• Marian Marton, Martin Konôpka, Jozef Dobrovodský, Dušan Vaňa, Sanath J. Shetty, Pavel Veis, Pavol Michniak, Vlastimil Reháček, Miroslav Behúl, Ľubomír Vančo, Marian Vojs, Alexander Kromka:
  Role of oxygen in suppression of boron incorporation in diamond films: Surface reactions insight, Applied Surface Science 709, 163832 (2025).
  
• Yuuki Adachi, Ján Brndiar, Martin Konôpka, Robert Turanský, Qiang Zhu, Huan Fei Wen, Yasuhiro Sugawara, Lev Kantorovich, Ivan Štich, Yan Jun Li:
  Tip-activated single-atom catalysis: CO oxidation on Au adatom on oxidized rutile TiO2 surface, Science Advances 9, eadi4799 (2023).
  
• Quanzhen Zhang, Ján Brndiar, Martin Konôpka, Huan Fei Wen, Yuuki Adachi, Masato Miyazaki, Robert Turanský, Rui Xu, Zhi Hai Cheng, Yasuhiro Sugawara, Ivan Štich, Yan Jun Li:
  Unraveling the Charge States of Au Nanoclusters on an Oxygen-Rich Rutile TiO2(110) Surface and Their Triboelectrification Overturn by nc-AFM and KPFM, J. Phys. Chem. C 125, 27607 (2021).
  
• Quanzhen Zhang, Ján Brndiar, Yuuki Adachi, Martin Konôpka, Huan Fei Wen, Masato Miyazaki, Yasuhiro Sugawara, Rui Xu, Zhi Hai Cheng, Hongqian Sang, Yan Jun Li, Lev Kantorovich, Ivan Štich:
  Voltage- and Redox State-Triggered Oxygen Adatom Conductance Switch, J. Phys. Chem. C 125, 26801 (2021).
  
• Katarína Gmucová, Martin Konôpka, Karol Vegso, Peter Bokes, Vojtech Nádaždy, Tomáš Váry:
  Correlation between Molecular Stereostructure, Film Microstructure, and Electronic Structure of Polyfluorene and Fluorene Based Alternating Copolymers F8BT and PFO−DBT, J. Phys. Chem. C 125, 8045 (2021).
  
• Martin Konôpka, Peter Dieška:
  Twin lead ballistic conductor based on nanoribbon edge transport, Physica E 97, 259 (2018).
  See also arXiv:1701.03815 (cond-mat).
  
• Martin Konôpka:
  Conductance of graphene flakes contacted at their corners, J. Phys.: Condens. Matter 27, 435005 (2015).
  See also arXiv:1509.05261 (cond-mat).
• Martin Konôpka, Peter Bokes:
  Wavepacket representation of leads for efficient simulations of time-dependent electronic transport, Phys. Rev. B 89, 125424 (2014).
  See also arXiv:1403.2223 (cond-mat).
• Martin Konôpka, Peter Bokes:
  Stroboscopic wave packet description of time-dependent currents through ring-shaped nanostructures, Eur. Phys. J. B 86, 114 (2013).
  See also arXiv:1301.6664 (cond-mat).
• Robert Turanský, Martin Konôpka, Nikos L. Doltsinis, Ivan Štich, Dominik Marx:
  Switching of functionalized azobenzene suspended between gold tips by mechanochemical, photochemical, and opto-mechanical means, Physical Chemistry Chemical Physics 12, 13922-13932 (2010).
• Robert Turanský, Martin Konôpka, Nikos L. Doltsinis, Ivan Štich, Dominik Marx:
  Optical, Mechanical, and Opto-Mechanical Switching of Anchored Dithioazobenzene Bridges, ChemPhysChem 11, 345-348 (2010).
• Martin Konôpka, Robert Turanský, Matúš Dubecký, Dominik Marx, Ivan Štich:
  Molecular Mechanochemistry Understood at the Nanoscale: Thiolate Interfaces and Junctions with Copper Surfaces and Clusters, J. Phys. Chem. C 113, 8878-8887 (2009).
• Martin Konôpka, Robert Turanský, Nikos L. Doltsinis, Dominik Marx, Ivan Štich:
  Organometallic Nanojunctions Probed by Different Chemistries: Thermo-, Photo-, and Mechano-Chemistry, Advances in Solid State Physics 48, 219-235 (Berlin Heidelberg: Springer Verlag London, 2009).
• Martin Konôpka, Robert Turanský, Joachim Reichert, Harald Fuchs, Dominik Marx, Ivan Štich:
  Mechanochemistry and Thermochemistry are Different: Stress-Induced Strengthening of Chemical Bonds, Phys. Rev. Lett. 100, 115503-1-4 (2008).
• Miroslava Diešková, Martin Konôpka, Peter Bokes:
  Atomic and electronic structure of ultra-thin Al/AlO$_x$/Al interfaces, Surf. Sci. 601, 4134-4137 (2007).
  See also arXiv:cond-mat/0608718.
• Martin Konôpka, Roger Rousseau, Ivan Štich, Dominik Marx:
  Electronic Origin of Disorder and Diffusion at a Molecule-Metal Interface: Self-Assembled Monolayers of CH$_3$S on Cu(111), Phys. Rev. Lett. 95, 096102-1-4 (2005).
• Martin Konôpka, Roger Rousseau, Ivan Štich, Dominik Marx:
  Detaching Thiolates from Copper and Gold Clusters: Which Bonds to Break?, J. Am. Chem. Soc. 126, 12103-12111 (2004).
• Martin Konôpka, Ivan Štich, Kiyoyuki Terakura:
  Structure and dynamics of atomic hydrogen on NiAl(110), Phys. Rev. B 65, 125418-1-7 (2002).


some of my older papers (from my PhD, on Quantum optics in photonics crystals):

• Martin Konôpka, Vladimír Bužek:
  Entangling atoms in photonic crystals, Eur. Phys. J. D 10, 285-293 (2000).
• Martin Konôpka:
  Stimulated emission from an atom in a photonic crystal, Phys. Rev. A 60 (5), 4183-4186 (1999).
• Martin Konôpka:
  Thermally induced decay of the atom in a photonic bandgap reservoir, J. mod. Opt. 46 (1), 15-33 (1999).
• Vladimír Bužek, Martin Konôpka:
  Dynamics of open systems governed by the Milburn equation, Phys. Rev. A 58 (3), 1735-1739 (1998).
• Martin Konôpka, Igor Jex:
  Exact solutions for nonlinear hamiltonians, Czech. J. Phys. 48, 1537 (1998).