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Ceramics are desirable materials for a range of mechanical, electrical and biomedical applications, but they can be difficult to form and process. Additive manufacture is increasingly being explored for producing ceramic parts without moulds. In this work, a method for controllably patterning filaments containing high volume fractions of ceramic particles was explored, using electrospinning as the deposition method. Inks containing 50 vol% alumina powder in mineral oil or wax were deposited from a 200 μm inner diameter blunt, grounded needle at distances from 0.5 to 5.0 mm from a conductive plate with positive voltages of up to 10 kV applied to it. For the oil-based ink, jets with widths down to 25 μm were produced and an empirical relationship between the minimum jet width, nozzle height, flow rate and voltage was established. An average electric field of 2.0-2.5 kV/mm was found to give the most stable jets. The substrate speed was found to have a major effect on the jet width and entirely determine the deposit diameter due to the ink still being molten upon impact, as predicted by thermal modelling. Patternable features were explored with the wax-based ink. It was found that filaments deposited within 0.5 mm of each other would be attracted together and that the ability to bridge gaps was limited. Sharp corners were rounded to a radius of 0.4 mm, with deviations up to 2 mm from the corner. Investigation was constrained by the speeds achievable with the motion platform used, resulting in filament diameters around 100 μm. Several lattices produced by this process were successfully sintered to pure alumina, although little consolidation was achieved and the filaments were very porous. These samples had approximately 15 % of the strength expected if they were made of solid alumina.

A prevalent morphology in the microscopic world of artificial microswimmers, bacteria and viruses is that of a helix. The intriguingly different physics at play at the small scale level make it necessary for bacteria to employ swimming strategies different from our everyday experience, such as the rotation of a helical filament. Bio-inspired microswimmers that mimic bacterial locomotion achieve propulsion at the microscale level using magnetically actuated, rotating helical filaments. A promising application of these artificial microswimmers is in non-invasive medicine, for drug delivery to tumours or microsurgery. Two crucial features need to be addressed in the design of microswimmers. First, the ability to selectively control large ensembles and second, the adaptivity to move through complex conduit geometries, such as the constrictions and curves of the tortuous tumour microvasculature. In this dissertation, a mechanics-based selective control mechanism for magnetic microswimmers is proposed, and a model and simulation of an elastic helix passing through a constricted microchannel are developed. Thereafter, a theoretical framework is developed for the propulsion by stiff elastic filaments in viscous fluids. In order to address this fluid-structure problem, a pertubative, asymptotic, elastohydrodynamic approach is used to characterise the deformation that arises from and in turn affects the motion. This framework is applied to the helical filaments of bacteria and magnetically actuated microswimmers. The dissertation then turns to the sub-bacterial scale of bacteriophage viruses, 'phages' for short, that infect bacteria by ejecting their genetic material and replicating inside their host. The valuable insight that phages can offer in our fight against pathogenic bacteria and the possibility of phage therapy as an alternative to antibiotics, are of paramount importance to tackle antibiotics resistance. In contrast to typical phages, flagellotropic phages first attach to bacterial flagella, and have the striking ability to reach the cell body for infection, despite their lack of independent motion. The last part of the dissertation develops the first theoretical model for the nut-and-bolt mechanism (proposed by Berg and Anderson in 1973). A nut being rotated will move along a bolt. Similarly, a phage wraps itself around a flagellum possessing helical grooves, and exploits the rotation of the flagellum in order to passively travel along and towards the cell body, according to this mechanism. The predictions from the model agree with experimental observations with respect to directionality, speed and the requirements for succesful translocation.

Abstract: This thesis focuses on the manufacturing of high carbide content wear-resistant parts by extrusion- based Additive Manufacturing (AM) based on the principles of Powder Metallurgy (PM). A new manufacturing technique, termed Fused Filament Fabrication of Cermets (FFFC) is presented. First, particle packing theory is applied to develop a methodology for maximizing packing density and carbide content in non-ideal binary powder mixtures. Based on this optimization, sinterable metal-ceramic polymer filaments suitable for Fused Filament Fabrication (FFF) are prepared and printed. It is shown that a traditional polymer 3D printer can be used to successfully deposit high- density polyethylene (HDPE) composite filaments containing up to 46 vol% Ni-TiC and Ni-WC fillers, to produce dense green parts for sintering. A characterization of the composite filaments and resultant printed parts is provided. An analysis of the random loose void fractions in dry fillers and the fraction of polymer in the composite after polymer is injected into the dry filler is presented. It is concluded that, the maximum void contraction (∆Θmax) is a function of the ratio of mean particles sizes (δ) in binary dry powder mixtures. As δ decreases and the particle sizes become more dissimilar, an increasing deviation from the ideal rule-of-mixtures law is observed. The critical δ is revealed to be 0.65. Furthermore, when dry filler is mixed with HDPE to form composite filaments for FFF, the particles are rearranged, and the polymer content of the filled composite is greater than the void fraction observed in dry filler packing. Fillers having lower dry void fractions, reported higher polymer contents in their composites. The important role of non- ideal particle packing in binary filler mixtures is emphasized, where the goal is to produce high carbide content cermet parts. Some remarks about process parameters that influence part quality and suggestions for future work are included.

During the first stage of cell division in bacteria, FtsZ filaments form a ring-like assembly, the Z-ring, which encircles the cell’s middle. This filament scaffold recruits a set of enzymes that synthesize the new cell wall, which divides the cell into two daughters. This dissertation addresses two questions related to the formation of the Z-ring. First, what molecular mechanism triggers Z-ring formation? Second, what are the intermediary structures through which the Z-ring assembly proceeds? The experiments are carried out in Escherichia coli (E.coli) bacteria, whose FtsZ molecules are fluorescently labelled. Using quantitative analysis of high temporal and spatial resolution time-lapse images, we show that the Z-ring formation at the midcell is preceded by a period when transient membrane-linked FtsZ assemblies form throughout the cell body. These transient assemblies result from the attachment of short FtsZ filaments to the inner membrane from the cytosol. We estimate these filaments to be less than 20 monomers long. Once attached filaments become more stable, but despite this stabilization they show treadmilling and periods of rapid growth and shrinkage. At the time of Z-ring formation one of the midcell assemblies is able to grow at the expense of the other transient assemblies indicating that FtsZ is a limiting factor for Z-ring assembly. The latter conclusion is further confirmed by our measurements of FtsZ concentration during the E. coli cell cycle. In slow growth conditions, we find a 4-fold upregulation of the FtsZ synthesis rate at the time of Z-ring formation. Altogether, our work shows that dynamic FtsZ filaments sample the cell surface for the possible location of the Z-ring and that there is a cell cycle control over the timing of the Z-ring formation, albeit not stringent.

This study of an upwelling cross-shore filament in the California Current System attempts to follow a parcel of water from upwelling source to offshore in order to characterize changes in silica cycling and associated impacts on carbon cycling under the influence of iron limitation. Water column samples were collected throughout the euphotic zone in conjunction with sediment traps following the filament in Lagrangian fashion (cycles); additional samples were taken across the filament (transects). The filament progressed from iron-replete to iron-limited throughout the study, identified by low silicic acid to nitrate ratios (Si:N) and elevated nitrate to iron (N:Fe) ratios in situ. Increases in biogenic silica to POC ratios (bSi:POC) in the water column were apparent with increasing iron limitation of the diatom-dominated community. The Lagrangian nature of the study improves overall understanding of the dynamics of biogenic silica as an upwelling filament develops to iron-limited, low Si:N water conditions. This work builds upon and adds context to previous studies which have shown that iron limitation affects silicic acid to carbon (Si:C) and silicic acid to nitrate (Si:N) uptake ratios in marine diatoms. These ratios have potential implications for both carbon and silica cycling in the ocean, impacting uptake and export of these elements. The filament was shown to transport biogenic silica laterally away from the coast, and enhanced silica ballasting was shown to be associated with increased export efficiency offshore.

Plasma blobs (filamentary structures extended along the magnetic field lines) are mesoscale turbulent structures that are usually observed in the scrape-off layer (SOL) of magnetic confinement devices. Electromagnetic fluid simulations for seeded high-beta blobs demonstrate that inhomogeneity of magnetic curvature or plasma pressure along the filament leads to bending of the filaments and magnetic field lines due to increased Alfven time. Moreover, the drift wave instabilities inside the filaments are modified by electromagnetic effects. A local linear analysis on an electromagnetic drift-kinetic equation with BGK-like collision operator proves to be valid for describing the linear growth rate of drift wave instabilities in a wide range of plasma parameters showing convergence to reference models for limiting cases. Finally, the development of the 5D version of the full-f gyrokinetic code COGENT and its application to the collisionless drift wave simulation are presented with discussion of the disturbance of the distribution function from the collisionless drift wave instability and the formation of a helical mode structure within the plasma filament.

Deciphering protein interaction and compartmentalization is crucial to understanding the molecular mechanisms that drive biological processes. Using various high throughput approaches, we have managed to score subcellular dynamic protein re-organization into supramolecular structures and map physical association networks to discover protein complexes on a proteome-wide level. However, the case by case studies of some of these novel structures and interactions reveal difficulties in interpreting their biological basis. This study offers insights into limits inherent in the molecular techniques used to investigate subcellular structures and protein interactions, describing a set of cautionary tales and critical analysis for deciphering cases of confounding data from orthogonal approaches. This study also offers a new experimental technique for high-throughput imaging assays with mammalian cell lines.

Tubulin is a universally conserved molecule, found in all three domains of life. Tubulin filaments use energy derived from GTP binding and hydrolysis to organize cytoplasm. Although tubulin homologues share the same fold to their monomers and similar protofilament architecture, they assemble filaments with unique geometric designs. Moreover, despite sharing the mechanism of self-assembly, wherein tubulin subunits require GTP binding to polymerize, and their polymerization stimulates GTP hydrolysis, tubulins exhibit distinctive dynamic properties. Together, unique filament architectures and dynamic properties determine a specific set of biological functions each tubulin family performs. The origins of tubulin filament architectural diversity and distinctive dynamic behavior are not well understood. We have been studying PhuZ tubulins, which are encoded by a few very large Pseudomonas ϕKZ-like bacteriophages. Our studies have shown that PhuZ assembles dynamically unstable spindle-like arrays that organize bacteriophage DNA at the cell midpoint, which somehow facilitates phage infectivity. Moreover, PhuZ monomer structure has the canonical tubulin fold, with a unique, highly conserved and extended C-terminus. The C-terminus mediates protofilament contacts and is critical for polymerization both in vitro and in vivo. The main focus of this manuscript is the structural investigation of the molecular mechanisms underlying PhuZ dynamic behavior. In an attempt to explain how GTP binding and hydrolysis drives PhuZ filament turnover, we have conducted a number of electron cryomicroscopy studies (cryo-EM) on PhuZ filaments in both pre- and post- hydrolysis states. PhuZ forms a polar three-stranded polymer with an unusual subunit orientation. Its C-terminus guides a cooperative assembly of the three-stranded filament by mediating both longitudinal and lateral interactions. Upon assembly, the longitudinal interface, C-terminus and tubulin fold undergo polymerization-competent rearrangements. We propose that the energy of GTP binding is stored in the displacement of these structural elements. Also, our structural studies have revealed how the energy of GTP hydrolysis is stored in the PhuZ filament lattice. In particular, GTP hydrolysis, initially sensed by the T3 loop and C-terminus, is accompanied by unwinding and supercoiling of the filament lattice. Based on these observations, we propose an assembly/disassembly pathway of PhuZ filament.

In this thesis, standard statistical methods are used to explore the relationships among solar activities such as coronal intensity, sunspot numbers, prominences/filaments, and solar flares. The statistical methods include correlation analysis, simple linear regression, analysis of variance, and multiple comparisons. The correlation, and simple linear regression methods show that the sunspot number and prominence/filament have significantly influenced the coronal intensity. The mean levels of coronal intensity in different solar flare classifications are also statistically different in ANOVA. With the multiple comparison methods, the treatment pairs, such as B & A, A & Others, M & X, and X & C, are statistically equal. Likewise, the mean numbers of sunspots over the solar cycles significantly differ.

We develop a general computational model for a elastic rod which allows for extension and shear.

The tubulin superfamily is a unique set of GTPases, which, while they have high sequence diversity, have remarkably similar tertiary structures. These proteins share a very conserved longitudinal interface, but are able to form a surprisingly wide variety of super structures within both eukaryotic and prokaryotic cells — from the familiar 13-protofilament microtubule assembled from αβ–tubulin heterodimers to the single protofilaments of the ubiquitous prokaryotic FtsZ seen in vitro. Additionally in eukaryotes, monomeric tubulin family members have the ability to affect the assembly of filaments, such as nucleation of microtubules with γ–tubulin, or involvement in the assembly of B– and C– microtubules in the centriole microtubule triplets (ε– and δ–tubulin respectively). Each tubulin family member, both prokaryotic and eukaryotic is exquisitely tuned to perform its cellular function, with a unique superstructure and dynamics. The main focus of this manuscript is a structural and biochemical investigation of a recently discovered bacterial tubulin TubZ–Bt. TubZ–Bt is located on the pBtoxis virulence plasmid in Bacillus thuringiensis, and is necessary to maintain stability of the pBtoxis plasmid in conjunction with an upstream DNA–adaptor protein (TubR) and DNAbinding site (tubC). We have determined that TubZ–Bt forms four–stranded filaments in the presence of GTP in vitro, whereas TubZ filaments formed with catalytically compromised protein or non-hydrolysable GTP analogs are predominantly two-stranded. These morphological changes were investigated by high–resolution cryo–electron microscopy of both two– and four–stranded TubZ–Bt filaments, as well as various biochemical approaches, and we propose that TubZ–Bt two–stranded filaments that we observed are an intermediate on pathway to four–stranded filament formation. In addition, we have begun preliminary investigations on the interaction of TubR bind to tubC DNA and the interaction of the TubRC complex with TubZ-Bt filaments. A minor focus of this manuscript is work on the eukaryotic tubulins, γ–, δ– and ε–tubulin. This work details preliminary attempts at purification of these tubulin family members in order to begin more detailed investigative work on their molecular function. Also included is a published manuscript of work done with Dr. Luke Rice investigating the conformational state of both αβ– and γ–tubulins using solution–state and crystallographic structural studies.

The time-resolved electrical conductivity of a short-pulse generated plasma filament in air was studied. Close-coupled metal electrodes were used to discharge the stored energy of a high-voltage capacitor and the resulting microsecond-scale electrical discharge was measured using fast current sensors. Significant differences in the time dependence of the current were seen with the two electrode geometries used. Using sharp-tipped electrodes additional peaks in the time-resolved conductivity were seen, relative to the single peak seen with spherical electrodes. We attribute these additional features to secondary electron collisional ionization brought about by field enhancement at the tips. Additional discrepancies in the currents measured leaving the high-voltage electrode and that returning to ground were also observed. Implications for potential laser-induced discharge applications will be discussed.

During pathfinding, growth cones alter their motility in response to filopodial contact with guidance cues. The first study shows that motile responses can be highly specific: filopodial contact with two, physiologically relevant cells differentially alters discrete motile elements. Contact with an inhibitory cell, posterior sclerotome, locally inhibits the ability of veils to extend down contacting filopodia without altering the frequency of veil initiation. In contrast, contact with a stimulatory cell, anterior sclerotome, elicits a bi-phasic response. First, contact stimulates extension generally, increasing the number of veil and filopodial initiations across the growth cone. Then, contacting processes consolidate. Filopodia contacting either cell type have similar lifetimes but different fates. Filopodia contacting posterior cells destabilize, whereas filopodia contacting anterior cells branch and ultimately consolidate. In the second study, we develop a novel model for veil extension and stabilization along filopodia. We expanded the findings in the first study by showing that veil extension down filopodia is controlled by fine patterns of filopodial adhesions and that these patterns can be altered differentially and specifically by filopodial contact with cellular cues that differentially induce (Schwann) or prohibit (posterior sclerotome) veil extension. Moreover, we show that the destabilization of filopodia contacting posterior sclerotome correlates with altered adhesion composition and premature F-actin withdrawal; both vinculin and F-actin withdraw, despite retention of phosphotyrosine-positive adhesions on both laminin and the cell. In the third study, we develop a novel model for filopodial initiation and both filopodial and lamellar stabilization. We examined the events underlying filopodial initiation by analyzing recorded filopodial histories. This analysis revealed three morphological features that consistently precede filopodial initiation: an influx of cytoplasm, a focal increase in phase density, and the later protrusion of a nub, thus permitting filopodial initiation sites to be identified and examined before the appearance of a frank filopodium. Both immunocytochemical and ultrastructural analyses indicate that focal densities presaging initiation correspond to adhesions, filament origins, and a focal ring with radiating filaments. We propose a model for filopodial initiation in which focal rings initiate filopodia and facilitate filopodial emergence by organizing and stabilizing actin filaments both within nascent filopodia and between filopodial bundles, which in turn provides stability to lamellar margins.