Atomic precision materials engineering

Research output

Publications per year 2018 2019 2021 2022 2023 2024

• 40 Article
• 7 Meeting abstract/Conference paper
• 1 Review

Publications per year

Publications per year

Search results

• 2024

  Automated image acquisition and analysis of graphene and hexagonal boron nitride from pristine to highly defective and amorphous structures

  Propst, D., Joudi, W., Längle, M., Madsen, J., Kofler, C., Mayer, B. M., Lamprecht, D., Mangler, C., Filipovic, L., Susi, T. & Kotakoski, J., 6 Nov 2024, In: Scientific Reports. 14, 1, 10 p., 26939.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• GPAW: An open Python package for electronic structure calculations

  Mortensen, J. J., Larsen, A. H., Kuisma, M., Ivanov, A. V., Taghizadeh, A., Peterson, A., Haldar, A., Dohn, A. O., Schäfer, C., Jónsson, E. Ö., Hermes, E. D., Nilsson, F. A., Kastlunger, G., Levi, G., Jónsson, H., Häkkinen, H., Fojt, J., Kangsabanik, J., Sødequist, J., Lehtomäki, J., & 27 othersHeske, J., Enkovaara, J., Winther, K. T., Dulak, M., Melander, M. M., Ovesen, M., Louhivuori, M., Walter, M., Gjerding, M., Lopez-Acevedo, O., Erhart, P., Warmbier, R., Würdemann, R., Kaappa, S., Latini, S., Boland, T. M., Bligaard, T., Skovhus, T., Susi, T., Maxson, T., Rossi, T., Chen, X., Schmerwitz, Y. L. A., Schiøtz, J., Olsen, T., Jacobsen, K. W. & Thygesen, K. S., 7 Mar 2024, In: Journal of Chemical Physics. 160, 9, 41 p., 092503.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Single atoms and metal nanoclusters anchored to graphene vacancies

  Trentino, A., Zagler, G., Längle, M., Madsen, J., Susi, T., Mangler, C., Åhlgren, E. H., Mustonen, K. & Kotakoski, J., Sept 2024, In: Micron. 184, 7 p., 103667.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2023

  Challenges for Scaling Up Electron-Beam Manipulation of Graphene Impurities

  Postl, A., Kozyrau, E., Madsen, J. & Susi, T., 22 Jul 2023, In: Microscopy and Microanalysis. 29, Suppl. 1, p. 1370-1371 2 p.

  Publications: Contribution to journal › Meeting abstract/Conference paper › Peer Reviewed

  Open Access

• Combined electronic excitation and knock-on damage in monolayer MoS₂

  Speckmann, C., Lang, J., Madsen, J., Ahmadpour Monazam, M. R., Zagler, G., Leuthner, G. T., McEvoy, N., Mangler, C., Susi, T. & Kotakoski, J., 1 Mar 2023, In: Physical Review B. 107, 9, 7 p., 094112.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

  • Molybdenum Sulfide 100%
  • Monolayer 100%
  • Electronic Excitation 100%
  • Reaction Mechanism 50%
  • Energy 50%

• Computationally Efficient Handling of Partially Coherent Electron Sources in (S)TEM Image Simulations via Matrix Diagonalization

  Li, Z., Rose, H., Madsen, J., Biskupek, J., Susi, T. & Kaiser, U., Feb 2023, In: Microscopy and Microanalysis. 29, 1, p. 364–373 10 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Creation of Single Vacancies in hBN with Electron Irradiation

  Bui, T. A., Leuthner, G. T., Madsen, J., Monazam, M. R. A., Chirita, A. I., Postl, A., Mangler, C., Kotakoski, J. & Susi, T., 27 Sept 2023, In: Small. 19, 39, 9 p., 2301926 .

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Deep reinforcement learning for data-driven adaptive scanning in ptychography

  Schloz, M., Müller, J., Pekin, T. C., Van den Broek, W., Madsen, J., Susi, T. & Koch, C. T., 30 May 2023, In: Scientific Reports. 13, 1, 10 p., 8732.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Direct Positioning of Point Defects in 3D Materials Using STEM

  Hudak, B. M., Markevich, A., Susi, T., Lupini, A. R. & Stroud, R. M., 22 Jul 2023, In: Microscopy and Microanalysis. 29, Suppl. 1, p. 1365 1 p.

  Publications: Contribution to journal › Meeting abstract/Conference paper › Peer Reviewed

  Open Access

• Linear indium atom chains at graphene edges

  Elibol, K., Susi, T., Mangler, C., Eder, D., Meyer, J. C., Kotakoski, J., Hobbs, R. G., van Aken, P. A. & Bayer, B. C., 25 Jan 2023, In: npj 2D Materials and Applications. 7, 1, 8 p., 2.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2022

  Accurate Computational Prediction of Core-Electron Binding Energies in Carbon-Based Materials: A Machine-Learning Model Combining Density-Functional Theory and GW

  Golze, D., Hirvensalo, M., Hernandez-Leon, P., Aarva, A., Etula, J., Susi, T., Rinke, P., Laurila, T. & Caro, M. A., 26 Jul 2022, In: Chemistry of Materials. 34, 14, p. 6240-6254 15 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Beam-driven dynamics of aluminium dopants in graphene

  Zagler, G., Stecher, M., Trentino, A., Kraft, F., Su, C., Postl, A., Längle, M., Pesenhofer, C., Mangler, C., Ahlgren, E. H., Markevich, A., Zettl, A., Kotakoski, J., Susi, T. & Mustonen, K., 1 Jul 2022, In: 2D Materials. 9, 3, 9 p., 035009.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Deep learning for electron and scanning probe microscopy: From materials design to atomic fabrication

  Kalinin, S., Ziatdinov, M., Spurgeon, S. R., Ophus, C., Stach, E. A., Susi, T., Agar, J. & Randall, J., Sept 2022, In: MRS Bulletin. 47, 9, p. 931-939 9 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Graphene Lattices with Embedded Transition-Metal Atoms and Tunable Magnetic Anisotropy Energy: Implications for Spintronic Devices

  Langer, R., Mustonen, K., Markevich, A., Otyepka, M., Susi, T. & Blonski, P., 28 Jan 2022, In: ACS Applied Nano Materials. 5, 1, p. 1562–1573 12 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Identifying and manipulating single atoms with scanning transmission electron microscopy

  Susi, T., 14 Nov 2022, In: Chemical Communications. 58, 88, p. 12274-12285 12 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Indirect measurement of the carbon adatom migration barrier on graphene

  Postl, A., Hilgert, P. P. P., Markevich, A., Madsen, J., Mustonen, K., Kotakoski, J. & Susi, T., 30 Aug 2022, In: Carbon. 196, p. 596-601 6 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Ion-Induced Surface Charge Dynamics in Freestanding Monolayers of Graphene and MoS₂ Probed by the Emission of Electrons

  Niggas, A., Schwestka, J., Balzer, K., Weichselbaum, D., Schlünzen, N., Heller, R., Creutzburg, S., Inani, H., Tripathi, M., Speckmann, C., McEvoy, N., Susi, T., Kotakoski, J., Gan, Z., George, A., Turchanin, A., Bonitz, M., Aumayr, F. & Wilhelm, R. A., 19 Aug 2022, In: Physical Review Letters. 129, 8, 9 p., 086802.

  Publications: Contribution to journal › Article › Peer Reviewed

• Three-dimensional ab initio description of vibration-assisted electron knock-on displacements in graphene

  Chirita, A., Markevich, A., Tripathi, M., Pike, N. A., Verstraete, M. J., Kotakoski, J. & Susi, T., 13 Jun 2022, In: Physical Review B. 105, 23, 6 p., 235419.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Toward Exotic Layered Materials: 2D Cuprous Iodide

  Mustonen, K., Hofer, C., Kotrusz, P., Markevich, A., Hulman, M., Mangler, C., Susi, T., Pennycook, T. J., Hricovini, K., Richter, C., Meyer, J. C., Kotakoski, J. & Skakalova, V., 3 Mar 2022, In: Advanced Materials. 34, 9, 9 p., 2106922.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Two-step implantation of gold into graphene

  Trentino, A., Mizohata, K., Zagler, G., Längle, M., Mustonen, K., Susi, T., Kotakoski, J. & Åhlgren, E. H., Apr 2022, In: 2D Materials. 9, 2, 7 p., 025011.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2021

  ab initio description of bonding for transmission electron microscopy

  Madsen, J., Pennycook, T. J. & Susi, T., Dec 2021, In: Ultramicroscopy. 231, 11 p., 113253.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Atomic-Level Structural Engineering of Graphene on a Mesoscopic Scale

  Trentino, A., Madsen, J., Mittelberger, A., Mangler, C., Susi, T., Mustonen, K. & Kotakoski, J., 23 Jun 2021, In: Nano Letters. 21, 12, p. 5179-5185 7 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Catalytic graphitization of single-crystal diamond

  Tulić, S., Waitz, T., Čaplovičová, M., Habler, G., Vretenár, V., Susi, T. & Skákalová, V., 15 Nov 2021, In: Carbon. 185, p. 300-313 14 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Chemistry at graphene edges in the electron microscope

  Leuthner, G. T., Susi, T., Mangler, C., Meyer, J. C. & Kotakoski, J., 29 Apr 2021, In: 2D Materials. 8, 3, 8 p., 035023.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Interferometric 4D-STEM for Lattice Distortion and Interlayer Spacing Measurements of Bilayer and Trilayer 2D Materials

  Zachman, M. J., Madsen, J., Zhang, X., Ajayan, P. M., Susi, T. & Chi, M., 15 Jul 2021, In: Small. 17, 28, 10 p., 2100388.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Mechanism of Electron-Beam Manipulation of Single-Dopant Atoms in Silicon

  Markevich, A., Hudak, B. M., Madsen, J., Song, J., Snijders, P. C., Lupini, A. R. & Susi, T., 19 Jul 2021, In: Journal of Physical Chemistry C. 125, 29, p. 16041–16048 8 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Single Indium Atoms and Few-Atom Indium Clusters Anchored onto Graphene via Silicon Heteroatoms

  Elibol, K., Mangler, C., O'Regan, D. D., Mustonen, K., Eder, D., Meyer, J. C., Kotakoski, J., Hobbs, R. G., Susi, T. & Bayer, B. C., 19 Aug 2021, In: ACS Nano. 15, 9, p. 14373–14383 11 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Step-By-Step Atomic Insights into Structural Reordering from 2D to 3D MoS₂

  Inani, H., Shin, D. H., Madsen, J., Jeong, H. J., Kwon, M. H., McEvoy, N., Susi, T., Mangler, C., Lee, S. W., Mustonen, K. & Kotakoski, J., 24 Mar 2021, In: Advanced Functional Materials. 31, 13, 9 p., 2008395.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Temperature-dependent displacement cross section of graphene and its impurities: measuring the carbon adatom migration barrier

  Postl, A., Madsen, J., Hilgert, P. P. P., Schreiber, M. T., Kotakoski, J. & Susi, T., 30 Jul 2021, In: Microscopy and Microanalysis. 27, S1, p. 3340 1 p.

  Publications: Contribution to journal › Meeting abstract/Conference paper › Peer Reviewed

  Open Access

• The abTEM code: Transmission electron microscopy from first principles

  Madsen, J. & Susi, T., 24 Mar 2021, In: Open Research Europe. 1, 24.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2020

  abTEM: ab Initio Transmission Electron Microscopy Image Simulation

  Madsen, J. & Susi, T., Aug 2020, In: Microscopy and Microanalysis. 26, S2, p. 448-450 3 p.

  Publications: Contribution to journal › Meeting abstract/Conference paper

• Tailoring Electronic and Magnetic Properties of Graphene by Phosphorus Doping

  Langer, R., Błoński, P., Hofer, C., Lazar, P., Mustonen, K., Meyer, J. C., Susi, T. & Otyepka, M., 29 Jul 2020, In: ACS Applied Materials and Interfaces. 12, 30, p. 34074-34085 12 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2019

  Automated Real-time Analysis of Atomic-resolution STEM Images

  Madsen, J., Postl, A. & Susi, T., 1 Aug 2019, In: Microscopy and Microanalysis. 25, S2, p. 166-167 2 p.

  Publications: Contribution to journal › Meeting abstract/Conference paper › Peer Reviewed

• Direct imaging of light-element impurities in graphene reveals triple-coordinated oxygen

  Hofer, C., Skákalová, V., Görlich, T., Tripathi, M., Mittelberger, A., Mangler, C., Monazam, M. R. A., Susi, T., Kotakoski, J. & Meyer, J. C., 8 Oct 2019, In: Nature Communications. 10, 1, 8 p., 4570.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Efficient first principles simulation of electron scattering factors for transmission electron microscopy

  Susi, T., Madsen, J., Ludacka, U., Mortensen, J. J., Pennycook, T. J., Lee, Z., Kotakoski, J., Kaiser, U. & Meyer, J. C., 1 Feb 2019, In: Ultramicroscopy. 197, p. 16-22 7 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Electron-Beam Manipulation of Lattice Impurities in Graphene and Single-Walled Carbon Nanotubes

  Susi, T., Tripathi, M., Mustonen, K., Markevich, A., Mangler, C., Su, C., Li, J., Idrobo, J. C., Meyer, J. & Kotakoski, J., 1 Aug 2019, In: Microscopy and Microanalysis. 25, S2, p. 938-939 2 p.

  Publications: Contribution to journal › Meeting abstract/Conference paper › Peer Reviewed

• Electron-Beam Manipulation of Silicon Impurities in Single-Walled Carbon Nanotubes

  Mustonen, K., Markevich, A., Tripathi, M., Inani, H., Ding, E. X., Hussain, A., Mangler, C., Kauppinen, E. I., Kotakoski, J. & Susi, T., 27 Dec 2019, In: Advanced Functional Materials. 29, 52, 7 p., 1901327.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Engineering single-atom dynamics with electron irradiation

  Su, C., Tripathi, M., Yan, Q. B., Wang, Z., Zhang, Z., Hofer, C., Wang, H., Basile, L., Su, G., Dong, M., Meyer, J. C., Kotakoski, J., Kong, J., Idrobo, J. C., Susi, T. & Li, J., 17 May 2019, In: Science Advances. 5, 5, 11 p., 2252.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Influence of temperature on the displacement threshold energy in graphene

  Chirita Mihaila, A. I., Susi, T. & Kotakoski, J., 10 Sept 2019, In: Scientific Reports. 9, 1, 7 p., 12981.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Microwave Energy Drives “On–Off–On” Spin-Switch Behavior in Nitrogen-Doped Graphene

  Zoppellaro, G., Bakandritsos, A., Tuček, J., Błoński, P., Susi, T., Lazar, P., Bad'ura, Z., Steklý, T., Opletalová, A., Otyepka, M. & Zbořil, R., 13 Sept 2019, In: Advanced Materials. 31, 37, 9 p., 1902587.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Quantifying Elastic and Inelastic Electron Irradiation Damage in Transmission Electron Microscopy of 2D Materials

  Susi, T., Lehnert, T., Kaiser, U., Meyer, J. & Kotakoski, J., 5 Aug 2019, In: Microscopy and Microanalysis. 25, S2, p. 454-455 2 p.

  Publications: Contribution to journal › Meeting abstract/Conference paper › Peer Reviewed

• Quantifying transmission electron microscopy irradiation effects using two-dimensional materials

  Susi, T., Meyer, J. C. & Kotakoski, J., Jun 2019, In: Nature Reviews Physics. 1, 6, p. 397-405 9 p.

  Publications: Contribution to journal › Review › Peer Reviewed

  Open Access

• Silicon Substitution in Nanotubes and Graphene via Intermittent Vacancies

  Inani, H., Mustonen, K., Markevich, A., Ding, E-X., Tripathi, M., Hussain, A., Mangler, C., Kauppinen, E. I., Susi, T. & Kotakoski, J., 23 May 2019, In: Journal of Physical Chemistry C. 123, 20, p. 13136-13140 5 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2018

  Atomic-Scale Deformations at the Interface of a Mixed-Dimensional van der Waals Heterostructure

  Mustonen, K., Hussain, A., Hofer, C., Reza Ahmadpour Monazam, M., Mirzayev, R., Elibol, K., Laiho, P., Mangler, C., Jiang, H., Susi, T., Kauppinen, E. I., Kotakoski, J. & Meyer, J. C., 28 Aug 2018, In: ACS Nano. 12, 8, p. 8512–8519 8 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Atomic-Scale in Situ Observations of Crystallization and Restructuring Processes in Two-Dimensional MoS2 Films

  Bayer, B. C., Kaindl, R., Reza Ahmadpour Monazam, M., Susi, T., Kotakoski, J., Gupta, T., Eder, D., Waldhauser, W. & Meyer, J. C., 28 Aug 2018, In: ACS Nano. 12, 8, p. 8758–8769 12 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Electron-Beam Manipulation of Silicon Dopants in Graphene

  Tripathi, M., Mittelberger, A., Pike, N., Mangler, C., Meyer, J. C., Verstraete, M., Kotakoski, J. & Susi, T., Aug 2018, In: Nano Letters. 18, 8, p. 5319–5323 5 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Intrinsic core level photoemission of suspended monolayer graphene

  Susi, T., Scardamaglia, M., Mustonen, K., Tripathi, M., Mittelberger, A., Al-Hada, M., Amati, M., Sezen, H., Zeller, P., Larsen, A. H., Mangler, C., Meyer, J. C., Gregoratti, L., Bittencourt, C. & Kotakoski, J., 23 Jul 2018, In: Physical Review Materials. 2, 7, 6 p., 074005.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Zigzag sp₂ Carbon Chains Passing through an sp₃ Framework: A Driving Force toward Room-Temperature Ferromagnetic Graphene

  Tuček, J., Holá, K., Zoppellaro, G., Bloński, P., Langer, R., Medved, M., Susi, T., Otyepka, M. & Zbořil, R., 5 Dec 2018, In: ACS Nano. 12, 12, p. 12847–12859 13 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access