1. O. Ranasingha, H. Wang, V. Zobač, P. Jelínek, G. Panapitiya, A. J. Neukirch∥, O. V. Prezhdo, J. P. Lewis
    Slow Relaxation of Surface Plasmon Excitations in Au55: The Key to Efficient Plasmonic Heating in Au/TiO2
    Journal of Physical Chemistry Letters 7 (2016) 1563-1569.
  2. 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).
  3. M. Ondráček, P. Hapala, P. Jelínek
    Charge-state dynamics in electrostatic force spectroscopy
    Nanotechnology 27 (2016) 274005(1)-274005(13).
  4. V. Zobač, J.P. Lewis, P. Jelínek
    Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions
    Nanotechnology 27 (2016) 285202(1)-285202(8).
  5. K. Kůsová, P. Hapala, P. Jelínek, I. Pelant
    Band Structure of Silicon Nanocrystals
    Chapter 4 in "Silicon Nanophotonics. Basic Principles, Present Status, and Perspectives". Second Edition, ed. by L. Khriachtchev, Pan Stanford Publishing 2016, pp 109-144.
  6. N. J. van der Heijden, P. Hapala, J. A. Rombouts, J. van der Lit, D. Smith, P. Mutombo, M. Švec, P. Jelínek, I. Swart
    Characteristic Contrast in Δfmin Maps of Organic Molecules Using Atomic Force Microscopy
    ACS Nano 10 (2016) 8517-8525.
  7. J. Berger, K. Kośmider, O. Stetsovych, M. Vondráček, P. Hapala, E. J. Spadafora, M. Švec, P. Jelínek
    Study of Ferrocene Dicarboxylic Acid on Substrates of Varying Chemical Activity
    Journal of Physical Chemistry C 120 (2016) 21955-21961.
  8. J. van der Lit, F. Di Cicco, P. Hapala, P. Jelínek, I. Swart
    Submolecular Resolution Imaging of Molecules by Atomic Force Microscopy: The Influence of the Electrostatic Force
    Physical Review Letters 116 (2016) 096102-1-096102-5.
  9. J. Sforzini, P. Hapala, M. Franke, G. van Straaten, A. Stöhr, S. Link, S. Soubatch, P. Jelínek, T.-L. Lee, U. Starke, M. Švec, F. C. Bocquet, F. S. Tautz
    Structural and Electronic Properties of Nitrogen-Doped Graphene
    Physical Review Letters 116 (2016) 126805(1)-126805(6).
  10. N. Kocić, X. Liu, S. Chen, S. Decurtins, O. Krejčí, P. Jelínek, J. Repp, S.-X. Liu
    Control of Reactivity and Regioselectivity for On-Surface Dehydrogenative Aryl–Aryl Bond Formation
    Journal of the American Chemical Society 138 (2016) 5585-5593.
  11. W. Kamiski, R. Topolnicki, P.Hapala, P. Jelínek, R. Kucharczyk
    Tuning the conductance of benzene-based single-molecule junctions
    Organic Electronics 34 (2016) 254-261.
  12. Pablo Merino, M. Švec, Jose Ignacio Martinez, P. Mutombo, César González, José Ángel Martin-Gago, Pedro L de Andrés Rodriguez, P. Jelínek
    Ortho and Para Hydrogen Dimers on G/SiC (0001): combined STM and DFT study
    Langmuir 31 (1) (2015) 233-239.
  13. V. Zobač, J.P. Lewis, E. Abad, J.I. Mendieta-Moreno, P. Hapala, P. Jelínek, J. Ortega
    Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism
    Journal of Physics: Condensed Matter 27 (2015) 175002(1)-175002(11).
  14. A.J. Neukirch, J. Park, V. Zobac, H. Wang, P. Jelínek, O. V. Prezhdo, H.-C. Zhou, J. P. Lewis
    Calculated photo-isomerization efficiencies of functionalized azobenzene derivatives in solar energy materials: azo-functional organic linkers for porous coordinated polymers
    Journal of Physics: Condensed Matter 27 (2015) 134208(1)-134208(11).
  15. Sh. Yamazaki, K. Maeda, Y. Sugimoto, M. Abe, V. Zobač, P. Pou, L. Rodrigo, P. Mutombo, R. Perez, P. Jelínek, S. Morita
    Interplay between Switching Driven by the Tunneling Current and Atomic Force of a Bistable Four-Atom Si Quantum Dot
    Nano Letters 15 (2015) 4356-4363.
  16. 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).
  17. 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.
  18. J. Berger, E. J. Spadafora, P. Mutombo, P. Jelínek, M. Švec
    Force-Driven Single-Atom Manipulation on a Low-Reactive Si Surface for Tip Sharpening
    Small 11 (2015) 3686-3693.
  19. 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).
  20. 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.
  21. P. Hapala, M. Ondráček, O. Stetsovych, M. Švec, P. Jelínek
    Simultaneous nc-AFM/STM Measurements with Atomic Resolution
    Noncontact Atomic Force Microscopy vol. 3
  22. Mykola Telychko, J. Berger, Zsolt Majzik, P. Jelínek, M. Švec
    Graphene on SiC (0001) inspected by dynamic atomic force microscopy at room temperature
    Beilstein Journal of Nanotechnology 6 (2015) 901-906.
  23. P. Jelínek
    Theoretical challenges of simultaneous nc-AFM/STM experiments
    Imaging and Manipulation of Adsorbates Using Dynamic Force Microscopy page 81-92 year 2015 ISBN 978-3-319-17400-6 Part of the series Advances in Atom and Single Molecule Machines
  24. 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.
  25. J. Berger, M. Švec, M. Müller, M. Ledinský, A. Fejfar, P. Jelínek, Z. Majzik
    Characterization of the mechanical properties of qPlus sensors
    Beilstein Journal of Nanotechnology 4 (2013) 1-9.
  26. 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).
  27. E. Abad, J. P Lewis, V. Zobač, P. Hapala, P. Jelínek, J. Ortega
    Calculation of non-adiabatic coupling vectors in a local-orbital basis set
    Journal of Chemical Physics 138 (2013) 154106(1)-154106(8).
  28. P. Hapala, K. Kůsová, I. Pelant, P. Jelínek
    Theoretical analysis of electronic band structure of 2- to 3-nm Si nanocrystals
    Physical Review B 87 (2013) 195420(1)-195420(13).
  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, M.R. Tchalala, M. Švec, P. Hapala, H. Enriquez, A. Kara, A. J. Mayne, G. Dujardin, P. Jelínek, H. Oughaddou
    Combined AFM and STM measurements of a silicene sheet grown on the Ag(111) surface
    Journal of Physics: Condensed Matter 25 (2013) 225301(1)- 225301(6).
  34. Y. Sugimoto, P. Pou, M. Abe, P. Jelínek, R. Pérez, S. Morita, Ó. Custance
    Chemical identification of individual surface atoms by atomic force microscopy.
    Nature 446 (2007) 64-67.
  35. Y.Sugimoto, P. Jelínek, P.Pou, M.Abe, S.Morita, R. Perez, O. Custance
    Mechanism for Room-Temperature Single-Atom Lateral Manipulations on Semiconductors using Dynamic force Microscopy.
    Physical Review Letters 98 (2007) 106104-1-106104-4.
  36. M.A. Basasnta, Y.J. Dappe, P. Jelínek, J. Ortega
    Optimized atomic-like orbitals fo first-principles tight-binding molecular dynamics.
    Computational Materials Science 39 (2007) 759-766.
  37. P. Jelínek, H. Wang, J. P. Lewis, O.F. Sankey, J.Ortega
    Multicenter approach to the exchange-correlation interactions in ab initio tight-binding methods
    Physical Review B 71 (2005) 235101(1)-235101(9).
  38. P. Jelínek, R. Pérez, J. Ortega, F. Flores
    Universal behaviour in the final stage of the breaking process for metal nanowires
    Nanotechnology 16 (2005) 1023-1028.
  39. J. M. Blanco, C. González, P. Jelínek, J. Ortega, F. Flores, R. Pérez, M. Rose, M. Salmeron, J. Méndez, J. Wintterlin, G. Ertl
    Origin of contrast in STM images of oxygen on Pd(111) and its dependence on tip structure and tunneling parameters
    Physical Review B 71 (2005) 113402(1)-113402(4).
  40. P. Jelínek, M. Ondřejček, J. Slezák, V. Cháb
    Experimental and theoretical studies of single Pb atom dynamics in one Si(111)-(7x7) unit cell.
    Surf. Sci. 544 (2003) 339 - 347
  41. P. Jelínek, R. Pérez, J. Ortega, F. Flores
    First-principles simulations of the stretching and final breaking of Al nanowires: Mechanical properties and electrical conductance
    Phys. Rev. B 68 (2003) 085403