Publikační činnost zaměstnanců ústavu

List of publications of the members of the Institute of Physics and Biophysics (2009 - to date)


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.

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.

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.


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.


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).


M. Karlický, H. Mészárosová,  P. Jelínek, Radio fiber bursts and fast magnetoacoustic wave trains, Astronomy and Astrophysics 550, A1, 2013.

P. Jelínek, K. Murawski, Numerical simulations of magnetoacoustic-gravity waves in the solar coronal curved magnetic field lines structure, Monthly Notices of the Royal Astronomical Society 435, 2347-2354, 2013.

Fuciman, M., Durchan, M., Šlouf, V., Keşan, G., Polívka, T.: Excited-state dynamics of astaxanthin aggregates. Chem. Phys. Lett. 568-569: 21-25, 2013.

M. Lísal, M. Předota and J. K. Brennan: “Molecular-Level Simulations of Chemical Reaction Equilibrium and Diffusion in Slit and Cylindrical Nanopores: Model Dimerization Reactions”, Mol. Sim. 39, 1103–1120, (2013).

M. Předota, M. L. Machesky, D. J. Wesolowski, and P. T. Cummings: “Electric Double Layer at the Rutile (110) Surface. 4. Effect of Temperature and pH on the Adsorption and Dynamics of Ions”, J. Phys. Chem. C 117, 22852-22866 (2013).

Šlouf V., Fuciman M., Johanning S., Hofmann E., Frank H.A., Polívka T.: Low-temperature time-resolved spectroscopic study of the major light-harvesting complex of Amphidinium carterae, Photosynth. Res. NOV 2013, 117 SI, 257-265.

Šlouf V., Fuciman M., Dulebo A., Kaftan D., Koblížek M., Frank H.A., Polívka T.: Carotenoid Charge Transfer States and Their Role in Energy Transfer Processes in LH1-RC Complexes from Aerobic Anoxygenic Phototrophs, J. Phys. Chem. B SEP 2013, 117 SI 10987-10999.

Kirakci K., Kubát P., Langmaier J., Polívka T., Fuciman M., Fejfarová K., Lang K.: A comparative study of the redox and excited state properties of (nBu4N)2[Mo6X14] and (nBu4N)2[Mo6X8(CF3COO)6] (X = Cl, Br, or I), Dalton Trans. 2013, 42, 7224-7232.


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.