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<p>  Peptide biomaterials have drawn great attention in recent decades owing to their tunability and biocompatibility. Coiled-coils specifically have become a well-studied scaffold with a clear sequence-to-structure relationship. As such, the Chmielewski lab has extensively studied peptide assemblies based on the GCN4 leucine zipper. First, we present the peptide <strong>TriCross</strong>, where nitrilotriacetic acid (NTA) and di-histidine ligands are installed at the N- and C-terminus, respectively, and a bipyridine ligand installed at a central, solvent exposed position. Through strategic placement of these metal-binding ligands, TriCross assembled into a three-dimensional (3D) mesh in the presence of zinc ions and dissembled following mild ethylenediaminetetraacetic acid (EDTA) treatment. These properties created a 3D network capable of encapsulating cells for extended periods of time (>1 week) and releasing cells upon metal-chelation. </p> <p>  Next, we describe a stabilized nanotube and enhanced crystal assembly through a heterocoiled-coil assembly. Nanotubes composed of the coiled-coil peptide <strong>TriNL</strong> that assembled likely through ionic interactions rapidly degraded in phosphate buffered saline (PBS). To improve stability, a peptide with metal-binding ligands, <strong>p2L</strong>, was introduced through thermal annealing of the two peptides. Low levels of <strong>p2L </strong>(up to 10:1 <strong>TriNL</strong>:<strong>p2L</strong>) retained nanotube morphology while simultaneously introducing NTA and di-histidine ligands. Upon addition of metal, metal-ligand interactions were established within the nanotube and increased stability of the material. Higher levels of <strong>p2L</strong> (2:1 <strong>TriNL</strong>:<strong>p2L</strong>) led to hexagonal crystals similar to <strong>p2L</strong> but now without the use of metal ions. These crystals expanded the scope of protein inclusion by removing the requirement for His-tags on proteins to be incorporated within the material.</p> <p>  Finally, a self-replicating and self-assembling coiled-coil peptide is reported. The coiled-coil <strong>TriNL</strong> was cysteine modified (N20C) to create a peptide capable of native chemical ligation. At low concentrations, the <strong>N20C FL</strong> peptide acted as a template for the cysteine and thioester fragments while high concentrations led to fibrillar structures. The size of the fibrils was controlled through the addition of preassembled seeds into the native chemical ligation system. </p>

Squaraine dyes have been a subject of extensive investigations lately due to their wide applications in important technological fields such as bioimaging probes, bioconjucation, second generation photosensitizers for photodynamic therapy, second harmonic generating organic dyes, two-photon absorbing materials with large cross section values, and, finally, photoconducting materials in photovoltaic cells. While a large number of patents and papers has been produced regarding their applications limited work has been done concerning their thermotropic behavior, including their liquid crystalline properties, or correlation of the crystalline structure to both the solid state aggregation and their photophysical properties. In the first chapter of this dissertation, a series of squaraine dyes, based on 2, 4-(4-(N,N-di-n-alkylamino)-2-hydroxyphenyl)squaraine including ethyl, propyl, butyl, pentyl, hexyl, and heptyl derivatives, were synthesized by condensation of the corresponding 4-(N,N-di-n-alkylamino)-2-hydroxyphenol with squaric acid. The thermal behavior of the series was recorded using both thermogravemetic analysis (TGA) and differential scanning calorimetry (DSC) while their crystalline structures were elucidated via single crystal X-ray diffraction. The length of the alkyl chain proved to have a significant effect on both the thermotropic behavior and the crystalline structure of the squaraine series. Two derivatives, butyl and heptyl, revealed the presence of liquid crystalline mesophases, smectic and nematic, respectively, that were confirmed and characterized via polarized light microscopy (PLM) and X-ray diffraction. In the second chapter, J- and H- aggregates were investigated in thin films by UV-vis spectroscopy; several of the derivatives formed H- and/or J-aggregates upon thin film formation via spin coating before and after thermal annealing, as indicated by UV-vis spectroscopy. The molecular structure, crystal structure, aggregation, and thermal behavior provide insight into the supramolecular assembly of this important class of materials. Photophysical measurements revealed large molar absorptivity, reasonably high fluorescence quantum yields, and significant fluorescence anisotropy, making these derivatives suitable candidates for a number of electro-optic and photonics applications. The third chapter was devoted to investigate liquid crystal-directed supramolecular assembly of a squaraine dye. Thus, The squaraine (SQ) dye, 2, 4-bis (4-(N,N-di-n-hexylamino)-2-hydroxyphenyl)squaraine was used to prepare a series of SQ dye/cholesteryl pelargonate mixtures with varying dye concentrations (1%, 3%, 7.5%, 10.8%, 15%, and 20% w/w). Their phase transitions were investigated using differential scanning calorimetry, polarized light microscopy and X-ray diffraction. The squaraine dye itself exhibits no liquid crystalline behavior. The concentration of the dye in the cholesteric compound proved to have a significant effect on the dye aggregation behavior and phase transitions in cholesteryl pelargonate manifested by the appearance of new mesophases and formation of J- and H- aggregates. The texture morphology, X-ray diffraction analyses, and UV-vis absorbance spectra provide compelling evidence of the viability of the self-assembly of squaraines in the liquid crystalline mesophase. In the last chapter we will discuss possible modifications that can improve the aggregation systems.

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The aim of this dissertation is to investigate self-assembled structures and the phase diagram of amphiphilic molecules of diverse geometric shapes using a number of different computer simulation methods. The semi-realistic coarse-grained model, used extensively for simulation of polymers and surfactant molecules, is adopted in an off-lattice approach to study how the geometric structure of amphiphiles affects the aggregation properties. The results of simulations show that the model system behavior is consistent with theoretical predictions, experiments and lattice simulation models. We demonstrate that by modifying the geometry of the molecules, self-assembled aggregates are altered in a way close to theoretical predictions. In several two and three dimensional off-lattice Brownian Dynamics simulations, the influence of the shape of the amphiphilic molecules on the size and form of the aggregates is studied systematically. Model phospholipid molecules, with two hydrophobic chains connected to one hydrophilic head group, are simulated and the formation of stable bilayers is observed. In addition, (practically very important) mixtures of amphiphiles with diverse structures are studied under different mixing ratios and molecular structures. We find that in several systems, with Poisson distributed chain lengths, the effect on the aggregation distribution is negligible compared to that of the pure amphiphilic system with the mean length of the Poisson distribution. The phase diagrams of different amphiphilic molecular structures are investigated in separate simulations by employing the Gibbs Ensemble Monte Carlo method with an implemented configurational-bias technique. The computer simulations of the above mentioned amphiphilic systems are done in an area where physics, biology and chemistry are closely connected and advances in applications require the use of new theoretical, experimental and simulation methods for a better understanding of their self-assembling properties. Obtained simulation results demonstrate the connection between the structure of amphiphilic molecules and the properties of their thermodynamically stable aggregates and thus build a foundation for many applications of the remarkable phenomena of amphiphilic self-assembly in the area of nanotechnology.

The self-assembly of chiral amphiphilic molecules in aqueous solutions is of particular interest because the chirality of individual molecules is often expressed in their supermolecular structures. Self-assembled tubes made of chiral amphiphilic molecules represent useful supramolecular architectures which hold promise as controlled release vehicles for drug delivery, encapsulates for functional molecules, and nanoreactors for chemical reactions. Lithocholic acid (LCA) is a secondary bile acid with the concentration being identical to that of cholesterol in the hepatic bile and gallbladder. It has a rigid, nearly planar hydrophobic steroid nucleus, with four hydrogen atoms and one hydroxyl group directed toward the concave side, and the convex side with three methyl groups. The ionic head with a carboxyl group is linked to the steroid nucleus through a short alkyl chain. In this thesis work, I study the self-assembly behavior of LCA at the liquid-solid interface, in confined spaces, and bulk solution. We find that the initially formed LCA vesicles further assemble into fractal tubes on glass slides by diffusion-limited aggregation and pronglike tubes by the capillary flow generated in an evaporating vesicle solution confined by two parallel glass slides. While in bulk solution, the LCA vesicles linearly aggregate and fuse into spiral tubes at pH 12.0. The spiral tubes can transition into a straight shape as the pH of solution is reduced to 7.4. The shape transition of the tubes is reversible as the pH of solution is adjusted back to 12.0. The pH-switchable shape transition suggests that the self-assembled LCA tubes can act as a supramolecular chemical spring. Finally, the LCA tubes are endowed with optical functionality by embedding cadmium sulfide nanopaticles (CdS) in the tube walls by the co-assembling synthesis of cadmium sulfide iv (CdS) nanoparticles with lithocholic acid (LCA) molecules. The fluorescent composite tubes can undergo pH switchable spiral/straight, which are a promising system for a variety of materials and biological applications.

My PhD work focuses on developing new methods to create the macroscopic patterns in a simple, robust, and versatile way. For macroscopic pattern formation, we first use flow coating as an assembly technique, uniquely balancing two driving forces: (i) evaporative deposition of nonvolatile solutes at a three-phase contact line and (ii) precision movement of a confined meniscus layer. This balance leads to the formation of line-based patterns that range in height and width from nanometers to microns, with lengths greater than centimeters. Moreover, we couple this deposition methodology with functional ligand chemistry on the nanoparticle surface, which allows us to create complex nanoparticle structures. By lifting crosslinked nanoparticle ribbons and ropes, exceptionally intriguing structures emanate from this process. The nanoparticle ribbons and ropes demonstrate a leap forward in nanomaterials fabrication, since the nanoscale properties are embedded within a macroscale object that can be manipulated with conventional methods and engineered into advanced technologies Using mechanical instability, we fabricate a simple, robust stimuli-responsive surface with periodic structures over a large area based upon osmotically-driven surface wrinkling. Although surface wrinkling has received considerable attention in the scientific literature, only a handful of papers have shown the ability to harness perhaps the greatest potential attribute of surface wrinkles: their active reversible nature. The ability to precisely control surface topographic morphologies in accordance with established scaling relationships opens a wide array of advanced materials applications, which do not rely upon cost-limiting fabrication techniques. Specifically, the surfaces respond to solvent exposure by developing well-defined topographic structures over laterally extensive areas due to osmotically-driven differential strains between a surface layer and underlying soft substrate. The observed wrinkling occurs spontaneously, forming hierarchical morphologies with controlled dimensions, and vanishes upon removal of the solvent driving force. The combined responsiveness and reversibility of wrinkling allow for the realization of functional devices, such as smart windows, smart microlens arrays, reversible channels in microfluidic devices. Moreover, by using thermal and osmotic approaches, we study the influence of geometry and material properties on surface instability such as cracking and wrinkling in a trilayer system consisting of a thin film on a soft foundation supported by a rigid substrate.

In this thesis, we studied the self-assembly of nanoparticles at liquid metal-water interfaces and oil-water interfaces. We demonstrated a simple approach to form nanostructured electronic devices by self-assembly of nanoparticles at liquid metal surfaces. In this approach, two liquid-metal droplets, which were coated with a monolayer of ligand-stabilized nanoparticles, were brought into contact. They did not coalesce but instead remained separated by the nanoparticles assembled at the interface. Devices formed by this method showed electron transport between droplets that was characteristic of the Coulomb blockade, where current was suppressed below a tunable threshold voltage because of the energy of charging individual nanoparticles. Further studies of this approach demonstrated the potential of interfacial assembly in fabricating microscopic electronic devices over a large area in a cost-effective and time-efficient fashion. Micrometer-scale Ga droplets coated with nanoparticles were fabricated using ultrasonication and then deposited on patterned substrates to form microscopic devices. I-V measurements showed Coulomb blockade effect in the devices containing more than one nanoparticle junction. The measured threshold voltages increased with number of junctions as expected for devices arranged in series. We also studied experimentally the energy of adsorption of nanoparticles and microparticles at the oil-water and Ga-water interfaces by monitoring the decrease of interfacial tension as the particles bind. For citrate-stabilized gold nanoparticles assembling on a droplet of octafluoropentyl acrylate, we found adsorption energy =-5.1 kBT for particle radius R = 2.5 nm, and adsorption energy scales R^2 for larger sizes. Gold nanoparticles with (1-mercaptoundec-11-yl) tetra(ethylene glycol) ligand had a much larger binding energy (-60.4 kBT) and an energy barrier against adsorption. For polystyrene spheres with R = 1.05 micrometer, we found adsorption energy =-0.9*10^6 kBT. We also found that the binding energy depended on the composition of the oil phase and could be tuned by the salt concentration of the nanoparticle suspension. At Ga-water interfaces, we found that adsorption energy of Au-cit and Au-TEG nanoparticles were much larger. We have also studied desorption of polystyrene microparticles from oil-water interfaces by changing experimental conditions, including addition of nanoparticles, cross-linking ligand molecules or in response to chemical interactions between the particles and the oil. We found that microparticles can desorb even though the adsorption energy is large. We also found that the desorbed particle formed a surprising `tail'-like structure.

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