Many animals including marine mammals and several seabird species dive in large groups, but the impacts that social interactions can have on diving behaviour are poorly understood. There are several potential benefits to social diving, such as access to social information or reduced predation risk. In this body of research I explore the use of social information by groups of diving animals by studying the behaviour of European shags (Phalacrocorax aristotelis) diving in “foraging rafts” in the Isles of Scilly. Using GPS tracking I establish where shags regularly forage in relation to bathymetry and areas where foraging rafts frequently formed. Using these data I show that the foraging ranges of different colonies overlap and that foraging ranges of individual shags are often predictable. This suggests that social information will be of less value while searching for foraging patches. However, using observational studies to further explore the conditions and areas in which foraging rafts formed, I show that advantages such as anti-predation or hydrodynamic benefits are unlikely to be the main drivers of rafting behaviour in the Scillies. I therefore suggest that access to social information from conspecifics at a foraging patch may be one of the main benefits diving in groups. Using a dynamic programming model I show that individuals diving in a group benefit from using social information, even when unable to assess conspecific foraging success. Finally I use video analysis to extract the positions and diving behaviour of individuals within a foraging raft and compare this to simulated data of collective motion and diving behaviour. The results of these studies indicate that an individual being able to utilise dives of conspecifics to inform their own diving decisions may be one of the main advantages of social diving.

The deposition of amyloid in the central nervous system is associated with prevalent neurological disorders such as Alzheimer's and Parkinson's disease. This thesis studies the mechanisms and prevention of amyloid formation in vitro. We specifically focus on Parkinson's disease associated α-synuclein (α-syn). Using novel labeling methods we introduce NMR observable labels onto lysosomal protein glucocerebrosidase (GCase), a leading cause of Parkinson's disease. By introducing NMR active labels we are able to study GCase dynamics and screen potential drug therapeutics (chapter 3). Furthermore, we analyze the three way interaction between GCase, α-syn and lipids. We conclude that GCase is able to effectively chaperone α-syn under lysosomal conditions, both preventing amyloidogenesis and destabilizing mature amyloid fibrils (chapter 4). Additionally, a model chaperone-aggregate system is investigated to gain insight into the mechanisms of small heat shock protein chaperoning, and how such mechanisms prevent aggregation (chapter 5). Finally, a high resolution crystal structure of RNA editing enzyme Cid1 is presented, whilst not directly linked to aggregation, many of the techniques used in this thesis were first developed on Cid1 (chapter 7). Together, we utilize NMR, X-ray crystallography, electron microscopy and native mass spectrometry to elucidate aspects of protein aggregation mechanisms and prevention.

Master of Science / Department of Physics / Christopher M. Sorensen / We investigated the effect of shear on the structure and aggregation kinetics of unstable colloids using small angle light scattering. We used an aqueous suspension of 20 nm polystyrene latex microspheres and MgCl2 to induce aggregation. The sample was only sheared once for approximately 33 seconds at different times, typically 1 min., 5 min., or 15 min., after the onset of aggregation. The average shear rate was in the range of 0.13 - 3.56 s-1, which was in a laminar regime. The unsheared sample gelled after ca. 45 min. When the sample was sheared soon after the onset of aggregation, the aggregation followed DLCA kinetics to yield = 1.80 ± 0.04 aggregates unaffected by the shear. The gel time also remained the same as the unsheared gel. Shearing at later stages of aggregation shortened the gel time and enhanced the scattered light intensity significantly indicating rapid growth. Then, depending on the shear rate, there were three different behaviors. At high shear rates, the aggregate structure was inhomogeneous after the shear was stopped with a crossover in slope in the scattered light intensity vs. q, to imply hybrid superaggregates with two different fractal dimensions. At intermediate shear rates far from the gel point, there was a similar crossover after the shear was stopped; however, the fractal dimension regained 1.80 ± 0.04 at the gel point. At low shear rates, the aggregation rate was increased, but the aggregate structure was uniform, and the fractal dimension remained 1.75 ± 0.05.

Doctor of Philosophy / Department of Physics / Amitabha Chakrabarti / This work is the result of a wide range of computer simulation research into the aggregation behavior of dispersed colloidal and aerosol particles in a number of different environments from the continuum to the free-molecular. The goal of this research has been to provide a bridge between experimental and theoretical researchers in this field by simulating the aggregation process within a known model. To this end, a variety of interparticle interactions has been studied in the course of this research, focusing on the effect of these interactions on the aggregation mechanism and resulting aggregate structures. Both Monte Carlo and Brownian Dynamics codes have been used to achieve this goal. The morphologies of clusters that result from aggregation events in these systems have been thoroughly analyzed with a range of diverse techniques, and excellent agreement has been found with other researchers in this field. Morphologies of these clusters include fractal, gel, and crystalline forms, sometimes within the same structure at different length scales. This research has contributed to the fundamental understanding of aggregation rates and size distributions in many physical system, having allowed for the development of improved models of the aggregation and gelation process. Systems studied include DLCA and BLCA in two and three dimension, free-molecular diffusional (Epstein) system, selective aggregation in binary colloids, ssDNA mediated aggregation in colloidal systems, and several others.

Doctor of Philosophy / Department of Physics / Christopher M. Sorensen / We investigated the effect of shear on the structure and aggregation kinetics of unstable colloids using small angle light scattering. We used an aqueous suspension of 20 nm polystyrene latex microspheres and MgCl[subscript]2 to induce aggregation. The sample was only sheared once for approximately 33 sec at different times, typically 1 min, 5 min, or 15 min, after the onset of aggregation. The average shear rate was in the range of 0.13 - 3.56 sec[superscript]−1 , which was in a laminar regime. The unsheared sample gelled after ca. 45 min. When the sample was sheared soon after the onset of aggregation, the aggregation followed the diffusion limited cluster cluster aggregation (DLCA) kinetics to yield D[subscript f] = 1.80 [plus or minus] 0.04 aggregates unaffected by the shear. The gel time also remained the same as the unsheared gel. Shearing at later stages of aggregation shortened the gel time and enhanced the scattered light intensity significantly indicating rapid growth. Then, depending on the shear rate, there were three different behaviors. At high shear rates, the aggregate structure was inhomogeneous after the shear was stopped with a crossover in slope in the scattered light intensity versus q, to imply hybrid superaggregates with two different fractal dimensions. At intermediate shear rates far from the gel point, there was a similar crossover after the shear was stopped; however, the fractal dimension regained 1.80 [plus or minus] 0.04 at the gel point. At low shear rates, the aggregation rate was increased, but the aggregate structure was uniform, and the fractal dimension remained 1.75 [plus or minus] 0.05.

Doctor of Philosophy / Department of Physics / Christopher M. Sorensen / We demonstrated that an aerosol can gel. This gelation was then used for a one-step method to produce an ultralow density porous carbon or silica material. This material was named an aerosol gel because it was made via gelation of particles in the aerosol phase. The carbon and silica aerosol gels had high specific surface area (200 – 350 sq m/g for carbon and 300 – 500 sq m/g for silica) and an extremely low density (2.5 – 6.0 mg/cm[superscript3]), properties similar to conventional aerogels. Key aspects to form a gel from an aerosol are large volume fraction, ca. 10[superscript-4] or greater, and small primary particle size, 50 nm or smaller, so that the gel time is fast compared to other characteristic times. Next we report the results of a study of the cluster morphology and kinetics of a dense aggregating aerosol system using the small angle light scattering technique. The soot particles started as individual monomers, ca. 38 nm radius, grew to bigger clusters with time and finally stopped evolving after spanning a network across the whole system volume. This spanning is aerosol gelation. The gelled system showed a hybrid morphology with a lower fractal dimension at length scales of a micron or smaller and a higher fractal dimension at length scales greater than a micron. The study of the kinetics of the aggregating system showed that when the system gelled, the aggregation kernel homogeneity attained a value 0.4 or higher. The magnitude of the aggregation kernel showed an increase with increasing volume fraction. We also used image analysis technique to study the cluster morphology. From the digitized pictures of soot clusters the cluster morphology was determined by two different methods: structure factor and perimeter analysis. We find a hybrid, superaggregate morphology characterized by a fractal dimension of D[subscript f] nearly equal to 1.8 between the monomer size, ca. 50 nm, and 1 micron and D[subscript f] nearly equal to 2.6 at larger length scales up to [similar to] 10 micron. The superaggregate morphology is a consequence of late stage aggregation in a cluster dense regime near a gel point.

Master of Science / Division of Biology / Bradley J. Olson / Unicellular organisms alter their behavior and morphology in response to environmental stresses, particularly in response to immediate threats to their survival. A common tactic of predator avoidance for unicellular green algae is to aggregate to form groups. We have found that the model unicellular green algae Chlamydomonas reinhardtii forms aggregates in response to the presence of the filter feeding zooplanktonic predator, Daphnia magna. Chalmydomonas is a member of the volvocine algae, a morphologically diverse group of closely related green algae that is often used to study multicellular development. We have characterized aggregation in Chlamydomonas reinhardtii and found that it is rapid, transient and induced by signals originating from the Daphnia predators. To understand the genetic basis of cooperative aggregation we used an RNA-seq approach. RNA-seq characterized the transcriptomic response by Chlamydomonas during aggregation, and we identified 131 genes are significantly differentially expressed between predated and unpredated cultures of Chlamydomonas. Several candidate genes were characterized based on existing annotations, evolutionary history and expression profile. Evolutionary relationships between candidate aggregation genes in Chlamydomonas and their orthologs in multicellular Volvocales suggest a possible role of aggregation genes in multicellular development. Our results demonstrate that Chlamydomonas dynamically alters its morphology based on its environment and identify several candidate genes for aggregation and multicellular development.

The formulation induced photooxidative stability of substituted 6, 13 trialkylsilylethynylpentacene derivatives is report for the first time. It is known that 6,13 trialkylsilylethynylpentacene derivatives undergo rapid oxidation through singlet oxidation and is believed to be primarily to the 6,13 endoperoxide. The effect of solvent, organic semiconductor concentration and the presence of polymeric binder on the rate of photooxidative degradation in oxygen saturated solutions on degradation kinetics have been investigated. The photochemical stability of 6,13 trialkysilylethynylpentacene has been studied in toluene, THF, dichloromethane, chloroform, decane and dodecane at concentrations ranging from 2.5×10-6 M to 5×10-2 M by measurement of the half-life by UV-visible spectroscopy. The predominant degradation products of TIPS-Pentacene are the same regardless of solvent and concentration, being predominantly an endo-peroxide resulting from O2 addition across the 6, 13 position of the pentacene. At low concentration (< 1×10 -3 M), the half- life of TIPS-Pentacene is observed to vary with solvent and the amount of dissolved oxygen, with half-life showing a strong, positive correlation between the product of the Hansen Solubility Parameter (HSP) and the mole-fraction oxygen solubility. In this range, the half-life is observed to increase markedly with increasing solution concentration, showing a linear correlation with mean intermolecular distance within the solution. From intermediate to high concentration, the half-life increase more rapidly with increasing concentration, which is attributed to aggregation. In most solvents, this behaviour shows a specific onset point, suggesting a cooperative rather than isodesmic aggregation mechanism. Photooxidative half-lives of TMTES-pentacene and fluorinated soluble pentacene derivatives were determined from 2.5 × 10-6 M to 5.0 × 10-3 M solutions in THF, toluene, chloroform and CH2Cl2. Independent of solvent and at constant concentration the relative ordering of photo-oxidative resistance was: α-di-FTIPS-pentacene > β-di-FTIPS-pentacene, α-mono -FTIPS-pentacene, β-mono-FTIPS-pentacene > TIPS-pentacene ≥ TMTES-pentacene. The same rank order for a particular derivative was generally maintained over the concentration range 2.5 x 10-6 M to 5 x 10-3 M the stability to photooxidation for all derivative increased with increasing concentration. All derivatives showed a mixture of endooxidation products as shown by APCI mass spectrometry, and 1H NMR.Added polystyrene and isotactic polystyrene were found to accelerate photooxidative degradation whist isotactic polymethylmethacrylate (i-PMMA) and poly (triaylamine) (PTAA) had no effect adding weight to the argument that anything which can act as an acceptor to the solution slows down the degradation and anything which impairs pair-wise energy transfer speeds up the degradation. Understanding of these phenomena is therefore essential for the further application of solution processing of organic materials.

The purpose of this thesis is to design a physical microchannel model for micro-Couette blood flow that provides constant and controlled conditions to study and analyze Red Blood Cell (RBC) aggregation. The innovation of this work is that the Couette blood flow is created by the motion of a second fluid with different properties, thereby entraining the blood. The experimental work is coupled with three-dimensional numerical simulations performed using a research Computational Fluid Dynamic (CFD) Solver, Nek5000, based on the spectral element method, while the experiments are conducted using a micro Particle Image Velocimetry (μPIV) system with a double frame CCD camera and an inverted laser imaging microscope. The design of the channel (150 × 33 μm and 170 × 64 μm microchannels) is based on several parameters determined numerically, such as the velocity and viscosity ratios and the degree of miscibility between the fluids, and the resulting configurations are fabricated in the laboratory using standard photolithography methods. The microchannel designed numerically is then tested experimentally, first, with a Newtonian fluid (glycerol), then with RBC suspensions to be compared to the simulations results. It was found that, numerically, using a velocity ratio of 4 between the two fluids, a third of the channel thickness corresponds to the blood layer. Within that range, it can be concluded, that the velocity profile of the blood layer is approximately linear as confirmed by experimental tests, resulting in the desired profile to study RBC aggregation in controlled conditions. The effect of several parameters, such as the hematocrit and the shear rate, on the RBC aggregates and the velocity profile is investigated, through experiments on the RBC suspensions. The final goal of this research is to ensure the compatibility of the results between the experiments and the Newtonian numerical model for several ranges of shear rate with the future intention of finding an accurate method to be able to quantitatively analyze aggregates and determine the number of RBC in each aggregate depending on the flow conditions (the shear rate).

The success of the internet over last few decades has mainly depended on various infrastructure technologies to run distributed applications. Due to diversification and multi-provider nature of the internet, radical architectural improvements which require mutual agreement between infrastructure providers have become highly impractical. This escalating resistance towards the further growth has created a rising demand for new approaches to address this challenge. Network virtualization is regarded as a prominent solution to surmount these limitations. It decouples the conventional Internet service provider’s role into infrastructure provider (InP) and service provider (SP) and introduce a third player known as virtual network Provider (VNP) which creates virtual networks (VNs). Resource discovery aims to assist the VNP in selecting the best InP that has the best matching resources for a particular VN request. In the current literature, resource discovery focuses mainly on static attributes of network resources highlighting the fact that utilization on dynamic attributes imposes significant overhead on the network itself. In this thesis we propose a resource discovery approach that is capable of utilizing the dynamic resource attributes to enhance the resource discovery and increase the overall efficiency of VN creation. We realize that recourse discovery techniques should be fast and cost efficient, enough to not to impose any significant load. Hence our proposed scheme calculates aggregation values of the dynamic attributes of the substrate resources. By comparing aggregation values to VN requirements, a set of potential InPs is selected. The potential InPs satisfy basic VN embedding requirements. Moreover, we propose further enhancements to the dynamic attribute monitoring process using a vector based aggregation approach.