IR Near-field Nanoscopy and Spectroscopy of Cells and Soft Matter

Infrared (IR) microscopy and spectroscopy, while being sensitive to the samples’ chemical composition, suffer from poor lateral resolution due to diffraction. Therefore, imaging of the cellular inner structure in the IR range of the electromagnetic spectrum proves to be challenging. An approach to overcome this limitation is by using scattering-type near-field optical microscopy (sSNOM) and nano-Fourier transform infrared (nanoFTIR) spectroscopy, achieved by combining the high spatial resolution of atomic force microscopy (AFM) and the chemical sensitivity of IR absorption. This methodology was applied to various biophysical systems with increasing complexity, starting with native membrane proteins, followed by aggregating peptides and light-induced surface patterning, concluding with investigation of cells. In this work I was able to resolve the subcellular structure of C. reinhardtii and assign the IR absorption of various organelles to molecular vibrations with spatial resolution of 20 nm. The necessity and power of chemical imaging was demonstrated by scanning the nuclear area, where several nuclear bodies were distinguished in the sSNOM images while remaining hidden in the AFM topography. Finally, a stack of sSNOM images, obtained by sequential scanning of serial sections, was used to reconstruct a three-dimensional image. Thus, we demonstrate that sSNOM tomography allows visualizing three-dimensional intracellular structures at nanometer resolution where the contrast originates from molecular vibrations of chemical bonds

Design and Fabrication of Integrated Plasmonic Platforms for Ultra-sensitive Molecular and Biomolecular Detections

One of the major challenges in analytical and biological sciences is to develop a device to obtain unambiguous chemical and structural properties of a material or a probe biomolecule with high reproducibility and ultra-high sensitivity. Moreover, in addition to such a high sensitivity, other cases such as minimum intrusiveness, small amounts of analyte, and short acquisition time and high reproducibility are key parameters that can be valued in any analytical measurements. Among the promising methods to achieve such endeavor, plasmon-mediated surface-enhanced spectroscopic techniques, such as surface-enhanced Raman spectroscopy (SERS), are considered as suitable options. Such techniques take advantage of the interaction between an optical field and a metallic nanostructure to magnify the electromagnetic (EM) field in the proximity of the nanostructure. This results in an amplified signal of the vibrational fingerprints of the adsorbed probe molecules onto the metallic surface. Keys to obtaining ultra-sensitive SERS measurements are the development of rationally-designed plasmonic nanostructures. Besides, a major challenge for controlled and reliable sensitive measurements of probe biomolecules on biological cells gives rise due to the intrinsic random positioning and proliferation of these cells over a substrate such as a glass coverslip. In this thesis, the rational design and development of a fluorocarbon thin film micropatterned platform is introduced for controlled programming of conventional and transfected cells proliferation over the substrate. They also provided high throughput capability of controlled neuronal network connections towards advanced imaging and sensitive detection of biomolecules of interest at nanoscale resolution. This micropatterned platform was also integrated with optimized plasmonic nanostructures fabricated by nanosphere lithography (NSL) for SERS biosensing of glycans using a Raman reporter over the positionally-controlled single cells surfaces. In addition to providing controlled plasmon-mediated measurements, the fabrications of two newly-developed 3D plasmonic nanostructures have been introduced in this thesis. These are nanopyramids arrays fabricated by NSL and arrays of nanoholes with co-registered nanocones fabricated by electron-beam lithography (EBL). These approaches have been used not only for ultra-sensitive molecular detection at the monolayer level in a variety of configurations, but also towards label-free single molecule detection at sub-femtomolar concentrations

Nanoscale local modification of PMMA refractive index by tip-enhanced femtosecond pulsed laser irradiation

Investigation techniques based on tip-enhanced optical effects, capable to yield spatial resolutions down to nanometers level, have enabled a wide palette of important discoveries over the past twenty years. Recently, their underlying optical setups are beginning to emerge as useful tools to modify and manipulate matter with nanoscale spatial resolution. We try to contribute to these efforts by reporting a method that we found viable to modify the surface refractive index of polymethyl methacrylate (PMMA), an acrylic polymer material. The changes in the refractive index are accomplished by focusing a femtosecond pulsed near-infrared laser beam on the apex of a metalized nano-sized tip, traditionally used in scanning probe microscopy (SPM) applications. The adopted illumination strategy yields circular-shaped modifications of the refractive index occurring at the surface of the PMMA sample, exhibiting a lateral size <200 nm, under 790 nm illumination, representing a four-fold increase in precision compared to the current state-of-the-art. The light intensity enhancement effects taking place at the tip apex makes possible achieving refractive index changes at low laser pulse energies (<0.5 nJ), which represents two orders of magnitude advantage over the current state-of-the art. The presented nanoimprinting method is very flexible, as it can be used with different power levels and can potentially be operated with other materials. Besides enabling modifications of the refractive index with high lateral resolution, this method can pave the way towards other important applications such the fabrication of photonic crystal lattices or surface waveguides

Synthetic, Crystallographic, and Computational Study of Copper(II) Complexes of Ethylenediaminetetracarboxylate Ligands

Copper(II) complexes of hexadentate ethylenediaminetetracarboxylic acid type ligands H4eda3p and H4eddadp (H4eda3p = ethylenediamine-N-acetic-N,N′,N′-tri-3-propionic acid; H4eddadp = ethylenediamine-N,N′-diacetic-N,N′-di-3-propionic acid) have been prepared. An octahedral trans(O6) geometry (two propionate ligands coordinated in axial positions) has been established crystallographically for the Ba[Cu(eda3p)]·8H2O compound, while Ba[Cu(eddadp)]·8H2O is proposed to adopt a trans(O5) geometry (two axial acetates) on the basis of density functional theory calculations and comparisons of IR and UV−vis spectral data. Experimental and computed structural data correlating similar copper(II) chelate complexes have been used to better understand the isomerism and departure from regular octahedral geometry within the series. The in-plane O−Cu−N chelate angles show the smallest deviation from the ideal octahedral value of 90°, and hence the lowest strain, for the eddadp complex with two equatorial β-propionate rings. A linear dependence between tetragonality and the number of five-membered rings has been established. A natural bonding orbital analysis of the series of complexes is also presented.

Advanced Photonic Sciences

The new emerging field of photonics has significantly attracted the interest of many societies, professionals and researchers around the world. The great importance of this field is due to its applicability and possible utilization in almost all scientific and industrial areas. This book presents some advanced research topics in photonics. It consists of 16 chapters organized into three sections: Integrated Photonics, Photonic Materials and Photonic Applications. It can be said that this book is a good contribution for paving the way for further innovations in photonic technology. The chapters have been written and reviewed by well-experienced researchers in their fields. In their contributions they demonstrated the most profound knowledge and expertise for interested individuals in this expanding field. The book will be a good reference for experienced professionals, academics and researchers as well as young researchers only starting their carrier in this field

Advanced photon counting techniques for long-range depth imaging

The Time-Correlated Single-Photon Counting (TCSPC) technique has emerged as a candidate approach for Light Detection and Ranging (LiDAR) and active depth imaging applications. The work of this Thesis concentrates on the development and investigation of functional TCSPC-based long-range scanning time-of-flight (TOF) depth imaging systems. Although these systems have several different configurations and functions, all can facilitate depth profiling of remote targets at low light levels and with good surface-to-surface depth resolution. Firstly, a Superconducting Nanowire Single-Photon Detector (SNSPD) and an InGaAs/InP Single-Photon Avalanche Diode (SPAD) module were employed for developing kilometre-range TOF depth imaging systems at wavelengths of ~1550 nm. Secondly, a TOF depth imaging system at a wavelength of 817 nm that incorporated a Complementary Metal-Oxide-Semiconductor (CMOS) 32×32 Si-SPAD detector array was developed. This system was used with structured illumination to examine the potential for covert, eye-safe and high-speed depth imaging. In order to improve the light coupling efficiency onto the detectors, the arrayed CMOS Si-SPAD detector chips were integrated with microlens arrays using flip-chip bonding technology. This approach led to the improvement in the fill factor by up to a factor of 15. Thirdly, a multispectral TCSPC-based full-waveform LiDAR system was developed using a tunable broadband pulsed supercontinuum laser source which can provide simultaneous multispectral illumination, at wavelengths of 531, 570, 670 and ~780 nm. The investigated multispectral reflectance data on a tree was used to provide the determination of physiological parameters as a function of the tree depth profile relating to biomass and foliage photosynthetic efficiency. Fourthly, depth images were estimated using spatial correlation techniques in order to reduce the aggregate number of photon required for depth reconstruction with low error. A depth imaging system was characterised and re-configured to reduce the effects of scintillation due to atmospheric turbulence. In addition, depth images were analysed in terms of spatial and depth resolution

Atomic Force Microscopy Tip-enhanced Laser Ablation

In the present work, an apertureless atomic force microscope (AFM) tip-enhanced laser ablation (TELA) system was developed and investigated. An AFM was coupled to an optical parametric oscillator (OPO) wavelength tunable laser for sample ablation with a submicron sampling size. The AFM was used to image the surface and hold the AFM tip 10 nm above the sample surface. The AFM tip is coated with a layer of gold with a thickness of 35 nm. The incident laser wavelength was tuned in the visible and near-infrared (IR) region and focused on the AFM tip. With the tip-enhancement effect, ablation craters on the surface with a submicron size were obtained. The mechanism of TELA was investigated using anthracene and three laser dyes: rhodamine B, methylene blue, and IR 797 chloride. All samples were prepared in thin films and the laser energy was set just below their far-field ablation threshold. The wavelength was tuned from 450 to 1100 nm to cover the visible and near-IR range. It was found that ablation is independent of the absorption of the compounds. The ablation crater volume was measured and found to have a maximum at 500 nm and an approximately linear drop to 800 nm. Craters could not be produced between 800 and 1200 nm and were slightly smaller at 450 nm compared to 500 nm. Apertureless TELA was then performed to sample plasmid DNA with 532 nm, which resulted in a sampling volume of 0.14 μm3 with 12% in variation. The captured DNA was amplified and the amount of sample transferred from each ablation crater was quantitated at 20 ag/spot

Modern lithographic techniques applied to stereographic imaging

The main aim of the research has been to produce and evaluate a high-quality diffusion screen to display projected film and television images. The screens have also been found to effectively de-pixelate LCD arrays viewed at a magnification of approximately 4x. The production process relies on the formation of localized refractive index gradients in a photopolymer. The photopolymer, specially formulated and supplied by Du Pont, is exposed to actinic light through a precision contact mask to initiate polymerization within the exposed areas. As polymerization proceeds, a monomer concentration gradient exists between the exposed and unexposed regions allowing the monomer molecules to diffuse. Since the longer polymer chains do not diffuse as readily, the molecular concentration of the material, which is related to its refractive index, is then no longer uniform. The generation of this refractive index profile can, to some extent, be controlled by careful exposure of the photopolymer through the correct mask so that the resulting diffusion screen can be tailored to suit specific viewing requirements. [Continues.

Development of Holographic Phase Masks for Wavefront Shaping

This dissertation explores a new method for creating holographic phase masks (HPMs), which are phase transforming optical elements holographically recorded in photosensitive glass. This novel hologram recording method allows for the fast production of HPMs of any complexity, as opposed to the traditional multistep process, which includes the design and fabrication of a master phase mask operating in the UV region before the holographic recording step. We holographically recorded transmissive HPMs that are physically robust (they are recorded in a silicate glass volume), can handle tens of kilowatts of continuous wave (CW) laser power, are un-erasable, user defined, require no power to operate, can work over a wavelength band ranging from 350 to 2500 nm, and can modify the wavefront of narrow line or broad band coherent sources. The HPMs can be wavelength-tunable by angular adjustment over tens or even hundreds of nanometers. The HPMs incorporate the phase information in the bulk of a volume Bragg grating (VBG) resulting in only a single diffraction order and up to 100% diffraction efficiency. Recording in thick photosensitive medium also enables the multiplexing of HPMs in a single monolithic element. While these HPMs are physically overlapped in the space, they provide independent phase profiles, efficiencies, spectral and angular acceptances. Multiplexing HPMs allows splitting or combining of multiple beams while affecting their wavefronts individually. We also developed a new holographic phase mask of reflective-type. This device provides us the ability of recording RBGs with transversely shifted parts in the larger aperture which upon reconstruction will produce different phases to different parts of the diffracted beam. RBG\u27s diffraction spectrum possesses a very narrow bandwidth, and the holographic recording technique allows to multiplex multiple gratings into a single volume of PTR glass. If each of these Bragg wavelengths is assigned with a specific spatial mode, it can be achieved simultaneous spatial and spectral multiplexing. As a separate research topic, we look at how holographic optical elements (HOEs) can be used for improving the capabilities of the existing generation of head-up displays (HUDs), resulting in smaller, lighter units with a larger eye-box. Currently, surface relief gratings recorded in photosensitive polymers that are susceptible to the environmental conditions are used in HOE-based HUDs. This has an impact on their reliability and overall lifespan. We investigated a specific holographically recorded in the volume of photo-thermo-refractive glass transmissive gratings that generated multiple diffracted beams due to their operation in Raman-Nath regime. The Raman Nath gratings were successfully used to create an array of images because in augmented reality systems, this approach can be used to enhance the size of the exit pupil. These image splitting elements, due to the features of PTR glass, have a great resistance to temperature gradients, mechanical shocks, vibrations, and laser radiation