Molecular devices for nanoelectronics and plasmonics

This thesis is focused on fabrication and characterization of molecular devices. In connection with molecular electronics the dielectrophoresis based method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. Moreover, the method was extended to self-assembled DNA nanostructures. The method allowed to obtain valuable information about electrical and dielectrophoretic properties of DNA. In addition, two general approaches to the utilization of DNA origami structures for the assembly of materials are described and experimentally demonstrated. In context of molecular plasmonics, a novel lithographic fabrication method for positioning dye molecules on …

DNA origami as a nanoscale template for protein assembly

We describe two general approaches to the utilization of DNA origami structures for the assembly of materials. In one approach, DNA origami is used as a prefabricated template for subsequent assembly of materials. In the other, materials are assembled simultaneously with the DNA origami, i.e. the DNA origami technique is used to drive the assembly of materials. Fabrication of complex protein structures is demonstrated by these two approaches. The latter approach has the potential to be extended to the assembly of multiple materials with single attachment chemistry.

Trapping and Immobilization of DNA Molecules Between Nanoelectrodes

DNA is one of the most promising molecules for nanoscale bottom-up fabrication. For both scientific studies and fabrication of devices, it is desirable to be able to manipulate DNA molecules, or self--assembled DNA constructions, at the single unit level. Efficient methods are needed for precisely attaching the single unit to the external measurement setup or the device structure. So far, this has often been too cumbersome to achieve, and consequently most of the scientific studies are based on a statistical analysis or measurements done for a sample containing numerous molecules in liquid or in a dry state. Here, we explain a method for trapping and attaching nanoscale double-stranded DNA …

Field-induced nanolithography for high-throughput pattern transfer.

Dielectrophoretic trapping of DNA origami.

In this thesis three-dimensional tube-shaped DNA-origamis were dielectrophoretically trapped within lithographically fabricated nanoelectrodes. The origamis had been premade while the electrodes were fabricated specifically for these experiments with two different gapsizes, 150 nm and 400 nm. The aim of the work was to capture individual nanotubes in the gap between the electrodes by utilizing the dielectrophoretic forces present in the structure when a solution containing the origamis was put onto the electrodes and a voltage was applied. It was observed during the experiments that the success of the dielectrophoretic trapping depended strongly on the trapping conditions. This caused the t…

Trapping of 27 bp–8 kbp DNA and immobilization of thiol-modified DNA using dielectrophoresis

Dielectrophoretic trapping of six different DNA fragments, sizes varying from the 27 to 8416 bp, has been studied using confocal microscopy. The effect of the DNA length and the size of the constriction between nanoscale fingertip electrodes on the trapping efficiency have been investigated. Using finite element method simulations in conjunction with the analysis of the experimental data, the polarizabilities of the different size DNA fragments have been calculated for different frequencies. Also the immobilization of trapped hexanethiol- and DTPA-modified 140 nm long DNA to the end of gold nanoelectrodes was experimentally quantified and the observations were supported by density functiona…

Molecular coupling of light with plasmonic waveguides.

We use molecules to couple light into and out of microscale plasmonic waveguides. Energy transfer, mediated by surface plasmons, from donor molecules to acceptor molecules over ten micrometer distances is demonstrated. Also surface plasmon coupled emission from the donor molecules is observed at similar distances away from the excitation spot. The lithographic fabrication method we use for positioning the dye molecules allows scaling to nanometer dimensions. The use of molecules as couplers between far-field and near-field light offers the advantages that no special excitation geometry is needed, any light source can be used to excite plasmons and the excitation can be localized below the d…

Vacuum Rabi splitting for surface plasmon polaritons and Rhodamine 6G molecules

We report on strong coupling between surface-plasmon polaritons and Rhodamine 6G molecules at room temperature. As a reference to compare with, we first determine the dispersion curve of (uncoupled) surface plasmon polaritons on a 50 nm thick film of silver. Consequently, we determine the dispersion curve of surface plasmon polaritons strongly coupled to Rhodamine 6G molecules, which exhibits vacuum Rabi splitting. Depending on the Rhodamine 6G concentration, we find splitting energies between 0.05 eV and 0.13 eV.

Dielectrophoresis as a tool for nanoscale DNA manipulation

The use of the dielectrophoresis as a tool for DNA manipulation is demonstrated experimentally, using both unmodified 48,500 base pairs long bacteriophage lambda dsDNA (λ-DNA), ∼16 μm in length and 414 base pairs long thiol modified natural dsDNA (avDNA), ∼140 nm in length. We show that both the dsDNA types used, are effectively directed between the planar gold electrodes by the positive dielectrophoresis while applying an AC voltage at frequencies between 500 kHz and 1 MHz. With high concentrations of dsDNA in buffer the attached dsDNA molecules are shown to form bundles or clumps (both λ-DNA and avDNA). Furthermore, we demonstrate the attaching of a single avDNA molecule to an electrode v…

Carbon nanotubes as electrodes for dielectrophoresis of DNA

Dielectrophoresis can potentially be used as an efficient trapping tool in the fabrication of molecular devices. For nanoscale objects, however, the Brownian motion poses a challenge. We show that the use of carbon nanotube electrodes makes it possible to apply relatively low trapping voltages and still achieve high enough field gradients for trapping nanoscale objects, e.g., single molecules. We compare the efficiency and other characteristics of dielectrophoresis between carbon nanotube electrodes and lithographically fabricated metallic electrodes, in the case of trapping nanoscale DNA molecules. The results are analyzed using finite element method simulations and reveal information abou…

Characterization of the conductance mechanisms of DNA origami by AC impedance spectroscopy.

Nanolithography: Small 23/2009

Frequency conversion of propagating surface plasmon polaritons by organic molecules

We demonstrate frequency conversion of surface plasmon polaritons (SPP) by utilizing the coupling between organic dye molecules and SPP. Launching of SPPs into a plasmonic waveguide is done in two ways: by optically excited molecules and by quantum dots (QDs). QDs are demonstrated to overcome the major problem of bleaching occurring with molecules. The SPP propagates tens of micrometers and clear frequency conversion is observed in the SPP spectrum after passing an area of converter molecules. The use of molecules and QDs as elements of all-plasmonic devices has the potential for high integration and use of self-assembly in fabrication. Peer reviewed

Vacuum Rabi Splitting and Strong-Coupling Dynamics for Surface-Plasmon Polaritons and Rhodamine 6G Molecules

We report on strong coupling between surface plasmon polaritons (SPP) and Rhodamine 6G (R6G) molecules, with double vacuum Rabi splitting energies up to 230 and 110 meV. In addition, we demonstrate the emission of all three energy branches of the strongly coupled SPP-exciton hybrid system, revealing features of system dynamics that are not visible in conventional reflectometry. Finally, in analogy to tunable-Q microcavities, we show that the Rabi splitting can be controlled by adjusting the interaction time between waveguided SPPs and R6G deposited on top of the waveguide. The interaction time can be controlled with sub-fs precision by adjusting the length of the R6G area with standard lith…

Creation of ordered 3D tubes out of DNA origami lattices

Funding Information: Funding from the Jane and Aatos Erkko Foundation (J.J.T. and A.K./M.V.-R.) and the Academy of Finland (#330584 and #350797 J.J.T./#308992 A.K. and A.K.N./#330896 M.V.-R.) is gratefully acknowledged. The authors also acknowledge the provision of facilities and technical support by Aalto University at OtaNano - Nanomicroscopy Center (Aalto-NMC). Publisher Copyright: © 2023 The Royal Society of Chemistry. Hierarchical self-assembly of nanostructures with addressable complexity has been a promising route for realizing novel functional materials. Traditionally, the fabrication of such structures on a large scale has been achievable using top-down methods but with the cost of…