2017

A. Charvátová Campbell, Pavel Jelínek, P. Klapetek
Study of uncertainties of height measurements of monoatomic steps on Si 5x5 using DFT
Meas. Sci. Technol. 28 (2017) 034005(1) - 034005(6).

T. Chutora, J. Redondo, B. de la Torre, M. ©vec, P. Jelínek, H. Vazquez
Stable Au–C bonds to the substrate for fullerene-based nanostructures
Beilstein J. Nanotechnol. 8 (2017) 1073 - 1079.

P. Jelínek
High resolution SPM imaging of organic molecules with functionalized tips
J. Phys.-Condens. Mat. 29 (2017) 343002(1) - 343002(18).

O. Krejčí, P. Hapala, M. Ondráček, P. Jelínek
Principles and simulations of high-resolution STM imaging with a flexible tip apex
Phys. Rev. B 95 (2017) 045407(1) - 045407(9).

J. LaRue, O. Krejčí, L. Yu, M. Beye , M. L. Ng, H. Öberg, H. Xin, G. Mercurio, S. Moeller, J. J. Turner, D. Nordlund, R. Coffee, M. P. Minitti, W. Wurth, L. G. M. Pettersson, H. Öström, A. Nilsson, F. Abild-Pedersen, H. Ogasawara
Real-Time Elucidation of Catalytic Pathways in CO Hydrogenation on Ru
J. Phys. Chem. Lett. 8 (2017) 3820 - 3825.

T. Meier, R. Pawlak, Sh. Kawai, Y. Geng, X. Liu, S. Decurtins, P. Hapala, A. Baratoff, Sh.-X. Liu, P. Jelínek, E. Meyer, Th. Glatzel
Donor–Acceptor Properties of a Single-Molecule Altered by On-Surface Complex Formation
ACS Nano XX (2017) 00 - 00.

J. Onoda, M. Ondáček, P. Jelínek, Y. Sugimoto
Electronegativity determination of individual surface atoms by atomic force microscopy
Nat. Commun. 8 (2017) 15155(1) - 15155(6).

O. Stetsovych, M. ©vec, J. Vacek, J. Vacek Chocholouąová, A. Jančařík, J. Rybáček, K. Kosmider, I. G. Stará, P. Jelínek, I. Starý
From helical to planar chirality by on-surface chemistry
Nat. Chem. 9 (2017) 213 - 218.


2016

J. Berger, K. Ko¶mider, O. Stetsovych, M. Vondráček, P. Hapala, E. J. Spadafora, M. ©vec, P. Jelínek
Study of Ferrocene Dicarboxylic Acid on Substrates of Varying Chemical Activity
J. Phys. Chem. C 120 (2016) 21955 - 21961.

N. J. van der Heijden, P. Hapala, J. A. Rombouts, J. van der Lit, D. Smith, P. Mutombo, M. ©vec, P. Jelinek, I. Swart
Characteristic Contrast in Δfmin Maps of Organic Molecules Using Atomic Force Microscopy
ACS Nano 10 (2016) 8517 - 8525.

J. van der Lit, F. Di Cicco, P. Hapala, P. Jelinek, I. Swart
Submolecular Resolution Imaging of Molecules by Atomic Force Microscopy: The Influence of the Electrostatic Force
Phys. Rev. Lett. 116 (2016) 096102-1 - 096102-5.

P. Hapala, M. Svec, O. Stetsovych, N. J. van der Heijden, M. Ondracek ,J. van der Lit, P. Mutombo, I. Swart, P. Jelinek
Mapping the electrostatic force field of single molecules from high-resolution scanning probe images
Nat. Commun. 7 (2016) 11560(1) - 11560(8).

W. Kamiski, R. Topolnicki, P.Hapala, P. Jelínek, R. Kucharczyk
Tuning the conductance of benzene-based single-molecule junctions
Org. Electron. 34 (2016) 254 - 261.

N. Kocić, X. Liu, S. Chen, S. Decurtins, O. Krejčí, P. Jelínek, J. Repp, S.-X. Liu
Control of Reactivity and Regioselectivity for On-Surface Dehydrogenative Aryl–Aryl Bond Formation
J. Am. Chem. Soc. 138 (2016) 5585 - 5593.

O. Krejčí, P. Matvija, P. Zimmermann, P. Sobotík, I. Oą»ádal, P. Kocán
Chemisorption of Acetophenone on Si(111)-7 x 7. Polar Aromatic Molecule on Electronically Complex Surface
J. Phys. Chem. C 120 (2016) 9200 - 9206.

P.Mutombo, R. Gubo, A. Berko
Interaction of Gold with a Pinwheel TiO∼1.2 Film Formed on Rh(111) Facet: STM and DFT Studies
J. Phys. Chem. C 120 (23) (2016) 12917 - 12923.

M. Ondráček, P. Hapala, P. Jelínek
Charge-state dynamics in electrostatic force spectroscopy
Nanotechnology 27 (2016) 274005(1) - 274005(13).

O. Ranasingha, H. Wang, V. Zobač, P. Jelínek, G. Panapitiya, A. J. Neukirch∥, O. V. Prezhdo, J. P. Lewis
Slow Relaxation of Surface Plasmon Excitations in Au55: The Key to Efficient Plasmonic Heating in Au/TiO2
J. Phys. Chem. Lett. 7 (2016) 1563 - 1569.

J. Sforzini, P. Hapala, M. Franke, G. van Straaten, A. Stöhr, S. Link, S. Soubatch, P. Jelínek, T.-L. Lee, U. Starke, M. ©vec, F. C. Bocquet, F. S. Tautz
Structural and Electronic Properties of Nitrogen-Doped Graphene
Phys. Rev. Lett. 116 (2016) 126805(1) - 126805(6).

J. Sforzini, M. Telychko, O. Krejčí, M. Vondráček, M. ©vec., F. C. Bocquet, F. S. Tautz
Transformation of metallic boron into substitutional dopants in graphene on 6H-SIC(0001)
Phys. Rev. B 93 (2016) 041302-1 - 041302-4.

V. Zobač, J.P. Lewis, P. Jelínek
Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions
Nanotechnology 27 (2016) 285202(1) - 285202(8).


2015

F. Albrecht, J. Repp, M. Fleischmann, M. Scheer, M. Ondráček, P. Jelínek
Probing Charges on the Atomic Scale by Means of Atomic Force Microscopy
Phys. Rev. Lett. 115 (2015) 076101-1 - 076101-5.

María Arroyo-Hernández, Martin ©vec, Celia Rogero, Carlos Briones, José Ángel Martín-Gago, José Luis Costa-Krämer
Structural modifications of gold thin films produced by thiol-derivatized single-stranded DNA immobilization
J. Phys.-Condens. Mat. 26 (5) (2015) 055010 - 055014.

J. Berger, E. J. Spadafora, P. Mutombo, P. Jelínek, M. ©vec
Force-Driven Single-Atom Manipulation on a Low-Reactive Si Surface for Tip Sharpening
Small 11 (2015) 3686 - 3693.

M. Corso, M. Ondráček, Ch. Lotze, P. Hapala, K. J. Franke, P. Jelínek, J. I. Pascual
Charge Redistribution and Transport in Molecular Contacts
Phys. Rev. Lett. 115 (2015) 136101(1) - 136101(5).

K. Iwata, Sh. Yamazaki, P. Mutombo, P. Hapala, M. Ondráček, P. Jelínek, Y. Sugimoto
Chemical structure imaging of a single molecule by atomic force microscopy at room temperature
Nat. Commun. 6 (2015) 7766(1) - 7766(6).

P. Kocán, O.Krejčí, H. Tochihara
Anomalous structural evolution and √ 3 x√ 3  reconstruction of a clean Si(111) surface observed after thermal desorption of thallium
J. Vac. Sci. Technol. A 33 (2015) 021408-1 - 021408-8.

Pablo Merino, Martin ©vec, Jose Ignacio Martinez, Pingo Mutombo, César González, José Ángel Martin-Gago, Pedro L de Andrés Rodriguez, Pavel Jelinek
Ortho and Para Hydrogen Dimers on G/SiC (0001): combined STM and DFT study
Langmuir 31 (1) (2015) 233 - 239.

César Moreno, Oleksandr Stetsovych, Tomoko K. Shimizu, Oscar Custance
Imaging Three-Dimensional Surface Objects with Submolecular Resolution by Atomic Force Microscopy
Nano Lett. 15 (2015) 2257 - 2262.

A.J. Neukirch, J. Park, V. Zobac, H. Wang, P. Jelinek, O. V. Prezhdo, H.-C. Zhou, J. P. Lewis
Calculated photo-isomerization efficiencies of functionalized azobenzene derivatives in solar energy materials: azo-functional organic linkers for porous coordinated polymers
J. Phys.-Condens. Mat. 27 (2015) 134208(1) - 134208(11).

O. Romanyuk, P. Mutombo, F. Grosse
Ab initio Study of Atomic Disorder on As-rich GaAs(111)A Surface
Surf. Sci. 641 (2015) 330 - 335.

Mykola Telychko, Jan Berger, Zsolt Majzik, Pavel Jelínek, Martin ©vec
Graphene on SiC (0001) inspected by dynamic atomic force microscopy at room temperature
Beilstein J. Nanotechnol. 6 (2015) 901 - 906.

M. Telychko, P. Mutombo, P. Merino, P. Hapala, M. Ondráček, F.C. Bocquet, J. Sforzini, O. Stetsovych, M. Vondráček, P. Jelínek, M. ©vec
Electronic and Chemical Properties of Donor, Acceptor Centers in Graphene
ACS Nano 9 (2015) 9180 - 9187.

Sh. Yamazaki, K. Maeda, Y. Sugimoto, M. Abe, V. Zobač, P. Pou, L. Rodrigo, P. Mutombo, R. Perez, P. Jelínek, S. Morita
Interplay between Switching Driven by the Tunneling Current and Atomic Force of a Bistable Four-Atom Si Quantum Dot
Nano Lett. 15 (2015) 4356 - 4363.

V. Zobač, J.P. Lewis, E. Abad, J.I. Mendieta-Moreno, P. Hapala, P. Jelínek, J. Ortega
Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism
J. Phys.-Condens. Mat. 27 (2015) 175002(1) - 175002(11).


2014

P. Hapala, G. Kichin, Ch. Wagner, F. S. Tautz, R. Temirov, P. Jelínek
Mechanism of high-resolution STM/AFM imaging with functionalized tips
Phys. Rev. B 90 (2014) 085421(1) - 085421(9).

P. Hapala, R. Temirov, F. S. Tautz, P. Jelínek
Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips
Phys. Rev. Lett. 113 (2014) 226101(1) - 226101(5).

K. Kůsová, P. Hapala, J. Valenta, P. Jelínek, O. Cibulka, L. Ondič, I. Pelant
Direct Bandgap Silicon: Tensile-Strained Silicon Nanocrystals
Adv. Mater. Interf. 1 (2014) 1300042(1) - 1300042(9).

P. Merino, M. ©vec, J.I. Martinez, P. Jelínek, P. Lacovig, M. Dalmiglio, S. Lizzit, P. Soukiassian, J. Cernicharo, J.A. Martin-Gago
Graphene etching on SiC grains as a path to interstellar polycyclic aromatic hydrocarbons formation
Nat. Commun. 5 (2014) 3054(1) - 3054(9).

P. Mutombo, O. Romanyuk
Ab initio density functional theory study of non-polar (10-10), (11-20) and semipolar {20-21} GaN surfaces
J. Appl. Phys. 115 (2014) 203508-1 - 203508-5.

J. Onoda, M. Ondráček, A, Yurtsever, P. Jelínek, Y. Sugimoto
Initial and secondary oxidation products on the Si(111)-(7x7) surface identified by atomic force microscopy and first principles calculations
Appl. Phys. Lett. 104 (2014) 133107(1) - 133107(4).

M. Setvín, X. Hao, B. Daniel, J. Pavelec, Z. Novotny, G. S. Parkinson, M. Schmid, G. Kresse, C. Franchini, U. Diebold
Charge Trapping at the Step Edges of TiO2 Anatase (101)
Angew. Chem. Int. Ed. 53 (2014) 4714 - 4716.

E. J. Spadafora, J. Berger, P. Mutombo, M. Telychko, M. ©vec, Z. Majzik, A. B. McLean, P. Jelínek
Identification of Surface Defects and Subsurface Dopants in a Delta-Doped System Using Simultaneous nc-AFM/STM and DFT
J. Phys. Chem. C 118 (2014) 15744 - 15753.

M. ©vec, P. Hapala, M. Ondráček, P. Merino, M. Blanco-Rey, P. Mutombo, M. Vondráček, Y. Polyak, V. Cháb, J. A. Martín Gago, P. Jelínek
Silicene versus two-dimensional ordered silicide: Atomic and electronic structure of Si-(√19×√19)R23.4◦/Pt(111)
Phys. Rev. B 89 (2014) 201412(1) - 201412(5).

M. Telychko, P. Mutombo, M. Ondráček, P. Hapala, F.C. Bocquet, J. Kolorenč, M. Vondráček, P. Jelínek, M. ©vec
Achieving High-Quality Single-Atom Nitrogen Doping of Graphene/SiC(0001) by Ion Implantation and Subsequent Thermal Stabilization
ACS Nano 8 (2014) 7318 - 7324.


2013

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
J. Chem. Phys. 138 (2013) 154106(1) - 154106(8).

J. Berger, M. ©vec, M. Müller, M. Ledinský, A. Fejfar, P. Jelínek, Z. Majzik
Characterization of the mechanical properties of qPlus sensors
Beilstein J. Nanotechnol. 4 (2013) 1 - 9.

Z. Chromcova, M. C. Tringides and Z. Chvoj
Nucleation on a stepped surface with an Ehrlich–Schwöbel barrier
J. Phys.-Condens. Mat. 25 (2013) 265003(1) - 265003(8).

P. Hapala, K. Kůsová, I. Pelant, P. Jelínek
Theoretical analysis of electronic band structure of 2- to 3-nm Si nanocrystals
Phys. Rev. B 87 (2013) 195420(1) - 195420(13).

Z. Majzik, B. Drevniok, W. Kamiński, M. Ondráček, A. B. McLean, P. Jelínek
Room Temperature Discrimination of Adsorbed Molecules and Attachment Sites on the Si(111)–7 × 7 Surface Using a qPlus Sensor
ACS Nano 7 (2013) 2686 - 2692.

Z. Majzik, M.R. Tchalala, M. ©vec, 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
J. Phys.-Condens. Mat. 25 (2013) 225301(1) - 225301(6).

M. Maąín, L. Bergqvist, J. Kudrnovský, M. Kotrla, V. Drchal
First-principles study of thermodynamical properties of random magnetic overlayers on fcc-Cu(001) substrate
Phys. Rev. B 87 (2013) 075452(1) - 075452(8).

M. Maąín, L. Bergqvist, J. Kudrnovský, M. Kotrla, V. Drchal
Critical Temperatures of Random Iron–Cobalt Overlayers on the fcc-Cu(001) Substrate
J. Superconductivity and Novel Magnetism 26 (2013) 809 - 812.

M. Maąín, M. Kotrla, B. Yang, M. Asta, M. O. Jahma, and T. Ala-Nissila
Multiscale modeling of submonolayer growth for Fe/Mo(110)
Eur. Phys. J. B 86 (2013) 359 - 365.

P.Shukrynau, P. Mutombo, M.Hietschold V.Cháb

Appl. Surf. Sci. 270 (2013) 157 - 162.

P. Sobotík, M. Setvín, P. Zimmermann, P. Kocán, I. Oąt’ádal, P. Mutombo, M. Ondráček, P. Jelínek
Emergence of state at Fermi level due to the formation of In-Sn heterodimers on Si(100)-2×1
Phys. Rev. B 88 (2013) 205406(1) - 205406(7).

Y. Sugimoto, M. Ondráček, M. Abe, P. Pou, S. Morita, R. Pérez, F. Flores, P. Jelínek
Quantum Degeneracy in Atomic Point Contacts Revealed by Chemical Force and Conductance
Phys. Rev. Lett. 111 (2013) 106803(1) - 106803(5).

Y. Sugimoto, A. Yurtsever, M. Abe, S. Morita, M. Ondráček, P. Pou, R. Pérez, P. Jelínek
Role of Tip Chemical Reactivity on Atom Manipulation Process in Dynamic Force Microscopy
ACS Nano 7 (2013) 7370 - 7376.

A. J. Weymouth, D. Meuer, P. Mutombo, T. Wutscher, M. Ondráček, P. Jelínek, F. J. Giessibl
Atomic Structure Affects the Directional Dependence of Friction
Phys. Rev. Lett. 111 (2013) 126103(1) - 126103(4).

A. Yurtsever, Y. Sugimoto, H. Tanaka, M. Abe, S. Morita, M. Ondráček, P. Pou, R. Pérez, P. Jelínek
Force mapping on a partially H-covered Si(111)-(7x7) surface: Influence of tip and surface reactivity
Phys. Rev. B 87 (2013) 155403(1) - 155403(10).

(Total number of publications: 60)