Department of Physics

Yläpalkki

Molecular electronics and plasmonics

The group studies nanoelectronics and plasmonics, especially 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 electronic and optical/plasmonic nanodevices. Another main interest, is the coupling between surface plasmons and molecules, especially on a strong coupling limit, which yields hybrid plasmon-molecule -states possessing new fundamental properties enabling, e.g., totally new ways for controlling chemistry in molecular level. Other topics studied are utilization of plasmonics for solar energy, surface enhanced Raman spectroscopy (SERS) of microbes, as well as optical and plasmonic properties of fluorescent proteins, carbon nanotubes, graphene and conducting polymers.

Contact person: Jussi Toppari

 

  • Group members »
    • Jussi Toppari, university lecturer
    • Andreas Johansson, university researcher
    • Janne Simonen, university researcher
    • Heli Lehtivuori, academic postdoctoral
    • Tibebe Lemma, postdoctoral researcher
    • Svitlana Baieva, doctoral student
    • Tommi Isoniemi, doctoral student
    • Boxuan Shen, doctoral student
    • Kosti Tapio, doctoral student
    • Jan Borovsky, doctoral student
    • Mikael Kautto, MSc student
    • Lauri Nuuttila, MSc student
    • Alex Saliniemi, MSc student
    • Kevin Roberts, MSc student
    • Vesa-Matti Hiltunen, MSc student
    • Jyrki Manninen, MSc student
  • Recent research
    • 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]. The work has been carried out in collaboration with Dr. V. Linko and Asst. Prof. M. Kostiainen (Aalto University). In order to push our process closer to industry, we have developed in collaboration with Asst. Prof. S. Tuukkanen (Tampere University of Technology) 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.

      [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 (2015) 11267-11272
      [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 (2015) 15634

      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.

    • Development of Near Infrared Fluorescence Dyes – Phytofluor »

       

      During the past decades, fluorophores active in the near infrared (NIR) have attracted ongoing attention due to their diverse applications in biomedical research, materials science and related fields. The phytochrome family of light-switchable proteins in NIR region has long been studied by biochemical, spectroscopic [2,3], crystallographic [3] and x-ray scattering [1] means. The discovery of bacteriophytochromes in the 1990s greatly accelerated this work. The NIR fluorescence properties of bacteriophytochromes, phytofluor, offer potential to tissue imaging, although high fluorescence quantum yield remains an elusive goal [2,3]. Our academic postdoc Heli Lehtivuori was able to improve the quantum yield to 9% as a Fulbright research fellow in University of Wisconsin-Madison [3].

      [1] H. Lehtivuori, S. Bhattacharya, N. M. Angenent-Mari, K. A. Satyshur, and K. T. Forest, Removal of Chromophore-proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor, Front. Mol. Biosci. 2 (2015) 65
      [2] J. A. Ihalainen, H. Takala and H. Lehtivuori, Fast photochemistry of prototypical Phytochromes - a species versus subunit specific comparison, Front. Mol. Biosci. 2 (2015) 75
      [3] A. Björling, O. Berntsson, H. Takala, K. D. Gallagher, H. Patel, E. Gustavsson, R. St. Peter, P. Duong, A. Nugent, F. Zhang, P. Berntsen, R. Appio, I. Rajkovic, H. Lehtivuori, M. R. Panman, M. Hoernke, S. Niebling, R. Harimoorthy, T. Lamparter, E.a A. Stojković, J. A. Ihalainen, and S. Westenhoff, Ubiquitous Structural Signaling in Bacterial Phytochromes, J. Phys. Chem. Lett 6 (2015) 3379

      A crystal structure of new phytofluor, WiPhy2, reveals that removal of polar interactions leads to enhanced fluorescence. WiPhy2 possesses the best compromise, achieved to date, between high fluorescence quantum yield and long illumination wavelength in this class of fluorophores.

      A crystal structure of new phytofluor, WiPhy2, reveal that removal of polar interactions leads to enhanced fluorescence. WiPhy2 possesses the best compromise, achieved to date, between high fluorescence quantum yield and long illumination wavelength in this class of fluorophores. [3]

    • Graphene and carbon nanotubes »

       

       

      Graphene, a single graphitic layer of carbon, has promising mechanical, electrical, magnetic, optical and thermal properties that have led to many experimental applications, e.g., in conductive inks, transistors, light emitting diodes and gas sensors. Plasmons in the infrared range can also be excited in graphene. The plasmon resonance can be controlled with the size of the structure and, as a specialty, by external electric fields and chemical doping. These factors and relatively low plasmon losses make graphene an interesting material for plasmonics.

      Our group is working on plasmons in graphene nanostructured by colloidal lithography and direct patterning by helium ion microscopy (HIM).  The strong interaction of these plasmons, tuned by gate voltage, with phonons in surrounding materials (hybridization) is the main focus of the research. Additionally, the spectroscopic properties of carbon nanotubes and their assemblies as well as their use in optoelectronics are topics of interest in our group. This research also extends to developing linked composites of porous silicon microparticles and carbon nanotubes for energy storage applications. We have also done work on the optical properties of conducting polymers with graphene additives, specifically on measuring anisotropy with total internal reflection spectroscopy.

      Exposure test for etching graphene with helium ions. Images starting from lowest magnification: optical dark-field, helium ion and atomic force microscopy.  The sample is single-layer graphene on oxidized silicon. 15 patterns were drawn ranging from doses of 1 µC/cm2 to 16.4 mC/cm2 increasing by factors of two from upper right.

      Exposure test for etching graphene with helium ions. Images starting from lowest magnification: optical dark-field, helium ion and atomic force microscopy.  The sample is single-layer graphene on oxidized silicon. 15 patterns were drawn ranging from doses of 1 µC/cm2 to 16.4 mC/cm2 increasing by factors of two from upper right.

    • 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 »


      B. Shen, V. Linko, H. Dietz and J.J. Toppari
      , Dielectrophoretic trapping of multilayer DNA origami nanostructures and DNA origami -induced local destruction of silicon dioxide, Electrophoresis, 36 (2015) 255–262

      B. Shen, V. Linko, T. Kosti, M.A. Kostiainen and J.J. Toppari, Custom-shaped metal nanostructures based on DNA origami silhouettes, Nanoscale 7 (2015) 11267-11272

      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 (2015) 15634

      T. Isoniemi, S. Tuukkanen, D.C. Cameron, J. Simonen, J.J. Toppari, Measuring optical anisotropy in poly(3,4-ethylene dioxythiophene):poly(styrene sulfonate) films with added graphene, Organic Electronics 25 (2015) 317–323

      H. Lehtivuori, S. Bhattacharya, N. M. Angenent-Mari, K. A. Satyshur, and K. T. Forest, Removal of Chromophore-proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor, Front. Mol. Biosci. 2 (2015) 65    

      J. A. Ihalainen, H. Takala and H. Lehtivuori, Fast photochemistry of prototypical Phytochromes - a species versus subunit specific comparison, Front. Mol. Biosci. 2 (2015) 75

      A. Björling, O. Berntsson, H. Takala, K. D. Gallagher, H. Patel, E. Gustavsson, R. St. Peter, P. Duong, A. Nugent, F. Zhang, P. Berntsen, R. Appio, I. Rajkovic, H. Lehtivuori, M. R. Panman, M. Hoernke, S. Niebling, R. Harimoorthy, T. Lamparter, E.a A. Stojković, J. A. Ihalainen, and S. Westenhoff, Ubiquitous Structural Signaling in Bacterial Phytochromes, J. Phys. Chem. Lett. 6 (2015) 3379

      J. Aumanen, A. Johansson, J. Koivistoinen, et al., Patterning and tuning of electrical and optical properties of graphene by l aser induced two-photon oxidation, Nanoscale  7 (2015) 2851

      J. Aumanen, A. Johansson, O. Herranen, et al.
        Local photo-oxidation of individual single walled carbon nanotubes probed by femtosecond four wave mixing imaging, Phys. Chem. Chem. Phys. 17 (2015) 209
    • Full Publication lists »

      Jussi Toppari     |    Andreas Johansson