Wong Yuen-yee. / Thesis submitted in: August 2005. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 121-125). / Abstracts in English and Chinese. / THESIS COMMITTEE --- p.ii / ABSTRACT --- p.iii / 摘要 --- p.iv / ACKNOWLEDGEMENTS --- p.v / TABLE OF CONTENT --- p.vi / LIST OF TABLES --- p.viii / LIST OF FIGURES --- p.xi / Chapter Chapter 1 --- Introduction --- p.1 / Chapter Chapter 2 --- Quantum Mechanical Background --- p.9 / Chapter 2.1 --- Molecular energy operator and the Born-Oppenheimer approximation --- p.9 / Chapter 2.2 --- Electronic wavefunctions --- p.16 / Chapter 2.3 --- Vibrational wavefunctions --- p.22 / Chapter 2.4 --- Rotational wave function --- p.28 / Chapter 2.5 --- Tunneling Phenomenon --- p.31 / Chapter Chapter 3 --- Implementation --- p.35 / Chapter 3.1 --- Inversion potential --- p.37 / Chapter 3.2 --- Zero-field vibrational wavefunctions --- p.39 / Chapter 3.3 --- Zero-field rovibrational levels --- p.43 / Chapter 3.4 --- Stark energy and rovibrational levels in DC fields --- p.49 / Chapter 3.5 --- Transition dipole moments and intensities calculations --- p.52 / Chapter Chapter 4 --- Results and Discussions --- p.57 / Chapter 4.1 --- "Inversion potentials, levels, and energies" --- p.57 / Chapter 4.2 --- Rovibrational levels and spectrum at zero-field --- p.70 / Chapter 4.3 --- Rovibrational spectrum in DC fields --- p.83 / Chapter 4.3.1 --- Localization of vibrational wavefunctions --- p.83 / Chapter 4.3.2 --- Rovibrational energies and spectra --- p.89 / Chapter 4.4 --- Discussion --- p.118 / REFERENCE --- p.121

The aim of this thesis is to use computer simulation methods to consider adsorption of both water and carbon dioxide onto oxide surfaces. The materials chosen have direct relevance to current environmental concerns, alkaline earth metal oxides for carbon sequestration and uranium dioxide for the storage and stability of nuclear materials. Chapter one outlines both previous experimental and computational work relevant to these research areas. The computational methodologies used in this thesis are described in chapters two and three. Chapter two outlines how the forces between atoms in the simulation are modelled using both potential-based and electronic structure models. Chapter three details how these are then used to find lowest energy configurations. The main results of the alkaline earth metal oxides are discussed in chapters four and five. Chapter four uses multiconfigurational static lattice simulations of water and CO2 surface adsorptions to identify the most probable adsorption sites and to generate surface phase diagrams as a function of surface composition. Whereas the focus of chapter five is to model interactions in liquid water with both surface and nanoparticles. Chapters six and seven describe the results of simulations on uranium dioxide. Chapter six uses electronic structure methods to model defects and nonstoichiometry in bulk and thin film structures. Chapter seven then describes the calculations of the interactions of water with uranium dioxide surfaces, in terms of both gas phase adsorption and the mineral – water interface with results showing the favourability of surface hydroxylation on the {100} and {110} surfaces. Finally, a summary of the main findings and achievements of this thesis are given in chapter nine, along with a discussion of possible future work.

The work in this thesis aims to gain fundamental understanding of several important types of disordered systems, including liquids, supercritical fluids and amorphous solids on the basis of extensive molecular dynamics simulations. I begin with studying the diffusion in amorphous zirconolite, a potential waste form to encapsulate highly radioactive nuclear waste. I find that amorphization has a dramatic effect for diffusion. Interestingly and differently from previous understanding, diffusion increases as a result of amorphization at constant density. Another interesting insight is related to different response of diffusion of different atomic species to structural disorder. I calculate activation energies and diffusion pre-factors which can be used to predict long-term diffusion properties in this system. This improves our understanding of how waste forms operate and provides a quantitative tool to predict their performance. I subsequently study the effects of phase coexistence and phase decomposition in Y-stabilized zirconia, the system of interest in many industrial applications including in encapsulating nuclear waste due to its exceptional resistance to radiation damage. For the first time I show how the microstructure emerges and evolves in this system and demonstrate its importance for self-diffusion and other properties. This has not been observed before and is important for better understanding of existing experiments and planning the new ones. I subsequently address dynamical properties of subcritical liquids and supercritical fluids. I start with developing a new empirical potential for CO2 with improved performance. Using this and other potentials, I simulate the properties of supercritical H2O, CO2 and CH4 and map their Frenkel lines in the supercritical region of the phase diagram. I observe that the Frenkel line for CO2 coincides with experimentally found maxima of solubility and explain this finding by noting that the Frenkel line corresponds to the optimal combination of density and temperature where the density is maximal and the diffusion is still in the fast gas-like regime. This can serve as a guide in future applications of supercritical fluids and will result in their more efficient use in dissolving and extracting applications. I extend my study to collective modes in liquids. Here, my simulations provide first direct evidence that a gap emerges and evolves in the reciprocal space in transverse spectra of liquids. I show that the gap increases with temperature and is inversely proportional to liquid relaxation time. Interestingly, the gap emerges and evolves not only in subcritical liquids but also in supercritical fluids as long as they are below the Frenkel line. Given the importance of phonons in condensed matter physics and other areas of physics, I propose that the discovery of the gap represents a paradigm change. There is an active interest in the dynamics of liquids and supercritical fluids, and I therefore hope that my results will quickly stimulate high-temperature and high-pressure experiments aimed at detecting and studying the gap in several important systems.

Integral Membrane Proteins (IMPs) are an important and scientifically interesting class of protein which span the lipid bilayer surrounding cells, cell compartments and many viruses. Molecular Dynamics (MD) simulation has revealed intimate and often highly specific relationships between membrane lipids and IMPs critical to many metabolic and signalling pathways. Meanwhile, the use of Coarse-Grained (CG) MD techniques has extended capabilities of biomolecular simulation to larger proteins over longer time periods. Several tools and resources for biomolecular simulations of IMPs are presented here, as well as two MD studies of specific IMPs. The previously developed MemProtMD pipeline automates the setup of MD simulations of IMPs; major extensions to this are presented here with the MemProtMD database and web server, automating the analysis of IMP simulations. The results of this can be viewed using the MemProtMD web server, an interactive, searchable online resource containing data from simulations of over 3000 experimentally determined IMP structures in explicit lipid bilayers. Using data from analysis of the entire MemProtMD database, MemProtMetrics has been developed to automate identification and orientation of IMP structures from Protein DataBank (PDB) depositions. This is shown to effectively predict membrane protein orientations seen in MD simulations. A tool for identification and classification of membrane lipids is also described, and used to identify over 500 IMPs structures with resolved lipids. CGMD simulations have also been used to assess dependence on side-chain ionisation state of interactions between lipids and two IMPs observed in mass spectrometry experiments. The simulations reveal similar trends to those seen in experiments. Finally, using multi-scale simulations, and through the development of a novel method for altering membrane composition in MD simulations, lipid-specific scramblase activity was shown for a novel structure of the TMEM16K scramblase IMP.

No description available.

Zhang Liang = 乙烯溴在異丁基杯(四)芳烴晶體中擴散機理的從頭算研究 / 章良. / Thesis submitted in: August 2004. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references. / Text in English; abstracts in English and Chinese. / Zhang Liang = Yi xi xiu zai yi ding ji bei (si) fang jing jing ti zhong kuo san ji li de cong tou suan yan jiu / Zhang Liang. / TITLE PAGE --- p.i / THESIS COMMUTE --- p.ii / ABSTRACT (English) --- p.iii / ABSTRACT (Chinese) --- p.iv / ACKNOWLEDGMENTS --- p.v / TABLE OF CONTENTS --- p.vi / LIST OF FIGURES --- p.viii / LIST OF TABLES --- p.ix / Chapter CHAPTER 1 --- Introduction / Chapter 1.1 --- Background Information of Calixarenes --- p.1 / Chapter 1.1.1 --- "History, Synthesis and Applications" --- p.1 / Chapter 1.1.2 --- Physical Properties --- p.2 / Chapter 1.1.3 --- Conformation of Calix[4]arenes --- p.3 / Chapter 1.1.4 --- Inclusion and Host-Guest Interactions --- p.4 / Chapter 1.2 --- Computational Theory --- p.8 / Chapter 1.2.1 --- Framework of Self-Consistent Field (SCF) --- p.8 / Chapter 1.2.2 --- Density function theory (DFT) --- p.9 / Chapter 1.3 --- Constrained Optimization Methods --- p.13 / Chapter 1.3.1 --- Introduction --- p.13 / Chapter 1.3.2 --- Augmented Lagrangian Method --- p.14 / Chapter 1.4 --- References --- p.16 / Chapter CHAPTER 2 --- Transformations of TBC4 Crystals / Chapter 2.1 --- Introduction and Experimental Results --- p.19 / Chapter 2.2 --- "II (""ab/ab"") to I (""ab/cd"") Transformation" --- p.21 / Chapter 2.3 --- "I (""ab/cd"") to III (Capsule) Transformation" --- p.25 / Chapter 2.4 --- Torsion of Capsulation --- p.27 / Chapter 2.5 --- References --- p.31 / Chapter CHAPTER 3 --- Diffusion through TBC4 Crystal / Chapter 3.1 --- Experimental Facts --- p.32 / Chapter 3.1.1 --- Kinds of TBC4 Inclusions --- p.32 / Chapter 3.1.2 --- "Inclusions of O2, vinyl bromide, toluene in TBC4" --- p.36 / Chapter 3.2 --- Diffusion of 02 in “ab/cd´ح TBC4 --- p.40 / Chapter 3.3 --- Diffusion of Vinyl Bromide through TBC4 --- p.44 / Chapter 3.3.1 --- "Vinyl bromide diffuses in ""ab/cd"" TBC4" --- p.45 / Chapter 3.3.2 --- Transformation/migration mechanism --- p.47 / Chapter 3.4 --- References --- p.51

"November 2002." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (p. 206-213). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Wong Chiu Tai, Andrew = 粒子懸浮液的自結合和場引發結合 / 黃昭泰. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 70-73). / Text in English; abstracts in English and Chinese. / Wong Chiu Tai, Andrew = Li zi xuan fu ye de zi jie he he chang yin fa jie he / Huang Zhaotai. / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Self assembly --- p.1 / Chapter 1.1.1 --- What is self assembly? --- p.1 / Chapter 1.1.2 --- Recent works --- p.1 / Chapter 1.2 --- Field induced assembly --- p.2 / Chapter 1.2.1 --- What is field induced assembly? --- p.2 / Chapter 1.2.2 --- Recent works --- p.3 / Chapter 1.3 --- Objective of the thesis --- p.4 / Chapter 2 --- Self Assembly of Binary Colloidal Alloys --- p.6 / Chapter 2.1 --- Interaction between colloidal suspensions --- p.7 / Chapter 2.1.1 --- Van der Waals interaction energy between two spheres --- p.7 / Chapter 2.1.2 --- Screened Coulomb Repulsion --- p.9 / Chapter 2.1.3 --- Derjaguin-Landau-Verwey-Overbeek potential --- p.12 / Chapter 2.1.4 --- DNA-mediated Colloidal Interaction --- p.13 / Chapter 2.2 --- 2D Molecular Dynamics Simulation --- p.14 / Chapter 2.2.1 --- One type of particles with attractive force --- p.16 / Chapter 2.2.2 --- Two type of particles --- p.18 / Chapter 2.2.3 --- Results --- p.19 / Chapter 2.2.4 --- Conclusion --- p.23 / Chapter 2.3 --- 3D Molecular Dynamics Simulation --- p.25 / Chapter 2.3.1 --- One type of particles with attractive force --- p.26 / Chapter 2.3.2 --- Two type of particles --- p.27 / Chapter 2.3.3 --- Results --- p.28 / Chapter 2.3.4 --- Conclusion --- p.32 / Chapter 3 --- Electrorheological Rotors --- p.34 / Chapter 3.1 --- Formalism --- p.35 / Chapter 3.2 --- MD Simulations and Results --- p.38 / Chapter 3.3 --- Discussion and conclusion --- p.39 / Chapter 4 --- Electrorheological Suspensions in Rotating Fields --- p.42 / Chapter 4.1 --- Long-range rotating field simulation --- p.43 / Chapter 4.1.1 --- Simulation method --- p.43 / Chapter 4.1.2 --- Result --- p.46 / Chapter 4.2 --- Uniform Rotating Shear Flow --- p.49 / Chapter 4.3 --- Discussion and conclusion --- p.50 / Chapter 5 --- Comparison between many body and multiple image effect --- p.53 / Chapter 5.1 --- Multiple image method --- p.54 / Chapter 5.2 --- Anisotropic many-body-MID model --- p.56 / Chapter 5.3 --- Computer simulation in the many-body-DID model --- p.59 / Chapter 5.4 --- Discussion and conclusion --- p.60 / Chapter 6 --- Conclusion --- p.68 / Bibliography --- p.70 / Chapter A --- Derivation of multiple image expression --- p.74 / Chapter A.1 --- Image of a point dipole on a sphere --- p.74 / Chapter A.2 --- Multiple images of induced dipole --- p.74 / Chapter B --- Derivation of anisotropic Maxwell-Garnett Approximation --- p.80 / Chapter B.1 --- Isotropic Maxwell-Garnett Approximation --- p.80 / Chapter B.2 --- Anisotropic Maxwell-Garnett Approximation --- p.82

Fusion of viral and host membranes is a key step during infection by membrane-enclosed viruses. The fusion pore plays a critical role, and must dilate to release the viral genome. Prior studies of fusion mediated by influenza A hemagglutinin (HA) revealed ~2-5 nm pores that flickered before dilating to >10 nm. The mechanisms involved are unknown. Here we studied HA-mediated fusion pore dynamics using a novel single-pore assay (supported by a novel, robust, single-cell optical assay for fusion between HA-expressing cells and nanodiscs), combined with computational simulations accessing extraordinarily long (ms) timescales. We measured pores between HA-expressing fibroblasts and bilayer nanodiscs. From pore currents we infer pore size with millisecond time resolution. Unlike previous in vitro studies, the use of nanodiscs limited the membrane contact areas and maximum pore sizes, better mimicking the initial phases of virus-endosome fusion. In wild-type (WT) HA-mediated fusion pores, pores flickered about a mean pore size ~1.7 nm. In contrast, fusion pores formed by GPI-anchored HA nucleated at less than half the WT rate; results were consistent with earlier findings that showed that while GPI-HA pores stabilize at larger initial conductances than WT, they were not able to enlarge beyond their initial size. We developed radically coarse-grained, explicit lipid molecular dynamics simulations of the fusion pore reconstituted with post-fusion, trans HA hairpins. With WT HA, fusion pores were small, similar to experiment. Over time hairpins gradually converted from trans to cis. With lipid-anchored HA, the trans → cis transition was much accelerated. Once most hairpins had converted to cis, because apposing membranes were released, the fusion pore was able to dilate to sizes close to protein-free. Additionally, in crowded simulations with HA densities approximating those found in HA clusters, we found that HA aggregation, promoted by TMD-TMD interactions, delayed fusion pore dilation by inhibiting the trans → cis transition. Our results suggest that pore dilation requires the trans → cis transition. We hypothesize that this transition is accelerated in GPI-HA by the more mobile lipid anchor, and may explain the larger observed nascent fusion pores.

In an attempt at studying tunneling motions in the solid para -H2, the infrared absorption spectrum of matrix-isolated ammonia molecules (NH3) has been studied using Fourier-transform infrared (FTIR) spectroscopy. The transitions of the ammonia molecule in the v2 fundamental band were observed to exhibit very different pattern compared to those observed in other matrix materials. A preliminary analysis of the observed spectrum was also discussed based on the effect of crystal annealing and nuclear spin conversion of NH3. Transitions have been assigned to ortho and para species of NH3 based on there behavior in the presence of O2. For a more definitive assignment, further experiments will be necessary. / In this thesis, high resolution infrared spectrum of tetrahexacontapole (64-pole)-induced rovibrational W transition of solid parahydrogen (para-H2) was studied in samples containing ∼0.05% of orthohydrogen (ortho-H2) using high resolution near infrared diode laser spectroscopy. The rovibrational W1(0) transition (v =1 ← 0,J = 6 ← 0) has been observed at ∼6441.73 cm-1 with resolved triplet structure. These components were interpreted as the splitting of the M levels in the v = 1, J = 6 state due to crystal field interaction. The corresponding crystal field parameters based on the model of localized exciton in the W1(0) transition were determined. The good agreement of the corresponding parameters between the W1(0) transition and the previous W0(0) transition confirms the localization of the J =6 roton in both v = 0 and 1 states for solid para-H2. In addition, the temperature dependence of the W1(0) transition was studied in the temperature range of 2.7-8.0 K. The observed frequency shift has been ascribed to the change of isotropic intermolecular interactions as a result of molar volume change at different temperature / Song, Yan. / "November 2009." / Source: Dissertation Abstracts International, Volume: 72-01, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 87-93). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.