Impact of Morphology and Scale on the Physical Properties of Periodic/Quasiperiodic Micro- and Nano- Structures by Lin Jia Bachelor of Science, Physics Peking University (2007) Submitted to the Department of Materials Science and Engineering in Partial fulfillment of the Requirements for the degree of Doctor of Philosophy in Materials Science and Engineering at the Massachusetts Institute of Technology June 2012 © 2012 Massachusetts Institute of Technology. All rights reserved. Signature of author ............................................................................................................................. Department of Materials Science and Engineering April 13th, 2012 Certified by ….................................................................................................................................... Edwin L. Thomas Morris Cohen Professor of Department of Materials Sciences and engineering Thesis Supervisor Accepted by ....................................................................................................................................... Gerbrand Ceder Chair, Departmental Committee on Graduate Students 1 Impact of Morphology and Scale on the Physical Properties of Periodic/Quasiperiodic Micro- and Nano- Structures by Lin Jia Submitted to the Department of Materials Science and Engineering on April 13th, 2012, in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy in Materials Science and Engineering ABSTRACT A central pillar of real-world engineering is controlled molding of different types of waves (such as optical and acoustic waves). The impact of these wave-molding devices is directly dependent on the level of wave control they enable. Recently, artificially structured metamaterials have emerged, offering unprecedented flexibility in manipulating waves. The design and fabrication of these metamaterials are keys to the next generation of real-world engineering. This thesis aims to integrate computer science, materials science, and physics to design novel metamaterials and functional devices for photonics and nanotechnology, and translate these advances into realworld applications. Parallel finite-difference time-domain (FDTD) and finite element analysis (FEA) programs are developed to investigate a wide range of problems, including optical micromanipulation of biological systems [1, 2], 2-pattern photonic crystals [3], integrated optical circuits on an optical chip [4], photonic quasicrystals with the most premier photonic properties to date [5], plasmonics [6], and structure-property correlation analysis [7], multiple-exposure interference lithography [8], and the world’s first searchable database system for nanostructures [9]. Thesis Supervisor: Edwin L. Thomas Title: Morris Cohen Professor of Department of Materials Sciences and engineering 2 Table of Contents List of figures………………………………………………………….……………5 List of tables………………………………………………………….…………...12 Acknowledgements……...………………………………………….…………….13 Chapter 1. Thesis overview.…………………….………………………………...15 Chapter 2. Optical micromanipulation in optical lattices…....……………….…22 2.1.Introduction…………………………………………….………..…..…22 2.2.Numerical approach to compute optical force and optical torque in Lorentz-Mie regime.………………..............................................................24 2.3.Optical forces from Optical lattices..……………………………..…….26 2.4.Optical torques from Optical lattices...…………………………………43 Chapter 3. Two-pattern photonic crystals and the associated optical devices.........46 3.1.Introduction………………….……………….………………………...46 3.2.Two-pattern photonic crystals….……………....…………...………….47 3.3.Integrated optical devices on a optical chip……………………...…….58 3.4.Summary ……………………………..………..………………………63 Chapter 4. Photonic quasicrystals……….………………………………………...64 4.1.Introduction………………..…………………………………………64 4.2.PBG maps of quasicrystals……………………………………………65 4.3.Summary…..…………………………………………………………79 Chapter 5. Structure-photonic properties correlation via statistical approach….…81 5.1.Introduction………………..…………………………………………...81 5.2.Statistical analysis on the structural morphologies…………………….82 5.3.Summary……………………………..……………………………...…94 3 Chapter 6. A searchable database for micro- and nano-structures………………..96 6.1.Introduction………………………...…………..……...……….………96 6.2.The protocol to process structures in the database……………………97 6.3.Inverse design of experiments to fabricate target structures…………...99 6.4.Discussion……………..……………………………………………...110 6.5.Summary……………..……………………………………………….112 Chapter 7. Acoustic wave modeling………………………………...……….…..114 Chapter 8. Summary and Future plans……..…………….……………………...120 8.1.Overview of research accomplishments.……………………………120 8.2.Future research directions.……………………………………………123 Bibliography……………………………………………………………………..130 4 List of figures Figure 2.1: optical forces for particles with (a) 120nm diameter, (b) 300nm diameter, (c) 540nm diameter. (d) The trends for optical forces acting on particles of different sizes superposed with the theoretical predictions. Figure 2.2: F0 in the range of 0 < d <1.5l . The broken line is ∇σ 0 . E02 Figure 2.3: optical forces for titanium particle of 300nm diameter. Figure 2.4: parameter η (nm , ns ) calculated by FDTD simulation, the two component method, and the ESA method. Figure 2.5: (a) optical forces on PS particles arising from the 3D optical lattice. The shapes of the optical force lines along different directions are similar. The amplitudes of the optical forces fulfill Fmax[1,0,0] = Fmax[1,1,0] 2 = Fmax[1,1,1] 3 . (b) Optical forces on absorbing particles arising from the 3D optical lattice. Figure 2.6: optical torques on three kinds of cylinders. For the 140nm length cylinder, we have not observed stable equilibrium orientations. For the 400nm length cylinder, θ = 0 is the stable equilibrium orientation. For the 800nm length cylinder, in addition to the stable equilibrium orientation at θ = 0 , metastable orientation is observed at θ = ±0.5π . Figure 3.1: (a) through (c): three sub-crystals with large TM PBG (rods of triangular lattice, rods of square lattice and eight-fold quasicrystals). The filling 5 ratio of the sub-crystals ( f ) are also given in the figure. For quasicrystals, the filling ratio is given by parameter r a . Here r is the radius of the rods and a is the quasicrystal lattice parameter. The DOS calculations of the sub-crystals are shown in (d) through (f). Two sub-crystals with large TE PBG (the honeycomb structure and rings on a triangular lattice) are shown in (g) and (h); the corresponding DOS calculations are shown in (i) and (j). Figure 3.2: (a): 2-pattern crystal from the sub-crystals in Figure 3.1(b) and Figure 3.1(h). (b): The DOS plot for a(TM) a(TE) = 0.559 . (c): The DOS plot for a(TM) a(TE) = 0.656 . Figure 3.3: (a): 2-pattern crystal from the sub-crystals in Figure 3.1(a) and Figure 3.1(g). (b): the TE PBG and the TM PBG of the 2-pattern crystal for different filling ratios of TE sub-crystal. (c): The DOS plot if the TE sub-crystal filling ratio f(TE) is 0.058. (d): DOS plot if f(TE) is 0.086. (e): DOS plot if f(TE) is 0.114. Figure 3.4: optimized 2-pattern crystals with large, complete PBG. (a): the 2pattern crystal from the sub-crystals in Figure 3.1(a) and Figure 3.1(g). Here the filling ratio of the TE sub-crystal f(TE) = 0.086 and the filling ratio of the TM subcrystal f(TM) = 0.086 . The ratio of the periodicities of the sub-crystals a(TM) a(TE) = 0.7157 . The DFT of the 2-pattern crystal and the corresponding DOS calculation are shown below the structure. (b): the 2-pattern crystal from the subcrystals in Figure 3.1(b) and Figure 3.1(g). Here f(TE) = 0.08 , f(TM) = 0.14 and a(TM) a(TE) = 0.67 . (c): the 2-pattern crystal from the sub-crystals in Figure 3.1(c) and Figure 3.1(g). Here f(TE) = 0.11 and r a = 0.22 . (d): the 2-pattern crystal from the sub-crystals in Figure 3.1(a) and Figure 3.1(h). Here f(TE) = 0.121 , f(TM) = 0.102 and 6 a(TM) a(TE) = 0.7258 . (e): the 2-pattern crystal from the sub-crystals in Figure 3.1(b) and Figure 3.1(h). Here f(TE) = 0.108 , f(TM) = 0.149 and a(TM) a(TE) = 0.6563 . (f): the champion structure from the sub-crystals in Figure 3.1(c) and Figure 3.1(h). Here f(TE) = 0.084 and r a = 0.189 . Figure 3.5: (a): the proposed crossed waveguide based on 2-pattern crystal in Figure 3.4(a). (b): the light intensity distribution for TE wave. The TE wave propagates in region 2 and 4. (c): the light intensity distribution for TM wave. The TM wave propagates in region 1 and 3. Figure 3.6: wavelength scale polarizer based on 2-pattern crystals. (a): the proposed polarizer based on 2-pattern crystal in Figure 3.4(a). TE and TM waves enter in channel 1 and they are separated to channel 2 and channel 3. (b): the light intensity distribution for TE wave. The TE wave propagates in region 1 and 3. (c): the light intensity distribution for TM wave. The TM wave propagates in region 1 and 2. Figure 3.7: (a): the filter structure. (b): the resonance peak for TE wave. (c): the resonance peak for TM wave. (d): the light intensity distribution of TE wave for on-resonance frequency: ωa 2πc = 0.438 . (e): the light intensity distribution of TE wave for off-resonance frequency: ωa 2πc = 0.466 . (f): the light intensity distribution of TM wave for on-resonance frequency: ωa 2πc = 0.475 . (g): the light intensity distribution of TM wave for off-resonance frequency: ωa 2πc = 0.456 . Figure 4.1: (a)-(e): structural evolution with fill factor for 8mm symmetric QCs defined by level set equation (4.1) as dielectric filling ratio is varied. Here the last 7 number behind LS − 8mm / is the filling ratio of the black component. For a negative photoresist, a black component indicates the dielectric; for a positive photoresist, the black color indicates air features in a dielectric surrounding; (f)-(j): structural evolution with fill factor for 10mm symmetric QCs defined by level set equation (4.1); (k)-(o): structural evolution with fill factor for 12mm symmetric QCs defined by level set equation (4.1). Figure 4.2: (a)-(e): QCs of 8mm rotational symmetry from quasiperiodic tiling patterns decorated with rods. Here the number after R − 8mm / is the filling ratio of the black component; (f)-(j): QCs of 10mm rotational symmetry from quasiperiodic tiling patterns decorated with rods; (k)-(o): QCs of 12mm rotational symmetry from quasiperiodic tiling patterns decorated with rods. For R-QCs, the black color indicates the dielectric and the white color indicates the air; whereas for AR-QCs, the black color indicates the air and the white color indicates the dielectric. Figure 4.3: (a)-(f): TM photonic LDOS maps for LS-8mm, LS-10mm, and LS12mm QCs, with log (LDOS) plotted vs. fill ratio and frequency. Figure 4.4: (a)-(d): TM photonic LDOS maps for periodic R-p6mm and the quasiperiodic R-8mm, R-10mm, and R-12mm QCs, with log (LDOS) plotted vs. fill ratio and frequency. Figure 4.5: (a)-(c): TM photonic LDOS maps for AR-8mm, AR-10mm and AR12mm QCs, with log (LDOS) plotted vs. fill ratio and frequency. The AR-QCs with a low filling ratio have a wide range of shapes and sizes of the discrete dielectric regimes (see Figure 4.2) and they provide relatively weak TM gaps. 8 Figure 4.6: (a): the champion AR-12mm structure with the largest TE PBG (56.5%). The filling ratio of the structure is 0.32; (b) schematic delineating the periodic honeycomb veins (AR-p6mm): honeycomb, rhombus, and triangles; (c) TE photonic LDOS maps for AR-12mm QCs, with log (LDOS) plotted vs. fill ratio and frequency; (d): the LDOS plot for the champion structure ( f = 0.32 ), the TE PBG is indicated in the figure; (e): the champion AR-12mm QC with the largest complete PBG at f = 0.18 . The “ninja star” shape dielectric resonator particles are indicated in the circles. This R/V (resonator-vein) structure exhibits good short range order. Figure 5.1: the 17 photonic structures examined. The structure index is shown above each figure. Here R stands for rods; O stands for oval; LS stands for level set equations and the rotational symmetry of the associated PQC is 2N. (a): rods in a triangular lattice; (b) rods in a triangular lattice, the rods have two area values: 1.2A and 0.6A 0.8A ; (c) rods in a triangular lattice, the rods have two area values: 1.4A and ; (d) rods in a square lattice; (e) rods in a parallelogram lattice; (f) through (h): QCs from placing rods in 8mm, 10mm, 12mm QC tilings; (i) through (k): QCs from placing ovals in 8mm, 10mm, 12mm QC tilings; (l) through (q) QCs from level set equations. The values in the end of the structural index ( 0π , stand for ϕ there is no ϕ values. For N=4, all ϕ 0.25π , 0.5π , 0.75π , 1π ) values lead to the same structure, therefore value at the end of the structural index. Figure 5.2: the relationship between the overall geometric factor q and the size of TM PBG for three permittivity contrasts. 9 Figure 6.1: the database is classified to a tree structure according to the symmetry of the periodic structures. Figure 6.2: the schematic of the database system incorporating structures uploaded by researchers. A user can upload a target structure which will be compared with the database structures. The most similar database structure is output with structural information such as experimental fabrication method and physical properties. Figure 6.3: two examples of the variation of the similarity function and the visual appearance of a particular structure and the target structure. (a). The structures are defined by the diamond family approximation level set equation: F ( x, y, z ) = cos ( 2π x ) cos ( 2π y ) cos ( 2π z ) + cos ( 2π x ) sin ( 2π y ) sin ( 2π z ) + sin ( 2π x ) cos ( 2π y ) sin ( 2π z ) + sin ( 2π x ) sin ( 2π y ) cos ( 2π z ) = t The target structure corresponds to t = 0 . The structure similarity function ( P ) increases as the structure deviates from the target structure. (b): the target stucture is defined by the simple cubic surface approximation: F ( x, y , z ) = cos ( 2π Qx ) + cos ( 2π Qy ) + cos ( 2π Qz ) = 0 The target structure corresponds to Qtarget = 1 and ΔQ = Q − Qtarget . Figure 6.4: the target photonic crystal structure with P4m2 symmetry. The enlarged unit cell is shown on the left. Figure 6.5: six types of phase mask are investigated. Every phase mask consists of two layers each with the same thickness h . The layer can be a one dimensional 10 grating or air posts on a square lattice in solid dielectric background. Here h , r1 and r2 are tunable parameters. Figure 6.6: photonic crystal structure with P4m2 space group. Comparison of the optimal phase mask fabricated structure (left) and the target structure (right). The skeletal graph of the target structure is shown in blue. The key 4 fold rotoinversion, diagonal mirror with perpendicular 2 fold rotation symmetries are captured in the phase mask structure using circularly polarized incident radiation. Figure 7.1: (a): a solid rectangular plate vibrates in water along the x direction. The vibration frequency is 1.43Hz and the vibration follows the sinusoidal function: U x = sin(2π ft ) . (b) the pressure ( p ) distribution in the water after the plate vibrates for 3.5 seconds; (c) the displacement along y direction ( u y ); (d) the displacement along x direction ( ux ). Figure 7.2: LDOS for a phononic wave propagating along Z direction. The 10layer woodpile structure is periodic in X and Y directions, and we show only one unit cell here. The green part of the structure is PMMA. Here c air is the sound velocity in air. 11 List of tables Table 4.1: Summary of key findings from the LDOS numerical calculations. The champion QCs with the largest TM, the largest TE, and the largest complete PBGs are shown by “italics”. The results are for ε 2 ε1 = 13:1 . Table 5.1: the geometric factors and the size of PBGs. α , β , γ are three geometric factors. The overall factors q for three permittivity contrasts is also shown. 12 Acknowledgements I feel that I cannot fully capture in words the gratitude I have for all those who have supported me throughout the past five years at MIT, but I will try. First and foremost, I would like to express my deepest gratitude for Prof. Edwin L. Thomas, who is the most influential mentor I’ve had in my life. His passion for science is contagious and his support for me has been unfailing. Throughout my Ph.D. training, he gave me important and helpful advices on both science and life. He granted me the freedom to explore different research areas, but always made himself available whenever I needed guidance. His mentoring enabled me to mature scientifically and allowed me to develop my own vision on science and technology. Thank you Ned, for your dedication, for your insight, and for being a powerful leader. I would like to thank Prof. Woosoo Kim for being an incredible colleague who not only showed me amazing science but also phenomenal kindness. Thanks for all the support Woosoo, and for telling me I need to sleep when I sent emails at 2AM. I would like to thank Dr. Ion Bita for being an inspiring colleague. Our long chats on quasicrystals laid down the basis for two chapters in this Thesis. I would like to thank Prof. Jeffrey C. Grossman and Prof. Mary C. Boyce, my thesis committee members, for their mentorship and insights on materials science. 13 I would like to thank Prof. John Joannopoulos, Prof. Lionel C. Kimerling, Prof. Eli Yablonovitch, and Prof. Steven G. Johnson for their help on my photonic crystal research. Their legendary pioneering works on photonics are truly inspiring. I would like to thank Dr. Jae-hwang Lee for many interesting research discussions, Dr. Martin Maldovan for his advice on numerical simulation, Dr. Henry Koh for his help on phase mask lithography, Miss Sisi Ni for her help on FIB, Dr. Steven Kooi for his help with various research equipments, Mr. William DiNatale for his help on SEM and AFM, Dr. Tz-Feng Lin and Miss Yin Fan for our interesting chats on life, and politics, and many, many others! I would like to thank Meghan Shan, for always telling me what I need to hear, even if it is not what I want to hear. Her unwavering faith in me keeps me grounded and she reminds me of the goodness in this world, which has been the most effective motivator. Lastly, I would like to thank my father and mother: Yang Qiu and Jingchun Jia. Thank you for your unconditional support, for giving me the freedom to do what I love even if it makes no sense to you and takes your only son half way across the planet. I dedicated this thesis to my family. 14 Chapter 1 Thesis overview Controlled molding of different types of waves (such as optical and elastic waves) is key to future applications of engineering. For example, controlling photonic waves at the nanoscale is crucial for next generation information technology (IT) such as quantum computing [10] and optical interconnect [11]; and controlling the flow of both optical and elastic waves is the basis for future cloaking devices [12-15]. The impact of these wave-molding devices is directly dependent on the level of control they enable. Recently, artificially structured devices have emerged (e.g., metamaterials, photonic and phononic crystals), offering unprecedented flexibility in manipulating waves. The modeling, design and fabrication of these devices have enabled unprecedented applications including negative refractive index [16, 17], super lenses [18], and sub-wavelength imaging [19]. This thesis utilizes computational tools (e.g., finite-difference time-domain) to design novel functional devices for manipulating waves: primarily optical and one chapter of elastic waves. We investigate six interconnected projects: optical micromanipulation (Chapter 2), 2-pattern photonic crystals and associated optical devices (Chapter 3), photonic quasicrystals (Chapter 4), the correlation of 15 structure-photonic properties via a statistical method (Chapter 5), a searchable nanostructure database (Chapter 6), and elastic wave modeling (Chapter 7). In Chapter 2, we discuss how we can use optical forces and optical torques to control the position and orientation of micro-scale objects in optical lattices. Maxwell pointed out that an electromagnetic wave can transfer momentum to matter and thus exert force [20]. However, it was not until nearly one hundred years later that Ashkin first demonstrated that this force could be useful to manipulate objects at the micro-scale using a tightly focused laser beam [21, 22]. This breakthrough quickly lead to the widespread development of “optical tweezers” with many important uses [23, 24], particularly in biology [25], microfluidics [26], and particle manipulation [27]. The notion of optical traps was also extended to atom traps [28]. An important extension of optical traps is the optical lattice, which comes from the interference of several laser beams. The large trapping area of an optical lattice enables it to be an effective tool for optical sorting and optical assembly [29]. In my thesis, I developed a novel numerical method combining the finitedifference time-domain (FDTD) and Maxwell stress tensor to compute optical forces and optical torques on Lorentz-Mie particles from optical lattices. We 16 compare our method to the two component method and the electrostatic approximation [30]. We also discuss how the particle refractive index, shape, size and morphology of the optical lattice influence optical forces and conditions to form stable optical trapping wells. In addition to optical forces, optical torque from the 1D optical lattices is discussed for particles having anisotropic shapes; metastable and stable equilibrium orientation states are found. A detailed understanding of the optical force and torque from optical lattices has significant implications for optical trapping, micromanipulation and sorting of particles. Chapter 2 shows how an optical field can control materials. Conversely, materials can also bring strong impact on optical fields. For example, one of the major recent revolutions in photonics, the photonic crystal, was proposed in 1987 [31]. Photonic crystals enable new approaches for controlling the flow of light primarily because of their photonic band gaps (PBG). Chapter 3 presents a new strategy to design two-dimensional (2D) structures with a large, complete PBG. These structures, “2-pattern crystals”, come from the superposition of two structures, each of which can be crystalline or quasicrystalline. One structure is selected to have an outstanding PBG for only one polarization (transverse magnetic, TM, for example) and it is paired with another structure that has an outstanding transverse electric (TE) gap. Compared to the many kinds of photonic crystals 17 proposed before, our 2-pattern photonic crystals offer opportunities to adjust the scale of each structure and the respective dielectric fill fractions to provide a compound photonic structure with superior TE and TM properties. Importantly, the TM and TE gaps of a 2-pattern photonic crystal are less interdependent than for conventional photonic crystals, affording capabilities for us to tune the PBGs. By superposing the two structures without regards to registration, we designed six new aperiodic PBG structures having a complete photonic band gap larger than 15% for ε 2 ε1 = 11.4 . The rod-honeycomb 2-feature photonic crystal provides the largest complete PBG to date. The structures present more design flexibility for on-chip photonic devices. By purposely introducing defects into the sub-photonic crystals, on chip photonic devices for different polarizations can be integrated to bend, split and resonate TM/TE waves simultaneously on the same plane. In addition to 2-pattern photonic crystals, another group of photonic structures explored in this thesis are the photonic quasicrystals (QCs). Photonic QCs have been shown to be promising PBG materials because of their nearly isotropic photonic band structures, defect-free localized modes [32, 33], and the possibility to open a PBG at lower refractive index contrast than typical PC structures [34, 35]. In Chapter 4, we provide a comprehensive analysis of the PBG 18 properties of 2D QCs, where rotational symmetry, dielectric fill factor and structural morphology were varied systematically in order to identify correlations between structure and PBG width at a given dielectric contrast (13:1, Si:air). The TE and TM PBGs of 12 types of QCs are investigated (a total of 588 structures). We discovered a 12mm QC with a 56.5% TE PBG, the largest reported TE PBG for an aperiodic crystal to date. We also found a QC morphology comprising “ninja star” like dielectric domains, with near circular air cores and interconnecting veins emanating radially from the core. This interesting morphology leads to a complete PBG of about 20%, which is the largest reported complete PBG for aperiodic crystals. In Chapters 3 and 4, photonic band gaps were calculated from the geometrical structure of the photonic structures. However, the formation mechanisms of PBGs in photonic crystals are not always clear, thus there is no general rule to predict the size and location of PBGs. In Chapter 5, we demonstrate a novel quantitative procedure to pursue statistical studies on the influence of geometric properties on PBGs of photonic crystals and photonic QCs which consist of separate dielectric particles. The geometric properties are quantified and correlated to the size of the PBG for a wide permittivity range using three characteristic parameters: dielectric particle shape anisotropy, size 19 distribution, and the feature-feature distance distribution. Our concept brings statistical analysis to photonic crystal research and offers the possibility to predict the PBG from a morphological analysis. Presently, there is no existing database system to incorporate the emerging number of newly designed functional micro- and nano-structures such as photonic crystals, phononic crystals, microtrusses, plasmonic structures, and metamaterials. Further, in micro- and nano- fabrication, the ability to achieve specific target structures is highly desirable as the morphology of a structure greatly influences its physical properties. In Chapter 6, we develop a database system to efficiently classify, store, analyze and compare 2D and 3D micro- and nano- structures. This system can also be used for high throughput experimental design for various fabrication techniques. The database is multi-functional: it can be used to analyze the impact of symmetry on physical properties of structures and it can also be used to find the best structure with a particular extremized objective function among a set of candidate structures. Further, we suggest initiation of a world-wide cooperation to establish a public website to incorporate millions or even billions of natural and human made structures in a comprehensive database. 20 In addition to modeling photonic waves, modeling elastic waves is important for a wide range of applications, including phononic crystals [36], ultrasound imaging [37, 38], seismic wave sensing [39, 40], and optomechanical interaction [41, 42]. In Chapter 7, we discuss the application of FDTD modeling to elastic waves. Here the partial differential equations governing elastic wave propagation are processed using Yee’s grid convention. In Chapter 8, we summarize the main accomplishments of this thesis and propose several future directions. 21 Chapter 2 Optical micromanipulation in optical lattices 2.1 Introduction An Electromagnetic field can apply forces on both static charges ( F = qE ) and moving charges ( F = qv × B ); therefore, when an EM wave propagates inside materials, it interacts with the electrons and protons. This microscopic interaction leads to the macroscopic effects of reflection, refraction and absorption of EM waves. Since the momentum of the EM waves is changed during the process, the EM waves exert forces on the materials to keep the total momentum conserved, as was first pointed out by Maxwell in 1873 [20]. The application of optical forces was first explored by Ashkin, using a highly focused laser beam to trap micro objects. This breakthrough was later termed “optical tweezers” or “optical traps”[22, 23, 25, 43]. Since then, various forms of optical fields have been developed to achieve optical micromanipulation and optical sorting, including optical vortex [44, 45], holographic optical tweezers [46, 47], interferometric optical tweezers [48-50], standing wave [51-53], plasmonic resonances [54-57], and optical lattices [26, 58, 59]. The rapid development of optical micromanipulation provide many applications in various fields, including sorting of cells, macromolecules, and colloids [51, 60, 61], colloidal crystals evolution [58, 22 62, 63], nanofabrication [29], quantum simulation [64], micro- and nano- motors [65, 66], and the study of the physical properties of biology systems including DNA at the molecular level [67, 68]. The numerical calculations of optical forces are clearly very important to support, design, and nurture the continued fast development of the experiments and the industrial applications of optical micromanipulation, trapping, and sorting. This fact has led to the development of multiple numerical techniques including 1) generalized Lorenz-Mie theory (GLMT) [69], which is suitable for calculating optical forces on objects of particular shapes including spherical, spheroid and cylinder shapes [69-71], 2) the gradient force intuitive approach [72], which is suitable for a strongly focused light source, 3) the T-matrix method [73, 74], which is suitable for highly symmetric systems, 4) the discrete dipole approximation (DDA) [75], which needs to satisfy two validate criteria and is computational cumbersome [75], and 5) the electrostatic approximation [30, 52, 76, 77], which calculates the optical forces on particles with refractive index close to the background medium. In this chapter, we combine a previously reported 3D finite-difference timedomain (FDTD) simulation [6] and the Maxwell stress tensor ( T ) to compute both optical forces and optical torques on particles in the Lorentz-Mie regime. Our approach can calculate optical forces and optical torques from various forms of 23 optical fields; we specifically focus on optical lattices in this chapter. Compared to other techniques, optical trapping and sorting using optical lattices have two advantages: 1) the number of trapping sites is high, up to hundreds; the trapping sites are periodic and can exhibit various optical intensity morphologies [78]; 2) the optical sorting area is large and control can be automated to offer high throughput sorting. These advantages enable interesting applications. For example, optical lattices can assemble particles to make optical matters including photonic and phononic crystals [63], or potentially even dual band gap crystals [79, 80]. Recently, optical lattices have been extended to a quasicrystalline substrate potential, which assembles particles to the Archimedean-like tiling [58]. In addition to micromanipulations, optical lattices can also be used to achieve passive, parallel, and high-throughput optical sorting [26, 59]. Furthermore, the opticalmechanical coupling is observed in optical lattices: the optical binding effect [81, 82] leads collective oscillations [83] and spatially localized vibration with multiple modes in optical matters [84]. 2.2. Numerical approach to compute optical force and optical torque in Lorentz-Mie regime The Maxwell stress tensor is a second rank tensor expressed as: Ti, j = Di E j + Bi H j − 0.5( E ⋅ D + B ⋅ H ) δi, j 24 (2.1) The force on an object at a specific time can be calculated by: ⋅ ndS f =∫ T ∂S0 (2.2) Here ∂ S 0 is a closed surface over the object and n is the surface normal vector. The Maxwell stress tensor is calculated by a FDTD simulation. Equation (2.2) is then used to calculate optical forces [1]. Noting that the EM wave varies with time, the time average force is calculated from: 1 τ f dt τ ∫0 F= (2.3) Here τ is the period of the light source. In addition to the net force, the torque can be calculated by: Ω=− 1 τ dt τ∫ ∫ 0 ∂S0 × rdS n⋅T (2.4) Here r is the vector from the center of mass of the object to the surface element ∂S0 . The method is versatile: it can be applied to calculate optical forces and torques on objects of arbitrary shape and does not require system symmetry. The calculation covers the Lorentz-Mie regime ( object size ≈ wavelength ) where most applications of optical trapping, micromanipulation and sorting reside. The method can be applied to both dielectric and absorbing objects. 25 2.3 Optical forces from optical lattices In our numerical calculation, the wavelength of the light source in vacuum ( λ) is fixed at 1064nm, to relate to the wavelength of the widely-used solid state lasers (Nd: YAG and Nd: YLF). All calculation results are applicable to other typical wavelengths via scaling along with incorporation of the dispersion of the refractive index. We first consider the simplest case of a one dimensional (1D) periodic optical lattice arising from the interference of two plane waves propagating along opposite directions in a uniform lossless medium. We assume that the medium is water and the refractive index nm is taken as 1.3. The light intensity is calculated by: I= 1 τ τ N N 0 i =1 i =1 ∫ ( ∑ Ei ) ⋅( ∑ Ei )dt (2.5) N is the number of the plane waves. The electronic component of the first plane Λ wave is given by E1 = E0 exp(ik0 y − iωt ) z , and the electronic vector of the second Λ plane wave is E2 = E0 exp(−ik0 y − iωt ) z ; here k0 = 2π nm λ and the polarization of the two plane waves is along ẑ direction. From equation (2.5), the light intensity is: 26 I = E 02 + E 02 cos(2 k 0 y ) (2.6) From equation (2.6), the period of the optical lattice ( l ) is 409nm. We next introduce a dielectric sphere with diameter d . The refractive index of the particle ( ns ) is taken as 1.58 ( ns nm = 1.2 ), which is typical for polystyrene spheres. We are interested in particles which have size that is comparable to the period of the optical lattice. Specifically, we focus on three kinds of particles: 120nm diameter ( d l = 0.293 ), 300nm diameter ( d l = 0.733 ) and 540nm diameter ( d l = 1.32 ). We change the positions of the centers of the particles ( y ) in the optical lattices and calculate the optical forces. From equations (2.1) though (2.4), optical forces are directly proportional to the light source power, thus we express the force in the form of F E 02 . The results are shown as the solid lines in Fig. 2.1(a), (b) and (c), and the dashed lines are the light intensity distribution. In Fig. 2.1(a) and (b), the optical forces push the sphere center to the high light intensity positions and trap it there. In Fig. 2.1(c), however, optical forces push the center of the sphere to the lowest light intensity positions. From Fig. 2.1(a), (b) and (c), we find that the optical force can be expressed as: F ( x, y, z ) = F0C ( x, y, z) (2.7) C(x, y, z) is a function of the particle position in the optical lattice and indicates how the optical force changes with the particle position. In the 1D optical lattices, 27 C(x, y, z) is only related to y due to the system symmetry, thus it can be expressed as C( y) . Comparing C( y) in Fig. 2.1(a), (b) and (c) demonstrates a perfect match, which is shown in Fig. 2.1(d). Figure 2.1: optical forces for particles with (a) 120nm diameter, (b) 300nm diameter, (c) 540nm diameter, (d) the trends for optical forces acting on particles of different sizes superposed with the theoretical predictions. The maximum force the particle experiences is F0 and it is a function of the particle size and permittivity. We assume that F0 is negative when optical forces push the particle center to the low light intensity positions. Fig. 2.2 shows how F0 changes with the diameter of the particle d . F0 increases with particle diameter until 28 the diameter is around the period of the optical lattice, and then F0 drops quickly with increasing diameter and becomes negative in some range. Figure 2.2: F0 in the range of 0 < d <1.5l . The broken line is ∇σ 0 . E02 We can understand how the optical forces on particles arise from optical lattices from examining the energy aspect. We first assume that the dielectric particle can be modeled as a set of multiple dipoles. The interaction energy between a single dipole p and the electric field E is −p ⋅ E . If the refractive index of the particle is near to the background material, p and E are generally in phase, so the particles are pushed into high light intensity positions to achieve minimum interaction energy. When the diameter of the particle is smaller than the period of the optical lattice, the optical forces push the particle center to the high light intensity positions and the particle stabilizes at the light intensity peaks. However, if the diameter of the particle is bigger than the period, the particle can span two 29 light intensity peaks within the particle when its center lies in the low light intensity positions. As the diameter increases continually, the particle center may return to high light intensity positions to hold three peaks in the material, so F0 oscillates as d increases. Fig. 2.2 shows the oscillation of F0 in the range of 6nm < d < 540nm ( 0.015 < d l < 1.320 ). To quantitatively explain Fig. 2.2, we define the following parameter to represent how much of the EM field is inside the particle: σ = − ∫∫∫ I(x, y,z)dxdydz (2.8) V0 Here V0 is the region occupied by the particle and I(x,y,z) is the light intensity of the optical lattice. The parameter σ represents the interaction energy between the particle and the optical lattice, thus the optical force should be directly proportional to the spatial derivative of the parameter σ : F ∝ −∇σ = ∫∫∫ ∇I(x, y,z)dV (2.9) V0 For the 1D optical lattice, the maximum optical force is: F0 = −∇σ 0 ≈ 2 E02 k0 ∫∫∫ sin [ 2k0 ( y + 0.25l )] dV V0 30 (2.10) In equation (2.10) the particle center is at the origin of the coordinates. We plot ∇ σ 0 E 02 as the dotted line in Fig. 2.2. The reason for the shape differences between ∇ σ 0 E 02 and F0 E 02 is that the light intensity in equation (2.8) are calculated from light intensity of the optical lattice, the actual field inside the particle is different from the field of the optical lattice. Despite this, ∇ σ 0 E 02 gives a very good approximation to F0 in the range of 0 < d <l . Except for the energy aspect, the optical force from optical lattices can also be understood by the two component method [85]. The trapping abilities of optical lattices mainly come from gradient force. The particle can be assumed as a set of dipoles. For a single dipole, its polarization is proportional to the electric field applied on it and can be expressed by Clausius-Mossotti relation: P(r ,t ) = 3ε mε 0 εs − εm E (r ,t ) ε s + 2ε m applied (2.11) By employing the above equation, the gradient force on the dipole can be expressed as: f grad (r ,t ) = 3ε 0ε m εs − εm ∇E2applied (r ,t )dV 2ε s + 4ε m (2.12) Here dV is the volume of the dipole. The total force on the particle is the integral of equation (2.12) over the volume of particle, thus: 31 Fgrad (r) = 3ε mε 0 εs − εm 2 ∇ Eapplied (r ,t ) dV ∫∫∫ τ 2ε s + 4ε m V (2.13) 0 In equations (2.11) through (2.13), the applied field E applied (r ,t ) on the dipole contains both the electric field from other dipoles and the electric field of the light source. If the particle is small and the refractive index of the particle is near to the background, the impact from other dipoles can be omitted, thus we have: Fgrad ( x, y, z ) ≈ 3ε mε 0 εs − εm ∇I ( x, y, z )dV 2ε s + 4ε m ∫∫∫ V (2.14) 0 We can also investigate the system using the electrostatic approximation [52, 76, 77]. The energy difference caused by introducing particles into optical lattices can be expressed by: ΔW = 0.5∫∫∫ (ED − Ei Di + HB − Hi Bi )dV (2.15) V Here V is the volume of the whole system, E,D,B,Hare the fields after the particle is introduced into the optical lattice and Ei , Di , Bi , Hi are the fields before the particle is introduced. Equation (2.15) can be transformed into: ΔW = −0.5ε 0ε m ( εs − 1) ∫∫∫ EEi dV εm V 0 Here V0 is the volume of the particle. From equation (2.16): 32 (2.16) Fgrad (r) = − ∇( ΔW ) τ = 0.5ε 0ε m ( εs − 1)∫∫∫ ∇( EEi τ )dV εm V (2.17) 0 The expression in equation (2.17) is not explicit because it needs information of the optical field inside the particle. E should be the sum of E i and the electric field from the material polarization. If the refractive index of the particle is near that of the background and the particle size is small, we can omit the material polarization and use E i to replace E ; this replacement is the so called “electrostatic approximation” [30], which leads to: Fgrad ( x, y, z) = 0.5ε 0ε m ( εs − 1)∫∫∫ ∇I ( x, y, z)dV εm V (2.18) 0 The two component method is a higher order approximation for calculating optical forces compared to the ESA method because the Clausius-Mossotti relation in the two component method gives an approximation to the electric field from the material polarization, which has been totally omitted in ESA method. Equation (2.14) can be deducted from equation (2.17): if the particle size is small compared to wavelength, we can assume that E = 3Eiε m (ε s + 2ε m ) Inserting equation (2.19) into equation (2.17) leads to equation (2.14). 33 (2.19) No matter what method we use to understand the optical forces from optical lattices, the forms of optical forces in equations (2.9), (2.14), and (2.18) are similar. Thus equation (2.7) can be expressed as: F = ε 0η (nm , ns ) ∫∫∫ ∇I ( x, y, z )dV (2.20) V0 In equation (2.20), the impact of the optical lattice morphology, the particle shape and size on optical forces is represented in the volume integral ∫∫∫ ∇I ( x, y, z )dV . We V0 calculate the volume integral to determine how the optical force changes for particles at different positions and plot it as a solid line in Fig. 2.1(d). Comparison of the FDTD simulation results with the predictions from physical theory shows an excellent match. Optical force is also impacted by refractive index of the particle. We next calculate the optical force on a titanium particle of 300nm diameter ( ns = 2.7; ns nm = 2.08 ), which is shown in Fig. 2.3. Figure 2.3: optical forces for titanium particle of 300nm diameter. 34 The shape of optical force line in Fig. 2.3 is very similar to Fig. 2.1 and the amplitude of the optical force increases. The impact of the particle refractive index relative to the background medium refractive index is represented in the parameter η (nm , ns ) in equation (2.20). From the two component method: η ( nm , ns ) = 3nm2 ( ns2 − nm2 ) ( 2 ns2 + 4 nm2 ) ; from the ESA method: η ( nm , n s ) = 0.5( n s2 − nm2 ) . We next compare parameter η (nm , ns ) from the FDTD simulation, the two component method, and the ESA method; the results are shown in Fig. 2.4. Compared with the ESA method, results from the two component method match the FDTD calculation very well in the low refractive index range because it is more accurate than ESA. The two component method can only be applied to low relative refractive index situations; thus it deviates from our calculation at high index contrast ( ns nm > 1.7 ). Figure 2.4: parameter η (nm , ns ) calculated by FDTD simulation, the two component method, and the ESA method. 35 From Fig. 2.4, optical forces increase as the refractive index contrast increases and then decrease. If we assume the particle as a set of dipoles, the electric field experienced by dipole N consists of electric fields of the light source and all the other dipoles: Eapplied , N = Eol , N + ∑ E NM (2.21) M Here E ol , N is the electric field of the optical lattice at the position of dipole N . E NM is the electric field of dipole M at the position of dipole N and it is given by: ⎡⎛ k 2 ik 1 E NM = exp(ikrNM ) ⎢⎜ + 2 − 3 ⎣⎝ rNM rNM rNM ⎤ ⎞ k 2 3ik 3 ( p + − − 2 + 3 )rˆNM (rˆNM ⋅ p M ) ⎥ ⎟ M rNM rNM rNM ⎠ ⎦ (2.22) rNM is the distance between dipole M and dipole N . The dipole moment of dipole N is: p N = α (Eol , N + ∑ ENM ) (2.23) M Here α = 3ε mε 0 εs − εm V and Vd is the volume of the dipole. ε s + 2ε m d From Equations (2.22-2.23) we have: ∑A NM p M = α Eol , N M 36 (2.24) Every dipole generates an equation like equation (2.24). In the matrix A , every component is a polynomial function of α . If we solve the set of equations, the final solution has the form: p M = Z M ,1 (α ) (2.25) Here Z M ,1 (α ) is a polynomial function of α . Inserting equation (2.25) into Equation (2.22), we have: ENM = Z NM (α ) (2.26) Thus: E applied , N = Eol , N + ∑ Z NM (α ) M = Eol , N + ∑ Z NM ⎡⎣ 3ε 0 εmVd ( ε s − εm ) ( ε s + 2 εm ) ⎤⎦ (2.27) M Inserting equation (2.27) into equation (2.13), we find that optical force is a complex polynomial function of the refractive index of the particle. Optical forces initially increase as the refractive index of the particle increases; after refractive index contrast exceeds some value (for 300nm spherical particles, this value is 1.8), the optical forces fluctuate as the refractive index increases. From Fig. 2.1, the optical force from the optical lattice is a restoring force, and trapping potential wells form at the stable equilibrium positions. The shape of 37 optical force lines in Fig. 2.1 is very near to a sinusoidal shape, thus the depth of the potential well is: 0.5 l U= ∫ 0.5 l F0C(x, y,z)dy ≈ 0 ∫ F0sin ( 2πy l ) dy = F0l π (2.28) 0 In real particle systems at finite temperatures, Brownian movement causes positional fluctuation. The effect of Brownian movement on optical trapping can be calibrated by a factor m that depends on the relative strength of the potential versus the thermal energy: m= U kT (2.29) It is assumed that the trapping force can overcome the effect of Brownian movement when m > 10 [22]. From equations (2.28) and (2.29): m= U Fl F0lQ ≈ 0 = kT πkT πkTcε0 nm E02 (2.30) Here Q represents the power of the optical lattice ( Q = cε 0 nm E02 ). If we assume typically that the power is 5mW μm2 and T = 300K , inserting these values into equation (2.30) gives: m ≈ F0 E 02 × 4.56 × 10 25 38 (2.31) From Fig. 2.2, F0 E 02 varies as d increases, therefore the trapping ability changes for particles of different sizes. For example, when the diameter is around the period of optical lattices, m ≈ 20 , the trapping force is sufficient to overcome the Brownian movement so particles mainly reside in the high light intensity positions. For other particle sizes such as d ≈ 1.3l , however, F0 E 02 is nearly zero. Here, the particles will wander among the optical lattice due to their dominant Brownian movement, and the trapping effect can be ignored. Next, we consider a three dimensional periodic optical lattice arising from the interference of six plane waves. Their electric fields are depicted by: Λ E1 = E0 exp(ik0 y − iωt ) z Λ E2 = E0 exp(−ik0 y − iωt ) z Λ E3 = E0 exp(ik0 z − iωt ) x Λ E4 = E0 exp(−ik0 z − iωt ) x Λ E5 = E0 exp(ik0 x − iωt ) y Λ E6 = E0 exp(−ik0 x − iωt ) y Here k0 = 2π nm λ (2.32) (2.33) (2.34) (2.35) (2.36) (2.37) and the light intensity is: I ( x, y, z ) = 3E02 + E02 cos(2k0 x) + E02 cos(2k0 y ) + E02 cos(2k0 z ) 39 (2.38) We now explain the behavior of particles in this 3D optical lattice. The highest light intensity positions are simple cubic lattice, and the period of the optical lattice ( l ) is 409nm. Equation (2.38) is a simple approximation to the P − minimal surface having Pm 3 m symmetry [86, 87]. From equation (2.40), the origin of the coordinate system is a high light intensity position. We calculate the optical force on two kinds of spherical particles: polystyrene particle with permittivity 2.56 and absorbing particles with permittivity 2.56 + i .The diameter of the particles is 300nm. We change the positions of the centers of the particles r = ( x2 + y 2 + z 2 ) 0.5 along [100 ] , [110 ] , and [111] directions and calculate the optical forces. The results are shown in Fig. 2.5. Figure 2.5: (a) optical forces on PS particles arising from the 3D optical lattice. The shapes of the optical force lines along different directions are similar. The amplitudes of the optical forces fulfill Fmax[1,0,0] = Fmax[1,1,0] 2 = Fmax[1,1,1] particles arising from the 3D optical lattice. 40 3 . (b) Optical forces on absorbing In Fig. Fmax[100] = Fmax[110] 2.5(a), optical 2 = Fmax[111] forces along different directions fulfill 3 . This can be understood from equation (2.9): F ∝∇I (x, y, z) . Inserting equation (2.38) into the above equation leads to: F ∝ sin(2k0 x) xˆ + sin(2k0 y) yˆ + sin(2k0 z) zˆ (2.39) From equation (2.39), the restoring force pushes the particle to high light intensity positions, where optical potential wells form. The depth of the potential well is different along different directions and the shallowest potential is along the [100 ] direction. Compared to the 1D optical lattice, the 3D optical lattice offers three dimensional trapping; the depth of the potential well in 3D optical lattice is similar to the 1D optical lattice. In addition to dielectric particles, optical trapping has been extended to absorbing particles [88-91]. The permittivity of absorbing particles has imaginary part: ε = ε1 + iε 2 . For Rayleigh particles, the gradient optical force is: F = 0.5 α ∇ E 2 In equation (2.40), α is the polarizability and can be expressed as: α = 3Veff ε 1 + iε 2 − ε m ε 1 + iε 2 + 2ε m (2.41) 41 (2.40) In equation (2.41), the effective volume ( Veff ) is smaller than the space volume of the particle due to the absorption [90]: Veff = 4π 0.5 d ∫ 0 ⎡ 0.5d − r ⎤ r 2 exp ⎢ − ⎥⎦dr δ ⎣ (2.42) δ is the skin depth and can be calculated from the permittivity of the particle: δ = λ ( 2π 0.5 ε 12 + ε 22 − 0.5ε 1 ) (2.43) 0.5 From equation (2.40) and (2.41), the effect of absorption on optical force is determined by the effect of absorption on polarizability: Fε =ε1 Fε =ε1 +iε2 = α ε =ε α ε =ε +iε 1 ⎡ ε −ε ⎤ = ⎢V 1 m ⎥ ⎣ ε1 + 2ε m ⎦ 1 2 (2.44) ⎡ ε1 + iε 2 − ε m ⎤ ⎢Veff ⎥ ε1 + iε 2 + 2ε m ⎦ ⎣ The permittivity absorption part ε2 increases the part ε1 + iε 2 − ε m and decreases the ε 1 + iε 2 + 2ε m part Veff = 4π 0.5 d ∫ 0 ⎡ 0.5d − r ⎤ . r 2 exp ⎢ − ⎥⎦dr δ ⎣ For absorbing Rayleigh particles, if the size of particles is much smaller than skin depth, from equation (2.42): V eff ≈ V , therefore absorption leads to higher gradient optical force; if the size of particles is much bigger than skin depth, from equation (2.42): Veff 42 << V , therefore absorption leads to smaller gradient optical force. For absorbing particles in Lorenz-Mie range, however, the size of particles is usually higher than the skin depth and the electric field inside the particle gets smaller due to the absorption. According to equation (2.17), absorption generally leads to smaller optical force. This is confirmed by comparing Fig. 2.5(a) and Fig. 2.5(b): absorption causes optical forces to decrease by 25%. 2.4. Optical torques from optical lattices Our discussions above concern spherical particles; to date, non-spherical micro and nanostructures have been fabricated in experiments through multiple methods such as holographic interference lithography [92], stop-flow interference lithography [93], the modification and aggregation of spherical particles [94, 95]. In addition to optical forces, optical lattices also apply optical torques on these non-spherical structures, offering the possibility to simultaneously control the position and orientation of particles. We now calculate the optical torque on particles in the 1D optical lattices discussed above. Three forms of particles are examined: a cylinder with 140nm length and 140nm diameter (aspect ratio 1), a cylinder with 400nm length and 80nm diameter (aspect ratio 5), and a cylinder with 800nm length and 60nm diameter (aspect ratio 13.3); the particles have nearidentical volumes. We fix their centers at the highest light intensity positions and rotate them along Z axis. The optical torques on them as a function of angle of the 43 cylinder axis are shown in Fig. 2.6, which shows that optical torques on particles of various shapes are very different. Optical torques on particles can also be understood from the aspect of energy. The interaction energy between a dielectric particle and optical lattice is expressed in equation (2.16), thus: Ω = − ∂ (ΔW ) ∂θ = 0.5ε 0ε m (ε s ε m − 1) ∂ ( ∫∫∫ EEi dV ) ∂θ (2.45) V0 Figure 2.6: optical torques on three kinds of cylinders. For the 140nm length cylinder, we have not observed stable equilibrium orientations. For the 400nm length cylinder, θ = 0 is the stable equilibrium orientation. For the 800nm length cylinder, in addition to the stable equilibrium orientation at θ = 0 , metastable orientation is observed at θ = ±0.5π . From the above equation, the physical origin of optical torque is that the particle adopts particular orientations to minimize the interaction energy. If the refractive index of particles is near to the background (e.g. polystyrene, silica particles in distilled water), we can assume E = 6ε mEi ; this leads to: 2ε s + 4ε m Ω = 3ε 0ε m (ε s − ε m ) (2ε s + 4ε m ) ∂ ( ∫∫∫ I ( x, y, z )dV ) ∂θ V0 44 (2.46) For particles with near spherical shape or with a size much smaller than the period of optical lattices, optical torques on them are small because the total light intensity inside does not change much as the particles rotate with respect to the optical lattice ( ∂ ∫∫∫ I ( x, y, z )dV ∂θ ≈ 0 ). Figure 2.6 confirms this: the 140nm length cylinder V0 has size much smaller than the period of the optical lattice ( 409nm ) and its shape is near to sphere compared to other cylinders calculated, thus the optical torque on it is nearly zero compared to other cylinders. For particles with large aspect ratio and sizes comparable to the period of optical lattices, θ = 0 is the stable equilibrium state. For the cylinder with aspect ratio 13.3, however, the two ends of the cylinder are both in at high intensity regimes at θ = 0.5π , so in addition to the stable equilibrium state of θ = 0 , a metastable state of θ = 0.5π exists. 45 Chapter 3 Integrated optical devices based on 2-pattern photonic crystals 3.1. Introduction It is generally believed that high structural symmetry is advantageous to open a large, complete photonic band gap (PBG); therefore most PBG structures investigated are periodic crystals or quasicrystals with high rotational symmetry incompatible with lattice translation. Here we design a new series of twodimensional (2D) ordered aperiodic structures with large, complete PBG but without any of the 2D symmetries: translation, rotation, mirror and glide reflection. These structures, “2-pattern crystals”, come from the simple superposition of two sub-crystals or quasicrystals. Our band gap optimization strategy is to first select distinct structures that have outstanding PBG properties. We then pair one structure that has a premier transverse magnetic (TM) gap with another structure that has a premier transverse electric (TE) gap, adjust the scale of each structure and their dielectric fill fractions to provide a composite structure with superior TE and TM properties. Using this approach, we have designed six aperiodic PBG structures having a complete photonic band gap larger than 15% for ε 2 ε1 = 11.4 . 46 Importantly, the TM and TE gaps of a 2-pattern crystal are less interdependent than for conventional photonic crystals, affording unique capabilities to simultaneously bend, split, couple and filter TM and TE waves. By separately altering the respective sub-crystals, we demonstrate novel 2-pattern crystal based polarizers, crossed waveguides, resonators and filters. 3.2. 2-pattern photonic crystals Many attempts have been made to achieve a complex system with interesting properties by the assembly of geometric elements with simple symmetries. For example, a 2D society consisting of lines, triangles, pentagons, etc was conjured by Abbott [96]. Here we design a novel series of 2D PBG structures by simply superposing geometric patterns without regards to preserving global symmetries in the composite. Photonic crystals, discovered in 1987 [31, 97], have attracted great interest due to their ability to control the flow of light [98-100]. A large number of PBG structures have been developed during the past twenty years. Up to now, PBG structures can be categorized into three types: periodic structures [31, 101-103], quasicrystals [104, 105] exhibiting higher rotational symmetries than consistent 47 with conventional periodic lattices, and even disordered structures[97, 106] with short range order. Moreover, it is generally believed that a highly symmetric structure, i.e. one possessing translational, rotational, mirror, and glide reflection symmetries is most advantageous to form the largest PBG. In our approach, we superpose a TM sub-crystal and a TE sub-crystal on the same plane to form 2-pattern photonic crystals. The chosen TM sub-crystal has separated dielectric features providing a large TM PBG and the chosen TE subcrystal has expanded dielectric features providing a large TE PBG. The subcrystals can be periodic or aperiodic. Interestingly, the 2-pattern crystal structures do not belong to any of the known PBG structural categories; they are both ordered and aperiodic. Moreover, they do not have global or even local symmetries. A crucial property of the photonic crystal devices is a complete PBG, a range of frequencies for which the propagation of an electromagnetic wave of arbitrary polarization in any direction is forbidden. Designing 2D structures with a large, complete PBG is challenging because the structural requirements are contrary: generally, TM PBG arises from a dielectric structure with separate features whereas TE PBG arises from a structure with a connected dielectric 48 network. In the previous literature, the complete PBG structure is mainly achieved by drilling holes in material background [104, 105] or by increasing the local fill fraction of a connected network at connection sites [106, 107]. Our approach is based on the rationale that the TE sub-crystal of 2-pattern crystals can be assumed a type of geometrical perturbation to the TM sub-crystal and vice versa. A random geometrical perturbation of a given structure shrinks the size of the PBG [108, 109], but the PBG is generally more robust to an ordered perturbation [110]. If the TE sub-crystal filling ratio is not high, the ordered geometrical perturbation is not strong enough to destroy the TM PBG; therefore the 2-pattern crystal may maintain a TM PBG, arising predominately from the TM sub-crystal. Conversely, the TM sub-crystal can be assumed as a geometrical perturbation to the TE PBG; therefore the 2-pattern crystal may maintain a TE PBG especially if the TM sub-crystal filling ratio is low. Since the dominant TM and TE PBGs mainly arise from the different sub-crystals, they should be essentially independent of each other. Importantly, this offers the possibility to separately tune the TM and TE PBGs by altering the respective sub-crystals and make them overlap to generate a composite structure with a larger, complete PBG than previously known structures. 49 In 2D, there are five factors which define the 2-pattern photonic crystal: the morphology of the sub-crystals, the filling ratio of each of sub-crystal, the relative scale of the sub-crystals, the relative position and the relative orientation of the sub-crystals. Next we analyze how those factors impact the complete PBG and demonstrate this PBG engineering strategy can successfully design a set of 2pattern crystals with large, complete PBGs. We then demonstrate several novel features for controlling light in one of our 2-pattern crystals. The first design factor is the morphology of the sub-crystals. Here it is desirable to select two sub-crystals: one with either a large TE PBG and one with a large TM PBG so as to open a large, complete PBG in the 2-pattern crystal. Here we assume that the dielectric material is GaAs with a permittivity of 11.4. We pick three candidates for the TM PBG sub-crystal: rods on a triangular lattice (Figure 3.1a, p6mm, the current champion structure with the largest TM PBG, 47.3% TM PBG for 0.1 filling ratio), rods on a square lattice (Figure 3.1b, p4mm, 37.5% TM PBG for 0.15 filling ratio), and an eight-fold quasicrystal of dielectric rods generated from hyperspace projection [111] (Figure 3.1c, 8mm, 42.1% TM PBG for r a = 0.185 , here r is the radius of the rods and a is the quasicrystalline length parameter). The two candidates for the TE PBG sub-crystal both have p6mm 50 symmetry: the connected honeycomb structure (Figure 3.1g, the current champion structure with the largest TE PBG [112], 42.5% TE PBG for 0.189 filling ratio) and circular rings on a triangular lattice (Figure 3.1h, 23.4% TE PBG for 0.114 filling ratio). Figure 3.1: (a) through (c): three sub-crystals with large TM PBG (rods of triangular lattice, rods of square lattice and eight-fold quasicrystals). The filling ratio of the subcrystals ( f ) are also given in the figure. For quasicrystals, the filling ratio is given by parameter r a . Here r is the radius of the rods and a is the quasicrystal lattice parameter. The DOS calculations of the sub-crystals are shown in (d) through (f). Two sub-crystals with large TE PBG (the honeycomb structure and rings on a triangular lattice) are shown in (g) and (h); the corresponding DOS calculations are shown in (i) and (j). 51 The second factor is the relative length scale of the two sub-crystals. For the 2-pattern crystals, if we tune the scale of the TE (TM) sub-crystal, the position of the TE (TM) PBG is shifted accordingly. The central frequency of the TE (TM) PBG is proportional to 1 a , here a is the characteristic scale of the sub-crystal [100]. An example is the 2-pattern crystal, shown in Figure 3.2a, made from the superposition of the sub-crystals depicted in Figure 3.1b and Figure 3.1h. The filling ratio of the TE sub-crystal is 0.102 and the filling ratio of the TM subcrystal is 0.149. The DOS plot for a(TM) / a(TE) = 0.559 is shown in Figure 3.2b. Note that the TE-PBG and the TM-PBG barely overlap. To maximize the complete PBG, we increase the periodicity of the TM sub-crystal to decrease the central frequency of the TM-PBG. The tuning is continued until the TE-PBG and the TMPBG fully overlap, which is shown in Figure 3.2c. Figure 3.2: (a): 2-pattern crystal from the sub-crystals in Figure 3.1(b) and Figure 3.1(h). (b): The DOS plot for a(TM) a(TE) = 0.559 . (c): The DOS plot for a(TM) a(TE) = 0.656 . 52 The third design factor of the 2-pattern crystals is the individual sub-crystal filling ratio. The filling ratio of each type of sub-crystal controls the respective TE or TM gap but also modifies the strength of the ordered geometrical perturbation on the PBG of the other sub-crystal. Therefore, altering the TE sub-crystal can in general shrink the size of the TM PBG and the shrinkage increases with the filling ratio of TE sub-crystal with the reverse situation holds for the TM sub-crystal. An example 2-pattern crystal made from superposition of the sub-crystals in Figure 3.1a and Figure 3.1g is shown in Figure 3.3a. In Figure 3.3b, we fix the filling ratio of the TM sub-crystal to 8.6% and increase the filling ratio of TE sub-crystal. If the filling ratio of the TE sub-crystal is too high (above 14%), the TM PBG is destroyed and the complete PBG closes. If the filling ratio is too low (below 3%), the TE PBG of the 2-pattern crystal is low or even closes, which is also obviously disadvantageous. Therefore, the filling ratios of the sub-crystals need to be adjusted carefully to maximize the complete PBG. For example, for the DOS plot shown in Figure 3.3c, the TE-PBG is smaller than TM-PBG and the complete PBG size is determined by the TE-PBG. To maximize the complete PBG, it is necessary to increase the TE-PBG size. Therefore we increase the filling ratio of the TE subcrystal. Although the TM-PBG shrinks because of this tuning, as shown in Figure 3.3b, the complete PBG size increases. We increase the filling ratio of the TE subcrystal until the TE-PBG and TM-PBG match with each other, which is shown in 53 Figure 3.3d. The complete PBG is maximized because if the filling ratio of the TE sub-crystal increases further, as shown in Figure 3.3e, the TM-PBG is smaller than the TE-PBG and the complete PBG is determined by the TM-PBG, which is relatively smaller than the complete PBG in Figure 3.3d. Figure 3.3: (a): 2-pattern crystal from the sub-crystals in Figure 3.1a and Figure 3.1g. (b): the TE PBG and the TM PBG of the 2-pattern crystal for different filling ratios of TE sub- 54 crystal. (c): The DOS plot if the TE sub-crystal filling ratio f(TE) is 0.058. (d): DOS plot if f(TE) is 0.086. (e): DOS plot if f(TE) is 0.114. The fourth and the fifth design factors are the relative position and orientation of the sub-crystals. Interestingly, it turns out these factors have essentially no influence on the PBG since the changes in the relative location of the TE sub-crystal, as an ordered geometrical perturbation to TM sub-crystal, should not substantially vary the TM PBG of the 2-pattern crystal with the same reasoning for the behavior of the TE PBG by the presence of the TM sub-crystal. Therefore, the relative position and orientation of the TE/TM sub-crystals only bring minor impact on the complete PBG of the 2-pattern crystal. The above fact is very advantageous for the fabrication of the 2-pattern crystals because it is not necessary to precisely adjust the relative position/orientation of the two subcrystals. For the three selected TE sub-crystals and two TM sub-crystals shown in Figure 3.1, six combinations can be constructed. For each combination, we maximize the complete PBG size by tuning the filling ratios of the sub-crystals and the relative scale of the sub-crystals. The optimized structures with their discrete Fourier transforms (DFT) and the associated DOS calculations are shown in Figure 55 3.4. The previous best 2D PBG structure with the largest complete band gap for a dielectric contrast of 11.4 (20.1%) is a complicated periodic dielectric network of various diameter rods and various width veins with four-fold rotational symmetry (p4mm) [113]. The six optimized 2-pattern crystals all have a complete PBG above 15% although as composite structures they do not possess any 2D symmetry. The aperiodic structure depicted in Figure 3.4a has the best complete PBG (20.4%), which is substantially the same as the current champion structure. Surprisingly, this is the first time that an aperiodic structure without any symmetry becomes the champion PBG structure. According to our experience, the optimized structures generally have almost equal sub-crystal filling ratios (around 0.1). Further, because the mid-gap frequency of the TE and TM PBGs corresponds to the wavelength near to the periodicity of the sub-crystals, to overlap the TE and TE PBGs, the periodicities of the sub-crystals need ( 0.1 < a(TM) a(TE) < 10 ). 56 to be on the same order Figure 3.4: optimized 2-pattern crystals with large, complete PBG. (a): the 2-pattern crystal from the sub-crystals in Figure 3.1a and Figure 3.1g. Here the filling ratio of the TE sub-crystal f(TE) = 0.086 and the filling ratio of the TM sub-crystal f(TM) = 0.086 . The ratio of the periodicities of the sub-crystals a(TM) a(TE) = 0.7157 . The DFT of the 2pattern crystal and the corresponding DOS calculation are shown below the structure. (b): the 2-pattern crystal from the sub-crystals in Figure 3.1b and Figure 3.1g. Here f(TE) = 0.08 , f(TM) = 0.14 and a(TM) a(TE) = 0.67 . (c): the 2-pattern crystal from the subcrystals in Figure 3.1c and Figure 3.1g. Here f(TE) = 0.11 and r a = 0.22 . (d): the 2-pattern crystal from the sub-crystals in Figure 3.1a and Figure 3.1h. Here f(TE) = 0.121 , f(TM) = 0.102 and a(TM) a(TE) = 0.7258 . (e): the 2-pattern crystal from the sub-crystals in 57 Figure 3.1b and Figure 3.1h. Here f(TE) = 0.108 , f(TM) = 0.149 and a(TM) a(TE) = 0.6563 . (f): the champion structure from the sub-crystals in Figure 3.1c and Figure 3.1h. Here f(TE) = 0.084 and r a = 0.189 . 3.3. Integrated optical devices on a optical chip 2D photonic crystal devices have wide applications, including components in optical computer chips [114, 115], spontaneous emission control devices [116, 117], quantum information devices [118, 119], waveguides [120-122], lasers [123126], and optical fibers [127]. The TM/TE PBGs of the 2-pattern photonic crystals are generally less interdependent, which is substantially different from the behavior of the photonic crystals reported before. The above advantages make 2-pattern crystals excellent candidates for novel optical devices because they can bend, split, couple, and filter TM/TE waves simultaneously on the scale of wavelength. For example, we can design waveguides and resonators which affect only the propagation of light of a particular polarization. A crossed waveguide is shown in Figure 3.5a. By locally removing the TM sub-crystal, we can create a TM waveguide in regions 1 and 3. Similarly, a TE waveguide can be created in regions 2 and 4 by simply removing the TE subcrystal. To illustrate how one can retain mode polarization through the crossing point, we introduce TM waves into region 1 and TE waves into in region 2. The 58 light intensity distributions for TE and TM waves are shown in Figure 3.5b and 3.5c, which demonstrate that the leakage of light of one polarization to the waveguide of the other polarization is very minor. Figure 3.5: (a): the proposed crossed waveguide based on 2-pattern crystal in Figure 3.4a. (b): the light intensity distribution for TE wave. The TE wave propagates in region 2 and 4. (c): the light intensity distribution for TM wave. The TM wave propagates in region 1 and 3. A novel type of wavelength scale polarizer device can be made from a 2pattern crystal optical circuit as shown in Figure 3.6a. Here the T-shape channel 59 consists of three regions: region 1 allows the propagation of both TE and TM waves; region 2 allows the propagation of TM waves while blocking TE waves; region 3 allows the propagation of TE waves while blocking TM waves. Thus, the T-shape channel can separate TM and TE waves, which are introduced to region 1 by radiating dipoles. The time-averaged light intensity distribution for the TE wave E2X + EY2 is shown in Figure 3.6b and the light intensity distribution for TM wave 2 E 2z is shown in Figure 3.6c. The transmittance of TM wave Ez over 40 % and the leakage of TM wave E2z Region 3 E2z Region 1 Region 2 E2z Region 1 is is less than 1%. The transmittance of the TE wave is nearly 90% and the leakage is again below 1%. The degree of polarization in region 2 ( E2Z − E2X + EY2 ) ( EX2 + EY2 + E2Z ) is 0.984; the degree of polarization in region 3 ( E2X + EY2 − E2Z ) ( EX2 + EY2 + E2Z ) is 0.985. 60 Figure 3.6: wavelength scale polarizer based on 2-pattern crystals. (a): the proposed polarizer based on 2-pattern crystal in Figure 3.4a. TE and TM waves enter in channel 1 and they are separated to channel 2 and channel 3. (b): the light intensity distribution for TE wave. The TE wave propagates in region 1 and 3. (c): the light intensity distribution for TM wave. The TM wave propagates in region 1 and 2. Creating other structures within a 2-pattern photonic crystal can lead to interesting phenomena such as optical coupling, resonance and optical confinement. In Figure 3.7a, we design a filter based on a ring resonator that can be used to select TM and TE waves of particular frequencies. To demonstrate this, we introduce light into region 1 covering the frequency range of the PBG. As the 61 optical waves propagate in the waveguide from region 1 to region 2, certain waves of resonance frequency are coupled to the ring resonator and dropped to region 3. Fourier analysis of the filtered waves inside region 3 is shown in Figures 3.7b and 3.7c. The resonance peaks are obvious for both TM and TE waves, which are filtered by the ring resonator. The light intensity distributions of TE and TM waves for on-resonance (drop) frequency and off-resonance (through) frequency are shown in Figure 3.7e through 3.7h. The filtered TM and TE waves are output from region 3. We can separate the TM and TE waves by connecting region 3 with the inlet of the T-shape polarizer shown in Figure 3.6. The quality factor of the filter device is around 100. The ring resonance frequency can be tuned by altering the ring morphology and the local refractive index of TM and TE sub-crystals. Figure 3.7: (a): the filter structure. (b): the resonance peak for TE wave. (c): the resonance peak for TM wave. (d): the light intensity distribution of TE wave for on-resonance frequency: ωa 2πc = 0.438 . (e): the light intensity distribution of TE wave for off-resonance 62 frequency: ωa 2πc = 0.466 . (f): the light intensity distribution of TM wave for on-resonance frequency: ωa 2πc = 0.475 . (g): the light intensity distribution of TM wave for offresonance frequency: ωa 2πc = 0.456 . 3.3. Summary In summary, a novel set of aperiodic PBG structures named “2-pattern crystals” consisting of two sub-crystals have been investigated. Although as a composite structure, these photonic crystals do not possess any symmetry, the six optimized 2-pattern crystals all have complete PBGs above 15%. Further, there is no precise translationally or orientational registration required between the two sub-structures. The above fact makes the fabrication of the 2-pattern crystals straightforward. Moreover, these 2-pattern crystals provide the ability to control TM and TE wave simultaneously on the scale of the wavelength. Our designs demonstrate strong potential for a set of novel optical circuit devices including 2pattern crystal based polarizer, crossed waveguide, and filter. 63 Chapter 4 Photonic quasicrystals 4.1. Introduction A large photonic band gap (PBG) is highly favorable for photonic crystal devices. One of the most important goals of PBG materials research is identifying structural design strategies for maximizing the gap size. We provide a comprehensive analysis of the PBG properties of two dimensional (2D) quasicrystals (QCs), where rotational symmetry, dielectric fill factor and structural morphology were varied systematically in order to identify correlations between structure and PBG width at a given dielectric contrast (13:1, Si:air). The transverse electric (TE) and transverse magnetic (TM) PBGs of 12 types of QCs are investigated (588 structures). We discovered a 12mm QC with a 56.5% TE PBG, the largest reported TE PBG for an aperiodic crystal to date. We also report here a QC morphology comprising “ninja star” like dielectric domains, with near circular air cores and interconnecting veins emanating radially around the core. This interesting morphology leads to a complete PBG of about 20%, which is the largest reported complete PBG for aperiodic crystals. 64 4.2. PBG maps of quasicrystals 2D photonic quasicrystals (PQCs) have been shown to be promising PBG materials because of their nearly isotropic photonic band structures stemming from their high rotational symmetries [128, 129], defect-free localized modes [32, 33, 130], and the possibility to open a PBG at lower refractive index contrast than typical PC structures [34, 35]. PQCs have attracted additional interest for a variety of photonic applications, including lensing [131], waveguiding [132, 133], negative refraction [134], and optical fiber devices [135]. An essential requirement for many applications of PBG materials is the gap size. The first study of PQC structures was published in 1998 and focused on 8mm symmetric QCs [136]. At a dielectric contrast of 10:1, Chan found a TM gap of 22% for structures consisting of isolated dielectric rods, while a corresponding 8mm vein-connected dielectric structure displayed a 25% TE gap and no complete PBGs [136]. In 2000, a published report on the properties of 12-fold rotationally symmetric QC suggested that even higher rotational symmetries could lead to significant improvements over conventional photonic crystals, and claimed finding a complete PBG of 30% at an astoundingly low dielectric contrast of only 4:1[104]. Unfortunately, the results from this paper were soon afterwards shown 65 to be erroneous, where structures with air rods decorating the vertices of a 12mm square-triangular tiling exhibited only a modest complete PBG that opens at a dielectric contrast greater than 7:1 [105]. Many theoretical investigations of QC PBG properties ensued, including Penrose structures [137], 5mm QCs[128], 8mm QCs [34, 138], various 12mm QCs [105, 139]. However, due to the various differences in the focus and material assumptions in these studies, it is quite difficult to conduct a direct comparison and detailed structure-property analysis to identify design elements for optimizing the PBG properties of 2D QCs of different symmetries and morphologies. For example, the impact of morphology on the size of TM PBG has been somewhat obscured, though recently the strong influence of the resonance of discrete dielectric features has been identified in independent studies [137, 140-144]. While the importance of large PBG sizes for applications of PBG material based devices has been well recognized, in the case of QC much work remains to be done towards identifying the champion QC structures, with the largest TM, TE and complete PBGs. In this chapter, we conduct a comprehensive study of the impact of rotational symmetry and morphology on the PBG of 12 different types of 588 QCs, assuming the constitutive materials are silicon and air ( ε 2 : ε1 = 13:1 ).The QCs investigated are 66 defined by level set equations [145, 146], that can be fabricated by interference lithography [147-151], and QCs generated by decorating quasiperiodic geometric tilings according to a particular recipe [152, 153], which can be fabricated via Ebeam lithography or focused ion beam lithography. We examined both TE and TM PBGs, for 8mm, 10mm, and 12mm rotational symmetries, for a very wide dielectric fill ratio range (0.02 to 0.98), and both structural morphologies (dielectric-filled, or air-filled). For each QC type in this extensive set of morphologies and symmetries, we used finite-difference time-domain (FDTD) simulations to find the optimum filling ratio that maximizes the TM or the TE PBG. Champion QCs with the largest TM, the largest TE, and the largest complete PBG are discussed and analyzed and the physical origin of the gaps is described. The first family of 2D QCs investigated is generated using the following level set equation: N −1 f ( x, y ) = ∑ cos(2π x cos(π n N ) a + 2π y sin(π n N ) a ) (4.1) n =0 The value of 2N in equation (4.1) sets the rotational symmetry of the associated QCs, and a represents the characteristic unit length. QCs defined by level set equation (4.1) can be fabricated by multiple-exposure interference lithography 67 (MEIL) [147, 154, 155]. Equation (4.1) can be used to generate two types of QC structure morphologies, using an analogy with the photoresist tone in MEIL: (i) positive tone, where the dielectric material of choice is found at all locations where f ( x, y ) < t (air fills the rest of the space), and (ii) negative tone, where the dielectric material occupies all locations where f ( x, y ) > t . Since large rotational symmetries involve increasing fabrication difficulties due to a reduced structural contrast associated with increasing the number of exposures, we focused our studies on QCs with N < 7 . For N = 1,2,3 , the structures are periodic. For N = 4,5,6 , the structures are quasiperiodic with rotational symmetries 8mm, 10mm, and 12mm respectively. Some representative QC morphologies from this study are shown in Figure 4.1. The rotation center of MEIL is assumed to be at the high light intensity position of the 1D periodic fringe pattern, which generates additional mirror symmetries. The resultant highest point group symmetries for 8, 10, and 12 fold QCs are 8mm, 10mm, and 12mm. Here we use LS-8mm, LS-10mm, and LS-12mm to denote 8mm, 10mm, and 12mm QCs generated from level set equation (4.1). 68 Figure 4.1: (a)-(e): structural evolution with fill factor for 8mm symmetric QCs defined by level set equation (4.1) as dielectric filling ratio is varied. Here the last number behind LS − 8mm / is the filling ratio of the black component. For a negative photoresist, a black component indicates the dielectric; for a positive photoresist, the black color indicates air features in a dielectric surrounding; (f)-(j): structural evolution with fill factor for 10mm symmetric QCs defined by level set equation (4.1); (k)-(o): structural evolution with fill factor for 12mm symmetric QCs defined by level set equation (4.1). The second set of QC structures studied is generated by decorating quasiperiodic geometric tilings obtained by 2D projection from a higher dimensional space [152, 153]. Here, we consider the approach of placing rods (dielectric or air) at the nodes of the chosen tilings, and filling the region between the rods with the complementary material (dielectric rods in air, or vice-versa for the opposite structural morphology). Representative QCs of various symmetries 69 are shown in Figure 4.2. We use R-QC (or AR-QC) to denote QCs generated from placing dielectric (or air) rods at the nodes of the chosen tilings. Figure 4.2: (a)-(e): QCs of 8mm rotational symmetry from quasiperiodic tiling patterns decorated with rods. Here the number after R − 8mm / is the filling ratio of the black component; (f)-(j): QCs of 10mm rotational symmetry from quasiperiodic tiling patterns decorated with rods; (k)-(o): QCs of 12mm rotational symmetry from quasiperiodic tiling patterns decorated with rods. For R-QCs, the black color indicates the dielectric and the white color indicates the air; whereas for AR-QCs, the black color indicates the air and the white color indicates the dielectric. The PBG of these 2D QC structures can be determined from maps of the local density of states (LDOS) [34, 138, 156-158] calculated using a FDTD solution to Maxwell’s equations [1, 6]. In a LDOS map, a continuous low LDOS region along the vertical frequency axis indicates a PBG. We first discuss the 70 results for TM polarized waves in QCs defined by the level set Equation (4.1). The LDOS maps for the 8mm, 10mm and 12mm QCs are shown in Figure 4.3. As the filling ratio of the structures ( f ) is varied from 0.02 to 0.98, a number of regions with gaps are found. For the negative tone LS-8mm QC shown in Figure 4.3(a), the largest TM PBG size is 37.0%, occurring at f = 0.18 . For the positive tone LS-8mm QC shown in Figure 4.3(b), a similar sized TM PBG also occurs at f = 0.18 . For the negative tone LS-10mm QC shown in Figure 4.3(c), an interesting observation is that the lowest TM PBG width remains almost constant for a wide range of filling fractions and this insensitivity makes it a good candidate for experimental photonic devices. For the positive tone LS-10mm QC shown in Figure 4.3(d), the largest TM PBG size is 37.2% at f = 0.12 . For the negative tone LS-12mm QC shown in Figure 4.3(e), the largest TM PBG size is 40.7% for f = 0.14 . For the positive tone LS-12mm QC shown in Figure 4.3(f), a large TM PBG of about 42% appears in the range of 0.1 ≤ f ≤ 0.2 , implying another excellent candidate for photonic devices. The comprehensive results of this study are collected in Table 4.1. 71 Figure 4.3: (a)-(f): TM photonic LDOS maps for LS-8mm, LS-10mm, and LS-12mm QCs, with log (LDOS) plotted vs. fill ratio and frequency. Quasicrystal type Mode f ωlower a 2π c ωupper a 2π c ωmiddlea 2π c Δω ωcenter Negative tone LS-8mm Positive tone LS-8mm Negative tone LS-10mm Positive tone LS-10mm Negative tone LS-12mm Positive tone LS-12mm R-8mm R-10mm R-12mm AR-8mm AR-10mm AR-12mm AR-12mm AR-12mm R-p6mm (crystal) R-p6mm (crystal) R-p6mm (crystal) Honeycomb (crystal) Honeycomb (crystal) AR-p6mm (crystal) AR-p6mm (crystal) AR-p6mm (crystal) TM TM TM TM TM TM TM TM TM TM TM TM TE Complete TM TE Complete TE TM TE TM Complete 0.18 0.18 0.24-0.38 0.12 0.14 0.1-0.2 0.12 0.12 0.12 0.08 0.1 0.16 0.32 0.18 0.12 0.44 any 0.22 any 0.36 0.1 0.18 0.22 0.22 ~0.21 0.235 0.225 ~0.285 0.292 0.280 0.294 0.225 0.26 0.417 0.26 0.41 0.297 0.292 0 0.225 0 0.252 0.483 0.413 0.32 0.32 ~0.28 0.3425 0.34 ~0.447 0.472 0.448 0.470 0.295 0.325 0.51 0.465 0.5 0.493 0.336 0 0.47 0 0.424 0.585 0.497 0.27 0.27 ~0.245 0.289 0.2825 ~0.366 0.382 0.364 0.382 0.26 0.2925 0.4635 0.362 0.455 0.395 0.314 0 0.3475 0 0.338 0.534 0.455 37.0% 37.0% ~28.5% 37.2% 40.7% ~44% 47.1% 46.1% 46.0% 26.9% 22.6% 21.2% 56.5% 19.8% 49.6% 13.77% 0 59.3% 0 50.9% 19.1% 18.5% Table 4.1: Summary of key findings from the LDOS numerical calculations. The champion QCs with the largest TM, the largest TE, and the largest complete PBGs are shown by “italics”. The results are for ε 2 ε1 = 13:1 . 72 Next we analyze the TM PBGs of QCs defined by placing solid rods (R-) or air rods (AR-) of desired diameter at the vertices of various QC geometric tilings obtained from hyperspace projection. Interestingly, for R-8mm, R-10mm and R12mm QCs, as well as the reference case of a triangular lattice PC (R-p6mm), the TM LDOS gaps are all found to be quite similar, see Figures 4.4(a) through 4.4(d). The similarity of the LDOS for these structures in the region with f < 0.25 is due to the dominant role of the Mie resonances generated by individual dielectric rods [141, 142, 144]. Although the rotational symmetries of the QCs are different, the identity of the individual scatterer is preserved and is found to lead to similar PBG properties for the various quasiperiodic arrangements we investigated. At larger fill fractions the rod-rod distance becomes small and the TM PBG closes quickly, which can be associated with a loss of distinct Mie resonances in the case of interconnected dielectric domains. The largest observed TM PBGs of R-p6mm, R8mm, R-10mm, and R-12mm QCs are listed in Table 4.1. The largest PBGs (above 45%) occur at f = 0.12 for the dielectric contrast of 13:1 used in this study. Compared to TM PBGs of R-QCs, AR-QCs are found to display smaller TM PBGs, as shown in Table 4.1 and Figure 4.5. 73 Figure 4.4: (a)-(d): TM photonic LDOS maps for periodic R-p6mm and the quasiperiodic R-8mm, R-10mm, and R-12mm QCs, with log (LDOS) plotted vs. fill ratio and frequency. Figure 4.5: (a)-(c): TM photonic LDOS maps for AR-8mm, AR-10mm and AR-12mm QCs, with log (LDOS) plotted vs. fill ratio and frequency. The AR-QCs with a low filling ratio have a wide range of shapes and sizes of the discrete dielectric regimes (see Figure 4.2) and they provide relatively weak TM gaps. In order to better understand why R-QCs have superior TM gap properties compared to AR-QCs and LS-QCs, we examine their corresponding structural characteristics. It is known that morphologies consisting of separate dielectric domains can have a large TM PBG, thus we start with exploring the impact of the 74 dielectric domain shapes and arrangements. Based on our calculations shown in Table 4.1 and from the data in reference [128], QCs consisting of entirely circular shape features, e.g. rods on the nodes of quasiperiodic tilings, have the best TM PBG properties. Further, the TM PBGs of QCs consisting of separated non-circular features (one group of level set equation: LS-8mm, LS-10mm and LS-12mm) are smaller than the TM PBGs of QCs consisting of near circular features (5-10 groups of level set equation, shown in reference [128]). A non-circular element has different scattering cross sections for waves incident from different angles, which is disadvantageous for wave propagation suppression for all in-plane directions. For example, the separated dielectric features of low dielectric fill AR-QCs, as shown in Figure 4.2, are star shaped or rectangular shape with sharp corners. Such features are strongly anisotropic scatterers; therefore their TM PBGs are small, as can be seen in Table 4.1 and Figure 4.5. Furthermore, besides the importance of optimizing the shape of the individual dielectric domain, it is important to emphasize the importance of their spatial arrangement. R-p6mm PC structures display larger TM PBG than the corresponding R-QCs, benefiting from added coherent Bragg scattering. In R-QC structures, the larger variation of nearest neighbor distances further limits the resonance optimization. 75 Figure 4.6: (a): the champion AR-12mm structure with the largest TE PBG (56.5%). The filling ratio of the structure is 0.32; (b) schematic delineating the periodic honeycomb veins (AR-p6mm): honeycomb, rhombus, and triangles; (c) TE photonic LDOS maps for AR12mm QCs, with log (LDOS) plotted vs. fill ratio and frequency; (d): the LDOS plot for the champion structure ( f = 0.32 ), the TE PBG is indicated in the figure; (e): the champion AR-12mm QC with the largest complete PBG at f = 0.18 . The “ninja star” shape dielectric resonator particles are indicated in the circles. This R/V (resonator-vein) structure exhibits good short range order. We now proceed to examine the results for the TE LDOS calculations. In general, TE PBGs are favored for a structure comprised of a network of connected veins. For example, the honeycomb vein structure is the champion photonic crystal structure with the largest TE PBG of 60% for ε1 ε 2 = 13.0 [159]. The TE PBGs of all the QC structures examined in this study are found to be much smaller (below 76 10%), with one notable exception. In the case of the AR-12mm QC structure, we found a very large TE PBG of 56.5% at f = 0.32 , which is the largest TE PBG observed to date for QCs and only slightly lower than the champion honeycomb structure [112]. The PBG gap map of AR-12mm QC and the LDOS plot for the champion AR-12mm QC are shown in Figures 4.6(c) and 4.6(d) and the corresponding AR-12mm morphology at f = 0.32 is shown in Figure 4.6(a). The high rotational symmetry leads to higher density of interconnected veins. To identify some correlations between structure and TE PBG properties, we also examine the case of the periodic honeycomb crystal (AR-p6mm) for which we compute the LDOS map and analyze the underlying morphology. Interestingly, we find a very similar TE gap range and, furthermore, many common structural motifs between the AR-12mm QC structure and the AR-p6mm PC structure, shown in Figure 4.6(a) and 4.6(b). The primary difference between the honeycomb structure and AR-12mm QC is that the nodes connecting the veins of the AR-12mm QC all contain a small round central dielectric core feature. We believe that the repeating motifs of the “ninja star” like dielectric domains, with near circular cores and interconnecting veins emanating radially, are key for simultaneously enabling complete gaps (overlapping TE and TM gaps), as discussed below. 77 To display a large complete PBG, the photonic structure needs to enable TM and TE gaps that are both large and have overlapping frequency intervals. The complete PBGs of most of the QCs examined in the present work are minimal (i.e. below 10%). AR-12mm is the only exception with a TM PBG and a TE PBG larger than 20%, as shown in Table 4.1. At f = 0.18 , the AR-12mm QC has the largest complete PBG (19.8%), which is essentially the same as the largest complete PBG found to date (20.1%) [113] and it is the largest reported value for aperiodic crystals. A portion of the champion AR-12mm QC is shown in more detail in Figure 4.6(e). Comparing the AR-12mm QC in Figure 4.6(a) ( f = 0.32 ) and the same structure with lower filling ratio in Figure 4.6(e) ( f = 0.18 ), we find that as we decrease the filling ratio, the dielectric veins become thinner compared to the dielectric core, causing the TE PBG to shrink rapidly from 56.5% to 20% while the TM PBG increases from 0% to around 20%. The physical reason for this behavior is that the veins contribute to the TE PBG through a destructive Bragg interference mechanism. As the vein thickness reduces, the strength of destructive interference decreases and the TE PBG shrinks. For thinner veins, their corresponding connection points consist of a relatively larger dielectric portion of the total and act as effective “particles”, as shown in Figure 4.6(e). The resonant scattering of these “particles” enables the formation of the TM PBG. Therefore the large, complete PBG of the AR-12mm at f = 0.18 is enabled by its morphology 78 comprising simultaneously a thin dielectric vein network, which contributes a large TE PBG, and the set of 4-fold shape dielectric particles, which contributes a large TM PBG. If the filling ratio is further decreased, e.g. to 0.12, the veins are broken and the QC is no longer self-connected, leaving isolated square shape dielectric particles – not surprisingly, in this case the corresponding TE PBG is zero while the TM PBG is still around 20%. 4.3. Summary In conclusion, we computed and analyzed in detail the LDOS of two families of 2D photonic QCs, generated from level set equations and from quasiperiodic tiling patterns decorated with rods, for 3 different rotational symmetries (8, 10, and 12). We found that (1) for QCs comprising individual dielectric features, TM PBGs are largely impacted by the feature shape and feature inter-distance. QCs consisting of dielectric rods with uniform diameter, as produced by decorating quasiperiodic tiling patterns, exhibit better TM PBGs than QCs consisting of non-circular features, as typically obtained in structures produced from level set equations. (2) R-8mm, R-10mm and R-12mm QCs are found to exhibit large TM PBGs (above 45%), close to the TM PBG of the current champion structure (~50% for the R-p6mm), supporting the conclusion that their 79 PBG properties are dominated by Mie resonances of the individual dielectric domains, with only a small impact from the particular rotational symmetry. (3) the TE PBGs of QCs investigated here are found to be very small (below or around 10%), except for the case of the AR-12mm QC where we find a very large TE PBG (56.5% at f = 0.32 ), which is only slightly lower than the champion TE PBG size (the honeycomb structure has a TE PBG ~ 60% for ε1 ε 2 = 13.0 at f = 0.2 ). The AR-12mm structure has a large amount of structural motifs of honeycomb veins and square veins, which are associated with the large TE PBG observed; (4) the AR-12mm QC is also found to have a large, complete PBG (19.8%) at f = 0.18 . In this case, the corresponding morphology consists of “ninja star” like dielectric domain motifs, with an “effective” particle in the center and interconnected veins radiating around the particle core, enabling formation of both TE and TM gaps; (5) the DOS maps provide detailed information about PBG properties obtained from different QC morphology design choices (symmetry, dielectric shapes, filling ratios, and structure morphology). The optimized QCs which have the largest PBGs are listed in Table 4.1, which enables direct comparison of the PBG properties of this large set of QCs, and provides useful guidance for further photonic QC device design and optimization. 80 Chapter 5 Structure-photonic properties correlation via statistical approach 5.1. Introduction Here we demonstrate a novel quantitative procedure to pursue statistical studies on the geometric properties of photonic crystals and photonic quasicrystals (PQCs) which consist of separate dielectric particles. The geometric properties are quantified and correlated to the size of the photonic band gap (PBG) for wide permittivity range using three characteristic parameters: shape anisotropy, size distribution, and feature-feature distribution. Our concept brings statistical analysis to the photonic crystal research and offers the possibility to predict the PBG from a morphological analysis. Topology optimization procedures for photonic crystals [112] and PQCs [128] have been developed to achieve premier PBG properties. However, the physical meanings behind the numerical optimization procedures have not been revealed and the detailed role of the particular geometric factors on determining the PBG size has not yet been clearly identified. 81 In this Chapter, we demonstrate a statistical analysis on the geometric properties of 2D photonic structures. Three geometric parameters (shape anisotropy parameter, size distribution parameter, and feature to feature distance distribution parameter) are identified to have strong correlation with the associated PBGs. 5.2. Statistical analysis on the structural morphologies Five periodic photonic crystals (Figures 5.1a through 5.1e) and 12 PQCs (Figures 5.1f through 5.1q), all with the same filling ratio ( f = 0.18 ), are analyzed. This particular filling ratio is selected in order for those structures to have large transverse magnetic (TM) PBGs. The structures are chosen to cover a wide range of morphologies and rotational symmetries (2, 4, 6, 8, 10, and 12-fold) to effectively represent the various types of 2D PBG structures. Structures in Figure 5.1(a) through 5.1(e) are made by placing rods on a periodic lattice. The characteristic length scale d 0 is the lattice constant. Structures in Figure 5.1(f) through 5.1(k) are made by placing rods or ovals on the vertices of the 8-fold, 10fold, and 12-fold quasicrystal tilings generated by projection into 2D from a higher dimensional space. The characteristic scale d 0 is the distance between the central 82 particle at rotational symmetric axis and its neighbor particles. PQCs in Figure 5.1(l) through 5.1(q) are defined by the following level set equation [145, 146]: N-1 f(x, y) = ∑ cos ⎡⎣ 2πxcos(πn N) d0 +2πysin(πn N) d0 +φ ⎤⎦ (5.1) n=0 Here f(x, y) is a numerical landscape in the 2D plane which assigns a value to the general point with coordinate (x, y) . In equation (5.1), d0 is the characteristic length scale of the PQCs. If f ( x , y ) > t , position ( x , y ) is occupied by material; if f ( x , y ) < t , position ( x , y ) is occupied by air. Here t is a parameter which can be tuned to change the filling ratio of the resultant structure. The PQCs have Fourier transform patterns with 2N-fold rotational symmetry. 83 Figure 5.1: the 17 photonic structures examined. The structure index is shown above each figure. Here R stands for rods; O stands for oval; LS stands for level set equations and the rotational symmetry of the associated PQC is 2N. (a): rods in a triangular lattice; (b) rods in a triangular lattice, the rods have two area values: 1.2A and 0.8A ; (c) rods in a triangular lattice, the rods have two area values: 1.4A and 0.6A ; (d) rods in a square lattice; (e) rods in a parallelogram lattice; (f) through (h): QCs from placing rods in 8mm, 10mm, 12mm QC tilings; (i) through (k): QCs from placing ovals in 8mm, 10mm, 12mm QC tilings; (l) through (q) QCs from level set equations. The values in the end of the structural index ( 0π , 0.25π , 0.5π , 0.75π , 1π ) stand for ϕ values. For N=4, all ϕ values lead to the same structure, therefore there is no ϕ value at the end of the structural index. 84 A large TM PBG is usually found in 2D structures consisting of separate dielectric particles and it is recognized that the particle resonances, which correspond to the peaks of the scattering cross section (SCS) [140], lead to the formation of the TM PBG [137, 140-144]. If the optical wave frequency is slightly higher than the first resonance frequency of the particle, the transmitted wave passing through the particles is anti-phase with the incoming wave, which leads to destructive interference and the reflectance of the incoming optical wave [140]. Resonance is believed to be the main physical reason for the formation of the TM PBGs for frequencies falling between the first and second resonance frequencies [140]. Such TM PBGs are rather insensitive to the positional disorder of the particles [141, 142]. Next, we provide a statistical analysis on the features of the PBG structures shown in Figure 5.1 and select three important geometric parameters which strongly influence the corresponding TM PBG. The first parameter is the shape anisotropy parameter ( α ). The particle shape brings strong impact on the scattering properties; therefore it is highly related to the TM PBG. For a typical non-circular particle, we can define the averaged radius: r = A π , here A is the area of the particle. For an arbitrary point on the surface of the particle, rG denotes G the vector from the center of mass to the surface point. Δr = r − r indicates the 85 deviation of the particle shape from the isotropic circular shape. For circular shape particle, Δr equals zero at all surface points. The normalized integration of Δr over the particle i is: Q = v∫∂S Δri2 ds Si ri (5.2) Here Si is the perimeter of the particle i and ∂S is the particle surface. The shape anisotropy factor α is defined by the averaged Q for the PBG structure: M α = ∑ ( v∫ ∂s Δ ri2 ds Si ri ) M (5.3) i =1 Here M is the total number of particles. For the structures investigated, we choose a fundamental domain with M M ~1000; ∑ is the sum for all i=1 M particles. The larger the α parameter, the more the particle shape deviates from the circular shape. A non-circular dielectric feature has different scattering cross section for waves incident from different angles, which is disadvantageous to achieve wave propagation suppression for all in-plane directions; therefore a larger value of α leads to a lower TM PBG consistent with the observation that the structures comprised of circular elements are found to open larger TM PBGs than the structures consisting of non-circular elements [128]. 86 The size of the particle determines the resonance frequency ( f ∝ 1 r ). The second structural characterization factor β is the standard deviation of the areas of the particles: M β = ∑ ( Ai − A)2 (M −1) A i =1 (5.4) Here A is the averaged area of the M particles. A larger β indicates a more polydisperse particle size distribution. Particles with various sizes correspond to different resonance frequencies, which are disadvantageous for uniform and isotropic wave propagation suppression; therefore a larger β leads to a lower TM PBG. Lastly, the neighbor-neighbor particle distribution is important because optical wave confinement, which is an important property of PBG, is a local effect. For every particle P0 , there are a group of n neighboring particles ( P1, P2.....Pn ) with particle to particle distance d0<−>i < 1.5d0 . Here d 0<−>i is the distance between the particle P0 and the particle Pi , and d 0 is the characteristic length scale for the structure defined previously. 1.5d 0 is selected as the criterion to identify whether two particles are neighbors. The normalized deviation of the particleneighbor particle distance for particle i is: 87 X= ni (5.5) ∑ (di <−> j − d 0 )2 (ni − 1) d 0 j =1 We define the third factor, γ , to represent the averaged X for the associated PBG structure: M ni i =0 j =1 γ = ∑ ∑ (di<−> j − d0 )2 (ni −1) Md0 (5.6) Here ni is the number of neighbor particles of particle Pi . A larger γ indicates a more poly-disperse neighbor particle distance distribution and lower local positional order. Loss of short range order is disadvantageous for coherent scattering and the isotropic local confinement of EM wave is hard to achieve due to the leakage from a non-uniform neighbor particle distribution; therefore a large γ leads to lower TM PBG. According to the above analysis, all three factors bring strong impact on the TM PBG size. We define an overall morphological factor ( q ) as a linear combination of three geometric factors: M M i=1 i=1 q = cα ∑ ( v∫∂s Δri2 ds Siri ) M + cβ ∑ ( Ai− A)2 (M −1) A M ni i=0 j=1 +cγ ∑ ∑ (di<−> j −d0)2 (ni−1) Md0 = cα α + cβ β + cγ γ 88 (5.7) Here cα , cβ and cγ are positive weighting coefficients for the geometric factors, which are functions of permittivity contrast ratio. Next, we calculate the individual geometric factors of the 17 structures and the associated TM PBGs for three permittivities: (1) silicon/air contrast ratio ( ε : ε 2 (ε :ε 2 1 = 11.4 : 1 ), 1 = 13 : 1 ); (2) GaAs/air contrast ratio and (3) silicon nitride/air contrast ratio ( ε : ε 2 1 = 4 : 1 ). The size of PBG is determined from the local density of states calculated via finite-difference time-domain (FDTD) method. The geometrical parameters of the 17 structures and the associated TM PBGs are shown in Table 5.1. According to the data, we propose a simple linear model to correlate the TM PBG and the overall geometrical factor: PBG size = Δω ω = b − kq For ε : ε 2 1 = 13 : 1 , values of cα = 0.97 , c β = 1.03 (5.8) , and cγ = 0.5 lead to the best correlation: the correlation coefficient ( R ) equals 0.95. The slope ( k ) in equation (5.8) equals 0.3 and the intercept ( b ) equals 0.46. For ε cα = 0.31 , cβ = 0.64 b = 0.45 . For ε : ε correlation: 2 1 , and = 4 :1 , R = 0.85 , cγ = 0.5 lead to the best correlation: values of k = 0.98 2 and cα = 0.05 , c β = 0.21 , b = 0.246 and : ε 1 = 11.4 : 1 , values of R = 0.94 , k = 0.58 cγ = 0.5 and lead to the best . From inspection of the weighting coefficients, the most important parameter at high refractive index contrast is the 89 standard deviation of the particle area distribution ( β ) while the particle distribution factor γ is the most important parameter at low refractive index contrast. The PBGs of the structures are plotted as the black squares in Figure 5.2 and the lines in Figure 5.2 are the linear models from equation (5.8). For ε 2 : ε 1 = 13 : 1 , the TM PBG sizes of the structures deviate less than 3.1% gap size from the linear relation. For ε 2 : ε 1 = 11.4 : 1 , the deviation is less than 4.5% gap size. For ε 2 : ε1 = 4 : 1 , the deviation is less than 6.0% gap size. Figure 5.2 indicates that the overall geometric factor q and the TM PBG size are related as the trend that PBG size decreases with increased q as expected. Figure 5.2: the relationship between the overall geometric factor q and the size of TM PBG for three permittivity contrasts. 90 Structure: α β γ 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.20 0.20 0.20 0.17 0.16 0.18 0.19 0.19 0.18 0.00 0.00 0.00 0.20 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.23 0.40 0.25 0.16 0.18 0.28 0.00 0.18 0.17 0.00 0.00 0.12 0.17 0.14 0.12 0.17 0.14 0.15 0.16 0.14 0.13 0.11 0.11 PBG(%) q PBG(%) PBG(%) Q 45.13 0.00 49.32 0.00 36.67 0.14 40.95 0.09 37.53 0.13 42.55 0.085 37.27 0.28 41.56 0.206 27.82 0.56 30.71 0.412 R - 6mm - 0.4ΔA 44.27 0.09 44.80 0.06 R -8mm 43.0 0.13 44.38 0.085 R -10mm 42.2 0.11 45.00 0.07 R -12mm 33.3 0.48 35.50 0.254 O - 8mm 37.0 0.52 37.55 0.279 O - 10mm 36.9 0.51 38.43 0.264 O -12mm 30.1 0.77 34.80 0.4768 LS_N = 4 22.2 1.00 27.70 0.6472 LS_N = 5_φ = 0π 27.8 0.81 30.21 0.5021 LS_N = 5_φ = 0.25π 29.0 0.70 31.20 0.4141 LS_N = 5_φ = 0.5π 30.1 0.71 34.10 0.4247 LS_N = 5_φ = 0.75π 32.1 0.84 32.80 0.518 LS_N = 5_φ = π Table 5.1: the geometric factors and the size of PBGs. α , β , γ are three geometric factors. R - p6mm R - p4mm R - p2 R - 6mm - 0.2ΔA 22.06 9.88 16.43 20.26 16.52 21.47 19.93 19.38 17.64 13.33 17.77 12.93 5.57 9.86 12.98 15.46 16.05 q 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.1 0.1 0.1 0.1 0.1 The overall factors q for three permittivity contrasts is also shown. In Figure 5.2, PCs and PQCs consisting of uniform circular rods (R-p6mm, 8mm, 10mm, and 12mm) have zero shape anisotropy parameter ( α = 0 ) and zero standard deviation of area ( β = 0 ). Therefore they have low overall factors. Further, circular particles lead to strong isotropic Mie resonance, therefore they have large PBGs and occupy up left corner of the figure. If R - p6mm - 0.2ΔA structure in Figure 5.1(b) and the A− A ≠ 0 , such as occurs for the R - p6mm - 0.4ΔA structure 5.1(c), the PBG size decreases as the area deviation increases. 91 in Figure Compared to PQCs consisting of rods, PQCs consisting of ovals (O-8mm, O-10mm, and O-12mm) have a higher overall factor q because of the non-circular features. The optical paths along the long axis ( nd long ) and the short axis ( nd short ) of the oval feature are different, which leads to an anisotropic resonance condition. Therefore they have smaller TM PBGs and occupy the middle area in Figure 5.2. PQCs defined by level set equations, according to Figure 5.1(l) through 5.1(q), have non-circular features ( α > 0 ), non-uniform particle area distribution (β > 0 ), and non-uniform neighbor particle distance distribution ( γ > 0 ). This leads to high overall morphological factors and low TM PBGs. Therefore these structures occupy the bottom right corner in Figure 5.2(a) and Figure 5.2(b). As refractive contrast decreases, the PBG sizes of the structures also decrease. PQCs are more robust compared to photonic crystals though they do not exhibit higher PBGs than photonic crystals. For high permittivity contrast, a noticeable case is LS_N = 5_φ = 0π : the particle area distribution is highly polydisperse ( β = 0.4 ), so the expected lowest TM PBG, which is supposed to be between the first and the second resonance frequencies [140, 144], is destroyed by leaky modes and the actual lowest TM PBG for this structure is between the second and the third 92 frequencies. Due to this shift toward higher frequency, the size of TM PBG is relatively lower than other LS-QCs. In the above discussion, we focused on the lowest PBG, which is usually the largest PBG for 2D photonic crystals. Among the 17 structures investigated, the structure of the triangular lattice ( R - p6mm ) is an interesting photonic crystal device platform due to its large PBG. Next we use geometrical factors to predict the impact of possible experimental errors on the size of TM PBG. For example, we introduce a random deviation of particle area ( A = A ± δ A ) to the R - p6mm structure with permittivity contrast ε 2 : ε 1 = 13 : 1 . The decrease of photonic band gap due to the experimental fabrication error δ A can be estimated using the prediction based on the associated geometrical factors and the linear approximation in equation (5.8). For δ A = 0.1A , the PBG size is predicted to be 43% and the FDTD simulation indicates that the actual PBG size is 46%. For δ A = 0.2A , the PBG size is predicted to be 39.8% and the FDTD simulation indicates that the actual PBG size is 42%. For δ A = 0.3A , the PBG size is predicted to be 36.7% and the FDTD simulation indicates that the actual PBG size is 34.6%. Next, we introduce three kinds of perturbations to the R - p6mm structure: in addition to the particle area deviation ( δ A = 0.2A ), every particle has 40% probability to have its center shifted from the 93 original coordinate ( x, y ) to ( x ± δ x, y ± δ y ) ; here δ x, δ y = 0.14d0 . Also, we assume the particle shape deforms to be oval with aspect ratio d long / d short = 1.5 and random orientation. Such a distorted structure has an overall factor ( q ) of 0.385 and the PBG size is predicted to be 34%. The FDTD simulation indicates that the actual PBG size is 31.9%. All 4 tests above show that the actual PBG sizes deviate from the predictions based on geometrical factors less than 4% PBG size. Our concept of developing a statistical parameter related to the structural geometry can be extended to 3D although in order to be self supporting, dielectric/air structures need to have the dielectric regions connected. For resonance dominant TM gap formation, a "tight binding" structure is necessary, requiring thin connecting "bonds" between the larger dielectric nodes. The q factor in 3D will then be related to variations in the shape, sizes and distances of the nodes as well as the overall isotropy of the structure. 5.3. Summary In conclusion, we employed a novel statistical procedure to correlate the geometric properties of 17 PBG structures and their TM PBG sizes. Based on our 94 analysis, to achieve a photonic crystal with a large TM PBG, one needs separate circular particles with uniform distribution. The physical meaning of the interesting optimization procedures proposed before [112, 128] are revealed: the PBG optimizations, which are done numerically by tuning the coefficients of level set equations [128] or the gradient-based algorithm known as topology optimization [112], are essentially tuning the particle shape to the near-circular shape ( α ≈ 0 ) and reaching a uniform particle distribution with nearly the same neighbor particle distance ( β ≈0 and γ ≈ 0 ). 95 Chapter 6 A searchable database for micro- and nano-structures 6.1. Introduction Periodic micro- and nano-structures are of importance in a variety of fields, including photonic crystals [31, 97], phononic crystals [160, 161], data storage devices [162, 163], fuel cells [164], microfluidics [165], biosensors [166], tissue engineering [167, 168], optical devices [169], impact absorption micro-trusses [170], plasmonic metamaterials [171], and energy applications including solar photovoltaics [172]. Though there are extensive ongoing investigations on functional micro and nano periodic structures, there is at present no system to comprehensively classify, store, process, and analyze the various functional structures that are continually emerging from these exciting research areas. Structure database system has been established for proteins [173-175], chemicals [176], crystal structures [122, 177, 178], minerals [119, 179], biotechnology information [180], standard references [181], and drug designs [182]. In this chapter, we propose a database system which incorporates various functional micro- and nano-structures. The database connects the morphologies, fabrication technologies, and physical properties of the functional structures. The 96 advantages of the database system include: (1) enabling the design of experiments for fabricating a given target structure; (2) finding the structure with an extremized objective function; (3) analyzing the impact of morphology on various physical properties. 6.2. The protocol to process structures in the database A periodic structure can be represented by a unit cell function S ( x, y , z ) . S ( x, y , z ) = i if the material i occupies position ( x, y , z ) within the unit cell of the periodic structure. If S ( x, y , z ) is directly stored, a large amount of storage space is required. For example, if the unit cell is meshed to 1000 × 1000 × 1000 grids, a single structure requires 240MB of storage space. A database consisting of one million structures would then need 2.4 × 105 GB of storage. To reduce the storage space, we take advantage of the periodicity of the structures: since all periodic structures can be described by a set of Fourier components, a small set of Fourier expansion coefficients of S ( x, y , z ) can be used to efficiently represent the structures. The structural unit cell function S ( x, y , z ) can be expressed as: S ( x, y, z ) = ∑a lmn l ,m, n cos(lπ x d x + mπ y d y + nπ z d z ) + ∑ blmn sin(lπ x d x + mπ y d y + nπ z d z ) l ,m,n 97 (6.1) Here d x , d y , d z are the periodicities of the structure along the x, y, z directions. We select one hundred Fourier coefficient groups which have the largest values of 2 2 almn + blmn to represent a given structure. The choice of the number of Fourier coefficient groups is a tradeoff between storage space, calculation time and structural description accuracy. Using our approach, the storage of one structure only needs 10kB and therefore a database consisting of one million structures only occupies 10 GB, which can be stored in a personal computer (PC) or ordinary external hard drive. The morphologies of human-made and naturally occurring periodic structures are unlimited. Thus any reasonably comprehensive database will be gigantic; therefore an efficient classification scheme for the database is necessary. We categorize the functional structures according to their symmetry using the seven crystal systems, 32 point groups and 230 space groups. Because of Neumann’s principle: that the macroscopic physical properties of any periodic structure have at least the symmetry of the structure, this scheme also helps researchers search for certain properties. The database is classified into a tree structure which is shown in Figure 6.1. 98 Figure 6.1: the database is classified to a tree structure according to the symmetry of the periodic structures. 6.3. Inverse design of experiments to fabricate target structures The vast applications of micro- and nano-structures have motivated the development of multiple fabrication techniques, ranging from bottom-up approaches including polymer phase and micro-phase separation [183, 184], molecular self-assembly [185], and colloidal self-assembly [186] to top-down 99 approaches including phase mask lithography [187-190], interference lithography [191-193], multiple-exposure interference lithography [194], electron-beam lithography [195], and Helium beam lithography [196, 197]. Each technique has its own particular group of ever growing accessible structures. By integrating various simulation results and actual experiments, we aim to establish a database comprised of a library of these mesoscale 3D and 2D periodic structures and their corresponding fabrication techniques and fabrication parameters. The structural length scale and material compositions are also included in the database structures. The database can indicate which kinds of structures can be fabricated using existing technologies. One important function of the database is to assist in the experimental design of the fabrication of a structure with particular morphology. After a database user uploads the target structure in various formats such as CAD images, level set equations, and Fourier coefficients, an automated program is used to both process the target structure (extract Fourier coefficients) and to compare it with the stored structures in the database. The most similar structures are selected and their 100 corresponding fabrication parameters are the output. Our method is schematically shown in Figure 6.2. Figure 6.2: the schematic of the database system incorporating structures uploaded by researchers. A user can upload a target structure which will be compared with the database structures. The most similar database structure is output with structural information such as experimental fabrication method and physical properties. In our method, we need to estimate the similarity of the target structure to the structures in the database. The similarity of two objects is normally judged visually and by one’s experience. To be more precise, we define the following similarity function P to quantify the correspondence between a database structure and the target structure: 101 P= ∑ (a lmn − a0 lmn ) 2 + l ,m ,n ∑ (b lmn − b0 lmn ) 2 (6.2) l ,m ,n Here almn , blmn are Fourier coefficients of a particular database structure and a0 lmn , b0 lmn are Fourier coefficients of the target structure. However, the unit cell function S ( x, y , z ) is not uniquely defined because the origin of the coordinate system is arbitrarily chosen; thus we need to calculate P for different origin definitions and select the smallest value of P to represent the closest similarity of the candidate structure and the database structure. In order to minimize additional computation we follow the convention of the International Tables for Crystallography: the origin of the coordinate system is the site of the highest symmetry of the space group. From equation (6.2), the similarity function P is a positive value, the smaller the similarity function; the closer the two structures. A value of P = 0 indicates that two structures are essentially the same. An example of the similarity function is shown in Figure 6.3. According to our experience (we employ one hundred Fourier coefficients to define a structures), if P < 0.01 , the two structures are visually the same; if P < 0.1 , the two structures are only slightly different; if P > 0.3 , the two structures are obviously visually different. 102 Figure 6.3: two examples of the variation of the similarity function and the visual appearance of a particular structure and the target structure. (a). The structures are defined by the diamond family approximation level set equation: F ( x, y, z ) = cos ( 2π x ) cos ( 2π y ) cos ( 2π z ) + cos ( 2π x ) sin ( 2π y ) sin ( 2π z ) + sin ( 2π x ) cos ( 2π y ) sin ( 2π z ) + sin ( 2π x ) sin ( 2π y ) cos ( 2π z ) = t The target structure corresponds to t = 0 . The structure similarity function ( P ) increases as the structure deviates from the target structure. (b): the target stucture is defined by the simple cubic surface approximation: F ( x, y , z ) = cos ( 2π Qx ) + cos ( 2π Qy ) + cos ( 2π Qz ) = 0 The target structure corresponds to Qtarget = 1 and ΔQ = Q − Qtarget . 103 For a PC with single 2.0GHz CPU, calculating the similarity function of the target structure and one database structure requires only about one second. By employing a 100 CPU server, the search time for a database of one million structures reduces to around two hours. Furthermore, the tree structure of the database avoids unnecessary computation: only the database structures which have the same symmetry as the target structure are needed to be visited during the search. After comparing the target structure with the database structures, a structure with Pmin is selected. If Pmin < 0.1 , we can assume that the structure is a close approximation of the target structure. Sometimes we have multiple sets of experimental parameters which all give Pmin < 0.1 . The user can then choose the structure with the most experimentally convenient set of fabrication parameters, for example, the highest contrast ratio ( I max I min ) in photolithography technology [191]. If Pmin > 0.1 , then additional corresponding experimental adjustments of the experimental parameters might be needed. By examining the structures in the database, users can observe the evolution of the structure as fabrication parameters change and decide on the adjustments. As the database evolves and new fabrication 104 technologies are realized, the chance to find database elements which precisely match a given target structure increases. Next, we illustrate how this approach can work by establishing a mini database for phase mask lithography [188, 198-200]. Here the task is to design a 2D periodic mask, located above a photoresist in the XY plane in order to fabricate a 3D targeted structure. When a coherent light source, such as plane wave, propagates along the Z direction and impinges on the mask, the incident light is reflected and diffracted such that an optical field pattern forms inside the photoresist, which can be used to fabricate 3D micro- and nano- structures. Compared to other techniques, phase mask lithography offers the advantages of fabrication over large areas with a very simple experimental setup [188, 190, 198]. However, the inverse design problem of phase mask lithography is challenging. We address this problem by creating a structural database consisting of phase mask lithography elements, to store phase mask lithography designs and their corresponding 3D periodic structures. We choose to explore the possibility to fabricate a layered photonic crystal structure [201]. The structure, shown in Figure 6.4, consists of alternating rod and 105 vein layers. It can be fabricated through layer-by-layer assembly [202], which is time-consuming and the structure size is limited. Therefore high throughput phase mask lithography, which can fabricate large area nanostructures (above cm 2 ) is designed to fabricate the structure. The target structure belongs to the tetragonal crystal system. The aspect ratio is d z d x, y = 1.09 and the filling ratio is 0.3. The target structure exhibits a large, complete photonic band gap (18% for silicon/air) and it is an excellent candidate for waveguide device [201]. Figure 6.4: the target photonic crystal structure with P4m2 symmetry. The enlarged unit cell is shown on the left. In phase mask lithography, there are three experimental parameters which strongly influence the morphology of the resulting structure: 1) the light source power ( I ). A higher laser power employed with a negative photoresist results in a higher filling fraction; whereas for a positive photoresist, the opposite occurs; 2) the depth of the phase mask surface profile ( h ). As h changes, the phase 106 modulation of the propagating light changes; 3) the symmetry of phase mask lithography system: the phase mask symmetry and the light source polarization. Each layer of the target structure has four-fold rotational symmetry in XY plane and the target structure has two-fold rotational symmetry; therefore we select circularly polarized light source to provide high rotational symmetry in XY plane. Further, we select the grating mask with two-fold rotational symmetry and the mask with four-fold rotational symmetry (posts on a square lattice). Those two phase mask patterns can be readily fabricated by nanoimprint lithography, interference lithography, and E-beam lithography. Based on these patterns, we select six phase masks with two layers [203] to create the database. The set of phase masks are shown in Figure 6.5. A different order stacking of the layers creates different phases between the diffracted beams from the first layer and the diffracted beams from the second layer. 107 Figure 6.5: six types of phase mask are investigated. Every phase mask consists of two layers each with the same thickness h . The layer can be a one dimensional grating or air posts on a square lattice in solid dielectric background. Here h , r1 and r2 are tunable parameters. The correct periodicity of the phase mask can be determined from the structural aspect ratio (see supplemental information). We choose light with λ = 810nm , a wavelength that is effective for two-photon lithography, which achieves a higher effective contrast ratio [199]. During the process of creating the mini database, structures are added to the database as we vary experimental parameters. If the variational step is too large, the resultant structures are too sparsely distributed and do not well represent all the structures available from the technique; if the variational step is too small, the neighboring structures are almost 108 identical and occupy unnecessary database storage space. A good selection of the variational step is that the neighboring structures should not be visually the same ( P > 0.1 ) but should be only slightly different ( P ≤ 0.3 ). The selected experimental parameter should be evenly distributed to cover all situations. For every phase mask, we pick three values for r1 and r2 : r1(2) d < 0.1 or r1(2) d > 0.9 , r1(2) d x , y = 0.27 , 0.54 and 0.81 because if the fabrication of the mask is difficult and the filling ratio of the resulting structures tends to be low. We pick three layer thickness values: h d x , y = 0.29, 0.58, 0.86 . We choose h d x , y < 1 to avoid high phase mask aspect ratio. The light source powers have ten levels to cover wide filling ratio range. Therefore every binary layer phase mask corresponds to 270 experimental designs. The minidatabase we construct thus has 1620 structures. We next calculate the similarity function between the target structure and the database structures. It takes a personal computer around thirty minutes to locate the minimum similarity function Pmin = 0.23 . The experimental design is: phase mask (3), d x , y = 520nm , h = 150nm , r1 = 420nm , r2 = 420nm , Ithres I = 0.75 . To further reduce the similarity function, we tuned the parameters and make a small database of 270 elements based on phase mask h = 120nm, 135nm, 150nm, 165nm, 180nm, 195nm 109 , (5). Here we choose r1(2) = 360nm, 420nm, 480nm , and I thres I = 0.65, 0.7, 0.75, 0.8, 0.85 . Then we calculate the similarity function between the target structures and database structures. The minimum similarity function is now Pmin = 0.219 . The new experimental design is: phase mask (3), d x , y = 520nm , h = 195nm , r1 = 420nm , r2 = 420nm , Ithres I = 0.8. The comparison between the target structure and the structure from experimental design is shown in Figure 6.6. Figure 6.6: photonic crystal structure with P4m2 space group. Comparison of the optimal phase mask fabricated structure (left) and the target structure (right). The skeletal graph of the target structure is shown in blue. The key 4 fold rotoinversion, diagonal mirror with perpendicular 2 fold rotation symmetries are captured in the phase mask structure using circularly polarized incident radiation. 6.4. Discussion To design structures with extremized physical properties is quite challenging and attracting [204]; for example, finding the photonic crystal with the largest photonic band gap [128, 205], or a microtruss with the maximum ratio of Young’s 110 modulus to density ( E ρ ), etc. If a physical property can be calculated from the structural morphology, it can be included as a structure element in the database. A comprehensive database, which incorporates hundreds of thousands of structures fabricated by various techniques, is an excellent reservoir to find a candidate structure with an extremized physical property. Furthermore, we can analyze the impact of changes in symmetry on the physical property by comparing the properties of structures residing in different symmetry branches of the database. Some functional mesostructures are non-periodic. If a functional structure has finite size, it can be assumed periodic by employing periodic boundary conditions. If a functional structure has unlimited size, for example, a photonic quasicrystal [104], a representing portion of the structure can be assumed as the unit cell and periodic boundaries are employed. Although the database is designed for periodic structures, non-periodic structures can also be included. For a functional mesostructure, if there is a way to link the fabrication parameters and the physical properties with the structure, it can be incorporated in the database. Given the fast development of nanotechnology, any comprehensive database will be gigantic. Constructing such a large database which contains 111 functional structures fabricated from various technologies would need a worldwide cooperation. The continual update and maintenance of the database would involve a sustained effort. If a user has a target structure in mind for a desired function, an automated program will search the database and locate structures that are the most similar to the target structure and output their fabrication. If a user does not know the target structure but specifies a desired physical property, the database can be used to find various candidates and even the optimal structure and output the design methodology. We hope that initiating such a system will strengthen world-wide scientific cooperation. 6.5. Summary We have developed a database system to efficiently classify, store, analyze and compare micro- and nano-structures. A multi-functional database incorporates a large number of natural and human made structures uploaded by contributors. High throughput experimental design and structural property analysis can be achieved using the database system. After a target structure is assigned by the user, a high throughput numerical engine compares the target structure with the structures inside the database and outputs the most similar database structure with associated experimental design and physical properties. The proposed database 112 incorporating millions or even billions of structures could be accessed through a public website, which is maintained and updated via a worldwide cooperation. 113 Chapter 7 Elastic wave modeling 7.1 Finite-difference time-domain modeling of elastic waves Controlling elastic waves have a wide range of engineering applications, such as acoustic cloaking [15], acoustic imaging [37, 38], seismic wave sensing [39, 40], opto-acoustic interaction [41, 42], and sub-wavelength imaging [206]. The theoretical modeling is indispensable in the development of phononic crystals and acoustic metamaterials. Here we discuss a finite-difference timedomain (FDTD) approach to model the propagation of acoustic waves. In the elastic range, the equation of motion is: ∂ 2ui ρ 2 = τ ij , j + f i ∂t (7.1) Here ρ is the density of the material, u is the displacement of the material, τ is the stress, and f is the body force applied to the material. We assume f = 0 and adopt the Einstein notation: τ ij , j = ∂τ i1 ∂τ i 2 ∂τ i 3 + + ∂x1 ∂x2 ∂x3 114 (7.2) The sub-indices i and j indicate the directions of the displacement, stress, and strain. Here we use a Cartesian coordinate system, and 1, 2, 3 ( x1, x2 , x3 ) refer to the X, Y, and Z directions, respectively. For fi = 0 , equation (7.1) can be expressed as: ∂ 2u1 ∂τ11 ∂τ12 ∂τ13 = + + ∂t 2 ∂x1 ∂x2 ∂x3 (7.3) ∂ 2u2 ∂τ 21 ∂τ 22 ∂τ 23 ρ 2 = + + ∂t ∂x1 ∂x2 ∂x3 (7.4) ∂ 2u3 ∂τ 31 ∂τ 32 ∂τ 33 = + + ∂t 2 ∂x1 ∂x2 ∂x3 (7.5) ρ ρ Equations (7.3) through (7.5) can be further rewritten as: ∂v1 ∂τ 11 ∂τ 12 ∂τ 13 = + + ∂t ∂x1 ∂x2 ∂x3 ∂v ∂τ ∂τ ∂τ ρ 2 = 21 + 22 + 23 ∂t ∂x1 ∂x2 ∂x3 ∂v ∂τ ∂τ ∂τ ρ 3 = 31 + 32 + 33 ∂t ∂x1 ∂x 2 ∂x 3 ρ (7.6) (7.7) (7.8) Here vi is the velocity along the direction i . Next we discuss how to express the stress τ ij in terms of the displacement. The constitutive law for a general material is τ ij = Cijkl ε kl C ijkl (7.9) is a fourth rank elastic tensor and has 81 components. Due to the symmetry of this system, τ ij = τ ji and ε kl = ε lk . The above facts lead to a simplified expression ( 6 × 6 matrix CIJ ) for the fourth rank elastic constant tensor C ijkl : 115 Cijkl ⎛ C11 C12 ⎜C ⎜ 21 C22 ⎜C C32 = C IJ = ⎜ 31 0 ⎜ 0 ⎜ 0 0 ⎜ 0 ⎝ 0 C13 C23 0 0 0 0 C33 0 0 C44 0 0 0 0 0 0 C55 0 0 ⎞ 0 ⎟⎟ 0 ⎟ ⎟ 0 ⎟ 0 ⎟ ⎟ C66 ⎠ (7.10) For isotropic structures (cubic crystal system), there are only 3 independent parameters. For transverse isotropic structures (tetragonal crystal system), there are 5 independent parameters. For anisotropic structures (orthotropic crystal system), there are 9 independent parameters. Here the sub-indices I , J = 1, 2, 3, 4, 5, 6 represent xx , yy , zz , yz , xz , xy respectively. Inserting equation (7.10) into equation (7.9) leads to: ∂τ 11 ∂t ∂τ 22 ∂t ∂τ 33 ∂t ∂τ 23 ∂t ∂τ 13 ∂t ∂τ 12 ∂t ∂v1 ∂v ∂v + C12 2 + C13 3 ∂x1 ∂x2 ∂x3 ∂v ∂v ∂v = C21 1 + C22 2 + C23 3 ∂x1 ∂x2 ∂ x3 ∂v ∂v ∂v = C31 1 + C32 2 + C33 3 ∂x1 ∂x 2 ∂ x3 ∂v ∂v = 0.5 × C44 × ( 2 + 3 ) ∂x3 ∂x2 ∂v ∂v = 0.5 × C55 × ( 1 + 3 ) ∂x3 ∂x1 ∂v ∂v = 0.5 × C66 × ( 1 + 2 ) ∂x2 ∂x1 = C11 (7.11) (7.12) (7.13) (7.14) (7.15) (7.16) For homogeneous isotropic solids: C44 = C55 = C66 = 2G = 116 E (1 +ν ) (7.17) C12 = C21 = C23 = C32 = C13 = C31 = C11 = C22 = C33 = Here E is the Young’s modulus, G νE (1 +ν )(1 − 2ν ) (1 −ν ) E (1 +ν )(1 − 2ν ) (7.18) (7.19) is shear modulus, and ν is Poisson’s ratio. For fluidic materials: C44 = C55 = C66 = 0 C11 = C12 = C13 = C21 = C22 = C23 = C31 = C32 = C33 = K τ 11 = τ 22 = τ 33 = − p Here K is the bulk modulus of the fluid and (7.20) (7.21) (7.22) p is the pressure. Equations (7.6) through (7.8) and equations (7.11) through (7.16) are then greatly simplified: ρ ∂v1 ∂p = ∂t ∂x1 (7.23) ρ ∂v2 ∂p = ∂t ∂x 2 (7.24) ρ ∂v3 ∂p = ∂t ∂x3 (7.25) ∂v ∂v ∂v ∂p = −K ( 1 + 2 + 3 ) ∂t ∂x1 ∂x2 ∂x3 (7.26) After the above mathematical transformation, the governing equations for elastic waves in fluids (acoustic waves) become linear partial differential equations which are readily solved. Here we give an exemplary simulation result: 117 Figure 7.1: (a): a solid rectangular plate vibrates in water along the x direction. The vibration frequency is 1.43Hz and the vibration follows the sinusoidal function: U x = sin(2π ft ) . (b) the pressure ( p ) distribution in the water after the plate vibrates for 3.5 seconds; (c) the displacement along y direction ( u y ); (d) the displacement along x direction ( ux ). Next, we test the computation method by comparing our results with the results from previous reference [207]. We calculate the local density of states (LDOS) for an elastic wave propagating in a 10-layer woodpile phononic crystal consisting of PMMA and air. The unit cell of the woodpile structure is shown in Figure 7.2. It is periodic along X and Y directions with periodicity a0 . According to LDOS, a phononic band gap along the Z direction between 0.6ωa 0 2πcair and 118 1ωa 0 2πcair exist, which matches very well with the result calculated from the finite element method [207]. Figure 7.2: LDOS for a phononic wave propagating along Z direction. The 10-layer woodpile structure is periodic in X and Y directions, and we show only one unit cell here. The green part of the structure is PMMA. Here c air is the sound velocity in air. 119 Chapter 8 Summary and future directions The last section reviews the main accomplishments of this thesis, and lists future directions of our research. 8.1 Overview of research accomplishments 1). Optical force and optical torque computation (Chapter 2) Using the three dimensional finite-difference time-domain (FDTD) and the Maxwell stress tensor, we calculated the radiation force and optical torque from optical lattices on various types of particles. We find that the optical force from optical lattices is a function of particle refractive index, size, shape, orientation, and the detailed morphology of optical lattice (equation 2.20). Absorption generally leads to smaller optical forces. The optical force reaches the maximum when the size of particle is around the period of the optical lattice. To form stable optical traps for polystyrene particles ( n = 1.58 ), the energy density of the optical lattice should be at or above 5mW μ m 2 . For particles near to a spherical shape or with a size much smaller than the period of the optical lattice, the optical torque is small compared to particles with size comparable to the period of the optical lattice and large aspect ratio. Both metastable and stable equilibrium orientation states exist for cylinder particles in the one dimensional optical lattice. 120 2). Optical devices on a chip (Chapter 3) Photonic crystal devices have demonstrated unique properties that enable wavelength-scale optical devices with ultra-high energy efficiency [31, 98, 208]. In Chapter 3, we developed a novel 2-pattern photonic crystal that offers the unique ability to integrate optical devices for different polarizations (TM, TE or both) on the same plane. Using these 2-pattern photonic crystals, we have further designed devices that can bend, split, couple, and filter TM/TE waves simultaneously [4]. These devices include a wavelength-scale polarizer, a low crosstalk circuit and a high-Q resonator for both TM and TE waves. Our work provides an important step towards absolute on-chip optical wave control by offering a versatile platform that can realize a wide range of important optical devices. 3). Photonic quasicrystals (Chapter 4) The ability of photonic crystals to mold the flow of optical waves is primarily due to the presence of a photonic band gap (PBG). Photonic quasicrystals demonstrate premier PBG properties at low refractive index contrast and therefore greatly expand the selection of suitable materials for photonic devices. Chapter 4 provides a comprehensive analysis of PBG properties of 558 two-dimensional (2D) quasicrystals (QCs). Importantly, we discovered two novel QCs, which have the best PBG properties to date [5]: a 12mm QC with a 56.5% TE PBG, the largest 121 reported TE PBG for an aperiodic crystal, and a QC comprising “throwing star”like dielectric domains, with near-circular air cores and interconnecting veins emanating radially around the core. This interesting morphology leads to a complete PBG of 20%. 4). Statistical analysis on structural morphology (Chapter 5) The size of the PBG in a photonic crystal device determines the quality of the device and the frequency range of waves that such a device can control. The fundamental formation mechanisms of PBGs in photonic crystals are not always clear, thus there is no general rule to design a given PBG. In Chapter 5, we develop a statistical approach for predicting band gaps of 2D photonic crystals and quasicrystals based on their morphology. The approach integrated knowledge from mathematics, scientific computing and physics to identify three geometric factors that correlate strongly with the size of PBG. This work helped elucidate the TM PBG formation mechanisms relevant to a given dielectric structure consisting of separated particles. 5). Searchable database of nanostructures (Chapter 6) Periodic nanostructures have a wide range of applications including fuel cells, photonic/phononic crystals, data storage devices and tissue engineering. As 122 new structural forms emerge, there is a need for a unified system to classify and store, as well as allow researchers to process and analyze these structures. In Chapter 6, we report the development of a database system to connect the morphologies, fabrication techniques and some physical properties of a library of two- and three-dimensional periodic structures. The system is empowered by an automated algorithm to efficiently store and compare structures (a database of one million structures requires only 10GB of storage and 2 hrs of searching based on 2011 IT technology). Users of this system input target structures, and the algorithm analyzes the target and compares it with structures in the database to output the fabrication parameters and physical properties of the most similar structure. 8.2 Future research directions Future research direction (1): 2-pattern photonic crystal fabrication In Chapter 3, we proposed a new set of photonic crystal devices based on 2pattern photonic crystals. Two advantages of 2-pattern crystals are the following: 1) the 2-pattern photonic crystals are reasonably tolerant of possible experimental errors, including variations of air gaps between dielectric regions. For example, we introduced a 40% random variation in the diameter of the rods ( r = r0 ++r0 , here + r0 is a random value between [ −0.4r0 , 0.4r0 ] ) and 40% random 123 variation in the thickness of the honeycomb walls ( h = h0 ++h0 , here +h0 is a random value between [ −0.4h0 , 0.4h0 ] ) to the rod-honeycomb structure, and the complete PBG is still large (16% for ε 2 : ε1 = 11.4 :1 , compared to the 20.4% PBG of the 2pattern photonic crystal without defects). Furthermore, we also introduced 30% G G G G random variation in the positions of rods ( r = r0 ++r0 , here +r0 is a random value between [0.3a(TM ), −0.3a(TM )] ) and the complete PBG only drops to 15%. 2) different from casual photonic crystal devices, 2-pattern photonic crystal devices mold the flow of both TM and TE waves on the same plane. In our previous work, we have demonstrated the design of various 2-pattern photonic crystal devices including wavelength scale polarizer, crossed waveguide, and a high-Q polarizer for both TM and TE waves [4]. One future research direction stemming from this work can be the experimental fabrication of 2-pattern photonic crystals and the optical characterization of the associated devices. In our previous work, we have demonstrated the morphology of six 2-pattern photonic crystals [3]. For the visible and near-IR frequency regimes ( 300nm < λ < 2 μ m ), experimental techniques that can be used to fabricate 2-pattern photonic crystals include nano-imprint lithography [209], electron beam lithography [162, 195], and focused ion beam 124 (FIB). The materials of photonic crystals for visible and near IR regime can be silicon or GaAs. The optical characterization can be performed using NSOM equipment. The TM and TE wave intensity can be measured to test the wave control abilities of 2-pattern photonic crystal devices, such as the 2-pattern photonic crystal polarizer and resonators shown in reference [4]. One important feature of photonic crystal devices is that photonic properties are not limited by frequency and length scale. Fabricating structures on a millimeter scale is much easier than on nanometer/micrometer scales. 2-pattern photonic crystals with millimeter scale features can be fabricated to control terahertz (THz) waves. One possible material for 2-pattern photonic crystal in THz regime is Aluminum ( ε Al : ε 0 ≈ 7 :1 ). Even though the permittivity contrast is lower than Silicon: air contrast ( ε Si : ε 0 ≈ 16 :1 ), the PBG is still quite large (10%). Future research direction (2): photonic quasicrystal devices In Chapter 4, we examined photonic quasicrystals based on level set equations and also created from a projection algorithm. Photonic QCs have rotational symmetries forbidden in periodic crystals; therefore they offer unique optical properties including isotropic photonic bands [128, 129], defect-free localized modes [32, 33, 130], polychromatic band gaps [210], and the possibility 125 to open a PBG at quite low refractive index contrast [34, 35]. Therefore photonic QCs are excellent candidates for nonlinear interaction [210, 211], waveguiding [132, 133, 212, 213], plasmonics [214], negative refraction [134], and optical communication [135]. Using the photonic QCs with large TE and TM PBGs as platforms [5, 8], we can create photonic devices (cavities, resonators, waveguides) within a medium with high local rotational symmetries (8-, 10-, and 12-fold). A negative tone LS10mm QC with filling ratio around 0.24-0.38 is an excellent candidate for photonic devices [5]. It can be readily fabricated using multiple exposure interference lithography [5, 147]. Its lowest TM PBG width remains almost constant for a wide range of filling fractions and this insensitivity makes it a good candidate for photonic devices. Photonic quasicrystal devices can be fabricated by removing or adding rows of features to the QC. Since the LS-10mm QC structures can be fabricated by MEIL, direct laser writing could be combined in the fabrication process to write devices directly. Several possible device designs can be envisioned: 126 1) A slow light waveguide via removing structural features. The photonic bands near the PBG edges are ultra-flat for quasicrystals, which offer slow light effects for all wave vectors. 2) Polychromatic resonators by removing/adding local features. A 2D structure with polychromatic PBGs offers fundamentally new abilities to manipulate photons on chips by allowing cavities with multiple resonance frequencies of integer ratios. Such cavities can be used to significantly enhance nonlinear interactions [215]. However, only one QC platform was shown and the cavity quality factors were not fully optimized [215]. We observed more than ten polychromatic PBGs in the PBG maps we plotted in Chapter 4 [5, 8]. One future direction for this work is to pursue a more comprehensive study to maximize cavity quality factors via Fourier analysis and gradient-based optimization, and to propose nonlinear devices based on QC cavities. 3) Phononic (acoustic/elastic wave) quasicrystals. In our previous work [5, 7], we created quasicrystals using level set equations and a projection algorithm and examined their photonic properties. Their phononic properties can be interesting from high symmetry. COMSOL software can be useful for phononic band gap simulation. 127 Future research direction (3): structural morphology-PBG analysis for three dimensional photonic crystals. In Chapter 5, we established a structural morphology-PBG analysis for 2D photonic crystals. Our concept of developing a statistical parameter (overall factor q) arising from various structural factors [7] can be extended to three dimensions (3D). In order to be self supporting, dielectric/air structures need to have connected dielectric regions. The PBG in 3D photonic crystals can arise from 2 aspects: 1) Bragg diffraction. The scattered fields from different structural portions interfere destructively with each other and form a photonic band gap; 2) resonance based PBG, a structure consisting of dielectric nodes is needed. The dielectric nodes act as strong electromagnetic (EM) field reflector to stop the propagation of EM waves. The correlation between the PBG and the structural morphology of a 3D photonic crystal could be more complex than an 2D case we investigated earlier [7]. The q factor in 3D will then be related to variations in the shape, sizes and distances of the nodes as well as the overall degree of isotropy of the structure. The q factor should incorporate the following parameters: 128 (1): Spatial isotropy parameter. The spatial distribution of materials should demonstrate some similarity for different directions to form a complete PBG. The isotropy parameter can be quantified from several aspects: (a) the Fourier coefficient signals along different directions. The strength, frequency distribution and signal peaks can be compared between different directions to judge the isotropy of the structure; (b) interface distribution. We can measure the interface distribution along different directions to judge isotropy. For example, the mean length of direction vector in different materials can be compared for different directions. (2): dielectric node analysis. In our previous work [7], the three parameters were used to analyze the geometric properties of dielectric nodes and to correlate with the size of PBG: (a) M the shape anisotropy factor α = ∑ ( v∫∂s Δri2 ds Si ri ) M ; (b) the standard deviation i =1 of the areas of the particles: β = of dielectric nodes M ∑ ( Ai − A)2 ( M − 1) A i =1 ; and (c) the spatial distribution n i . ∑ ( di<−> j − d 0 )2 ( ni − 1) Md 0 i =0 j =1 M γ= ∑ also be used to analyze dielectric nodes in 3D. 129 Those three parameters can Bibliography 1. L. Jia, and E. L. Thomas, "Radiation forces on dielectric and absorbing particles studied via the finite-difference time-domain method," Journal of the Optical Society of America BOptical Physics 26, 1882-1891 (2009). 2. L. Jia, and E. L. Thomas, "Optical forces and optical torques on various materials arising from optical lattices in the Lorentz-Mie regime," Physical Review B 84, 125128 (2011). 3. L. Jia, and E. L. Thomas, "Two-pattern compound photonic crystals with a large complete photonic band gap," Physical Review A 84, 033810 (2011). 4. L. Jia, and E. L. Thomas, "Theoretical study on photonic devices based on a commensurate two-pattern photonic crystal," Optics Letters 36, 3416-3418 (2011). 5. L. Jia, I. Bita, and E. L. Thomas, "Photonic density of states of two-dimensional quasicrystalline photonic structures," Physical Review A 84, 023831 (2011). 6. W. S. Kim, L. Jia, and E. L. Thomas, "Hierarchically Ordered Topographic Patterns via Plasmonic Mask Photolithography," Advanced Materials 21, 1921-1926 (2009). 7. L. Jia, I. Bita, and E. L. Thomas, "Impact of Geometry on the TM Photonic Band Gaps of Photonic Crystals and Quasicrystals," Physical Review Letters 107, 193901 (2011). 8. L. Jia, I. Bita, and E. L. Thomas, "Level Set Photonic Quasicrystals with Phase Parameters," Advanced Functional Materials 22, 1150-1157 (2012). 9. L. Jia, and E. L. Thomas, "Initiation of a Database of Functional Micro- and Nanostructures," Small 7, 2981-2989 (2011). 10. H. J. Kimble, "The quantum internet," Nature 453, 1023-1030 (2008). 11. D. A. B. Miller, "Rationale and challenges for optical interconnects to electronic chips," Proceedings of the Ieee 88, 728-749 (2000). 12. W. Cai, U. K. Chettiar, A. V. Kildishev, and V. M. Shalaev, "Optical cloaking with metamaterials," Nature Photonics 1, 224-227 (2007). 13. D. Schurig, J. J. Mock, B. J. Justice, S. A. Cummer, J. B. Pendry, A. F. Starr, and D. R. Smith, "Metamaterial electromagnetic cloak at microwave frequencies," Science 314, 977-980 (2006). 130 14. S. A. Cummer, B.-I. Popa, D. Schurig, D. R. Smith, J. Pendry, M. Rahm, and A. Starr, "Scattering theory derivation of a 3D acoustic cloaking shell," Physical Review Letters 100, 024301 (2008). 15. S. A. Cummer, and D. Schurig, "One path to acoustic cloaking," New Journal of Physics 9, 45 (2007). 16. V. M. Shalaev, "Optical negative-index metamaterials," Nature Photonics 1, 41-48 (2007). 17. V. M. Shalaev, W. S. Cai, U. K. Chettiar, H. K. Yuan, A. K. Sarychev, V. P. Drachev, and A. V. Kildishev, "Negative index of refraction in optical metamaterials," Optics Letters 30, 3356-3358 (2005). 18. N. Fang, H. Lee, C. Sun, and X. Zhang, "Sub-diffraction-limited optical imaging with a silver superlens," Science 308, 534-537 (2005). 19. J. Li, L. Fok, X. Yin, G. Bartal, and X. Zhang, "Experimental demonstration of an acoustic magnifying hyperlens," Nature Materials 8, 931-934 (2009). 20. J. C. Maxwell, A treatise on Electricity and Magnetism (Oxford, 1873). 21. A. Ashkin, "Acceleration and Trapping of Particles by Radiation Pressure," Physical Review Letters 24, 156-159 (1970). 22. A. Ashkin, J. M. Dziedzic, J. E. Bjorkholm, and S. Chu, "OBSERVATION OF A SINGLE-BEAM GRADIENT FORCE OPTICAL TRAP FOR DIELECTRIC PARTICLES," Optics Letters 11, 288-290 (1986). 23. K. C. Neuman, and S. M. Block, "Optical trapping," Review of Scientific Instruments 75, 2787-2809 (2004). 24. E. R. Dufresne, G. C. Spalding, M. T. Dearing, S. A. Sheets, and D. G. Grier, "Computer- generated holographic optical tweezer arrays," Review of Scientific Instruments 72, 1810-1816 (2001). 25. A. Ashkin, J. M. Dziedzic, and T. Yamane, "OPTICAL TRAPPING AND MANIPULATION OF SINGLE CELLS USING INFRARED-LASER BEAMS," Nature 330, 769-771 (1987). 26. M. P. MacDonald, G. C. Spalding, and K. Dholakia, "Microfluidic sorting in an optical lattice," Nature 426, 421-424 (2003). 131 27. S. C. Chapin, V. Germain, and E. R. Dufresne, "Automated trapping, assembly, and sorting with holographic optical tweezers," Optics Express 14, 13095-13100 (2006). 28. S. Chu, J. E. Bjorkholm, A. Ashkin, and A. Cable, "Experimental-Observation of Optically Trapped Atoms," Physical Review Letters 57, 314-317 (1986). 29. P. Korda, G. C. Spalding, E. R. Dufresne, and D. G. Grier, "Nanofabrication with holographic optical tweezers," Review of Scientific Instruments 73, 1956-1957 (2002). 30. D. Torrent, and J. Sanchez-Dehesa, "Broadband acoustic cloaks based on the homogenization of layered materials," Wave Motion 48, 497-504 (2011). 31. E. Yablonovitch, "INHIBITED SPONTANEOUS EMISSION IN SOLID-STATE PHYSICS AND ELECTRONICS," Physical Review Letters 58, 2059-2062 (1987). 32. K. Mnaymneh, and R. C. Gauthier, "Mode localization and band-gap formation in defect- free photonic quasicrystals," Optics Express 15, 5089-5099 (2007). 33. A. Della Villa, S. Enoch, G. Tayeb, F. Capolino, V. Pierro, and V. Galdi, "Localized modes in photonic quasicrystals with Penrose-type lattice," Optics Express 14, 10021-10027 (2006). 34. J. L. Yin, X. G. Huang, S. H. Liu, and S. J. Hu, "Photonic bandgap properties of 8-fold symmetric photonic quasicrystals," Optics Communications 269, 385-388 (2007). 35. G. Zito, T. P. Rose, E. Di Gennaro, A. Andreone, E. Santamato, and G. Abbate, "BANDGAP PROPERTIES OF LOW-INDEX CONTRAST APERIODICALLY ORDERED PHOTONIC QUASICRYSTALS," Microwave and Optical Technology Letters 51, 2732-2737 (2009). 36. A. Khelif, B. Djafari-Rouhani, J. O. Vasseur, and P. A. Deymier, "Transmission and dispersion relations of perfect and defect-containing waveguide structures in phononic band gap materials," Physical Review B 68, 024302 (2003). 37. P. Pignoli, E. Tremoli, A. Poli, P. Oreste, and R. Paoletti, "INTIMAL PLUS MEDIAL THICKNESS OF THE ARTERIAL-WALL - A DIRECT MEASUREMENT WITH ULTRASOUND IMAGING," Circulation 74, 1399-1406 (1986). 38. J. Ophir, I. Cespedes, H. Ponnekanti, Y. Yazdi, and X. Li, "ELASTOGRAPHY - A QUANTITATIVE METHOD FOR IMAGING THE ELASTICITY OF BIOLOGICAL TISSUES," Ultrasonic Imaging 13, 111-134 (1991). 132 39. B. L. N. Kennett, S. Widiyantoro, and R. D. van der Hilst, "Joint seismic tomography for bulk sound and shear wave speed in the Earth's mantle," Journal of Geophysical Research-Solid Earth 103, 12469-12493 (1998). 40. P. Kumar, and E. FoufoulaGeorgiou, "Wavelet analysis for geophysical applications," Reviews of Geophysics 35, 385-412 (1997). 41. M. Eichenfield, R. Camacho, J. Chan, K. J. Vahala, and O. Painter, "A picogram- and nanometre-scale photonic-crystal optomechanical cavity," Nature 459, 550 (2009). 42. M. Eichenfield, J. Chan, R. M. Camacho, K. J. Vahala, and O. Painter, "Optomechanical crystals," Nature 462, 78-82 (2009). 43. A. Ashkin, and J. M. Dziedzic, "OPTICAL TRAPPING AND MANIPULATION OF VIRUSES AND BACTERIA," Science 235, 1517-1520 (1987). 44. L. Paterson, M. P. MacDonald, J. Arlt, W. Sibbett, P. E. Bryant, and K. Dholakia, "Controlled rotation of optically trapped microscopic particles," Science 292, 912-914 (2001). 45. A. T. O'Neil, I. MacVicar, L. Allen, and M. J. Padgett, "Intrinsic and extrinsic nature of the orbital angular momentum of a light beam," Physical Review Letters 88 (2002). 46. J. Leach, G. Sinclair, P. Jordan, J. Courtial, M. J. Padgett, J. Cooper, and Z. J. Laczik, "3D manipulation of particles into crystal structures using holographic optical tweezers," Optics Express 12, 220-226 (2004). 47. G. Sinclair, P. Jordan, J. Courtial, M. Padgett, J. Cooper, and Z. J. Laczik, "Assembly of 3-dimensional structures using programmable holographic optical tweezers," Optics Express 12, 5475-5480 (2004). 48. A. E. Chiou, W. Wang, G. J. Sonek, J. Hong, and M. W. Berns, "Interferometric optical tweezers," Optics Communications 133, 7-10 (1997). 49. A. Casaburi, G. Pesce, P. Zemanek, and A. Sasso, "Two- and three-beam interferometric optical tweezers," Optics Communications 251, 393-404 (2005). 50. E. Schonbrun, R. Piestun, P. Jordan, J. Cooper, K. D. Wulff, J. Courtial, and M. Padgett, "3D interferometric optical tweezers using a single spatial light modulator," Optics Express 13, 3777-3786 (2005). 51. T. Cizmar, M. Siler, M. Sery, P. Zemanek, V. Garces-Chavez, and K. Dholakia, "Optical sorting and detection of submicrometer objects in a motional standing wave," Physical Review B 74 (2006). 133 52. P. Zemanek, A. Jonas, P. Jakl, J. Jezek, M. Sery, and M. Liska, "Theoretical comparison of optical traps created by standing wave and single beam," Optics Communications 220, 401412 (2003). 53. W. Mu, Z. Li, L. Luan, G. C. Spalding, G. Wang, and J. B. Ketterson, "Force measurement on microspheres in an optical standing wave," Journal of the Optical Society of America B-Optical Physics 25, 763-767 (2008). 54. X. Y. Miao, and L. Y. Lin, "Trapping and manipulation of biological particles through a plasmonic platform," Ieee Journal of Selected Topics in Quantum Electronics 13, 1655-1662 (2007). 55. M. Righini, A. S. Zelenina, C. Girard, and R. Quidant, "Parallel and selective trapping in a patterned plasmonic landscape," Nature Physics 3, 477-480 (2007). 56. M. Sukharev, and T. Seideman, "Light trapping and guidance in plasmonic nanocrystals," Journal of Chemical Physics 126 (2007). 57. L. Huang, S. J. Maerkl, and O. J. F. Martin, "Integration of plasmonic trapping in a microfluidic environment," Optics Express 17, 6018-6024 (2009). 58. J. Mikhael, J. Roth, L. Helden, and C. Bechinger, "Archimedean-like tiling on decagonal quasicrystalline surfaces," Nature 454, 501-504 (2008). 59. R. L. Smith, G. C. Spalding, K. Dholakia, and M. P. MacDonald, "Colloidal sorting in dynamic optical lattices," Journal of Optics a-Pure and Applied Optics 9, S134-S138 (2007). 60. I. Ricardez-Vargas, P. Rodriguez-Montero, R. Ramos-Garcia, and K. Volke-Sepulveda, "Modulated optical sieve for sorting of polydisperse microparticles," Applied Physics Letters 88 (2006). 61. Y. Y. Sun, X. C. Yuan, L. S. Ong, J. Bu, S. W. Zhu, and R. Liu, "Large-scale optical traps on a chip for optical sorting," Applied Physics Letters 90 (2007). 62. P. T. Korda, G. C. Spalding, and D. G. Grier, "Evolution of a colloidal critical state in an optical pinning potential landscape," Physical Review B 66 (2002). 63. D. Maystre, and P. Vincent, "Making photonic crystals using trapping and binding optical forces on particles," Journal of Optics a-Pure and Applied Optics 8, 1059-1066 (2006). 64. R. A. Williams, J. D. Pillet, S. Al-Assam, B. Fletcher, M. Shotter, and C. J. Foot, "Dynamic optical lattices: two-dimensional rotating and accordion lattices for ultracold atoms," Optics Express 16, 16977-16983 (2008). 134 65. Z. P. Luo, Y. L. Sun, and K. N. An, "An optical spin micromotor," Applied Physics Letters 76, 1779-1781 (2000). 66. K. D. Bonin, B. Kourmanov, and T. G. Walker, "Light torque nanocontrol, nanomotors and nanorockers," Optics Express 10, 984-989 (2002). 67. J. M. Cruz, and F. J. Garcia-Diego, "Dielectrophoretic motion of oblate spheroidal particles. Measurements of motion of red blood cells using the Stokes method," Journal of Physics D-Applied Physics 31, 1745-1751 (1998). 68. P. M. Hansen, V. K. Bhatia, N. Harrit, and L. Oddershede, "Expanding the optical trapping range of gold nanoparticles," Nano Letters 5, 1937-1942 (2005). 69. G. Gouesbet, B. Maheu, and G. Grehan, "LIGHT-SCATTERING FROM A SPHERE ARBITRARILY LOCATED IN A GAUSSIAN-BEAM, USING A BROMWICH FORMULATION," Journal of the Optical Society of America a-Optics Image Science and Vision 5, 1427-1443 (1988). 70. J. P. Barton, "INTERNAL AND NEAR-SURFACE ELECTROMAGNETIC-FIELDS FOR A SPHEROIDAL PARTICLE WITH ARBITRARY ILLUMINATION," Applied Optics 34, 5542-5551 (1995). 71. G. Gouesbet, and L. Mees, "Generalized Lorenz-Mie theory for infinitely long elliptical cylinders," Journal of the Optical Society of America a-Optics Image Science and Vision 16, 1333-1341 (1999). 72. T. Tlusty, A. Meller, and R. Bar-Ziv, "Optical gradient forces of strongly localized fields," Physical Review Letters 81, 1738-1741 (1998). 73. B. Peterson, and S. Strom, "T-MATRIX FORMULATION OF ELECTROMAGNETIC SCATTERING FROM MULTILAYERED SCATTERERS," Physical Review D 10, 2670-2684 (1974). 74. M. I. Mishchenko, L. D. Travis, and D. W. Mackowski, "T-matrix computations of light scattering by nonspherical particles: A review," Journal of Quantitative Spectroscopy & Radiative Transfer 55, 535-575 (1996). 75. B. T. Draine, and P. J. Flatau, "DISCRETE-DIPOLE APPROXIMATION FOR SCATTERING CALCULATIONS," Journal of the Optical Society of America a-Optics Image Science and Vision 11, 1491-1499 (1994). 135 76. P. Zemanek, A. Jonas, and M. Liska, "Simplified description of optical forces acting on a nanoparticle in the Gaussian standing wave," Journal of the Optical Society of America a-Optics Image Science and Vision 19, 1025-1034 (2002). 77. A. Jonas, L. Sramek, M. Liska, and P. Zemanek, "Theoretical study of the optical forces and other characteristical parameters in the standing wave trap," 11th Slovak-Czech-Polish Optical Conference on Wave and Quantum Aspects of Contemporary Optics 3820, 70-76 (1999). 78. K. I. Petsas, A. B. Coates, and G. Grynberg, "Crystallography of Optical Lattices," Physical Review A 50, 5173-5189 (1994). 79. M. Maldovan, and E. L. Thomas, "Simultaneous complete elastic and electromagnetic band gaps in periodic structures," Applied Physics B-Lasers and Optics 83, 595-600 (2006). 80. M. Maldovan, and E. L. Thomas, "Simultaneous localization of photons and phonons in two-dimensional periodic structures," Applied Physics Letters 88 (2006). 81. M. M. Burns, J. M. Fournier, and J. A. Golovchenko, "OPTICAL BINDING," Physical Review Letters 63, 1233-1236 (1989). 82. M. M. Burns, J. M. Fournier, and J. A. Golovchenko, "OPTICAL MATTER - CRYSTALLIZATION AND BINDING IN INTENSE OPTICAL-FIELDS," Science 249, 749754 (1990). 83. F. J. G. de Abajo, "Collective oscillations in optical matter," Optics Express 15, 11082- 11094 (2007). 84. J. Ng, and C. T. Chan, "Localized vibrational modes in optically bound structures," Optics Letters 31, 2583-2585 (2006). 85. A. Rohrbach, and E. H. K. Stelzer, "Optical trapping of dielectric particles in arbitrary fields," Journal of the Optical Society of America a-Optics Image Science and Vision 18, 839853 (2001). 86. C. Ullal, M. Maldovan, S. Yang, G. Chen, Y. J. Han, J. Aizenberg, R. Rapaport, C. White, and E. L. Thomas, "Photonic crystals through interference lithography: A level set approach," Nontraditional Approaches to Patterning, 179-181 (2004). 87. M. Wohlgemuth, N. Yufa, J. Hoffman, and L. E. Thomas, "Triply periodic bicontinuous cubic microdomain morphologies by symmetries," Macromolecules 34, 6083-6089 (2001). 88. H. Furukawa, and I. Yamaguchi, "Optical trapping of metallic particles by a fixed Gaussian beam," Optics Letters 23, 216-218 (1998). 136 89. A. T. O'Neil, and M. J. Padgett, "Three-dimensional optical confinement of micron-sized metal particles and the decoupling of the spin and orbital angular momentum within an optical spanner," Optics Communications 185, 139-143 (2000). 90. K. Svoboda, and S. M. Block, "OPTICAL TRAPPING OF METALLIC RAYLEIGH PARTICLES," Optics Letters 19, 930-932 (1994). 91. Q. W. Zhan, "Trapping metallic Rayleigh particles with radial polarization," Optics Express 12, 3377-3382 (2004). 92. J. H. Jang, C. K. Ullal, M. Maldovan, T. Gorishnyy, S. Kooi, C. Y. Koh, and E. L. Thomas, "3D micro- and nanostructures via interference lithography," Advanced Functional Materials 17, 3027-3041 (2007). 93. J. H. Jang, D. Dendukuri, T. A. Hatton, E. L. Thomas, and P. S. Doyle, "A route to three- dimensional structures in a microfluidic device: Stop-flow interference lithography," Angewandte Chemie-International Edition 46, 9027-9031 (2007). 94. P. Jiang, J. F. Bertone, and V. L. Colvin, "A lost-wax approach to monodisperse colloids and their crystals," Science 291, 453-457 (2001). 95. V. N. Manoharan, M. T. Elsesser, and D. J. Pine, "Dense packing and symmetry in small clusters of microspheres," Science 301, 483-487 (2003). 96. E. A. Abbott, Flatland: A romance of many dimensions (Seeley & Co, London, 1884). 97. S. John, "STRONG LOCALIZATION OF PHOTONS IN CERTAIN DISORDERED DIELECTRIC SUPERLATTICES," Physical Review Letters 58, 2486-2489 (1987). 98. J. D. Joannopoulos, P. R. Villeneuve, and S. H. Fan, "Photonic crystals: Putting a new twist on light," Nature 386, 143-149 (1997). 99. M. Maldovan, and E. L. Thomas, Periodic Materials and Interference Lithography (Wiley-VCH Verlag Gmbh& Co. KGaA Weinheim, 2009). 100. J. D. Joannopoulos, S. G. Johnson, J. N. Winn, and R. D. Meade, Photonic crystals: molding the flow of light (Princeton University Press, Princeton, 2008). 101. S. Noda, K. Tomoda, N. Yamamoto, and A. Chutinan, "Full three-dimensional photonic bandgap crystals at near-infrared wavelengths," Science 289, 604-606 (2000). 102. S. G. Johnson, S. H. Fan, P. R. Villeneuve, J. D. Joannopoulos, and L. A. Kolodziejski, "Guided modes in photonic crystal slabs," Physical Review B 60, 5751-5758 (1999). 137 103. S. Y. Lin, J. G. Fleming, D. L. Hetherington, B. K. Smith, R. Biswas, K. M. Ho, M. M. Sigalas, W. Zubrzycki, S. R. Kurtz, and J. Bur, "A three-dimensional photonic crystal operating at infrared wavelengths," Nature 394, 251-253 (1998). 104. M. E. Zoorob, M. D. B. Charlton, G. J. Parker, J. J. Baumberg, and M. C. Netti, "Complete photonic bandgaps in 12-fold symmetric quasicrystals," Nature 404, 740-743 (2000). 105. X. D. Zhang, Z. Q. Zhang, and C. T. Chan, "Absolute photonic band gaps in 12-fold symmetric photonic quasicrystals," Physical Review B 63 (2001). 106. M. Florescu, S. Torquato, and P. J. Steinhardt, "Designer disordered materials with large, complete photonic band gaps," Proceedings of the National Academy of Sciences of the United States of America 106, 20658-20663 (2009). 107. R. L. Chern, C. C. Chang, and R. R. Hwang, "Large full band gaps for photonic crystals in two dimensions computed by an inverse method with multigrid acceleration," Physical Review E 68 (2003). 108. X. Wang, and K. Kempa, "Effects of disorder on subwavelength lensing in two- dimensional photonic crystal slabs," Physical Review B 71 (2005). 109. R. Meisels, and F. Kuchar, "Density-of-states and wave propagation in two-dimensional photonic crystals with positional disorder," Journal of Optics a-Pure and Applied Optics 9, S396S402 (2007). 110. R. Biswa, I. kady, and K. Ho, "Enhanced complete photonic band gap in the optimized planar diamond struture," Photonics and Nanostructures-Fundamentals and Applications 1, 15-21 (2003). 111. I. Bita, "Breaking symmetries in ordered materials: spin polarized light transport in magnetized noncentrosymmetric 1D photonic crystals, and photonic gaps and fabrication of quasiperiodic structured materials from interference lithography," in Department of Materials Science and Engineering(Massachusetts Institute of Technology, Cambridge, 2006), pp. 120-124. 112. O. Sigmund, and K. Hougaard, "Geometric properties of optimal photonic crystals," Physical Review Letters 100 (2008). 113. L. F. Shen, Z. Ye, and S. He, "Design of two-dimensional photonic crystals with large absolute band gaps using a genetic algorithm," Physical Review B 68 (2003). 138 114. R. S. Jacobsen, K. N. Andersen, P. I. Borel, J. Fage-Pedersen, L. H. Frandsen, O. Hansen, M. Kristensen, A. V. Lavrinenko, G. Moulin, H. Ou, C. Peucheret, B. Zsigri, and A. Bjarklev, "Strained silicon as a new electro-optic material," Nature 441, 199-202 (2006). 115. A. Chutinan, S. John, and O. Toader, "Diffractionless flow of light in all-optical microchips," Physical Review Letters 90 (2003). 116. P. Lodahl, A. F. van Driel, I. S. Nikolaev, A. Irman, K. Overgaag, D. L. Vanmaekelbergh, and W. L. Vos, "Controlling the dynamics of spontaneous emission from quantum dots by photonic crystals," Nature 430, 654-657 (2004). 117. M. Fujita, S. Takahashi, Y. Tanaka, T. Asano, and S. Noda, "Simultaneous inhibition and redistribution of spontaneous light emission in photonic crystals," Science 308, 1296-1298 (2005). 118. T. Tanabe, M. Notomi, E. Kuramochi, A. Shinya, and H. Taniyama, "Trapping and delaying photons for one nanosecond in an ultrasmall high-Q photonic-crystal nanocavity," Nature Photonics 1, 49-52 (2007). 119. T. Yoshie, A. Scherer, J. Hendrickson, G. Khitrova, H. M. Gibbs, G. Rupper, C. Ell, O. B. Shchekin, and D. G. Deppe, "Vacuum Rabi splitting with a single quantum dot in a photonic crystal nanocavity," Nature 432, 200-203 (2004). 120. J. S. Foresi, P. R. Villeneuve, J. Ferrera, E. R. Thoen, G. Steinmeyer, S. Fan, J. D. Joannopoulos, L. C. Kimerling, H. I. Smith, and E. P. Ippen, "Photonic-bandgap microcavities in optical waveguides," Nature 390, 143-145 (1997). 121. E. Chow, S. Y. Lin, S. G. Johnson, P. R. Villeneuve, J. D. Joannopoulos, J. R. Wendt, G. A. Vawter, W. Zubrzycki, H. Hou, and A. Alleman, "Three-dimensional control of light in a two-dimensional photonic crystal slab," Nature 407, 983-986 (2000). 122. T. F. Krauss, R. M. DeLaRue, and S. Brand, "Two-dimensional photonic-bandgap structures operating at near infrared wavelengths," Nature 383, 699-702 (1996). 123. O. Painter, R. K. Lee, A. Scherer, A. Yariv, J. D. O'Brien, P. D. Dapkus, and I. Kim, "Two-dimensional photonic band-gap defect mode laser," Science 284, 1819-1821 (1999). 124. M. Law, D. J. Sirbuly, J. C. Johnson, J. Goldberger, R. J. Saykally, and P. D. Yang, "Nanoribbon waveguides for subwavelength photonics integration," Science 305, 1269-1273 (2004). 139 125. H. G. Park, S. H. Kim, S. H. Kwon, Y. G. Ju, J. K. Yang, J. H. Baek, S. B. Kim, and Y. H. Lee, "Electrically driven single-cell photonic crystal laser," Science 305, 1444-1447 (2004). 126. E. Yablonovitch, T. J. Gmitter, R. D. Meade, A. M. Rappe, K. D. Brommer, and J. D. Joannopoulos, "DONOR AND ACCEPTOR MODES IN PHOTONIC BAND-STRUCTURE," Physical Review Letters 67, 3380-3383 (1991). 127. D. N. Christodoulides, F. Lederer, and Y. Silberberg, "Discretizing light behaviour in linear and nonlinear waveguide lattices," Nature 424, 817-823 (2003). 128. M. C. Rechtsman, H. C. Jeong, P. M. Chaikin, S. Torquato, and P. J. Steinhardt, "Optimized structures for photonic quasicrystals," Physical Review Letters 101 (2008). 129. M. Florescu, S. Torquato, and P. J. Steinhardt, "Complete band gaps in two-dimensional photonic quasicrystals," Physical Review B 80 (2009). 130. R. C. Gauthier, and K. Mnaymneh, "FDTD analysis of 12-fold photonic quasi-crystal central pattern localized states," Optics Communications 264, 78-88 (2006). 131. E. Di Gennaro, C. Miletto, S. Savo, A. Andreone, D. Morello, V. Galdi, G. Castaldi, and V. Pierro, "Evidence of local effects in anomalous refraction and focusing properties of dodecagonal photonic quasicrystals," Physical Review B 77 (2008). 132. C. J. Jin, B. Y. Cheng, B. Y. Man, Z. L. Li, D. Z. Zhang, S. Z. Ban, and B. Sun, "Band gap and wave guiding effect in a quasiperiodic photonic crystal," Applied Physics Letters 75, 1848-1850 (1999). 133. H. H. Tao, C. Ren, S. Feng, Y. Z. Liu, Z. Y. Li, B. Y. Cheng, D. Z. Zhang, and A. Z. Jin, "Optical improvement of photonic devices fabricated by Ga+ focused ion beam micromachining," Journal of Vacuum Science & Technology B 25, 1609-1614 (2007). 134. X. H. Deng, Y. G. Peng, J. T. Liu, J. R. Yuan, and L. Zou, "Omnidirectional reflection band extension using Fibonacci photonic heterostructures containing negative-index materials," Journal of Modern Optics 57, 325-329. 135. S. Kim, and C. S. Kee, "Dispersion properties of dual-core photonic-quasicrystal fiber," Optics Express 17, 15885-15890 (2009). 136. Y. S. Chan, C. T. Chan, and Z. Y. Liu, "Photonic band gaps in two dimensional photonic quasicrystals," Physical Review Letters 80, 956-959 (1998). 140 137. A. Della Villa, S. Enoch, G. Tayeb, V. Pierro, V. Galdi, and F. Capolino, "Band gap formation and multiple scattering in photonic quasicrystals with a Penrose-type lattice," Physical Review Letters 94 (2005). 138. G. Zito, B. Piccirillo, E. Santamato, A. Marino, V. Tkachenko, and G. Abbate, "FDTD analysis of photonic quasicrystals with different tiling geometries and fabrication by single-beam computer-generated holography," Journal of Optics a-Pure and Applied Optics 11 (2009). 139. R. C. Gauthier, and K. Mnaymneh, "Photonic band gap properties of 12-fold quasi- crystal determined through FDTD analysis," Optics Express 13, 1985-1998 (2005). 140. C. Rockstuhl, U. Peschel, and F. Lederer, "Correlation between single-cylinder properties and bandgap formation in photonic structures," Optics Letters 31, 1741-1743 (2006). 141. E. Lidorikis, M. M. Sigalas, E. N. Economou, and C. M. Soukoulis, "Gap deformation and classical wave localization in disordered two-dimensional photonic-band-gap materials," Physical Review B 61, 13458-13464 (2000). 142. C. Rockstuhl, and F. Lederer, "The effect of disorder on the local density of states in two- dimensional quasi-periodic photonic crystals," New Journal of Physics 8 (2006). 143. L. N. Shi, X. Y. Jiang, and C. F. Li, "Effects induced by Mie resonance in two- dimensional photonic crystals," Journal of Physics-Condensed Matter 19 (2007). 144. R. L. Chern, and S. D. Chao, "Optimal higher-lying band gaps for photonic crystals with large dielectric contrast," Optics Express 16, 16600-16608 (2008). 145. C. K. Ullal, M. Maldovan, M. Wohlgemuth, and E. L. Thomas, "Triply periodic bicontinuous structures through interference lithography: a level-set approach," Journal of the Optical Society of America a-Optics Image Science and Vision 20, 948-954 (2003). 146. A. Avgeropoulos, B. J. Dair, N. Hadjichristidis, and E. L. Thomas, "Tricontinuous double gyroid cubic phase in triblock copolymers of the ABA type," Macromolecules 30, 5634-5642 (1997). 147. I. Bita, T. Choi, M. E. Walsh, H. L. Smith, and E. L. Thomas, "Large-area 3D nanostructures with octagonal quasicrystalline symmetry via phase-mask lithography," Advanced Materials 19, 1403-+ (2007). 148. J. B. Yeo, S. D. Yun, N. H. Kim, and H. Y. Lee, "Fabrication of Si-based two- dimensional photonic quasicrystals by using multiple-exposure holographic lithography," Journal of Vacuum Science & Technology B 27, 1886-1889 (2009). 141 149. X. Wang, J. Xu, J. C. W. Lee, Y. K. Pang, W. Y. Tam, C. T. Chan, and P. Sheng, "Realization of optical periodic quasicrystals using holographic lithography," Applied Physics Letters 88 (2006). 150. W. Y. Tam, "Icosahedral quasicrystals by optical interference holography," Applied Physics Letters 89 (2006). 151. J. Xu, R. Ma, X. Wang, and W. Y. Tam, "Icosahedral quasicrystals for visible wavelengths by optical interference holography," Optics Express 15, 4287-4295 (2007). 152. D. Levine, and P. J. Steinhardt, "QUASICRYSTALS - A NEW CLASS OF ORDERED STRUCTURES," Physical Review Letters 53, 2477-2480 (1984). 153. M. Senechal, Quasicrystals and Geometry (Cambridge University Press, Cambridge, 1996). 154. N. D. Lai, J. H. Lin, Y. Y. Huang, and C. C. Hsu, "Fabrication of two- and three- dimensional quasi-periodic structures with 12-fold symmetry by interference technique," Optics Express 14, 10746-10752 (2006). 155. R. C. Gauthier, and A. Ivanov, "Production of quasi-crystal template patterns using a dual beam multiple exposure technique," Optics Express 12, 990-1003 (2004). 156. K. Busch, and S. John, "Photonic band gap formation in certain self-organizing systems," Physical Review E 58, 3896-3908 (1998). 157. V. I. Kopp, B. Fan, H. K. M. Vithana, and A. Z. Genack, "Low-threshold lasing at the edge of a photonic stop band in cholesteric liquid crystals," Optics Letters 23, 1707-1709 (1998). 158. S. Y. Zhu, Y. P. Yang, H. Chen, H. Zheng, and M. S. Zubairy, "Spontaneous radiation and lamb shift in three-dimensional photonic crystals," Physical Review Letters 84, 2136-2139 (2000). 159. M. Florescu, S. Torquato, and P. J. Steinhardt, "Effects of random link removal on the photonic band gaps of honeycomb networks," Applied Physics Letters 97. 160. I. E. Psarobas, N. Stefanou, and A. Modinos, "Scattering of elastic waves by periodic arrays of spherical bodies," Physical Review B 62, 278-291 (2000). 161. J. O. Vasseur, P. A. Deymier, B. Chenni, B. Djafari-Rouhani, L. Dobrzynski, and D. Prevost, "Experimental and theoretical evidence for the existence of absolute acoustic band gaps in two-dimensional solid phononic crystals," Physical Review Letters 86, 3012-3015 (2001). 142 162. B. H. Cumpston, S. P. Ananthavel, S. Barlow, D. L. Dyer, J. E. Ehrlich, L. L. Erskine, A. A. Heikal, S. M. Kuebler, I. Y. S. Lee, D. McCord-Maughon, J. Q. Qin, H. Rockel, M. Rumi, X. L. Wu, S. R. Marder, and J. W. Perry, "Two-photon polymerization initiators for threedimensional optical data storage and microfabrication," Nature 398, 51-54 (1999). 163. D. A. Parthenopoulos, and P. M. Rentzepis, "3-Dimensional Optical Storage Memory," Science 245, 843-845 (1989). 164. J. W. Long, B. Dunn, D. R. Rolison, and H. S. White, "Three-dimensional battery architectures," Chemical Reviews 104, 4463-4492 (2004). 165. J. P. Fu, R. B. Schoch, A. L. Stevens, S. R. Tannenbaum, and J. Y. Han, "A patterned anisotropic nanofluidic sieving structure for continuous-flow separation of DNA and proteins," Nature Nanotechnology 2, 121-128 (2007). 166. R. S. Kane, S. Takayama, E. Ostuni, D. E. Ingber, and G. M. Whitesides, "Patterning proteins and cells using soft lithography," Biomaterials 20, 2363-2376 (1999). 167. L. Boldrin, N. Elvassore, A. Malerba, M. Flaibani, E. Cimetta, M. Piccoli, M. D. Baroni, M. V. Gazzola, C. Messina, P. Gamba, L. Vitiello, and P. De Coppi, "Satellite cells delivered by micro-patterned scaffolds: A new strategy for cell transplantation in muscle diseases," Tissue Engineering 13, 253-262 (2007). 168. C. J. Bettinger, E. J. Weinberg, K. M. Kulig, J. P. Vacanti, Y. D. Wang, J. T. Borenstein, and R. Langer, "Three-dimensional microfluidic tissue-engineering scaffolds using a flexible biodegradable polymer," Advanced Materials 18, 165-+ (2006). 169. A. Yariv, and M. Nakamura, "Periodic Structures for Integrated-Optics," Ieee Journal of Quantum Electronics 13, 233-253 (1977). 170. L. F. Wang, M. C. Boyce, C. Y. Wen, and E. L. Thomas, "Plastic Dissipation Mechanisms in Periodic Microframe-Structured Polymers," Advanced Functional Materials 19, 1343-1350 (2009). 171. J. Henzie, M. H. Lee, and T. W. Odom, "Multiscale patterning of plasmonic metamaterials," Nature Nanotechnology 2, 549-554 (2007). 172. M. Nedelcu, J. Lee, E. J. W. Crossland, S. C. Warren, M. C. Orilall, S. Guldin, S. Huttner, C. Ducati, D. Eder, U. Wiesner, U. Steiner, and H. J. Snaith, "Block copolymer directed synthesis of mesoporous TiO2 for dye-sensitized solar cells," Soft Matter 5, 134-139 (2009). 173. "http://www.pdb.org/pdb/home/home.do." 143 174. A. Bateman, L. Coin, R. Durbin, R. D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E. L. L. Sonnhammer, D. J. Studholme, C. Yeats, and S. R. Eddy, "The Pfam protein families database," Nucleic Acids Research 32, D138-D141 (2004). 175. W. Gish, and D. J. States, "IDENTIFICATION OF PROTEIN CODING REGIONS BY DATABASE SIMILARITY SEARCH," Nature Genetics 3, 266-272 (1993). 176. "http://www.chemspider.com/." 177. S. Grazulis, D. Chateigner, R. T. Downs, A. F. T. Yokochi, M. Quiros, L. Lutterotti, E. Manakova, J. Butkus, P. Moeck, and A. Le Bail, "Crystallography Open Database - an openaccess collection of crystal structures," Journal of Applied Crystallography 42, 726-729 (2009). 178. "http://www.fiz-karlsruhe.de/icsd.html." 179. "http://rruff.geo.arizona.edu/AMS/amcsd.php." 180. "http://www.ncbi.nlm.nih.gov/guide/." 181. "http://www.nist.gov/srd/onlinelist.cfm." 182. O. Guner, O. Clement, and Y. Kurogi, "Pharmacophore modeling and three dimensional database searching for drug design using catalyst: Recent advances," Current Medicinal Chemistry 11, 2991-3005 (2004). 183. E. L. Thomas, D. B. Alward, D. J. Kinning, D. C. Martin, D. L. Handlin, and L. J. Fetters, "Ordered Bicontinuous Double-Diamond Structure of Star Block Copolymers - a New Equilibrium Microdomain Morphology," Macromolecules 19, 2197-2202 (1986). 184. I. Bita, J. K. W. Yang, Y. S. Jung, C. A. Ross, E. L. Thomas, and K. K. Berggren, "Graphoepitaxy of self-assembled block copolymers on two-dimensional periodic patterned templates," Science 321, 939-943 (2008). 185. S. G. Zhang, "Fabrication of novel biomaterials through molecular self-assembly," Nature Biotechnology 21, 1171-1178 (2003). 186. A. D. Dinsmore, A. G. Yodh, and D. J. Pine, "Phase-Diagrams of Nearly Hard-Sphere Binary Colloids," Physical Review E 52, 4045-4057 (1995). 187. D. J. Shir, S. Jeon, H. Liao, M. Highland, D. G. Cahill, M. F. Su, I. F. El-Kady, C. G. Christodoulou, G. R. Bogart, A. V. Hamza, and J. A. Rogers, "Three-dimensional nanofabrication with elastomeric phase masks," Journal of Physical Chemistry B 111, 1294512958 (2007). 144 188. S. Jeon, J. U. Park, R. Cirelli, S. Yang, C. E. Heitzman, P. V. Braun, P. J. A. Kenis, and J. A. Rogers, "Fabricating complex three-dimensional nanostructures with high-resolution conformable phase masks," Proceedings of the National Academy of Sciences of the United States of America 101, 12428-12433 (2004). 189. S. Jeon, V. Malyarchuk, J. O. White, and J. A. Rogers, "Optically fabricated three dimensional nanofluidic mixers for microfluidic devices," Nano Letters 5, 1351-1356 (2005). 190. D. J. Shir, S. Jeon, H. Liao, M. Highland, D. G. Cahill, M. F. Su, I. F. El-Kady, C. G. Christodoulou, G. R. Bogart, A. V. Hamza, and J. A. Rogers, "Three-dimensional nanofabrication with elastomeric phase masks," Journal of Physical Chemistry B 111, 1294512958 (2007). 191. M. Campbell, D. N. Sharp, M. T. Harrison, R. G. Denning, and A. J. Turberfield, "Fabrication of photonic crystals for the visible spectrum by holographic lithography," Nature 404, 53-56 (2000). 192. C. K. Ullal, M. Maldovan, E. L. Thomas, G. Chen, Y. J. Han, and S. Yang, "Photonic crystals through holographic lithography: Simple cubic, diamond-like, and gyroid-like structures," Applied Physics Letters 84, 5434-5436 (2004). 193. J. H. Jang, C. K. Ullal, T. Gorishnyy, V. V. Tsukruk, and E. L. Thomas, "Mechanically tunable three-dimensional elastomeric network/air structures via interference lithography," Nano Letters 6, 740-743 (2006). 194. S. H. Zaidi, and S. R. J. Brueck, "MULTIPLE-EXPOSURE INTERFEROMETRIC LITHOGRAPHY," Journal of Vacuum Science & Technology B 11, 658-666 (1993). 195. Y. N. Xia, J. A. Rogers, K. E. Paul, and G. M. Whitesides, "Unconventional methods for fabricating and patterning nanostructures," Chemical Reviews 99, 1823-1848 (1999). 196. J. D. Gillaspy, "Highly charged ions," Journal of Physics B-Atomic Molecular and Optical Physics 34, R93-R130 (2001). 197. S. Nowak, T. Pfau, and J. Mlynek, "Nanolithography with metastabile helium," Applied Physics B-Lasers and Optics 63, 203-205 (1996). 198. D. Shir, H. W. Liao, S. Jeon, D. Xiao, H. T. Johnson, G. R. Bogart, K. H. A. Bogart, and J. A. Rogers, "Three-dimensional nanostructures formed by single step, two-photon exposures through elastomeric Penrose quasicrystal phase masks," Nano Letters 8, 2236-2244 (2008). 145 199. D. Shir, E. C. Nelson, Y. C. Chen, A. Brzezinski, H. Liao, P. V. Braun, P. Wiltzius, K. H. A. Bogart, and J. A. Rogers, "Three dimensional silicon photonic crystals fabricated by two photon phase mask lithography," Applied Physics Letters 94 (2009). 200. S. Jeon, D. J. Shir, Y. S. Nam, R. Nidetz, M. Highland, D. G. Cahill, J. A. Rogers, M. F. Su, I. F. El-Kady, C. G. Christodoulou, and G. R. Bogart, "Molded transparent photopolymers and phase shift optics for fabricating three dimensional nanostructures," Optics Express 15, 6358-6366 (2007). 201. D. Roundy, and J. Joannopoulos, "Photonic crystal structure with square symmetry within each layer and a three-dimensional band gap," Applied Physics Letters 82, 3835-3837 (2003). 202. M. H. Qi, E. Lidorikis, P. T. Rakich, S. G. Johnson, J. D. Joannopoulos, E. P. Ippen, and H. I. Smith, "A three-dimensional optical photonic crystal with designed point defects," Nature 429, 538-542 (2004). 203. Y. K. Lin, A. Harb, D. Rodriguez, K. Lozano, D. Xu, and K. P. Chen, "Fabrication of two-layer integrated phase mask for single-beam and single-exposure fabrication of threedimensional photonic crystal," Optics Express 16, 9165-9172 (2008). 204. S. Torquato, S. Hyun, and A. Donev, "Optimal design of manufacturable three- dimensional composites with multifunctional characteristics," Journal of Applied Physics 94, 5748-5755 (2003). 205. M. C. Rechtsman, and S. Torquato, "Method for obtaining upper bounds on photonic band gaps," Physical Review B 80 (2009). 206. J. Zhu, J. Christensen, J. Jung, L. Martin-Moreno, X. Yin, L. Fok, X. Zhang, and F. J. Garcia-Vidal, "A holey-structured metamaterial for acoustic deep-subwavelength imaging," Nature Physics 7, 52-55 (2011). 207. L.-Y. Wu, and L.-W. Chen, "Acoustic band gaps of the woodpile sonic crystal with the simple cubic lattice," Journal of Physics D-Applied Physics 44 (2011). 208. M.-K. Kim, J.-Y. Kim, J.-H. Kang, B.-H. Ahn, and Y.-H. Lee, "On-demand photonic crystal resonators," Laser & Photonics Reviews 5, 479-495 (2011). 209. S. Y. Chou, P. R. Krauss, and P. J. Renstrom, "Nanoimprint lithography," Journal of Vacuum Science & Technology B 14, 4129-4133 (1996). 146 210. S. M. Thon, W. T. M. Irvine, D. Kleckner, and D. Bouwmeester, "Polychromatic Photonic Quasicrystal Cavities," Physical Review Letters 104. 211. J. Ma, and M. L. Povinelli, "Mechanical Kerr nonlinearities due to bipolar optical forces between deformable silicon waveguides," Optics Express 19, 10102-10110. 212. Z. F. Yu, G. Veronis, Z. Wang, and S. H. Fan, "One-way electromagnetic waveguide formed at the interface between a plasmonic metal under a static magnetic field and a photonic crystal," Physical Review Letters 100 (2008). 213. M. L. Povinelli, and S. H. Fan, "Radiation loss of coupled-resonator waveguides in photonic-crystal slabs," Applied Physics Letters 89 (2006). 214. A. Gopinath, S. V. Boriskina, N. N. Feng, B. M. Reinhard, and L. Dal Negro, "Photonic- plasmonic scattering resonances in deterministic aperiodic structures," Nano Letters 8, 24232431 (2008). 215. S. M. Thon, W. T. M. Irvine, D. Kleckner, and D. Bouwmeester, "Polychromatic Photonic Quasicrystal Cavities," Physical Review Letters 104 (2010). 147