1. P. Galář, J. Kopenec, R. Král, F. Matějka, P. Zemenová, M. Dopita, P. Hapala, D. König, P. Vrbka, K. Kůsová
    Engineering the Thermal and Energy-Storage Properties in Quantum Dots Using Dominant Faceting: The Case Study of Silicon
    ACS Nano 19 (2025) 2196-2122.
  2. I. Mal, M. Kočí, P. Nicolini, P. Hapala
    GridFF: Efficient Simulation of Organic Molecules on Rigid Substrates
    Journal of Chemical Theory and Computation 21 (2025) 12214-12226.
  3. 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).
  4. J. Carracedo-Cosme, P. Hapala, P. Rubén
    Atomic force microscopy simulations for CO-functionalized tips with deep learning
    Machine Learning - Science and Technology 5 (2024) 025025(1)-025025(11).
  5. M. Manikandan, P. Nicolini, P. Hapala
    Computational design of photosensitive polymer templates to drive molecular nanofabrication
    ACS Nano 18 (2024) 9969-9979.
  6. 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.
  7. 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-.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. P. Hapala, M. Ondráček, O. Stetsovych, M. Švec, P. Jelínek
    Simultaneous nc-AFM/STM Measurements with Atomic Resolution
    Noncontact Atomic Force Microscopy vol. 3
  13. 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.
  14. 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).
  15. 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).
  16. 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).
  17. 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).
  18. 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).
  19. 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).
  20. 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).
  21. 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.
  22. 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).