Publications

Complete list of publications with downloadable copies whenever possible. Please send me an email if you can't access a paper you would like to see.

Peer-reviewed publications

 
[47]    C. Herbig, E.H. Åhlgren, W. Jolie, C. Busse, J. Kotakoski, A.V. Krasheninnikov & Thomas Michely,
Interfacial Carbon Nanoplatelet Formation by Ion Irradiation of Graphene on Ir(111),
ACS Nano, accepted for publication (2014).
DOI: 10.1021/nn503874n (Open Access)
 
[46]    G. Argentero, C. Mangler, J. Kotakoski, F.R. Eder & J.C. Meyer,
Towards weighing individual atoms by high-angle scattering of electrons,
Ultramicroscopy, accepted for publication (2014).
 
[45]    B.C. Bayer, C. Baehtz, P.R. Kidambi, R.S. Weatherup, C. Mangler, J. Kotakoski, C.J.L. Goddard, S. Caneva, A. Cabrero-Vilatela, J.C. Meyer & S. Hofmann,
Nitrogen controlled iron catalyst phase during carbon nanotube growth,
Appl. Phys. Lett. 105, 143111 (2014).
PDF: Download a preprint
DOI: 10.1063/1.4897950 (Open Access)
 
[44]    J. Kotakoski, C. Mangler & J. C. Meyer,
Imaging Atomic-Level Random Walk of a Point Defect in Graphene,
Nat. Commun. 5, 4991 (2014).
ArXiv: 1404.7434
DOI: 10.1038/ncomms4991 (Open Access)
animation
 
[43]    T. Susi, J. Kotakoski, D. Kepaptsoglou, C. Mangler, T.C. Lovejoy, O.L. Krivanek, R. Zan, U. Bangert, P. Ayala, J.C. Meyer & Q. Ramasse,
Silicon-carbon bond inversions driven by 60 keV electrons in graphene,
Phys. Rev. Lett. 113, 115501 (2014).
DOI: 10.1103/PhysRevLett.113.115501 (Open Access)
ArXiv: 1407.4274
 
[42]    A.W. Cummings, D.L. Duong, V.L. Nguyen, D.V. Tuan, J. Kotakoski, Y.H. Lee & S. Roche,
Charge Transport in Polycrystalline Graphene: Challenges and Opportunities,
Adv. Mater. 26, 5079-5094 (2014).
PDF: Download a postprint
DOI: 10.1002/adma.201401389
 
[41]    J. Kotakoski, F.R. Eder & J.C. Meyer,
Atomic structure and energetics of large vacancies in graphene,
Phys. Rev. B 89, 201406(R) (2014).
PDF: Download a preprint
ArXiv: 1404.5396
DOI: 10.1103/PhysRevB.89.201406 (Open Access)
 
[40]    F.R. Eder, J. Kotakoski, U. Kaiser & J.C. Meyer,
A Journey from Order to Disorder — Atom by Atom Transformation from Graphene to a 2D Carbon Glass,
Sci. Rep. 4, 4060 (2014).
DOI: 10.1038/srep04060 (Open Access)
PDF: Download a preprint, Download the supplement
ZIP: Download the supplementary structures
 
[39]    D. Jimenez, A. W. Cummings, F. Chaves, D. V. Tuan, J. Kotakoski & S. Roche,
Impact of graphene polycrystallinity on the performance of graphene field-effect transistors,
Appl. Phys. Lett. 104, 043509 (2014).
DOI: 10.1063/1.4863842
ArXiv: 1402.0734
 
[38]    T. Björkman, S. Kurasch, O. Lehtinen, J. Kotakoski, O.V. Yazyev, A. Srivastava, V. Skakalova, J.H. Smet, U. Kaiser & A.V. Krasheninnikov,
Defects in bilayer silica and graphene: common trends in diverse hexagonal two-dimensional systems,
Sci. Rep. 3, 3482 (2013).
DOI: 10.1038/srep03482 (Open Access)
 
[37]    J. C. Meyer, J. Kotakoski & C. Mangler,
Atomic structure from large-area, low-dose exposures of materials: A new route to circumvent radiation damage,
Ultramicroscopy 145, 13-21 (2014).
DOI: 10.1016/j.ultramic.2013.11.010 (Open Access via Austrian Science Fund (FWF))
 
[36]    E.H. Åhlgren, S. Hämäläinen, O. Lehtinen, P. Liljeroth & J. Kotakoski,
Structural manipulation of the graphene/metal-interface with Ar+ irradiation,
Phys. Rev. B 88, 155419 (2013).
DOI: 10.1103/PhysRevB.88.155419
ArXiv: 1310.1755
 
[35]    D.V. Tuan, J. Kotakoski, T. Louvet, F. Ortman, J.C. Meyer & S. Roche,
Scaling Properties of Charge Transport in Polycrystalline Graphene,
Nano Lett. 13, 1730-1735 (2013).
DOI: 10.1021/nl400321r
ACS Articles on Request: Free Download (50 copies first year, then unlimited)
 
[34]    S. Standop, O.J. Lehtinen, C. Herbig, G. Lewes-Malandrakis, F. Craes, J. Kotakoski, T. Michely, A.V. Krasheninnikov & C. Busse,
Ion Impacts on Graphene/Ir(111): Interface Channeling, Vacancy Funnels, and a Nanomesh,
Nano Lett. 13, 1948-1955 (2013).
DOI: 10.1021/nl304659n
ACS Articles on Request: Free Download (50 copies first year, then unlimited)
 
[33]    F. Eder, J. Kotakoski, K. Holzweber, C. Mangler, V. Skakalova & J.C. Meyer,
Probing from both sides: Reshaping the graphene landscape via face-to-face dual-probe microscopy,
Nano Lett. 13, 1934-1940 (2013).
DOI: 10.1021/nl3042799 (Open Access via Austrian Science Fund (FWF))
PDF: Download a reprint
 
[32]    A. Santana, A. Zobelli, J. Kotakoski, A. Chuvilin & E. Bichoutskaia
Inclusion of radiation damage dynamics in high resolution transmission electron microscopy image simulations: The example of graphene,
Phys. Rev. B 87, 094110 (2013).
DOI: 10.1103/PhysRevB.87.094110 (Open Access)
PDF: Download a preprint
 
[31]    H.-P. Komsa, J. Kotakoski, S. Kurasch, O. Lehtinen, U. Kaiser & A. V. Krasheninnikov
Two-dimensional transition metal dichalcogenides under electron irradiation: Defect production and doping,
Phys. Rev. Lett., 109, 035503 (2012).
DOI: 10.1103/PhysRevLett.109.035503
arXiv: 1206.4407
 
[30]    J. Kotakoski & J.C. Meyer,
Mechanical properties of polycrystalline graphene based on a realistic atomistic model,
Phys. Rev. B 85, 195447 (2012).
DOI: 10.1103/PhysRevB.85.195447
arXiv: 1203.4196
 
[29]    T. Susi, J. Kotakoski, H. Jiang, S. Kurasch, H.J. Park, V. Skakalova, U. Kaiser, A.V. Krasheninnikov, E.I. Kauppinen & J.C. Meyer,
Atomistic Description of Electron Beam Damage in Nitrogen-Doped Graphene and Single-Walled Carbon Nanotubes,
ACS Nano 6, 8837-8846 (2012).
DOI: 10.1021/nn303944f
ACS Articles on Request: Free download (50 copies first year, then unlimited)
 
[28]    E. H. Åhlgren, J. Kotakoski, O. Lehtinen & A.V. Krasheninnikov,
Ion irradiation tolerance of graphene as studied by atomistic simulations,
Appl. Phys. Lett., 100, 233108 (2012).
DOI: 10.1063/1.4726053
arXiv: 1205.1826
 
[27]    S. Kurasch, J. Kotakoski, O. Lehtinen, V. Skakalova, J. Smet, C.E. Krill III, A.V. Krasheninnikov & U. Kaiser,
Atom-by-atom observation of grain boundary migration in graphene,
Nano Lett., 12, 3168-3173 (2012).
DOI: 10.1021/nl301141g
ACS Articles on Request: Free download (50 copies first year, then unlimited)
 
[26]    J.C. Meyer, F. Eder, S. Kurasch, V. Skakalova, J. Kotakoski, H.J. Park, S. Roth, A. Chuvilin, A.V. Krasheninnikov & U. Kaiser,
An accurate measurement of electron beam induced displacement cross sections for single-layer graphene,
Phys. Rev. Lett., 108, 196102 (2012).
DOI: 10.1103/PhysRevLett.108.196102
arXiv: 1203.2372
 
[25]    E. Holmström, J. Kotakoski, L. Lechner, U. Kaiser & K. Nordlund,
Atomic-scale effects behind structural instabilities in Si lamellae during ion beam thinning,
AIP Advances 2, 012186 (2012).
DOI: 10.1063/1.3698411 (Open Access)
 
[24]    P. Huang, S. Kurasch, A. Srivastava, V. Skakalova, J. Kotakoski, A. Krasheninnikov, H. Robert, Q. Mao, J. Meyer, J. Smet, D. Muller & U. Kaiser,
Direct Imaging of a Two-Dimensional Silica Glass on Graphene,
Nano Lett. 12, 1081-1086 (2012).
DOI: 10.1021/nl204423x
ACS Articles on Request: Free download
 
[23]    J. Kotakoski, D. Santos-Cottin, & A.V. Krasheninnikov,
Stability of Graphene Edges under Electron Beam: Equilibrium Energetics vs. Dynamic Effects,
ACS Nano 6, 671-676 (2012).
DOI: 10.1021/nn204148h
ACS Articles on Request: Free download
 
[22]    J. Kotakoski, J.C. Meyer, S. Kurasch, D. Santos-Cottin, U. Kaiser & A.V. Krasheninnikov
Stone-Wales-type transformations in carbon nanostructures driven by electron irradiation,
Editors's suggestion: Phys. Rev. B 83, 245420 (2011).
DOI: 10.1103/PhysRevB.83.245420
arXiv: 1105.1617
 
[21]    D. Şopu, J. Kotakoski & K. Albe
Finite-size effects in the phonon density of states of nanostructured germanium: A comparative study of nanoparticles, nanocrystals, nanoglasses and bulk phases,
Phys. Rev. B, 83, 245416 (2011).
DOI: 10.1103/PhysRevB.83.245416
PDF: Download a preprint
 
[20]    O. Lehtinen, J. Kotakoski, A.V. Krasheninnikov & J. Keinonen
Cutting and controlled modification of graphene with ion beams,
Nanotechnology 22, 175306 (2011).
DOI: 10.1088/0957-4484/22/17/175306
arXiv: 1102.0737
 
[19]    E. H. Åhlgren, J. Kotakoski & A.V. Krasheninnikov
Atomistic simulations of the implantation of low energy boron and nitrogen ions into graphene,
Phys. Rev. B 83, 115424 (2011).
DOI: 10.1103/PhysRevB.83.115424
arXiv: 1102.0645
 
[18]    J. Kotakoski, A.V. Krasheninnikov, U. Kaiser & J.C. Meyer,
From point defects in graphene to two-dimensional amorphous carbon,
Phys. Rev. Lett. 106, 105505 (2011).
DOI: 10.1103/PhysRevLett.106.105505
arXiv: 1102.0174
 
[17]    F. Banhart, J. Kotakoski & A.V. Krasheninnikov,
Structural Defects in Graphene (review),
ACS Nano 5, 26-41 (2011).
DOI: 10.1021/nn102598m
ACS Articles on Request: Free download
 
[16]    O. Lehtinen, E. Dumur, J. Kotakoski, K. Nordlund & A.V. Krasheninnikov,
Production of defects in hexagonal boron nitride monolayer under ion irradiation,
Nucl. Instr. Meth. Phys. Res. B 269, 1327-1331 (2011).
DOI: 10.1016/j.nimb.2010.11.027
PDF: Download a preprint
 
[15]    J. Kotakoski, C.H. Jin, O. Lehtinen, K. Suenaga & A.V. Krasheninnikov,
Knock-on damage in hexagonal boron nitride monolayers,
Phys. Rev. B 82, 113404 (2010).
DOI: 10.1103/PhysRevB.82.113404
PDF: Download a reprint
 
[14]    O. Lehtinen, J. Kotakoski, A.V. Krasheninnikov, A. Tolvanen, K. Nordlund & J. Keinonen,
Effects of ion bombardment on a two-dimensional target: Atomistic simulations of graphene irradiation,
Phys. Rev. B 81, 153401 (2010).
DOI: 10.1103/PhysRevB.81.153401
PDF: Download a reprint
 
[13]    Y. Ma, A. R. Oganov, Z. Li, Y. Xie & J. Kotakoski,
Novel high pressure structures of polymeric nitrogen,
Phys. Rev. Lett. 102, 065501 (2009).
DOI: 10.1103/PhysRevLett.102.065501
PDF: Download a reprint
 
[12]    J. Kotakoski & K. Albe,
First principles calculations on solid nitrogen: A comparative study of high pressure phases,
Phys. Rev. B 77, 144109 (2008).
DOI: 10.1103/PhysRevB.77.144109
PDF: Download a reprint
 
[11]    Y. Gan, J. Kotakoski, A.V. Krasheninnikov, K. Nordlund & F. Banhart,
The diffusion of interstitial atoms in carbon nanotubes,
New J. Phys. 10, 023022 (2008).
DOI: 10.1088/1367-2630/10/2/023022
PDF: Download a reprint
 
[10]    A. Tolvanen, J. Kotakoski, A.V. Krasheninnikov & K. Nordlund,
Relative abundance of single and double vacancies in irradiated single-walled carbon nanotubes,
Appl. Phys. Lett. 91, 173109 (2007).
DOI: 10.1063/1.2800807
PDF: Download a reprint
 
[9]    J. Kotakoski, A.V. Krasheninnikov & K. Nordlund,
Kinetic Monte Carlo simulations of the response of carbon nanotubes to electron irradiation,
J. Comp. Theor. Nanosci. 4, 1153-1159 (2007).
URL: Link to the article
PDF: Download a reprint
 
[8]    J. Kotakoski,
Irradiation-mediated tailoring of carbon nanotubes,
Report Series in Physics, HU-P-D137 (2007), Ph.D. Thesis.
ISBN: 978-952-10-3239-4
PDF: Download a reprint
 
[7]    J. Kotakoski, A.V. Krasheninnikov & K. Nordlund,
Atomistic simulations of irradiation effects in carbon nanotubes: an overview,
Rad. Eff. and Def. in Solids 162, 157 (2007), ICTP 2006 (Trieste) workshop.
DOI: 10.1080/10420150601132537
PDF: Download a preprint
 
[6]    J. Kotakoski, A.V. Krasheninnikov & K. Nordlund,
Energetics, structure and long-range interaction of vacancy defects on carbon nanotubes: Atomistic simulations,
Phys. Rev. B 74, 245420 (2006).
DOI: 10.1103/PhysRevB.74.245420
PDF: Download a reprint
 
[5]    J. Kotakoski & K. Nordlund,
Binding a carbon nanotube to the Si (100) surface using ion irradiation - an atomistic simulation study,
New J. Phys. 8, 115 (2006).
DOI: 10.1088/1367-2630/8/7/115
PDF: Download a reprint
 
[4]    J. Kotakoski, A.V. Krasheninnikov & K. Nordlund,
A molecular dynamics study of the clustering of implanted potassium in multiwalled carbon nanotubes,
Nucl. Instr. Meth. Phys. Res. B 240, 810-818 (2005).
DOI: 10.1016/j.nimb.2005.06.200
PDF: Download a reprint
 
[3]    J. Samela, J. Kotakoski, K. Nordlund & J. Keinonen,
A quantitative and comparative study of sputtering yields in Au,
Nucl. Instr. Meth. Phys. Res. B 239, 331-346 (2005).
DOI: 10.1016/j.nimb.2005.05.047
PDF: Download a reprint
 
[2]    J. Kotakoski, A.V. Krasheninnikov, Y. Ma, A. S. Foster, K. Nordlund & R. M. Nieminen,
B and N implantation onto carbon nanotubes: insight from atomistic simulations,
Phys. Rev. B 71, 205408 (2005).
DOI: 10.1103/PhysRevB.71.205408
PDF: Download a reprint
 
[1]    J. Kotakoski, J.A.V. Pomoell, A.V. Krasheninnikov & K. Nordlund,
Irradiation-induced substitution of carbon atoms with nitrogen and boron in single-walled carbon nanotubes,
Nucl. Instr. Meth. Phys. Res. B 228, 31-36 (2005).
DOI: 10.1016/j.nimb.2004.10.018
PDF: Download a reprint

Conference papers

[5]    F. Eder, J. C. Meyer, S. Kurasch, U. Kaiser, V. Skakalova, J. Kotakoski, A. V. Krasheninnikov & A. Chuvilin,
Quantitative Analysis of Electron Beam-Induced Destruction of Graphene Membranes under an Electron Microscope,
Microscopy and Microanalysis 18, 1500-1501 (2012).
DOI: 10.1017/S143192761200935X
 
[4]    P. Huang, R. Hovden, Q. Mao, D. A. Muller, S. Kurasch, U. Kaiser, A. Srivastava, V. Skakalova, J. Smet, J. Kotakoski, A. V. Krasheninnikov & J. C. Meyer,
Imaging the Atoms in a Two-Dimensional Silica Glass on Graphene,
Microscopy and Microanalysis 18, 1496-1497 (2012).
DOI: 10.1017/S1431927612009336
 
[3]    P. Huang, R. Hovden, Q. Mao, D. A. Muller, S. Kurasch, U. Kaiser, J. Kotakoski, A. V. Krasheninnikov, A. Srivastava, V. Skakalova, J. Smet & J. C. Meyer,
Quantitative Atomic-resolution Imaging and Spectroscopy of a 2D Silica Glass,
Microscopy and Microanalysis 18, 340-341 (2012).
DOI: 10.1017/S1431927612003558
 
[2]    J. Kotakoski & O. Lehtinen,
Nanomachining Graphene with Ion Irradiation,
in Graphene Materials and Devices (Mater. Res. Soc. Symp. Proc. Vol. 1259E, Warrendale, PA, 2010), 1259-S18-02.
DOI: 10.1557/PROC-1259-S18-02
PDF: Download a reprint
 
[1]    J. Kotakoski & K. Nordlund,
Ion irradiation-induced welding of a carbon nanotube to a Si (100) surface,
in Growth, Modification, and Analysis by Ion Beams at the Nanoscale, edited by Joerg K. N. Lindner, Marcel Toulemonde, William J. Weber, Barney L. Doyle (Mater. Res. Soc. Symp. Proc. Vol. 908E, Warrendale, PA, 2006), 0908-OO15-01.
DOI: 10.1557/PROC-0908-OO15-01
PDF: Download a reprint

Other publications

[10]    T. Susi & J. Kotakoski,
Kohti avointa verkkojulkaisemista – hinnalla millä hyvänsä?,
Signum 6:2012, Finnish Research Library Association, Finland.
 
[9]    J. Kotakoski & T. Susi,
Tiedejulkaisemisen noidankehää purkamassa,
Tiedetoimittaja 02/2012, 22-24, Finnish Association of Science Editors and Journalists, Turku, Finland.
URL: Available here (pdf)
 
[8]    J. Kotakoski & T. Susi,
Akateeminen kevät,
Yliopisto 05/2012, 52, Helsinki, Finland.
URL: Available here (jpg)
 
[7]    J. Kotakoski & T. Susi,
Koittiko viimein "avoimen julkaisun kevät"?,
Kajahdus 01/2012, 22-24, Helsinki, Finland.
URL: Available on this website
 
[6]    J. Kotakoski,
Atom-scale modification in graphene and hexagonal boron nitride, Research highlight of the Division of materials physics in "Annual report 2010, Department of physics, University of Helsinki (2011).
PDF: Download the submitted version
 
[5]    J. Kotakoski & A.V. Krasheninnikov,
Native and irradiation-induced defects in graphene: What can we learn from atomistic simulations?, book chapter published in "Computational Nanoscience" monograph (edited by Elena Bichoutskaia) in the RSC Theoretical and Computational Chemistry Series (2011), ISBN: 978-1-84973-133-1.
PDF: Download the submitted version
 
[4]    J. Kotakoski,
Atomistic simulations on polymeric nitrogen,
published in Schriften des Forschungszentrums Jülich, IAS Series, Vol. 3, pp. 105-110, edited by Münster, Wolf and Kremer (FZ Jülich GmbH, Jülich, Germany, 2010).
URL: Available through FZ Jülich website
PDF: Download a reprint
 
[3]    J. Kotakoski,
opinion Ateistille riittää elämä itsessään, published in newspaper Helsingin Sanomat (4.3.2010, Helsinki, Finland).
URL: Available on this website
 
[2]    J. Kotakoski,
contributed images to book Universumi tietokoneessa, by Leena Tähtinen, Chris Flynn and Esko Valtaoja (Tähtitieteellinen yhdistys Ursa, Helsinki, Finland, 2009).
 
[1]    K. Nordlund, A. Krasheninnikov & J. Kotakoski,
The exciting science of imperfect carbon nanotubes, CSC News 4, 26-27 and cover (2006).