Submitted to the faculty of Indiana University In partial fulfillment of the requirements for the degree Master in Bioinformatics In the School of Informatics, Indiana University, December 2004 / The aggregation rate of B-Lactoglobulin (BLG) was studied using turbidimetry and dynamic light scattering in the range 5.8<pH,3.5 at a fixed ionic strength of 4.5 mM, and in the range 4.5 - 500mM NACl at a fixed pH of 5.0. The initial slope of turbidity vs time curve was used to define an initial rate. The highest initial rates of aggregation were observed in the pH range 4.50 to 4.75 but the increase in aggregation rate when the pH was reduced from 5.0 to 4.69 was large compared to its decrease when the pH was reduced from pH 4.69 to 4.20; i.e. the dependence of initial rate on pH was highly asymmetric. The rate of aggregation at pH 5.0 strongly increased with decrease in ionic strength I from 100 to 4.5 mM and was found to be nearly linear with 1/ I. QELS measurements at pH 5.22 and 5.40 at I = 4.5mM revealed that particle size increased with time. Eventual appearances of bimodal distributions showed fast and slow modes corresponding to the BLG dimer and to hydrodynamic diameter 100-800 nm. Measurements at 4.0 and 4.2 indicated the consumption of dimers in the first few minutes to form higher order aggregates. Electrostatic modeling via Delphi was used to visualize the electrostatic poetnetial around the BLG dimer in order to elucidate the pH and ionic strength dependence of BLG aggregation rates. The aggregation process appears to comprise firstly an initial fast consumption of dimer, whose dependence on pH and I arises from the interaction of the positive and negative domains of interacting dimers; and secondly, the slow formation of much larger aggregates with relatively little sensitivity to pH and I. The open-ended nature of BLG aggregation is thought to arise from the asymmetry of the dimer charge distribution in the range 4.2<pH<5.2. Polyanions appear to inhibit aggregation. However, the role of polyanions in minimizing BLG aggregation was observed immediately after the addition of polyanioin to the protein. / Bioinformatics

Understanding the mechanisms that structure biological systems is a primary goal of biology. My research shows that the biological structure is constrained in important ways by general variables such as the number of base pairs in a genome and the number of individuals and species in a community. I used a combination of macroecology, bioinformatics, statistics, mathematics, and advanced computing to pursue my research and published several peer-reviewed scientific manuscripts and open-source software as a result.I was funded through a combination of fellowships and scholarships awarded by the Utah State University School of Graduate Studies, College of Science, and Department of Biology, as well as teaching assistantships awarded through the Department of Biology at Utah State University, and research assistantships funded through a CAREER grant from the U.S. National Science Foundation (DEB-0953694) awarded to my advisor, Dr. Ethan White. With the help of my advisor, I also obtained a computing grant from Amazon Web Services in the amount of $7,500. Altogether, funding for my research and education totaled approximately $123,500. Using over 9000 communities of plants, animals, fungi, and microorganisms, I demonstrated that the forms of empirical species abundance distributions (SADs) are constrained by total abundance and species richness. Using over 300 microbial genomes, I demonstrate that nucleotide aggregation is constrained by genome length and differs between regions of coding and noncoding DNA. General state variables of genomes and ecological communities (i.e. genome length, total abundance and species richness) constrain simple structural properties of each system.

The present thesis demonstrates how different thermodynamic aspects of self-assembly and stimuli-responsive properties in water can be encoded on the structure of π-amphiphiles, consisting of perylene or naphthalene bisimide cores. Initially, quantitative thermodynamic insights into the entropically-driven self-assembly was studied for a series of naphthalene bisimides with UV/Vis and ITC measurements, which demonstrated that their thermodynamic profile of aggregation is heavily influenced by the OEG side chains. Subsequently, a control over the bifurcated thermal response of entropically driven and commonly observed enthalpically driven self-assembly was achieved by the modulation of glycol chain orientation. Finally, Lower Critical Solution Temperature (LCST) phenomenon observed for these dyes was investigated as a precise control of this behavior is quintessential for self-assembly studies as well as to generate ‘smart’ materials. It could be shown that the onset of phase separation for these molecules can be encoded in their imide substituents, and they are primarily determined by the supramolecular packing, rather than the hydrophobicity of individual monomers. / Die vorliegende Arbeit zeigt, wie verschiedene thermodynamische Aspekte der Selbstorganisation sowie die Stimuli-responsiven Merkmale in Wasser mittels der Struktur von π-Amphiphilen mit Perylen- oder Naphthalinbisimidkernen programmiert werden können. Zunächst wurden quantitative thermodynamische Einblicke in die entropisch getriebene Selbstorganisation für eine Reihe von Naphthalinbisimiden mit UV / Vis- und ITC-Messungen untersucht. Diese zeigten, dass ihr thermodynamisches Aggregationsprofil stark von den Oligoethylenglykol-Seitenketten beeinflusst wird. Anschließend wurde durch gezielte Modulation der Glykolketten und der daraus resultierenden Neuorientierung der Ketten, eine Kontrolle über die Thermodynamik der Selbstassemblierung zwischen der häufiger beobachtbaren enthalpisch getriebenen und der entropisch getriebenen Selbstorganisation erreicht. Schließlich wurde das für diese Farbstoffe beobachtete Phänomen der niedrigeren kritischen Lösungstemperatur (LCST) untersucht, da eine genaue Kontrolle dieses Verhaltens für Selbstorganisationsstudien sowie für die Erzeugung „intelligenter“ Materialien von entscheidender Bedeutung ist. Es konnte gezeigt werden, dass der Beginn der Phasentrennung für diese Moleküle von ihren Imidsubstituenten und hauptsächlich durch die supramolekulare Packung bestimmt werden und nicht durch die Hydrophobie einzelner Monomere.

Smartphones now account for the majority of all cell phones in use today [23]. Ubiquitous Internet access is a valuable feature offered by these devices and the vast majority of smartphone applications make use of the Internet in one way or another. However, the bandwidth offered by these cellular networks is often much lower than we typically experience on our standard home networks, leading to a less-than-optimal user experience. This makes it very challenging and frustrating to access certain types of web content such as video streaming, large file downloads, loading large webpages, etc. Given that most modern smartphones are multi-homed and are capable of ac- cessing multiple networks simultaneously, this thesis attempts to utilize all available network interfaces in order to achieve the aggregated bandwidth of each to improve the overall network performance of the phone. To do so, I implement a bandwidth aggregation system for iOS that combines the bandwidths of multiple devices located within close proximity of each other. Deployed on up to three devices, speedups of up to 1.82x were achieved for downloading a single, 10mb file. Webpage loading saw speedups of up to 1.55x.

Aggregation-induced emission (AIE) is a phenomenon with many applications, such as chemical sensors, biological probes, immunoassay markets, and active layers in fabricating organic light-emitting diodes. AIE materials in polymers can enhance the emissivity of such materials while having the benefits of polymeric materials. This thesis examines the use of AIE polymers to study the effect of structure on the properties. This is done by first synthesizing a monomer with AIE characteristics, tetraphenylethylene-methacrylate (TPEMA). Secondly, polymerizing TPEMA using free and controlled radical polymerizations. Finally, the copolymerization of TPEMA with methyl methacrylate (MMA) to understand the effect of spaced-out TPE groups in the polymer chain on the photoluminescence of the polymer. The structures of all intermediates and final products were characterized by nuclear magnetic resonance (NMR) and size exclusion chromatography (SEC). The AIE characteristics were proven and compared using the photoluminescence graphs, showing that the homopolymer had increased emission intensity than its monomer. The copolymer had higher emission intensity than TPEMA and higher normalized emission intensity than that of the homopolymer, showing the effect of structure on the photoluminescence. Both the homopolymer and the copolymer were easier to aggregate than the monomer, making it more effective to utilize the material in applications where it needs to be emissive in diluted solutions. The glass transition temperature and the tacticity of the homopolymer and copolymer were also compared. The thesis is divided into the following five chapters; 1. Introduction, where a brief background along with the scope of the thesis is provided; 2. Literature Review, where a summary of controlled radical polymerization and AIE is given; 3. Experimental Section, where the materials' detailed procedure and characterization are provided; 4. Results and Discussion, where results of successful experiments are discussed; 5. Concluding Remarks, where the results are summarized, and future work is discussed.

Protein aggregation is a phenomenon that plays a major role in protein crystallization and in protein formulation. In protein crystallization, aggregation is the prerequisite step; however, in protein formulation it has to be suppressed to assure therapeutic efficiency of the product. Light scattering techniques are the most promising methods to study the hydrodynamic properties of macromolecular solutions, which directly measures protein aggregation. Unfortunately, the normal dynamic light scattering technique is regarded as expensive because of the amount of protein used for these experiments. In order to address this problem, a scale down dynamic light scattering device has been designed. The osmotic second virial coefficient, a dilute solution parameter helps in identifying solution conditions for protein crystal growth. The second part of this thesis involves comparison of osmotic second virial coefficient (B) measurements of lysozyme using laser light scattering techniques with B measurements of lysozyme performed using self-interaction chromatography (SIC).

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