This dissertation presents methods to design and fabricate direct optical bio- and chemical sensors that offer high sensitivity and low limit of detection (LOD). To enhance sensitivity and reduce LOD of the sensors over sensors reported in previous works, the two “materials” are implemented: Photonic crystal (PhC) and Porous Silicon (PSi). If PhC structures enhance sensitivity and reduce LOD with their ability to confine exciting electrical field energy of resonance mode to increase interaction with analytes, then the PSi structures enhance sensitivity with their high porosity that allows large amount of analytes absorbed on increased surfaces as well as penetrating into the porous structures for interaction with electrical fields.
This dissertation is divided into six chapters and has five appendices. In Chapter 1 are Introduction to PhC structures and their fabrication methods. PhC structures 1D-, 2D-, and 3D, their origins of bandgaps and calculations method are introduced. Special properties of PhCs like bandgaps and nonlinearity make them potential candidates for miniature components for high integrated optical circuits. Different fabrication methods are listed, among them EBeam lithography is the most popular method for nanopatterns especially for prototypes and small fabrication lot and it will be described in detail. With advantages in bandgaps and IC compatible fabrication, PhC structures are widely implemented to fabricate a series of photonics devices including optical biosensors.
In Chapter 2 some published PhC-based label-free biosensors devices are presented showing their structures and results in biosensing. Two of them were based on resonance of a PhC-cavity placed on/close to a PhC-waveguide. In-plane excitation was coupled from fibers to devices and transmission signal was coupled out carrying information of change of environment in cavity region. Three devices were based on off-plane 1D or 2D PhC grating resonances. This configuration eliminates difficulty in alignment existing in the in-plane configuration still gives high sensitivity.
Chapter 3 presents our Device design and simulation. From knowledge of PhC (Chapter 1) and overview of PhC-based biosensors (Chapter 2), a motivation was raised to fabricate label-free biosensors that would be based on PhC structures in combination with porous silicon (PSi) and suspension structures. The “3 in 1” feature would enhance sensitivity and minimize limit of detection (LOD) in chemical and biosensing. We introduce two of our devices – one was based on in-plane PhC-cavity - PhC waveguide configuration, and the other was based on off-plane 1D-PhC porous silicon. The device design and simulation are presented in the chapter.
Chapter 4 focuses on Device fabrication. With silicon and silicon on insulator (SOI) as main substrates, photolithography and EBeam lithography followed by RIE etching silicon, PhC structures were fabricated based on designed and simulated results. For PSi formation, electrochemical etching in HF based solution was applied. For a fixed etching solution (concentration and temperature), different current density decides different porosities (pore density and size) on silicon substrates with different doping type and doping level (resistivity) while etching time decides PSi thickness. Various porosities and PhC lattices were fabricated to estimate sensitivity and LOD of the devices to some chemicals and bioanalytes.
Chapter 5 presents Device testing for some chemistry and bioanalytes. Two setups for two devices are introduced: in-plane and off-plane measurement. In the first setup, a near IR laser scanning from 1.2 m to 1.6 m and a spectrometer were used to excite and construct the spectra of devices. Polarizers were used since the device is polarization dependent and single-mode fibers were for light coupling to/from device. In the second measurement setup we used two instrument sets. The first set included an inverse microscope equipped high magnification objective lens (50X), white light source and high resolution spectrometer. Some standard chemicals were used to estimate device characteristics in visible wavelength range. The second setup reflectance spectrometry using high sensitive VIS-670 and FTIR4000 (Jasco, USA) and devices were characterized with some chemicals and proteins in the mid-IR wavelength range. The results of the two kinds of devices gave the sight of device sensitivities and LOD.
Chapter 6 Conclusion and future works emphasizes the main achievements in our research on micro-, nanofabrication and chemical and biosensoring. The design of a SOI 2D PhC cavity placed next to a 2D PhC waveguide enhanced the device sensitivity and decreased LOD. 3D SU8 prism with ultra small inclined angle placed in adjustment to SOI waveguide much reduced insertion-loss of fiber waveguide interconnection while kept the signal undistorted. Other kind of chemical and biosensors was made based on PSi structures of single and multilayers designed and produced to work in UVIS and Mid-IR and tested by spectrometry in UVIS and FTIR4000 in Mid-IR. Thank to the high porosity of PSi structure the made devices had very high sensitivity and very low LOD for both liquid chemical and solid biolayers. FTIR also helped to detect and assign characteristic peaks to functional groups existing in analyzed biomatters.
Appendices. Can be found here details of some processes concerning our PhC based device such as PhC structure fabrication, 3D SU8 prism fabrication, electroless and electrochemical etching, preparation of bioanalytes for testing.
Publication lists publications on PhD program duration.

本論文提出一直接式光學生化傳感器之設計與製造的方法，其具有高靈敏度和低檢出限制(limit of detection, LOD)。根據先前研究指出，為了提高此傳感器的靈敏度和降低LOD，常使用以下兩種材料來實現：光子晶體(Photonic crystal, PhC)和多孔矽(Porous silicon, PSi)。如果光子晶體結構藉由侷限共振模式的電場能量來增加與分析物相互作用的能力，然後使用多孔矽本身結構的高孔隙率以允許大量的分析物的吸收於所增加的表面與穿透至多孔結構與電場相互作用。

本論文共分為6章和5個附錄。在第1章中介紹光子晶體結構及其製造方法。首先是有關光子晶體結構的一維、二維與三維能隙和計算方法。光子晶體像能隙和非線性的特殊性質使得它們有潛力發展成一高整合光路的微型元件。其中列出了不同的製造方法，包括eBeam蝕刻奈米圖形化結構，尤其應用於原型和小製造元件上，為一最常用的方法，後續也將進行詳細說明。挾帶著能隙和IC兼容製造的優勢，光子晶體結構被廣泛的應用於製作一系列的光電子裝置，包括光學生物感測器。

在第2章中，回顧一些已發表以光子晶體為基礎之無需標記生物傳感器，展示它們的結構設計和在生物感測上的結果。其中兩篇討論到接近光子晶體波導之光子晶體腔共振現象。在in-plane激發耦合從纖維至設備與發送信號被耦合出來承載腔區域的環境變化信息。三種設備是基於off-plane一維或二維光子晶體光柵共振方式，該in-plane配置解決現存難以對準的問題但仍具有高靈敏度。

第3章介紹我們的實驗裝置設計和模擬。從光子晶體的知識(第1章)與以光子晶體為基礎的生物傳感器概述(第2章)，引發我們製作一無需標記生物傳感器的動機，提出以光子晶體結構為基礎並結合多孔矽和懸浮的結構。此“3合1”功能將提高檢測的靈敏度和最小化生化傳感檢測限制。我們介紹二種裝置：一為in-plane光子晶體腔 - 光子晶體波導配置，另一為off-plane一維光子晶體之多孔矽結構。該裝置的設計和模擬將於本章內詳細介紹。

第4章著重於裝置的製造。利用矽與絕緣層覆矽(silicon on insulator, SOI)作為基板，透過微影、ebeam蝕刻技術與反應離子蝕刻矽基材，光子晶體結構依據設計和模擬結果來進行製作。多孔矽結構的形成係利用於氫氟酸溶液中進行電化學蝕刻方式來完成—固定蝕刻溶液(即濃度和反應溫度)，以不同的電流密度來決定矽基材上不同的孔隙率(孔洞密度和尺寸)，並可選擇具有不同的摻雜類型和摻雜程度(電阻率)的矽基材，而蝕刻時間將決定多孔矽的厚度。不同的孔隙度和光子晶體的晶格將製作來評估對於某些化學品和生物分析物的靈敏度和檢測極限。

第5章介紹為一些化學和生化分析相關之裝置測試。本論文中分別介紹兩個實驗裝置的設置方式：in-plane與off-plane的測量。第一方式設置中，利用一個近紅外雷射掃描範圍從1.2至1.6微米和一台光譜儀用於激發與建構一光譜設備。偏振器被使用於該設備是偏振依賴性和單模光纖的光耦合設備。在第二次方式之測量設置中，我們使用了兩組儀器設備：第一組包括倒立式顯微鏡配備高倍率物鏡(50X)、光源和高分辨率的光譜儀。一些標準使用的化學品在可見光波長範圍內被用於評估裝置的特性；第二組為使用高靈敏度的反射光譜設備VIS-670和FTIR4000(JASCO, USA)運用於中紅外波長範圍內的一些化學物質和蛋白質檢測。上述兩種裝置檢測的結果將得到的該裝置的靈敏度和檢測限制。

第6章結論和未來工作部份強調研究中就微奈米結構的製作與化學、生物檢測方面的成果等。以一個絕緣層覆矽為基材之二維光子晶體設計在一個二維光子晶體波導旁邊將提高了該裝置的靈敏度和降低檢測限制。三維的SU8菱鏡與超小角度放置以調整絕緣層覆矽波導來大大降低光纖波導相互聯繫的插入損耗，同時能夠保持信號不失真。其他類型的化學和生物傳感器是基於多孔矽結構的單一和多層設計和工作在UVIS和中紅外光範圍並在UVIS和FTIR4000光譜範圍中進行測試。由於高孔隙率的多孔矽結構所製成的裝置對於液體化學品與固體生物層結構有很高的靈敏度和非常低的檢測限制。另外，傅立葉轉換紅外光譜技術也有助於檢測並指出所分析存在於生物物質中官能基的特徵峰。

附錄。在這裡可以找到關於本論文所提及光子晶體的裝置，如光子晶體結構製作、三維SU8菱鏡製造、化學和電化學蝕刻技術以及生物分析物相關製備過程的詳細訊息。

發表。修習博士學位課程期間所發表相關論文著作。

Chapter 1:
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[1.7] M. Soljacˇic´ and J. D. Joannopoulos, “Enhancement of nonlinear effects using photonic crystals,” Nature Materials 3, pp211-219 (2004).
[1.8] Jacob B. Khurgin et al, “Tunable wideband optical delay line based on balanced coupled resonator structures,” Optics Letters 34 (17), pp. 2655-2657 (2009).
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[1.12] J. Pedersen et al, “Slow-light enhanced absorption for bio-chemical sensing applications: potential of low-contrast lossy materials,” http://www.mendeley.com/ research/slowlight-enhanced-absorption-for-biochemical-sensing-applications-potential-of-lowcontrast-lossy-materials/
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Chapter 2:
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[2.13] Y. Nazirizadeh et al, “Low-cost label-free biosensors using photonic crystals embedded between crossed polarizers,” Opt. Exp. 18 (18), pp. 19120-19128 (2010).
[2.14] X. Wei et al, “Guided mode biosensor based on grating coupled porous silicon waveguide,” Opt. Exp. 19 (12), pp. 11330-11339 (2011).
[2.15] Minh-Hang Nguyen, Chia-Jung Chang, Ming-Chang Lee, and Fan-Gang Tseng, “SU8 3D prisms with ultra small inclined angle for low-insertion-loss fiber/waveguide interconnection,” Opt. Express 19 (20), 18956–18964 (2011).
[2.16] Minh-Hang Nguyen, Hau-Jie Tsai, Jen-Kuei Wu, Yi-Shiuan Wu, Ming-Chang Lee, and Fan-Gang Tseng “Cascaded Nano-Porous Silicons for High Sensitive Biosensing and Functional Group Distinguishing by Mid-IR Spectra,” to be submitted.
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[2.18] R. Yanga, S. A. Soperb and W. Wanga, “Microfabrication of pre-aligned fiber bundle couplers using ultraviolet lithography of SU-8,” Sens. Actuators A Phys. 127(1), 123–130 (2006)
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[2.20] C. S. Jao and H. Y. Lin, “Ultrasensitive guided-mode resonance biosensors superimposed with vertical-sidewall roughness,” App. Opt. 50 (26), pp. 5139-5148 (2011).
[2.21] M. El Beheiry, V. Liu, S. Fan, and O. Lev, “Sensitivity enhancement in photonic crystal slab biosensors,” Opt. Exp. 18 (22), pp. 22702-22714 (2010).
[2.22] J. J. Wang, L. Chen, S. Kwan, F. Liu, and X. Deng, “Resonant grating filters as refractive index sensors for chemical and biological detections,” J. Vac. Sci. Technol. 23 (6), pp. 3006-3010 (2005).
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[2.24] W. Zhange et al, “High sensitivity photonic crystal biosensor incorporating nanorod structures for enhanced surface area,” Sensors and Actuators B 131, pp. 279-284 (2008).
[2.25] M. M. Lee et al, “Integrated photonic structures for parallel fluorescence and refractive index biosensing,” Proc. of SPIE 8034, pp. 803406-1 (2011).

Chapter 3:
[3.1] H. Y. Hsieh et al, ”Au-Coated Polystyrene Nanoparticles with High-Aspect-Ratio Nanocorrugations via Surface-Carboxylation-Shielded Anisotropic Etching for Significant SERS Signal Enhancement,” J. Phys. Chem. C 115, pp. 16258–16267 (2011).
[3.2] J. M. Obliosca et al, “Probing quenched dye fluorescence of Cy3-DNA-Au-nanoparticle hybrid conjugates using solution and array platforms,” J. Colloid Interface Sci. 371 (1), pp. 34-41 (2012)
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[3.5] John D. Joannopoulos at al, “Photonic Crystals Molding the Flow of Light,” Second Edition, Princeton University Press • Princeton And Oxford (2008).
[3.6] M. Loncˇa et al, “Experimental and theoretical confirmation of Bloch-mode light propagation in planar photonic crystal waveguides,” Applied Physics Letters 80 (10), pp. 1689-1691 (2002).
[3.7] S. Ha et al, “Slow-light switching in nonlinear Bragg-grating couplers,” Optics Letters 32 (11), pp. 1429-1431 (2007).
[3.8] B. S. Song et al, “Physical origin of the small modal volume of ultra-high-Q photonic double-heterostructure nanocavities,” New Journal of Physics 8 (209), pp. 1-13 (2006).
[3.9] Minh-Hang Nguyen, Chia-Jung Chang, Ming-Chang Lee, and Fan-Gang Tseng, “SU8 3D prisms with ultra small inclined angle for low-insertion-loss fiber/waveguide interconnection,” Opt. Express 19 (20), 18956–18964 (2011).
[3.10] S. Mandal et al, “Nanoscale optofluidic sensor arrays,” Optics Ex, 16, 1623 (2008)
[3.11] E. Guillermain et al, “Multi-channel biodetection via resonance microcavities coupled to a photonic crystal waveguide,” Proc. of SPIE Vol. 7167, 71670D-1 (2009)
[3.12] M. El Beheiry, V. Liu, S. Fan, and O. Lev, “Sensitivity enhancement in photonic crystal slab biosensors,” Opt. Exp. 18 (22), pp. 22702-22714 (2010).
[3.13] S. S. Wang et al, “Theory and applications of guided-mode resonance filters,” Appl. Optics 32 (14), pp. 2606-2613 (1993).
[3.14] X. Wei et all, “ Guided mode biosensor based on grating coupled porous silicon waveguide,” Optics Express 19 (12), pp. 11330-1339 (2011)
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[3.17] P. M. Fauchet, “Biodetection using Silicon Photonic Bandgap Devices” Biophotonics Winter School 2007.

Chapter 4:
[4.1] Minh-Hang Nguyen, Chia-Jung Chang, Ming-Chang Lee, and Fan-Gang Tseng, “SU8 3D prisms with ultra small inclined angle for low-insertion-loss fiber/waveguide interconnection,” Opt. Express 19 (20), 18956–18964 (2011).
[4.2] N. Megouda et al, “Au-assisted electroless etching of silicon in aqueous HF/H2O2 solution,” Applied Surface Science 255, pp. 6210–6216 (2009).
[4.3] R. Douani et al, “Silver-assisted electroless etching mechanism of silicon,” Phys. Stat. Sol. (a) 205 (2), pp. 225–230 (2008).
[4.4] C. Y. Chen et al, “Vertically-Aligned of Sub-Millimeter Ultralong Si Nanowire Arrays and Its Reduced Phonon Thermal Conductivity,” J. of The Electrochemical Society, 158 (5), pp. D302-D306 (2011).
[4.5] N. Megouda et al, “Au-assisted electroless etching of silicon in aqueous HF/H2O2 solution,” Applied Surface Science 255, pp. 6210–6216 (2009).
[4.6] R. Douani et al, “Silver-assisted electroless etching mechanism of silicon,” Phys. Stat. Sol. (a) 205 (2), pp. 225–230 (2008).
[4.7] C. Y. Chen et al, “Vertically-Aligned of Sub-Millimeter Ultralong Si Nanowire Arrays and Its Reduced Phonon Thermal Conductivity,” J. of The Electrochemical Society, 158 (5), pp. D302-D306 (2011).
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[4.10] V. Lehmann et al, “On the morphology and the electrochemical formation mechanism of mesoporous silicon,” Materials Science and Engineering B69–70, pp. 11– 22 (2000).
[4.11] P. M. Fauchet, “Biodetection using Silicon Photonic Bandgap Devices” Biophotonics Winter School 2007.
[4.12] H. Ouyang et al, “Biosensing using Porous Silicon PhotonicBandgap Structures,” SPIE Optics East 2005.
[4.13] F. A. Harraza et all, “Cylindrical pore array in silicon with intermediate nano-sizes: A template for nanofabrication and multilayer applications,” Electrochimica Acta 53, pp. 6444-6451 (2008).
[4.14] Philippe M. Fauchet, “Lecture 1: Biodetection using Silicon Photonic Bandgap Devices,” University of Rochester, http://www.powershow.com/view/1b0b85-ZjZiY/Lecture_1_Biodetection_using_Silicon_Photonic_Bandgap_Devices_flash_ppt_presentation.
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[4.19] H. Ouyang et al, “Macroporous Silicon Microcavities for Macromolecule Detection,” Adv. Funct. Mater. 15, pp. 1851-1859 (2005).

Chapter 5:
[5.1] F. A. Harraza et all, “Cylindrical pore array in silicon with intermediate nano-sizes: A template for nanofabrication and multilayer applications,” Electrochimica Acta 53, pp. 6444-6451 (2008).
[5.2] H. Ouyang et al, “Macroporous Silicon Microcavities for Macromolecule Detection,” Adv. Funct. Mater. 15, pp. 1851-1859 (2005).
[5.3] M. E. Beheiry et al, “Sensitivity enhancement in photonic crystal slab biosensors,” Opt. Exp. 18 (22), pp. 22701-22714 (2010).
[5.4] Y. Nazirizadeh et al, “Low-cost label-free biosensors using photonic crystals embedded between crossed polarizers,” Opt. Exp. 18 (18), pp. 19120-19128 (2010).
[5.5] X. Wei et al, “Guided mode biosensor based on grating coupled porous silicon waveguide,” Opt. Exp. 19 (12), pp. 11330-11339 (2011).
[5.6] A. S. Hovhannisyan, “Investigation of Glucose Sensitivity of Porous Silicon,” http://ajp.asj-oa.am/32/1/Bio-sens-AJP.pdf, pp. 38-42 (2008).
[5.7] K. E. Toghill and R. G. Compton, “Electrochemical Non-enzymatic Glucose Sensors: A Perspective and an Evaluation,” Int. J. Electrochem. Sci., 5, pp. 1246 – 1301 (2010).
[5.8] Y. H. Kwak et al, “Flexible glucose sensor using CVD-grown graphene-based field effect transistor,” Biosensors and Bioelectronics 37, pp. 82–87 (2012).
[5.9] M. Brandstetter et al, “Tunable external cavity quantum cascade laser for the simultaneous determination of glucose and lactate in aqueous phase,” Analyst 135 (12), pp. 3260-5 (2010).
[5.10] Z. Movasaghi et al, “Fourier Transform Infrared (FTIR) Spectroscopy of Biological Tissues,” Applied Spectroscopy Reviews 43, pp.134–179 (2008).
[5.11] C. Vrančić, “Continuous glucose monitoring by means of mid-infrared transmission laser spectroscopy in vitro,” Analyst 136, pp. 1192-1198 (2011).
[5.12] http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/InfraRed/infrared.htm
[5.13] B.H. Stuart, “Infrared Spectroscopy of Biological Applications,” Published Online: 15 JUN 2012, DOI: 10.1002/9780470027318.a0208.pub2.
[5.14] P. I. Haris and F. Severcan, “FTIR spectroscopic characterization of protein structure in aqueous and non-aqueous media,” Journal of Molecular Catalysis B: Enzymatic 7, pp. .207–221 (1999).