Three dimensional (3-D) seismic reflection surveying is accepted as the preferred method for imaging complex geology for proving and developing commercial oil and gas fields. However, the cost of 3-D seismic recording and processing is substantial and often can be as expensive as the cost of production drilling. This is particularly the case for land oil field development, where the cost of 3-D surveying is often unacceptably high. Such high costs also restrict its application in coal exploration, where 2-D seismic methods have long been accepted.During the early 1980's, a low fold technique for recording land 3-D data was devised which offered significant cost savings. The technique was adapted by the author for land 3-D surveying over coal fields. Inherent in the technique was a requirement that the data must have a high signal-to-noise ratio, which is not generally the case in land surveying due to the presence of strong source generated surface wave noise. A further major impediment to the technique was its inability to perform an acceptable stacking velocity analysis because of the low number of seismic traces generated. This thesis defines three data collection and processing advancements in low fold 3-D technology which go some way towards resolving these impediments.The first advancement is a method to enhance the signal-to-noise ratio of the stacked seismic data, and consists of a Radon-based transform which stacks shot domain data along a curved trajectory, thereby attenuating surface waves on swath recorded data. This transform is termed the 'Radial Transform' of 3-D data.The second advancement is a statics method to improve the stacked image from a low number of input traces. The method uses the concept that if both the reflected and refracted waves pass through a weathering layer with very similar travel paths, then static corrections to remove the ++ / effects of weathering variations on the refraction travel times would be very similar to those required for the reflections. This method, which was patented, is used equally for both 2-D and 3-D field data, and is regularly used in high resolution seismic processing for coal at Curtin University.The third advancement resolves the problem of azimuthal variation of stacking velocities. By predicting the true reflector dip and its azimuth, apparent dip can be included in the normal moveout equation, which is named the Generalized Moveout equation. The requirement for an azimuthally dependent stacking velocity is then no longer an impediment in low fold 3-D processing of coal data.After developing these transforms and applying them to synthetic data, they were tested with success on modelled field data. All field data used within this thesis were either recorded in the field by the author, or were produced with a physical modelling system, which was built by the author at the University of Houston and later at Curtin University.Results indicate that the procedures described in this thesis enable the low fold 3-D technique to be used as a viable method for recording seismic data when survey economics are a major issue. Furthermore, all three advancements are suitable for application in conventional two dimensional (2-D) and swath seismic surveying.

This thesis discusses the effects of basal friction and basement configuration on the deformation of the fold-and-thrust belts in convergent zones. A series of analogue models were conducted with adjacent different basal configuration and frictional properties to observe and gain a better understanding of these basal effects and their interactions. The results from these side-by-side systematic models demonstrate that the kinematics and geometry of the deformation wedges are strongly influenced by the mechanical and geometrical basal effects. In these experiments, high accuracy laser scanner and digital camera were used to record the evolution of the surface topography of the deformed sand packs. Comparison between models with different basal friction shows that the basal friction plays a significant role on the propagation and topography of the deformation structures in aspects such as wedge height, taper angle, number of imbricates and deformation front. The models with a basal viscous material, which acts as low friction substrate, illustrates that the propagation of deformation above viscous material is faster and further than above the adjacent mechanically different frictional decollement. In the experiments with a moving plate under the part of the sand pack, the velocity discontinuity was introduced by either rigid, i.e. frontal edge of the metal plate, or deformable like distal end of the viscous materials. The results of these kinds of experiments, applicable to for example basement faults, salt decollements and tectonic underplating simulations, illustrate that the deformation localizes and develops continuously above the velocity discontinuities. Besides, the different rate and distance of the propagation of deformation fronts caused by different substrate distribution between the adjacent zones also lead to the formation of transpressive zones at the boundary of these adjacent domains with different basal friction/configurations.

The 3D structures of proteins may provide important clues to their functions and roles in complex biological pathways. Traditional methods such as X-ray crystallography and NMR are not feasible for all proteins, while theoretical models are typically not validated by experimental data. This project investigates the use of chemical crosslinkers as an experimental means of validating these models. Five target proteins were successfully purified from yeast whole cell extract: Transketolase (TKL1), inorganic pyrophosphatase (IPP1), amidotransferase/cyclase HIS7, phosphoglycerate kinase (PGK1) and enolase (ENO1). These TAP-tagged target proteins from yeast <em>Saccharomyces cerevisiae</em> allowed the protein to be isolated in two affinity purification steps. Subsequent structural analysis used the homobifunctional chemical crosslinker BS³ to join pairs of lysine residues on the surface of the purified protein via a flexible spacer arm. Mass spectrometry (MS) analysis of the crosslinked protein generated a set of mass values for crosslinked and non-crosslinked peptides, which was used to identify surface lysine residues in close proximity. The Automatic Spectrum Assignment Program was used to assign sequence information to the crosslinked peptides. This data provided inter-residue distance constraints that can be used to validate or refute theoretical protein structure models generated by structure prediction software such as SWISS-MODEL and RAPTOR. This approach was able to validate the structure models for four of the target proteins, TKL1, IPP1, HIS7 and ENO1. It also successfully selected the correct models for TKL1 and IPP1 from a protein model library and provided weak support for the HIS7, PGK1 and ENO1 models.

Protein structure prediction has been a fundamental challenge in the biological field. In this post-genomic era, the need for automated protein structure prediction has never been more evident and researchers are now focusing on developing computational techniques to predict three-dimensional structures with high throughput. Consensus-based protein structure prediction methods are state-of-the-art in automatic protein structure prediction. A consensus-based server combines the outputs of several individual servers and tends to generate better predictions than any individual server. Consensus-based methods have proved to be successful in recent CASP (Critical Assessment of Structure Prediction). In this thesis, a Support Vector Machine (SVM) regression-based consensus method is proposed for protein fold recognition, a key component for high throughput protein structure prediction and protein function annotation. The SVM first extracts the features of a structural model by comparing the model to the other models produced by all the individual servers. Then, the SVM predicts the quality of each model. The experimental results from several LiveBench data sets confirm that our proposed consensus method, SVM regression, consistently performs better than any individual server. Based on this method, we developed a meta server, the Alignment by Consensus Estimation (ACE).

The 3D structures of proteins may provide important clues to their functions and roles in complex biological pathways. Traditional methods such as X-ray crystallography and NMR are not feasible for all proteins, while theoretical models are typically not validated by experimental data. This project investigates the use of chemical crosslinkers as an experimental means of validating these models. Five target proteins were successfully purified from yeast whole cell extract: Transketolase (TKL1), inorganic pyrophosphatase (IPP1), amidotransferase/cyclase HIS7, phosphoglycerate kinase (PGK1) and enolase (ENO1). These TAP-tagged target proteins from yeast <em>Saccharomyces cerevisiae</em> allowed the protein to be isolated in two affinity purification steps. Subsequent structural analysis used the homobifunctional chemical crosslinker BS³ to join pairs of lysine residues on the surface of the purified protein via a flexible spacer arm. Mass spectrometry (MS) analysis of the crosslinked protein generated a set of mass values for crosslinked and non-crosslinked peptides, which was used to identify surface lysine residues in close proximity. The Automatic Spectrum Assignment Program was used to assign sequence information to the crosslinked peptides. This data provided inter-residue distance constraints that can be used to validate or refute theoretical protein structure models generated by structure prediction software such as SWISS-MODEL and RAPTOR. This approach was able to validate the structure models for four of the target proteins, TKL1, IPP1, HIS7 and ENO1. It also successfully selected the correct models for TKL1 and IPP1 from a protein model library and provided weak support for the HIS7, PGK1 and ENO1 models.

A study of packing constructs a critique of the everyday: a dialogue between chaos and order, surface and area, interior and exterior, gravity and lightness. In search of tangible expression of the spatial processes I am responsible for, I have become both master architect and expert packer. I have composed this thesis the same way I pack: I have assembled piles of fragments, regrouped them, reconsidered, edited, alloted them more or less space. Things have become more and less valuable. Quotes and images are precious, like artifacts, tucked delicately between text-filled pages. Each word I write, each line I draw, creates a boundary, a parcel, a unit of space set apart from the white of the page. This book is my suitcase.

The research presented here deals with synthetic materials for application in tissue engineering, primarily poly(ethylene glycol) (PEG) and poly(dimethyl siloxane)star (PDMS)star. Tissue engineering seeks to repair or replace damaged tissue through implantation of cell encapsulated in an artificial scaffold. Cell differentiation and extracellular matrix (ECM) deposition can be influenced through a wide variety of in vitro culture techniques including biochemical stimuli, cell-cell interactions, mechanical conditioning and scaffold physical properties. In order to systematically optimize in vitro conditions for tissue engineering experiments, the individual effects of these different components must be studied. PEG hydrogels are a suitable scaffold for this because of their biocompatibility and biological "blank slate" nature. This dissertation presents data investigating: the effects of glycosaminoglycans (GAGs) as biochemical stimuli on pig vocal fold fibroblasts (PVFfs); the effects of mechanical conditioning and cell-cell interactions on smooth muscle cells (SMCs); and the effects of scaffold physical properties on SMCs. Results show that GAGs influence PVFf behavior and are an important component in scaffold design. Hyaluronic acid (HA) formulations showed similar production in collagen I and III as well as reduced levels of smooth muscle a-actin (SMa-actin), while chondroitin sulfate (CSC) and heparin sulfate showed enriched collagen III environments with enhanced expression of SMa-actin. A physiological flow system was developed to give comprehensive control over in vitro mechanical conditioning on TEVGs. Experiments performed on SMCs involved creating multi-layered TEVGs to mimic natural vascular tissue. Constructs subjected to mechanical conditioning with an endothelial cell (EC) layer showed enhanced expression of SMC differentiation markers calponin h1 and myocardin and enhanced deposition of elastin. Consistent with other studies, EC presence diminished overall collagen production and collagen I, specifically. Novel PDMSstar-PEG hydrogels were studied to investigate the effects of inorganic content on mesenchymal stem cell differentiation for use in TEVGs. Results agree with previous observations showing that a ratio of 5:95 PDMSstar: PEG by weight enhances SMC differentiation markers; however, statistically significant conclusions could not be made. By studying and optimizing in vitro culture conditions including scaffold properties, mechanical conditioning and multi-layered cell-cell interactions, TEVGs can be designed to maximize SMC differentiation and ECM production.

Vocal fold scarring, caused by injury and inflammation, presents significant treatment challenges. Tissue engineering might be a promising treatment for vocal fold restoration or regeneration. It is important to investigate how scaffold properties alter cell behavior instead of screening thousand of materials, which is fundamental knowledge for rational scaffold design. This work studies how tuning only one parameter, mechanical strength of the hydrogel scaffold, influences the extracellular matrix production of encapsulated porcine vocal fold fibroblast (PVFF). PVFF cells were encapsulated by photopolymerization in 10 wt%, 20 wt%, and 30 wt% poly(ethylene glycol) diacrylate (PEGDA) hydrogels (MW 10,000), with the similar biochemical environment and network structure but different mechanical properties. Cell adhesive peptide, RGDS, was grafted into each hydrogel network to mimic a cell adhesive environment. The glycosaminoglycans (GAGs) production per cell increased from 10 wt% to 20 wt%, 30 wt% gels, with an increase in hydrogel stiffness. The collagen production per cell increased from 10 wt% to 20 wt% gels but no further increase occurred with the increasing modulus from 20 wt% to 30 wt% gels. Interestingly, in hydrogels of intermediate modulus (20% PEGDA hydrogels), the highest elastin per cell was observed compared with gels with higher and lower storage modulus after day 30. Histological analysis showed GAGs, collagen and elastin were distributed pericellularly. However, the organization of collagen type I appeared to be influenced by gel mechanical properties, which was confirmed by immunohistological analysis. Furthermore, the immunohistological analysis showed that the phenotype of PVFF is regulated by the stiffness of the PEG hydrogel. This study demonstrates that different levels of VFF ECM formation may be achieved by varying the mechanical properties of PEG hydrogels and validates a systematic and controlled platform for further research of cell-biomaterials interaction.

Subject to a sufficiently large compression, materials may undergo mechanical instabilities of various types. When the material is homogeneous, creases set in. When the material is a bilayer consisting of a stiff thin film on a thick compliant substrate, wrinkles set in. Creases are localized self-contact regions with large strain deviating from the smooth state, while wrinkles are undulations finite in space with infinitesimal strain deviating from the smooth state. After the formation of wrinkles, if the compression further increases, wrinkles double their period and form localized folds. If the substrate is subject to a sufficiently large pre-tension, wrinkles transit to ridges. This thesis explores different types of mechanical instabilities: creases, wrinkles, folds, and ridges. We start with studying creases in different materials. Soft tissues growing under constraint often form creases. We adopt the model of growth that factors the deformation gradient into a growth tensor and an elastic deformation tensor, and show that the critical conditions for the onset of creases take a remarkably simple form. We then perform simulations to explore creases in strain-stiffening materials. For a solid that stiffens steeply at large strains, as the compression increases, the surface is initially smooth, then forms creases, and finally becomes smooth again. For a solid that stiffens steeply at small strains, creases never form for all levels of compression. In order to better control the formation and disappearance of creases, we design a soft elastic bilayer with same moduli of the film and substrate but the substrate pre-compressed, and show that the bilayer can snap between the flat and creased states reproducibly with tunable hysteresis in a large strain range. We also show that an interface between two soft materials can form creases under compression. We then investigate the critical conditions for the onset of wrinkles and creases in bilayers with arbitrary thicknesses and moduli of the two layers, and show several new types of bifurcation behavior when the film and substrate have comparable moduli and thicknesses. We study the effect of substrate pre-stretch on post-wrinkling bifurcations, and show that pre-tension stabilizes wrinkles while pre-compression destabilizes wrinkles. When the pre-compression is sufficiently large, `chaotic' morphologies emerge. When the pre-tension is sufficiently large, we realize ridge localizations and networks under an equi-biaxial compression, and study the mechanics of ridge formation and propagation. / Engineering and Applied Sciences

This investigation focuses on the Jurassic-Eocene sedimentary record of northwestern Montana and the geometry and kinematics of the thrust belt, in order to develop a unifying geodynamic-stratigraphic model to explain the evolution of the Cordilleran retroarc of this region. Provenance and subsidence analyses suggest the onset of a foreland basin system by Middle Jurassic time. U-Pb ages of detrital zircons and detrital modes of sandstones indicate provenance from accreted terranes and deformed miogeoclinal rocks. Subsidence commenced at ∼170 Ma and followed a sigmoidal pattern characteristic of foreland basin systems. Jurassic deposits of the Ellis Group and Morrison Formation accumulated in a back-bulge depozone. A regional unconformity/paleosol zone separates the Morrison from Cretaceous deposits. This unconformity was possible result of forebulge migration, decreased dynamic subsidence, and eustatic sea level fall. The late Barremian(?)-early Albian Kootenai Formation is the first unit in the foreland that consistently thickens westward. The subsidence curve at this time begins to show a convex-upward pattern characteristic of foredeeps. The location of thrust belt structures during the Late Jurassic and Early Cretaceous is uncertain, but provenance information indicates exhumation of the Intermontane and Omineca belts, and deformation of miogeocline strata, possibly on the western part of the Purcell anticlinorium. By Albian time, the thrust belt had propagated to the east and incorporated Proterozoic rocks of the Belt Supergroup as indicated by provenance data in the Blackleaf Formation, and by cross-cutting relationships in thrust sheets involving Belt rocks. From Late Cretaceous to early Eocene time the retroarc developed a series of thrust systems including the Moyie, Snowshoe, Libby, Pinkham, Lewis-Eldorado-Steinbach-Hoadley, the Sawtooth Range and the foothills structures. The final stage in the evolution of the compressive retroarc system is recorded by the Paleocene-early Eocene Fort Union and Wasatch Formations, which are preserved in the distal foreland. A new ∼145 Km balanced cross-section indicates ∼130 km of shortening. Cross-cutting relationships, thermochronology and geochronology suggest that most shortening along the frontal part of the thrust belt occurred between the mid-Campanian to Ypresian (∼75-52 Ma), indicating a shortening rate of ∼5.6 mm/y. Extensional orogenic collapse began during the middle Eocene.