1. 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).
  2. 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).
  3. Z. Majzik, M. Setvín, A. Bettac, A. Feltz, V. Cháb, P. Jelínek
    Simultaneous current, force and dissipation measurements on the Si(111) 7×7 surface with an optimized qPlus AFM/STM technique
    Beilstein Journal of Nanotechnology 3 (2012) 249-259.
  4. 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.
  5. 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.
  6. A. Yurtsever, D. Fernandez-Torre, C. Gonzalez, P. Jelínek, P. Pou, Y. Sugimoto, M. Abe, R. Perez, S. Morita
    Understanding image contrast formation in TiO2 with force spectroscopy
    Physical Review B 85 (2012) 125416(1)-125416(9).
  7. M. Švec, P. Merino, Y. J. Dappe, C. González, E. Abad, P. Jelínek, J. A. Martín-Gago
    van der Waals interactions mediating the cohesion of fullerenes on graphene
    Physical Review B 86 (2012) 121407(R)-121412(R).
  8. W. Kaminski, W. Rozsíval, P. Jelínek
    Theoretical study of electronic and transport properties of PPy-Pt(111) and PPy-C(111):H interfaces
    Journal of Physics: Condensed Matter 22 (2010) 045003(1)-045003(10).
  9. S. Lindsay, J. He, O. Sankey, P. Hapala, P. Jelínek, P. Zhang, S.Chang, S. Huang
    Recognition tunneling
    Nanotechnology 21 (2010) 262001(1)-262001(12).
  10. C.Sánchez-Sánchez, C.González, P. Jelínek, J.Méndez, P.L.deAndres, J.A. Martín-Gago, M.F. López
    Understanding atomic-resolved STM images on TiO.2.(110)-(1x1) surface by DFT calculations.
    Nanotechnology 21 (2010) 405702(1)-405702(10).
  11. H. Vázquez, P. Jelínek, M. Brandbyge, A.P. Jauho, F. Flores
    Corrections to the density-functional theory electronic spectrum: copper phthalocyanine.
    Applied Physics A-Materials Science & Processing 95 (2009) 257-263.
  12. M. Švec, V. Dudr, M. Vondráček, P. Jelínek, P. Mutombo, V. Cháb, F. Šutara, V. Matolín, K. Prince
    Intra-atomic charge re-organization at the Pb Si interface: Bonding mechanism at low cover.
    Surface Science 603 (2009) 2861-2869.
  13. P. Pou, S.A. Ghasemi, P. Jelínek, T. Lenosky, S. Goedecker, R. Perez
    Structure and stability of semiconductor tip apexes for atomic force microscopy.
    Nanotechnology 20 (2009) 264015-1-264015-10.
  14. R. Bechstein, C. González, J. Schütte, P. Jelínek, R. Pérez, A. Kühnle
    'All-inclusive' imaging of the rutile TiO.2.(110) surface using NC-AFM.
    Nanotechnology 20 (2009) 505703(1)-505703(7).
  15. K. Košmider, A. Krupski, P. Jelínek, L. Jurczyszyn
    Atomic and electronic properties of the Pb/Mo(110) adsorption system.
    Physical Review B 80 (2009) 115424(1)-115424(7).
  16. S. Sadewasser, P. Jelínek, Ch.K. Fang, O.Custance, Y. Yamada, Y.Sugimoto, M.Abe, S.Morita
    New Insights on Atomic-Resolution Frequency-Modulation Kelvin-Probe Force-Microscopy Imaging of Semiconductors.
    Physical Review Letters 103 (2009) 266103(1)-266103(4).
  17. P. Pou, P. Jelínek, R. Pérez
    Basic Mechanisms for Single Atom Manipulation in Semiconductor Systems with the FM-AFM.
    Chapter 11 in Noncontact Atomic Force Microscopy, eds. S.Morita, F.J. Giessibl, R. Wiesendanger, in series NanoScience and Technology, vol. 2, Springer-Verlag Berlin Heidelberger 2009 pp. 227-248.
  18. 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.
  19. 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.
  20. 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.
  21. N.Oyabu, P.Pou, Y.Sugimoto, P. Jelínek, M.Abe, S.Morita, R.Pérez, Ó.Custance
    Single atomic contact adhesion and dissipation in dynamic force microscopy
    Physical Review Letters 96 č.10 (2006) 106101/1-106101/4.
  22. P. Jelínek, R.Pérez, J.Ortega, F.Flores
    Hydrogen dissociation over Au nanowires and the fractional conductance quantum
    Physical Review Letters 96, č.4 (2006) 046803/1-046803/4.
  23. Y.Sugimoto, P.Pou, O.Custance, P. Jelínek, S.Morita, R.Peréz, M.Abe.
    Real topography, atomic relaxations and short-range chemical interactions in atomic force microscopy: The case of the α-Sn/Si(111)-(√3 x √3) R30o surface.
    Physical Review B 73 (2006) 205329-1-205329-9.
  24. Z. Kuntová, P. Jelínek, V. Cháb, Z. Chvoj
    Single atom diffusion of Pb on a Si(111)-7x7 surface.
    Surf. Sci. 566-568 (2004) 130 - 136
  25. W. Kaminski, P. Jelínek, R. Pérez, F. Flores, J. Ortega
    Si-substitutional defects on the alpha-Sn-Si(111)-(r3xr3) surface.
    Appl. Surf. Sci. 234 (2004) 286 - 291
  26. P. Jelínek, R. Peréz, J. Ortega, F. Florez
    Mechanical properties and electrical conductance of different Al nanowire submitted to an homogeneous deformation: a first-principles simulation.
    Surf. Sci. 566-568 (2004) 13 - 23
  27. J. M. Blanco, C. Gonzáles, P. Jelínek, J. Ortega, F. Flores, R. Peréz
    First-principles simulations of STM images: From tuneling to the contact regime.
    Phys. Rev. B 70 (2004) 85405