynamic Oscillations in the Solar Corona and Earth's Magnetosphere: Towards Consolidated Understanding, Space Sci. Rev., 200(1), 75, 2016. https://doi.org/10.1007/s11214-015-0233-0

O. Kroutil, M. Předota, and Z. Chval, Pt···H Nonclassical Interaction in Water-Dissolved Pt(II) Complexes: Coaction of Electronic Effects with Solvent-Assisted Stabilization, Inorg. Chem. 55, 3252–3264 (2016).

Keşan, G., Litvín, R., Bína, D., Durchan, M., Šlouf, V. Polívka, T. Efficient light-harvesting using non-carbonyl carotenoids: Energy transfer dynamics in the VCP complex from Nannochloropsis oceanica. Biochim. Biophys. Acta, 1857, 370-379, 2016.

Kvíčalová, Z., Alster, J., Johanning, S., Hofmann, E., Khoroshyy, P., Litvín, R., Bína, D., Polívka, T., Pšenčík, J. Triplet-triplet energy transfer from chlorophylls to carotenoids in two antenna complexes from dinoflagellate Amphidinium carterae. Biochim. Biophys. Acta, 1857, 341-349, 2016.

Adamec, F., Greco, J.A., LaFountain, A.M., Magdaong, N.M., Fuciman, M., Birge, R.R., Polívka, T., Frank, H.A. Spectroscopic investigation of a brightly colored psittacofulvin pigment from parrot feathers. Chem. Phys. Lett, 648, 195-199, 2016.

West, R., Keşan, G., Trsková, E., Sobotka, R., Kaňa, R., Fuciman, M., Polívka, T. Spectroscopic properties of the triple bond carotenoid alloxanthin. Chem. Phys. Lett. 653, 167-172, 2016.

Niedzwiedzki, D.M., Tronina, T., Liu, H., Staleva, H., Komenda, J., Sobotka, R., Blankenship, R.E., Polívka, T. Carotenoid-induced non-photochemical quenching in the cyanobacterial chlorophyll synthase-HliC/D complex. BBA-Bioenergetics, 1857, 1430-1439, 2016.

Kloz, M., Weissenborn, J., Polívka, T., Frank, H. A., Kennis, J.T.M. Spectral watermarking in Raman spectroscopy. Phys. Chem. Chem. Phys. 18, 14619-14628, 2016.

Balevičius, V., Abramavicius, D., Pour, A. G., Polívka, T., Hauer, J. A unified picture of S* in carotenoids. J. Phys. Chem. Lett. 7, 3347-3352, 2016.

Pinnola, A., Staleva-Musto, H., Capaldi, S., Ballottari, M., Bassi, R., Polívka, T. Electron transfer between carotenoid and chlorophyll contributes to quenching in the LHCSR1 protein from Physcomitrella patens.  BBA-Bioenergetics 1857, 1870-1878, 2016.

Kesan G., Durchan M., Tichý J., Minofar B., Kuznetsova V., Fuciman M., Šlouf V., Parlak C., Polívka T. Different Response of Carbonyl Carotenoids to Solvent Proticity Helps To Estimate Structure of the Unknown Carotenoid from Chromera velia. J. Phys. Chem. B 119, 12653-12663, 2015.

P. Jelínek, M. Karlický, K. Murawski,  Electric current filamentation at a non-potential magnetic null-point due to pressure perturbation, The Astrophysical Journal 812, 105, 2015.

P. Jelínek, A. K. Srivastava, K. Murawski, P. Kayshap, B.N. Dwivedi, Spectroscopic Observations and Modelling of Impulsive Alfven Waves Along a Polar Coronal Jet, Astronomy and Astrophysics 581, A131, 2015.

P. Jelínek, M. Karlický, Structured mass density slab as a waveguide of fast magnetoacoustic waves, Cent. Eur. Aphys. Bull 39 (1), 51, 2015.

Fuciman, M., Keşan, G., LaFountain, A., Frank, H.A., Polívka, T. Tuning the spectroscopic properties of aryl carotenoids by slight changes in structure. J. Phys. Chem. B. 119, 1457–1467, 2015.

Staleva, H., Komenda, J., Shukla, M., K., Šlouf, V., Kaňa, R., Polívka, T., Sobotka, R. Mechanism of photoprotection in the cyanobacterial ancestor of plant antenna proteins. Nat. Chem. Biol. 11, 287-291, 2015.

Kroutil, O., Chval, Z., Skelton, A. A., Předota, M. Computer Simulations of Quartz (101)–Water Interface over a Range of pH Values, J. Phys. Chem. C,119, 9274–9286, 2015.

Machesky, M. L., Předota, M.,  Ridley, M. K., Wesolowski, D. J.: Constrained Surface Complexation Modeling: Rutile in RbCl, NaCl, and NaCF3SO3 Media to 250 °C, J. Phys. Chem. C 119, 15204–15215, 2015.

Ptacek, L., Machlica, L., Linhart, P., Jaska, P., Muller, L.: Automatic Recognition of Bird Individual on the Open Set using as-is Recordings. Bioacoustic Journal, 2015. DOI: 10.1080/09524622.2015.1089524.

A. Majumdar, S.Ch. Das, V. Stranak, R. Hippler, Electronic Bond Structure of Carbon Nitride Thin Film Deposited by HiPIMS and dc Magnetron Plasma. J. Coat. Sci. Technol. 2, (2015), 28-37.

J. Alami, V. Stranak, A-P. Herrendorf, Z. Hubicka, R. Hippler, Design of magnetic field configuration for controlled discharge properties in highly ionized plasma, Plasma Sources Sci. Technol. 24 (2015) 045016.

P. Dytrych, P. Kluson, O. Solcova, S. Kment, V. Stranak, M. Cada, Z. Hubicka, Shape selective photoinduced electrochemical behavior of thin ZnO layers prepared by surfatron, Thin Solid Films 597, (2015), 131.

Staleva, H., Zeeshan, M., Chábera, P., Partali, V., Sliwka, H.R., Polívka, T. Ultrafast dynamics of long homologs of carotenoid zeaxanthin. J. Phys. Chem. A, 119, 11304-11312, 2015.

Durchan, M., Keşan, G., Šlouf, V., Fuciman, M., Staleva, H., Tichý, J., Litvín, R., Bína, D., Vácha, F., Polívka, T. Highly efficient energy transfer from a carbonyl carotenoid to chlorophyll-a in the main light harvesting complex of Chromera velia. Biochim. Biophys. Acta, 1837, 1748-1755, 2014.

Polívka, T., Hofmann, E. Structure-function relationship in peridinin-chlorophyll proteins. In: The Structural Basis of Biological Energy Generation (ed. M. F. Hohmann-Marriott). Vol. 39 of the series Advances in Photosynthesis and Respiration. p. 39-58, Springer, Dordrecht, The Netherlands, 2014.

Polívka, T., Frank, H. A. Spectroscopic investigation of carotenoids involved in nonphotochemical quenching. In: Nonphotochemical Quenching and Energy Dissipation in Plants, Algae and Cyanobacteria (ed. B. Demmig-Adams). Vol. 40 of the series Advances in Photosynthesis and Respiration. p. 203-227, Springer, Dordrecht, The Netherlands, 2014.

H. Mészárosová, M. Karlický, P. Jelínek, J. Rybák, Magnetoacoustic waves propagating along a dense slab and Harris current sheet and their wavelet spectra, The Astrophysical Journal 788, 44, 2014.

S. Parez, M. Předota, and M. Machesky: “Dielectric Properties of Water at Rutile and Graphite Surfaces: Effect of Molecular Structure”, J. Phys. Chem. C 118, 4818-4834 (2014).

P. Jelínek, M. Karlický, Magnetoacoustic waves in diagnostics of the flare current sheets, Astronomy and Astrophysics 537, A46, 2012.

P. Jelínek, M. Karlický, K. Murawski, Magnetoacoustic waves in a vertical flare current-sheet in a gravitationally stratified solar atmosphere, Astronomy and Astrophysics 546, A49, 2012.

Vredenberg, W., Durchan, M., Prášil, O.: The analysis of PS II photochemical aktivity using single and multi-turnover excitations. J. Photochem. Photobiol. B 107: 45-54, 2012.

Durchan, M., Tichý, J., Litvin, R., Šlouf, V., Gardian, Z., Hříbek, P., Vácha, F., Polívka, T.: Role of carotenoids in light-harvesting processes in an antenna protein from the chromophyte Xanthonema debile. J. Phys. Chem. B 116: 8880-8889, 2012.

Durchan, M., Fuciman, M., Šlouf, V., Keşan, G., Polívka, T.: Excited-state dynamics of monomeric and aggregated carotenoid 8´-apo-β-carotenal. J. Phys. Chem. A 116: 12330-12338, 2012.

S. Pařez and M. Předota: “Determination of Distance-dependent Viscosity of Mixtures in Parallel Slabs using Non-equilibrium Molecular Dynamics”, Phys. Chem. Chem. Phys. 14, 3640-3650 (2012).

I. Romancová, Z. Chval and M. Předota: “Influence of the Environment on the Specificity of the Mg(II) Binding to Uracil”, J. Phys. Chem. A 116, 1786−1793 (2012).

M. Kabeláč, O. Kroutil, M. Předota, F. Lankaš and M. Šíp: “Influence of a Charged Graphene Surface on the Orientation and Conformation of Covalently Attached Oligonucleotides: A Molecular Dynamics Study”, Phys. Chem. Chem. Phys. 14, 4217–4229 (2012).

D. J. Wesolowski, J. O. Sofo, A. V. Bandura, Z. Zhang, E. Mamontov, M. Předota, N. Kumar, J. D. Kubicki, P. R. C. Kent, L. Vlcek, M. L. Machesky, P. A. Fenter, P. T. Cummings, L. M. Anovitz, A. Skelton, J. Rosenqvist: “The Rutile (110)-Water Interface: A comment on “Structure and Dynamics of Liquid Water on Rutile TiO2(110)” by L.-M. Liu, C. Zhang, G. Thornton and A. Michaelides”, Phys. Rev. B 85, 167401 (2012).

Dall’Osto L., Holt N.E., Kaligotla S., Fuciman M., Cazzaniga S., Carbonera D., Frank H.A., Alric J., Bassi R.: Zeaxanthin Protects Plant Photosynthesis by Modulating Chlorophyll Triplet Yield in Specific Light-harvesting Antenna Subunits, J. Biol. Chem. DEC 2012, 287, 41820-41834.

Fuciman M., Enriquez M.M., Polívka T., Dall’Osto L., Bassi R., Frank H.A.: Role of Xanthophylls in Light Harvesting in Green Plants: A Spectroscopic Investigation of Mutant LHCII and Lhcb Pigment-Protein Complexes, J. Phys. Chem. B MAR 2012, 116, 3834-3849.

Maiuri M., Polli D., Brida D., Lueer L., LaFountain A.M., Fuciman M., Cogdell R.J., Frank H.A., Cerullo G.: Solvent-dependent activation of intermediate excited states in the energy relaxation pathways of spheroidene, Phys. Chem. Chem. Phys. 2012, 14, 6312-6319.

V. Šlouf, P. Chábera, J.D. Olsen, E.C. Martin, P. Qian, C.N. Hunter, T. Polívka. Photoprotection in a purple phototrophic bacterium mediated by oxygen-dependent alteration of carotenoid excited-state properties. Proc. Natl. Acad. Sci. U.S.A. 109, 8570–8575, 2012.

M. Karlický, P. Jelínek, H. Mészárosová, Magnetoacoustic waves in the narrowband dm-spikes sources, Astronomy and Astrophysics 529, A96, 2011.

P. Jelínek, G. Hensler, The Collisions of High Velocity Clouds with Galactic Halo, Comp. Phys. Commun. 182, 1784-1789, 2011.

Chábera, P., Durchan, M., Shih, P.M., Kerfeld, C.A., Polívka, T.: Excited-state properties of the 16 kDa red carotenoid protein from Arthrospira maxima. Biochim. Biophys. Acta 1807: 30-35, 2011.

M. Machesky, D. Wesolowski, J. Rosenqvist, M. Předota, L. Vlcek, M. Ridley, V. Kohli, Z. Zhang, P. Fenter, P. Cummings, S. Lvov, M. Fedkin, V. Rodriguez-Santiago, J. Kubicki, and A. Bandura: “Comparison of Cation Adsorption by Isostructural Rutile and Cassiterite”, Langmuir 27, 4585–4593 (2011).

Niedźwiedzki D., Fuciman M., Kobayashi M., Frank H.A., Blankenship R.E.: Ultrafast time-resolved spectroscopy of the light-harvesting complex 2 (LH2) from the photosynthetic bacterium Thermochromatium tepidum, Photosynth. Res. OCT 2011, 110, 49-60.

Bould J., Base T., Londesborough M.G.S., Oro L.A., Macias R., Kennedy J.D., Kubát P., Fuciman M., Polívka T., Lang K.: Reversible Capture of Small Molecules On Bimetallaborane Clusters: Synthesis, Structural Characterization, and Photophysical Aspects, Inorg. Chem. AUG 2011, 50, 7511-7523.

Niedźwiedzki D.M., Fuciman M., Frank H.A., Blankenship R.E.: Energy transfer in an LH4-like light harvesting complex from the aerobic purple photosynthetic bacterium Roseobacter denitrificans, BBA-Bioenergetics MAY 2011, 1807, 518-528.

Fuciman M., Enriquez M.M., Kaligotla S., Niedźwiedzki D.M., Kajikawa T., Aoki K., Katsumura S., Frank H.A.: Singlet and Triplet State Spectra and Dynamics of Structurally Modified Peridinins, J. Phys. Chem. B APR 2011, 115, 4436-4445.

Zhang Y., LaFountain A.M., Magdaong N., Fuciman M., Allen J.P., Frank H.A., Rusling J.F.: Thin Film Voltammetry of Wild Type and Mutant Reaction Center Proteins from Photosynthetic Bacteria, J. Phys. Chem. B MAR 2011, 115, 3226-3232.

Kubát P., Šebera J., Záliš S., Langmaier J., Fuciman M., Polívka T., Lang K.: Charge transfer in porphyrin-calixarene complexes: ultrafast kinetics, cyclic voltammetry, and DFT calculations, Phys. Chem. Chem. Phys. 2011, 13, 6916-6923.

V. Šlouf, S.P. Balashov, J.K. Lanyi, T. Pullerits, T. Polívka. Carotenoid response to retinal excitation and photoisomerization dynamics in xanthorhodopsin. Chem. Phys. Lett. 516, 96–101, 2011.

P. Jelínek, M. Karlický, Impulsively Generated Wave Trains in a Solar Coronal Loop, IEEE Trans. Plasma Sci. 38, No. (9), 2243-2248, 2010.

Durchan, M., Herbstová, M., Fuciman, M., Gardian, Z., Vácha, F., Polívka, T.: Carotenoids in energy transfer and quenching processes in Pcb and Pcb-PS I complexes from Prochlorothrix hollandica. J. Phys. Chem. B 114: 9275-9282, 2010.

M. Předota, I. Nezbeda, and S. Pařez: “Coarse-grained potential for interaction with a spherical colloidal particle and planar wall”, Collect. Czech. Chem. Commun. 75, 527-545 (2010).

Fuciman M., Chábera P., Župčanová A., Hříbek P., Arellano J.B., Vácha F., Pšenčík J., Polívka T.: Excited state properties of aryl carotenoids, Phys. Chem. Chem. Phys. 2010, 12, 3112-3120.

Enriquez M.M., Fuciman M., LaFountain A.M., Wagner N.L., Birge R.R., Frank H.A.: The Intramolecular Charge Transfer State in Carbonyl-Containing Polyenes and Carotenoids, J. Phys. Chem. B OCT 2010, 114, 12416-12426.

Chábera P., Fuciman M., Naqvi K.R., Polívka T.: Ultrafast dynamics of hydrophilic carbonyl carotenoids - Relation between structure and excited-state properties in polar solvents, Chem. Phys. JUL 2010, 373, 56-64.

Enriquez M.M., LaFountain A.M., Budarz J., Fuciman M., Gibson G.N., Frank H.A.: Direct determination of the excited state energies of the xanthophylls diadinoxanthin and diatoxanthin from Phaeodactylum tricornutum, Chem. Phys. Lett. JUN 2010, 493, 353-357.

P. Jelínek, M. Karlický, Computational Study of Impulsively Generated Waves in a Solar Coronal Loop, Eur. Phys. J. D 54, 305-311, 2009.

P. Bartoš, J. Blažek, P. Jelínek, P. Špatenka, Hybrid Computer Simulations: Electrical Charging of Dust Particles in Low-Temperature Plasma, Eur. Phys. J. D 54, 319-323, 2009.

Pavlovič, A., Demko, V., Durchan, M., Hudák, J.: Feeding with aminolevulinic acid increased chlorophyll content in Norway spruce (Picea abies) in the dark. Photosynthetica 47: 631-634, 2009.

Pavlovič, A., Slováková, Ľ., Demko, V., Durchan, M., Mikulová, K., Hudák, J.: Chlorophyll biosynthesis and chloroplast development in etiolated seedlings of Ginkgo biloba L. Photosynthetica 47: 510-516, 2009.

Vredenberg, W., Durchan, M., Prášil, O.: Photochemical and photoelectrochemical quenching of chlorophyll fluorescence in photosystem II. Biochim. Biophys. Acta 1787: 1468-1478, 2009.

Chábera P., Fuciman M., Hříbek P., Polívka T.: Effect of carotenoid structure on excited-state dynamics of carbonyl carotenoids, Phys. Chem. Chem. Phys. 2009, 11, 8795-8803.

Polívka, T., Pšenčík, J., Kroh, P., Engst, D., Prášil, O., Falkowski, P.G., Hála, J. Hole-burning study of energy transfer in antenna proteins of Dunaliella tertiolecta affected by iron-limitation. Mol. Cryst. Liq. Cryst. 291, 111, 1996.

Engst, D., Kroh, P., Polívka, T., Pšenčík, J., Nedbal L., Hála, J.: Hole burning and low temperature absorption and fluorescence spectroscopy of algae affected by UV-B stress, Mol. Cryst. Liq. Cryst. 291, 103, 1996.

Kroh, P., Pšenčík, J., Polívka, T., Engst, D., Hála, J.: Laser induced hole filling in bacteriochlorophyll d monomers and aggregates of  green sulphur photosynthetic bacteria antennae, Mol. Cryst. Liq. Cryst. 291, 201, 1996

Polívka, T., Kroh, P., Pšenčík, J., Engst, D., Komenda, J., Hála, J