Efficient design and optimization of bio-photonic sensing cells (BICELLs) for label free biosensing

In previous works we demonstrated the benefits of using micro–nano patterning materials to be used as bio-photonic sensing cells (BICELLs), referred as micro–nano photonic structures having immobilized bioreceptors on its surface with the capability of recognizing the molecular binding by optical transduction. Gestrinone/anti-gestrinone and BSA/anti-BSA pairs were proven under different optical configurations to experimentally validate the biosensing capability of these bio-sensitive photonic architectures. Moreover, Three-Dimensional Finite Difference Time Domain (FDTD) models were employed for simulating the optical response of these structures. For this article, we have developed an effective analytical simulation methodology capable of simulating complex biophotonic sensing architectures. This simulation method has been tested and compared with previous experimental results and FDTD models. Moreover, this effective simulation methodology can be used for efficiently design and optimize any structure as BICELL. In particular for this article, six different BICELL's types have been optimized. To carry out this optimization we have considered three figures of merit: optical sensitivity, Q-factor and signal amplitude. The final objective of this paper is not only validating a suitable and efficient optical simulation methodology but also demonstrating the capability of this method for analyzing the performance of a given number of BICELLs for label-free biosensing.

Photonic Logic Based on Molecular Reorientation of Nematic Liquid Crystals

A new type of photonic logic, based on the use of nematic liquid crystals is proposed. The system takes advantage of the refractive-index changes induced by laser beams. Examples of AND, OR and NOR functions are presented.

Learning from the living bodies: New principles and techniques for photonic sensing

Signal processing in any living being is much more complex than the one performed in artificial systems. Cortex architecture, although only partly known, gives some useful ideas to be employed in sensing technology. To analyze some of these structures is the objective of this paper. Among the points to be analyzed are the parallel transfer of information, the similarity of the different systems and the massive amount of data analyzed by physical techniques. As an example of these concepts, the possibility to transmit images in a parallel way will be reported.

Photonic switching architectures with logic cells

Possible switching architectures, with Optically Programmable Logic Cells - OPLCs - will be reported in this paper. These basic units, previously employed by us for some other applications mainly in optical computing, will be employed as main elements to switch optical communications signals. The main aspect to be considered is that because the nternal components of these cells have nonlinear behaviors, namely either pure bistable or SEED-like properties, several are the possibilities to be obtained. Moreover, because their properties are dependent, under certain condition, of the signal wavelength, they are apt to be employed in WDM systems and the final result will depend on the orresponding optical signal frequency. We will give special emphasis to the case where self-routing is achieved, namely to structures of the Batcher or Banyan type. In these cases, as it will be shown, there is the possibility to route any packet input to a certain direction according to its first bits. The number of possible outputs gives the number of bits needed to route signals. An advantage of this configuration is that a very versatile behavior may be allowed. The main one is the possibility to obtain configurations with different kinds of behavior, namely, Strictly Nonblocking, Wide-Sense Nonblocking or Rearrangeably Nonblocking as well as to eliminate switching conflicts at a certain intermediate stages.

Photonic processing subsystem based on visual cortex architecture

Optical signal processing in any living being is more complex than the one obtained in artificial systems. Cortex architecture, although only partly known, gives some useful ideas to be employed in communications. To analyze some of these structures is the objective of this paper. One of the main possibilities reported is handling signals in a parallel way. As it is shown, according to the signal characteristics each signal impinging onto a single input may be routed to a different output. At the same time, identical signals, coming to different inputs, may be routed to the same output without internal conflicts. This is due to the change of some of their characteristics in the way out when going through the intermediate levels. The simulation of this architecture is based on simple logic cells. The basis for the proposed architecture is the five layers of the mammalian retina and the first levels of the visual cortex.

Integrable high order UWB pulse photonic generator based on cross phase modulation in a SOA-MZI

We propose and experimentally demonstrate a potentially integrable optical scheme to generate high order UWB pulses. The technique is based on exploiting the cross phase modulation generated in an InGaAsP Mach-Zehnder interferometer containing integrated semiconductor optical amplifiers, and is also adaptable to different pulse modulation formats through an optical processing unit which allows to control of the amplitude, polarity and time delay of the generated taps.

Tunable liquid crystal-photonic crystal fiber interferometer

In this work, we present a novel interferometer based on liquid crystal and photonic crystal fiber technology. The objective of this project is the development of a tunable (switchable) modal (Mach-Zehnder) interferometer for optical communications or sensing.

Photonic liquid crystal fiber intermodal interferometer

In this work, we present a novel interferometer based on liquid crystal and photonic crystal fiber technology. The objective of this project is the development of a tunable (switchable) modal (Mach-Zehnder) interferometer for optical communications or sensing. This interferometer has been manufactured splicing a short portion (between 15 and 30 mm) of photonic crystal fiber with two single mode fiber pigtails. The study shows a high sensitivity of the interferometer to the polarization of the launching light.

Some relations between visual perception and non-linear photonic structures

The main objective of this work is to present a way to emulate some functions of the mammalian visual system and a model to analyze subjective sensations and visual illusions

Polarization properties of polymer-based photonic crystal fibers

Selectively filled photonic crystal fibers with polydimethylsiloxane (PDMS), a silicon-type material, have been studied. Is has been demonstrated that polarization properties of these hybrid devices and the properties of the guided light in relation with the temperature changes, finding that the state of polarization (SOP) change with the increasing temperature but remains constant for a wide spectrum of wavelengths for a determinate temperature.

Infiltration of a photonic crystal fiber with cholesteric liquid crystal and blue phase

Photonic crystal fibers (PCF) have been selectively filled with a cholesteric liquid crystal (ChLC) with special interest in the blue phase (BP) of the liquid crystal. It has been observed thermal tuning of the guided light in the visible region. A dramatically enhance appears when the phase of the liquid crystal changes from cholesteric to blue phase I (BPI). When a thermal range of the blue phase I is achieved, no changes are observed while increasing temperature from BPI through BPII and to the isotropic phase.

Silicon oxides as alignment surfaces for vertically-aligned nematics in photonic devices

A comparative study on alignment performance and microstructure of inorganic layers used for liquid crystal cell conditioning has been carried out. The study has focused on two specific materials, SiOx and SiO2, deposited under different conditions. The purpose was to establish a relationship between layer microstructure and liquid crystal alignment. The surface morphology has been studied by FESEM and AFM. An analysis on liquid crystal alignment, pretilt angle, response time, contrast ratio and the conditions to develop backflow effect (significant rise time increase due to pure homeotropic alignment) on vertically-aligned nematic cells has been carried out. A technique to overcome the presence of backflow has been identified. The full comparative study of SiOx and SiO2 layer properties and their influence over liquid crystal alignment and electrooptic response is presented.

Scalable UWB photonic generator based on the combination of doublet pulses

We propose and experimentally demonstrate a scalable and reconfigurable optical scheme to generate high order UWB pulses. Firstly, various ultra wideband doublets are created through a process of phase-tointensity conversion by means of a phase modulation and a dispersive media. In a second stage, doublets are combined in an optical processing unit that allows the reconfiguration of UWB high order pulses. Experimental results both in time and frequency domains are presented showing good performance related to the fractional bandwidth and spectral efficiency parameters.

Thermally tunable polarization by nanoparticle plasmonic resonance in photonic crystal fibers

A photonic crystal fiber selectively filled with silver nanoparticles dispersed in polydimethylsiloxane has been numerically studied via finite elements analysis. These nanoparticles possess a localized surface plasmon resonance in the visible region which depends on the refractive index of the surrounding medium. The refractive index of polydimethylsiloxane can be thermally tuned leading to the design of polarization tunable filters. Filters found with this setup show anisotropic attenuation of the x-polarization fundamental mode around ?x = 1200dB/cm remarkably higher than the y-polarization mode. Moreover, high fiber birefringence and birefringence reversal is observed in the spectral region of the plasmon.

Selectively filled photonic liquid crystal fibers = Fibras de cristal fotónico selectivamente llenas con cristal líquido

El presente trabajo de Tesis se ha centrado en el diseño, fabricación y caracterización de dispositivos basados en fibras de cristal fotónico infiltrado selectivamente con cristales líquidos, polímeros y una mezcla de ambos. Todos los dispositivos son sintonizables, y su área de aplicación se centra en comunicaciones ópticas y sensores. La manipulación y fusionado de fibras fotónicas, el llenado selectivo de determinadas cavidades y la alineación recíproca de fibras mantenedoras de polarización son tareas muy específicas y delicadas para las que se requieren protocolos muy estrictos. Previo a la fabricación de dispositivos ha sido necesaria por tanto una tarea de sistematización y creación de protocolos de fabricación. Una vez establecidos se ha procedido a la fabricación y caracterización de dispositivos. Los dispositivos fabricados se enumeran a continuación para posteriormente detallar una a una las singularidades de cada uno. • Interferómetros intermodales hechos a partir de una porción de fibra fotónica soldada entre dos fibras estándar, bien monomodo o PANDA (mantenedora de polarización). Estos interferómetros han sido sumergidos o bien llenados selectivamente con cristales líquidos para así sintonizar la señal interferométrica guiada a través de la fibra. • Infiltración de fibras fotónicas con cristales líquidos colestéricos con especial énfasis en la fase azul (blue phase) de estos materiales. Las moléculas de cristal líquido se autoalinean en volumen por lo que la infiltración de fibras fotónicas con estos cristales líquidos es muy interesante, pues es conocida la dificultad de alinear apropiadamente cristales líquidos dentro de cavidades micrométricas de las fibras fotónicas. • Grabación de redes holográficas de forma selectiva en las cavidades de una fibra fotónica. Estas redes holográficas, llamadas POLICRYPS (POlymer-LIquid CRYstal-Polymer Slices), son redes fabricadas a base de franjas de polímero y cristal líquido alineado perpendicularmente a dichas franjas. Las franjas son a su vez perpendiculares al eje de la fibra como lo puede ser una red de Bragg convencional. El cristal líquido, al estar alineado perpendicularmente a dichos franjas y paralelo al eje de la fibra, se puede conmutar aplicando un campo eléctrico externo, modificando así el índice efectivo de la red. Se puede fabricar por lo tanto una red de Bragg sintonizable en fibra, muy útil en comunicaciones ópticas. • Llenado selectivo de fibras fotónicas con polidimetilsiloxano (PDMS), un polímero de tipo silicona. Si se realiza un llenado selectivo asimétrico se puede inducir birrefringencia en la fibra. El índice de refracción del PDMS tiene una fuerte dependencia térmica, por lo que se puede sintonizar la birrefringencia de la fibra. • Estudio teórico de llenado selectivo de fibras fotónicas con PDMS dopado con nanopartículas de plata de 5, 40 y 80 nm. Estas nanopartículas poseen un pico de absorción en torno a los 450 nm debido a resonancias superficiales localizadas de plasmones (LSPR). La resonancia del plasmon tiene una fuerte dependencia con el índice de refracción del material colindante, y al ser éste PDMS, la variación de índice de refracción se ve amplificada, obteniendo una absorción sintonizable. Se ha propuesto la fabricación de polarizadores sintonizables usando esta técnica. Como ya se ha dicho, previamente a la fabricación ha sido necesaria la protocolización de diversos procedimientos de fabricación de alta complejidad, así como protocolizar el proceso de toma de medidas para optimizar los resultados. Los procedimientos que han requerido la formulación de protocolos específicos han sido los siguientes: • Llenado selectivo de cavidades en una fibra fotónica. Dichas fibras tienen generalmente un diámetro externo de 125 μm, y sus cavidades son de entre 5 y 10 μm de diámetro. Se han desarrollado tres técnicas diferentes para el llenado/bloqueado selectivo, pudiéndose combinar varios protocolos para la optimización del proceso. Las técnicas son las siguientes: o Llenado y bloqueado con un prepolímero. Dicho prepolímero, también llamado adhesivo óptico, está inicialmente en estado líquido y posee una cierta viscosidad. Las cavidades de la fibra fotónica que se desea llenar o bloquear poseen un diámetro diferente al resto, por lo que en el proceso de llenado aparecen dos frentes de llenado dependientes de su diámetro. A mayor diámetro, mayor velocidad de llenado. Polimerizando cuando existe dicha diferencia en los frentes se puede cortar por medio, obteniendo así una fibra parcialmente bloqueada. o Colapsamiento de las cavidades de menor diámetro mediante aplicación de calor. El calor producido por un arco voltaico de una soldadora de fibra estándar fusiona el material exterior de la fibra produciendo el colapsamiento de las cavidades de menor diámetro. En esta técnica también es necesaria una diferencia de diámetros en las cavidades de la fibra. o Bloqueo una a una de las cavidades de la fibra fotónica con adhesivo óptico. Este procedimiento es muy laborioso y requiere mucha precisión. Con este sistema se pueden bloquear las cavidades deseadas de una fibra sin importar su diámetro. • Alineación de una fuente de luz linealmente polarizada con una fibra mantenedora de polarización ya sea PANDA o fotónica. Así mismo también se han alineado entre sí fibras mantenedoras de polarización, para que sus ejes rápidos se fusionen paralelos y así el estado de polarización de la luz guiada se mantenga. • Sistematización de toma de medidas para caracterizar los interferómetros modales. Éstos son altamente sensibles a diversas variables por lo que el proceso de medida es complejo. Se deben aislar variables de forma estrictamente controlada. Aunque todos los dispositivos tienen en común el llenado selectivo de cavidades en una fibra fotónica cada dispositivo tiene sus peculiaridades, que van a ser explicadas a continuación. ABSTRACT The present Thesis has been centered in the design, fabrication and characterization of devices based on photonic crystal fibers selectively filled with liquid crystals, polymers and a mixture of both. All devices are tunable and their work field is optical communications and sensing The handling and splicing of photonic crystal fibers, the selective filling of their holes and the aligning of polarization maintaining fibers are very specific and delicate tasks for which very strict protocols are required. Before the fabrication of devices has therefore been necessary task systematization and creation of manufacturing protocols. Once established we have proceeded to the fabrication and characterization of devices. The fabricated devices are listed below and their peculiarities are detailed one by one: • Intermodal interferometers made with a portion of photonic crystal fiber spliced between two optical communication fiber pigtails, either single mode or PANDA (polarization-maintaining) fiber. These interferometers have been submerged or selectively filled with liquid crystals to tune the interferometric guided signal. • Infiltration of photonic fibers with cholesteric liquid crystals with special emphasis on their blue phase (blue phase). The liquid crystal molecules are self-aligning in volume so the infiltration of photonic fibers with these liquid crystals is very interesting. It is notoriously difficult to properly align liquid crystals within micron cavities such as photonic fibers. • Selectively recording of holographic gratings in the holes of photonic crystal fibers. These holographic gratings, called POLICRYPS (POlymer-LIquid CRYstal-Polymes Slices), are based on walls made of polymer and liquid crystal aligned perpendicular to them. These walls are perpendicular to the axis of the fiber as it can be a conventional Bragg grating. The liquid crystal is aligned perpendicular to the walls and parallel to the fiber axis, and can be switched by applying an external electric field and thus change the effective index of the grating. It is thus possible to manufacture a tunable Bragg grating fiber, useful in optical communications. •Asymmetrically selective filling of photonic crystal fibers with a silicone polymer like called polydimethylsiloxane (PDMS) to induce birefringence in the fiber. The refractive index of PDMS has temperature dependence, so that the birefringence of the fiber can be tuned. • Theoretical study of photonic crystal fibers selectively filled with PDMS doped with silver nanoparticles of 5, 40 and 80 nm. These nanoparticles have an absorption peak around 450 nm due to localized surface plasmon resonances (LSPR). Plasmon resonance has a strong dependence on the refractive index of the adjacent material, and as this is PDMS, the refractive index variation is amplified, obtaining a tunable absorption. Fabrication of tunable polarizers using this technique has been proposed. Before starting the fabrication, it has been necessary to optimize several very delicate procedures and different protocols have been designed. The most delicate procedures are as follows: • Selective filling of holes in a photonic crystal fiber. These fibers generally have an outer diameter of 125 μm, and their holes have a diameter around between 5 and 10 μm. It has been developed three different techniques for filling / selective blocking, and they can be combined for process optimization. The techniques are: o Filling and blocked with a prepolymer. This prepolymer also called optical adhesive is initially in liquid state and has a certain viscosity. The holes of the photonic crystal fiber that are desired to be filled or blocked should have a different diameter, so that in the filling process appear two different fronts depending on the hole diameter. The holes with larger diameter are filled faster. Then the adhesive is polymerized when there is such a difference on the front. A partially blocked fiber is obtained cutting between fronts. o Collapsing of holes of smaller diameter by application of heat. The heat produced by an arc of a standard fusion splicer fuses the outer fiber material producing the collapsing of the cavities of smaller diameter. In this technique also you need a difference of diameters in the fiber holes. o Blocking one by one the holes of photonic crystal fiber with optical adhesive. This procedure is very laborious and requires great precision. This system can block unwanted cavities regardless fiber diameter. • Aligning a linearly polarized light source with a polarization-maintaining fiber (either a PANDA fiber as a photonic crystal fiber). It is needed also an aligning between polarization-maintaining fibers, so that their fast axes parallel merge and that is state of polarization of light guided is maintained. • Systematization of taking measurements to characterize the modal interferometers. These are highly sensitive to several variables so the measurement process is very complicated. Variables must be fixed in a very controlled manner. Although all devices have the common characteristic of being selectively filled PCFs with some kind of material, each one has his own peculiarities, which are explained below.