List of publications; pre-/postprints for download

Publication list

Peer-reviewed publications

[141]		H.M. Fruehwald, Y. Liebsch, U. Javed, H. Lebius, C. Grygiel, J. Kotakoski, M. Schleberger & R.D.L. Smith,
		Introducing basal-plane pores to activate monolayer MoS2 for the hydrogen evolution,
		In preparation (2024).

[140]		C. Speckmann, K. Mustonen, D. Propst, C. Mangler & J. Kotakoski,
		Electron-irradiation effects in monolayer MoS2 at elevated temperatures,
		Submitted for publication (2024).
		arXiv: 2411.03200

[139]		C. Speckmann, A. Angeletti, L. Kyvala, D. Lamprecht, F. Herterich, C. Mangler, L. Filipovic, C. Dellago, C. Franchini & J. Kotakoski,
		Electron-beam-induced adatom-vacancy-complexes in mono- and bilayer phosphorene,
		Adv. Mater. Interfaces, accepted for publication (2024).
		arXiv: 2409.11102

[138]		S.M. Noisternig, Gammer, H.P. Karnthaler, J. Kotakoski & Ch. Rentenberger,
		Probing the interaction range of electron beam-induced etching in STEM by a non-contact electron beam,
		Ultramicroscopy 265, 114019 (2024).
		DOI: 10.1016/j.ultramic.2024.114019

[137]		D. Propst, W. Joudi, M. Längle, J. Madsen, C. Kofler, B.M. Mayer, D. Lamprecht, C. Mangler, L. Filipovic, T. Susi, & J. Kotakoski,
		Automated image acquisition and analysis of graphene and hBN from pristine to highly defective and amorphous structures,
		Sci. Rep. 14, 26939 (2024).
		DOI: 10.1038/s41598-024-77740-9

[136]		M. Längle, B.M. Mayer, J. Madsen, D. Propst, A. Bo, C. Kofler, V. Hana, C. Mangler, T. Susi, & J. Kotakoski,
		Defect-engineering hexagonal boron nitride using low-energy Ar+ irradiation,
		Submitted for publication (2024).
		ArXiv: 2404.07166

[135]		B. Fickl, T.M. Seifried, E. Rait, J. Genser, Th. Wicht, J. Kotakoski, G. Rupprechter, A. Lugstein, D. Zhang, Ch. Dipolt, H. Grothe, D. Eder, & B.C. Bayer,
		Controllable Freezing Transparency for Water Ice on Scalable Graphene Films on Copper,
		Submitted for publication (2024).
		ArXiv: 2403.15629

[134]		V. Chesnyak, D. Perilli, M. Panighel, A. Nomar, A. Markevich, T.A. Bui, A. Ugolotti, A. Farooq, M. Stredansky, C. Kofler, C. Cepek, G. Comelli, J. Kotakoski, C. di Valentin & C. Africh,
		Scalable Bottom-Up Synthesis of Exceptionally Stable Co-Ni-Doped Graphene,
		Sci. Adv. 10, eado8956 (2024).
		DOI: 10.1126/sciadv.ado8956

[133]		M. Längle, K. Mizohata, C. Mangler, A. Trentino, K. Mustonen, E.H. Åhlgren & J. Kotakoski,
		Two-dimensional few-atom noble gas clusters in a graphene sandwich,
		Nat. Mater. 23, 762 (2024).
		DOI: 10.1038/s41563-023-01780-1
		ArXiv: 2306.15436

[132]		M. Lucherelli, L. Stiegler, F. Steiger, E.H. Åhlgren, J. Requena-Ramírez, E. Castro, L. Echegoyen, A. Hirsch, W. Peukert, J. Kotakoski, J. Walter, M.E. Pérez-Ojeda, & G. Abellán,
		Carbon nano-onions: individualization and enhanced water solubility,
		Carbon 31, 118760 (2024).
		DOI: 10.1016/j.carbon.2023.118760

[131]		A. Trentino, G. Zagler, M. Längle, J. Madsen, T. Susi, C. Mangler, E.H. Åhlgren, K. Mustonen & J. Kotakoski,
		Single metal atoms and nanoclusters anchored to graphene vacancies,
		Micron 184, 103667 (2024).
		DOI: 10.1016/j.micron.2024.103667

[130]		D. Propst, J. Kotakoski & E.H. Åhlgren,
		Impurity atom configurations in diamond and their visibility via scanning transmission electron microscopy imaging,
		Electron. struct. 5, 033004 (2023).
		DOI: 10.1088/2516-1075/acf9d3
		ArXiv: 2308.16141

[129]		A. Niggas, K. Fischer, S. Kretschmer, M. Werl, H. Biber, C. Speckmann, N. McEvoy, J. Kotakoski, F. Aumayr, A.V. Krasheninnikov & R.A. Wilhelm,
		Charge-exchange dependent energy loss of H and He in freestanding monolayers of graphene and MoS2,
		Phys. Rev. A 108, 062823 (2023).
		DOI: 10.1103/PhysRevA.108.062823

[128]		T.A. Bui, G.T. Leuthner, J. Madsen, M.R.A. Monazam, A.I. Chirita, A. Postl, C. Mangler, J. Kotakoski & T. Susi,
		Creation of single vacancies in hBN with electron irradiation,
		Small 19, 2301926 (2023).
		DOI: 10.1002/smll.202301926
		ArXiv: 2303.00497

[127]		C. Speckmann, J. Lang, J. Madsen, M. Monazam, G. Zagler, G.T. Leuthner, N. McEvoy, C. Mangler, T. Susi, & J. Kotakoski,
		Combined electronic excitation and knock-on damage in monolayer MoS2,
		Phys. Rev. B 107, 094112 (2023).
		DOI: 10.1103/PhysRevB.107.094112
		ArXiv: 2302.10529

[126]		K. Elibol, T. Susi, C. Mangler, D. Eder, J.C. Meyer, J. Kotakoski, R.G. Hobbs, P.A. van Aken, & B.C. Bayer,
		Linear indium atom chains at graphene edges,
		npj 2D Materials and Applications 7, 2 (2023).
		DOI: 10.1038/s41699-023-00364-6

[125]		R. Singh, D. Scheinecker, U. Ludacka & J. Kotakoski,
		Corrugations in free-standing graphene,
		Nanomaterials 12, 3562 (2022).
		DOI: 10.3390/nano12203562

[124]		E.H. Åhlgren, A. Markevich, S. Scharinger, B. Fickl, G. Zagler, F. Herterich, N. McEvoy, C. Mangler & J. Kotakoski,
		Atomic-scale Oxygen-mediated Etching of 2D MoS₂ and MoTe₂,
		Adv. Mater. Interfaces, 2200987 (2022).
		DOI: 10.1002/admi.202200987
		ArXiv: 2205.00855

[123]		G. Zagler, A. Trentino, K. Mustonen, C. Mangler & J. Kotakoski,
		Interface effects on titanium growth on graphene,
		2D Mater. 10, 045025 (2023).
		DOI: 10.1088/2053-1583/acf22e
		ArXiv: 2204.09669

[122]		G. Zagler, M. Stecher, A. Trentino, et al.,
		Beam-driven Dynamics of Aluminium Dopants in Graphene,
		2D Mater. 9, 035009 (2022).
		DOI: 10.1088/2053-1583/ac6c30

[121]		A. Postl, P.P.P. Hilgert, A. Markevich, J. Madsen, K. Mustonen, J. Kotakoski & T. Susi,
		Indirect measurement of the carbon adatom migration barrier on graphene,
		Carbon 196, 596-601 (2022).
		DOI: 10.1016/j.carbon.2022.05.039
		ArXiv: 2202.04485

[120]		A. Niggas, J. Schwestka, K. Balzer, D. Weichselbaum, et al.,
		Ion-induced surface charge dynamics in freestanding monolayers of graphene and MoS2 probed by the emission of electrons,
		Phys. Rev. Lett. 129, 086802 (2022).
		DOI: 10.1103/PhysRevLett.129.086802

[119]		A. Trentino, K. Mizohata, G. Zagler, M. Längle, K. Mustonen, T. Susi, J. Kotakoski & E.H. Åhlgren,
		Two-step implantation of gold into graphene,
		2D Mater. 9, 025011 (2022).
		DOI: 10.1088/2053-1583/ac4e9c

[118]		C. Kröckel, U. Ludacka, R. Singh, J. Kotakoski, S. Reich, F. Hauke, J.C. Chacón-Torres & A. Hirsch,
		Recovery process in chemically doped single-walled carbon nanotubes,
		submitted for publication (2022).

[117]		A. Chirita, A. Markevich, M. Tripathi, N.A. Pike, M.J. Verstraete, J. Kotakoski & T. Susi,
		Three-dimensional ab initio description of vibration-assisted electron knock-on displacements in graphene,
		Phys. Rev. B 105, 235419 (2022).
		DOI:: 10.1103/PhysRevB.105.235419
		ArXiv: 2111.14498

[116]		K. Mustonen, Ch. Hofer, P. Kotrusz, A. Markevich, M. Hulman, C. Mangler, T. Susi, T.J. Pennycook, J.C. Meyer, J. Kotakoski & V. Skakalova,
		Towards exotic layered materials: 2D Cuprous Iodide,
		Adv. Mater., 202106922 (2022).
		DOI: 10.1002/adma.202106922
		ArXiv: 2109.08456

[115]		Ma.E.Pérez-Ojeda, E. Castro, C. Kröckel, M.A. Lucherelli, U. Ludacka, J. Kotakoski, K. Werbach, H. Peterlik, M. Melle-Franco, J.C. Chacón-Torres, F. Hauke, L. Echegoyen, A. Hirsch & G. Abellán,
		Carbon Nano-onions (Multilayer Fullerenes): Potassium Intercalation and Reductive Covalent Functionalization,
		J. Am. Chem. Soc. 143, 18997-19007 (2021).
		DOI: 10.1021/jacs.1c07604


[114]		K. Zhussupbekov, L. Ansari, K. Elibol, A. Zhussupbekova, J. Kotakoski, I.V. Shvets, G.S. Duesberg, P.K. Hurley, N. McEvoy, C.Ó. Coileáin & F. Gity,
		Revealing the influence on edge states on the electronic properties of PtSe2,
		Applied Materials Today 35, 101926 (2023).
		DOI: 10.1016/j.apmt.2023.101926

[113]		A. Trentino, J. Madsen, A. Mittelberger, C. Mangler, T. Susi, K. Mustonen & J. Kotakoski,
		Atomic-level structural engineering of graphene on a mesoscopic scale,
		Nano Lett. 21, 5179-5185 (2021).
		DOI: 10.1021/acs.nanolett.1c01214

[112]		G.T. Leuthner, T. Susi, C. Mangler, J.C. Meyer & J. Kotakoski,
		Chemistry at graphene edges in the electron microscope,
		2D Mater. 8, 035023 (2021).
		DOI: 10.1088/2053-1583/abf624
		ArXiv: 2012.03703

[111]		S. Hummel, K. Elibol, D. Zhang, K. Sampathkumar, O. Frank, D. Eder, C. Schwalb, J. Kotakoski, J.C. Meyer & B.C. Bayer,
		Direct visualization of local deformations in suspended graphene membranes by coupled in-situ atomic force and scanning electron microscopy,
		Appl. Phys. Lett. 118, 103104 (2021).
		DOI: 10.1063/5.0040522

[110]		A.E. Goldt, O.T. Zaremba, M.O. Bulavskiy, F.S. Fedorov, K.V. Larionov, A.P. Tsapenko, Z.I. Popov, P. Sorokin, A.S. Anisimov, H. Inani, J. Kotakoski, K. Mustonen & A.G. Nasibulin,
		Highly efficient bilateral doping of single-walled carbon nanotubes,
		J. Mater. Chem. C 9, 4514-4521 (2021).
		DOI: 10.1039/d0tc05996j
		arXiv: 2104.00757

[109]		H. Inani, D.H. Shin, J. Madsen, H.J. Jeong, M.H. Kwon, N. McEvoy, T. Susi, C. Mangler, S.W. Lee, K. Mustonen & J. Kotakoski,
		Step-by-step atomic insights into structural reordering from 2D to 3D MoS2,
		Adv. Func. Mater. 31, 2008395 (2021).
		DOI: 10.1002/adfm.202008395

[108]		C. Brand, M.R.A. Monazam, C. Mangler, Y. Lilach, O. Cheshnovsky, M. Arndt & J. Kotakoski,
		The morphology of doubly-clamped graphene nanoribbons,
		2D Mater. 8, 025035 (2021).
		DOI: 10.1088/2053-1583/abe952

[107]		K. Elibol, C. Mangler, D.D. O'Regan, K. Mustonen, D. Eder, J.C. Meyer, J. Kotakoski, T. Susi & B.C. Bayer,
		Single indium atoms and few-atom indium clusters anchored onto graphene via silicon heteroatoms,
		ACS Nano 15, 14373−14383 (2021).
		ArXiv: 2009.00063
		DOI: 10.1021/acsnano.1c03535

[106]		J. Schwestka, H. Inani, M. Tripathi, A. Niggas, N. McEvoy, F. Libisch, F. Aumayr, J. Kotakoski & R.A. Wilhelm,
		Atomic-scale carving of nanopores into a van-der-Waals heterostructure with slow highly charged ions,
		ACS Nano 14, 10536-10543 (2020).
		DOI: 10.1021/acsnano.0c04476

[105]		M. Mostaghelchi, J. Kotakoski, C. Rentenberger & C.L. Lengauer,
		Kiruna-Type Ore as a Novel Precursor for Large-Scale Production of Small Uniform Iron Oxide Nanoparticles,
		J. Nanosci. Nanotech. 20, 6625-6531 (2020).
		DOI: 10.1166/jnn.2020.18438

[104]		S. Creutzburg, J. Schwestka, A. Niggas, et al.,
		Vanishing influence of the band gap on charge exchange of slow highly charged ions in freestanding single layer MoS2,
		Phys. Rev. B 102, 045408 (2020).
		DOI: 10.1103/PhysRevB.102.045408

[103]		S. Ahmad, K. Mustonen, B. McLean, H. Jiang, Q. Zhang, A. Hussain, A.T. Khan, E.-X. Ding, Y. Liao, N. Wei, M.R.A. Monazam, A.G. Nasibulin, J. Kotakoski, A.J. Page & E.I. Kauppinen,
		Hybrid Low-Dimensional Carbon Allotropes Formed in Gas Phase,
		Adv. Func. Mater. 30, 2005016 (2020).
		DOI: 10.1002/adfm.202005016

[102]		T. Hartl, M. Will, D. Capeta, et al.,
		Cluster Superlattice Membranes,
		ACS Nano 14, 13629-13637 (2020).
		DOI: 10.1021/acsnano.0c05740

[101]		J.H. Choi, D.H. Shin, H. Inani, M.H. Kwon, K. Mustonen, C. Mangler, M. Park, H. Jeong, D.S. Lee, J. Kotakoski & S.W. Lee,
		Transformation and Evaporation of Surface Adsorbents on a Graphene “Hot Plate”,
		ACS Appl. Mater. Interfaces 12, 26313-26319 (2020).
		DOI: 10.1021/acsami.0c02056

[100]		K. Elibol, C. Mangler, G. Tushar, G. Zagler, D. Eder, J.C. Meyer, J. Kotakoski & B.C. Bayer
		Process Pathway Controlled Evolution of Phase and Van-der-Waals Epitaxy in In/In2O3 on Graphene Heterostructures,
		Adv. Func. Mater. 30, 2003300 (2020).
		DOI: 10.1002/adfm.202003300

[99]		G. Zagler, M. Reticcioli, C. Mangler, D. Scheinecker, C. Franchini & J. Kotakoski,
		CuAu, a hexagonal two-dimensional metal,
		2D Mater. 7, 045017 (2020).
		DOI: 10.1088/2053-1583/ab9c39
		ArXiv: 1909.06372

[98]		C. Hofer, V. Skakalova, T. Goerlich, M. Tripathi, A. Mittelberger, C. Mangler, M.R.A. Monazam, T. Susi, J. Kotakoski & J.C. Meyer,
		Direct imaging of light-element impurities in graphene reveals triple-coordinated oxygen,
		Nat. Commun. 10, 4570 (2019).
		DOI: 10.1038/s41467-019-12537-3

[97]		A. Hussain, E.-X. Ding, S. Ahmad, K. Mustonen, Y. Liao, M. Tavakkoli, Q. Zhang, H. Jiang, J. Kotakoski & E.I. Kauppinen,
		Scalable Growth of Single-Walled Carbon Nanotubes with Highly Uniform Structure,
		Nanoscale 12, 12263-12267 (2020).
		DOI: 10.1039/D0NR01919D

[96]		M.R.A. Monazam, U. Ludacka, H.-P. Komsa & J. Kotakoski,
		Substitutional Si impurities in monolayer hexagonal boron nitride,
		Appl. Phys. Lett. 115, 071604 (2019).
		DOI: 10.1063/1.5112375
		ArXiv: 1904.02432

[95]		Y. Liao, K. Mustonen, S. Tulić, V. Skákalová, S.A. Khan, P. Laiho, Q. Zhang, C. Li, M. Monazam, J. Kotakoski, H. Lipsanen & E. Kauppinen,
		Enhanced Tunnelling in a Hybrid of Single-Walled Carbon Nanotubes and Graphene,
		ACS Nano 13, 11522-11529 (2019).
		DOI: 10.1021/acsnano.9b05049
		ArXiv: 1903.06449

[94]		K. Mustonen, A. Markevich, M. Tripathi, H. Inani, E.-X. Ding, A. Hussain, C. Mangler, E.I. Kauppinen, J. Kotakoski & T. Susi,
		Electron-Beam Manipulation of Silicon Impurities in Single-Walled Carbon Nanotubes,
		Adv. Funct. Mater. 29, 1901327 (2019).
		DOI: 10.1002/adfm.201901327
		ArXiv: 1902.03972

[93]		H. Inani, K. Mustonen, A. Markevich, E.-X. Ding, M. Tripathi, A. Hussain, C. Mangler, E.I. Kauppinen, T. Susi & J. Kotakoski,
		Si Substitution in Nanotubes and Graphene via Intermittent Vacancies,
		J. Phys. Chem. C 123, 13136-13140 (2019).
		DOI: 10.1021/acs.jpcc.9b01894
		ArXiv: 1902.02611

[92]		C. Brand, M. Debiossac, T. Susi, F. Aguillon, J. Kotakoski, P. Roncin & M. Arndt,
		Coherent diffraction of hydrogen through the 246 pm lattice of graphene,
		New J. Phys. 21, 033004 (2019).
		DOI: 10.1088/1367-2630/ab05ed

[91]		T. Susi, J.C. Meyer & J. Kotakoski,
		Quantifying electron irradiation effects in transmission electron microscopy using 2D materials,
		Nat. Rev. Phys. 1, 397-405 (2019).
		DOI: 10.1038/s42254-019-0058-y
		ArXiv: 1912.01877

[90]		R. Kozubek, M. Tripathi, M. Ghorbani-Asl, et al.,
		Perforating freestanding molybdenum disulfide monolayers with highly charged ions,
		J. Phys. Chem. Lett. 10, 904-310 (2019).
		DOI: 10.1021/acs.jpclett.8b03666
		ArXiv: 1907.01171

[89]		A.I. Chirita, T. Susi & J. Kotakoski,
		Influence of temperature on the displacement threshold energy in graphene,
		Sci. Rep. 9, 12981 (2019).
		DOI: 10.1038/s41598-019-49565-4
		ArXiv: 1811.04011

[88]		C. Hofer, V. Skakalova, M.R.A. Monazam, C. Mangler, J. Kotakoski, T. Susi & J.C. Meyer,
		Direct visualization of the 3D structure of silicon impurities in graphene,
		Appl. Phys. Lett. 114, 053102 (2019).
		DOI: 10.1063/1.5063449
		ArXiv: 1809.08946

[87]		G.T. Leuthner, S. Hummel, C. Mangler, T.J. Pennycook, T. Susi, J.C. Meyer & J. Kotakoski,
		Scanning transmission electron microscopy under controlled low-pressure atmospheres,
		Ultramicroscopy 203, 76-81 (2019).
		DOI: 10.1016/j.ultramic.2019.02.002
		ArXiv: 1811.04266

[86]		B.C. Bayer, R. Kaindl, M.R.A. Monazam, T. Susi, J. Kotakoski, T. Gupta, D. Eder, W. Waldhauser & J.C. Meyer,
		Atomic Scale In Situ Observations of Crystallization and Restructuring Processes in Two-Dimensional MoS2 Films,
		ACS Nano 12, 8758-8769 (2018).
		DOI: 10.1021/acsnano.8b04945

[85]		M. Schleberger & J. Kotakoski,
		2D Material Science: Defect Engineering by Particle Irradiation,
		Materials 11, 1885 (2018).
		DOI: 10.3390/ma11101885

[84]		U. Ludacka, M.R.A. Monazam, C. Rentenberger, M. Friedrich, U. Stefanelli, J.C. Meyer & J. Kotakoski,
		In situ control over graphene ripples and strain in the electron microscope,
		npj 2D Materials and Applications 2, 25 (2018).
		DOI: 10.1038/s41699-018-0069-z

[83]		T. Susi, J. Madsen, U. Ludacka, J.J. Mortensen, T.J. Pennycook, Z. Lee, J. Kotakoski, U. Kaiser & J.C. Meyer,
		Efficient first principles simulation of electron scattering factors for transmission electron microscopy,
		Ultramicroscopy 197, 16-22 (2019).
		DOI: 10.1016/j.ultramic.2018.11.002
		ArXiv: 1803.05338

[82]		K. Mustonen, A. Hussain, C. Hofer, M. Monazam, R. Mirzayev, K. Elibol, P. Laiho, C. Mangler, H. Jiang, T. Susi, E. Kauppinen, J. Kotakoski & J.C. Meyer,
		Atomic-Scale Deformations at the Interface of a Mixed-Dimensional van der Waals Heterostructure,
		ACS Nano 12, 8512-8519 (2018).
		DOI: 10.1021/acsnano.8b04050

[81]		C. Su, M. Tripathi, Q.-B. Yan, Z. Wang, Z. Zhang, L. Basile, G. Su, M. Dong, J. Kotakoski, J. Kong, J.-C. Idrobo, T. Susi & J. Li,
		Engineering single-atom dynamics with electron irradiation,
		Sci. Adv. 5, eaav2252 (2019).
		DOI: 10.1126/sciadv.aav2252
		ArXiv: 1803.01369

[80]		M. Tripathi, A. Markevich, R. Böttger, S. Facsko, E. Besley, J. Kotakoski & T. Susi,
		Implanting germanium into graphene,
		ACS Nano 12, 4641-4647 (2018).
		DOI: 10.1021/acsnano.8b01191
		ArXiv: 1802.04660

[79]		T. Susi, M. Scardamaglia, K. Mustonen, et al.,
		Intrinsic core level photoemission of suspended monolayer graphene,
		Phys. Rev. Mater. 2, 074005 (2018).
		DOI: 10.1103/PhysRevMaterials.2.074005
		ArXiv: 1807.11870

[78]		C. Hofer, C. Kramberger, M.R.A. Monazam, C. Mangler, A. Mittelberger, G. Argentero, J. Kotakoski & J.C. Meyer,
		Revealing the 3D structure of graphene defects,
		2D Mater. 5, 045029 (2018).
		DOI: 10.1088/2053-1583/aaded7
		ArXiv: 1807.00677

[77]		M. Tripathi, A. Mittelberger, N. A. Pike, C. Mangler, J.C. Meyer, M. J. Verstraete, J. Kotakoski & T. Susi,
		Electron-beam manipulation of silicon dopants in graphene,
		Nano Lett. 18, 5319-5323 (2018).
		DOI: 10.1021/acs.nanolett.8b02406
		ArXiv: 1712.08755

[76]		K. Elibol, T. Susi, G. Argentero, M.R.A. Monazam, T.J. Pennycook, J.C. Meyer & J. Kotakoski,
		Atomic structure of intrinsic and electron-irradiation-induced defects in MoTe2,
		Chem. Mater. 30, 1230-1238 (2018).
		DOI: 10.1021/acs.chemmater.7b03760
		ArXiv: 1802.01552

[75]		V. Skakalova, P. Kotrusz, M. Jergel, T. Susi, A. Mittelberger, V. Vretenar, P. Siffalovic, J. Kotakoski, J.C. Meyer & M. Hulman,
		Chemical Oxidation of Graphite: Evolution of the Structure and Properties,
		J. Phys. Chem. C 122, 929-935 (2018).
		DOI: 10.1021/acs.jpcc.7b10912

[74]		Y.K. Mishra, N.A. Murugan, J. Kotakoski & J. Adam,
		Progress in electronics and photonics with nanomaterials,
		Vacuum 146, 304-307 (2017).
		DOI: 10.1016/j.vacuum.2017.09.035

[73]		R. Nieman, A.J.A. Aquino, T.P. Hardcastle, J. Kotakoski, T. Susi & H. Lischka,
		Structure and Electronic States of a Graphene Double Vacancy with Embedded Si Dopant,
		J. Chem. Phys. 147, 194702 (2017).
		DOI: 10.1063/1.4999779
		ArXiv: 1711.07250

[72]		T. Susi, D. Kepaptsoglou, Y.-C. Lin, Q. Ramasse, J.C. Meyer, K. Suenaga & J. Kotakoski,
		Towards atomically precise manipulation of 2D nanostructures in the electron microscope,
		2D Mater. 4, 042004 (2017).
		DOI: 10.1088/2053-1583/aa878f
		PDF: Download a preprint

[71]		X. Zhao, J. Kotakoski, J.C. Meyer, E. Sutter, P. Sutter, A.V. Krasheninnikov, U. Kaiser & W. Zhou,
		Engineering and modifying two-dimensional materials by electron beams,
		MRS Bulletin 42, 667-676 (2017).
		DOI: 10.1557/mrs.2017.184

[70]		D. Nosraty Alamdary, J. Kotakoski & T. Susi,
		Structure and energetics of embedded Si structures in graphene,
		Phys. Status Solidi B 254, 1700188 (2017).
		DOI: 10.1002/pssb.201700188
		ArXiv: 1704.08019

[69]		M. Tripathi, A. Mittelberger, K. Mustonen, C. Mangler, J. Kotakoski, J.C. Meyer & T. Susi
		Cleaning graphene: comparing heat treatments in air and in vacuum,
		Phys. Status Solidi (RRL) 11, 1700124 (2017).
		DOI: 10.1002/pssr.201700124
		ArXiv: 1704.08038

[68]		R. Mirzayev, K. Mustonen, M.R.A. Monazam, A. Mittelberger, T.J. Pennycook, C. Mangler, T. Susi, J. Kotakoski & J.C. Meyer,
		Buckyball Sandwiches,
		Sci. Adv. 3, e1700176 (2017).
		DOI: 10.1126/sciadv.1700176
		ArXiv: 1706.05947

[67]		B.C. Bayer, S. Caneva, T.J. Pennycook, J. Kotakoski, C. Mangler, S. Hofmann & J.C. Meyer,
		Introducing Overlapping Grain Boundaries in Chemical Vapor Deposited Hexagonal Boron Nitride Monolayer Films,
		ACS Nano 11, 4521-4527 (2017).
		DOI: 10.1021/acsnano.6b08315

[66]		T. Susi, V. Skakalova, A. Mittelberger, P. Kotrusz, M. Hulman, T.J. Pennycook, C. Mangler, J. Kotakoski & J.C. Meyer,
		Computational insights and the observation of SiC nanograin assembly: towards 2D silicon carbide,
		Sci. Rep. 7, 4399 (2017).
		DOI: 10.1038/s41598-017-04683-9
		ArXiv: 1701.07387

[65]		H. Vázquez, E. H. Åhlgren, O. Ochedowski, et al.,
		Creating nanoporous graphene with swift heavy ions,
		Carbon 114, 511-518 (2017).
		DOI: 10.1016/j.carbon.2016.12.015

[64]		K. Elibol, T. Susi, M. O’Brien, B.C. Bayer, T.J. Pennycook, N. McEvoy, G.S. Duesberg, J.C. Meyer & J. Kotakoski,
		Grain boundary-mediated nanopores in molybdenum disulfide grown by chemical vapor deposition,
		Nanoscale 9, 1591-1598 (2017).
		DOI: 10.1039/C6NR08958E
		ArXiv: 1612.07852

[63]		G. Argentero, A. Mittelberger, M.R.A. Monazam, Y. Cao, T.J. Pennycook, C. Mangler, C. Kramberger-Kaplan, J. Kotakoski, A.K. Geim & J.C. Meyer,
		Unraveling the 3D atomic structure of a suspended graphene/hBN van der Waals heterostructure,
		Nano Lett. 17, 1409-1416 (2017).
		DOI: 10.1021/acs.nanolett.6b04360
		ArXiv: 1702.02836

[62]		T. Susi, T.P. Hardcastle, H. Hofsäss, A. Mittelberger, T.J. Pennycook, C. Mangler, R. Drummond-Brydson, A.J. Scott, J.C. Meyer & J. Kotakoski,
		Single-atom spectroscopy of phosphorus dopants implanted into graphene,
		2D Mater. 4, 021013 (2017).
		DOI: 10.1088/2053-1583/aa5e78
		ArXiv: 1610.03419

[61]		T. Susi, J.C. Meyer & Jani Kotakoski,
		Manipulating low-dimensional materials down to the level of single atoms with electron irradiation,
		Ultramicroscopy 180, 163-172 (2017).
		DOI: 10.1016/j.ultramic.2017.03.005
		ArXiv: 1703.02429

[60]		L. Madauß, O. Ochedowski, H. Lebius, B. Ban-d'Etat, C. Naylor, A. Johnson, J. Kotakoski & M. Schleberger,
		Defect engineering of single- and few-layer MoS2 by swift heavy ion irradiation,
		2D Materials 4, 015034 (2017).
		DOI: 10.1088/2053-1583/4/1/015034

[59]		T. Susi, C. Hofer, G. Argentero, G.T. Leuthner, T.J. Pennycook, C. Mangler, J.C. Meyer & J. Kotakoski,
		Isotope analysis in the transmission electron microscope,
		Nat. Commun. 7, 13040 (2016).
		DOI: 10.1038/ncomms13040
		ArXiv: 1608.04676
		Press release: Deutsch, English, Infographic (pdf): Deutsch, English


[58]		C. Yim, K. Lee, N. McEvoy, M. O'Brien, S. Riazimehr, N.C. Berner, C.P. Cullen, J. Kotakoski, J.C. Meyer, M.C. Lemme & G.S. Duesberg,
		High-performance hybrid electronic devices from layered PtSe2 films grown at low temperature,
		ACS Nano 10, 9550-9558 (2016).
		DOI: 10.1021/acsnano.6b04898
		ArXiv: 1606.08673

[57]		K. Elibol, B.C. Bayer, S. Hummel, J. Kotakoski, G. Argentero & J.C. Meyer,
		Visualising the strain distribution in suspended two-dimensional materials under local deformation,
		Sci. Rep. 6, 28485 (2016).
		DOI: 10.1038/srep28485

[56]		D. Emmrich, A. Beyer, A. Nadzeyka, S. Bauerdick, J.C. Meyer, J. Kotakoski & A. Gölzhäuser,
		Nanopore fabrication and characterization by helium ion microscopy,
		Appl. Phys. Lett. 108, 163103 (2016).
		DOI: 10.1063/1.4947277

[55]		L. Shi, P. Rohringer, K. Suenaga, Y. Niimi, J. Kotakoski, J.C. Meyer, H. Peterlik, P. Ayala & T. Pichler,
		Confined linear carbon chains as a route to bulk carbyne,
		Nat. Mater. 15, 634-639 (2016).
		DOI: 10.1038/nmat4617
		ArXiv: 1507.04896

[54]		J.C. Chacon-Torres, S. Dzsaber, S. Vega-Diaz, J. Akbarzadeh, H. Peterlik, J. Kotakoski, G. Argentero, J.C. Meyer, T. Pichler, F. Simon, M. Terrones & S. Reich,
		Potassium intercalated multiwalled carbon nanotubes,
		Carbon 105, 90-95 (2016).
		DOI: 10.1016/j.carbon.2016.04.016

[53]		T. Susi & J. Kotakoski,
		Comment on "Temperature dependence of atomic vibrations in mono-layer graphene" [J. Appl. Phys. 118, 074302 (2015)],
		J. Appl. Phys. 119, 066101 (2016).
		DOI: 10.1063/1.4941385

[52]		M. O'Brien, N. McEvoy, C. Motta, J.-Y. Zheng, N.C. Berner, J. Kotakoski, K. Elibol, T.J. Pennycook, J.C. Meyer, C. Yim, M. Abid, T. Hallam, J.F. Donegan, S. Sanvito & G.S. Duesberg,
		Raman Characterization of Platinum Diselenide Thin Films,
		2D Materials 3, 021004 (2016).
		DOI: 10.1088/2053-1583/3/2/021004
		ArXiv: 1512.09317

[51]		C. Herbig, E.H. Åhlgren, U.A. Schröder, A.J. Martinez-Galera, M.A. Arman, J. Kotakoski, J. Knudsen, A.V. Krasheninnikov & T. Michely,
		Xe Irradiation of Graphene on Ir(111): From Trapping to Blistering,
		Phys. Rev. B 92, 085429 (2015).
		DOI: 10.1103/PhysRevB.92.085429
		ArXiv: 1508.02915

[50]		J. Kotakoski, C. Brand, Y. Lilach, O. Cheshnovsky, C. Mangler, M. Arndt & J.C. Meyer,
		Toward two-dimensional all-carbon heterostructures via ion beam patterning of single-layer graphene,
		Nano Lett. 15, 5944-5949 (2015).
		DOI: 10.1021/acs.nanolett.5b02063 (Open Access)

[49]		C. Brand, M. Sclafani, C. Knobloch, Y. Lilach, T. Juffmann, J. Kotakoski, C. Mangler, A. Winter, A. Turchanin, J.C. Meyer, O. Cheshnovsky & M. Arndt,
		An atomically thin matter-wave beam splitter,
		Nature Nanotech. 10, 845-848 (2015).
		ArXiv: 1602.07578
		DOI: 10.1038/nnano.2015.179

[48]		C. Herbig, E.H. Åhlgren, U. Schröder, A. Martinez-Galera, M. Arman, W. Jolie, C. Busse, J. Kotakoski, J. Knudsen, A.V. Krasheninnikov & Thomas Michely,
		Comment on "Interfacial Carbon Nanoplatelet Formation by Ion Irradiation of Graphene on Ir(111)",
		ACS Nano 9, 4664-4665 (2015).
		DOI: 10.1021/acsnano.5b02303
		ACS Articles on Request: Free Download (50 copies first year, then unlimited)

[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 8, 12208-12218 (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 151, 23-30 (2015).
		ArXiv: 1501.05541
		DOI: 10.1016/j.ultramic.2014.11.031

[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)


[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).
		ArXiv: 1407.4274
		DOI: 10.1103/PhysRevLett.113.115501 (Open Access)

[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).
		ArXiv: 1507.06272
		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, R. Arenal, S. Kurasch, H. Jiang, V. Skakalova, O. Stephan, A.V. Krasheninnikov, E. Kauppinen, U. Kaiser & 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,
		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,
		Electron 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

Patents

[1]		J. Kotakoski, T. Susi, J.C. Meyer,
		Method and Apparatus for Determination of an Isotope Concentration using a Microscope with Energetic Particles,
		application submitted (2016).

Conference papers

[30]		T. Susi, N. Dellby, R. Hayner, C. Hofer, J. Kotakoski, T.C. Lovejoy, C. Mangler, A. Mittelberger, T.J. Pennycook & B. Plotkin-Swing
		Open-source Phase Reconstruction of Focused-Probe 4D-STEM Data with Near-Ideal Direct-Electron Detection,
		Microsc. Microanal. 30 S1, ozae044.920 (2024).
		DOI: 10.1093/mam/ozae044.920

[29]		U. Javed, C. Speckmann, W. Joudi, M. Längle, A. Trentino, E.H. Åhlgren, D. Lamprecht, C. Mangler, K. Mustonen, T. Susi & J. Kotakoski,
		Scanning Transmission Electron Microscopy as a Part of an Integrated Vacuum Setup for Growth and Manipulation of 2D Materials,
		Microsc. Microanal. 30 S1, ozae044.547 (2024).
		DOI: 10.1093/mam/ozae044.547

[28]		K. Elibol, T. Susi, C. Mangler, J.C. Meyer, J. Kotakoski, R.G. Hobbs, P.A. van Aken & B.C. Bayer
		Formation of Metal Atom Chains at the Edges of Graphene Nanoribbons Supported by Graphene,
		Microsc. Microanal. 30 S1, ozae044.778 (2024).
		DOI: 10.1093/mam/ozae044.778

[27]		A. Trentino, G. Zagler, M. Längle, D. Propst, E.H. Åhlgren, C. Mangler, K. Mustonen, T. Susi & J. Kotakoski,
		Single Heteroatom Configurations in Graphene and Diamond,
		Microsc. Microanal. 29 S1, 1364 (2023).
		DOI: 10.1093/micmic/ozad067.700

[26]		C. Mangler, J. Meyer, A. Mittelberger, K. Mustonen, T. Susi & J. Kotakoski,
		A Materials Scientist's CANVAS: A System for Controlled Alteration of Nanomaterials in Vacuum Down to the Atomic Scale,
		Microsc. Microanal. 28 S1, 2940 (2022).
		DOI: 10.1017/S1431927622009977

[25]		W. Joudi, A. Trentino, K. Mustonen, C. Mangler & J. Kotakoski,
		Correlated AFM/STEM Study on the Mechanical Stiffness of Defect-Engineered Graphene,
		Microsc. Microanal. 28 S1, 2626 (2022).
		DOI: 10.1017/S1431927622009977

[24]		A. Postl, T.A. Bui, F. Kraft, A. Chirita, G. Leuthner, H. Inani, C. Mangler, K. Mustonen, J. Kotakoski & T. Susi,
		Adventures in Atomic Resolution in situ STEM,
		Microsc. Microanal. 28 S1, 2342 (2022).
		DOI: 10.1017/S1431927622008996

[23]		A. Chirita, A. Markevich, J. Kotakoski & T. Susi,
		Atomistic understanding of damage and beam-driven dynamics in 2D materials,
		Microsc. Microanal. 26 S2, 542-543 (2020).
		DOI: 10.1017/S1431927620015007

[22]		M. Längle, K. Mizohata, E.H. Åhlgren, A. Trentino, K. Mustonen & J. Kotakoski,
		2D Noble Gas Crystals Encapsulated in Few-Layer Graphene,
		Microsc. Microanal. 26 S2, 1086-1089 (2020).
		DOI: 10.1017/S1431927620016918

[21]		C. Brand, T. Susi, J. Kotakoski, M. Arndt, M. Debiossac, F. Aguillon & P. Roncin,
		Diffraction of 80 eV hydrogen through suspended graphene,
		J. Phys. Conf. Ser. 20, 202036 (2020).
		DOI: 10.1088/1742-6596/1412/20/202036

[20]		J. Schwestka, H. Inani, M. Tripathi, P.L. Grande, R. Heller, N. Klingner, A. Niggas, R. Kozubek, L. Madauss, S. Facsko, J. Kotakoski, M. Schleberger, F. Aumayr & R.A. Wilhelm,
		Energy deposition of highly charged ions transmitted through single layer MoS2,
		J. Phys. Conf. Ser. 1412, 162018 (2020).
		DOI: 10.1088/1742-6596/1412/16/162018

[19]		G. Leuthner, T.A. Bui, G. Zagler, B. Fickl, M. Monazam, A. Chirita, T. Susi & J. Kotakoski,
		Quantitative measurement and utilization of electron irradiation effects in 2D materials,
		Microsc. Microanal. 26 S2, 166 (2020).
		DOI: 10.1017/S1431927620013653

[18]		T. Susi, T. Lehnert, U. Kaiser, J.C. Meyer & J. Kotakoski,
		Quantifying Elastic and Inelastic Electron Irradiation Damage in Transmission Electron Microscopy of 2D Materials,
		Microsc. Microanal. 25 S2, 454-455 (2019).
		DOI: 10.1017/S1431927619003003

[17]		M.R.A. Monazam, U. Ludacka, H.-P. Komsa & J. Kotakoski
		Silicon Substitution in Monolayer Hexagonal Boron Nitride,
		Microsc. Microanal. 25 S2, 2082-2083 (2019).
		DOI: 10.1017/S1431927619011140

[16]		H. Inani, K. Mustonen, A. Markevich, E.-X. Ding, M. Tripathi, A. Hussian, C. Mangler, E.I. Kauppinen, T. Susi & J. Kotakoski,
		Substitutional Si Doping of Graphene and Nanotubes through Ion Irradiation-Induced Vacancies,
		Microsc. Microanal. 25 S2, 1574-1575 (2019).
		DOI: 10.1017/S1431927619008602

[15]		G.T. Leuthner, C. Mangler, J.C. Meyer, T. Susi & J. Kotakoski,
		Atomic-scale Chemical Manipulation of Materials in the Scanning Transmission Electron Microscope under Controlled Atmospheres,
		Microsc. Microanal. 25 S2, 1398-1399 (2019).
		DOI: 10.1017/S1431927619007724

[14]		G. Zagler, C. Mangler & J. Kotakoski,
		Patterned Ultra-Thin Gold Nanostructures on Graphene,
		Microsc. Microanal. 25 S2, 1530-1531 (2019).
		DOI: 10.1017/S1431927619008389

[13]		T. Susi, M. Tripathi, K. Mustonen, A. Markevich, C. Mangler, C. Su, J. Li, J.C. Idrobo, J.C. Meyer & J. Kotakoski,
		Electron-Beam Manipulation of Lattice Impurities in Graphene and Single-Walled Carbon Nanotubes,
		Microsc. Microanal. 25 S2, 938-939 (2019).
		DOI: 10.1017/S1431927619005427

[12]		C. Hofer, K. Mustonen, A. Mittelberger, M.R.A. Monazam, A. Hussain, C. Mangler, C. Kramberger, E.I. Kauppinen, T. Susi, J. Kotakoski & J.C. Meyer,
		Graphene hybrids and extended defects: Revealing 3D structures and new insights to radiation damage,
		Microsc. Microanal. 24 S1, 1582-1583 (2018).
		DOI: 10.1017/S1431927618008395

[11]		T. Susi, A. Mittelberger, C. Kramberger, C. Mangler, C. Hofer, T. Pennycook, J. Kotakoski & J.C. Meyer,
		Understanding and exploiting the interaction of electron beams with low-dimensional materials—From controlled atomic-level manipulation to circumventing radiation damage,
		Microsc. Microanal. 23 S1, 196-197 (2017).
		DOI: 10.1017/S1431927617002987

[10]		G. Argentero, K. Mustonen, R. Mirzayev, A. Mittelberger, T. Susi, G. Leuthner, Y. Cao, M. Monazam, T. Pennycook, C. Mangler, C. Kramberger, A.K. Geim, J. Kotakoski & J.C. Meyer,
		A new detection scheme for van der Waals heterostructures, imaging individual fullerenes between graphene sheets, and controlling the vacuum in scanning transmission electron microscopy,
		Microsc. Microanal. 23 S1, 460-461 (2017).
		DOI: 10.1017/S1431927617002987

[9]		J.C. Meyer, J. Kotakoski, G. Argentero, C. Mangler, B. Bayer, C. Kramberger-Kaplan, F. Eder, S. Hummel, K. Elibol & A. Mittelberger,
		Exploring low-dimensional carbon materials by high-resolution electron and scanning probe microscopy,
		Microsc. Microanal. 21 S3, 1147-1148 (2015).
		DOI: 10.1017/S1431927615006522

[8]		J. Kotakoski, F. Eder, G. Argentero, S. Hummel, D. Lindner & J.C. Meyer,
		Atomic structure of amorphous 2D carbon structures as revealed by scanning transmission electron microscopy,
		Microsc. Microanal. 21 S3, 997-998 (2015).
		DOI: 10.1017/S1431927615005784

[7]		Q.M. Ramasse, D.M. Kepapstoglou, F.S. Hage, T. Susi, J. Kotakoski, C. Mangler, P. Ayala, J. Meyer, J.A. Hinks, S. Donnelly, R. Zan, C.T. Pan, S.J. Haigh & U. Bangert,
		Atom-by-Atom STEM Investigation of Defect Engineering in Graphene,
		Microsc. Microanal. 20, 1736-1737 (2014).
		DOI: 10.1017/S1431927614010411

[6]		J. Kotakoski, F. Eder, U. Kaiser, C. Mangler & J. C. Meyer,
		Irradiation-induced Modifications and Beam-driven Dynamics in Low-dimensional Materials,
		Microsc. and Microanal. 20 S2, 1726-1727 (2014).
		DOI: 10.1017/S1431927614010368

[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,
		Microsc. Microanal. 18 S2, 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,
		Microsc. Microanal. 18 S2, 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,
		Microsc. Microanal. 18 S2, 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

[11]		O. Lehtinen & J. Kotakoski,
		Structural changes in 2D materials due to scattering of light ions,
		Helium Ion Microscopy. Ed. G. Hlawacek, A. Gölzhäuser. Springer, 2016. p. 63-88 (Nanoscience and Technology).

[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).