Polythiophenes have great potential as semiconductors for use in organic field effect transistors and light emitting diodes. Recent research has been focused on the design, synthesis and characterization of fluorinated polythiophenes and oligothiophenes. Various fluoroalkyl side chains have been introduced to induce polymer self-assembly, to control the electronic properties of the conjugated backbone, and to modify the solubility of the polymer in supercritical CO2. This work led to the preparation of poly(3-(perfluorooctyl)thiophene), which is one of only a few examples of n-dopable polythiophenes, and is the first supercritical CO2-soluble conducting polymer. An alternating copolymer consisting of 3-perfluoroakyl and 3-alkylthiophene units has been synthesized. This polymer, with alternating electron-donating and withdrawing substituents, has a high quantum yield for fluorescence in solution relative to the two homopolymers, and strong fluorescence in solid state. Based on the study on its nanocrystals, the unusual photophyiscs may be due to the formation of the supramolecular structure with hexagonal packing. A novel thiophene monomer, 3-(1,1-difluorooctyl)thiophene, was prepared to further tune the electronic structure of polythiophenes by changing the fluorination pattern of side chains, while retaining solubility in organic solvents by virtue of the hydrocarbon side chain. a-Hexyl-w-perfluorohexylsexithiophene was synthesized to make a novel amphiphilic material for use in TFTs. Models for interchain charge transfer in doped conducting polymers were also developed. Stacked and unstacked conjugated oligomers have been synthesized as models for conducting polymers. The bis(radical cation) form and the dication-neutral form of compounds in which conjugated oligomers are held in a stacked arrangement are shown to coexist and in equilibrium with each other. The coexistence of these two forms further suggests that both may serve as charge carriers. Interconversion between these forms by disproportionation mimics a possible mechanism for charge migration in doped conjugated polymers.

Stacking sequence design is a combinatorial problem when the fiber orientations in each layer are restricted to certain angles. In addition, there often exist many optimal or nearoptimal designs for the stacking sequence of a composite pressure vessel under different loading conditions. Genetic algorithms are quite well suited for finding the optimal designs for such a combinatorial problem. In this thesis, a genetic algorithm code is developed in Matlab, optimizing the stacking sequence of a composite pressure vessel subjected to internal and external pressures, axial load and body force due to rotation. For testing of the code and identification of the effects of optimization parameters, a problem, whose optimum solution is obvious, is defined and the optimum design is tried to be found by using the developed code. The results have shown that the code was quite successful in finding the best design. Afterwards, the code is used for the optimization of the stacking sequence of a composite pressure vessel under different loading conditions. Again the code has proven its reliability in finding the optimal designs. The developed genetic algorithm optimization code also has the infrastructure to be easily adapted to the solution of different combinatorial problems.

The move into deeper waters in the Gulf of Mexico has produced new opportunities for petroleum production, but it also has produced new challenges as different reservoir problems are encountered. This integrated reservoir characterization effort has provided useful information about the behavior and characteristics of a typical unconsolidated, overpressured, fine-grained, turbidite reservoir, which constitutes the majority of the reservoirs present in the Outer Continental Shelf of the Gulf of Mexico. Reservoirs in the Green Canyon 18 (GC 18) field constitute part of a turbidite package with reservoir quality typically increasing with depth. Characterization of the relatively shallow 8 reservoir had hitherto been hindered by the difficulty in resolving its complex architecture and stratigraphy. Furthermore, the combination of its unconsolidated rock matrix and abnormal pore pressure has resulted in severe production-induced compaction. The reservoir's complex geology had previously obfuscated the delineation of its hydrocarbon accumulation and determination of its different resource volumes. Geological and architectural alterations caused by post-accumulation salt tectonic activities had previously undermined the determination of the reservoir's active drive mechanisms and their chronology. Seismic interpretation has provided the reservoir geometry and topography. The reservoir stratigraphy has been defined using log, core and seismic data. With well data as pilot points, the spatial distribution of the reservoir properties has been defined using geostatistics. The resulting geological model was used to construct a dynamic flow model that matched historical production and pressure data.. The reservoir's pressure and production behavior indicates a dominant compaction drive mechanism. The results of this work show that the reservoir performance is influenced not only by the available drive energy, but also by the spatial distribution of the different facies relative to well locations. The study has delineated the hydrocarbon bearing reservoir, quantified the different resource categories as STOIIP/GIIP = 19.8/26.2 mmstb/Bscf, ultimate recovery = 9.92/16.01 mmstb/Bscf, and reserves (as of 9/2001) = 1.74/5.99 mmstb/Bscf of oil and gas, respectively. There does not appear to be significant benefit to infill drilling or enhanced recovery operations.

This work investigates pathways of conformational transitions in ubiquitous RNA structural motifs. In our lab, we have developed multi-scale structural datamining techniques for identification of three-dimensional structural patterns in high-resolution crystal structures of globular RNA. I have applied these techniques to identify variations in the conformations of RNA double-helices and tetraloops. The datamined structural information is used to propose reaction coordinates for conformational transitions involved in double-strand helix propagation and tetraloop folding in RNA. I have also presented an algorithm to identify stacked RNA bases. In this work, experimentally derived thermodynamic evaluation of the conformations has been used to as an additional parameter to add detail to RNA structural transitions. RNA conformational transitions help control processes in small systems such as riboswitches and in large systems such as ribosomes. Adopting functional conformations by globular RNA during a folding process also involves structural transitions. RNA double-helices and tetraloops are common, ubiquitous structural motifs in globular RNA that independently fold in to a thermodynamically stable conformation. Folding models for these motifs are proposed in this work with probable intermediates ordered along the reaction coordinates. We hypothesize that frequently observed structural states in crystals structures are analogous in conformation to stable thermodynamic â on-pathwayâ folded states. Conversely, we hypothesize that conformations that are rarely observed are improbable folding intermediates, i.e., these conformational states are â off-pathwayâ states. In general on-pathway states are assumed to be thermodynamically more stable than off-pathway states, with the exception of kinetic traps. Structural datamining shows that double helices in RNA may propagate by the â stack-ratchetâ mechanism proposed here instead of the commonly accepted zipper mechanism. Mechanistic models for RNA tetraloop folding have been proposed and validated with experimentally derived thermodynamic data. The extent of stacking between bases in RNA is variable, indicating that stacking may not be a two-state phenomenon. A novel algorithm to define and identify stacked bases at atomic resolution has also been presented in this work.

The main objective of this research is to efficiently enable 3D die-stacked memory and heterogeneous memory systems. 3D die-stacking is an emerging technology that allows for large amounts of in-package high-bandwidth memory storage. Die-stacked memory has the potential to provide extraordinary performance and energy benefits for computing environments, from data-intensive to mobile computing. However, incorporating die-stacked memory into computing environments requires innovations across the system stack from hardware and software. This dissertation presents several architectural innovations to practically deploy die-stacked memory into a variety of computing systems. First, this dissertation proposes using die-stacked DRAM as a hardware-managed cache in a practical and efficient way. The proposed DRAM cache architecture employs two novel techniques: hit-miss speculation and self-balancing dispatch. The proposed techniques virtually eliminate the hardware overhead of maintaining a multi-megabytes SRAM structure, when scaling to gigabytes of stacked DRAM caches, and improve overall memory bandwidth utilization. Second, this dissertation proposes a DRAM cache organization that provides a high level of reliability for die-stacked DRAM caches in a cost-effective manner. The proposed DRAM cache uses error-correcting code (ECCs), strong checksums (CRCs), and dirty data duplication to detect and correct a wide range of stacked DRAM failures—from traditional bit errors to large-scale row, column, bank, and channel failures—within the constraints of commodity, non-ECC DRAM stacks. With only a modest performance degradation compared to a DRAM cache with no ECC support, the proposed organization can correct all single-bit failures, and 99.9993% of all row, column, and bank failures. Third, this dissertation proposes architectural mechanisms to use large, fast, on-chip memory structures as part of memory (PoM) seamlessly through the hardware. The proposed design achieves the performance benefit of on-chip memory caches without sacrificing a large fraction of total memory capacity to serve as a cache. To achieve this, PoM implements the ability to dynamically remap regions of memory based on their access patterns and expected performance benefits. Lastly, this dissertation explores a new usage model for die-stacked DRAM involving a hybrid of caching and virtual memory support. In the common case where system’s physical memory is not over-committed, die-stacked DRAM operates as a cache to provide performance and energy benefits to the system. However, when the workload’s active memory demands exceed the capacity of the physical memory, the proposed scheme dynamically converts the stacked DRAM cache into a fast swap device to avoid the otherwise grievous performance penalty of swapping to disk.

This thesis is based on nine research publications (I – IX) on structure and reactivity of RNA vis-à-vis DNA. The DNA and RNA are made of flexible pentose sugar units, polyelectrolytic phosphodiester backbone, and heterocyclic nucleobases. DNA stores our genetic code, whereas RNA is involved both in protein biosynthesis and catalysis. Various ligand-binding and recognition properties of DNA/RNA are mediated through inter- and intra-molecular H-bonding and stacking interactions, beside hydration, van der Waal and London dispersion forces. In this work the pH dependant chemical shift, pKa values of 2'-OH group as well as those the nucleobases in different sequence context, alkaline hydrolysis of the internucleotidic phosphodiester bonds and analysis of NOESY footprints along with NMR constrained molecular dynamics simulation were used as tools to explore and understand the physico-chemical behavior of various nucleic acid sequences, and the forces involved in their self-assembly process. Papers I – II showed that the ionization of 2'-OH group is nucleobase-dependant. Paper III showed that the chemical characters of internucleotidic phosphate are non-identical in RNA compared to that of DNA. Papers IV – VI show that variable intramolecular electrostatic interactions between electronically coupled nearest neighbor nucleobases in a ssRNA can modulate their respective pseudoaromatic character, and result in creation of a unique set of aglycons with unique properties depending on propensity and geometry of nearest neighbor interaction. Paper VII showed that the cross-modulation of the pseudoaromatic character of nucleobases by the nearest neighbor is sequence-dependant in nature in oligonucleotides. Paper VIII showed that the purine-rich hexameric ssDNA and ssRNA retain the right-handed helical structure (B-type in ssDNA and A-type in ssRNA) in the single-stranded form even in absence of intermolecular hydrogen bonding. The directionality of stacking geometry however differs in ssDNA compared to ssRNA. In ssDNA the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in the 5' to 3' direction, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA. Paper IX showed that the pKa values of the nucleobases in monomeric nucleotides can be used to show that a RNA-RNA duplex is more stable than a DNA-DNA duplex. The dissection of the relative strength of base-pairing and stacking showed that the relative contribution of former compared to that of the latter in an RNA-RNA over the corresponding DNA-DNA duplexes decreases with the increasing content of A-T/U base pairs in a sequence.

ABSTRACT Rationale: Respiratory insufficiency is one of the most common causes of death in patients with neuromuscular disorders (NMD). Due to weakness and cognitive level, children with NMD often cannot perform required maneuvers to recruit lung volume. Data from cooperative adults suggest that breath stacking with a mask and one-way valve can obtain significantly higher lung volumes. Methods: To study the effectiveness of a breath stacking mask in patients with NMD, we studied 23 children (17 male, 6 female) over 3 years, mean age 11 y (range 3-19 y) and body mass 43.8 kg (range 12-80 kg). Fifteen were cognitively aware and able to communicate verbally. For involuntary breath stacking a one-way valve and pneumotach were attached to a cushioned mask that was held to the face, covering around nose and mouth with a tight seal. Flow signals were acquired to computer (AcqKnowledge BIOPAC Inc.). Tidal volumes (Vt) and minute ventilation (VE) were calculated from the recording for 30 s before and 30 s after 15 s of valve closure during which expiration was prevented. Oxygen saturation (SaO2) was measured. Results: The mean Vt before valve closure was 277 ml (range 29-598 ml). The mean increase in volume by stacking was 599 ± 558 ml (range -140 to 2,916 ml). When normalized to body mass, mean increase above normal end inspiratory level was 14.7 ± 14.7 ml/kg (range -2.7 to 52.2 ml/kg). The mean number of stacked breaths was 4.5 ± 3.6 (range 0-17). VE increased on average by 18% after stacking (p<0.05, paired t-test). There was no change in SaO2 after stacking. Four of the 23 children did not stack. Conclusions: Our findings show that breath stacking with a mask and a one-way valve can achieve breath volumes approximately 3x Vt. The mask was tolerated well, and cooperation of the child was not required.

The field of organic electronics has received much attention over the last few years, and engineering of organic crystals to grow with pi-electron systems arranged in a face-to-face motif has been shown to be beneficial in electronic devices. The effects of combining aromatic and perfluorinated aromatic derivatives have shown that the intramolecular stacking pattern can be changed from an edge-to-face arrangement to that of a face-to-face motif. Before the work described herein, there were no reported studies of the supramolecular behavior of fused polycyclic aromatic compounds with partial peripheral fluorination, inducing the desired face-to-face behavior. This is the main focus of the thesis. Furthermore, by exploiting the interactions between the fluorinated and non-fluorinated faces of the molecule, columnar liquid crystalline behavior can be achieved through variations of the alkyl substituents on the molecule.

The centrepiece of this thesis is a deep, new, high-resolution 1.4-GHz image covering the United Kingdom Infrared (IR) Telescope IR Deep Sky Survey (UKIDSS) Ultra Deep Survey (UDS) legacy field. Deep pseudo-continuum observations were made using the Very Large Array, prior to its recent upgrade, in its A, B and DnC configurations. The resulting mosaic has a full-width-at-half-maximum synthesised beam width of ≈ 1.7 arcsec and a point-source sensitivity of ≈ 60μJy (6σ ) across the central 0.6 deg2, while conserving flux from sources of extended emission. The full image covers 1.3 deg2. I also present a catalogue containing over 1,000 radio emitters, having chosen the 6-σ threshold by maximising the number of radio sources with secure optical/near-IR counterparts. Most of the sources in the catalogue (≈ 90 per cent) lie in the sub-mJy flux density regime. Deep, complementary data covering a wide range of wavelengths was used to explore this faint radio population, whose nature remains controversial. It was found that 53 per cent of the sample comprise active galactic nuclei (AGN). AGN dominate at & 0.2mJy and remain a significant population down to 0.1mJy; at lower fluxes – the so-called μJy radio population – star-forming galaxies become dominant. The radio sample presented here was also matched to Hubble Space Telescope imaging of the UDS field (which is part of the Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey – CANDELS) to classify the faint radio population morphologically. These classifications were done using the Gini–M20 method. It was found that a low fraction of AGN and SFGs are undergoing interactions and mergers, 33 ± 9 and 13 ± 7 per cent, respectively. The merger fraction does not appear to have evolved significantly since z ∼ 3. This suggests that mergers have played a relatively minor role in the assembly of galaxies and super-massive black holes – certainly less significant than previously thought. Finally, I present a study of cosmic star-formation activity as a function of stellar mass and redshift, exploiting panchromatic stacking. Mid-IR–through–radio images, including new data from Herschel, are stacked at the positions of a K-selected (i.e. an approximately mass-selected) sample in the UDS field. Specific star-formation rates (SSFR, i.e. star-formation rate per stellar mass, or the rate at which a galaxy is converting its gas into stars) were derived from UDS radio luminosities measured here and stellar masses from the literature. The SSFR was found to be poorly correlated with stellar mass; it decreases with decreasing redshift; at a given mass, SSFR rises with redshift. These results indicate that at early epochs, galaxies were forming stars more efficiently and at a higher rate.

ABSTRACT Rationale: Respiratory insufficiency is one of the most common causes of death in patients with neuromuscular disorders (NMD). Due to weakness and cognitive level, children with NMD often cannot perform required maneuvers to recruit lung volume. Data from cooperative adults suggest that breath stacking with a mask and one-way valve can obtain significantly higher lung volumes. Methods: To study the effectiveness of a breath stacking mask in patients with NMD, we studied 23 children (17 male, 6 female) over 3 years, mean age 11 y (range 3-19 y) and body mass 43.8 kg (range 12-80 kg). Fifteen were cognitively aware and able to communicate verbally. For involuntary breath stacking a one-way valve and pneumotach were attached to a cushioned mask that was held to the face, covering around nose and mouth with a tight seal. Flow signals were acquired to computer (AcqKnowledge BIOPAC Inc.). Tidal volumes (Vt) and minute ventilation (VE) were calculated from the recording for 30 s before and 30 s after 15 s of valve closure during which expiration was prevented. Oxygen saturation (SaO2) was measured. Results: The mean Vt before valve closure was 277 ml (range 29-598 ml). The mean increase in volume by stacking was 599 ± 558 ml (range -140 to 2,916 ml). When normalized to body mass, mean increase above normal end inspiratory level was 14.7 ± 14.7 ml/kg (range -2.7 to 52.2 ml/kg). The mean number of stacked breaths was 4.5 ± 3.6 (range 0-17). VE increased on average by 18% after stacking (p<0.05, paired t-test). There was no change in SaO2 after stacking. Four of the 23 children did not stack. Conclusions: Our findings show that breath stacking with a mask and a one-way valve can achieve breath volumes approximately 3x Vt. The mask was tolerated well, and cooperation of the child was not required.