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Conjugated polymers represent a class of semi-conducting materials with numerous applications in optoelectronic devices, including organic light-emitting diodes, field-effect transistors, and photovoltaics. Because of the numerous advantages of macromolecular systems, including solution processing and mechanical flexibility, conjugated polymers have become a burgeoning field of research with the hopes of producing cost-effective solution-based electronics. Importantly, optoelectronic device performance is heavily influenced by conjugated polymer backbone orientation and overall thin film morphology. As such, the processing conditions of these systems are important to the construction of high- performance optoelectronics. Polythiophenes are model conjugated polymers that have been studied extensively in halogenated organic solvents. However, the self- assembly of these systems from dilute solution to the solid state remains ambiguous for solvents with high dielectric constants. Here, two derivative compounds of poly(3-hexylthiophene) are correspondingly investigated in high dielectric solvents by way of ultraviolet-visible absorption and fluorescence spectroscopy, Fourier transform infrared spectroscopy, small-angle X-ray scattering, polarized optical microscopy, and four- point probe conductivity measurements. In dilute solutions, both systems are found to undergo self-assembly when exposed to various stimuli, including temperature, solvent composition, and side-chain characteristics. The kinetics of these transitions are investigated, and a model is put forth to explain contrasting self-assembly mechanisms. At higher concentrations, both systems form lyotropic liquid crystalline phases. Characteristics of the liquid crystalline phases are found to be heavily influenced by dilute solution self-assembly mechanisms and processing. Through the application of a mechanical shear force along still-wet liquid crystal films, alignment of the polythiophene long axis is attained. This morphological characteristic is found to carry over to the solid-state for both systems, and clear optoelectronic anisotropy of the thin films is observed. As such, these methodologies may provide a route to the production of environmentally friendly high-performance optoelectronic devices.

The three projects utilized polymer physics theories to investigate polymer aggregation mechanics. Dynamic light scattering (DLS), static light scattering (SLS) and small angle light scattering (SALS) were the primary characterization tools. The goal of the first project was to study the aggregation of bovine βL-crystallin and apply that knowledge towards cataract formation, which is caused by aggregation of the crystallins. The first series of experiments characterized the kinetics of α-crystallin and βL-crystallin in water at room temperature. α-crystallin’s equilibrium hydrodynamic radius value was kinetically independent. βL-crystallin formed an aggregate with an Rh that was kinetically dependent. The packing structure of the aggregate formed by βL-crystallin was determined to be loosely packed using SLS. α -crystallin was uniquely demonstrated to be a chaperone in a way that indicated electrostatics played a significant role in aggregation. The role of electrostatics led to an investigation into sodium chloride. Sodium chloride proved to reduce the βL-crystallin aggregate size. The next series of experiments simulated biological conditions using a phosphate buffered saline (PBS). The experiments were performed at 35oC. α -crystallin and βL-crystallin were shown to be kinetically independent and demonstrate equilibrium Rh values on the time scale that the experiments were performed. A pH study revealed that multiple size-scales were present only at physiological pH. Above and below physiological pH, only two aggregate size-scales existed. A charge model was made of βL-crystallin to compare theory with experimental results. The future goal of project is to reproduce these experiments with human crystallins. In the second project, by changing the order and arrangement of β-spiral elastin (E) and α -helical COMPcc (C) the macroscopic structure was controlled. The EC diblock exhibited a fast and slow mode below the transition temperature of 25oC and single mode behavior above the transition. Phase separation occurred above the transition. CE showed three different size-scales below the transition of 15oC and demonstrated spinodal decomposition above the transition. The ECE triblock demonstrated bimodal behavior below the transition of 25oC and one micellar size above the transition. α-helical COMPcc has the ability to bind to small molecules, making the findings from this project instrumental in creating a drug delivery vehicle. The third project investigated sodium polystyrene sulfonate and polyethylene oxidepolypropylene oxide-polyethylene oxide in solution. Both systems self-assemble into aggregate structures at specific conditions. The significant difference between these two polymers is that sodium polystyrene sulfonate is a polyelectrolyte. It is well known that aggregate structures can be formed by variation in temperature and concentration. However, by having a charged polymer in solution with a neutral polymer the aggregate structure can also be controlled by changing the pH and adding salt to the solution, as was performed in the first project. The third project is an excellent conclusion to the previous two because it allows for the aggregate structure to be controlled even more so than in the previous projects by mediating the polydispersity index, molecular weight and concentration of each component. Each project focused on a different method of mediating the aggregate structure. A better understanding of aggregation has applications in industry and medicine. Polymer physics theory is instrumental in understanding aggregation mechanics.

In this thesis, we use the self-consistent field theory (SCFT) to study neutral and charged block copolymer melts and blends in thin films and bulk. We showcase the utility of the SCFT by applying it to a number of different model systems. In our first study, we examined the elastic properties of multi-component bilayer membranes composed of amphiphilic AB/ED diblock copolymers. We focused on the effects of chain architecture and interactions between the amphiphilic molecules on the line tension or edge energy of a membrane pore. We discovered a direct relationship between the effective volume of the amphiphilic molecules, which is dictated by their architecture, and the line tension. We found that the addition of cone-shaped molecules to the membrane results in a decrease in the line tension. The opposite effect is seen for inverse cone-shaped amphiphiles, where an increase in their concentration results in an increase of the line tension. Studies two and three fall under the theme of directed self assembly of block copolymer thin films. First we examined the effects of ion concentration on the strength of the external electric field required to reori- ent lamellar domains from the parallel to the perpendicular orientation. The change in the critical electric field is found to be dependent on whether the neutral or charged polymer species is favoured by the top and bottom surfaces. In the second study, we examined the mechanism of using the entropic effect to direct the self assembly of micro domains in star block copolymer thin films. We control the architecture of star block copolymers by varying the number of arms, ranging from a linear chain with 1-arm to 4-arm star block copolymers. Using both experiments and SCFT, we showed that the entropic effect is enhanced in star block copolymer blends with greater number of arms. Furthermore, we showed that the entropic effect can be used to direct the self assembly of micro domains perpendicular to the substrate. In our last study, we examined the unbinding transition of the α-BN phase in pentablock terpolymer/ homopolymer blends. We constructed a phase diagram of the system as a function of homopolymer con- centration. We discovered that the unbinding transition is preempted by the macrophase separation of the blends into block copolymer rich/ homopolymer rich domains. The results presented in this thesis help advance our understanding of various properties of polymeric systems, such as the elastic properties of multi-component membranes, directed self assembly in block copolymer thin films and the phase behaviour of block copolymers in bulk. / Thesis / Doctor of Philosophy (PhD)

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This work is a numerical examination of a semiflexible polymer exposed to a disorder landscape consisting of hard disks. For a small parameter range and simple constraints it is known that disorder leads to structural transitions of the equilibrium properties of polymers. The scope of this work strongly extends this range by going to both high disorder densities and large stiffnesses of the polymers. The competing length scales of polymer stiffness and average distance between the obstacles of the potential along with the way of assembling the disorder lead to a wide range of effects such as crumpling and stretching of polymer configurations due to the disorder or a modulation of the polymer’s characterizing observables with the correlation function of the potential. The high accuracy results presented in this work have been obtained by means of sophisticated Monte Carlo simulations. The refinement of a rarely applied but highly promising method to a state of the art algorithm in connection with latest numerical techniques made it possible to investigate the impact of hard-disk disorder on semiflexible polymer conformations on a broad scale.

Studies show that dynamical properties of ultra-thin polymer films deviate from those of bulk materials. Despite some controversial issues, there is growing evidence indicating that the interfacial properties play a key role for observed dynamical anomalies. However, how and how much the interfacial properties affect the average dynamics of the nanometer scale systems are still elusive. In this work, we developed several novel techniques to investigate near-free-surface dynamics of thin polymer films. We studied surface dynamics of glassy i-PMMA films using a nano surface hole relaxation technique: a strong substrate property dependence and an unexpected molecular weight dependence were observed; we found that a local Tg of ~40K below bulk Tg could be assigned to the surface region. We used nano gold particle embedding to study PS surface dynamics: enhanced surface dynamics and weak temperature dependence were observed for the surface region; a depth profile with the nm resolution was observed; viscous liquid-like and soft solid-like properties were observed in the first 5.5nm and next 3.3 nm regions in PS films; no molecualr weight dependence was found in glassy PS films. We built a low level noise measurement system to study the thermal polarization noise in PVAc films: cooperative rearranging dynamics were evidenced; the noise power spectral density (PSD) is found to fluctuate around a certain average level without discernable peak shift; we observed some relatively big jumps or fluctuations in successive integrated PSD’s, which indicate some energy exchange between different microscopic domains in glassy polymer systems. We developed a novel nano rheology AFM technique to study the near-free-surface dynamics of thin polymer films: enhanced near-free-surface dynamics with weak temperature dependence are observed for PVAc films, which is similar with the PS case.

Studies show that dynamical properties of ultra-thin polymer films deviate from those of bulk materials. Despite some controversial issues, there is growing evidence indicating that the interfacial properties play a key role for observed dynamical anomalies. However, how and how much the interfacial properties affect the average dynamics of the nanometer scale systems are still elusive. In this work, we developed several novel techniques to investigate near-free-surface dynamics of thin polymer films. We studied surface dynamics of glassy i-PMMA films using a nano surface hole relaxation technique: a strong substrate property dependence and an unexpected molecular weight dependence were observed; we found that a local Tg of ~40K below bulk Tg could be assigned to the surface region. We used nano gold particle embedding to study PS surface dynamics: enhanced surface dynamics and weak temperature dependence were observed for the surface region; a depth profile with the nm resolution was observed; viscous liquid-like and soft solid-like properties were observed in the first 5.5nm and next 3.3 nm regions in PS films; no molecualr weight dependence was found in glassy PS films. We built a low level noise measurement system to study the thermal polarization noise in PVAc films: cooperative rearranging dynamics were evidenced; the noise power spectral density (PSD) is found to fluctuate around a certain average level without discernable peak shift; we observed some relatively big jumps or fluctuations in successive integrated PSD’s, which indicate some energy exchange between different microscopic domains in glassy polymer systems. We developed a novel nano rheology AFM technique to study the near-free-surface dynamics of thin polymer films: enhanced near-free-surface dynamics with weak temperature dependence are observed for PVAc films, which is similar with the PS case.

<p>Small-angle X-ray scattering (SAXS) is a biophysical technique that allows one to study the statistical conformation of a biopolymer in solution. The two-dimensional data obtained from SAXS is a low-resolution probe of the statistical conformation- it is a population weighted orientational average of all conformers within a conformational ensemble. Traditional biological SAXS experiments seek to describe an "average" structure of a protein, or enumerate a "minimal ensemble" of a protein at the atomic resolution scale. However, for highly flexible proteins, an average structure or minimal ensemble may be insufficient for enumeration of conformational space, and may be an over-parameterized model of the statistical conformation. This work describes a SAXS analysis of highly flexible proteins and presents a protocol for describing the statistical conformation based on minimally parameterized polymer physics models and judicious use of ensemble modeling. This protocol is applied to the structural characterization of S. aureus protein A - a crucial virulence factor - and Fibronectin III domains 1-2 - an important structural protein.</p> / Dissertation

The pericellular matrix (PCM) is a voluminous polymer network adhered to and surrounding many different types of mammalian cells, and which extends out into the environment outside the cell for distances ranging up to twenty microns. It is comprised of very long flexible polymers (hyaluronan) which are tethered to the cell surface and which have binding sites for large, highly charged bottle brush proteoglycans (aggrecan). The PCM plays an important role in many cell functions such as cell proliferation, cell adhesion, cell migration, and cancer development, however the precise way it influences these processes remains unclear. Three original biophysical tools are developed in this thesis in order to study the PCM: the quantitative particle exclusion assay (qPEA), optical force probe assay (OFPA), and exogenous fluorescent aggrecan mapping assays. These tools are used to measure the polymeric and biophysical properties of the matrix in order to make further advancements in the understanding the PCMs role in adhesion, transport to and from the cell surface, its purported function as a chemical micro-reservoir, as well as basic studies on the kinetics of its formation, turnover and maintenance. The qPEAs measure the penetration and distribution of sub-micron particles after they diffuse into the cell coat, where their distribution maps the interior structure of the PCM. The qPEA assays reveal that the PCM acts a sieve, separating incoming particles by their size, preventing micron sized particles from entering the PCM while allowing sub 100 nm particles to pass to the cell surface. The OFPA uses an optically-trapped bead to study the force response of the matrix as it encounters the probe. The assay not only reveals new details about the PCM such as the fact that it is larger than initially thought, having a two layer structure, but when combined with a polymer physics model which relates the observed equilibrium forces to an existing osmotic pressure gradient within the PCM, the OFPA studies produce the first discovery and measurement of the correlation length distribution in the cell coat. The OFPA and qPEA assays are also performed on cells modified with exogenous aggrecan, resulting in a model for possible proteoglycan mediated cell coat transformations. The fluorescent exogenous aggrecan assays measure the dynamics of the exogenous aggrecan binding to and releasing from the coat, revealing that the PCM can be rapidly modified by a changing environment, and quantitatively measure how the exogenous aggrecan modifies the existing PCM. Together, these assays provide an unprecedented look into the interior structure of the PCM, and the mechanisms responsible both for this structure and its modification.