1.      Sh. Farhangfar, K.P. Hirvi, J.P. Kauppinen, J.P. Pekola, J.J.  Toppari, D.V. Averin, and A.N. Korotkov. "One Dimensional Arrays and Solitary Tunnel Junctions in the Weak Coulomb Blockade Regime: CBT Thermometry", J. Low Temp. Phys. 108, 191 (1997).

2.      J.P. Pekola, J.J. Toppari, J.P. Kauppinen, K.M. Kinnunen, and A.J. Manninen "Coulomb blockade-based nanothermometry in strong magnetic fields" J. Appl. Phys. 83, 5582 (1998).

3.      Sh. Farhangfar, J.J. Toppari, Yu. Pashkin, A.J. Manninen, and J.P. Pekola "Experiments on tunnelling in small normal-metal junctions influenced by dissipative environment: Critical comparison to the theories of quantum fluctuations" Europhys. Lett. 43, 59 (1998).

4.      J.P. Pekola, J.J. Toppari, M. Aunola, M.T. Savolainen, and D.V. Averin "Adiabatic transport of Cooper pairs in arrays of Josephson junctions" Phys. Rev. B 60, R9931 (1999).

5.      M. Aunola, J.J. Toppari, and J.P. Pekola "Arrays of Josephson junctions in an environment with vanishing  impedance" Phys. Rev. B 62, 1296 (2000).

6.      J.P. Pekola, and J.J. Toppari: "Decoherence in circuits of small Josephson junctions", Phys. Rev. B 64, 172509 (2001).

7.      N. Kim, K. Hansen, J.J. Toppari, T. Suppula, and Jukka Pekola: "Fabrication of mesoscopic superconducting Nb wires using conventional  electron-beam lithographic techniques", J. Vac. Sci. Technol. B 20(1), 386-388 (2002).

8.      M. Aunola, and J.J. toppari: “Connecting Berry’s phase and the pumped charge in a Cooper pair pump”, Phys. Rev. B 68, 020502 (2003). [Virtual Journal of Applications of Superconductivity, July 15 (2003)]

9.      J.J. Toppari, J.M. Kivioja, J.P. Pekola, and M.T. Savolainen: “Turnstile behaviour of the Cooper pair pump”, J. Low Temp. Phys. 136 (1-2): 57-91 (2004).

10.    S. Tuukkanen, J.J. Toppari, V.P. Hytönen, A. Kuzyk, M.S. Kulomaa, and P. Törmä, “Dielectrophoresis as a tool for nanoscale DNA manipulation”, Int. J. Nanotechnology 2, No. 3, 280–291 (2005).

11.   S. Tuukkanen, A. Kuzyk, J.J. Toppari, V.P. Hytönen, T. Ihalainen and P. Törmä, “Dielectrophoresis of nanoscale double-stranded DNA and humidity effects on its electrical conductivity”, Appl. Phys. Lett. 87, 183102 (2005).

12.    S. Tuukkanen, J.J. Toppari, A. Kuzyk, L. Hirviniemi, V.P. Hytönen, T. Ihalainen, and P. Törmä, “Carbon nanotubes as electrodes for dielectrophoresis of DNA”, Nanoletters 6, 1339 (2006).

13.    T.K. Hakala, J.J. Toppari, and P. Törmä, “A hybrid method for calorimetry with subnanolitre samples using Schottky junctions”, J. Appl. Phys. 101, 034512 (2007). [Virtual Journal of Nanoscale Science & Technology, February 26 (2007)]

14.    S. Tuukkanen, A. Kuzyk, J.J. Toppari, H. Häkkinen, V.P. Hytönen, E. Niskanen, M. Rinkiö, and P. Törmä “Trapping of 27 bp - 8 kbp DNA and immobilization of thiol-modified DNA using dielectrophoresis,” Nanotechnology 18, 295204 (2007). [Chosen as the Nanotechnology Journal Highlight, see http://nanotechweb.org/articles/journal/6/6/8/1]

15.    A. Kuzyk, M. Pettersson, J.J. Toppari, T.K. Hakala, H. Tikkanen, H. Kunttu, and P. Törmä, "Molecular coupling of light with plasmonic waveguides," Opt. Express 15, 9908 (2007).

16.    J.J. Toppari, T. Kühn, A.P. Halvari, J. Kinnunen, M. Leskinen and G.S. Paraoanu, “Cooper-pair resonances and subgap Coulomb blockade in a superconducting single-electron transistor”, Physical Review B 76, 172505 (2007). [Virtual Journal of Applications of Superconductivity, December 1 (2007)]

17.    M.Y. Zavodchikova, A. Johansson, M. Rinkiö, J.J. Toppari, A.G. Nasibulin, E.I. Kauppinen, and P. Törmä, “Fabrication of carbon nanotube-based field-effect transistors for studies of their memory effects,” Physica Status Solidi (b) 244, 4188 (2007).

18.     A. Kuzyk, B. Yurke, J.J. Toppari, V. Linko, and P. Törmä, “Dielectrophoretic trapping of DNA origami”, Small 4, 447 (2008).

19.    M. Rinkiö, A. Johansson, M.Y. Zavodchikova, J.J. Toppari, A.G. Nasibulin, E.I. Kauppinen, and P. Törmä: “High-yield of memory elements from carbon nanotube field-effect transistors with atomic layer deposited gate dielectric,” to appear in New Journal of Physics (2008).

20.    T.K. Hakala, J.J. Toppari, M. Pettersson, A. Kuzyk, H. Tikkanen, H. Kunttu, and P. Törmä, “Frequency conversion of propagating surface plasmon polaritons by organic molecules”, Appl. Phys. Lett. 93, 123307 (2008).

21.    T.K. Hakala, J.J. Toppari, A. Kuzyk, M. Pettersson, H. Tikkanen, H. Kunttu, and P. Törmä, “Vacuum Rabi splitting and strong coupling dynamics for surface plasmon polaritons and Rhodamine 6G molecules”, Phys. Rev. Lett. 103, 053602 (2009).

22.    V. Linko, S.-T. Paasonen, A. Kuzyk, P. Törmä, and J.J. Toppari, “Characterisation of the Conductance Mechanisms of the DNA Origami by AC Impedance Spectroscopy”, Small 5, 2382 (2009).

23.    T.K. Hakala, V. Linko, A.-P. Eskelinen, J.J. Toppari, A. Kuzyk, and P. Törmä, “ Field induced nanolithography for high-throughput pattern transfer”, Small 5, 2683 (2009).

24.    V. Linko, J. Leppiniemi, S.-T. Paasonen, V.P. Hytönen and J.J. Toppari, “Defined-sized DNA triple crossover construct for molecular electronics: modification, positioning and conductance properties”, Nanotechnology 22, 275610 (2011).

25.    V. Linko, J. Leppiniemi, B. Shen, E. Niskanen, V.P. Hytönen and J.J. Toppari, “ Growth of immobilized DNA by polymerase: bridging nanoelectrodes with individual dsDNA molecules”, Nanoscale 3, 3788 (2011).

26.    T. Isoniemi, A. Johansson, T.K. Hakala, M. Rinkiö, P. Törmä, J.J. Toppari, and H. Kunttu, “ Surface plasmon effects on carbon nanotube field effect transistors”, Appl. Phys. Lett. 99, 031105 (2011).

27.    L.J. Antila, M.J. Heikki, V. Mäkinen, N. Humalamäki, M. Laitinen, V. Linko, P. Jalkanen, J.J. Toppari, V. Aumanen, M. Kemell, P. Myllyperkiö, K. Honkala, H. Häkkinen, M. Leskelä, and J.E.I. Korppi-Tommola, “ ALD Grown Aluminum Oxide Submonolayers in Dye-Sensitized Solar Cells: The Effect on Interfacial Electron Transfer and Performance”, J. Phys. Chem. C 115, 16720 (2011).

Proceedings

1.   J.J. Toppari, K. Hansen, N. Kim, M.T. Savolainen, L. Taskinen and J.P. Pekola, "Characterisation of Cooper pair boxes for quantum computing", Phys. C 352 (1-4) 177-180 (2001).

2.   J.P. Pekola, J.J. Toppari, N. Kim, M.T. Savolainen, L. Taskinen, and K.Hansen: "Adiabatic transport of Cooper pairs in arrays of Josephson junctions", Proceedings of 'Macroscopic Quantum Coherence 2', Napoli, 2000: "Macroscopic Quantum Coherence and Quantum Computing", D. Averin, B. Ruggiero, and P. Silvestrini (eds.) Plenum Publishers, New York (2001) 127.

3.   M.T. Savolainen, J.J. Toppari, L. Taskinen, N. Kim, K. Hansen, and  J.P. Pekola: "Characterization of Cooper pair boxes for quantum bits", Proceedings of 'Macroscopic Quantum Coherence 2', Napoli, 2000: "Macroscopic Quantum Coherence and Quantum Computing", D. Averin, B. Ruggiero, and P. Silvestrini (eds.) Plenum Publishers, New York (2001) 145.

4.   J.J. Toppari: “Kvanttilaskenta ja squbitit”, Juhani Hämäläinen, and Riitta Lähdemäki-Taipalus (eds.), Finnish Defence Forces Technical Research Centre, publications 5, Ylöjärvi (2002)

5.   J.J. Toppari, T. Kühn, A.P. Halvari, and G.S. Paraoanu, “Method for finding the critical temperature of the island in a SET structure”, J. Phys.: Conf. Ser. 150, 022088 (2009).

6.   Editors: J.-L. Mergny, A. Bourdoncle, and L. Spindler, "Meeting report: Guanosines and quadruplexes (London, September 15–17, 2010)", Biochimie 93, 121 (2011).

7.   R.J. Moerland, T.K. Hakala, A.I. Väkeväinen, A.-P. Eskelinen, G. Sharma, J.J. Toppari, A. Kuzyk, M. Pettersson, H. Kunttu, and P. Törmä, "Vacuum Rabi splitting for surface plasmon polaritons and Rhodamine 6G molecules", Metamaterials VI, Eds. V. Kuzmiak, P. Markos, T. Szoplik, Proc. of SPIE2011 8070, 80700D (2011).

Scientific monographs

J.J. Toppari, ”TRANSPORT PHENOMENA AND DECOHERENCE IN SHORT JOSEPHSON JUNCTION ARRAYS”, PhD thesis, Department of Physics, University of Jyväskylä, Research report No.  9/2003, ISBN 951-39-1631-6, ISSN 0075-465X (2003).

Popular publications etc. published in Finland

1.   Sampo Tuukkanen, Jussi Toppari and Päivi Törmä, “Dna-kone kokoaa itse itsensä”, Tiede 9/2006, 48-51 (2006).

2.   Markus Ahlskog and Jussi Toppari, “Kohti molekyylielektroniikkaa”, Prosessori 11/2006, 26-27 (2006).

3.   One part of a TV-show YLE/Teema “Aineen Arvoituksia” Producer: Jari Mäkinen, Producer at YLE: Elina Saksala, Pruducing company: Kupla Productions Oy

Conference talks and seminars

·         J.J. Toppari, J. Kuhalainen, M.T. Savolainen, A.J. Manninen, and J.P. Pekola: "Cooper pair tunneling in small tunnel junctions", XXXII conference of the finnish physical society, 19-21 March , Tampere, Finland (1998).

·         J.P. Pekola, J.J. Toppari, M. Aunola, M.T. Savolainen, and D.V. Averin: "Quantum Inaccuracy of single Cooper pair transfer", Mesoscopic Days, 7-9 May, Copenhagen, Denmark (1999).

·         J.J. Toppari, J.P. Pekola, M. Aunola, and D.V. Averin: "Quantum inaccuracy of a Single Cooper Pair Pump" Invited, XXII international conference on low temperature  physics, (LT 22), 4-11 August, Helsinki university of technology, Finland (1999).

·         J.P. Pekola, J.J. Toppari, M. Aunola, M.T. Savolainen, and D.V. Averin: "Quantum inaccuracy of single Cooper pair transfer", Symposium on micro- and nanocryogenics, 1-3 August,  Jyväskylä, Finland (1999).

·         J.J. Toppari, K. Hansen, N. Kim, M.T. Savolainen, L. Taskinen, and J.P. Pekola: "Progress on the Experiment of the Transport of Cooper pairs", TMR/IST joint meeting, 24-26 September, Catania, Italy (2000).

·         J.J. Toppari, A. Halvari, K. Hansen, N. Kim, J. Pekola, M. Savolainen, and L. Taskinen: "Characterization of Cooper pair pumps", SQUBIT project review meeting, 20-23 September, Delft, Holland (2001).

·         J.J. Toppari: “Kvanttilaskenta ja squbitit”, Invited, Research seminar: Modelling and simulation, Finnish Defence Forces Technical Research Centre, Riihimäki 7. March, (2002).

·         J.J. Toppari, S. Tuukkanen, V.P. Hytönen, A. Kuzyk, M.S. Kulomaa and P. Törmä, ”Dielectrophoresis as a tool for nanoscale DNA manipulation: Developing sequence-specific DNA sensor”, Nano and Giga Challenges in Microelectronics, Symposium and Summer School, Research and Development Opportunities, Cracow (Poland), September 13-17, (2004). 

·         J.J. Toppari, S. Tuukkanen, A. Kuzyk, L. Hirviniemi, V.P. Hytönen, T. Ihalainen and P. Törmä, “Dielectrophoresis of nanoscale dsDNA using metallic and CNT-electrodes: Humidity effects on dsDNA’s electrical conductivity”, DNA-Based Nanoscale Integration, International Symposium, 18-20 May, Jena, Germany (2006).

·         J.J. Toppari: “Molecular electronics and nanoscale photonics”, Invited, Nanolitho-graphy seminar, 26-27 February, Dortmund, Germany (2007).

·         J.J. Toppari, S. Tuukkanen, A. Kuzyk, V.P. Hytönen, T. Ihalainen, and P. Törmä, “Dielectrophoresis of nanoscale DNA”, The 41st conference of the finnish physical society, 15-17 March, Tallinn, Estonian (2007).

·         J.J. Toppari, A. Johansson, S. Tuukkanen, A. Kuzyk, M. Rinkiö, M. Zavodchikova, V. Linko, E. Niskanen, T. Ihalainen and P. Törmä, “CNT Memory Elements & Electrical Assembly and Conductance Measurements of DNA molecules”, Icon 2007: The Second International Conference on One-dimensional Nanomaterials, 26–29 September, Malmö, Sweden (2007).

·         J.J. Toppari, A. Kuzyk, B. Yurke, V. Linko, K. Laitinen and P. Törmä, “Dielectrophoretic Trapping of DNA Molecules and Selfassembled Structures”, ICN+T 2008, International conference on nanoscoemce + technology, 20-25 July, Keystone, Colorado, USA (2008).

·         J.J. Toppari T. Hakala, A. Kuzyk, M. Pettersson, H.-M. Tikkanen, H. Kunttu, and P. Törmä, “Frequency conversion of waveguided surface plasmon polaritons by organic molecules”, Nanometa 2009, 5-8 January, Seefeld/Tirol, Austria (2009).

·         J.J. Toppari, “Trapping and Electrical Measurements of Single dsDNA Molecules and DNA-origamis”, 21 October, Seminar in Saint Petersburg State University (2009).

·         J.J. Toppari, T.K. Hakala, A. Kuzyk, M. Pettersson, H. Tikkanen, H. Kunttu, and P. Törmä, “Vacuum Rabi splitting and strong coupling dynamics for surface plasmon polaritons and Rhodamine 6G molecules”, The 44th conference of the finnish physical society, 11-13 March, Jyväskylä, Finland (2010).

·         J.J. Toppari, V. Linko, S.-T. Paasonen, A. Kuzyk , P. Törmä, “Characterization of the Conductance Mechanisms of DNA Origami by AC Impedance Spectroscopy”, TDNA-Based MicroNano Integration, International Symposium, 27-29 May, Jena, Germany (2010).

·         J.J. Toppari, V. Linko, S.-T. Paasonen, J. Leppiniemi, A. Kuzyk, P. Törmä, V. Hytönen, “Characterization of the Conductance Mechanisms of Self-assembled DNA Structures by AC Impedance Spectroscopy”, Invited, COST ACTION MP0802 Annual Conference, 15-17 september, The London School of Pharmacy, London, Great-Britain (2010).