Alpan Bek

Nanoscale chemical mapping using three-dimensional adiabatic compression of surface plasmon polaritons

The fields of plasmonics, Raman spectroscopy and atomic force microscopy have recently undergone considerable development, but independently of one another. By combining these techniques, a range of complementary information could be simultaneously obtained at a single molecule level. Here, we report the design, fabrication and application of a photonic-plasmonic device that is fully compatible with atomic force microscopy and Raman spectroscopy. Our approach relies on the generation and localization of surface plasmon polaritons by means of adiabatic compression through a metallic tapered waveguide to create strongly enhanced Raman excitation in a region just a few nanometres across. The tapered waveguide can also be used as an atomic force microscope tip. Using the device, topographic, chemical and structural information about silicon nanocrystals may be obtained with a spatial resolution of 7 nm.

Modulation of alpha-synuclein aggregation by dopamine analogs.

The action of dopamine on the aggregation of the unstructured alpha-synuclein (α-syn) protein may be linked to the pathogenesis of Parkinsons disease. Dopamine and its oxidation derivatives may inhibit α-syn aggregation by non-covalent binding. Exploiting this fact, we applied an integrated computational and experimental approach to find alternative ligands that might modulate the fibrillization of α-syn. Ligands structurally and electrostatically similar to dopamine were screened from an established library. Five analogs were selected for in vitro experimentation from the similarity ranked list of analogs. Molecular dynamics simulations showed they were, like dopamine, binding non-covalently to α-syn and, although much weaker than dopamine, they shared some of its binding properties. In vitro fibrillization assays were performed on these five dopamine analogs. Consistent with our predictions, analyses by atomic force and transmission electron microscopy revealed that all of the selected ligands affected the aggregation process, albeit to a varying and lesser extent than dopamine, used as the control ligand. The in silico/in vitro approach presented here emerges as a possible strategy for identifying ligands interfering with such a complex process as the fibrillization of an unstructured protein.

A Revertible, Autonomous, Self-Assembled DNA-Origami Nanoactuator

A DNA-origami actuator capable of autonomous internal motion in accord to an external chemical signal was designed, built, operated and imaged. The functional DNA nanostructure consists of a disk connected to an external ring in two, diametrically opposite points. A single stranded DNA, named probe, was connected to two edges of the disk perpendicularly to the axis of constrain. In the presence of a hybridizing target molecule, the probe coiled into a double helix that stretched the inner disk forcing the edges to move toward each other. The addition of a third single stranded molecule that displaced the target from the probe restored the initial state of the origami. Operation, dimension and shape were carefully characterized by combining microscopy and fluorescence techniques.

Understanding the plasmonic properties of dewetting formed Ag nanoparticles for large area solar cell applications

The effects of substrates with technological interest for solar cell industry are examined on the plasmonic properties of Ag nanoparticles fabricated by dewetting technique. Both surface matching (boundary element) and propagator (finite difference time domain) methods are used in numerical simulations to describe plasmonic properties and to interpret experimental data. The uncertainty on the locations of nanoparticles by the substrate in experiment is explained by the simulations of various Ag nanoparticle configurations. The change in plasmon resonance due to the location of nanoparticles with respect to the substrate, interactions among them, their shapes, and sizes as well as dielectric properties of substrate are discussed theoretically and implications of these for the experiment are deliberated.

Infrared microspectroscopy: a multiple-screening platform for investigating single-cell biochemical perturbations upon prion infection.

Prion diseases are a group of fatal neurodegenerative disorders characterized by the accumulation of prions in the central nervous system. The pathogenic prion (PrP(Sc)) possesses the capability to convert the host-encoded cellular isoform of the prion protein, PrP(C), into nascent PrP(Sc). The present work aims at providing novel insight into cellular response upon prion infection evidenced by synchrotron radiation infrared microspectroscopy (SR-IRMS). This non-invasive, label-free analytical technique was employed to investigate the biochemical perturbations undergone by prion infected mouse hypothalamic GT1-1 cells at the cellular and subcellular level. A decrement in total cellular protein content upon prion infection was identified by infrared (IR) whole-cell spectra and validated by bicinchoninic acid assay and single-cell volume analysis by atomic force microscopy (AFM). Hierarchical cluster analysis (HCA) of IR data discriminated between infected and uninfected cells and allowed to deduce an increment of lysosomal bodies within the cytoplasm of infected GT1-1 cells, a hypothesis further confirmed by SR-IRMS at subcellular spatial resolution and fluorescent microscopy. The purpose of this work, therefore, consists of proposing IRMS as a powerful multiscreening platform, drawing on the synergy with conventional biological assays and microscopy techniques in order to increase the accuracy of investigations performed at the single-cell level.

Tip enhanced Raman scattering with adiabatic plasmon focusing tips

Tip-Enhanced Raman spectroscopy (TERS) is a promising microscopy technique which combines, in principle, outstanding spatial resolution with a detailed chemical analysis of the sample. However, as yet, it is not routinely used although an increasing number of research groups are becoming more actively involved in the field. Among the several reasons which can explain the relatively low usage of TERS, the lack of reproducibility of tips as field enhancers is probably the most critical. Here we propose and demonstrate a TERS microscope which uses photonic engineered tips. These tips are based on standard silicon nitride atomic force microscope (AFM) cantilevers. A photonic crystal together with a plasmonic waveguide focuses the Raman excitation laser to the apex of the waveguide, enabling a photon confinement equivalent to the radius of curvature of the nanofabricated tip. These tips were successfully applied here in both AFM imaging and high resolution Raman spectroscopy. The new tips produced AFM imaging performances comparable with the best AFM commercial tips. Moreover, we demonstrate that the photonic crystal combined with the plasmonic waveguide acts effectively as a localized near field emitter.

Structural Insights into Alternate Aggregated Prion Protein Forms

The conversion of the cellular form of the prion protein (PrP(C)) to an abnormal, alternatively folded isoform (PrP(Sc)) is the central event in prion diseases or transmissible spongiform encephalopathies. Recent studies have demonstrated de novo generation of murine prions from recombinant prion protein (recPrP) after inoculation into transgenic and wild-type mice. These so-called synthetic prions lead to novel prion diseases with unique neuropathological and biochemical features. Moreover, the use of recPrP in an amyloid seeding assay can specifically detect and amplify various strains of prions. We employed this assay in our experiments and analyzed in detail the morphology of aggregate structures produced under defined chemical constraints. Our results suggest that changes in the concentration of guanidine hydrochloride can lead to different kinetic traces in a typical thioflavin T(ThT) assay. Morphological and structural analysis of these aggregates by atomic force microscopy indicates a variation in the structure of the PrP molecular assemblies. In particular, ThT positive PrP aggregates produced from rec mouse PrP residues 89 to 230 lead to mostly oligomeric structures at low concentrations of guanidine hydrochloride, while more amyloidal structures were observed at higher concentrations of the denaturant. These findings highlight the presence of numerous and complex pathways in deciphering prion constraints for infectivity and toxicity.

Effect of surface type on structural and optical properties of Ag nanoparticles formed by dewetting

Integration of an array of Ag nanoparticles in solar cells is expected to increase light trapping through field enhancement and plasmonic scattering. Requirement of Ag nanoparticle decoration of cell surfaces or interfaces at the macro-scale, calls for a self-organized fabrication method such as thermal dewetting. Optical properties of a 2D array of Ag nanoparticles are known to be very sensitive to their shape and size. We show that these parameters depend on the type of the substrate used. We observe that the average nanoparticle size decreases with increasing substrate thermal conductivity and nanoparticle size distribution broadens with increasing surface roughness.

Fabrication of Ag Nanoparticles Embedded in Al:ZnO as Potential Light-Trapping Plasmonic Interface for Thin Film Solar Cells

Incident photon conversion efficiency of the absorbing materials at either side of a thin film solar module can be enhanced by integrating a plasmonic interface. Silver nanoparticles represent a good candidate that can be integrated to a thin film solar cell for efficient light-trapping. The aim of this work is to fabricate plasmonically active interface consisting of Ag nanoparticles embedded in Al:ZnO that has the potential to be used at the front surface and at the back reflector of a thin film solar cell to enhance light-trapping and increase the photoconversion efficiency. We show that Ag can readily dewet the Al:ZnO surface when annealed at temperatures significantly lower than the melting temperature of Ag, which is beneficial for lowering the thermal budget and cost in solar cell fabrication. We find that such an interface fabricated by a simple dewetting technique leads to plasmonic resonance in the visible and near infrared regions of the solar spectrum, which is important in enhancing the conversion efficiency of thin film solar cells.

Engineering nonlinear response of nanomaterials using Fano resonances

We show that nonlinear optical processes of nanoparticles can be controlled by the presence of interactions with a molecule or a quantum dot. By choosing the appropriate level spacing for the quantum emitter, one can either suppress or enhance the nonlinear frequency conversion. We reveal the underlying mechanism for this effect, which is already observed in recent experiments: (i) suppression occurs simply because transparency induced by Fano resonance does not allow an excitation at the converted frequency, and (ii) enhancement emerges since the nonlinear process can be brought to resonance. The path interference effect cancels the nonresonant frequency terms. We demonstrate the underlying physics using a simplified model, and we show that the predictions of the model are in good agreement with the three-dimensional boundary element method (MNPBEM toolbox) simulations. Here, we consider the second harmonic generation in a plasmonic converter as an example to demonstrate the control mechanism. The phenomenon is the semi-classical analog of nonlinearity enhancement via electromagnetically induced transparency.