1. N. Oinonen, A. V. Yakutovich, A. J. Gallardo Caparrós, M. Ondráček, P. Hapala, O. Krejčí
    Advancing scanning probe microscopy simulations: A decade of development in probe-particle models
    Computer Physics Communications 305 (2024) 109341(1)-109341(12).
  2. C. G. Ayani, M. Bosnar, F. Calleja, A. P. Solé, O. Stetsovych, I. M. Ibarburu, C. Rebanal, M. Garnica, R. Miranda, M. M. Otrokov, M. Ondráček, P. Jelínek, A. Arnau, A. L. V. de Parga
    Unveiling the Interlayer Interaction in a 1H/1T TaS2 van der Waals Heterostructure
    Nano Letters 24 (2024) 10805-10812.
  3. A. Cahlík, M. Ondráček, Christian Wäckerlin, Andres Pinar Solé, Olivier Siri, M. Švec, P. Jelínek
    Light-Controlled Multiconfigurational Conductance Switching in a Single 1D Metal-Organic Wire
    ACS Nano 1 (2024) 1-9.
  4. B. J. Mallada Faes, M. Ondráček, M. Lamanec, A. J. Gallardo Caparrós, A. Jiménez-Martín, B. De La Torre Cerdeño, P. Hobza, P. Jelínek
    Visualization of π-hole in molecules by means of Kelvin probe force microscopy
    Nature Communications 14 (2023) 4954 -4954 .
  5. F. Frezza, A. Sánchez-Grande, M. Ondráček, M. Vondráček, Q. Chen, O. Stetsovych, V. Villalobos-Vilda, E. Tosi, F. J. Palomares, M. F. López, C. Sánchez-Sánchez, K.-H. Ernst, J. A. Martín-Gago, J. Honolka, P. Jelínek
    Epitaxial growth and characterization of SnSe phases on Au(111)
    Journal of Physics: Condensed Matter 35 (2023) 335001(1)-335001(9).
  6. Ch. Wäckerlin, A. Cahlík, J. Goikoetxea, O. Stetsovych, D. Kývala, J. R. López Roso Redondo, M. Švec, B. Delley, M. Ondráček, A. Pinar Solé, M. Blanco-Rey, J. Kolorenč, A. Arnau, P. Jelínek
    Role of the Magnetic Anisotropy in Atomic-Spin Sensing of 1D Molecular Chains
    ACS Nano 16 (2022) 16402-16413.
  7. B. Lowe, J. Hellerstedt, A. Matěj, P. Mutombo, D. Kumar, M. Ondráček, P. Jelínek, A. Schiffrin
    Selective Activation of Aromatic C−H Bonds Catalyzed by Single Gold Atoms at Room Temperature
    Journal of the American Chemical Society 144 (2022) 21389-21397.
  8. V. M. Santhini, Ch. Wäckerlin, A. Cahlík, M. Ondráček, S. Pascal, A. Matěj, O. Stetsovych, P. Mutombo, P. Lazar, O. Siri, P. Jelínek
    1D Coordination π–d Conjugated Polymers with Distinct Structures Defined by the Choice of the Transition Metal: Towards a New Class of Antiaromatic Macrocycles
    Angewandte Chemie International Edition 60 (2021) 439-445.
  9. V. M. Santhini, O. Stetsovych, M. Ondráček, J. I. Mendieta Moreno, P. Mutombo, B. De La Torre Cerdeño, M. Švec, J. Klívar, I. G. Stará, H. Vázquez, I. Starý, P. Jelínek
    On-Surface Synthesis of Polyferrocenylene and its Single-Chain Conformational and Electrical Transport Properties
    Advanced Functional Materials 31 (2021) 2006391(1)-2006391(11).
  10. J. Su, W. Fan, P. Mutombo, X. Peng, Sh. Song, M. Ondráček, P. Golub, J. Brabec, L. Veis, M. Telychko, P. Jelínek, J. Wu, J. Lu
    On-Surface Synthesis and Characterization of [7]Triangulene Quantum Ring
    Nano Letters 21 (2021) 861-867.
  11. J. Berger, M. Ondráček, O. Stetsovych, P. Malý, P. Holý, J. Rybáček, M. Švec, I.G. Stará, T. Mančal, I. Starý, P. Jelínek
    Quantum dissipation driven by electron transfer within a single molecule investigated with atomic force microscopy
    Nature Communications 11 (2020) 1337-1-1337-10.
  12. K. Scheil, M. Gruber, M. Ondráček, R. Berndt
    Force Spectroscopy of Iron Tetraphenylporphyrin Molecules with Cl Tips
    Journal of Physical Chemistry C 124 (2020) 26889-26896.
  13. B. Cirera, B. De La Torre Cerdeño, D. Moreno, M. Ondráček, R. Zbořil, R. Miranda, P. Jelínek, D. Écija
    On-Surface Synthesis of Gold Porphyrin Derivatives via a Cascade of Chemical Interactions: Planarization, Self-Metalation, and Intermolecular Coupling
    Chemistry of Materials 31 (2019) 3248-3256.
  14. M. Ondráček, P. Hapala, M. Švec, P. Jelínek
    Imaging Charge Distribution Within Molecules by Scanning Probe Microscopy
    Chapter 16 in Kelvin Probe Force Microscopy, eds. S. Sadewasser & T. Glatzel, Springer Series in Surface Sciences, vol. 65, Springer, Cham, 2018, pp. 499-518
  15. P. Brázda, P. Mutombo, M. Ondráček, C. Antunes Correa, J. Kopeček, L. Palatinus
    Silicene-terminated surface of calcium and strontium disilicides: properties and comparison with bulk structures by computational methods
    Philosophical Magazine 98 (2018) 1131-1150.
  16. J. Peng, J. Guo, P. Hapala, D. Cao, R. Ma, B. Cheng, L. Xu, M. Ondráček, P. Jelínek, E. Wang, Y. Jiang
    Weakly perturbative imaging of interfacial waterwith submolecular resolution by atomic forcemicroscopy
    Nature Communications 9 (2018) 122(1)-122(7).
  17. O. Krejčí, P. Hapala, M. Ondráček, P. Jelínek
    Principles and simulations of high-resolution STM imaging with a flexible tip apex
    Physical Review B 95 (2017) 045407(1)-045407(9).
  18. J. Onoda, M. Ondráček, P. Jelínek, Y. Sugimoto
    Electronegativity determination of individual surface atoms by atomic force microscopy
    Nature Communications 8 (2017) 15155(1)-15155(6).
  19. P. Hapala, M. Švec, O. Stetsovych, N. J. van der Heijden, M. Ondráček, J. van der Lit, P. Mutombo, I. Swart, P. Jelínek
    Mapping the electrostatic force field of single molecules from high-resolution scanning probe images
    Nature Communications 7 (2016) 11560(1)-11560(8).
  20. M. Ondráček, P. Hapala, P. Jelínek
    Charge-state dynamics in electrostatic force spectroscopy
    Nanotechnology 27 (2016) 274005(1)-274005(13).
  21. K. Iwata, Sh. Yamazaki, P. Mutombo, P. Hapala, M. Ondráček, P. Jelínek, Y. Sugimoto
    Chemical structure imaging of a single molecule by atomic force microscopy at room temperature
    Nature Communications 6 (2015) 7766(1)-7766(6).
  22. M. Corso, M. Ondráček, Ch. Lotze, P. Hapala, K. J. Franke, P. Jelínek, J. I. Pascual
    Charge Redistribution and Transport in Molecular Contacts
    Physical Review Letters 115 (2015) 136101(1)-136101(5).
  23. M. Telychko, P. Mutombo, P. Merino, P. Hapala, M. Ondráček, F.C. Bocquet, J. Sforzini, O. Stetsovych, M. Vondráček, P. Jelínek, M. Švec
    Electronic and Chemical Properties of Donor, Acceptor Centers in Graphene
    ACS Nano 9 (2015) 9180-9187.
  24. F. Albrecht, J. Repp, M. Fleischmann, M. Scheer, M. Ondráček, P. Jelínek
    Probing Charges on the Atomic Scale by Means of Atomic Force Microscopy
    Physical Review Letters 115 (2015) 076101-1-076101-5.
  25. P. Hapala, M. Ondráček, O. Stetsovych, M. Švec, P. Jelínek
    Simultaneous nc-AFM/STM Measurements with Atomic Resolution
    Noncontact Atomic Force Microscopy vol. 3
  26. M. Švec, P. Hapala, M. Ondráček, P. Merino, M. Blanco-Rey, P. Mutombo, M. Vondráček, Y. Polyak, J. A. Martín Gago, P. Jelínek
    Silicene versus two-dimensional ordered silicide: Atomic and electronic structure of Si-(√19×√19)R23.4◦/Pt(111)
    Physical Review B 89 (2014) 201412(1)-201412(5).
  27. M. Telychko, P. Mutombo, M. Ondráček, P. Hapala, F.C. Bocquet, J. Kolorenč, M. Vondráček, P. Jelínek, M. Švec
    Achieving High-Quality Single-Atom Nitrogen Doping of Graphene/SiC(0001) by Ion Implantation and Subsequent Thermal Stabilization
    ACS Nano 8 (2014) 7318-7324.
  28. J. Onoda, M. Ondráček, A, Yurtsever, P. Jelínek, Y. Sugimoto
    Initial and secondary oxidation products on the Si(111)-(7x7) surface identified by atomic force microscopy and first principles calculations
    Applied Physics Letters 104 (2014) 133107(1)-133107(4).
  29. A. J. Weymouth, D. Meuer, P. Mutombo, T. Wutscher, M. Ondráček, P. Jelínek, F. J. Giessibl
    Atomic Structure Affects the Directional Dependence of Friction
    Physical Review Letters 111 (2013) 126103(1)-126103(4).
  30. Y. Sugimoto, M. Ondráček, M. Abe, P. Pou, S. Morita, R. Pérez, F. Flores, P. Jelínek
    Quantum Degeneracy in Atomic Point Contacts Revealed by Chemical Force and Conductance
    Physical Review Letters 111 (2013) 106803(1)-106803(5).
  31. Y. Sugimoto, A. Yurtsever, M. Abe, S. Morita, M. Ondráček, P. Pou, R. Pérez, P. Jelínek
    Role of Tip Chemical Reactivity on Atom Manipulation Process in Dynamic Force Microscopy
    ACS Nano 7 (2013) 7370-7376.
  32. P. Sobotík, M. Setvín, P. Zimmermann, P. Kocán, I. Ošt’ádal, P. Mutombo, M. Ondráček, P. Jelínek
    Emergence of state at Fermi level due to the formation of In-Sn heterodimers on Si(100)-2×1
    Physical Review B 88 (2013) 205406(1)-205406(7).
  33. Z. Majzik, B. Drevniok, W. Kamiński, M. Ondráček, A. B. McLean, P. Jelínek
    Room Temperature Discrimination of Adsorbed Molecules and Attachment Sites on the Si(111)–7 × 7 Surface Using a qPlus Sensor
    ACS Nano 7 (2013) 2686-2692.
  34. A. Yurtsever, Y. Sugimoto, H. Tanaka, M. Abe, S. Morita, M. Ondráček, P. Pou, R. Pérez, P. Jelínek
    Force mapping on a partially H-covered Si(111)-(7x7) surface: Influence of tip and surface reactivity
    Physical Review B 87 (2013) 155403(1)-155403(10).
  35. M. Ondráček, C. González, P. Jelínek
    Reversal of atomic contrast in scanning probe microscopy on (111) metal surfaces
    Journal of Physics: Condensed Matter 24 (2012) 084003(1)-084003(7).
  36. P. Jelínek, M. Ondráček, F. Flores
    Relation between the chemical force and the tunnelling current in atomic point contacts: a simple model
    Journal of Physics: Condensed Matter 24 (2012) 084001(1)-084001(10).
  37. M. Setvín, P. Mutombo, M. Ondráček, Z. Majzik, M. Švec, V. Cháb, I. Ošťádal, P. Sobotík, P. Jelínek
    Chemical Identification of Single Atoms in Heterogeneous III-IV Chains on Si(100) Surface by Means of nc-AFM and DFT Calculations
    ACS Nano 6 (2012) 6969-6976.
  38. M. Ondráček, P. Mutombo, Z. Chvoj, A. G. Mark, Z. Chromcová, A.B. McLean, P. Jelínek
    Stability, interaction and influence of domain boundaries in Ge/Si(111)-5 × 5
    Journal of Physics: Condensed Matter 24 (2012) 445003-445016.
  39. A. Campbellová, M. Ondráček, P. Pou, R. Pérez, P. Klapetek, P. Jelínek
    'Sub-atomic' resolution of non-contact atomic force microscope images induced by a heterogeneous tip structure: a density functional theory study
    Nanotechnology 22 (2011) 295710(1)-295710(7).
  40. M. Ondráček, P. Pou, V. Rozsíval, C. González, P. Jelínek, R. Pérez
    Forces and Currents in Carbon Nanostructures: Are We Imaging Atoms?
    Physical Review Letters 106 (2011) 176101(1)-176101(4).
  41. J. Kudrnovský, M. Ondráček, O. Bengone, F. Máca
    Disorder-induced antiferromagnetic to ferromagnetic transition in magnetic overlayers: (Fe,Mn)/W(001) as a case study
    e-Journal of Surface Science and Nanotechnology 8 (2010) 184-189.
  42. V. Drchal, M. Ondráček, J. Kudrnovský, O. Bengone, I. Turek, F. Máca
    Exchange interactions in the bcc Fe/TaW(001) system
    e-Journal of Surface Science and Nanotechnology 8 (2010) 157-160.
  43. M. Ondráček, O. Bengone, J. Kudrnovský, V. Drchal, F. Máca, I. Turek
    Magnetic phase stability of monolayers: Fe on TaxW1-x(001) random alloy as a case study
    Physical Review B 81 (2010) 064410(1)-064410(8).
  44. A. Šik, F. Máca, M. Ondráček, O. Mryasov, T. Jungwirth
    Large magnetic anisotropy and tunneling anisotropic magnetoresistance in bi-metallic layered nanostructures: Case study of Mn/W(001)
    Physical Review B 78 (2008) 054413-1-054413-6.
  45. M. Ondráček, J. Kudrnovský, F. Máca
    Magnetic order of FeMn alloy on the W(001) surface
    Surface Science 601 (2007) 4261-4265.
  46. M. Ondráček, J. Kudrnovský, I. Turek, F. Máca
    Magnetism of 3d transition metal atoms on W(001): submonlayer films.
    Journal of Physics: Conference Series 61 (2007) 894-898.
  47. M. Ondráček, F. Máca, J. Kudrnovský, J. Redinger
    Surface resonance on the NiFe(001) alloy surface
    Czechoslovak Journal of Physics 56 č.1 (2006) 69-74.
  48. M. Ondráček, F. Máca, J. Kudrnovský, J.Redinger, A.Biedermann, C.Fritscher, M.Schmid, P.Varga
    Chemical ordering and composition fluctuations at the (001) surface of the Fe64Ni36 Invar alloy.
    Physical Review B 74 (2006) 235437(1)-235437(7).
  49. M. Ondráček, F. Máca
    Theoretical calculations for the interpretation of STM images.
    Československý časopis pro fyziku 56 (2006) 65-73.