Publications - Dr. Tech. Sami Paavilainen

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1 Publications - Dr. Tech. Sami Paavilainen June 15, 2016 Articles in refereed scientific journals 1. J.A. Nieminen and S. Paavilainen, Surface Science Letters 405, L573 (1998). Adsorption site and STM image of O 2 on Pt{111}. 2. J.A. Nieminen and S. Paavilainen, Physical Review B 60, 2921 (1999). Bridging the gap over size scales: A Green s function method to combine tight-binding and semiempirical force calculations. 3. M. Hirsimäki, S. Paavilainen, J.A. Nieminen, and M. Valden, Surface Science , 171 (2001). Role of translational and vibrational energy in the dissociative chemisorption of methane on Pd{110}(1x1). 4. S. Paavilainen and J.A. Nieminen, Surface Science Letters 486, L489 (2001). Effect of Translational and Vibrational Energies on Dissociation of Methane on Pd(110) - A Molecular Dynamics Study. 5. S. Paavilainen and J.A. Nieminen, Physical Review B 66, (2002). Path and energy dependence of CH 4 dissociation on Pd(110) and Pd(320). 6. S. Paavilainen and J.A. Nieminen, Surface Science 521, 69 (2002). Molecular dynamics studies of STM manipulation of oxygen on Pt(111). 7. J.A. Nieminen, S. Lahti, S. Paavilainen and K. Morgenstern, Physical Review B 66, (2002). Contrast Changes in STM Images and Relations between Different Tunneling Models. 8. J. Repp, G. Meyer, S. Paavilainen, F.E. Olsson and M. Persson, Physical Review Letters 95, (2005). Scanning tunneling spectroscopy of Cl-vacancies in NaCl-films: Strong electron-phonon coupling in double-barrier tunneling junctions. 9. J. Repp, G. Meyer, S. Paavilainen, F.E. Olsson and M. Persson, Science 312, 1196 (2006). Imaging Bond Formation Between a Gold Atom and Pentacene on an Insulating Surface. 10. S. Paavilainen and M. Persson, Physical Review B 74, (2006). Vibrational assignments and line shapes in inelastic tunnelling spectroscopy: Cu(100). H on

2 11. E. Niemi, V. Simic-Milosevic, K. Morgenstern, A. Korventausta, S. Paavilainen, and J.A. Nieminen, Journal of Chemical Physics 125, (2006). Submolecular imaging of chloronitrobenzene isomers on Cu(111). 12. F. E. Olsson, S. Paavilainen, M. Persson, J. Repp, and G. Meyer, Physical Review Letters 98, (2007). Multiple charge states of Ag atoms on ultrathin NaCl films. 13. A. Korventausta, S. Paavilainen, E. Niemi, and J.A. Nieminen, Surface Science 603, 437 (2009). STM Simulation of Molecules on Ultrathin Insulating Overlayers using Tight-Binding: Au-Pentacene on NaCl bilayer on Cu. 14. P. Liljeroth, I. Swart, S. Paavilainen, J. Repp, and G. Meyer, Nano Letters 10, 2475 (2010). Single molecule synthesis and characterization of metal-ligand complexes by low-temperature STM. 15. S. Paavilainen, T. Róg, and I. Vattulainen, The Journal of Physical Chemistry B, 115, 3747 (2011). Analysis of twisting in cellulose nanofibrils during molecular dynamics simulations. 16. S. Paavilainen, J. L. McWhirter, T. Róg, J. Järvinen, I. Vattulainen and J. A. Ketoja, Nord. Pulp Pap. Res. 27, 282 (2012). Mechanical properties of cellulose nanofibrils determined through atomistic molecular dynamics simulations. 17. M. Ropo, S. Paavilainen, E. Räsänen, and J. Akola, Physical Review B, 90, (2014). Density-functional investigation of molecular graphene: CO on Cu(111). 18. A. Orlowski, T. Róg, S. Paavilainen, M. Manna, I. Heiskanen, K. Backfolk, J. Timonen, and I. Vattulainen, Cellulose, 22, 2911 (2015). How endoglucanase enzymes act on cellulose nanofibrils: role of amorphous regions revealed by atomistic simulations 19. B. Schuler, M. Persson, S. Paavilainen, N. Pavlicek, L. Gross, G. Meyer and J. Repp, Physical Review B 91, (2015). Effect of electron-phonon interaction on the formation of one-dimensional electronic states in coupled Cl vacancies 20. S. Paavilainen, M. Ropo, J. Nieminen, E. Räsänen, and J. Akola, Nano Lett. 16, 3519(2016), Co-existing honeycomb and Kagome characteristics in the electronic band structure of molecular graphene

3 21. A. Paajanen, Y. Sonavane, D. Ignasiak, J. A. Ketoja, T. Maloney, S. Paavilainen, submitted (2016) Atomistic molecular dynamics simulations on the interaction of TEMPO-oxidized cellulose nanofibrils in water Articles in non-refereed journals 1. P. Liljeroth and S. Paavilainen, Arkhimedes 2/2008, 23. Molekyylielektroniikan ensiaskelia ultraohuilla kalvoilla. Articles in refereed conference proceedings 1. S. Paavilainen and J.A. Nieminen, Proc. of the XXXII Ann. Conf. of the Finnish Phys. Soc. (1998). Calculation of cohesion energy and interatomic forces of CO on Pt{111} surface. 2. J.A. Nieminen and S. Paavilainen, Proc. of the XXXII Ann. Conf. of the Finnish Phys. Soc. (1998). Dynamical simulation of adsorption and calculation of STM image of O 2 on Pt{111}. 3. S. Paavilainen (oral) and J.A. Nieminen, Proc. of the XXXIII Ann. Conf. of the Finnish Phys. Soc. (1999). A Green s function method to combine tight-binding and semiempirical calculations: Dissociation of O 2 on Pd{110}. 4. M. Hirsimäki, S. Paavilainen, J.A. Nieminen and M. Valden, Proc. of the XXXIV Ann. Conf. of the Finnish Phys. Soc. (2000). Activated adsorption of methane on Pd{110} and Pd{320}. 5. J.A. Nieminen and S. Paavilainen, Proc. of the XXXIV Ann. Conf. of the Finnish Phys. Soc. (2000). Dissociative adsorption of oxygen on transition metals. 6. S. Paavilainen and J.A. Nieminen, Proc. of the XXXV Ann. Conf. of the Finnish Phys. Soc. (2001). Effect of Translational and Vibrational Energies on Dissociation of Methane on Pd(110) - A Molecular Dynamics Study. 7. S. Paavilainen and J.A. Nieminen, Proc. of the XXXVI Ann. Conf. of the Finnish Phys. Soc. (2002). Vibrational mode dependence of dissociation of methane on Pd(110). 8. S. Paavilainen and M. Persson, IVC-16/ICSS-12/NANO-8/AIV-17, Venice (2004). Stability of Assembled Molecular Nanostructures on Surfaces. 9. S. Paavilainen and M. Persson, IVC-16/ICSS-12/NANO-8/AIV-17, Venice (2004).

4 Calculations of Vibrationally Inelastic Tunneling Spectroscopy and Microscopy of Single Hydrogen Atoms on a Copper Surface. 10. S. Paavilainen (oral), F.E. Olsson, M. Persson, J. Repp and G. Meyer, 5th Nordic Conference on Surface Science, Tampere (2004). Color centers in ultrathin sodiumchloride films on a stepped copper surface. 11. S. Paavilainen (oral), F.E. Olsson and M. Persson, Research Conference on Molecular Nano-machines, Les Houches (2005). DFT simulations of STM and STS of Cl vacancies in ultrathin NaCl films on Cu. 12. S. Paavilainen (oral), F.E. Olsson and M. Persson, 23rd European Conference on Surface Science, Berlin (2005). DFT simulations of scanning tunneling spectroscopy in double barrier tunneling junctions. 13. S. Paavilainen (oral), F.E. Olsson and M. Persson, Proc. of the XL Ann. Conf. of the Finnish Phys. Soc. (2006). Modeling of scanning tunneling spectroscopy on ultrathin insulating film. 14. S. Paavilainen (oral), F.E. Olsson, M. Persson, J. Repp, and G. Meyer, 24th European Conference on Surface Science, Paris (2006). Imaging frontier orbital reorganization in single-molecule chemistry. 15. A. Korventausta, S. Paavilainen and J. Nieminen, Proc. of the XLI Ann. Conf. of the Finnish Phys. Soc. (2007). Applying Various Approaches in Modelling STM on Molecules on Ultrathin Insulating Overlayers, 16. S. Paavilainen (oral), F.E. Olsson, M. Persson, J. Repp, and G. Meyer, International Conference on Nano Science and Technology, Stockholm (2007). Imaging frontier orbital reorganization in single-molecule chemistry. 17. S. Paavilainen (oral), F.E. Olsson and M. Persson, Proc. of the XLII Ann. Conf. of the Finnish Phys. Soc. (2008). Charge state multiplicity of single atoms on an ultrathin insulating film. 18. S. Paavilainen (oral) and M. Persson, 25th European Conference on Surface Science, Liverpool (2009). Pentacene molecule interaction with a gold atom in a chlorine vacancy in an ultrathin NaCl film, 19. A. Korventausta, S. Paavilainen, and J. Nieminen, 25th European Conference on Surface Science, Liverpool (2009). Analysis of STM imaging in Molecular Bonding of Adsorbates on Insulating Films, 20. S. Paavilainen, T. Róg and I. Vattulainen, Proc. of the XLIII Ann. Conf. of the Finnish Phys. Soc. (2009). Molecular dynamics simulations of cellulose nanofibrils, 21. S. Paavilainen (oral), T. Róg, J. Järvinen, and I. Vattulainen, Proc. of the XLIV

5 Ann. Conf. of the Finnish Phys. Soc. (2010). Modeling cellulose nanofibrils with non-crystalline parts, 22. S. Paavilainen, J. L. McWhirter, T. Róg, and I. Vattulainen, 2010 TAPPI International Conference on Nanotechnology for the Forest Products Industry Atomistic modeling of cellulose nanofibrils and their interactions, 23. J. L. McWhirter, S. Paavilainen, T. Róg, and I. Vattulainen, 2010 TAPPI International Conference on Nanotechnology for the Forest Products Industry Atomistic Modeling of Cellulose Nanofibrils: Elastic Properties, 24. S. Paavilainen, J. L. McWhirter, A. Orlowski, T. Róg, and I. Vattulainen(oral), 2010 TAPPI International Conference on Nanotechnology for the Forest Products Industry Computational perspective to cellulose nanofibrils through atomistic simulations,