1. F. Slanina, M. Kotrla
    Hydrodynamic approximations for driven dense colloidal mixtures in narrow pores
    Physical Review E 107 (2023) 064606 (1)-064606 (14).
  2. F. Slanina, M. Kotrla, K. Netočný
    Short-range and long-range correlations in driven dense colloidal mixtures in narrow pores
    Physical Review E 106 (2022) 014610(1)-014610(12).
  3. Y. Humenyuk, M. Kotrla, F. Slanina
    Continuous and discontinuous waves in an ASEP with pockets
    Journal of Statistical Mechanics: Theory and Experiment 2021 (2021) 1-18.
  4. Y. Humenyuk, M. Kotrla, K. Netočný, F. Slanina
    Separation of dense colloidal suspensions in narrow channels: A stochastic model
    Physical Review E 101 (2020) 032608(1)-032608(21).
  5. M. Mašín, L. Bergqvist, J. Kudrnovský, M. Kotrla, V. Drchal
    Critical Temperatures of Random Iron–Cobalt Overlayers on the fcc-Cu(001) Substrate
    Journal of Superconductivity and Novel Magnetism 26 (2013) 809-812.
  6. M. Mašín, M. Kotrla, B. Yang, M. Asta, M. O. Jahma, T. Ala-Nissila
    Multiscale modeling of submonolayer growth for Fe/Mo(110)
    European Physical Journal B - Condensed Matter and Complex Systems 86 (2013) 359-365.
  7. M. Mašín, L. Bergqvist, J. Kudrnovský, M. Kotrla, V. Drchal
    First-principles study of thermodynamical properties of random magnetic overlayers on fcc-Cu(001) substrate
    Physical Review B 87 (2013) 075452(1)-075452(8).
  8. M. Mašín, M. Kotrla
    Influence of control and material parameters on island density in early stage of pulsed laser deposition
    Thin Solid Films 520 (2012) 4965-4970.
  9. M.Mašín, M. Kotrla
    Pulsed Depositions vs. Continuous Growth: Monte Carlo Study of Submonolayer Regime.
    e-Journal of Surface Science and Nanotechnology 8 (2010) 65-68.
  10. M. Mašín, M. Kotrla
    Effect of persistence of compact surface clusters during pulsed-laser deposition on submonolayer growth.
    Europhysics Letters 90 (2010) 18006-p1-18006-p6.
  11. D. Goykolov, M. Kotrla
    Study of the island morphology at the early stages of Fe/Mo(110) MBE growth
    Central European Journal of Physics 7 (2009) 220-226.
  12. S. Weber, M. Biehl, M. Kotrla, W. Kinzel
    Simulation of self-assembled nanopatterns in strained 2D alloys on the face centered cubic(111) surface
    Journal of Physics: Condensed Matter 20 (2008) 265004(1)-265004(7).
  13. M. Kotrla, S. Weber, F. Much, M. Biehl, W. Kinzel
    Self-assembled nano-patterns in strained 2D metalic alloys: stripes vs. islands
    Acta Metallurgica Slovaca 13 (2007) 70-75.
  14. C. Polop, H. Hansen, W. Langenkamp, Z. Zhong, C. Busse, U. Linke, M. Kotrla, P. Feibelman, T. Michely
    Oscillatory interaction between O impurities and Al adatoms on Al(111) and its effect on nucleation and growth
    Surface Science 575 (2005) 89(1)-89(13).
  15. F. Slanina, J. Krug, M. Kotrla
    Kinetics of step bunching during growth: A minimal model.
    Physical Review E 71 (2005) 041605(1)-041605(8).
  16. T. Volkmann, F. Much, M. Biehl, M. Kotrla
    Interplay of strain relaxation and chemically induced diffusion barriers: Nanostructure formation in 2D alloys
    Surface Science 586 (2005) 157(1)-157(17).
  17. P. Kocan, P. Sobotik, I. Ostadal, M. Kotrla
    Continuous and correlated nucleation during nonstandard island growth at Ag/Si(111)-7x7 heteroepitaxy
    Phys. Rev. B 69 (2004) 165409
  18. P. Kocan, P. Sobotik, I. Ostadal, M. Kotrla
    Self-organized growth of Ag islands on Si(111)-(7x7)-optimization of an STM experiment by means of KMC simulations
    Surf. Sci. 566 (2004) 216
  19. J. Kallunki, J. Krug, M. Kotrla
    Competing mechanisms for step meandering in unstable growth
    Phys. Rev. B 65 (2002) 205411
  20. M. Kotrla, F. Slanina, J. Steiner
    Dynamic scaling and universality in evolution of fluctuating random networks
    Europhys. Lett. 60 (2002) 14
  21. M. Kotrla, J. Krug, P. Šmilauer
    Effects of mobile and immobile impurities on two-dimensional nucleation
    Surface Science 482-485 (2001) 840-843.
  22. M. Kotrla, J. Krug, P. Šmilauer
    Effects of adsorbates on submonolayer growth
    Collective Diffusion on Surfaces: Correlation Effects and Adatom Interactions, Eds. M.C. Tringides and Z. Chvoj, Kluwer Academic Publisher, 2001, pp. 247-257. ISBN: 978-0-7923-7115-1, 978-0-7923-7116-8.
  23. M. Kotrla, J. Krug, P. Smilauer
    Effects of mobile and immobile impurities on two-dimensional nucleation
    Surf. Sci. 482 (2001) 840
  24. M. Kotrla, Joachim Krug, Pavel Šmilauer
    Submonolayer growth with decorated island edges
    Surface Science 454-456 (2000) 681-685.
  25. M. Kotrla, J. Krug, P. Smilauer
    Submonolayer epitaxy with impurities: Kinetic Monte Carlo simulations and rate-equation analysis
    Phys. Rev. B 62 (2000) 2889
  26. M. Kotrla, J. Krug, P. Smilauer
    Submonolayer growth with decorated island edges
    Surf. Sci. 454 (2000) 681
  27. F. Máca, M. Kotrla, O. S. Trushin
    Energy barriers for diffusion on stepped Rh(111) surfaces
    Surface Science 454 (2000) 579-584.
  28. F. Slanina, M. Kotrla
    Random networks created by biological evolution
    Phys. Rev. E 62 (2000) 6170
  29. F. Máca, M. Kotrla, O. S. Trushin
    Energy barriers for interlayer diffusion in Pt/Pt(111) and Rh/Rh(111) homoepitaxy: Small islands
    Czechoslovak Journal of Physics 49 (1999) 1591-1596.
  30. F. Máca, M. Kotrla, O. S. Trushin
    Energy barriers for diffusion on stepped Pt(111) surface
    Vacuum 54 (1999) 113-117.
  31. F. Slanina, M. Kotrla
    Extremal dynamics model on evolving networks
    Phys. Rev. Lett. 83 (1999) 5587
  32. F. Slanina, M. Kotrla
    Weak pinning: surface growth in the presence of a defect
    Physica A 256 (1998) 1
  33. M. Kotrla, M. Predota, F. Slanina
    Kinetic roughening and phase ordering in the two-component growth model
    Surf. Sci. 402 (1998) 249
  34. M. Kotrla, F. Slanina, M. Predota
    Scaling in a two-component surface-growth model.
    Phys. Rev. B 58 (1998) 10003
  35. A. C. Levi, M. Kotrla
    Theory and simulation of crystal growth.
    J. Phys. C 9 (1997) 299
  36. O. S. Trushin, K. Kokko, P. T. Salo, W. Hergert, M. Kotrla
    Step roughening effect on adatom diffusion
    Phys. Rev. B 56 (1997) 12135
  37. O. S. Trushin, M. Kotrla, F. Máca
    Energy barriers on stepped Ir/Ir(111) surfaces a molecular statics calculation.
    Surface Science 389 (1997) 55-65.
  38. M. Kotrla, M. Predota
    Interplay between kinetic roughening and phase ordering.
    Europhys. Lett. 39 (1997) 251
  39. M. Kotrla, P. Šmilauer
    Nonuniversality in models of epitaxial growth
    Physical Review B 53 (1996) 13777-13792.
  40. M. Kotrla
    Numerical simulations in the theory of crystal growth
    Comput. Phys. Comm. 97 (1996) 82
  41. M. Predota, M. Kotrla
    Stochastic equations for simple discrete models of epitaxial growth
    Phys. Rev. E 54 (1996) 3933
  42. P. Šmilauer, M. Kotrla
    Crossover effects in the Wolf-Villain model of epitaxial growth in 1+1 and 2+1 dimensions
    Physical Review B 49 (1994) 5769-5772.
  43. M. Kotrla, P. Šmilauer
    Kinetic Roughening in Models of Molecular-Beam Epitaxy Growth
    Acta Physica Slovaca 44 (1994) 237-244.
  44. P. Šmilauer, M. Kotrla
    Kinetic roughening in growth models with diffusion in higher dimensions
    Europhysics Letters 27 (1994) 261(1)-261(6).
  45. M. Kotrla, A. C. Levi
    Kinetics of crystal growth near the roughening transition: A Monte Carlo study
    Surf. Sci. 317 (1994) 183
  46. V. Drchal, M. Kotrla
    Moment expansion of the two-particle Green function for the Hubbard Hamiltonian
    J. Phys.-Condens. Mat. 5 (1993) 171
  47. A. C. Levi, G. Garrod, M. Kotrla, M. Touzani
    Growth modes and models for smooth and rough surfaces
    Phys. Scr. T 49 (1993) 593
  48. A. C. Levi, M. Kotrla
    A poor man's interpretation of the Nozieres-Gallet effect
    Il Nuovo Cimento 15 D, No. 2-3 (1993) 485-491
  49. M. Kotrla
    Growth of rough surfaces (review article)
    Czech. J. Phys. 42 (1992) 449
  50. M. Kotrla, V. Drchal
    Two-particle excitations of the Hubbard Hamiltonian: Alloy analogy solution
    J. Phys.-Condens. Mat. 4 (1992) 4251