Department of Physics

Yläpalkki

Molecular electronics and plasmonics


Group leader: Jussi Toppari  |  CV


The group studies nanoelectronics and -plasmonics/-photonics,
concentrating on phenomena related to molecules.

  • One of the main interests, on which the group has a long experience, is self-assembled DNA structures. The main focus is on DNA origami structures; their modifications and utilization in nanofabrication of electrical and optical/plasmonic nanodevices.
  • Another main interest is the coupling between surface plasmons or cavity photons and molecules, especially in a strong coupling limit. This limit brings about hybrid plasmon-molecule -states possessing new fundamental properties. For example, it enables totally new ways for controlling chemistry.
  • Other topics studied are molecular level mechanisms and properties of fluorescent proteins, enhancing their fluorescence for bioimaging by plasmonics, and utilization of plasmonics for solar energy, as well as plasmonic/optical properties of graphene and conducting polymers.

  • Group members »
  • Recent research
    • Towards DNA-based single electron electronics »
    • Dynamics of strongly coupled modes between surface plasmon polaritons and photoactive molecules: the effect of the Stokes shift »
    • Custom-shaped plasmonic metal nanostructures based on DNA origami silhouettes »

       

      The plasmonic metal nanostructures have gained huge interest due to the promising applications of their unique optical properties. However, the fabrication of nanoshaped structures with desired properties by conventional methods, remains challenging. DNA self-assembly, especially the DNA origami, provides a precise and programmable way to form nanoscale structures. Although numerous efforts have been made to synthesize metallic nanostructures by DNA constructs, the quality and uniformity of such nanostructures have been far from ideal so far.

      By combining the precision of the DNA origami and the maturity of conventional nanofabrication techniques, we have developed a novel method for fabrication of smooth sub-100-nanometer visible-range plasmonic nanostructures with designable shapes. The method employs a selectively grown SiO2 layer with DNA origami silhouettes as hard mask for metal evaporation on silicon substrate. The resulting nanostructures have the shape of the origami template within a nanometer accuracy, and thus has much higher resolution compared to other approaches so far [1]. In order to push our process closer to industry, we have developed a cost-effective spray-coating-based deposition method for covering large scale substrates with DNA origami structures [2]. These metal nanostructures have ready applications in fluorescence enhancement, SERS and can even be used to construct metamaterials in visible range.

      The work has been carried out in collaboration with Dr. V. Linko and Asst. Prof. M. Kostiainen (Aalto University) [1-3], Asst. Prof. S. Tuukkanen (Tampere University of Technology) [2], (California Institute of Technology) [3] and Prof. K.V. Gothelf (iNano / Univ. of Aarhus) [3].

      [1] B. Shen, V. Linko, T. Kosti, M.A. Kostiainen and J.J. Toppari, Custom-shaped metal nanostructures based on DNA origami silhouettes, Nanoscale 7, 11267-11272 (2015).
      [2] V. Linko, B. Shen, K. Tapio, J.J. Toppari, M.A. Kostiainen and S. Tuukkanen, One-step large-scale deposition of salt-free DNA origami nanostructures. Scientific Reports 5, 15634 (2015).
      [3] B. Shen, V. Linko, K. Tapio, S. Pikker, T. Lemma, A. Gopinath, K.V. Gothelf, M.A. Kostiainen, J.J. Toppari, Plasmonic nanostructures through DNA-assisted lithography, In Review.

      Top: Illustrations of a DNA origami and a fabricated metal nanostructure with the same shape (upper row). Atomic force microscope image of a cross-shaped DNA origami and a false-color scanning electron micrograph of the gold nanostructure fabricated from it (lower row). Bottom: Large-area scanning electron micrograph of cross-shaped metal nanostructures and zoom-ins of individual ones. Inset scale bar 50 nm.

      Illustrations of a DNA origami and a fabricated metal nanostructure with the same shape (upper row). Atomic force microscope image of a cross-shaped DNA origami and a false-color scanning electron micrograph of the gold nanostructure fabricated from it (lower row). Large-area scanning electron micrograph of cross-shaped metal nanostructures and zoom-ins of individual ones. Inset scale bar 50 nm.

    • Growth of Oxidized Graphene by Two-Photon Oxidation »


      We studied the formation of graphene oxide in the two-photon oxidation process by detailed atomic force microscopy (AFM) at different stages of the oxidation process. The study revealed that the initial oxidation seeds appear randomly in the graphene layer as demonstrated in Figure below. Once an oxidation seed is established, it starts to grow into an island with an oxidation rate for nearest neighbor sites being five orders of magnitude higher than for the initial seeding.

      Oxide growth process
      Left: Schematic of the oxide growth process during the two-photon oxidation. Right: AFM image of oxide islands appearing on graphene.

      Real-time monitoring of graphene patterning with wide-field four-wave mixing microscopy 

      Our in-house discovery of a two-photon oxidation process in graphene driven by a femto-second laser with a spot size of about 300 nm motivated us to develop a way to monitor the oxidation in real-time, as it happens. We chose wide-field four-wave mixing (FWM) imaging as it has shown to be very sensitive to changes made in graphene. A series of snapshots in Figure below display successful FWM imaging of a free-standing graphene window. The yellow dot is the intense femto-second laser performing two-photon oxidation of the graphene. The areas where graphene has been converted into graphene-oxide, loose their resonance in the FWM imaging and appear black in the snapshots. This technique may prove useful for developing scaled up oxidation patterning of graphene.

      Wide-field four-wave mixing snap shots of two-photon oxidation patterning
      Wide-field four-wave mixing snap shots of two-photon oxidation patterning on a suspended graphene window. Yellow dot is the oxidation laser.

      [1] J. Koivistoinen, L. Sladkova, J. Aumanen, Pekka Koskinen, Kevin Roberts, A. Johansson, P. Myllyperkiö, and M. Pettersson, From Seeds to Islands: Growth of Oxidized Graphene by Two-Photon Oxidation, J. Phys. Chem. C, 120, 22330 (2016).
      [2] J. Koivistoinen, J. Aumanen, Vesa-Matti Hiltunen, P. Myllyperkiö, A. Johansson, and M. Pettersson, Real-Time Monitoring of Graphene Patterning with Wide-Field Four-Wave Mixing Microscopy, Appl. Phys. Lett. 108, 153112 (2016).

    • Chemical composition of two-photon oxidized graphene »


      In this study we collaborated with a Taiwanese group to analyze the chemical composition of two-photon oxidized graphene, using μm X-ray photoelectron spectroscopy at National Synchrotron Radia­tion Research Center (Hsinchu, Taiwan). We were able to follow how the first hydroxyl groups appear and dominate, followed by a minor formation of epoxy groups at higher two-photon exposures as shown in Figure below. Carboxylic groups did not seem to form, with a very small and constant signal throughout. The study shows a significant difference of composition compared to chemically produced graphene oxide, which typically has a higher fraction of epoxy groups and a clear presence of carboxylic groups. The take-home-message is that two-photon oxidation is a more controlled and gentle oxidation process, leaving graphene more structurally intact than chemical oxidation.

      Graphene oxide during two-photon oxidation
      Illustration of the chemical composition of graphene oxide during two-photon oxidation.

      A. Johansson, H.-C. Tsai, J. Aumanen, J. Koivistoinen, P. Myllyperkiö, Y.-Z. Hung, M.-C. Chuang, C.-H. Chen, W.Y. Woon, M. Pettersson, Chemical Composition of Two-Photon Oxidized Graphene, Carbon, 115 (2017) 77
    • To understand light sensing mechanism in plants and bacteria »
    • Manipulating conformation of individual biomolecules »


      Biological systems in nature possess interesting complex functions that would offer solutions to many material science applications such as biosensors and bioactuators, but are inherently difficult to control. Meanwhile, non-biological systems are relatively easy to control, but applicability is limited. The goal is to combine the biological and non-biological domains so that one can influence conformation of the studied biomolecule and hence the functionality of the biomolecule. To achieve this, one can utilize e.g. pH and electric and magnetic field to elongate, shrink, bent and twist the biomolecules, which are typically immobilized on a substrate.

      The first biomolecule we have tested for the method is a DNA-hairpin, which consist of two ssDNA arms and a loop, where the objective is to open and close loop of the hairpin in controllable fashion, by help of a charged gold nanoparticle (AuNP) attached to a one arm of the DNA-hairpin. Distance, which is related to the conformation of the hairpin, can be tracked by measuring the localized surface plasmon resonance (LSPR) of AuNP, which depends on the distance between the AuNP and the Au-surface. This scheme can be implemented to study other biomolecules also.

    • More Research
  • Publications
    • Recent publications »


      T. Lemma, A. Saliniemi, V. Hynninen, V.P. Hytönen, J.J. Toppari,
      SERS detection of cell surface and intracellular components of microorganisms using nano-aggregated Ag substrate, Vib. Spectrosc. 83 (2016) 36–45

      J. Wang, K. Tapio, A. Habert, S. Sorgues, C. Colbeau-Justin, B. Ratier, M. Scarisoreanu, J.J. Toppari, N. Herlin-Boime, and J. Bouclé, Influence of Nitrogen Doping on Device Operation for TiO2-Based Solid-State Dye-Sensitized Solar Cells: Photo-Physics from Materials to Devices, Nanomaterials 6(3) (2016) 35

      V. Hynninen, L. Vuori, M. Hannula, K. Tapio, K. Lahtonen, T. Isoniemi, E. Lehtonen, M. Hirsimäki, J.J. Toppari, M. Valden, V.P. Hytönen, Improved antifouling properties and selective biofunctionalization of stainless steel by employing heterobifunctional silane-polyethylene glycol overlayers and avidin-biotin technology” Sci. Rep., 6 (2016) 29324

      V. Linko, S. Nummelin, L. Aarnos, K. Tapio, J.J. Toppari, and M.A. Kostiainen, DNA-Based Enzyme Reactors and Systems, (Review) Nanomaterials 6 (2016) 139

      B. Shen, K. Tapio, V. Linko, M.A. Kostiainen and J.J. Toppari, Metallic Nanostructures Based on DNA Nanoshapes, (Review) Nanomaterials 6 (2016) 146

      K. Tapio, J. Leppiniemi, B. Shen, V.P. Hytönen, W. Fritzsche, J.J. Toppari, Toward Single Electron Nanoelectronics Using Self-Assembled DNA Structure, Nano Lett., 16 (2016) 6780

      L. Qiu, W. Wang, A. Zhang, N. Zhang, T. Lemma, H. Ge, J.J. Toppari, V.P. Hytönen, J. Wang, Core-Shell Nanorod Columnar Array Combined with Gold Nanoplate-Nanosphere Assemblies Enable Powerful In Situ SERS Detection of Bacteria. ACS Appl. Mater. Interf. 8 (2016) 24394

      WQ. Wang, V. Hynninen, L. Qiu, AW. Zhang, T. Lemma, NN. Zhang, HH. Ge, J.J. Toppari, V.P. Hytönen, J. Wang, Synergistic enhancement via plasmonic nanoplate-bacteria-nanorod supercrystals for highly efficient SERS sensing of food-borne bacteria, Sensors and Actuators B, 239 (2017) 515

      S. Baieva, O. Hakamaa, G. Groenhof, T.T. Heikkilä, J.J. Toppari, Dynamics of strongly coupled modes between surface plasmon polaritons and photoactive molecules: the effect of the Stokes shift, ACS Phot., 4 (2017) 28

      F. Heimbach, A. Arndt, H. Nettelbeck, F. Langner, U. Giesen, H. Rabus, S. Sellner, J.J. Toppari, B. Shen, and W.Y. Baek, Measurement of changes in impedance of DNA nanowires due to radiation induced structural damage: A novel approach for a DNA-based radiosensitive device, Eur. Phys. J. D, 71 (2017) 211

      HL. Luk, J. Feist, J.J. Toppari, G. Groenhof, Multi-scale Molecular Dynamics Simulations of Polaritonic Chemistry, J. Chem. Theory Comput. 13 (2017) 4324

      B. Shen, V. Linko, K. Tapio, S. Pikker, T. Lemma, A. Gopinath, K.V. Gothelf, M.A. Kostiainen, J.J. Toppari, Plasmonic nanostructures through DNA-assisted lithography, In Review

      J. Koivistoinen, L. Sladkova, J. Aumanen, Pekka Koskinen, Kevin Roberts, A. Johansson, P. Myllyperkiö, and M. Pettersson, From Seeds to Islands: Growth of Oxidized Graphene by Two-Photon Oxidation, J. Phys. Chem. C, 120 (2016) 22330

      J. Koivistoinen, J. Aumanen, Vesa-Matti Hiltunen, P. Myllyperkiö, A. Johansson, and M. Pettersson, Real-Time Monitoring of Graphene Patterning with Wide-Field Four-Wave Mixing Microscopy, Appl. Phys. Lett. 108 (2016) 153112

      A. Johansson, H.-C. Tsai, J. Aumanen, J. Koivistoinen, P. Myllyperkiö, Y.-Z. Hung, M.-C. Chuang, C.-H. Chen, W.Y. Woon, M. Pettersson, Chemical Composition of Two-Photon Oxidized Graphene, Carbon, 115 (2017) 77

      H. Takala, S. Niebling, O. Berntsson, A.  Björling, H. Lehtivuori, H. Häkkänen, M. Panman, E. Gustavsson, M. Hoernke, G. Newby, F. Zontone, M. Wulff, A. Menzel, J.A. Ihalainen, S. Westenhoff, Light-induced structural changes in a monomeric bacteriophytochrome, Structural Dynamics, 3 (2016) 054701

      A. Björling, O. Berntsson, H. Lehtivuori, T. Takala, A.J. Hughes, M. Panman, M. Hoernke, S. Niebling, L. Henry, R. Henning, I. Kosheleva, V. Chukharev, N.V. Tkachenko, A. Menzel, G. Newby, D. Khakhulin, M. Wulff, J.A. Ihalainen, S. Westenhoff, Structural photoactivation of a full-length bacterial phytochrome, Science Advances, 2 (2016) e1600920

      P. Edlund, H. Takala, E. Claesson, L. Henry, R. Dods, H. Lehtivuori, M. Panman, K. Pande, T. White, T. Nakane, O. Berntsson, E. Gustavsson, P. Båth, V. Modi, S. Roy-Chowdhury, J.  Zook, P. Berntsen, S. Pandey, I. Poudal, J. Tenboer, C. Kupitz, A. Barty, P. Fromme, J.D. Koralek, T. Tanaka, J. Spence, M. Liang, M. Hunter, S. Boutet, E. Nango, K. Moffat, G. Groenhof, J.A. Ihalainen, E. Stojkovic, M. Schmidt, S. Westenhoff, The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography, Scientific Reports, 6 (2016) 35279

      J. Chen, D., Liu, M.J. Al-Marri, L. Nuuttila, H. Lehtivuori, K., Zheng, Photostability of CsPbBr3 Perovskite quantum dots, Science China Materials, 59 (2016) 719

      T. Mathes, J.T.M., Kennis, eds. Optogenetic Tools in the Molecular Spotlight. Lausanne: Frontiers Media. (2016)

    • Full Publication lists »

      Jussi Toppari
      Andreas Johansson