Seeding is an important variable in controlling or directing the assembly of peptides. The presence of impurities, responsible for creating a 'dip' in the surface tension versus peptide concentration profile, is used to determine the critical aggregation concentration (CAC). This phenomenon is investigated to differentiate crude and high purity EAK16-II peptide. The purified peptide did not show this 'dip' and clearly indicated a critical aggregation concentration for EAK16-II at 0. 09 mg/mL by surface tension measurements. Conversely, a surface tension 'dip' is clearly observed for the crude EAK16-II peptide. Atomic Force Microscopy imaged the nanostructures of aggregates. The presence of impurities induces fibre formation below the CAC. This study provides information about the seeding effect of peptide assembly at low concentrations as well as the modification of surface activity of assembled peptide particles. Alanine, glutamic acid and lysine were used as model seeding agents to simulate the seeding phenomenon and better understand the nucleation mechanism of peptide assembly. All amino acid monomers were able to induce fibre formations at low peptide concentrations. However, only glutamic acid and lysine were able to produce the surface tension dip profile observed in the crude peptide. This information may be of importance in understanding fibrillogenesis occurring in conformational diseases and other biomedical applications including drug delivery.

Seeding is an important variable in controlling or directing the assembly of peptides. The presence of impurities, responsible for creating a 'dip' in the surface tension versus peptide concentration profile, is used to determine the critical aggregation concentration (CAC). This phenomenon is investigated to differentiate crude and high purity EAK16-II peptide. The purified peptide did not show this 'dip' and clearly indicated a critical aggregation concentration for EAK16-II at 0. 09 mg/mL by surface tension measurements. Conversely, a surface tension 'dip' is clearly observed for the crude EAK16-II peptide. Atomic Force Microscopy imaged the nanostructures of aggregates. The presence of impurities induces fibre formation below the CAC. This study provides information about the seeding effect of peptide assembly at low concentrations as well as the modification of surface activity of assembled peptide particles. Alanine, glutamic acid and lysine were used as model seeding agents to simulate the seeding phenomenon and better understand the nucleation mechanism of peptide assembly. All amino acid monomers were able to induce fibre formations at low peptide concentrations. However, only glutamic acid and lysine were able to produce the surface tension dip profile observed in the crude peptide. This information may be of importance in understanding fibrillogenesis occurring in conformational diseases and other biomedical applications including drug delivery.

In this study, we develop self-assembled nano-metal-dots etching mask techniques to fabricate quantum dots (QDs) nano-pillars. We explain the self-assembled nano-metal-dots formation processes by using Dewetting model. Two important experimental factors including (1) interaction force between film and vapor during annealing (£^FV),¡]2¡^interaction force between film and substrate (£^FS) are study to investigate the self-assembled processes. A 200nm thick SiO2 buffer layer is first deposited on the GaAs substrate to congregate thermal energy during the RTA process. In our group, the QDs optimum grown temperature condition is 570¢J, so we develop Au-Ge nano-dots process especially for GaAs based QDs samples. The 8nm thick Au-Ge is annealed at lower 500oC for 60sec under the pressure of 5 E6 Torr to format the nano-dots on QDs samples. The Au-Ge nano-dots have a size and density of 250 ¡Ó 50 nm and 4 E8 cm-2,respectively. We use the Au-Ge nano-dots as mask and dry etching process to fabricate the 9-layer vertical coupled QDs nano-pillars. The diameter and height of the QDs nano-pillar are 250, and 800nm, respectively. According to the QDs density, each nano-pillar contains 1600 QDs in it. The QDs nano-pillar resonance signals are observed by the low temperature cryogenic cathode-luminescence measurement. A strong nano-pillar resonance signal in 1050 nm matched to our simulation results is observed.

Development of nanoscience and nanotechnology requires rapid and robust nanomanufacturing processes to produce nanoscale materials, structures and devices. The dissertation aims to contribute to two major challenging and attractive topics in nanomanufacturing. Firstly, this research develops fabrication techniques for three dimensional (3D) structures and integrates them into functional devices and systems. Secondly, a novel process is proposed and studied for rapid and efficient manipulation of nanomaterials using a directed self-assembly process. The study begins with the development of nanoimprint lithography for nanopatterning and fabrication of 3D multilayer polymeric structures in the micro- and nano-scale, by optimizing the layer-transfer and transfer-bonding techniques. These techniques allow the integration of microfluidic and photonic systems in a single chip for achieving ultracompact lab-on-a-chip concept. To exemplify the integration capability, a monolithic fluorescence detection system is proposed and the approaches to design and fabricate the components, such as a tunable optical filter and optical antennas are addressed. The nanoimprint lithography can also be employed to prepare nanopatterned polymer structures as a template to guide the self-assembly process of nanomaterials, such as single-walled carbon nanotubes (SWNTs). By introducing the surface functionalization, electric field and ultrasonic agitation into the process, we develop a rapid and robust approach for effective placement and alignment of SWNTs. These nanomanufacturing processes are successfully developed and will provide a pathway to the full realization of the lab-on-a-chip concept and significantly contribute to the applications of nanomaterials.

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The use of organic compounds as templates to assemble inorganic materials with structures over multiple length scales has received much attention due to the potential applications that can be developed from these materials. Many organisms synthesize organic/inorganic composites with exceptional control over morphology, physical properties, and nanoscale organization of these materials. Materials such as bone, nacre, and silica diatoms are excellent examples of the complex yet highly controllable hierarchically structured materials nature can form at ambient conditions. The ability to mimic these organisms through the design of supramolecular assemblies and use them to direct the growth of hierarchically structured materials has increased significantly in recent years. In this dissertation, block copolypeptide templated inorganic materials were synthesized and characterized using a wide range of analytical techniques. There are three major conclusions from this dissertation. First, the conformation of a polypeptide chain can be used to manipulate the porosity of oxide materials obtained. Second, individual supramolecular objects (vesicles) formed by block copolypeptides can be used as templates to form nanostructured hard materials. Third, polypeptide chemistry and solution conditions can be used to control both the morphology and porosity of the hard materials they assemble. This dissertation also describes preliminary work toward designing the block copolypeptides derivatives for biomimetic inorganic synthesis and gene delivery. This work includes the synthesis of these block copolypeptides derivatives and of the templated oxide materials. Some interesting silica materials such as porous silicas and silica nanocapsules were synthesized using double hydrophilic block copolypeptides derivatives as templates. Also, the preliminary work of using these block copolypeptides derivatives for gene delivery is included and shows these copolypeptide derivatives are potential delivery vehicles.

Conformational stability of the collagen triple helix affects its turnover and determines tissue homeostasis. Although it is known that the presence of imino acids (prolines or hydroxyprolines) confer stability to the molecule, little is known regarding the stability of the imino-poor region lacking imino acids, which plays a key role in collagen cleavage. In particular, there have been continuing debates about the role of water in collagen stability. We addressed these issues using molecular dynamics simulations on 30-residue long collagen triple helices, including a structure that has a biologically relevant 9-residue imino-poor region from type III collagen (Protein Data Bank ID: 1BKV). We characterized the conformational motion of the molecule that differs between imino-rich and imino-poor regions using a torsional map approach. At temperatures of 300 K and above, unwinding initiates at a common cleavage site, the glycine-isoleucine bond in the imino-poor region. This provides a linkage between previous observations that unwinding of the imino-poor region is a requirement for collagenase cleavage, and that isolated collagen molecules are unstable at body temperature. Unwinding of the imino-poor region is controlled by dynamic water bridges between backbone atoms with average lifetimes on the order of a few picoseconds, as the degree of unwinding strongly correlated with the loss of water bridges, and unwinding could be either prevented or enhanced, respectively by enforcing or forbidding water bridge formation. While individual water bridges were short-lived in the imino-poor region, the hydration shell surrounding the entire molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 Â, in good agreement with the experimentally measured inter-collagen distances. These results elucidate the general role of water in collagen turnover: water not only affects collagen cleavage by controlling its torsional motion, but it also forms a larger-scale lubrication layer mediating collagen self-assembly.

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