1. 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).
  2. M. Ternes, C. González, Ch. P. Lutz, P. Hapala, F.J. Giessibel, P. Jelínek, A.J. Heinrich
    Interplay of Conductance, Force, and Structural Change in Metallic Point Contacts.
    Physical Review Letters 106 (2011) 016802(1)-016802(4).
  3. J.P. Lewis, P. Jelínek, J. Ortega, A.A. Demkov, D.G. Trabada, B. Haycock, H. Wang, G. Adams, J.K. Tomfohr, E. Abad, H. Wang, D.A. Drabold
    Advances and applications in the FIREBALL ab initio tight-binding molecular-dynamics formalism
    physica status solidi (b) 248 (2011) 1989-2007.
  4. L. Wang, H. Wang, P. Hapala, L. Zhu, L. Ren, X. Meng, J. P. Lewis, F.-S. Xiao
    Superior catalytic properties in aerobic oxidation of olefins over Au nanoparticles on pyrrolidone-modified SBA-15
    Journal of Catalysis 281 (2011) 30-39.
  5. 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).
  6. 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.
  7. 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.
  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. P. Mutombo, V. Cháb
    The interaction of carbon with Si(111):As and Si(111):H surfaces, a theoretical study
    Surface Science 603 (2009) 590-596.
  12. 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.
  13. 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.
  14. P. Shukrynau, V. Dudr, M. Švec M. Vondráček, P. Mutombo, T. Skála, F. Šutara, V. Matolín, K.C. Prince, V. Cháb
    Core level photoemission and STM characterization of Ta/Si(111)-7x7 interfaces.
    Surface Science 603 (2009) 469-476.
  15. M. Švec, V. Cháb, M.C. Tringides
    Resolving the coverage puzzle of the Pb/Si(111) -\sqrt 7 x  \sqrt 3 phase
    Journal of Applied Physics 106 (2009) 053501(1)-053501(3).
  16. 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.
  17. 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).
  18. 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).
  19. 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).
  20. 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.
  21. P. Mutombo, A.M. Kiss, A. Berkó, V. Cháb
    Atomic geometry and STM simulations of a TiO2(110) surface upon formation of an oxygen vacancy and hydroxyl group.
    Modelling and Simulation in Materials Science and Engineering 16 (2008) 025007(1)-025007(9).
  22. M. Švec, P. Jelínek, P. Shukrynau, C. González, V. Cháb, V. Drchal
    Local atomic and electronic structure of the Pb/Si(111) mosaic phase: STM and ab initio study.
    Physical Review B 77 (2008) 125104(1)-125104(8).
  23. 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.
  24. P. Jelínek, M. Švec, P. Pou, R. Perez, V. Cháb
    Tip-Induced Reduction of the Resonant Tunneling Current on Semiconductor Surfaces.
    Physical Review Letters 101 (2008) 176101(1)-176101(4).
  25. P. Jelínek, R. Pérez, J. Ortega, F. Flores
    Ab initio study of evolution of mechanical and transport properties of clean and contaminated Au nanowires along the deformation path.
    Physical Review B 77 (2008) 115447(1)-115447(11).
  26. B. Pieczyrak, C. González, P. Jelínek, R. Peréz, J. Ortega, F. Flores
    Mechanical and electrical properties of stretched clean and H-contaminated Pd-nanowires.
    Nanotechnology 19 (2008) 335711(1)-335711(8).
  27. Y.Sugimoto, P. Pou, O. Custance, P. Jelínek, M. Abe, R. Perez, S. Morita
    Complex Patterning by Vertical Interchange Atom Manipulation Using Atomic Force Microscopy.
    Science 322 (2008) 413-417.
  28. 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.
  29. M. Ondráček, J. Kudrnovský, F. Máca
    Magnetic order of FeMn alloy on the W(001) surface
    Surface Science 601 (2007) 4261-4265.
  30. O.Plekan, V. Feyer, F. Šutara, T. Skála, M. Švec, V. Cháb, V. Matolín, K.C. Prince
    The adsorption of adenine on mineral surfaces: Iron pyrite and silicon dioxide
    Surface Science 601 (2007) 1973-1980.
  31. M. Švec, V. Dudr, F. Šutara, N. Tsud, T. Skála, V. Cháb, V. Matolín, K.C. Prince
    A valence band photoemission study of Pb adsorption on Rh(100) and Rh(110)
    Surface Science 601 (2007) 5673-5677.
  32. A. Berkó, A.M. Kiss, M. Švec, F. Šutara, V. Cháb
    Ar+ assited carbidization of TiO2(110) supported Mo nanparticles by decomposition of C2H4
    Vacuum 82 (2007) 125-129.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. P. Mutombo, A.M.Kiss, A.Berkó, V.Cháb
    The effect of potassium on the adsorption of gold on the TiO2 (110) –1 x 1 surface.
    Nanotechnology 17 (2006) 4112-4116.
  38. P. Mutombo, V.Cháb
    Density functional theory study of the formation of Si nanostructures on a Si(111) unreconstructed surface.
    Surface Science 600 (2006) 4081-4085.
  39. M. Švec, P. Mutombo, P.Shukrinov, V.Dudr, V.Cháb
    Phase-sensitive lock-in imaging of surface densities of states.
    Nanotechnology 17 (2006) 213-216.
  40. 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).
  41. M. Ondráček, F. Máca
    Theoretical calculations for the interpretation of STM images.
    Československý časopis pro fyziku 56 (2006) 65-73.
  42. 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.
  43. 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.
  44. 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.
  45. A.M.Kiss, M. Švec, A.Berkó
    The effect of preadsorbed K on the size distribution of Au nanoparticles on TiO2(110) surface.
    Surface Science 600 (2006) 3352-3360.
  46. P. Mutombo, P. Shukrinov, V. Cháb
    Experimental and theoretical characterization of Cu adsorption sites on the Si(111) - 7x7 surface
    Surface Science 583 (2005) 173-178.
  47. 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).
  48. 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.
  49. 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).
  50. 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