Multiscale model reduction methods for deterministic and stochastic partial differential equations

Partial differential equations (PDEs) with multiscale coefficients are very difficult to solve due to the wide range of scales in the solutions. In the thesis, we propose some efficient numerical methods for both deterministic and stochastic PDEs based on the model reduction technique.

For the deterministic PDEs, the main purpose of our method is to derive an effective equation for the multiscale problem. An essential ingredient is to decompose the harmonic coordinate into a smooth part and a highly oscillatory part of which the magnitude is small. Such a decomposition plays a key role in our construction of the effective equation. We show that the solution to the effective equation is smooth, and could be resolved on a regular coarse mesh grid. Furthermore, we provide error analysis and show that the solution to the effective equation plus a correction term is close to the original multiscale solution.

For the stochastic PDEs, we propose the model reduction based data-driven stochastic method and multilevel Monte Carlo method. In the multiquery, setting and on the assumption that the ratio of the smallest scale and largest scale is not too small, we propose the multiscale data-driven stochastic method. We construct a data-driven stochastic basis and solve the coupled deterministic PDEs to obtain the solutions. For the tougher problems, we propose the multiscale multilevel Monte Carlo method. We apply the multilevel scheme to the effective equations and assemble the stiffness matrices efficiently on each coarse mesh grid. In both methods, the $\KL$ expansion plays an important role in extracting the main parts of some stochastic quantities.

For both the deterministic and stochastic PDEs, numerical results are presented to demonstrate the accuracy and robustness of the methods. We also show the computational time cost reduction in the numerical examples.

The isolation and partial biochemical analysis of Sindbis virus proteins

Recently, the amino acid sequences have been reported for several proteins, including the envelope glycoproteins of Sindbis virus, which all probably span the plasma membrane with a common topology: a large N-terminal, extracellular portion, a short region buried in the bilayer, and a short C-terminal intracellular segment. The regions of these proteins buried in the bilayer correspond to portions of the protein sequences which contain a stretch of hydrophobic amino acids and which have other common characteristics, as discussed. Reasons are also described for uncertainty, in some proteins more than others, as to the precise location of some parts of the sequence relative to the membrane.

The signal hypothesis for the transmembrane translocation of proteins is briefly described and its general applicability is reviewed. There are many proteins whose translocation is accurately described by this hypothesis, but some proteins are translocated in a different manner.

The transmembraneous glycoproteins E1 and E2 of Sindbis virus, as well as the only other virion protein, the capsid protein, were purified in amounts sufficient for biochemical analysis using sensitive techniques. The amino acid composition of each protein was determined, and extensive N-terminal sequences were obtained for E1 and E2. By these techniques E1 and E2 are indistinguishable from most water soluble proteins, as they do not contain an obvious excess of hydrophobic amino acids in their N-terminal regions or in the intact molecule.

The capsid protein was found to be blocked, and so its N-terminus could not be sequenced by the usual methods. However, with the use of a special labeling technique, it was possible to incorporate tritiated acetate into the N-terminus of the protein with good specificity, which was useful in the purification of peptides from which the first amino acids in the N-terminal sequence could be identified.

Nanomole amounts of PE2, the intracellular precursor of E2, were purified by an immuno-affinity technique, and its N-terminus was analyzed. Together with other work, these results showed that PE2 is not synthesized with an N-terminal extension, and the signal sequence for translocation is probably the N-terminal amino acid sequence of the protein. This N-terminus was found to be 80-90% blocked, also by Nacetylation, and this acetylation did not affect its function as a signal sequence. The putative signal sequence was also found to contain a glycosylated asparagine residue, but the inhibition of this glycosylation did not lead to the cleavage of the sequence.

The rate and mechanism of the partial oxidation of acetaldehyde by PPM concentrations of nitrogen dioxide

The thermal reaction between nitrogen dioxide and acetaldehyde in the gas phase was investigated at room temperature and atmospheric pressure. The initial rate of disappearance of nitrogen dioxide was 1.00 ± 0.03 order with respect to nitrogen dioxide and 1.00 ± 0.07 order with respect to acetaldehyde. An initial second order rate constant of (8.596 ± 0.189) x 10^-3 1.mole^-1 sec^-1 was obtained at 22.0 ± 0.1 °C and a total pressure of one atmosphere. The activation energy of the reaction was 12,900 cal/mole in the temperature range between 22°C and 122°C.

The products of the reaction were nitric oxide, carbon dioxide, methyl nitrite, nitromethane and a trace amount of trans-dimeric nitrosomethane. The addition of nitric oxide increased the rate of formation of nitromethane and decreased the rate of formation of methyl nitrite. There were no measurable surface effects due to the addition of glass wool or glass beads to the reactor.

Reactants and products were analyzed by gas chromatography. A mechanism was proposed incorporating the principal features of the reaction.

Optical properties of a square-lattice photonic crystal within the partial bandgap

Optical properties of a two-dimensional square-lattice photonic crystal are systematically investigated within the partial bandgap through anisotropic characteristics analysis and numerical simulation of field pattern. Using the plane-wave expansion method and Hellmann-Feynman theorem, the relationships between the incident and refracted angles for both phase and group velocities are calculated to analyze light propagation from air to photonic crystals. Three kinds of flat slab focusing are summarized and demonstrated by numerical simulations using the multiple scattering method. (c) 2007 Optical Society of America

Laser-induced damage threshold of ZrO2 thin films prepared at different oxygen partial pressures by electron-beam evaporation

ZrO2, films were deposited by electron-beam evaporation with the oxygen partial pressure varying from 3 X 10(-3) Pa to I I X 10(-3) Pa. The phase structure of the samples was characterized by x-ray diffraction (XRD). The thermal absorption of the films was measured by the surface thermal lensing technique. A spectrophotometer was employed to measure the refractive indices of the samples. The laser-induced damage threshold (LIDT) was assessed using a 1064, nm Nd: yttritium-aluminium-garnet pulsed laser at pulse width of 12 ns. The influence of oxygen partial pressure on the microstructure and LIDT of ZrO2 films was investigated. XRD data revealed that the films changed from polycrystalline to amorphous as the oxygen partial pressure increased. The variation of refractive index at 550 nm wavelength indicated that the packing density of the films decreased gradually with increasing oxygen partial pressure. The absorptance of the samples decreased monotonically from 125.2 to 84.5 ppm with increasing oxygen partial pressure. The damage threshold, values increased from 18.5 to 26.7 J/cm(2) for oxygen partial pressures varying from 3 X 10(-3) Pa to 9 X 10(-3) Pa, but decreased to 17.3 J/cm(2) in the case of I I X 10(-3) Pa. (C) 2005 American Vacuum Society.

Laser-induced damage threshold of ZrO2 thin films prepared at different oxygen partial pressures by electron-beam evaporation

ZrO2, films were deposited by electron-beam evaporation with the oxygen partial pressure varying from 3 X 10(-3) Pa to I I X 10(-3) Pa. The phase structure of the samples was characterized by x-ray diffraction (XRD). The thermal absorption of the films was measured by the surface thermal lensing technique. A spectrophotometer was employed to measure the refractive indices of the samples. The laser-induced damage threshold (LIDT) was assessed using a 1064, nm Nd: yttritium-aluminium-garnet pulsed laser at pulse width of 12 ns. The influence of oxygen partial pressure on the microstructure and LIDT of ZrO2 films was investigated. XRD data revealed that the films changed from polycrystalline to amorphous as the oxygen partial pressure increased. The variation of refractive index at 550 nm wavelength indicated that the packing density of the films decreased gradually with increasing oxygen partial pressure. The absorptance of the samples decreased monotonically from 125.2 to 84.5 ppm with increasing oxygen partial pressure. The damage threshold, values increased from 18.5 to 26.7 J/cm(2) for oxygen partial pressures varying from 3 X 10(-3) Pa to 9 X 10(-3) Pa, but decreased to 17.3 J/cm(2) in the case of I I X 10(-3) Pa. (C) 2005 American Vacuum Society.

Influence of oxygen partial pressure on the structure and photoluminescence of direct current reactive magnetron sputtering ZnO thin films

The effects of oxygen partial pressure on the structure and photoluminescence (PL) of ZnO films were studied. The films were prepared by direct current (DC) reactive magnetron sputtering with various oxygen concentrations at room temperature. With increasing oxygen ratio, the structure of films changes from zinc and zinc oxide phases, single-phase ZnO, to the (002) orientation, and the mechanical stresses exhibit from tensile stress to compressive stress. Films deposited at higher oxygen pressure show weaker emission intensities, which may result from the decrease of the oxygen vacancies and zinc interstitials in the film. This indicates that the emission in ZnO film originates from the oxygen vacancy and zinc interstitial-related defects. From optical transmittance spectra of ZnO films, the plasma edge shifts towards the shorter wavelength with the improvement of film stoichiometry. (C) 2004 Elsevier B.V. All rights reserved.

The effects of oxygen partial pressure on the optical absorption edge and the UV emission energy of ZnO films

The optical absorption edge and ultraviolet (UV) emission energy of ZnO films deposited by direct current (DC) reactive magnetron sputtering at room temperature have been investigated. With the oxygen ratio increasing, the structure of films changes from zinc and zinc oxide coexisting phase to single-phase ZnO and finally to the highly (002) orientation. Both the grain size and the stress of ZnO film vary with the oxygen partial pressure. Upon increasing the oxygen partial pressure in the growing ambient, the visible emission in the room-temperature photoluminescence spectra was suppressed without sacrificing the band-edge emission intensity in the ultraviolet region. The peaks of photoluminescence spectra were located at 3.06---3.15 eV. From optical transmittance spectra of ZnO films, the optical band gap edge was observed to shift towards shorter wavelength with the increase of oxygen partial pressure.

Effects of oxygen partial pressure on packing density and laser damage threshold of TiO2 thin films

TiO2 films are deposited by electron beam evaporation as a function of oxygen partial pressure. The packing density, refractive index, and extinction coefficient all decrease with the increase of pressure, which also induces the change of the film's microstructure, such as the increase of voids and H2O concentration in the film. The laser-induced damage threshold (LIDT) of the film increases monotonically with the rise of pressure in this experiment. The porous structure and low nonstoichiometric defects absorption contribute to the film's high LIDT. The films prepared at the lowest and the highest pressure show nonstoichiometric and surface-defects-induced damage features, respectively.(C) 2007 American Institute of Physics.