Woo, Kat Choi = 以時域有限差分法模擬貴金屬的納米結構 / 胡吉才. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 84-86). / Abstracts in English and Chinese. / Woo, Kat Choi = Yi shi yu you xian cha fen fa mo ni gui jin shu de na mi jie gou / Hu Jicai. / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- The Importance of Nanoscale Plasmonic Physics --- p.1 / Chapter 1.2 --- The Driving Forces behind Plasmon Physics --- p.2 / Chapter 1.3 --- Computation Method --- p.3 / Chapter 1.4 --- Conclusion and Interesting Topics --- p.5 / Chapter 2 --- The FDTD Mechanism --- p.6 / Chapter 2.1 --- Algorithm Method --- p.6 / Chapter 2.2 --- The Dielectric Function --- p.9 / Chapter 2.2.1 --- Drude Model Definition --- p.9 / Chapter 2.2.2 --- Drude Model Discretization --- p.10 / Chapter 2.2.3 --- Discussion on Models --- p.11 / Chapter 2.3 --- Accuracy and Stability --- p.12 / Chapter 2.3.1 --- Numerical Dispersion --- p.12 / Chapter 2.3.2 --- Courant Condition --- p.14 / Chapter 2.4 --- Time Dependence of the Methods --- p.15 / Chapter 2.5 --- Perfectly Matched Layer (PML) --- p.16 / Chapter 2.5.1 --- Boundaries Problem --- p.16 / Chapter 2.5.2 --- PML Main Theme --- p.17 / Chapter 2.5.3 --- Different Types of PMLs --- p.20 / Chapter 2.6 --- Conclusion: Simulation Laboratory --- p.20 / Chapter 3 --- Software Comparison and Scaling Usage --- p.22 / Chapter 3.1 --- Physical Quantity Interested --- p.22 / Chapter 3.1.1 --- Cross-sections and Relation to Surface Plasmon Excitation --- p.23 / Chapter 3.2 --- Mie Theory --- p.24 / Chapter 3.2.1 --- Spherical Harmonics --- p.24 / Chapter 3.2.2 --- Expressing the terms in Spherical Harmonics --- p.26 / Chapter 3.2.3 --- Matching Boundaries --- p.27 / Chapter 3.2.4 --- Scattering and Extinction Cross-sections --- p.28 / Chapter 3.3 --- Software Used --- p.29 / Chapter 3.3.1 --- Meep --- p.29 / Chapter 3.3.2 --- Lumerical FDTD Solution --- p.30 / Chapter 3.4 --- Machines Used for Comparison --- p.30 / Chapter 3.5 --- Ease of Usage --- p.30 / Chapter 3.5.1 --- Installation --- p.31 / Chapter 3.5.2 --- Support --- p.32 / Chapter 3.5.3 --- Parallel Computation --- p.33 / Chapter 3.6 --- The Check Case Building --- p.33 / Chapter 3.6.1 --- Monitor Measurement Related to Time for Simulation --- p.34 / Chapter 3.6.2 --- Meep's Implementation --- p.34 / Chapter 3.6.3 --- Total Field Scattering Field (TFSF) Source --- p.35 / Chapter 3.6.4 --- Lumerical FDTD Solutions' Implement at ion --- p.36 / Chapter 3.7 --- Comparison --- p.37 / Chapter 3.7.1 --- Accuracy of the Programs --- p.37 / Chapter 3.7.2 --- Time Needed for the Programs --- p.43 / Chapter 3.8 --- Conclusion: How to Build Reasonable Running Cases --- p.46 / Chapter 4 --- The Projects on Nanorods --- p.47 / Chapter 4.1 --- Basic Understanding of Nanorods --- p.47 / Chapter 4.1.1 --- Geometry Dependence on Localized Surface Plasmon Resonance in Au Nanorods --- p.48 / Chapter 4.1.2 --- Plasmonic Coupling in Au Nanorod Dimers --- p.49 / Chapter 4.2 --- Size-Dependent Scattering and Absorption Cross-sections for Au Nanocrystals --- p.51 / Chapter 4.2.1 --- Measurement of Data --- p.51 / Chapter 4.2.2 --- Setup of Simulation --- p.52 / Chapter 4.2.3 --- Results and Conclusion --- p.54 / Chapter 4.3 --- Angle-Dependent Plasmon Coupling in Au Nanorod Dimers --- p.56 / Chapter 4.3.1 --- Setup of Experiment --- p.56 / Chapter 4.3.2 --- Setup of Simulation --- p.57 / Chapter 4.3.3 --- Results of Simulation --- p.59 / Chapter 4.3.4 --- The Dipolar Model Discussion --- p.62 / Chapter 4.3.5 --- Conclusion --- p.65 / Chapter 4.4 --- Plasmon Coupling in Linear Au Nanorod Dimers --- p.65 / Chapter 4.4.1 --- Experimental Results --- p.66 / Chapter 4.4.2 --- Energy Dependent Plasmon Coupling of Au Nanorod Dimers --- p.67 / Chapter 4.4.3 --- Dependency of the Plasmon Coupling on the Inter-particle Distance --- p.70 / Chapter 4.4.4 --- Dependency of the Plasmon Coupling on the Head Shape of Au Nanocrystals --- p.74 / Chapter 4.4.5 --- Coupling-induced Fano-Resonance in Au Nanorod Het- erodimers --- p.74 / Chapter 4.4.6 --- Conclusion --- p.78 / Chapter 4.5 --- Conclusion --- p.80 / Chapter 5 --- Conclusion --- p.81 / Bibliography --- p.84

Histone post-translational modifications (PTMs) are key determinants of the local chromatin landscape and critical for regulation of eukaryotic gene expression. These histone marks are deposited by a vast number of chromatin modifying enzymes and preferentially recognized by specific associated histone reader domains. Recognition of histone PTMs by histone reader domains is important for either targeting these complexes to chromatin or regulating their enzymatic activity once there. The Polycomb repressive complex 1 and 2 (PRC1 and PRC2) are two such chromatin modifying complexes that are critical for developmental gene repression. The enzymatic activity of PRC2 is tightly regulated by many histone reader domains whereas the PRC1 complex is targeted to chromatin through these domains. In this thesis, I explore how PRC1 and PRC2 functions are regulated by histone reader domains. I identify a previously unrecognized histone reader domain within the PRC2 complex, the EZH2 SANT1 domain, which has important implications for regulating PRC2 enzymatic activity. In addition, I explore the mechanism through which the CBX8 chromodomain targets the PRC1 complex to chromatin. Together, these studies provide significant insight into the regulation of chromatin modifying complexes by histone reader domains and how this occurs via multiple mechanisms.

We have constructed a new finite-difference time-domain (FDTD) method in this project. Our new algorithm focuses on the most important and more challenging transverse electric (TE) case. In this case, the electric field is discontinuous across the interface between different dielectric media. We use an electric permittivity that stays as a constant in each medium, and magnetic permittivity that is constant in the whole domain. To handle the interface between different media, we introduce new effective permittivities that incorporates electromagnetic fields boundary conditions. That is, across the interface between two different media, the tangential component, Er(x,y), of the electric field and the normal component, Dn(x,y), of the electric displacement are continuous. Meanwhile, the magnetic field, H(x,y), stays as continuous in the whole domain. Our new algorithm is built based upon the integral version of the Maxwell's equations as well as the above continuity conditions. The theoretical analysis shows that the new algorithm can reach second-order convergence O(∆x2)with mesh size ∆x. The subsequent numerical results demonstrate this algorithm is very stable and its convergence order can reach very close to second order, considering accumulation of some unexpected numerical approximation and truncation errors. In fact, our algorithm has clearly demonstrated significant improvement over all related FDTD methods using effective permittivities reported in the literature. Therefore, our new algorithm turns out to be the most effective and stable FDTD method to solve Maxwell's equations involving multiple media.

The motion of domain walls due to the spin torque generated by coherent carrier transport is of considerable interest for the development of spintronic devices. We model the charge and spin transport through domain walls in ferromagnetic semiconductors for various systems. With an appropriate model Hamiltonian for the spin– dependent potential, we calculate wavefunctions inside the domain walls which are then used to calculate transmission and reflection coefficients, which are then in turn used to calculate current and spin torque. Starting with a simple approximation for the change in magnetization inside the domain wall, and ending with a sophisticated transfer matrix method, we model the common π wall, the less–studied 2π wall, and a system of two π walls separated by a variable distance. We uncover an interesting width dependence on the transport properties of the domain wall. 2π walls in particular, have definitive maximums in resistance and spin torque for certain domain wall widths that can be seen as a function of the spin mistracking in the system — when the spins are either passing straight through the domain wall (narrow walls) or adiabatically following the magnetization (wide walls), the resistance is low as transmission is high. In the intermediate region, there is room for the spins to rotate their magnetization, but not necessarily all the way through a 360 degree rotation, leading to reflection and resistance. We also calculate that there are widths for which the total velocity of a 2π wall is greater than that of a same–sized π wall. In the double–wall system, we model how the system reacts to changes in the separation of the domain walls. When the domain walls are far apart, they act as a spin–selective resonant double barrier, with sharp resonance peaks in the transmission profile. Brought closer and closer together, the number and sharpness of the peaks decrease, the spectrum smooths out, and the domain walls brought together have a transmission spectrum with many of the similar features from the 2π wall. Looking at the individual walls, we find an interesting interaction that has three distinct regimes: 1) repulsion, where the left wall moves to the left and the right wall to the right; 2) motion together, where the two walls both move to the right, even at the same velocity for one special value of separation; and 3) attraction, where the left wall moves to the right and the right wall moves to the left. This speaks to a kind of natural equilibrium distance between the domain walls. This is of major interest for device purposes as it means that stacks of domain walls could be self–correcting in their motions along a track. Much experimental work needs to be done to make this a reality, however.

Graduation date: 1999

A new second order accurate nonuniform grid spacing technique which does not depend on supraconvergence is developed for Finite Difference Time Domain (FDTD) simulation of general three dimensional structures. The technique is useful for FDTD simulations of systems which require finer details in small regions of the simulation space by providing the ability to utilize nonuniform grid spacing. The stability conditions of the new technique are derived and shown to be consistent with uniform grid formulation and the accuracy of the technique is investigated and shown to be second order. The advantage of the new technique is that it allows for greater simulation detail while reducing the computational and memory requirements compared to the current uniform grid FDTD techniques. Additionally, the derivation of the expressions associated with the inclusion of material properties in the FDTD simulation with nonuniform grids is presented allowing for the development of a nonuniform FDTD simulator for general lossy 3D systems associated with on and off chip interconnects, electronic packages and microwave circuits. In order to illustrate the utility of this simulator, time domain electromagnetic simulation of a 3-D lossy interconnect structure associated with a generic surface mount IC package is presented. The time domain currents and fields are computed in the structure to investigate ground bounce, signal degradation, and crosstalk associated with the interconnects and packaging structure. The supply plane conductivities are included in the simulation allowing the observation of the current densities in the power/ground planes as a function of time. Finally, the FDTD simulation tool is proposed and used as a Virtual TDR (V-TDR) to extract the circuit models associated with complex 3D structures. The time domain response of a multiport structure is used to extract the equivalent circuit parameters to characterize the multiport by using the multiport time domain reflection (TDR) based general deconvolution algorithm. Examples of coupled interconnects and transmission lines are presented to illustrate this technique. / Graduation date: 1997

The purpose of this study is to develop accuracy enhancement techniques for the Time Domain Reflection/Transmission (TDR/T) measurements including the analysis of the error sources for the Enhanced Accuracy TDR/T (EA-TDR/T). These TDR/T techniques are used for IC and IC package interconnect characterization and equivalent circuit model extraction, which are important for evaluating the overall system performance in today's digital IC design. The frequency domain error correction has been used to get parameters for a Device Under Test (DUT) from time domain measurements. The same technique can be used as an intermediate step for obtaining the EA-TDR/T. Careful choice of the acquisition window and precise alignment of the DUT and calibration standard waveforms are necessary to get the accuracy enhancement for the TDR/T. Improved FFT techniques are used in order to recover the actual spectra of the step-like time domain waveforms acquired with an acquisition window with a finite time length. The EA-TDR/T waveform are recovered from error corrected frequency domain parameters of the DUT by launching an ideal excitation at the DUT and finding the response. The rise time of the ideal excitation can be faster than that of the physical excitation in the measurement system. However, excessive high-frequency noise can enter the system if the rise time of the ideal excitation is chosen to be too high. The resulting EA-TDR/T waveforms show significantly less aberrations than the conventional TDR/T waveforms, hence allow us to extract accurate equivalent circuit model for the DUT, which in our case is IC interconnects. / Graduation date: 1995

The improved accuracy of Time Domain Reflection and Transmission (TDR/T) measurements made possible by the calibration process known as Time Domain Network Analysis (TDNA) is applied to the problem of characterization and modeling of electronic interconnect and packaging structures. TDNA uses measurements of known and partially known calibration standards to characterize the measurement system allowing for the correction of the raw measurements of an unknown network to eliminate the effects of system non-idealities and resulting in a significant improvement of the measurement quality. The correction process is shown to be analogous to the well established Frequency Domain Vector Network Analyzer calibrations and to have the same capabilities for high precision metrology applications. Methods are developed to extract electrical circuit models from time domain measurements of lossless, nonuniform, multiconductor transmission lines for two broad classes of structures. Although unique solutions are not feasible for general structures that scatter the propagating wave-front, approximate solutions have been identified using the assumption of a single velocity wave-front, the case for homogeneous media. For structures with identical lines, such as a parallel line bus structure, the propagation behavior (eigenvector matrix) is determined only by the number of conductors, N, and is therefore known a priori for the entire structure allowing decoupling of the system into N orthogonal nonuniform transmission lines. Circuit models have been developed for these decoupled nonuniform lines as well as for the equal modal velocity assumption which relies on a matrix impedance profile to fully describe the system. The implications of non-ideal grounding of interconnection circuits is explored. Traditional lumped element methods for modeling these effects are examined and typical examples where distributed circuit models are necessary to adequately describe the system are identified. Techniques for examining power-planes and substrate connections in integrated circuits and integrated circuit packages using the distributed ground model are presented. Novel circuit design methods to circumvent the limitations imposed by non-ideal grounds and nonzero length transmission structures are also proposed. / Graduation date: 1994

[by] Charles Kittel. / "Reprinted from the Physical review, vol. 70, nos. 11 and 12, 965-971, Dec. 1 and 15, 1946." / Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Dallas, 2006. / Includes vita. Includes bibliographical references (leaves 253-256).