With the miniaturization of devices, block copolymers (BCPs) are emerging as promising candidates for scaffolds and templates in the fabrication of nanoscopic structures. Key to the use of BCPs is control of the orientation and lateral ordering of their microdomains in thin films. An external electric field was previously shown to effectively orient BCP microdomains in a desired direction. However, complete alignment of microdomains in BCP thin films remains a challenge due to achieve due to the preferential interactions of blocks at the interfaces with the electrodes. Here, we demonstrate that lithium-PMMA complexes, formed by adding lithium salts to polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) copolymer, markedly enhanced alignment of BCP microdomains in thin films under an electric field, mainly by the increased dielectric contrast and mediated surface interactions, which significantly reduced the critical field strength. In addition, formation of lithium-PMMA complexes induces a transition in the reorientation process of lamellar microdomains, from disruption/re-formation to grain rotation. The transition arises in an increase in the segmental interaction parameter, χeffc., of the ion-complexed copolymer, which drives stronger phase segregation. This feature is evidenced by increase of microdomain spacing and ordering, the induced disorder-to-order transition (DOT), and order-to-order (OOT) transitions (sphere-to-cylinder, S-to-C). The increase in χeffc is further confirmed by small-angle neutron scattering (SANS) from the complexed copolymers in the disordered state. Moreover, the temperature dependence of χ effc for the complexed copolymer becomes weaker than that of the neat copolymer. The electric-field-induced sphere-to-cylinder transition in thin films depends on the strength of the interfacial interactions. As a result, a strong preferential interfacial interaction suppresses the transition. However, the formation of ion-complexes enhances the ability of an applied electric field to induce S-to-C transition even on a surface with unbalanced interfacial interactions, providing a simple route to ordered arrays of high aspect ratio cylinders oriented normal to the surface.

Over recent decades, molecular biology has been transformed by the progression towards a more physical understanding of biological macromolecules, such that familiar biochemical behavior can be understood in terms of individual macromolecular structure. Such physical insight now guides modern approaches to biotechnology and fundamental biology. Langevin dynamics simulations offer the opportunity to build upon static structural models by treating macromolecules as dynamic entities. Results will be presented of the application of Langevin dynamics simulations to viral genome packaging and voltage-induced polyelectrolyte translocation. An overview will be given demonstrating how Langevin dynamics, taken together with remarkable experimental efforts, has revealed the central importance of DNA/RNA dynamics in each of these phenomena. Based on the success of these studies, it is suggested that Langevin dynamics, in coordination with experimental efforts, represents a powerful tool for improving the fundamental understanding of various phenomena of biological and biotechnological import.

This dissertation describes computer simulations and theoretical analyses of polymer crystallization and amyloid fibrillization. Langevin Dynamics simulations of polymer chains in dilute solutions suggest that chains are prefolded before crystallization, in contradiction with the traditional view that chain folding occurs only on the growth front. The prefolded chain reveals a thickness plateau in low-temperature region (solving the puzzle of "δL catastrophe"), suggesting that lamellar thickness might be a predetermined equilibrium result. Based on the above prefolding and predetermined thickness concepts, the prefolded chains are then taken as the smallest dynamic units in Monte Carlo simulations, where an anisotropic aggregation model is proposed to study single crystals, shish-kebab crystals, and crystal melting. This model is further extended to amyloid fibrillization. The single crystal study shows a rough-flat-rough habit transition, solving a long-standing puzzle for the existing theories. The lamellar growth rate is confirmed to vary exponentially with temperature and concentration. The shish-kebab study confirms that the distribution of kebab spacings is lognormal. In contrast to Pennings' and Hill's models, a new model is proposed to describe the relation between the spacing and temperature: the logarithm of the spacing growth rate is proportional to the inverse of temperature. The spacing is also found to be proportional to the inverse of polymer concentration. A broad melting transition for shish-kebab crystals is observed in simulations. The melting point is confirmed to be proportional to the square root of heating rate, increase exponentially with crystallization temperature, and increase with the logarithm of crystallization time in sigmoidal fashion. It is proposed that the melting point is related to the lamellar diameter, rather than the lamellar thickness in the traditional view. The seeding phenomenon for amyloid fibrils is reproduced in simulations. It is proposed that nucleation of the amyloid fibril is due to its semi-two-dimensional nature, because a pure one-dimensional growth does not require nucleation and does not exhibit sigmoidal curves. The importance of the second layer of β-sheet is stressed. It is proposed that Ostwald ripening (bigger fibrils grow at the expense of smaller ones) is the dominating mechanism for amyloid fibril growth.

The research presented in this thesis focuses on the development of novel functional hybrid organic-inorganic architectures containing chemically-tethered icosohedral carboranes. The motivation behind this work was to understand and overcome the challenges associated with the incorporation of inorganic boron clusters into a variety of well-defined polymeric architectures. This task was critical for the advancement of scientific understanding, as well as the improvement and implementation of novel hybrid materials towards technological applications. Chapter 1 illustrates some of these potential target applications, and highlights the advantages associated with the utilization of hybrid materials, in particular those containing boron. The synthesis of a novel silyl-protected oxanorbornene imide carborane (SONIC) monomer as well as its copolymerization by ring-opening metathesis polymerization (ROMP) to obtain amphiphilic diblock copolymers is described in Chapter 2. The subsequent functionalization and labeling of the polymers, and their solution behavior have been investigated. Initial biological studies have shown the incorporation of the carborane-containing polymers in carcinoma cells. These findings pave the way for future investigations of these polymeric architectures as delivery agents for boron neutron capture therapy in cancer treatment. The random copolymerization of SONIC and cyclooctene is reported in Chapter 3. Polymers with varying compositions have been obtained and hydrogenated to afford polyethylene-like materials. The structural and thermal properties of these materials have been evaluated and compared to model compounds. Carboranes have also been introduced into conjugated polyaromatic structures as side chains. The synthesis of a polyfluorene monomer having two pendant silylcarborane groups is reported in Chapter 4. The homopolymerization of this monomer, and its copolymerization with 2,7-dibromo-9,9-di-n-hexylfluorene by microwave-assisted nickel(0)-mediated coupling was investigated. The advantage offered by the presence of bulky silylcarborane groups is described. Finally, the versatility of carborane-containing polymers is demonstrated through their utilization as resists for nanoimprint lithography (NIL). A novel silylcarborane-containing acrylate has been synthesized as described in Chapter 5. The utilization of only 10 wt% of the carborane-containing resist lead to a two-fold decrease in etch rate. Excellent image transfer was also observed, allowing for the fabrication of gold interdigitated electrodes. This work provides a new set of tools for the efficacious implementation of NIL.

The complexity of biological processes manifests itself in many ways, with the most notable being the high level of dynamical control they possess. For the full potential of biological mimicry to be unlocked, it is essential for the scientific community to partake in an exhaustive search to understand the governing dynamics behind these biological processes. In this vein, this work investigates the bulk conductivity behavior of sodium polystyrene sulfonate (NaPSS) as a function of polymer (Cp) and salt (Cs) concentrations. This was carried out in an attempt to understand the individual contributions from each of the conducting species of a polyelectrolyte solution (chain, counter-ions, and/or salt) to the bulk conductivity in its most simple aqueous environment. The translocation behavior of NaPSS through α-hemolysin protein pores was also investigated. We demonstrate how single molecules of NaPSS, varying over two orders of magnitude in the degree of polymerization, can be pulled in aqueous media by an externally applied electric field through the α-hemolysin channel embedded in a lipid bilayer. We propose a two-barrier free energy landscape for polyelectrolyte translocation through α-hemolysin protein pores. Based on the proposed energy landscape, a detailed mechanism behind the array of interactions between a charged polymer and the α-hemolysin protein pore is described. Although the experimental setup and the measurement protocol are identical to the original investigation involving DNA, this work demonstrates that synthetic polymer translocation displays many significant distinguishing features when compared to the behavior of DNA or RNA. We have also investigated the sculpting of synthetic nanopores for translocation of bottle-brush polyelectrolytes towards understanding the transport behavior of more complex chain architectures. The use of synthetic nanopores allows for the custom tailoring of pore diameter, allowing for the translocation properties for a variety of chain architectures to be studied.

The glass transition temperature, the equilibrium modulus, the relaxation behavior in the glass transition region, and the swelling behavior in mixed solvents of two structurally different model network systems, the PPG-DRF system and the PIP-HDI system, were studied. These materials are important since they mimic the behavior of the theoretically described "perfect networks" closely. A range in material properties was induced by introducing stoichiometric imbalances and different molecular weights of the network components in the system. Several theories for each aspect of the properties of these two systems were tested against the experiment. It can be concluded that the PPG-DRF system behaves as a copolymer, following from the glass transition temperature and relaxation, and the swelling behavior. The end group contribution was important for the glass transition temperature. The PIP-HDI system does not behave as a copolymer. The Constrained Chain model was applicable to the equilibrium modulus data for both systems. The trapped entanglement contribution was not explicitly relevant. The swelling in mixed solvents could only be explained when azeotropic behavior of the solvent mixture is assumed.

The study of molecules in restricted geometries is an important topic in the chemical sciences. Surfaces and ultra-thin films are examples of restricted geometries because they alter the structure of the molecules confined due to the presence of an air interface. The structural changes that occur in these restricted geometries directly influence the fields of adhesion, coatings, lithography, photography, printing, filtration, transport properties, surfactants, sensors, microelectronics, electrodes, biology, biological compatibility and membrane function. The structure of ultra-thin polyurethane films is studied to determine effect of the air-polymer interface on the degree of phase separation and the orientation of the hard segments in both the hard and soft domains. External reflection infrared spectroscopy studies show that as the film thickness is decreased, the degree of phase separation decreased and the hard segments oriented into the plane of the film in both domains. The phase separation process in ultra-thin polyurethane films are also studied. The added free volume of the air-polymer interface allows phase mixing to occur at a much lower temperature than in the bulk. The isothermal phase separation of the ultra-thin films is characterized by a much lower Avrami coefficient than the bulk. A simulation of the phase separation process shows that the decrease in the Avrami coefficients can be attributed to the small film thickness compared to the hard domain size, the hard segment concentration change over the course of the phase separation and the disk like shape of the growing domains. In addition, the overall degree of phase separation observed in the ultra-thin films is kinetically controlled due to the directional grow of the disk like hard domains which is limited not by the amount of isotropic phase, but by the film thickness. Finally, the structures of insoluble monolayers at the air-water interface are studied. The frequency and approximate S to P dichroic ratio are used to characterize the structure of H(CH$\sb2)\sb{18}$OH as a function of area per molecule. F(CF$\sb2)\sb{8}$(CH$\sb2)\sb2$OH and F(CF$\sb2)\sb{10}$(CH$\sb2)\sb2$OH are also studied at the air-water interface. In both cases, the C-H stretching region indicated that the water surface is covered by a monolayer however only the longer fluorinated chain gives consistently useful information in the C-F stretching region. This is attributed to changes in the structure of the shorter chain amphiphiles just after they are spread at the air-water interface that the longer chain molecules do not exhibit.

This dissertation describes research performed using siloxane polymers. This includes the reactions of siloxane polymers with inorganic oxide surfaces to form covalently attached monolayers, and the electrical properties of crosslinked silicone composite films fabricated by compounding with nickel particles. In addition to these topics, the use of contact line pinning as a practical and controllable method for the deposition of materials on superhydrophobic and chemically patterned surfaces is also described The first chapter provides a general review of siloxane polymer chemistry, focusing in particular on the relationship between molecular structure and physical properties. The use and fabrication of silicone composite materials is also discussed, including typical methods for crosslinking siloxane polymers and the effects of filler materials. Finally, contact angle hysteresis and contact line pinning phenomena are presented. Following this introduction, four separate but interrelated projects are presented. First, the surface modification of titania via hydridomethylsiloxanes is discussed. This work represents an extension of the reaction of hydridosilanes and provides an environmentally clean method for the hydrophobization of titania. Linear and cyclic hydridomethylsiloxanes, as well as hydridomethylsiloxane-co-dimethylsiloxane polymers, are used as reagents and the resulting surfaces are discussed. Unpredicted results from this method lead to the consideration of poly(dimethylsiloxane) as a previously unconsidered reagent presented in the next project. The second project discusses the covalent attachment of siloxane polymers, particularly poly(dimethylsiloxane), to a range of inorganic oxide surfaces, including titania, nickel oxide, alumina, and silica. This reaction is presented as a thermally activated equilibrium process, and offers insight into certain aging processes found in silicone materials. Particular focus is made on the development of a highly reproducible method for the fabrication of low contact angle hysteresis surfaces. Furthermore, this reaction is shown to be general for the siloxane bond through the reaction of functional and cyclic siloxanes. The third project describes the preparation of electrically conductive silicone coatings, containing nickel and titania particles. The effect of nickel concentration and geometry on the electrical properties of these coatings is examined and the effects on the percolation threshold are presented. In addition to this, the addition of titania nanoparticles to diminish electrical conductance is also investigated. The fourth project discusses the contact line pinning of liquids on hydrophobic surfaces. In this chapter, the use of ionic liquids exhibiting no vapor pressure is used to experimentally determine the de-wetting process of liquids from pillared, superhydrophobic surfaces through micro-capillary bridge rupture. Furthermore, this technique is used as a preparative technique for the fabrication of individual salt crystals supported on pillared surfaces.

Geometrically hindered motions of a single large solute (particle or polymer) can be imaged in real time via optical microscopy. The dynamics of fluorescent colloidal particles near surfaces and in porous membranes were monitored using confocal microscopy. A method of analysis to estimate diffusivity of particles in the axial direction by observing their intensity fluctuations was developed. The intensity fluctuations correspond to the Brownian motion of the particles in the axial direction. The method was successful in capturing the hindered diffusion of particles close to surfaces and in pores. This study provides a novel route to monitor the dynamics of particles, including biomacromolecules, near surfaces, through porous substrates and biological tissues. Ionic liquid (IL) as a medium for room temperature preservation of biomacromolecules has been proposed and, to investigate the possibility, physicochemical and enzymatic properties of proteins in the neat hydrophilic IL, ethylmethyl imidazolium ethyl sulfate [EMIM][EtSO4] were studied. Spectroscopic techniques were employed to probe the secondary and tertiary structure of proteins whereas light scattering and viscometry were used to estimate the hydrodynamic size. The secondary structure of the protein was retained in the ionic liquid but the tertiary structure was found to change. Alterations in protein conformation/activity were investigated after transfer of the dissolved protein from the IL to buffer. Further, suitability of ionic liquid gels as protein encapsulation and preservation media was assessed.

Reaction of poly(chlorotrifluoroethylene) (PCTFE) with trimethyl 4-lithioorthobutyrate and hydrolysis produces a surface containing carboxylic acids (PCTFE-CO$\sb2$H). The advancing water contact angle ($\Theta\sb{\rm A}$) varies from ${\sim56}\sp\circ$ at low pH to ${\sim30}\sp\circ$ at high pH. The receding water contact angle ($\Theta\sb{\rm R}$) is 0$\sp\circ$ at all pH values. PCTFE-CO2H could be reduced to the alcohol, creating a less hydrophilic surface $\rm (\Theta\sb{A}/\Theta\sb{R} = 62\sp\circ/22\sp\circ)$ or converted to the n-octyl ester, rendering a hydrophobic surface $\rm (\Theta\sb{A}/\Theta\sb{R} = 99\sp\circ/47\sp\circ).$ PCTFE reacts with acetaldehyde 3-lithiopropyl ethyl acetal at $-$78-$-$15$\sp\circ$C to introduce the acetal into the outer $\sim$30-1000 A of the surface (PCTFE-PEAA). Hydrolysis produces a hydrophilic $\rm (\Theta\sb{A}/\Theta\sb{R} = 67\sp\circ/17\sp\circ),$ alcohol-functionalized surface (PCTFE-OH) which was derivatized to prepare a series of linear hydrocarbon and fluorocarbon ester surfaces. Reactions with multifunctional reagents produced crosslinked surfaces. Gravimetric, XPS, ATR-IR and contact angles results are consistent with the proposed surface structures and high reaction yields. Water contact angles on the hydrocarbon ester surfaces range from 82$\sp\circ/46\sp\circ$ (acetate) to 108$\sp\circ/90\sp\circ$ (stearate), while those on the fluorocarbon esters range from 92$\sp\circ/51\sp\circ$ (trifluoroacetate) to 120$\sp\circ/69\sp\circ$ (perfluorodecanoate). Hexadecane contact angles and XPS results show that the stearate and perfluorodecanoate esters form ordered surfaces. Friction properties of these modified surfaces were also investigated. The effects of varying the ester chain length, crosslinking the surface and varying the modification depth were studied. Contrary to expectations, the perfluorinated surfaces exhibited greater friction than their hydrocarbon analogs. The results show that chemical interactions at the sliding interface have little influence on friction and that it is the deformation behavior of the polymer near the interface that dictates the magnitude of the energy losses. Mixed surfaces were prepared to study the effect of surface composition on wetting. Randomly mixed hydroxyl/hydrocarbon ester surfaces were prepared by kinetic control of the esterification of PCTFE-OH, while compositionally similar, patchy surfaces were prepared by kinetic control of the hydrolysis of PCTFE-Esters. Esterification of the alcohol groups in these two sets of mixed surfaces was utilized to prepare the corresponding hydrocarbon ester/fluorocarbon ester mixed surfaces. As expected, greater contact angle hysteresis was observed on the patchy surfaces.