Mgr. Markéta Paloncýová, Ph.D.

Tel: 58 563 4423, E-mail:, Room: 3.004

Research interests



International experience




  1. Langer M, Paloncýová M, Medved' M, Pykal M, Nachtigallová D, Shi B, Aquino AJA, Lischka H, Otyepka M: Progress and challenges in understanding of photoluminescence properties of carbon dots based on theoretical computations. Appl. Mater. Today, 22, 100924, 2021. (DOI)


  1. Langer M, Paloncýová M, Medved' M, Otyepka M: Molecular Fluorophores Self-Organize into C-Dot Seeds and Incorporate into C-Dot Structures. J. Phys. Chem. Lett., 11(19), 8252–8258, 2020. (DOI)
  2. Paloncýová M, Aniander G, Larsson E, Knippenberg S: Cyanine dyes with tail length asymmetry enhance photoselection: A multiscale study on DiD probes in a liquid disordered membrane. Spectrochim. Acta, Part A, 224, 117329, 2020. (DOI)
  3. Paloncýová M, Tornmalm J, Sen S, Piguet J, Widengren J, Knippenberg S: The Photoisomerization of DiD: Molecular Dynamics Calculations Reveal the Influence of the Tail Lengths. J. Phys. Chem. C, 124(10), 5829-5837, 2020. (DOI)
  4. Siddique F, Langer M, Paloncýová M, Medved M, Otyepka M, Nachtigallová D, Lischka H, Aquino AJ: Conformational Behavior and Optical Properties of a Fluorophore Dimer as Model of Luminescent Centers in Carbon Dots. J. Phys. Chem. C, 124(26), 14327–14337, 2020. (DOI)


  1. Kosina P, Paloncýová M, Svobodová AR, Zálešák B, Biedermann D, Ulrichová J, Vostálová J: Dermal Delivery of Selected Polyphenols from Silybum marianum. Theoretical and Experimental Study Molecules , 24(1), 61, 2019. (DOI)


  1. Knippenberg S, Fabre G, Osella S, Di Meo F, Paloncýová M, Ameloot M, Trouillas P: Atomistic Picture of Fluorescent Probes with Hydrocarbon Tails in Lipid Bilayer Membranes: An Investigation of Selective Affinities and Fluorescent Anisotropies in Different Environmental Phases. Langmuir, 34(30), 9072-9084, 2018. (DOI)
  2. Paloncýová M, Langer M, Otyepka M: Structural Dynamics of Carbon Dots in Water and N,N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations. J. Chem. Theory Comput., 14(4), 2076–2083, 2018. (DOI)
  3. Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M: Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem, 183, 117-136, 2018. (DOI)


  1. Navrátilová V, Paloncýová M, Berka K, Mise S, Haga Y, Matsumura C, Sakaki T, Inui H, Otyepka M: Molecular Insights into the Role of a Distal F240A Mutation that Alters CYP1A1 Activity towards Persistent Organic Pollutants. Biochim. Biophys. Acta, Gen. Subj., 1861(11), 2852-2860, 2017. (DOI)


  1. Di Meo F, Fabre G, Berka K, Ossman T, Chantemargue B, Paloncýová M, Marquet P, Otyepka M, Trouillas P: In Silico Pharmacology: Drug Membrane Partitioning and Crossing. Pharmacol. Res., 111, 471–486, 2016. (DOI)
  2. Navrátilová V, Paloncýová M, Berka K, Otyepka M: Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4. J. Phys. Chem. B, 120(43), 11205–11213, 2016. (DOI)
  3. Paloncýová M, Navrátilová V, Berka K, Laio A, Otyepka M: Role of Enzyme Flexibility in Ligand Access and Egress to Active Site – Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4 J. Chem. Theory Comput., 12(4), 2101–2109, 2016. (DOI)
  4. Scott EE, Wolf CR, Otyepka M, Humphreys SC, Reed JR, Henderson CJ, McLaughlin LA, Paloncýová M, Navrátilová V, Berka K, Anzenbacher P, Dahal UP, Barnaba C, Brozik JA, Jones JP, Estrada DF, Laurence JS, Park JW, Backes WL: The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function. Drug. Metab. Dispos., 44(4), 576-590, 2016. (DOI)


  1. Fabre G, Bayach I, Berka K, Paloncýová M, Starok M, Rossi C, Duroux J, Otyepka M, Trouillas P: Synergism of antioxidant action of vitamins E, C and quercetin is related to formation of molecular associations in biomembranes. Chem. Commun., 51(36), 7713-7716, 2015. (DOI)
  2. Navrátilová V, Paloncyová M, Kajšová M, Berka K, Otyepka M: Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. J. Chem. Inf. Model., 55(3), 628–635, 2015. (DOI)
  3. Paloncýová M, Vávrová K, Sovová Ž, DeVane R, Otyepka M, Berka K: Structural Changes in Ceramide Bilayers Rationalize Increased Permeation through Stratum Corneum Models with Shorter Acyl Tails. J. Phys. Chem. B., 119(30), 9811-9819, 2015. (DOI)


  1. Paloncýová M, DeVane R, Murch B, Berka K, Otyepka M: Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region. J. Phys. Chem. B, 118(4), 1030-1039, 2014. (DOI)
  2. Paloncýová M, DeVane RH, Murch BP, Berka K, Otyepka M: Rationalization of Reduced Penetration of Drugs through Ceramide Gel Phase Membrane. Langmuir, 30(46), 13942-13948, 2014. (DOI)
  3. Paloncýová M, Fabre G, DeVane RH, Trouillas P, Berka K, Otyepka M: Benchmarking of Force Fields for Molecule–Membrane Interactions. J. Chem. Theory Comput., 10(9), 4143-4151, 2014. (DOI)


  1. Berka K, Paloncýová M, Anzenbacher P, Otyepka M: Behavior of Human Cytochromes P450 on Lipid Membranes. J. Phys. Chem. B, 117(39), 11556-11564, 2013. (DOI)
  2. Paloncýová M, Berka K, Otyepka M: Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers. J. Phys. Chem. B, 117(8), 2403-2410, 2013. (DOI)
  3. Podloucká P, Berka K, Fabre G, Paloncýová M, Duroux J, Otyepka M, Trouillas P: Lipid Bilayer Membrane Affinity Rationalizes Inhibition of Lipid Peroxidation by a Natural Lignan Antioxidant. J. Phys. Chem. B, 117(17), 5043-5049, 2013. (DOI)


  1. Paloncýová M, Berka K, Otyepka M: Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. J. Chem. Theory Comput., 8(4), 1200-1211, 2012. (DOI)