Inspired by the dilute spray regime in spray combustion, this dissertation explores the evaporation and combustion of an isolated droplet. Under a highly convective environment inside a gas combustor, due to imbalance of inertial and surface tension forces, the droplets of larger size in sprays exhibit notable deformations from spherical to non-spherical shapes. Such shape changes are generally observed but not quantified in experimental studies. Therefore, the effect of this deformation on droplet combustion dynamics is unknown yet. To bridge this gap, a comprehensive investigation of an isolated freely deforming droplet can be insightful as it can reveal more about the interaction of droplet shape with its evaporation and combustion. This work attempts to analyze and quantify the impact of such deformations on evaporation and combustion using interface-capturing Direct Numerical Simulation approach. With the focus on small-scale processes involved in evaporation as it is a pre-step for combustion, this dissertation first covers a thorough examination on evaporation of a deformable droplet under both natural and forced convection. A single component jet-fuel surrogate n-decane is chosen. To ensure that the droplet remains stationary throughout its lifetime, a novel numerical method called "gravity update method" is developed and implemented. The results obtained from these two separate studies are validated against experimental results and analytical correlations respectively. The findings from the investigation of droplet evaporation under forced convective flow at moderate Reynolds numbers are noteworthy. The droplet shape under such flow conditions is governed by Weber number (We) which is a ratio of inertial force to surface tension force. The results demonstrated upto 20% en- hancement in total evaporation rate for highly deformed droplets. This improvement is a net results of increased droplet surface area and alteration in the distribution of local evaporation flux ( m'' ). It is found that m'' is proportional to its curvature up to the point of flow separation which agrees with low Re theories on droplet evaporation by Tonini and Cossalli (International Journal of Heat and Mass Transfer 2013), Palmore (Journal of Heat Transfer 2022). Beyond the flow separation point, evaporation flux distribution depends on the boundary layer development and flow evolution downstream of the droplet. For highly deformed droplets, a larger wake region creates favorable fuel vapor gradients and promotes mixing in droplet wake, hence higher evaporation flux. Such positive impact of droplet deformation on total evaporation rate motivated further investigation on droplet combustion under a low Reynolds number convective flow. High pressure and temperature gas flow leads to Damköhler number is higher than 1. This fa- vors the generation of envelope type flame. The results show overall little sensitivity to combustion related parameters despite the droplet shape change and significant (upto 9%) enhancement in total evaporation rate. It is also noted that while burning, droplets do not reach critical deformation conditions and break-up even beyond the critical Weber number, suggesting the suppression of deformation due to faster evaporation rate. The findings presented in these studies provide substantial evidence for the interaction between droplet shape and flow dynamics. Therefore, it demonstrates the potential for enhancing the existing numerical models and analytical correlations by accounting the influence of droplet shape. / Doctor of Philosophy / This work is inspired by the spray combustion in gas turbines where the pressurized liquid fuel jet is injected in the combustion chamber and converted into dilute sprays after undergoing a series of processes. Due to the presence of higher air to fuel ratio for these spray droplets, they become the localized combustion sites with rapid evaporation rates. Understanding the evaporation of these droplets becomes crucial, as it sets the stage for their subsequent combustion. In an attempt to understand this chemically and fluid-dynamically complex phenomenon, abundant experimental studies are available with focus on overall atomization process and velocity field evolution. However, they lack in resolving the small-scale processes which govern the evaporation, therefore combustion. With the intent to investigate in detail about the combustion aspect, this problem is reduced to analyzing behavior of isolated droplets. Despite the sophisticated measurement technologies particle-scale processes such as temperature and species mass fraction evolution are yet unknown. Moreover, the majority of these studies are performed with simplifying assumptions. assumption has been that the droplet remains spherical throughout its lifetime. However, in practical applications, particularly when exposed to convective and turbulent environments, droplets can undergo significant deformation due to the presence of inherent surface tension of liquid. This deformation can influence their evaporation and burning rates. Additionally, the droplet's shape governs the flow field around it, potentially altering droplet-droplet interactions. Direct Numerical Simulation (DNS) approach is one of the numerical methods which can resolve both the phases. It offers a promising approach to reveal these small-scale details, such as droplet shape, vapor and temperature field around a droplet, droplet-droplet interaction, droplet motion etc. With the aim to bridge this gap, this dissertation focuses on the study of evaporation and combustion of an isolated deformable droplet under various conditions.

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Droplets as precursor are extensively applied in diverse fields of science and engineering. Various contributions are provided previously towards analysis of single phase and multi-phase droplets of single and multiple components. This thesis describes modelling of multi-phase (nano fluid) droplet vaporization. The evaporation of liquid phase along with migration of dispersed particles in two-dimensional plane within droplet is detailed using the governing transport equations along with the appropriate boundary and interface conditions. The evaporation model is incorporated with aggregate kinetics to study agglomeration among nano silica particles in base water. Agglomeration model based on population balance approach is used to track down the aggregation kinetics of nano particles in the droplet. With the simulated model it is able to predict different types of final structure of the aggregates formed as observed in experimental results available in literature. High spatial resolution in terms of agglomeration dynamics is achieved using current model. Comparison based study of aggregation dynamics is done by heating droplet in convective environment as well as with radiations and using different combination of heating and physical parameters. The effect of internal flow field is also analysed with comparative study using levitation and without levitation individually. For levitation, droplet is stabilized in an acoustic standing wave. It is also attempted to study the transformation of cerium nitrate to ceria in droplets when heated under different environmental conditions. Reaction kinetics based on modified rate equation is modelled along with vaporization in aqueous cerium nitrate droplet. The thermo physical changes within the droplet along with dissociation reaction is analysed under different modes of heating. The chemical conversion of cerium nitrate to ceria during the process is predicted using Kramers' reaction velocity equation in a modified form. The model is able to explain the kinetics behind formation of ceria within droplet at low temperatures. Transformation of chemical species is observed to be influenced by temperature and configuration of the system. Reaction based model along with CFD (computational fluid dynamics) simulation within the droplet is able to determine the rate of chemical dissociation of species and predict formation of ceria within the droplet. The prediction shows good agreement with experimental data which are obtained from literature.

Bloodstain pattern analysis has been used in criminal investigations for more than 100 years. It provides valuable information about the events that took place prior to the formation of bloodstains at a crime scene. Forensic scientists use empirical laws to make a deduction from bloodstains, but the validity of these conclusions has been challenged in courts due to a lack of understanding of the underlying fluid mechanics. With this motivation, this thesis illustrates how mathematical modeling and numerical simulation can help gain insight into the spreading of blood droplets which eventually leads to the formation of a bloodstain. Understanding the fluid mechanics of droplet spreading and sliding has been accomplished with the help of the lubrication approximation which simplifies the Navier-Stokes equations to a more tractable form, i.e. a coupled set of non-linear partial differential equations. The resulting highly non-linear coupled set of equations is discretized using Finite-Difference. The resulting algebraic system is solved via an efficient Multigrid algorithm. These equations are modified to understand the effects of contact angle hysteresis, fluid rheology and absorptive properties of substrates on sliding dynamics. Variations in the inclination of the substrate cause the droplets to attain different advancing and receding contact angles as they slide down the incline under gravitational pull. This work explores a new way to introduce contact angle hysteresis in the numerical simulation to predict the different phases of a sliding droplet. Experiments of fluid droplet spreading/sliding on inclined surfaces have been performed to measure the terminal sliding velocity. A simplified hysteresis model has been proposed. This model automatically locates the section of the contact line which is advancing and the section which is receding which enables the application of the contact angles for the advancing and receding fronts and therefore takes into account contact angle hysteresis. A simplified analytical model is also suggested for droplets moving down the incline with near circular footprints. With the inclusion of the contact angle hysteresis, simulation results were brought in closer agreement with the experimental ones and the results from both were compared with the results from the analytical model. Blood is a shear-thinning fluid. One of the main objectives of this study is to investigate numerically the effect on the spreading and/or sliding of non-Newtonian fluid droplets on surfaces. To achieve this, the effect of rheology on the leveling of thin fluid films on horizontal solid substrates is first investigated as a preliminary investigation since this problem does not involve a contact line and is therefore more tractable. A mathematical model based on the lubrication approximation which defines non-Newtonian rheology using a power-law model is presented. Results for the leveling of sinusoidal perturbations of the fluid film highlight important differences between the leveling of shear-thinning and shear-thickening fluids. Namely, the onset of leveling occurs earlier for the shear-thinning fluid than for the shear-thickening one. However, the rate of leveling is higher for the shear-thickening fluid than the shear-thinning one. An important aspect of this part of the work is the verification of the numerical implementation using the Method of Manufactured Solutions (MMS). This leveling study also highlights differences between the leveling of two-dimensional and three-dimensional perturbations. This verified numerical formulation is then used to study the effects of rheology on the spreading/sliding of droplets. Results for the spreading of fully wetting droplets on a horizontal substrate show that, for all other quantities being equal, an increase of the flow index leads to a more rapid wetting. It also shows that, even for non-Newtonian fluids, the droplet velocity asymptotes to a constant value when sliding down an inclined substrate. This terminal velocity is strongly dependent on the rheological parameters and as it is reached, the droplets travel with a visibly constant profile. Finally, the numerical simulations revealed the formation of a tail at the rear of the droplet as it slides down the incline plane in the case of shear-thickening fluids. Finally, a more complex dynamics of fluid being absorbed in a porous substrate as it slides/spreads is considered. A mathematical model based on the lubrication approximation which defines the absorptive property of a substrate using a Darcy’s model is presented. This numerical model is verified with the help of comparison between the analytical and numerical solutions for the absorption of thin film on horizontal porous substrates. Results show that physical properties of the substrates, i.e. permeability, porosity, capillary pressure and equilibrium contact angle affect the rate of absorption of the fluid. Adding inclination to the problem, introduces the gravitational pull in the absorption dynamics. This directly shows its effects on the footprints formed inside the porous substrates. The following papers, based on sections of this thesis, have appeared or been accepted for publication: - Ahmed, G., Sellier, M., Lee, Y., Jermy, M., and Taylor, M. (2013). Modeling the spreading and sliding of power-law droplets. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 432:2–7. - Ahmed, G., Sellier, M., Lee, Y., Jermy, M., and Taylor, M. (2014). Rheological effects on the leveling dynamics of thin fluid films. Accepted for publication in the International Journal of Numerical Methods for Heat and Fluid Flow. - Ahmed, G., Sellier, M., Jermy, M., and Taylor, M. (2014). Modelling the effects of contact angle hysteresis on sliding of droplets on inclined surfaces. Submitted for peer review in The European Journal of Mechanics - B/Fluids.

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<p>Advances in modern medicine have helped to prolong human life. These advancements coupled with an ever-increasing population means that diseases associated with aging will become more prevalent in the coming years. As such, it is critical to understand the pathogenesis of disease where aging is the main risk factor. While not widely known, age is in fact a large risk factor in development of obesity and metabolic syndrome. More widely known and discussed are the neurodegenerative diseases that occur late in life. While age as a risk factor is a common point between these types of pathology, there are other similarities, such as the interaction between lipid metabolism and mitochondrial health. </p><p>To study the overlap between obesity and neurodegeneration, we investigated two pathways that regulate both. First, we find that loss of cytoplasmic deacetylase HDAC6 leads to aberrant accumulation of lipid in vitro and in vivo. HDAC6 knock-out (KO) mice gain more weight than WT counterparts after a high-fat diet regimen. Additionally, the intermediary metabolism of cells lacking HDAC6 is disrupted as they increase glucose uptake while downregulating fatty acid oxidation. HDAC6 not only plays a role in lipid metabolism, but regulates mitochondrial dynamics. Upon glucose-withdrawal, HDAC6 KO cells fail to elongate their mitochondria and display increased levels of mitochondrial toxic by-products. Therefore, HDAC6 has critical roles in lipid homeostasis and mitochondrial health. </p><p>The other pathway we investigated is critical in neurodegenerative disease, Parkinson's disease. Parkin, an E3 ubiquitin ligase, flags damaged mitochondria for destruction so they do not poison the other functional organelles. We found that Parkin promotes lipid remodeling at the surface of the mitochondria. Phosphatidic acid (PA) accumulates shortly after mitochondrial damage while diacylglycerol (DAG) appears several hours later. This lipid accumulation is dependent upon Parkin's translocation and E3 ligase activity. Additionally, we found that lipin-1, a PA phosphatase, and endophilin B1 (EndoB1) are critical for DAG accumulation and effective mitochondrial clearance. </p><p>Through this work, we show that two proteins critical in quality control mechanisms also play significant roles in energy homeostasis. We aim to highlight this overlap and posit that common diseases of aging, though presenting differently, might have disruptions in the same basic process.</p> / Dissertation

Thesis advisor: Michelle Meyer / The primary bacterial targets for most antibiotics are well known. To survive the stress of an antibiotic a bacterium must decrease the antibiotic to target binding ratio to escape from harmful effects. This can occur through a number of different functions including down-regulation of the target, mutation of the binding site on the target, and decreasing the intake or increasing the efflux of the antibiotic. However, it is becoming more evident that an antibiotic stress response influences more than just the primary target, and that a wave of secondary responses can be triggered throughout the bacterium. As a result resistance mutations may arise in genes that are indirectly affected by the initial interaction between the antibiotic and target. These indirect responses have been found to be associated with metabolism, regulation, cell division, oxidative stress, and other critical pathways. One technique recently developed in our lab, called transposon insertion sequencing (Tn-seq), can be used to further understand the complexity of these indirect responses by profiling growth rates (fitness) of mutants at a genome-wide level. However, Tn-seq is normally performed with large libraries of pooled mutants and thus it remains unclear how this may influence fitness of some independent mutants that may be compensated by others in the population. Additionally, since the original method has only utilized planktonic culture, it is also not clear how higher order bacterial structures, such as biofilms or microcolonies, influence bacterial fitness. To better understand the dynamics of pooled versus individual mutant culture, as well as the effect of community structure in microcolony development on the influence of fitness, we adapted a droplet microfluidics-based technique to encapsulate and culture single mutants. We were able to successfully encapsulate at least 7 different species of bacterial pathogens, including Streptococcus pneumoniae, and culture them planktonically, or as microcolonies, in either monodisperse liquid or agarose droplets. These experiments, however, raised an important challenge: the DNA yield from one encapsulation experiment is insufficient to generate samples for sequencing by means of the traditional Tn-seq method. This led us to develop a novel Tn-seq DNA library preparation method, which is able to generate functional Tn-seq library molecules from picogram amounts of DNA. This method is not ideal yet because fitness data generated through the new method currently does not correlate well with data from traditional Tn-seq library preparation. However, we have identified one major culprit that should be easily solvable. We expect by modifying the binding site of the primer used for linear amplification of transposon ends that the new preparation method will be able recapitulate results from the traditional Illumina preparation method for Tn-seq. This will enable us to prepare robust Tn-seq samples from very small amounts of DNA in order to probe stress responses in single mutants as well as in microcolonies in a high-throughput manner. / Thesis (MS) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Many droplet microfluidic assays have been described in the literature over the last decade of research, however, there has been little reported industrial use of droplet microfluidics in drug discovery compound screening, and in particular that of P450 enzyme inhibition assays for profiling drug-drug interactions. This is partly for Intellectual Property reasons, since Pharmaceutical companies do not wish to give away trade secrets in a competitive market, but also because the technology is not yet 'proven' and remains in the proof-of-concept stage. In droplet microfluidics, where at least two liquid phases are encountered, it is important that leakage of material between phases is addressed. This effect has been extensively reported in the literature using fluorescent dyes, however there is very little evidence of research using large compound sets of diverse chemistry. This is probably because few researchers have access to the large pharmaceutical libraries necessary for this work. This project assessed the feasibility of translating a widely used microtitre plate-based P450 enzyme inhibition assay to droplet format; determined the extent of partitioning from droplets using a large pharmaceutical library set and attempted to model this behaviour, and thirdly, considered the pharmacological impact the droplet format may have on the assay. The P450 cytochrome 1A2 enzyme type (isoform) was chosen for translation to the micro-droplet format. Assays of this type are often conducted using fluorogenic substrates, making them favourable for relatively easy fluorescent detection in droplet format using simple optical detection assemblies. Oil selection was investigated to determine which oil systems would be better suited in respect of droplet formation. The use of surfactants in the oil phase and its impact on droplet formation was studied and the synthesis, preparation and characterisation of a custom perfluoropolyether (PFPE) surfactant ('AZF') conducted. Droplet chips were designed and fabricated to produce droplets of 200-300 µm diameter using novel channel designs and sealing techniques. The droplets were analysed by fluorescence spectroscopy using bespoke detector apparatus. Partitioning from aqueous to oil phase was studied for a small range of compounds and oils (with and without surfactant for fluorous oils). Partitioning was lowest using fluorous oils alone, and increased substantially when surfactant was included. Results from the large pharmaceutical test set suggested the percentage of compounds that may partition readily to the oil phase is low even when using surfactant. However, attempts to correlate this to known physicochemical properties and to develop a predictive model for fluorous solubility proved largely unsuccessful. Partitioning in the droplet chip using a droplet collection pooling method was difficult to quantify as a consequence of the profound impact turbulence had on partitioning. Miniaturisation of the P450 cytochrome inhibition assay to the droplet format initially gave poorly reproducible low signals. Possible causes included detector insensitivity, partitioning of reagent and/or fluorescent metabolite over longer incubation times, and binding of the 1A2 P450 cytochrome enzyme-protein at the droplet interface. Protein interaction at the droplet-oil boundary was studied by fluorescence labelling a protein contained in 200µm droplets and observing the extent of fluorescence localisation at the interface by epifluorescent and confocal fluorescence microscopy. The data from this work indicates a pronounced localisation of protein at the droplet interface, possibly leading to enzyme deactivation and the loss of signal seen for the assay in the droplet chip. A number of protein titrations were co-added to the droplets as 'blocking proteins' which were found to improve the reaction output, however were also noted to affect the pharmacology of the assay, noted by an order of magnitude shift in the reported IC50 for the test inhibitor used (fluvoxamine). The effects of compound leakage from droplets, and the possible detrimental impact on biological reagents by interaction at the droplet-oil interface, is a challenge that may limit widespread adoption of droplet MF systems in drug screening operations. Appropriate control measures and/or a means to reduce these effects are essential to enable accurate quantification with industrial drug discovery environments. The findings in this work highlight the challenges that have to be addressed for droplet microfluidic technology to be successfully incorporated into key areas of assay screening within drug discovery. In terms of further research, there is a significant requirement for the research community to delve further into these challenges and work closely with the industry sector to understand the beneficial role microfluidics can have and how to develop effective robust strategies the industry can easily adopt to progress this area of science.

Materials on the nanoscale have very interesting properties. Hence, they are commonly used for a variety of applications such as drug delivery, bio-imaging and sensing devices. Moreover, coating these particles with other materials forming core@shell or Janus particles can further enhance their properties. However, for the particles to be used in medical and electronic devices, their properties such as size, shape and composition need to be precisely controlled. In this PhD., an emulsification technique was chosen to investigate the synthesis of nanoparticles; it is a simple process, does not require any harsh chemicals or temperature and is fast. Emulsification occurs when two or more immiscible liquids and surfactants are mixed. Here, emulsion droplets were produced using a microfluidic device which allowed for the creation of uniform droplets. These were employed as templates to synthesise and assemble nanomaterials. The main aim of the Ph.D. was to develop a droplet based synthesis process to generate nanoparticles and then assemble them into core@shell particles. This Ph.D., starts by synthesising Fe3O4 nanoparticles (~ 12 nm) and assembling them into microparticles (~ 1µm 2µm) using emulsion droplets as microreactors. By tuning the surfactant, droplet size and evaporation rate of the dispersed phase, microparticles of varying shapes and sizes, such as spherical or crumbled shapes, were produced. When these particles are compared with the commercially available particles, the magnetic content of the in-house particles, or sometimes referred to as Loughborough University Enterprises Ltd. (LUEL), are much higher and more uniform, hence resulting in faster separation when used for extraction of analytes. LUEL particles were supplied as part of commercial collaboration. The use of Pickering emulsions were then explored to create core@shell particles using gold nanoparticles instead of a surfactant to produce gold shells and the addition of pre-synthesised Fe3O4 nanoparticles results in Fe3O4@Au core@shell particles. This is the first time Pickering emulsions were used to produce Fe3O4@Au core@shell particles (~ 1.5 µm) within a microfluidic device. However, the shells were not uniform in thickness. In order to improve the coverage, nanoparticles were synthesised in situ at the droplet interface. By placing the gold chloride (AuCl4-) in the continuous phase and by varying the concentration of the electron donor in hexane droplet, single crystal gold nanoparticles and platelets were formed. The reaction is spontaneous at room temperature, creating gold nanoparticles at the interface of the emulsion droplet. The size and shape of the gold nanoparticles were controlled by varying the concentration of the reactants and the size of the droplets. By adding pre-synthesised particles (Fe3O4 nanoparticles) to the droplet, Au@Fe3O4 core@shell particles were formed with an approximate size of 250 nm. The same concept of forming core@shell particles using gold nanoparticles was further expanded by using other metal ions; palladium and silver. Unlike gold, palladium and silver only formed spherical nanoparticles, no platelets were observed. The addition of preformed iron oxide nanoparticles to the palladium results in core@shell particles. However, in the case of silver, no core@shell particles were formed. The study of the rate of reaction was conducted to understand the details of the mechanism. Overall, the process developed in this Ph.D. study allows for the facile synthesis of core@shell particles in a rapid, high throughput reaction. In the future, it is believed it could be scaled up for commercial purposes.

We investigate the formation of droplets in a thin liquid film on a solid substrate due to the combined action of surface tension and van der Waals forces. Current models for droplet formation assume that droplets have a shallow profile. By removing that assumption and numerically solving for stable droplet profiles, we have modelled droplets that separate from the substrate on which they sit.