Thesis (Ph. D.)--Lehigh University, 2003. / Includes vita. Includes bibliographical references (leaves 80-85).

Thesis (Ph. D.)--University of Chicago, Department of Chemistry, August 2003. / CD-ROM reproduces the entire dissertation in PDF format. Includes bibliographical references. Also available on the Internet.

Molecular self-assembly through non-covalent interactions is an integral part of countless natural and synthetic materials. The Iverson group specifically focuses on aromatic donor-acceptor interactions and the subsequent self-assembly of molecules containing these functionalities. The work has predominately utilized association between the electron-rich 1,5-dialkoxynaphthalene (DAN) and the electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) to create numerous self-assembled structures through intramolecular or intermolecular aromatic donor-acceptor interactions. The self-assembly and inherent electronic properties of aromatic units have made them attractive candidates for nature-inspired molecules, molecular machines and organic electronic materials. The focus of these D-A interactions now shifts from an aqueous environment as solid state aromatic D-A interactions are promising modes of driven self-assembly for molecular architectures geared towards material applications. Aromatic units have long been applied in areas such as organic electronic materials due to their inherent charge transport properties. NDI has become a molecule of considerable interest among the organic electronics community due its electron transporting properties and ability to self-assemble. Therefore a thorough understanding of NDI and DAN-NDI self-assembly in the solid state should be of importance for the improvement and development of molecular architectures for organic electronic devices. The following dissertation chapters focus on NDI or its aromatic D-Acomplex with DAN. Chapter 2 investigates an unusual thermochromic behavior that occurred in our previous study when several solid state DAN:NDI mixtures lost their characteristic red color while crystallizing from the mesophase. Chapter 3 describes the synthetic progress towards a rigid, non-conjugated DAN-NDI molecule that retains electrostatic complementarity and ultimately led us to explore solid state non-covalent interactions of conjugated aromatic NDI-donor polymers. Chapter 5 describes an approach to synthesize conjugated NDI polymers and a diyne NDI to serve as an important synthetic intermediate. The work in chapter 6 tests the solid state association between neutral aromatic donor and acceptor polymer strands. The work enhances the present understanding of these D-A interactions in different phases. The results also support recent discussions about aromatic stacking dominated by interactions between highly polarized groups on the periphery of aromatic units rather than overall polarization of the aromatic ring itself (i.e. D-A interactions). / text

Self-assembly provides an efficient way to build complex structures with great flexibility in terms of components and properties. This dissertation presents two different forms of self-assembly for technical applications. The first example is the molecular assembly of liquid crystals (LCs). Attaching appropriate side chains on anthracene, oligothiophene, and oligoarenethiophene successfully constructed liquid crystalline organic semiconductors. The phase transitions of the LC semiconductors were analyzed by differential scanning calorimetry (DSC) and polarized optical microscopy (POM). The effect of the LC phase change on charge transport was probed by the space-charge limited current (SCLC) method and the field-effect transistor (FET) method. Mobility in the LC phase rose in anthracenyl esters but decreased in oligothiophenes and oligoarenethiophenes. The different electronic behavior of LC semiconductors may be caused by the difference in domain size and/or the difference in response to electric field. The second example of self-assembly in this dissertation is DNA-guided self-assembly of micrometer-sized particles. Patternable bioconjugation polymers were synthesized to allow for lithographic patterning and DNA conjugation. The base pairing of DNA was then used to drive the self-assembly of DNA-conjugated particles. The DNA conjugation chemistry was studied in detail using a fluorescence-based reaction test platform. The conjugated DNA on the polymer surface retained its ability to hybridize with its complement and was efficient in binding microspheres with complementary strands. Highly specific bead-to-bead assembly was analyzed using imaging flow cytometry, and the fractions of self-assembly products were explained on the basis of chemical equilibrium. The process of particle fabrication using photolithography was successfully developed, and the self-assembly of lithographically-patterned particles was demonstrated. We envision that the technologies described in this dissertation will be useful in a variety of fields ranging from microelectronics to biotechnology. / text

The development of novel, peptide based structures for tissue engineering materials has been widely researched, and its popularity can be attributed to advancements in technological analysis methods. Using principles based on protein structure and organization, this work describes the novel self-assembly of depsipeptides, which incorporate alternating esters within a native peptide backbone. Chapter 1 introduces and reviews peptide mimics for their utility for tissue engineering applications. Chapter 2 describes the methodology in synthesizing and characterization a depsipeptide library using both solution and solid phase methods. Chapter 3 discusses the effects of depsipeptide length, concentration, and sequence within a range of ionic concentrations and pH ranges on the self-assembly of depsipeptides into spherical nanostructures, fibers, or hydrogels. Chapter 4 describes proposed methods to increase the rate of gelation, followed by discussions of biocompatibility studies from other self-assembling peptide and modified-peptide systems in vitro and in vivo. The work described in this dissertation demonstrates that the synthesis and self-assembly of a depsipeptide family which alternates esters into a native peptide backbone does not disrupt the formation of higher order structures. This study illustrates the potential to synthesize a wide range of depsipeptides with variable side chains and hydrophobic character, as understanding these effects on self-assembly is imperative to the development of biomimetic materials for tissue engineering applications. / text

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As the feature size of new devices continues to decrease so too does the feasibility of top-down methods of patterning them. In many cases bottom-up methods are replacing the existing methods of assembly, as having building blocks self-organize into the desired structure appears, in many cases, to be a much more advantageous route. Self-assembled nanoparticulate films have a wide range of potential applications; high-density magnetic media, sensing arrays, meta-materials and as seeds for 3D photonic crystals to name a few. Thus, it is critical that we understand the fundamental dynamics of pattern formation on the nanoparticulate and colloidal scale so that we may have better control over the formation and final quality of these structures. We study computationally the self-organization of colloidal particles in 2D using both Monte Carlo and dynamic simulation We present 3 studies employing Monte Carlo simulation. In the first study, Monte Carlo simulations were used to understand the experimental observation of highlyordered 2D arrays of bidisperse, stabilized gold nanoparticles. It was shown that the LS lattice forms with the addition of interparticle forces and a simple compressive force, revealing that bidisperse lattice formation is, in fact, a dynamic process. It was evident that the LS lattice forms in large part because the particles within the lattice reside in their respective interparticle potential wells. In the second Monte Carlo study, this information was used to predict size-ratios and surface coverages for novel lattice structures. These predictions are intended to guide experimentalists in their search for these exciting new structures. In the third study it was shown that polydisperse amounts of amorphous-silicon nanoparticles could form 2D clusters exhibiting long-range orientational order even in the absence of translational order. Monte Carlo simulations were performed, which included lateral capillary forces and a simple stabilizing repulsion, resulting in structures that were strikingly similar to the experimentally observed In the fourth study we used dynamic simulation to study the hydrodynamicallyassisted self-organization of DNA-functionalized colloids in 2D. It was shown that hydrodynamic forces allow a more thorough sampling of phase space than through thermal or Brownian forces alone.

<p>Pattern formation is a mysterious phenomenon occurring at all scales in nature. The beauty of the resulting structures and myriad of resulting properties occurring in naturally forming patterns have attracted great interest from scientists and engineers. One of the most convenient experimental models for studying pattern formation are colloidal particle suspensions, which can be used both to explore condensed matter phenomena and as a powerful fabrication technique for forming advanced materials. In my thesis, I have focused on the study of colloidal patterns, which can be conveniently tracked in an optical microscope yet can also be thermally equilibrated on experimentally relevant time scales, allowing for ground states and transitions between them to be studied with optical tracking algorithms. </p><p>In particular, I have focused on systems that spontaneously organize due to particle-surface and particle-particle interactions, paying close attention to systems that can be dynamically adjusted with an externally applied magnetic or acoustic field. In the early stages of my doctoral studies, I developed a magnetic field manipulation technique to quantify the adhesion force between particles and surfaces. This manipulation technique is based on the magnetic dipolar interactions between colloidal particles and their "image dipoles" that appear within planar substrate. Since the particles interact with their own images, this system enables massively parallel surface force measurements (>100 measurements) in a single experiment, and allows statistical properties of particle-surface adhesion energies to be extracted as a function of loading rate. With this approach, I was able to probe sub-picoNewton surface interactions between colloidal particles and several substrates at the lowest force loading rates ever achieved. </p><p>In the later stages of my doctoral studies, I focused on studying patterns formed from particle-particle interaction, which serve as an experimental model of phase transitions in condensed matter systems that can be tracked with single particle resolution. Compared with other research on colloidal crystal formation, my research has focused on multi-component colloidal systems of magnetic and non-magnetic colloids immersed in a ferrofluid. Initially, I studied the types of patterns that form as a function of the concentrations of the different particles and ferrofluid, and I discovered a wide variety of chains, rings and crystals forming in bi-component and tri-component systems. Based on these results, I narrowed my focus to one specific crystal structure (checkerboard lattice) as a model of phase transformations in alloy. Liquid/solid phase transitions were studied by slowly adjusting the magnetic field strength, which serves to control particle-particle interactions in a manner similar to controlling the physical temperature of the fluid. These studies were used to determine the optimal conditions for forming large single crystal structures, and paved the way for my later work on solid/solid phase transitions when the angle of the external field was shifted away from the normal direction. The magnetostriction coefficient of these crystals was measured in low tilt angle of the applied field. At high tilt angles, I observed a variety of martensitic transformations, which followed different pathways depending on the crystal direction relative to the in-plane field. </p><p>In the last part of my doctoral studies, I investigated colloidal patterns formed in a superimposed acoustic and magnetic field. In this approach, the magnetic field mimics "temperature", while the acoustic field mimics "pressure". The ability to simultaneously tune both temperature and pressure allows for more efficient exploration of phase space. With this technique I demonstrated a large class of particle structures ranging from discrete molecule-like clusters to well ordered crystal phases. Additionally, I demonstrated a crosslinking strategy based on photoacids, which stabilized the structures after the external field was removed. This approach has potential applications in the fabrication of advanced materials. </p><p> My thesis is arranged as follows. In Chapter 1, I present a brief background of general pattern formation and why I chose to investigate patterns formed in colloidal systems. I also provide a brief review of field-assisted manipulation techniques in order to motivate why I selected magnetic and acoustic field to study colloidal patterns. In chapter 2, I present the theoretical background of magnetic manipulation, which is the main technique used in my research. In this chapter, I will introduce the basic knowledge on magnetic materials and theories behind magnetic manipulation. The underlining thermodynamic mechanisms and theoretical/computational approaches in colloidal pattern formation are also briefly reviewed. In Chapter 3, I focus on using these concepts to study adhesion forces between particle and surfaces. In Chapter 4, I focus on exploring the ground states of colloidal patterns formed from the anti-ferromagnetic interactions of mixtures of particles, as a function of the particle volume fractions. In Chapter 5, I discuss my research on phase transformations of the well-ordered checkerboard phase formed from the equimolar mixture of magnetic and non-magnetic beads in ferrofluid, and I focus mainly on phase transformations in a slowly varying magnetic field. In Chapter 6, I discuss my work on the superimposed magnetic and acoustic field to study patterns formed from monocomponent colloidal suspensions under vertical confinement. Finally, I conclude my thesis in Chapter 7 and discuss future directions and open questions that can be explored in magnetic field directed self-organization in colloidal systems.</p> / Dissertation

The formation of large, complex structures from small building blocks through self-assembly is widely seen in proteins and provides a tool for the creation of functional nanoscale devices. However, the factors controlling protein self-assembly are complex and often poorly understood. Peroxiredoxins are a large family of proteins, many of which are able to form a variety of large structures from a small, basic unit. This assembly has been shown to be strongly influenced by the redox state of the enzyme, which functions as a switch, controlling self-assembly. This thesis uses a protein from this family, human peroxiredoxin 3 (hPrx3) as a model system to investigate whether the self-assembly properties of hPrx3 can be influenced by rational protein engineering. Three forms of hPrx3 were purified and examined. These were the wild type and two variants: a mutant (S78A) and a His-tagged form. Size exclusion chromatography showed that each form showed a different ratio of dimers and larger species. Both variants showed preference for larger species, especially in the His-tagged form. This was shown to be partially dependent on metal binding in the His-tagged form. Larger species formed from multiple rings were also identified. SAXS measurement indicated that in the wild type enzyme, higher order species were dodecameric rings. For the His-tagged variant, SAXS measurement showed that the species observed had a different structure than that of the wild type. Electron microscopy showed that higher order structures seen in both wild type hPrx3 and His-tagged hPrx3 were ring shaped, with dimensions consistent with dodecamers. A competitive assay showed that the wild type, with kcat/km values near 2 x 10⁷, consistent with published results. Both variant forms showed evidence of slightly higher activity than the wild type, indicating a link between activity and assembly. A peroxiredoxin from the thermophilic bacteria Thermus aquaticus, TaqPrx was also examined, in an attempt to investigate a peroxiredoxin capable of self-assembly at high temperatures, which would be very useful for a nanoscale device. TaqPrx was cloned, purified and examined, however, no evidence of self-assembly was observed. Protein modelling and dynamic light scattering measurement indicated that the protein purified was monomeric and had a structure. Sparse matrix crystal screening identified conditions that allowed crystal formation, although strongly diffracting crystals were not produced. A novel assay for peroxiredoxin activity was developed, and suggested that TaqPrx shows peroxiredoxin activity. This thesis shows that peroxiredoxins are a useful model system for the investigation of how protein self-assembly is controlled, and how it can be influenced by protein engineering.

Αυτή η μεταπτυχιακή εργασία έχει στόχο την ανάπτυξη ενός ολοκληρωμένου ενσωμματωμένου συστήματος, με βάση τον επεξεργαστή ARM9, για την χρήση στα εργαστήρια Συμβολικής γλώσσας, Μικροϋπολογιστών και Αρχιτεκτονικής του τμήματος Μηχανικών Η/Υ & Πληροφορικής, Πανεπιστημίου Πατρών. / The objective of this master thesis is the development of an embedded system, based on ARM9 CPU, that is going to be used in Assembly, Micro and Architecture Labs, in the Computer Engineering and Informatics Department, of University of Patras