VictorJuiz/thesis huggingface dataset:
The Development and Evolution of Complex Patterns: The Drosophila Sex Comb as a Model System

One of the best-known structures in Drosophila is the sex comb, an arrangement of modified bristles on the tarsal forelegs of males. This complex, sexually-dimorphic trait shows striking variation among closely related species, although most other aspects of the tarsal bristle pattern have been conserved. I studied the development of the sex comb in the model organism Drosophila melanogaster and six related species. I confirmed that the D. melanogaster sex comb, although longitudinal in the adult, originates in a transverse orientation and rotates during development, and showed that this process occurs through male-specific convergent extension. However, in the species that I examined that have longitudinally-oriented sex combs that extend the full length of the tarsus, including D. ficusphila and two species of the montium subgroup, the sex comb does not rotate, and instead forms from two longitudinal rows that converge during development. Another species of the montium subgroup, D. nikananu, has a sex comb that is convergently similar to D. melanogaster, but forms in a manner typical of its subgroup, showing that very similar combs can be formed through different processes. In all species, there is a strong correlation between the position of the sex comb and the transverse bristle row on the foreleg tarsus just proximal to it. To test whether it is possible to violate this apparent constraint on development, I perturbed the expression of the leg patterning gene dachshund to generate ectopic sex combs in D. melanogaster. I found that while most patterns showed the same correlation, a few circumvent the constraint. I also demonstrated that the ectopic combs were formed non-autonomously and that overexpression of dachshund can transform certain aspects of the sex comb phenotype to resemble the transverse bristles to which they are homologous.

Keywords: evolution
development
complexity
patterning
developmental constraints
Drosophila
sex comb
tarsus
bristle pattern
live imaging
convergent extension
cell intercalation
Advisor: Larsen, Ellen
An Integrated Multi-model Approach for Predicting the Impact of Household Travel on Urban Air Quality and Simulating Population Exposure

The population and economic growth experienced by Canadian metropolitan areas in the past twenty years, has been associated with increased levels of car ownership and vehicle kilometres travelled leading to a deterioration of air quality and public health and an increase in greenhouse gas emissions. The need to modify urban growth patterns has motivated planning agencies in Canada to develop a broad range of policies aiming at achieving a more sustainable transportation sector. The challenge however, remains in the ability to test the effectiveness of proposed policy measures. This situation has led to a renewed interest in integrated land-use and transport models to support transport policy appraisal. This research is motivated by the need to improve transport policy appraisal through the use of integrated land-use and transport models linked with a range of sub-models that can reflect transport externalities. This research starts with an exploration of the transport policy environment in Canada through a questionnaire-based survey conducted with planners and policy-makers. The survey results highlight the need for tools reflecting the sustainability impacts of proposed policies. While the second part of this research explores sustainability indicators and recommends a set of social, economic, and environmental measures, linked with integrated land-use and transport models; effort is dedicated to estimate the environmental indicators as part of this thesis. As such, the third part of this research involves the development of an emission-dispersion-exposure modelling framework. The framework includes a suite of sub-models including an activity-based travel demand model (TASHA), an emission factor model (Mobile6.2C), a meteorological model (CALMET), and a dispersion model (CALPUFF). The framework is used to estimate link-based emissions of light-duty vehicles in the Greater Toronto Area under a base scenario for 2001. Dispersion of emissions is then conducted and linked with population in order to estimate exposure to air pollution.

Keywords: Transportation Emissions Modelling
Air Quality Modelling
Transport Policy Appraisal
Environmental Impacts of Transport
Advisor: Miller, Eric
Performance Assessment of Shear-critical Reinforced Concrete Plane Frames

Current analysis procedures for new reinforced concrete structures are typically based on linear-elastic principles. However, under certain conditions, it may be necessary to analyze a structure to more accurately predict its structural behaviour. Such an analysis can be performed using nonlinear analysis procedures which typically require specialized software. This type of software is limited in number and most available programs do not adequately capture shear-related influences, potentially severely overestimating strength and ductility in shear-critical structures. The purpose of this study is to develop and verify an analytical procedure for the nonlinear analysis of frame structures with the aim of capturing shear-related mechanisms as well as flexural and axial effects. A previously developed analysis program, VecTor5, is further developed for this purpose. Originally formulated in the early 1980s at the University of Toronto, VecTor5 is based on the Modified Compression Field Theory (MCFT) and is capable of performing nonlinear frame analyses under temperature and monotonic loading conditions. Although providing generally satisfactory simulations, there are a number of deficiencies present in its computational algorithms. This study consists of three major parts: improvement of the original analysis procedure for monotonic loading conditions, expansion of the procedure for general loading conditions including the special cases of cyclic and reversed-cyclic loading, and further development of the procedure for dynamic loading conditions including time-varying base accelerations, impulse, impact and blast forces, initial mass velocities, and constant mass accelerations. Each part is supported by verification studies performed on a large number and variety of previously tested structures available in the literature. In addition, considerations in nonlinear modelling are discussed with the aim of providing guidelines for general modelling applications. Analyses of 63 previously tested structures, half of which are shear-critical, demonstrate that the developed analytical procedure is highly successful in simulating the experimental responses in terms of load-deflection response, reinforcement strains, crack widths, failure mode, failure displacement, total energy dissipation, displacement ductility ratio, and post-peak vibrational characteristics.

Keywords: shear-critical
reinforced concrete
nonlinear
analysis
performance
frame
shear
non-linear
Advisor: Vecchio, Frank J.
Developing New Strategies for the Preparation of Micro- and Nano-structured Polymer Materials

This thesis described the development of new strategies for the preparation of micro- and nano-structured polymer materials. In particular, this thesis focused on: i) the synthesis of polymer particles in microreactors, and ii) the self-assembly of inorganic nanorods. First, this thesis presented the synthesis of polymer particles and capsules with pre-determined sizes and narrow size distributions (CV<2%) in continuous microfluidic reactors. The method includes (i) the emulsification of monomers in a microfluidic flow-focusing device and (ii) in-situ solidification of droplets via photopolymerization. This microfluidic synthesis provides a novel strategy for the control over the shapes, compositions, and morphologies of polymer particles. In particular, we demonstrated the control over particle shapes by producing polymer ellipsoids, disks, rods, hemispheres, plates, and bowls. We produced polymer particles loaded with dyes, liquid crystals, quantum dots, and magnetic nanoparticles. We generated core-shell particles, microcapsules, Janus and three-phasic polymer particles. Control over the number of cores per droplet was achieved by manipulating the flow rates of liquids in the microchannels. We further investigated the hydrodynamic mechanism underlying the emulsification of droplets, which helps in guiding scientists and engineers to utilize this technique. Second, we described the self-assembly of inorganic nanorods by using a striking analogy between amphiphilic ABA triblock copolymers and the hydrophilic nanorods tethered with hydrophobic polystyrene chains at both ends. We organized metal nanorods in structures with various geometries such as nanorings, nanochains, bundles, bundled nanochains, and nanospheres by tuning solely the quality of solvents. The self-assembly was tunable and reversible. This approach paved the way for the organization of anisotropic nanoparticles by using the strategies that are well-established for the self-assembly of block copolymers. We further described a systematic study of the self-assembly of polymer-tethered gold nanorods as a function of solvent composition in the system and the molecular weight of the polystyrene blocks. We found that the structure of the polymer pom-poms played an important role on the organization of polymer-tethered gold NRs. The 'supramolecular' assembly was governed by the competition between the end-to-end and side-by-side association of NRs and resulted in the controlled variation of the plasmonic properties of NRs, reflected in a 3-D plasmonic graph.

Keywords: microfluidics, microreactors, polymer particles, core-shell, microcapsules, Janus particles, three-phasic particles, self-assembly, gold nanorods, block copolymers, plasmonic band
Advisor: Kumacheva, Eugenia
Phase Transitions in Polymeric Systems: A Directed Walk Study

In this thesis several classes of directed paths are considered as models of linear polymers in a dilute solution. We obtain the generating functions for each model by considering factorization arguments. Information about the polymer behaviour can be extracted from the singularity structure of the associated generating functions. By using modified versions of these models we study the adsorption and localization of polymer molecules, the behaviour of polymers subject to a tensile force, the effects of stiffness, as well as the behaviour of polymers in confined geometries. In each of these situations the resulting generating functions contain at least two physical singularities. We identify the phase transitions in these systems by a changeover in the dominant singularity of the generating function. In the study of localization and polymers subject to a force, we utilize both homopolymer and random copolymer models. For copolymers, the physically relevant properties are obtained by considering a quenched average of the free energy over all possible monomer sequences. This procedure is intractable even for the simplest models. By considering the Morita approximation for several walk models we obtain results which give a bound on the corresponding features of the quenched system. We use a mapping between a simple model of duplex DNA and an adsorbing Motzkin path in order to study the mechanical unzipping of duplex DNA. From this model, we obtain force-temperature diagrams which show re-entrant behaviour of the force. We also develop a simple low temperature theory to describe the behaviour of the force close to T=0 and find that the shape of the force-temperature curve is associated with entropy in the ground state of the system. We consider the effect of stiffness on polymer adsorption and find that the phase transition is second order for all finite stiffness parameters. For systems of polymers in confined geometries, we find that the behaviour of the polymer depends on the distance between the confining surfaces and the associated interactions with each surface. In this problem, there exist regimes where the polymer exerts a force on the surfaces which can be attractive, repulsive or zero.

Keywords: statistical mechanics
polymers
directed walks
phase transition
Advisor: Whittington, Stuart
Quantum-Classical Master Equation Dynamics: An Analysis of Decoherence and Surface-hopping Techniques

In this thesis quantum-classical dynamics is applied to the study of quantum condensed phase processes. This approach is based on the quantum-classical Liouville equation where the dynamics of a small subset of the degrees of freedom are treated quantum mechanically while the remaining degrees of freedom are treated by classical mechanics to a good approximation. We use this approach as it is computationally tractable, and the resulting equation of motion accurately accounts for the quantum and classical dynamics, as well as the coupling between these two components of the system. By recasting the quantum-classical Liouville equation into the form of a generalized master equation we investigate connections to surface-hopping. The link between these approaches is decoherence arising from interaction of the subsystem with the environment. We derive an evolution equation for the subsystem which contains terms accounting for the effects of the environment. One of these terms involves a memory kernel that accounts for the coherent dynamics. If this term decays rapidly, a Markovian approximation can be made. By lifting the resulting subsystem master equation into the full phase space, we obtain a Markovian master equation that prescribes surface-hopping-like dynamics. Our analysis outlines the conditions under which such a description is valid. Next, we consider the calculation of the rate constant for a quantum mechanical barrier crossing process. Starting from the reactive-flux autocorrelation function, we derive a quantum-classical expression for the rate kernel. This expression involves quantum-classical evolution of a species operator averaged over the initial quantum equilibrium structure of the system making it possible to compute the rate constant via computer simulation. Using a simple model for a proton transfer reaction we compare the results of the rate calculation obtained by quantum-classical Liouville dynamics with that of master equation dynamics. The master equation provides a good approximation to the full quantum-classical Liouville calculation for our model and a more stable algorithm results due to the elimination of oscillating phase factors in the simulation. Finally, we make use of the theoretical framework established in this thesis to analyze some aspects of decoherence used in popular surface-hopping techniques.

Keywords: Quantum-classical molecular dynamics
decoherence
surface-hopping schemes
nonadiabatic dynamics
Advisor: Kapral, Raymond E.
Silicon Inverse Opal-based Materials as Electrodes for Lithium-ion Batteries: Synthesis, Characterisation and Electrochemical Performance

Three-dimensional macroporous structures (‘opals’ and ‘inverse opals’) can be produced by colloidal crystal templating, one of the most intensively studied areas in materials science today. There are several potential advantages of lithium-ion battery electrodes based on inverse opal structures. High electrode surface, easier electrolyte access to the bulk of electrode and reduced lithium diffusion lengths allow higher discharge rates. Highly open structures provide for better mechanical stability to volume swings during cycling. Silicon is one of the most promising anode materials for lithium-ion batteries. Its theoretical capacity exceeds capacities of all other materials besides metallic lithium. Silicon is abundant, cheap, and its use would allow for incorporation of microbattery production into the semiconductor manufacturing. Performance of silicon is restricted mainly by large volume changes during cycling. The objective of this work was to investigate how the inverse opal structures influence the performance of silicon electrodes. Several types of silicon-based inverse opal films were synthesised, and their electrochemical performance was studied. Amorphous silicon inverse opals were fabricated via chemical vapour deposition and characterised by various techniques. Galvanostatic cycling of these materials confirmed the feasibility of the approach taken, since the electrodes demonstrated high capacities and decent capacity retentions. The rate performance of amorphous silicon inverse opals was unsatisfactory due to low conductivity of silicon. The conductivity of silicon inverse opals was improved by crystallisation. Nanocrystalline silicon inverse opals demonstrated much better rate capabilities, but the capacities faded to zero after several cycles. Silicon-carbon composite inverse opal materials were synthesised by depositing a thin layer of carbon via pyrolysis of a sucrose-based precursor onto the silicon inverse opals in an attempt to further increase conductivity and achieve mechanical stabilisation of the structures. The amount of carbon deposited proved to be insufficient to stabilise the structures, and silicon-carbon composites demonstrated unsatisfactory electrochemical behaviour. Carbon inverse opals were coated with amorphous silicon producing another type of macroporous composites. These electrodes demonstrated significant improvement both in capacity retentions and in rate capabilities. The inner carbon matrix not only increased the material conductivity, but also resulted in lower silicon pulverisation during cycling.

Keywords: batteries
lithium-ion batteries
Li-ion batteries
anode
negative electrode
silicon
inverse opal
inverse colloidal crystal
macroporous material
Advisor: Ozin, Geoffrey Alan
Elastic Scattering Phenomena in Molecularly-linked Gold Nanoparticle Films

We have investigated the conductance, g, of 1,4-butanedithiol linked Au nanoparticle films as a function of temperature, T, bias potential, V, and applied magnetic field, B. An interesting temperature dependence is observed for non-metallic films with thicknesses just below a critical film thickness: g ~ exp [-(T_0/T)^(1/2)] for 20 K < T < 300 K. We show that this temperature dependence is incompatible with an Efros-Shklovskii "variable range hopping" model, since "hopping distances" are too large to be consistent with tunneling processes, and tend to scale with size of super-clusters of molecularly-linked nanoparticles. We propose a "quasilocalized hopping" model based on competition between single-electron charging of super-clusters and electron backscattering within super-clusters to explain the observed temperature dependence. Various electron scattering time scales are extracted from magnetoconductance data using a modified "weak localization" model. Elastic scattering time scales are comparable to those required for an electron to traverse a nanoparticle, while inelastic and spin-orbit scattering time scales are consistent with those found in studies of conventionally-prepared granular Au films. At interfaces between metallic 1,4-butanedithiol-linked Au nanoparticle films and conventional superconductors, we find that g consistently exhibits peaks, as well as oscillations, that depend simultaneously on both V and B. Such peaks and correlated conductance oscillations are predicted by an enhanced Andreev reflection process due to disorder-driven elastic scattering and electron-hole interference in the nanoparticle film. While oscillations have been predicted by a so-called "reflectionless tunneling" model, they have not been observed at other normal-superconductor interfaces. We speculate that oscillations are observable in this system due to synthetically controlled uniformity of elastic scattering length (i.e., nanoparticle diameter) and a reduced number of current-carrying pathways, especially near the interface. Contrary to predictions of existing "reflectionless tunneling" models, we find that the periods of oscillation in B decrease as T increases. This suggests that the area of interfering pathways increases with T. We propose that this increasing area can be attributed to magnetic field penetration into the superconductor. Conductance data agrees remarkably well with known temperature dependence of penetration depth predicted by BCS theory. Our study shows that this additional region of flux must be considered in experimental and theoretical studies of "reflectionless tunneling", and underscores the utility of molecularly-linked nano\-particle films as a platform for studying charge transport.

Keywords: electronic scattering
conductance
self-assembled nanoparticle film
quasilocalized hopping
weak localization
reflectionless tunneling
Advisor: Dhirani, Al-Amin
NMR Studies of SH3 Domain Structure and Function

SH3 domains are excellent models for probing folding and protein interactions. This thesis describes NMR studies of several SH3 domains, including the N-terminal SH3 domain of the Drosophila adaptor protein Drk (drkN SH3 domain), the SH3 domain of the proto-oncogene tyrosine-kinase Fyn, and the SH3 domains of the human adaptor protein CIN85, involved in Cbl-mediated downregulation of epidermal growth factor receptor (EGFR) and other receptor tyrosine kinases (RTKs). The drkN SH3 domain is an ideal system for studying disordered states. The unique quality of this isolated domain is that it exists in an approximately 50/50 equilibrium between its folded and unfolded states under non-denaturating buffer conditions. Interestingly, the single T22G mutation dramatically stabilizes the domain. Here the NMR structures of the drkN SH3 domain and its T22G mutant are determined and compared in order to illuminate the causes of the marginal stability of the domain. Solvent exposure of the folded and the unfolded drkN SH3 domains are probed and compared with a novel NMR technique using molecular oxygen dissolved in solution as a paramagnetic probe. The changes in partial molar volume along the folding trajectories of the drkN SH3 and Fyn SH3 domains are also studied and analyzed here in terms of changes in protein hydration and packing accompanying folding. Finally, the interactions between the SH3 domains of CIN85 and ubiquitin are discussed. All three are shown to bind ubiquitin. The structure of the SH3-C domain in complex with ubiquitin is presented and the effect of disruption of ubiquitin binding on ubiquitination of CIN85 and EGFR in vivo is discussed. SH3 domains are easily amendable to a wide range of NMR approaches and provide a good system for development and testing of novel methods. Through the use of these approaches significant insights into details of SH3 domain structure, stability, mechanisms of folding and cellular function have been gained.

Keywords: SH3 domain
NMR
drk
fyn
CIN85
ubiquitination
protein folding
Advisor: Kay, Lewis E.
Forman-Kay, Julie Deborah