1. M. Manikandan, P. Nicolini, P. Hapala
    Computational design of photosensitive polymer templates to drive molecular nanofabrication
    ACS Nano 18 (2024) 9969-9979.
  2. 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).
  3. J. Carracedo-Cosme, P. Hapala, P. Rubén
    Atomic force microscopy simulations for CO-functionalized tips with deep learning
    Journal: Machine Learning: Science and Technology
  4. J. Doležal, S. Canola, P. Hapala, R. C. de Campos Ferreira, P. Merino, M. Švec
    Real space visualization of entangled excitonic states in charged molecular assemblies
    ACS Nano 16 (2022) 1082-1088.
  5. J. Doležal, S. Canola, P. Hapala, R. C. de Campos Ferreira, P. Merino, M. Švec
    Evidence of exciton-libron coupling in chirally adsorbed single molecules
    Nature Communications 13 (2022) 6008-.
  6. K. Dohnalová, P. Hapala, K. Kůsová, I. Infante
    Electronic Structure Engineering Achieved via Organic Ligands in Silicon Nanocrystals
    Chemistry of Materials 32 (2020) 6326-6337.
  7. A. Liebig, P. Hapala, A. J. Weymouth, F. J. Giessibl
    Quantifying the evolution of atomic interaction of a complex surface with a functionalized atomic force microscopy tip
    Scientific Reports 10 (2020) 14104-14104.
  8. B. Alldritt, P. Hapala, N. Oinonen, F. Urtev, O. Krejci, F. F. Canova, J. Kannala, F. Schulz, P. Liljeroth, A. S. Foster
    Automated structure discovery in atomic force microscopy
    Science Advances 6 (2020) eaay6913-eaay6913.
  9. 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.
  10. P. Hapala, M. Ondráček, O. Stetsovych, M. Švec, P. Jelínek
    Simultaneous nc-AFM/STM Measurements with Atomic Resolution
    Noncontact Atomic Force Microscopy vol. 3
  11. P. Hapala, R. Temirov, F. S. Tautz, P. Jelínek
    Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips
    Physical Review Letters 113 (2014) 226101(1)-226101(5).
  12. K. Kůsová, P. Hapala, J. Valenta, P. Jelínek, O. Cibulka, L. Ondič, I. Pelant
    Direct Bandgap Silicon: Tensile-Strained Silicon Nanocrystals
    Advanced Materials Interfaces 1 (2014) 1300042(1)-1300042(9).
  13. 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).
  14. 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.
  15. 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).
  16. 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).
  17. 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).
  18. 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).
  19. 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.
  20. 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).