The development of an automated nano sampling handling system for nanometre protein crystallography experiments

As the world's synchrotrons and X-FELs endeavour to meet the need to analyse ever-smaller protein crystals, there grows a requirement for a new technique to present nano-dimensional samples to the beam for X-ray diffraction experiments.The work presented here details developmental work to reconfigure the nano tweezer technology developed by Optofluidics (PA, USA) for the trapping of nano dimensional protein crystals for X-ray crystallography experiments. The system in its standard configuration is used to trap nano particles for optical microscopy. It uses silicon nitride laser waveguides that bridge a micro fluidic channel. These waveguides contain 180 nm apertures of enabling the system to use biologically compatible 1.6 micron wavelength laser light to trap nano dimensional biological samples. Using conventional laser tweezers, the wavelength required to trap such nano dimensional samples would destroy them. The system in its optical configuration has trapped protein molecules as small as 10 nanometres.

The development of an automated nano sampling handling system for nanometne protein crystallography experiments

As the world's synchrotrons and X-FELs endeavour to meet the need to analyse ever-smaller protein crystals, there grows a requirement for a new technique to present nano-dimensional samples to the beam for X-ray diffraction experiments.The work presented here details developmental work to reconfigure the nano tweezer technology developed by Optofluidics (PA, USA) for the trapping of nano dimensional protein crystals for X-ray crystallography experiments. The system in its standard configuration is used to trap nano particles for optical microscopy. It uses silicon nitride laser waveguides that bridge a micro fluidic channel. These waveguides contain 180 nm apertures of enabling the system to use biologically compatible 1.6 micron wavelength laser light to trap nano dimensional biological samples. Using conventional laser tweezers, the wavelength required to trap such nano dimensional samples would destroy them. The system in its optical configuration has trapped protein molecules as small as 10 nanometres.

Miniature optical delay lines and buffers

Creation of miniature optical delay lines and buffers is one of the greatest challenges of the modern photonics which can revolutionize optical communications and computing. Several remarkable designs of slow light optical delay lines employing coupled ring resonators and photonic crystal waveguides has been suggested and experimentally demonstrated. However, the insertion loss of these devices is too large for their practical applications. Alternatively, the recently developed photonic fabrication platform, Surface Nanoscale Axial Photonics (SNAP) allows us to fabricate record small delay lines with unprecedentedly small dispersion and low loss. In this report, we review the recent progress in fabrication and design of miniature slow light devices and buffers, in particular, those based on the SNAP technology.

Fractional order of poling period for broadly tunable second harmonic generation

We demonstrate the possibility to use a fractional order of poling period of nonlinear crystal waveguides for tunable second harmonic generation. This approach allows one to extend wavelength coverage in the visible spectral range by frequency doubling in a single crystal waveguide.

Nonlinear optics with cold Rb atoms using tapered optical nanofibres

Optical nanofibres (ONFs) are very thin optical waveguides with sub-wavelength diameters. ONFs have very high evanescent fields and the guided light is confined strongly in the transverse direction. These fibres can be used to achieve strong light-matter interactions. Atoms around the waist of an ONF can be probed by collecting the atomic fluorescence coupling or by measuring the transmission (or the polarisation) of the probe beam sent through it. This thesis presents experiments using ONFs for probing and manipulating laser-cooled 87Rb atoms. As an initial experiment, a single mode ONF was integrated into a magneto-optical trap (MOT) and used for measuring the characteristics of the MOT, such as the loading time and the average temperature of the atom cloud. The effect of a near-resonant probe beam on the local temperature of the cold atoms has been studied. Next, the ONF was used for manipulating the atoms in the evanescent fields region in order to generate nonlinear optical effects. Four-wave mixing, ac Stark effect (Autler-Townes splitting) and electromagnetically induced transparency have been observed at unprecedented ultralow power levels. In another experiment, a few-mode ONF, supporting only the fundamental mode and the first higher order mode group, has been used for studying cold atoms. A higher pumping rate of the atomic fluorescence into the higher order fibreguided modes and more interactions with the surrounding atoms for higher order mode evanescent light, when compared to signals for the fundamental mode, have been identified. The results obtained in the thesis are particularly for a fundamental understanding of light-atom interactions when atoms are near a dielectric surface and also for the development of fibre-based quantum information technologies. Atoms coupled to ONFs could be used for preparing intrinsically fibre-coupled quantum nodes for quantum computing and the studies presented here are significant for a detailed understanding of such a system.

Exploring a new transmission window for telecommunications in the 2 μm waveband

In this paper, we will demonstrate the possibility of opening a new telecommunications transmission window around the 2 μm wavelength, in order to exploit the potential low loss of hollow-core photonic bandgap fibers, with the benefits of significantly lower non-linearity and latency. We will show recent efforts developing a dense wavelength division multiplexing testbed at this waveband, with 100 GHz spacing wavelength channels and 105 Gbit/s total capacity achieved.

Hybrid photonic crystal lasers

Energy efficient Wavelength Division Multiplexing (WDM) is the key to satisfying the future bandwidth requirements of datacentres. As the silicon photonics platform is regarded the only technology able to meet the required power and cost efficiency levels, the development of silicon photonics compatible narrow linewidth lasers is now crucial. We discuss the requirements for such laser systems and report the experimental demonstration of a compact uncooled external-cavity mW-class laser architecture with a tunable Si Photonic Crystal resonant reflector, suitable for direct Frequency Modulation.

A Micro-Opto-Electro-Mechanical System (MOEMS) for Microstructure Manipulation

Microstructure manipulation is a fundamental process to the study of biology and medicine, as well as to advance micro- and nano-system applications. Manipulation of microstructures has been achieved through various microgripper devices developed recently, which lead to advances in micromachine assembly, and single cell manipulation, among others. Only two kinds of integrated feedback have been demonstrated so far, force sensing and optical binary feedback. As a result, the physical, mechanical, optical, and chemical information about the microstructure under study must be extracted from macroscopic instrumentation, such as confocal fluorescence microscopy and Raman spectroscopy. In this research work, novel Micro-Opto-Electro-Mechanical-System (MOEMS) microgrippers are presented. These devices utilize flexible optical waveguides as gripping arms, which provide the physical means for grasping a microobject, while simultaneously enabling light to be delivered and collected. This unique capability allows extensive optical characterization of the structure being held such as transmission, reflection, or fluorescence. The microgrippers require external actuation which was accomplished by two methods: initially with a micrometer screw, and later with a piezoelectric actuator. Thanks to a novel actuation mechanism, the “fishbone”, the gripping facets remain parallel within 1 degree. The design, simulation, fabrication, and characterization are systematically presented. The devices mechanical operation was verified by means of 3D finite element analysis simulations. Also, the optical performance and losses were simulated by the 3D-to-2D effective index (finite difference time domain FDTD) method as well as 3D Beam Propagation Method (3D-BPM). The microgrippers were designed to manipulate structures from submicron dimensions up to approximately 100 µm. The devices were implemented in SU-8 due to its suitable optical and mechanical properties. This work demonstrates two practical applications: the manipulation of single SKOV-3 human ovarian carcinoma cells, and the detection and identification of microparts tagged with a fluorescent “barcode” implemented with quantum dots. The novel devices presented open up new possibilities in the field of micromanipulation at the microscale, scalable to the nano-domain.

Graphene-based waveguide resonators for submillimeter-wave applications

Utilization of graphene covered waveguide inserts to form tunable waveguide resonators is theoretically explained and rigorously investigated by means of full-wave numerical electromagnetic simulations. Instead of using graphene-based switching elements, the concept we propose incorporates graphene sheets as parts of a resonator. Electrostatic tuning of the graphene surface conductivity leads to changes in the electromagnetic field boundary conditions at the resonator edges and surfaces, thus producing an effect similar to varying the electrical length of a resonator. The presented outline of the theoretical background serves to give phenomenological insight into the resonator behavior, but it can also be used to develop customized software tools for design and optimization of graphene-based resonators and filters. Due to the linear dependence of the imaginary part of the graphene surface impedance on frequency, the proposed concept was expected to become effective for frequencies above 100 GHz, which is confirmed by the numerical simulations. A frequency range from 100 GHz up to 1100 GHz, where the rectangular waveguides are used, is considered. Simple, all-graphene-based resonators are analyzed first, to assess the achievable tunability and to check the performance throughout the considered frequency range. Graphene–metal combined waveguide resonators are proposed in order to preserve the excellent quality factors typical for the type of waveguide discontinuities used. Dependence of resonator properties on key design parameters is studied in detail. Dependence of resonator properties throughout the frequency range of interest is studied using eight different waveguide sections appropriate for different frequency intervals. Proposed resonators are aimed at applications in the submillimeter-wave spectral region, serving as the compact tunable components for the design of bandpass filters and other devices.

A Frequency-Dependent Equivalence Between Groove Gap Waveguide and Rectangular Waveguide

Recently gap waveguides have been shown as a potential alternative to conventional waveguides in the millimeter-wave band. Groove Gap Waveguide (GGW) has until now been studied though direct correspondence with rectangular waveguide with the same propagation channel dimensions. However there have been observed differences in the above cutoff propagation characteristics between these waveguide types. Furthermore, the behaviour of GGW below cutoff remains unknown. This work presents a discussion of below and above cutoff propagation characteristics, and introduces a simple model that explains observed GGW behavior and establishes its propagation characteristics.

Nonlinear Optics and Carrier Dynamics in Nanostructured and Two-Dimensional Materials

Understanding and measuring the interaction of light with sub-wavelength structures and atomically thin materials is of critical importance for the development of next generation photonic devices.  One approach to achieve the desired optical properties in a material is to manipulate its mesoscopic structure or its composition in order to affect the properties of the light-matter interaction.  There has been tremendous recent interest in so called two-dimensional materials, consisting of only a single to a few layers of atoms arranged in a planar sheet.  These materials have demonstrated great promise as a platform for studying unique phenomena arising from the low-dimensionality of the material and for developing new types of devices based on these effects.  A thorough investigation of the optical and electronic properties of these new materials is essential to realizing their potential.  In this work we present studies that explore the nonlinear optical properties and carrier dynamics in nanoporous silicon waveguides, two-dimensional graphite (graphene), and atomically thin black phosphorus. We first present an investigation of the nonlinear response of nanoporous silicon optical waveguides using a novel pump-probe method. A two-frequency heterodyne technique is developed in order to measure the pump-induced transient change in phase and intensity in a single measurement. The experimental data reveal a characteristic material response time and temporally resolved intensity and phase behavior matching a physical model dominated by free-carrier effects that are significantly stronger and faster than those observed in traditional silicon-based waveguides.  These results shed light on the large optical nonlinearity observed in nanoporous silicon and demonstrate a new measurement technique for heterodyne pump-probe spectroscopy. Next we explore the optical properties of low-doped graphene in the terahertz spectral regime, where both intraband and interband effects play a significant role. Probing the graphene at intermediate photon energies enables the investigation of the nonlinear optical properties in the graphene as its electron system is heated by the intense pump pulse. By simultaneously measuring the reflected and transmitted terahertz light, a precise determination of the pump-induced change in absorption can be made. We observe that as the intensity of the terahertz radiation is increased, the optical properties of the graphene change from interband, semiconductor-like absorption, to a more metallic behavior with increased intraband processes. This transition reveals itself in our measurements as an increase in the terahertz transmission through the graphene at low fluence, followed by a decrease in transmission and the onset of a large, photo-induced reflection as fluence is increased.  A hybrid optical-thermodynamic model successfully describes our observations and predicts this transition will persist across mid- and far-infrared frequencies.  This study further demonstrates the important role that reflection plays since the absorption saturation intensity (an important figure of merit for graphene-based saturable absorbers) can be underestimated if only the transmitted light is considered. These findings are expected to contribute to the development of new optoelectronic devices designed to operate in the mid- and far-infrared frequency range.  Lastly we discuss recent work with black phosphorus, a two-dimensional material that has recently attracted interest due to its high mobility and direct, configurable band gap (300 meV to 2eV), depending on the number of atomic layers comprising the sample. In this work we examine the pump-induced change in optical transmission of mechanically exfoliated black phosphorus flakes using a two-color optical pump-probe measurement. The time-resolved data reveal a fast pump-induced transparency accompanied by a slower absorption that we attribute to Pauli blocking and free-carrier absorption, respectively. Polarization studies show that these effects are also highly anisotropic - underscoring the importance of crystal orientation in the design of optical devices based on this material. We conclude our discussion of black phosphorus with a study that employs this material as the active element in a photoconductive detector capable of gigahertz class detection at room temperature for mid-infrared frequencies.

Mid-infrared photonic sensors based on metamaterial structures

In this work three different metallic metamaterials (MMs) structures such as asymmetric split ring resonators (A-SRRs), dipole and split H-shaped (ASHs) structures that support plasmonic resonances have been developed. The aim of the work involves the optimization of photonic sensor based on plasmonic resonances and surface enhanced infrared absorption (SEIRA) from the MM structures. The MMs structures were designed to tune their plasmonic resonance peaks in the mid-infrared region. The plasmonic resonance peaks produced are highly dependent on the structural dimension and polarisation of the electromagnetic (EM) source. The ASH structure particularly has the ability to produce the plasmonic resonance peak with dual polarisation of the EM source. The double resonance peaks produced due to the asymmetric nature of the structures were optimized by varying the fundamental parameters of the design. These peaks occur due to hybridization of the individual elements of the MMs structure. The presence of a dip known as a trapped mode in between the double plasmonic peaks helps to narrow the resonances. A periodicity greater than twice the length and diameter of the metallic structure was applied to produce narrow resonances for the designed MMs. A nanoscale gap in each structure that broadens the trapped mode to narrow the plasmonic resonances was also used. A thickness of 100 nm gold was used to experimentally produce a high quality factor of 18 in the mid-infrared region. The optimised plasmonic resonance peaks was used for detection of an analyte, 17β-estradiol. 17β-estradiol is mostly responsible for the development of human sex organs and can be found naturally in the environment through human excreta. SEIRA was the method applied to the analysis of the analyte. The work is important in the monitoring of human biology and in water treatment. Applying this method to the developed nano-engineered structures, enhancement factors of 10^5 and a sensitivity of 2791 nm/RIU was obtained. With this high sensitivity a figure of merit (FOM) of 9 was also achieved from the sensors. The experiments were verified using numerical simulations where the vibrational resonances of the C-H stretch from 17β-estradiol were modelled. Lastly, A-SRRs and ASH on waveguides were also designed and evaluated. These patterns are to be use as basis for future work.

Efficient split eld FDTD analysis of third-order nonlinear materials in two-dimensionally periodic media

In this work the split-field finite-difference time-domain method (SF-FDTD) has been extended for the analysis of two-dimensionally periodic structures with third-order nonlinear media. The accuracy of the method is verified by comparisons with the nonlinear Fourier Modal Method (FMM). Once the formalism has been validated, examples of one- and two-dimensional nonlinear gratings are analysed. Regarding the 2D case, the shifting in resonant waveguides is corroborated. Here, not only the scalar Kerr effect is considered, the tensorial nature of the third-order nonlinear susceptibility is also included. The consideration of nonlinear materials in this kind of devices permits to design tunable devices such as variable band filters. However, the third-order nonlinear susceptibility is usually small and high intensities are needed in order to trigger the nonlinear effect. Here, a one-dimensional CBG is analysed in both linear and nonlinear regime and the shifting of the resonance peaks in both TE and TM are achieved numerically. The application of a numerical method based on the finite- difference time-domain method permits to analyse this issue from the time domain, thus bistability curves are also computed by means of the numerical method. These curves show how the nonlinear effect modifies the properties of the structure as a function of variable input pump field. When taking the nonlinear behaviour into account, the estimation of the electric field components becomes more challenging. In this paper, we present a set of acceleration strategies based on parallel software and hardware solutions.

Aluminum nanoholes for optical biosensing

Sub-wavelength diameter holes in thin metal layers can exhibit remarkable optical features that make them highly suitable for (bio)sensing applications. Either as efficient light scattering centers for surface plasmon excitation or metal-clad optical waveguides, they are able to form strongly localized optical fields that can effectively interact with biomolecules and/or nanoparticles on the nanoscale. As the metal of choice, aluminum exhibits good optical and electrical properties, is easy to manufacture and process and, unlike gold and silver, its low cost makes it very promising for commercial applications. However, aluminum has been scarcely used for biosensing purposes due to corrosion and pitting issues. In this short review, we show our recent achievements on aluminum nanohole platforms for (bio)sensing. These include a method to circumvent aluminum degradation—which has been successfully applied to the demonstration of aluminum nanohole array (NHA) immunosensors based on both, glass and polycarbonate compact discs supports—the use of aluminum nanoholes operating as optical waveguides for synthesizing submicron-sized molecularly imprinted polymers by local photopolymerization, and a technique for fabricating transferable aluminum NHAs onto flexible pressure-sensitive adhesive tapes, which could facilitate the development of a wearable technology based on aluminum NHAs.