Ma Nap Tak. / Thesis submitted in: December 2004. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 109-114). / Abstracts in English and Chinese. / ABSTRACT (ENGLISH) --- p.iii / ABSTRACT (CHINESE) --- p.iv / ACKNOWLEDGMENTS --- p.v / ABBREVIATION --- p.vi / TABLE OF CONTENTS --- p.vii / LIST OF FIGURES --- p.x / LIST OF TABLES AND GRAPHS --- p.xii / Chapter CHAPTER 1 --- Introduction and Background --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- Hydrogen bonds (H-bonds) in DNA --- p.2 / Chapter 1.2.1 --- Experimental Evidences of Hydrogen Bonding --- p.3 / Chapter 1.3 --- Three-centered hydrogen bond (TCHB) --- p.4 / Chapter 1.3.1 --- Definition of Three-centered hydrogen bond (TCHB) --- p.5 / Chapter 1.3.2 --- Significance of Three-centered hydrogen bond (TCHB) --- p.6 / Chapter 1.3.3 --- Characterization of Three-centered hydrogen bond (TCHB) --- p.7 / Chapter 1.3.4 --- Classification of Three-centered hydrogen bond (TCHB) --- p.7 / Chapter 1.4 --- Charge transfer in DNA --- p.9 / Chapter 1.4.1 --- Theory of DNA charge transfer --- p.9 / Chapter 1.4.2 --- Short and long range hole transfer in DNA --- p.10 / Chapter 1.4.3 --- Electron transfer in DNA --- p.12 / Chapter 1.4.4 --- Summary of DNA charge transfer --- p.12 / Chapter 1.5 --- Thesis Scope --- p.13 / Chapter CHAPTER 2 --- Theory and methodology --- p.16 / Chapter 2.1 --- Introduction --- p.16 / Chapter 2.2 --- Theory --- p.17 / Chapter 2.2.1 --- Density Functional Theory (DFT) --- p.17 / Chapter 2.2.2 --- Basis set selection --- p.18 / Chapter 2.2.3 --- Natural Bond Orbital (NBO) --- p.19 / Chapter 2.2.3.1 --- Natural Population Analysis (NPA) --- p.20 / Chapter 2.2.3.2 --- E(2) --- p.20 / Chapter 2.2.3.2 --- bond index --- p.21 / Chapter 2.2.4 --- spin-spin coupling constants --- p.22 / Chapter 2.2.5 --- Molecular Orbital (MO) --- p.23 / Chapter 2.3 --- Methodology --- p.24 / Chapter 2.3.1 --- Test calculation for TCHBs by NBO --- p.24 / Chapter 2.3.2 --- Geometry Optimization --- p.24 / Chapter 2.3.3 --- NBO analysis --- p.25 / Chapter 2.3.4 --- J-coupling constants (lhJnx) and MO calculations --- p.26 / Chapter 2.4 --- Summary --- p.26 / Chapter CHAPTER 3 --- Results and Discussion --- Hydrogen bonding in DNA --- p.27 / Chapter 3.1 --- Introduction --- p.27 / Chapter 3.2 --- Method for extracting DNA dimer models --- p.27 / Chapter 3.3 --- Computed results of Inter H-bonds of the ten dimer models --- p.33 / Chapter 3.3.1 --- Geometric parameters --- p.33 / Chapter 3.3.2 --- Natural Bond Orbital (NBO) Analysis --- p.36 / Chapter 3.3.2.1 --- E(2) and Wiberg Bond index --- p.36 / Chapter 3.3.2.2 --- The relationship of E(2) and bond distance --- p.40 / Chapter 3.3.2.3 --- The relationship of E(2) and bond angle --- p.42 / Chapter 3.3.2.4 --- The relationship of E(2) and bond index --- p.44 / Chapter 3.3.3 --- Spin-Spin Coupling Constants of inter-H bonds --- p.46 / Chapter 3.3.3.1 --- The relationship of spin-spin coupling constant and distance --- p.49 / Chapter 3.3.3.2 --- The relationship of spin-spin coupling constant and bond angle --- p.50 / Chapter 3.3.3.3 --- The relationship of spin-spin coupling constant and E(2) energy --- p.52 / Chapter 3.4 --- Experimental Characterization of Three-centered H-bonds --- p.54 / Chapter 3.5 --- Theoretical Characterization of Three-centered H-bonds --- p.55 / Chapter 3.5.1 --- Geometry properties (360°C Rule) --- p.55 / Chapter 3.5.2 --- NMR properties (Spin-Spin Coupling Constants) --- p.55 / Chapter 3.5.3 --- NBO properties (E(2) and Wiberg bond index) --- p.56 / Chapter 3.6 --- Computed results of Three-centered hydrogen bonds (TCHBs) of the ten dimer models --- p.56 / Chapter 3.6.1 --- Natural Bond Orbital (NBO) Analysis --- p.56 / Chapter 3.6.1.1 --- Determination of TCHBs in the ten dimer models --- p.56 / Chapter 3.6.1.2 --- Analysis of TCHB interactions (E(2) and bond index) --- p.62 / Chapter 3.6.1.3 --- The relationship between E(2) and bond distance of TCHBs --- p.63 / Chapter 3.6.1.4 --- The relationship between E(2) and bond angle of TCHBs --- p.65 / Chapter 3.6.2 --- Spin-Spin Coupling Constants of TCHBs --- p.66 / Chapter 3.6.2.1 --- The relationship between spin-spin coupling constant and bond distance of TCHBs --- p.68 / Chapter 3.6.2.2 --- The relationship between spin-spin coupling constant and E(2) energy of TCHBs --- p.69 / Chapter 3.6.3 --- Geometry of TCHBs --- p.71 / Chapter 3.7 --- Summary --- p.72 / Chapter CHAPTER 4 --- Results and Discussion --- Charge location and charge transfer in DNA --- p.77 / Chapter 4.1 --- Introduction --- p.77 / Chapter 4.2 --- Method --- p.78 / Chapter 4.3 --- Computed results of the charge location of the trimer models --- p.81 / Chapter 4.3.1 --- Location of excess positive charge --- p.81 / Chapter 4.3.2 --- Location of excess negative charge --- p.90 / Chapter 4.4 --- Role of TCHBs in charge transfer --- p.95 / Chapter 4.4.1 --- Introduction --- p.95 / Chapter 4.4.2 --- "Analysis of G1G2C3, C3A4A5 and A8A9C10 trimers" --- p.96 / Chapter 4.4.3 --- Analysis of A7A8A9 and A8A9C10 trimers --- p.103 / Chapter 4.5 --- Summary --- p.105 / Chapter CHAPTER 5 --- Concluding Remarks --- p.107 / REFERENCES / APPENDIX

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Techniques from representation theory (Diaconis, 1988) and algebraic geometry (Drton et al., 2008) have been applied to the statistical analysis of discrete data with log-linear models. With these ideas in mind, we discuss the selection of sparse log-linear models, especially for binary data and data on other structured sample spaces. When a sample space and its symmetry group satisfy certain conditions, we construct a natural spanning set for the space of functions on the sample space which respects the isotypic decomposition; these vectors may be used in algorithms for model selection. The construction is explicitly carried out for the case of binary data.

Musculoskeletal injuries are the most common injuries sustained by athletes and military recruits and can result in decreased performance and lifelong disability. So common and costly are these injuries that the American Academy of Orthopedic Surgeons has provided guidelines for future research, including recommendations for the development of a large animal model of bone injury (USDA 2001). In human and veterinary medicine, digital radiography represents the primary diagnostic tool the physician uses to diagnose skeletal injury. Advances in digital radiography have provided the veterinarian with opportunities to make both simple and complex radiographic assessments. We investigated a simple quantitative measurement of the solar, concave aspect of the distal phalanx in the horse, termed the Palmar-Metric (PM). The PM was a significant predictor of solar cup volume (p < 0.001) and negatively correlated with age (r2 = 0.28, p < 0.05) as determined from 544 radiographs of the distal phalanx from the left and right front feet. Therefore, veterinarians should be aware of the age related change in the solar, concave aspect of the distal phalanx in the horse. We hypothesized that the decrease in the degree of concavity with age may be due to demineralization and subsequent loss of bone density along the solar margin of the distal phalanx. Therefore, we investigated the quantification of optical bone density (bone OD) via complex radiographic calibration. By developing a brightness/darkness index (BDI), the greyscale of radiographs, calibrated with an aluminum marker of varying known thickness, can be compared to the average density of a cross-section of bone. At varying radiographic exposure intensity (kV) and exposure time (mAs), Al BDI was a significant predictor of bone BDI (r2 = 0.960, p < 0.001) and bone OD (r2 = 0.971, p < 0.001). This method of calibration can be utilized by the radiologist to accurately assess bone OD regardless of technique, and allow direct comparison of radiographs taken under different exposure settings. This method successfully quantifies bone OD via measurement of BDI from standardized digital radiographs, allowing for the opacity of radiographs to be truly comparable when taken under different circumstances.

acase@tulane.edu / 1 / YD

This study measures the electron-induced luminescence (cathodoluminescence) for various samples of fused silica. With a band gap of ~8.9 eV, visible and near-IR (NIR) luminescence occurs only if there are states (localized defect or trap states) within the forbidden band gap for electrons to occupy. A model is presented based on the electronic band structure and defect density of states—used to explain electron transport in highly disordered insulating materials—which has been extended to describe the relative cathodoluminescent intensity and spectral bands as a function of incident beam energy and current density, sample temperatures, and emitted photon wavelength. Tests were conducted on two types of disordered SiO2 samples, the first type containing two variations: (i) thin (~60 nm) coatings on reflective metal substrates, and (ii) ~80 μm thick bulk samples. Luminescence was measured using a visible range SLR CCD still camera, a VIS/NIR image-intensified video camera, a NIR video camera, and a UV/VIS spectrometer. Sample temperature was varied from ~295 K to 40 K. The results of these tests were fit with the proposed model using saturation dose rate and mean shallow trap energy as fitting parameters and are summarized below. First, each incident energy has a corresponding penetration depth, or range, which determines the fraction of energy absorbed in the material. In the thinner samples, the range exceeds the thickness of the sample; therefore, the intensity decreases with increasing energy. However, for the thicker samples, the range is less than the sample thickness and the intensity increases linearly with incident energy. Next, at low current densities, luminescent intensity is linearly proportional to incident current density through the dose rate. At very high current densities, saturation is observed. Finally, the overall luminescent intensity increased exponentially as T decreased, until reaching an optimum temperature, where it falls off to zero (as the model predicts). The spectra show four distinct bands of emitted photon wavelengths, corresponding to four distinct energy distributions of defect states within the band gap, each behaving differently with temperature. The response of each band to temperature is indicative of the extent to which it is filled.

Systems involving quantisation arise in many areas of engineering, especially when digital implementations are involved. In this thesis we consider different aspects of quantisation in feedback control systems. We study two topics of interest: (a) quantisers that quadratically stabilise a given system and are efficient in the use of their quantisation levels and (b) the derivation of ultimate bounds for perturbed systems, especially when the perturbations arise from the use of quantisers. In the first part of the thesis we address problem (a) above. We consider quadratic stabilisation of discrete-time multiple-input systems by means of quantised static feedback and we measure the efficiency of a quantiser via the concept of quantisation density. Intuitively, the lower the density of a quantiser is, the more separated its quantisation levels are. We thus deal with the problem of optimising density over all quantisers that quadratically stabilise a given system with respect to a given control Lyapunov function. Most of the available results on this problem treat single-input systems, and the ones that deal with the multiple-input case consider only two-input systems. In this thesis, we derive several new results for multiple-input systems and also provide an alternative approach to deal with the single-input case. Our new results for multiple-input systems include the derivation of the structure of optimal quantisers and the explicit design of multivariable quantisers with finite density that are able to quadratically stabilise systems having an arbitrary number of inputs. For single-input systems, we provide an alternative approach to the analysis and design of optimal quantisers by establishing a link between the separation of the quantisation levels of a quantiser and the size of its quantisation regions. In the second part of the thesis we address problem (b) above. In the presence of perturbations, asymptotic stabilisation may not be possible. However, there may exist a bounded region that contains the equilibrium point and has the property that the system trajectories converge to this bounded region. When this bounded region exists, we say that the system trajectories are ultimately bounded, and that this bounded region is an ultimate bound for the system. The size of the ultimate bound quantifies the performance of the system in steady state. Hence, it is important to derive ultimate bounds that are as tight as possible. This part of the thesis addresses the problem of ultimate bound computation in settings involving several scalar quantisers, each having different features. We consider each quantised variable in the system to be a perturbed copy of the corresponding unquantised variable. This turns the original quantised system into a perturbed system, where the perturbation has a natural \emph{componentwise} bound. Moreover, according to the type of quantiser employed, the perturbation bound may depend on the system state. Typical methods to estimate ultimate bounds are based on the use of Lyapunov functions and usually require a bound on the norm of the perturbation. Applying these methods in the setting considered here may disregard important information on the structure of the perturbation bound. We therefore derive ultimate bounds on the system states that explicitly take account of the componentwise structure of the perturbation bound. The ultimate bounds derived also have a componentwise form, and can be systematically computed without having to, e.g. select a suitable Lyapunov function for the system. The results of this part of the thesis, though motivated by quantised systems, apply to more general perturbations, not necessarily arising from quantisation. / PhD Doctorate

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Optimal nutritional management of growing pigs is constrained by lack of quantitative information on the response of animals between 30 and 110 kg live weight to dietary energy content. Under 'ideal' conditions modern genotypes appear to adjust feed intake to maintain a constant DE intake over a much wider range of dietary energy concentrations than previously thought (Mullan et al, 1998). However, under commercial pen conditions, voluntary feed intake is lower, pigs respond in terms of both growth rate and feed conversion to dietary DE density considerably above the levels currently thought to maximise biological and economic responses. The present study was designed to provide information on the response of growing pigs to dietary energy content under ideal and commercial housing conditions for two growth periods 30-60kg liveweight and 60-100kg liveweight. The results of the pigs kept under individual (ideal) housed conditions were consistent with the literature in that they adjusted their voluntary feed intake with digestible energy density to maintain a constant energy intake. The results of the pigs kept in groups (commercial) housing conditions tended to increase their daily energy intake as the energy density of the feed increased. This increase in energy intake improved the growth rate of the pigs and increased the fat deposition of those pigs. Economic analysis of the experiments involving pigs in groups indicates that formulating diets to a least cost per megajoule of digestible energy is not the most profitable point to set the digestible energy density. Modelling programs need to be used to determine where the least cost per unit of growth of the pig occurs. This is the most economical digestible energy density to formulate too. This will have major impact on the cost of production of piggery operations as the cost of energy is the single most important parameter in the cost of producing a pig.

Bibliography: leaves [71]-[72]