Optimization of a label-free biosensor vertically characterized based on a periodic lattice of high aspect ratio SU-8 nano-pillars with a simplified 2D theoretical model

We have recently demonstrated a biosensor based on a lattice of SU8 pillars on a 1 μm SiO2/Si wafer by measuring vertically reflectivity as a function of wavelength. The biodetection has been proven with the combination of Bovine Serum Albumin (BSA) protein and its antibody (antiBSA). A BSA layer is attached to the pillars; the biorecognition of antiBSA involves a shift in the reflectivity curve, related with the concentration of antiBSA. A detection limit in the order of 2 ng/ml is achieved for a rhombic lattice of pillars with a lattice parameter (a) of 800 nm, a height (h) of 420 nm and a diameter(d) of 200 nm. These results correlate with calculations using 3D-finite difference time domain method. A 2D simplified model is proposed, consisting of a multilayer model where the pillars are turned into a 420 nm layer with an effective refractive index obtained by using Beam Propagation Method (BPM) algorithm. Results provided by this model are in good correlation with experimental data, reaching a reduction in time from one day to 15 minutes, giving a fast but accurate tool to optimize the design and maximizing sensitivity, and allows analyzing the influence of different variables (diameter, height and lattice parameter). Sensitivity is obtained for a variety of configurations, reaching a limit of detection under 1 ng/ml. Optimum design is not only chosen because of its sensitivity but also its feasibility, both from fabrication (limited by aspect ratio and proximity of the pillars) and fluidic point of view. (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Electromagnetic analysis of periodic structures under a waveguide viewpoint

The fundamental objective of this Ph. D. dissertation is to demonstrate that, under particular circumstances which cover most of the structures with practical interest, periodic structures can be understood and analyzed by means of closed waveguide theories and techniques. To that aim, in the first place a transversely periodic cylindrical structure is considered and the wave equation, under a combination of perfectly conducting and periodic boundary conditions, is studied. This theoretical study runs parallel to the classic analysis of perfectly conducting closed waveguides. Under the light shed by the aforementioned study it is clear that, under certain very common periodicity conditions, transversely periodic cylindrical structures share a lot of properties with closed waveguides. Particularly, they can be characterized by a complete set of TEM, TE and TM modes. As a result, this Ph. D. dissertation introduces the transversely periodic waveguide concept. Once the analogies between the modes of a transversely periodic waveguide and the ones of a closed waveguide have been established, a generalization of a well-known closed waveguide characterization method, the generalized Transverse Resonance Technique, is developed for the obtention of transversely periodic modes. At this point, all the necessary elements for the consideration of discontinuities between two different transversely periodic waveguides are at our disposal. The analysis of this type of discontinuities will be carried out by means of another well known closed waveguide method, the Mode Matching technique. This Ph. D. dissertation contains a sufficient number of examples, including the analysis of a wire-medium slab, a cross-shaped patches periodic surface and a parallel plate waveguide with a textured surface, that demonstrate that the Transverse Resonance Technique - Mode Matching hybrid is highly precise, efficient and versatile. Thus, the initial statement: ”periodic structures can be understood and analyzed by means of closed waveguide theories and techniques”, will be corroborated. Finally, this Ph. D. dissertation contains an adaptation of the aforementioned generalized Transverse Resonance Technique by means of which the analysis of laterally open periodic waveguides, such as the well known Substrate Integrated Waveguides, can be carried out without any approximation. The analysis of this type of structures has suscitated a lot of interest in the recent past and the previous analysis techniques proposed always resorted to some kind of fictitious wall to close the structure. vii Resumen El principal objetivo de esta tesis doctoral es demostrar que, bajo ciertas circunstancias que se cumplen para la gran mayoría de estructuras con interés práctico, las estructuras periódicas se pueden analizar y entender con conceptos y técnicas propias de las guías de onda cerradas. Para ello, en un primer lugar se considera una estructura cilíndrical transversalmente periódica y se estudia la ecuación de onda bajo una combinación de condiciones de contorno periódicas y de conductor perfecto. Este estudio teórico y de caracter general, sigue el análisis clásico de las guías de onda cerradas por conductor eléctrico perfecto. A la luz de los resultados queda claro que, bajo ciertas condiciones de periodicidad (muy comunes en la práctica) las estructuras cilíndricas transversalmente periódicas guardan multitud de analogías con las guías de onda cerradas. En particular, pueden ser descritas mediante un conjunto completo de modos TEM, TE y TM. Por ello, ésta tesis introduce el concepto de guía de onda transversalmente periódica. Una vez establecidas las similitudes entre las soluciones de la ecuación de onda, bajo una combinación de condiciones de contorno periódicas y de conductor perfecto, y los modos de guías de onda cerradas, se lleva a cabo, con éxito, la adaptación de un conocido método de caracterización de guías de onda cerradas, la técnica de la Resonancia Transversal Generalizada, para la obtención de los modos de guías transversalmente periódicas. En este punto, se tienen todos los elementos necesarios para considerar discontinuidades entre guías de onda transversalmente periódicas. El analisis de este tipo de discontinuidades se llevará a cabo mediante otro conocido método de análisis de estructuras cerradas, el Ajuste Modal. Esta tesis muestra multitud de ejemplos, como por ejemplo el análisis de un wire-medium slab, una superficie de parches con forma de cruz o una guía de placas paralelas donde una de dichas placas tiene cierta textura, en los que se demuestra que el método híbrido formado por la Resonancia Transversal Generalizada y el Ajuste Modal, es tremendamente preciso, eficiente y versátil y confirmará la validez de el enunciado inicial: ”las estructuras periódicas se pueden analizar y entender con conceptos y técnicas propias de las guías de onda cerradas” Para terminar, esta tésis doctoral incluye también una modificación de la técnica de la Resonancia Transversal Generalizada mediante la cual es posible abordar el análisis de estructuras periódica abiertas en los laterales, como por ejemplo las famosas guías de onda integradas en sustrato, sin ninguna aproximación. El análisis de este tipo de estructuras ha despertado mucho interés en los últimos años y las técnicas de análisis propuestas hasta ix el momento acostumbran a recurrir a algún tipo de pared ficticia para simular el carácter abierto de la estructura.

Analysis of the railway track as a spatially periodic structure

This article presents a new and computationally efficient method of analysis of a railway track modelled as a continuous beam of 2N spans supported by elastic vertical springs. The main feature of this method is its important reduction in computational effort with respect to standard matrix methods of structural analysis. In this article, the whole structure is considered to be a repetition of a single one. The analysis presented is applied to a simple railway track model, i.e. to a repetitive beam supported on vertical springs (sleepers). The proposed method of analysis is based on the general theory of spatially periodic structures. The main feature of this theory is the possibility to apply Discrete Fourier Transform (DFT) in order to reduce a large system of q(2N + 1) linear stiffness equilibrium equations to a set of 2N + 1 uncoupled systems of q equations each. In this way, a dramatic reduction of the computational effort of solving the large system of equations is achieved. This fact is particularly important in the analysis of railway track structures, in which N is a very large number (around several thousands), and q = 2, the vertical displacement and rotation, is very small. The proposed method allows us to easily obtain the exact solution given by Samartín [1], i.e. the continuous beam railway track response. The comparison between the proposed method and other methods of analysis of railway tracks, such as Lorente de Nó and Zimmermann-Timoshenko, clearly shows the accuracy of the obtained results for the proposed method, even for low values of N. In addition, identical results between the proposed and the Lorente methods have been found, although the proposed method seems to be of simpler application and computationally more efficient than the Lorente one. Small but significative differences occur between these two methods and the one developed by Zimmermann-Timoshenko. This article also presents a detailed sensitivity analysis of the vertical displacement of the sleepers. Although standard matrix methods of structural analysis can handle this railway model, one of the objectives of this article is to show the efficiency of DFT method with respect to standard matrix structural analysis. A comparative analysis between standard matrix structural analysis and the proposed method (DFT), in terms of computational time, input, output and also software programming, will be carried out. Finally, a URL link to a MatLab computer program list, based on the proposed method, is given

A panel method free-wake code for aeroelastic rotor predictions

A panel method free-wake model to analyse the rotor flapping is presented. The aerodynamic model consists of a panel method, which takes into account the three-dimensional rotor geometry, and a free-wake model, to determine the wake shape. The main features of the model are the wake division into a near-wake sheet and a far wake represented by a single tip vortex, and the modification of the panel method formulation to take into account this particular wake description. The blades are considered rigid with a flap degree of freedom. The problem solution is approached using a relaxation method, which enforces periodic boundary conditions. Finally, several code validations against helicopter and wind turbine experimental data are performed, showing good agreement

Tilted excitation implies odd periodic resonances

This work was supported by the Brazilian agencies FAPESP and CNPq. MSB also acknowledges the Engineering and Physical Sciences Research Council grant Ref. EP/I032606/1. GID thanks Felipe A. C. Pereira for fruitful discussions.

Detecting finite bandwidth periodic signals in stationary noise using the signal coherence spectrum

All signals that appear to be periodic have some sort of variability from period to period regardless of how stable they appear to be in a data plot. A true sinusoidal time series is a deterministic function of time that never changes and thus has zero bandwidth around the sinusoid's frequency. A zero bandwidth is impossible in nature since all signals have some intrinsic variability over time. Deterministic sinusoids are used to model cycles as a mathematical convenience. Hinich [IEEE J. Oceanic Eng. 25 (2) (2000) 256-261] introduced a parametric statistical model, called the randomly modulated periodicity (RMP) that allows one to capture the intrinsic variability of a cycle. As with a deterministic periodic signal the RMP can have a number of harmonics. The likelihood ratio test for this model when the amplitudes and phases are known is given in [M.J. Hinich, Signal Processing 83 (2003) 1349-13521. A method for detecting a RMP whose amplitudes and phases are unknown random process plus a stationary noise process is addressed in this paper. The only assumption on the additive noise is that it has finite dependence and finite moments. Using simulations based on a simple RMP model we show a case where the new method can detect the signal when the signal is not detectable in a standard waterfall spectrograrn display. (c) 2005 Elsevier B.V. All rights reserved.

Comparative Analysis of Structural and Morphological Properties of Large-Pore Periodic Mesoporous Organosilicas and Pure Silicas

A systematic study on the structural properties and external morphologies of large-pore mesoporous organosilicas synthesized using triblock copolymer EO20PO70EO20 as a template under low-acid conditions was carried out. By employing the characterization techniques of SAXS, FE-SEM, and physical adsorption of N-2 in combination with alpha(s)-plot method, the structural properties and external morphologies of large-pore mesoporous organosilicas were critically examined and compared with that of their pure-silica counterparts synthesized under similar conditions. It has been observed that unlike mesoporous pure silicas, the structural and morphological properties of mesoporous organosilicas are highly acid-sensitive. High-quality mesoporous organosilicas can only be obtained from synthesis gels with the molar ratios of HCl/H2O between 7.08 x 10(-4) and 6.33 x 10(-3), whereas mesoporous pure silicas with well-ordered structure can be obtained in a wider range of acid concentration. Simply by adjusting the HCl/H2O molar ratios, the micro-, meso-, and macroporosities of the organosilica materials can be finely tuned without obvious effect on their structural order. Such a behavior is closely related to their acid-controlled morphological evolution: from necklacelike fibers to cobweb-supported pearl-like particles and to nanosized particulates.

Numerical implementation of the coarse step method with a varying differential group delay

The effect of having a fixed differential group delay term in the coarse step method results in a periodic pattern in the inserting a varying DGD term at each integration step, according to a Gaussian distribution. Simulation results are given to illustrate the phenomenon and provide some evidence about its statistical nature.

Numerical implementation of the coarse step method with a varying differential group delay

The effect of having a fixed differential-group delay term in the coarse-step method results in a periodic pattern in the autocorrelation function. We solve this problem by inserting a varying DGD term at each integration step, according to a Gaussian distribution. Simulation results are given to illustrate the phenomenon and provide some evidence, about its statistical nature.

Algorithm BIDIMS for Automated Systematization of Data Array. Case Study: Rediscovering Mendeleev’s Periodic Table of Chemical Elements

The method (algorithm BIDIMS) of multivariate objects display to bidimensional structure in which the sum of differences of objects properties and their nearest neighbors is minimal is being described. The basic regularities on the set of objects at this ordering become evident. Besides, such structures (tables) have high inductive opportunities: many latent properties of objects may be predicted on their coordinates in this table. Opportunities of a method are illustrated on an example of bidimentional ordering of chemical elements. The table received in result practically coincides with the periodic Mendeleev table.

Optical communication based on the periodic nonlinear Fourier transform signal processing

In this work we introduce the periodic nonlinear Fourier transform (PNFT) and propose a proof-of-concept communication system based on it by using a simple waveform with known nonlinear spectrum (NS). We study the performance (addressing the bit-error-rate (BER), as a function of the propagation distance) of the transmission system based on the use of the PNFT processing method and show the benefits of the latter approach. By analysing our simulation results for the system with lumped amplification, we demonstrate the decent potential of the new processing method.

Periodic polymer photonic bandgap structures for on-chip optical cavities

Integrated on-chip optical platforms enable high performance in applications of high-speed all-optical or electro-optical switching, wide-range multi-wavelength on-chip lasing for communication, and lab-on-chip optical sensing. Integrated optical resonators with high quality factor are a fundamental component in these applications. Periodic photonic structures (photonic crystals) exhibit a photonic band gap, which can be used to manipulate photons in a way similar to the control of electrons in semiconductor circuits. This makes it possible to create structures with radically improved optical properties. Compared to silicon, polymers offer a potentially inexpensive material platform with ease of fabrication at low temperatures and a wide range of material properties when doped with nanocrystals and other molecules. In this research work, several polymer periodic photonic structures are proposed and investigated to improve optical confinement and optical sensing. We developed a fast numerical method for calculating the quality factor of a photonic crystal slab (PhCS) cavity. The calculation is implemented via a 2D-FDTD method followed by a post-process for cavity surface energy radiation loss. Computational time is saved and good accuracy is demonstrated compared to other published methods. Also, we proposed a novel concept of slot-PhCS which enhanced the energy density 20 times compared to traditional PhCS. It combines both advantages of the slot waveguide and photonic crystal to localize the high energy density in the low index material. This property could increase the interaction between light and material embedded with nanoparticles like quantum dots for active device development. We also demonstrated a wide range bandgap based on a one dimensional waveguide distributed Bragg reflector with high coupling to optical waveguides enabling it to be easily integrated with other optical components on the chip. A flexible polymer (SU8) grating waveguide is proposed as a force sensor. The proposed sensor can monitor nN range forces through its spectral shift. Finally, quantum dot - doped SU8 polymer structures are demonstrated by optimizing spin coating and UV exposure. Clear patterns with high emission spectra proved the compatibility of the fabrication process for applications in optical amplification and lasing.

Study of Periodic and Quasi-Periodic Structures in Silicon-on-Insulator

In this thesis, a numerical design approach has been proposed and developed based on the transmission matrix method in order to characterize periodic and quasi-periodic photonic structures in silicon-on-insulator. The approach and its performance have been extensively tested with specific structures in 2D and its validity has been verified in 3D.

Periodic nonlinear Fourier transform for fiber-optic communications, Part I:theory and numerical methods

In this work, we introduce the periodic nonlinear Fourier transform (PNFT) method as an alternative and efficacious tool for compensation of the nonlinear transmission effects in optical fiber links. In the Part I, we introduce the algorithmic platform of the technique, describing in details the direct and inverse PNFT operations, also known as the inverse scattering transform for periodic (in time variable) nonlinear Schrödinger equation (NLSE). We pay a special attention to explaining the potential advantages of the PNFT-based processing over the previously studied nonlinear Fourier transform (NFT) based methods. Further, we elucidate the issue of the numerical PNFT computation: we compare the performance of four known numerical methods applicable for the calculation of nonlinear spectral data (the direct PNFT), in particular, taking the main spectrum (utilized further in Part II for the modulation and transmission) associated with some simple example waveforms as the quality indicator for each method. We show that the Ablowitz-Ladik discretization approach for the direct PNFT provides the best performance in terms of the accuracy and computational time consumption.

Periodic nonlinear Fourier transform for fiber-optic communications, Part II:eigenvalue communication

In this paper we propose the design of communication systems based on using periodic nonlinear Fourier transform (PNFT), following the introduction of the method in the Part I. We show that the famous "eigenvalue communication" idea [A. Hasegawa and T. Nyu, J. Lightwave Technol. 11, 395 (1993)] can also be generalized for the PNFT application: In this case, the main spectrum attributed to the PNFT signal decomposition remains constant with the propagation down the optical fiber link. Therefore, the main PNFT spectrum can be encoded with data in the same way as soliton eigenvalues in the original proposal. The results are presented in terms of the bit-error rate (BER) values for different modulation techniques and different constellation sizes vs. the propagation distance, showing a good potential of the technique.