Model glassy polymers, polymethyl methacrylate (PMMA) and polycarbonate (PC) are used to experimentally probe several aspects of polymer fracture. In Chapter 1, the method of pre-stress is employed as a means of improving the fracture properites of brittle PMMA. Samples are tested under equi-biaxial compression, simple shear and a combination of biaxial compression and shear. Equi-biaxial compression is shown to increase the threshold stress level for projectile penetration whereas shear pre-stress has a large effect on the overall energy absorbed during an impact. There is also an apparent interaction observed between compression and shear to dramatically increase the threshold stress. Pre-stressed laminates of PMMA and PC show an increase in damage area because of the unique formation of a secondary cone. In Chapter 2, the effect of stress state on stress relaxation in PMMA and PC is investigated. Direct comparisons are made between uniaxial and biaxial loading conditions. The experimental methods used highlight the effect of hydrostatic stress on the relaxation process. The data shows an increase in relaxation time and increase in the breadth of the relaxation spectrum with increases in hydrostatic stress. This suggests that the stress state can have a significant effect on the useful lifetime of pre-stressed articles. In Chapter 3, Mode I and II fracture studies are performed from quasi-static to low velocity impact rates on PMMA and PC. Mode II testing utilizes an angled double-edge notched specimen loaded in compression. The shear banding response of PMMA is shown to be highly sensitive to rate, with diffuse shear bands forming at low rates and sharp distinct shear bands forming at high rates. As the rate increases, shear deformation becomes more localized to the point where Mode II fracture occurs. PC is much less rate dependent and stable shear band propagation is observed over the range of rates studied with lesser amounts of localization. A new theory is formulated relating orientation in a shear band to intrinsic material properties obtained from true-stress true-strain tests. In a qualitative sense the theory predicts the high rate sensitivity of PMMA. A kinematic limit for orientation within a shear band is also derived based on entanglement network parameters. Mode II fracture in PMMA is shown to occur at this kinematic limit. For the case of PC, the maximum impact rates were not high enough to reach the kinematic limit. In Chapter 4, the deformation response, as observed in a shear band is interpreted through the characterization of the "intrinsic material properties" obtained from true stress—true strain 8compression tests. The relatively high rate sensitivity of PMMA deformed at room temperature is related to the proximity of the beta transition to the test temperature. This is also shown in corollary experiments on PC where deformation near the beta transition is accompanied by an increase in rate sensitivity. Physical aging results in a more narrow alpha transition and is shown to increase strain localization and decrease rate sensitivity at low strain rates.

The rise in bacterial resistance and the declining approval rate of novel anti-infective drugs are a major threat to global public health. Antimicrobial peptides (AMPs), found in almost every multicellular organism, have attracted considerable attention as models for the design of new therapeutic agents due to their broad spectrum activity and reduced bacterial resistance development. This dissertation focuses on the development of a new series of synthetic mimics of antimicrobial peptides (SMAMPs) from simple aryl scaffolds using Suzuki Miyaura coupling. This novel design allows easy tuning of the conformation, overall hydrophobicity of the molecule, amphiphilicity, and the number of charges in order to develop a structure-activity relationship. The antimicrobial activities of the SMAMPs against both gram-positive and gram-negative bacteria suggest that improving the selectivity requires fine-tuning of one or more of these parameters, with overall hydrophobicity and charge having a more significant impact than conformational rigidity. Furthermore, comparing the activities of SMAMPS with facially amphiphilic and disrupted amphiphilic topologies confirmed that amphiphilicity is an important design parameter for attaining antimicrobial activity, especially against gram-negative bacteria. This aryl scaffold design has led to the development of several highly active SMAMPs with selectivities >200 against both gram-positive S. aureus and gram-negative E. coli, which is nearly 20 times higher than that of the conventional AMP, MSI-78. One of these SMAMPs also shows a unique immunomodulatory response involving the induction of both cytokines and chemokines, which can have significant therapeutic potential. Similar chemistry was employed in the development of novel lipopeptide mimics (LPMs), where the attachment of pendant aliphatic chains to the tri-aryl backbone structure can be used to modulate the activity. The second project in this dissertation concerns the investigation of the influence of the cobalt density in the phase-separated domains in the ferromagnetic block copolymer materials A series of metal-containing block-random copolymers composed of an alkyl-functionalized homo block (C16 ) and a random block of cobalt complex- (Co) and ferrocene complex-functionalized (Fe) units was synthesized via ring-opening metathesis polymerization (ROMP). Taking advantage of the block-random architecture, the influence of dipolar interactions on the magnetic properties of these nanostructured BCPs was studied by systematically varying the molar ratio of the Co units to the Fe units, while maintaining the cylindrical phase-separated morphology. A decrease in the cobalt density weakens the dipolar interactions between the cobalt nanoparticles, leading to the transition from a room temperature ferromagnetic material to a superparamagnetic material. These results confirm that the dipolar interactions of the cobalt nanoparticles within the phase-separated domains are responsible for the (unexpected) room temperature ferromagnetic properties of the nanostructured BCPs.

Currently, most of the commercially available therapeutics are all targeting cell surface receptors which constitutes only a small portion of the targets found in the cells. Therefore, reaching intracellular targets would provide many new opportunities to treat various diseases. However, intracellular delivery of therapeutic molecules has always been a challenge due to the poor permeability of cell membrane to large, negatively charged macromolecules and their restricted biodistribution. In the past decades, cell penetrating peptides (CPPs), also known as protein transduction domains (PTDs), are shown to improve the intracellular delivery of bioactive molecules and among the PTDs, arginine-rich peptides are highlighted as the most effective subclass. In the light of this information, using the power of polymer chemistry, protein transduction domain mimics (PTDMs) based on ring opening metathesis polymerization (ROMP) of functionalized oxanorbornene derivatives are aimed to be designed. This thesis demonstrates that these PTDMs can adopt cell penetrating activity and show superior properties compared to peptide analogues (i.e. nonaarginine, R9, Pep-1). The structure-activity relationship is studied by guanidinium functionalized monomers. The impact of number of guanidiniums, density of guanidiniums, molecular length and hydrophobicity on cellular internalization is investigated. Further, the siRNA delivery ability of designed PTDMs is also studied. Efficient downregulation of NOTCH1 protein using PTDM-based non-covalent siRNA delivery system in T cell lines and primary blood cells is demonstrated. Two different structures of PTDMs are studied to understand the structural requirements for an efficient carrier. Apart from in vitro testing of PTDM/siRNA complexes, their size and surface charge are also characterized. Further, PTDM-based siRNA delivery system is used to study the function of NOTCH1 in in vitro in primary human blood cells and as well as in humanized mouse model of graft vs host disease as an in vivo environment. In addition to siRNA delivery, novel protein transporter PTDMs which are inspired by primary amphipathic peptides is introduced. The effects of different functional groups and different block lengths on protein delivery efficiency are studied. Successful delivery of functional proteins is demonstrated using Cre Recombinase and Runx1.d190.

Macromolecular assemblies constitute the world in which we live. The work contained within this thesis has studied three different types of macromolecular assemblies: human gamma-crystallin protein aggregation, the synthesis of glutamic acid bottle brushes, and cross-linked hyaluronic acid hydrogels. The in vitro study of human lens gamma-crystallin protein aggregation is the main component of this thesis. Separate projects that aid the body of this work include a description for the synthesis of glutamic acid bottle brush macromolecules and novel cross-linked networks of hyaluronic acid hydrogels. Cataract is the number one cause of blindness worldwide. Despite being a widespread disease, the epidemiology of cataract is still largely unknown. Cataracts are protein aggregates consisting of alpha-, beta-, and gamma-crystallin protein which are the major components of the lens in the human eye. In this work, in vitro investigations of protein-protein interactions were performed on dilute solutions of recombinant human alpha- and gamma-crystallin protein using dynamic light scattering technique. It was discovered that in phosphate buffered solutions, gamma-crystallin exists as two distinct populations of unaggregated and large aggregated protein. On the other hand, alpha-crystallin protein does not aggregate, but forms small oligomeric assemblies. Upon mixing alpha- and gamma-crystallin the aggregation of gamma-crystallin was removed. The impact of temperature, protein concentration, the reducing agent dithiothreitol, salt concentration, and pH on gamma-crystallin were all subsequently investigated. It was concluded that in vitro aggregation of gamma-crystallin protein arises from non-covalent electrostatic interactions. To further investigate the electrostatic hypothesis, point mutations were performed on human gamma-crystallin in an attempt to prevent protein aggregation. Using recombinant DNA technology, twelve different gammaS-crystallin protein mutants were created. The mutations were designed to change the proteins overall surface charge by substituting positively charged amino acids with neutral hydrophilic amino acids. The aggregation behavior of the mutant proteins was then studied by dynamic light scattering. It was observed that all gamma-crystallin mutants resulted in continued aggregation. The result suggests that the in vitro aggregation behavior of gamma-crystallin is likely due to electrostatic interactions between specific amino acids not probed in this work. Due to the time consuming nature of point mutations, chemical modifications of gamma-crystallin were subsequently performed in an alternative method to disrupt electrostatic interactions which are believed to cause gamma-crysatllin protein aggregation. GammaD- and GammaS-crystallin proteins were chemically modified with seven different molecules. Chemical modifications were characterized with a combination of mass spectroscopy, circular dichroism spectroscopy, and dynamic light scattering. The results demonstrated that modifying positively charged amino acids of human gamma-crystallin protein with poly(ethylene) glycol prevented in vitro protein aggregation. The chemical modification of lens crystallin protein provides a possible route by which protein aggregation and ultimately cataract can be prevented, arrested or reversed. In a separate project, glutamic acid bottle brushes were synthesized for future translocation experiments. Translocation is viewed as a potential method by which genomic DNA can be sequenced. In an attempt to understand the effect of polymer diameter on translocation kinetics, bottle brush polymers with varying thicknesses were synthesized. The complex synthesis and subsequent characterization by nuclear magnetic resonance, atomic force microscopy, capillary electrophoresis, static and dynamic light scattering are described herein. In summary, glutamic acid bottle brushes of three different thicknesses were successfully synthesized, characterized, and purified. Finally, the novel synthesis of thiol cross-linked hyaluronic acid hydrogels is described. Hyaluronic acid is a polysaccharide which is of interest for potential biomedical applications. The biopolymer was modified with cystamine and placed under reducing conditions which provides free thiol groups capable of crosslinking under oxidizing conditions. The synthesis, characterization, and gelation procedure for the cross-linked hyaluronic acid hydrogels is described in detail. The modified hyaluronic acid is a material capable of in situ gelation.

Analogous disproportionation processes lead to similarities in the structures present at incipient coacervation to those within the subsequent dense phase. Coacervation in polyelectrolyte/mixed micelle system is induced by temperature to explore structural evolution before, during and after coacervation. Assemblies of polyelectrolyte-micelle primary complexes appear to be governed by the interparticle interaction, a delicate balance between short-range attraction and long-range repulsion. Dilution-induced coacervation in opposite to self-suppression is facilitated by the presence of smaller particles in size but larger in number as a result of the favourable interparticle interaction. While dilution leads to formation of smaller particles that can phase separate easily, larger particles can achieve coacervation by increase in temperature, a greater entropy contribution. Dynamic light scattering reveals a progressive increase in aggregate size with temperature up to the phase transition at Tphi;, followed by splitting of these aggregates into respectively smaller and larger particles. The fact that the process of coacervation itself is accompanied by the expulsion of smaller aggregates to form near-neutral aggregates is known as a type of macroion disproportionation. At incipient coacervation, the transfer among soluble complexes of excess macroions to achieve near-neutrality is found to be analogous to the expulsion (with counterions) of excess macroions into dilute domains in the coacervates. The driving forces of ion-pairing and counterion release, in one-phase and dense phase states, use similar strategies of disproportionation and local charge neutralization to form analogous transient structures. The transient nature of coacervate structure is further investigated by rheology and total internal reflection microscopy in PDADMAC/BSA coacervates. While polyelectrolyte-colloid coacervates exhibit structural rearrangement in the coacervate correlated with the compositional difference between supernatant and coacervate, heteroprotein coacervation appears to have a fixed stoichiometry in both phases. The absence of disproportionation is suggested to be responsible for the highly limited conditions of pH, ionic strength I, total protein concentration Cp, and BLG:LF stoichiometry under which Lactoferrin (LF) and B-lactoglobulin (BLG) form optically clear coacervates. These constraints on conditions for pure coacervation were also attributed to the requirements for the formation of a basic primary unit, LF(BLG)4 , characterized in the supernatant and coacervate. Coacervate is characterized as a solidlike transient network of primary units embedded into a viscoelastic suspending fluid.

Polymer materials have become important tools in nanomanufacturing due to their facile processing and ready attainment of the necessary feature sizes. The development of cleavable junctions has led to advances in the production of polymer nanotemplates. Photocleavage strategies have come to the forefront of the field because photons, as a cleavage stimulus, do not have the mass-transport limitations of chemical methods, and provide for targeted two- and three-dimensional feature control. This dissertation presents a method for producing photocleavable materials by one-pot copper-catalyzed azide-alkyne "click" chemistry (CuAAC), activator regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) and activated ester substitution methods that have each block labeled with a fluorescent dye, enabling exploration of the polymer physics of these systems by correlation fluorescence spectroscopy. It also introduces a novel photocleavable linker, the o-nitrobenzyl-1,2,3-triazole, its behavior on photocleavage, and a facile method for the production of the o-nitrobenzyl azides necessary for their synthesis. The synthesis and properties of a bulk photodegradable polytriazole are reported, as are proof of concept experiments demonstrating its potential as a directly photoetchable material. Lastly, this dissertation contains a perspective on possible avenues of new research on the topics presented.

This dissertation explores the design, synthesis, and structure of aromatic molecules with the goal of understanding the forces which affect packing of conjugated molecules in the solid state. Two approaches were applied to direct the assembly of aromatic materials. The first one involved the use of coordination bonds between aromatic nitriles and silver(I) triflate. Several acridine-based ligands were synthesized and crystallized, alone and complexed to silver(I) triflate. Generally, ligands that possessed three peripheral coordination sites formed sheet-like crystal structures. Ligands with only one coordination site crystallized into columnar arrangements with significant edge-to-face interactions. The second approach studied the effect of mutually phobic side-chains on the properties of dyads - molecules comprised of linked electron-rich and electron-poor aromatic moieties. It was shown that, despite attractive electrostatic forces between electron-rich and electron-poor aromatic species, aliphatic hydrocarbon and fluorocarbon side-chains form segregated domains in single crystals. Finally, the mutually phobic side-chain approach was extended to materials based on oligo- or poly-thiophene and naphthalenediimide.

Materials with nanoscale dimensions display electronic, photonic, and magnetic properties different from those observed by their respective bulk materials. This thesis work has focused on the utilization of molecular recognition for modular self-assembly of nano-sized building blocks into two or three-dimensional aggregates and the precise control over their structural parameters and morphologies. Special attention will be given to the design and synthesis of molecular and macromolecular building blocks to generate micron and nanometer-scale order, to tailor local surface properties through site-selective immobilization, and to create responsive/adaptive functional materials in a controlled, reproducible, and reversible manner. The advantages, potential applications, and current challenges associated with this "bottom up" self-assembly approach will also be discussed. I am going to demonstrate in the following chapters how we synthesized functionalized Au and CdSe nanoparticles (NPs), styrene based block copolymer with pended recognition units, and diamidopyridine ( DAP)—thymine (Thy) three-point hydrogen bonding dyads that induced recognition-mediated self-assembly of polymers and NPs into ordered and tunable/responsive nanocomposites. The resultant composite materials were addressed onto photo-lithographically defined surface regions. Desired electrical conductivity, surface wettability and biocompatibility were achieved by choosing appropriate polymers and NPs—the versatile building blocks for nanocomposite functional materials.

A hydrogel is a crosslinked network of polymer chains swollen by water. When immersed in an aqueous medium, a hydrogel will swell by taking up water until the osmotic pressure set by mixing between water and polymer is balanced by the free energy required to stretch polymer chains. When considered at a length scale greater than the sub-micrometer scale inhomogeneity of the gel network structure, the unconstrained gel swells isotropically and reaches a macroscopically stress free state. However, when a sheet of gel is attached to either a non-swelling rigid substrate or a gel that swells by a different amount, the resulting mechanical constraints generate stress within the gel, leading to the out-of-plane deformations of the gel. In this thesis, we study and harness the instabilities of these mechanically constrained hydrogels, especially thin hydrogel sheets with thicknesses of 10–100 micrometers that swell and deswell rapidly (less than 10 seconds for sufficiently hydrophilic gels). We create hydrogel based micro-systems, where we locally apply mechanical constraints on the swelling of hydrogel sheets, and therefore, the gels deform out-of-plane into 3D shapes. Next, we experimentally characterize and analyze the deformed hydrogels, elucidate the mechanisms underlying the observed deformation using finite element analysis, and finally utilize these methods to fabricate stimuli-responsive surfaces and structures. As the first example, we attach a thin film of hydrogel on a rigid substrate, inducing an elastic creasing instability in which the surface of the hydrogel locally folds against itself. Through the chemical modification of the hydrogel surfaces that undergo the creasing instability, we fabricate dynamic surfaces that hide and display biomolecular patterns in response to an external stimulus and show how these materials hold promise for applications in studying cell mechanics and creating lab-on-a-chip devices. Next, we use a grayscale gel lithography to two-dimensionally patterned discretely varying swelling ratios within a hydrogel sheet of ∼ 10 micrometer thickness. This finite-thickness, differentially growing hydrogel sheet undergoes out-of-plane deformation as it swells and adopts a configuration that is determined by the initially prescribed local swelling ratios and minimizes the overall elastic deformation energy, i.e. the sum of stretching and bending energies. Additionally, we introduce a halftone-style two-level grayscale gel lithography, which prescribes effectively continuous metrics on the hydrogel sheets by patterning hexagonal arrays of dots that locally vary in their sizes and swell less than the background. This platform, grayscale gel lithography, provides opportunities both for asking fundamental questions about the mechanics of non-Euclidean plates, as well as for designing stimuli-responsive micro-devices.

The development of highly selective and very sensitive methods to detect peptides and proteins of interest in complex mixtures remains an important goal in proteomics applications. This dissertation focuses on the use of reverse-micelle forming amphiphilic homopolymers as part of liquid-liquid extraction to selectively extract and concentrate peptides from an aqueous solution into an immiscible organic phase. After extraction, the polymer-peptide mixtures are amenable to direct analysis by matrix assisted laser desorption ionization mass spectrometry (MALDI-MS). The charged interiors of the reverse micelles enable oppositely charged peptides to be selectively extracted into the aggregate’s cores via coulombic attraction. Reverse micelles formed by negatively charged carboxylic acid or positively charged quaternary amine groups can be used alone or in sequence to selectively extract and fractionate peptides according to their isoelectric points (pIs). Furthermore, the pI cutoff can be readily tuned by adjusting the extraction pH. The coalescence of polymer-peptide conjugates into hotspots on the MALDI target plate during MALDI-MS analysis results in significant signal enhancement for the enriched peptides, enabling reproducible ion signals at concentrations as low as 10 fM. Interestingly, reverse micelles formed by positively charged polymers with quaternary amine substituents can selectively enrich acidic peptides that are undetectable during regular MALDI-MS analysis. The extraction protocol along with MALDI-MS can also be used for the selective enrichment and detection of low abundance peptide/protein biomarkers in human serum at physiologically relevant concentrations. Overall, the results described in this dissertation reveal that this selective extraction protocol along with MALDI-MS analysis might have a significant impact on protein identification and early stage screening of biomarkers.