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In vitro studies have shown that the major membrane phospholipid phosphatidylcholine (PC) can positively influence the incorporation of cholesterol in lipid membranes. The influence of PC on the cellular trafficking of LDL-derived free cholesterol was investigated. Sterol regulatory-defective (SRD)-4 cells are Chinese hamster ovary (CHO)-derived fibroblasts that display vastly elevated rates for the synthesis and catabolism of PC. SRD-4 cells harbor two known gene mutations: a mutation in the functional allele for SCAP, resulting in defective feedback suppression of cholesterol biosynthesis; and a loss-of-function mutation in the functional allele for acyl-CoA:cholesterol acyl transferase (ACAT), an endoplasmic reticulum (ER)-localized enzyme that esterifies free cholesterol. Incubation of SRD-4 cells with 50 µg/ml low density lipoprotein (LDL) for 18 h resulted in lysosomal accumulation of free cholesterol as revealed by filipin staining. This accumulation was not evident following LDL treatment of parental CHO7 cells, and was blunted in SRD-2 cells that express a constitutively-active form of SREBP-2 and overproduce cholesterol but have functional ACAT activity. Treatment of SRD-2 cells with LDL in the presence of an ACAT inhibitor 58-035 resulted in robust lysosomal cholesterol accumulation that was reversible upon drug washout, supporting that cholesterol trafficking in cholesterol-loaded cells is dependent on ACAT activity and, more specifically, ER free cholesterol levels. Lysosomal accumulation of LDL-derived cholesterol was prevented in SRD-4 cells supplemented with lyso-PC (50 µM), a substrate for PC synthesis through the reacylation pathway, and also in cells treated with bromoenol lactone (BEL), an inhibitor of phospholipase A2 implicated in bulk PC turnover. In a counter study, lysosomal LDL-derived cholesterol accumulation was induced in parental CHO-7 cells using R-propranolol, which inhibits the conversion of phosphatidic acid to diacylglycerol (DAG), a substrate in the CDP-choline pathway. This blockage was also relieved through co-treatment with lyso-PC. These studies support that PC to free cholesterol ratios in downstream organellar membranes can influence cholesterol trafficking out of lysosomal compartments in cholesterol-loaded cells.

Addition of nanopacticles in a base solvent leads to suspensions with enhanced physiochemical properties, compared to base solvent. This new type of suspensions is called nanofluids, with applications ranging from biomedicine to automotives. As a consequence extensive research is being conducted in the field, in particular, on the evaporation of these fluids as it leads to well-defined and highly ordered coffee-rings. However, the exact physics governing this phenomenon remain elusive. The goal of this experimental investigation is to elucidate how various parameters affect the progression of nanofluid coffee-stain formation. Examination of the coffee-ring structuring, produced by the free evaporation of sessile droplets containing nanoparticles, revealed an unexpected, disordered region at the exterior edge of the ring. A self-assembly mechanism with two components, particle velocity and wedge constraints, was proposed to describe the deposition of particles at contact lines of evaporating drops. Environmental pressure was used as a method to control particle crystallinity in the coffee-rings. Essentially, evaporation rate and pressure were found to be inversely proportional. Macroscopically, lowering pressure led to a transition from “stick-slip” to constant pinning. Nanoscopically, lowering pressure promoted crystallinity. Findings supported the proposed, in this thesis, particle self-assembly mechanism. Particle aspect ratio and flexibility were subsequently examined. Pinning strength was found to be a function of particle aspect ratio and rigidity, leading to constant pinning. The proposed, in this thesis, particle self-assembly mechanism was found to be applicable to a variety of aspect ratios and flexibilities. Lastly, particulate crystals grew following different pathways depending on particle flexibility.

Philosophiae Doctor - PhD / Sequencing an HIV quasispecies with next generation sequencing technologies yields a dataset with significant amplification bias and errors resulting from both the PCR and sequencing steps. Both the amplification bias and sequencing error can be reduced by labelling each cDNA (generated during the reverse transcription of the viral RNA to DNA prior to PCR) with a random sequence tag called a Primer ID (PID). Processing PID data requires additional computational steps, presenting a barrier to the uptake of this method. MotifBinner is an R package designed to handle PID data with a focus on resolving potential problems in the dataset. MotifBinner groups sequences into bins by their PID tags, identifies and removes false unique bins, produced from sequencing errors in the PID tags, as well as removing outlier sequences from within a bin. MotifBinner produces a consensus sequence for each bin, as well as a detailed report for the dataset, detailing the number of sequences per bin, the number of outlying sequences per bin, rates of chimerism, the number of degenerate letters in the final consensus sequences and the most divergent consensus sequences (potential contaminants). We characterized the ability of the PID approach to reduce the effect of sequencing error, to detect minority variants in viral quasispecies and to reduce the rates of PCR induced recombination. We produced reference samples with known variants at known frequencies to study the effectiveness of increasing PCR elongation time, decreasing the number of PCR cycles, and sample partitioning, by means of dPCR (droplet PCR), on PCR induced recombination. After sequencing these artificial samples with the PID approach, each consensus sequence was compared to the known variants. There are complex relationships between the sample preparation protocol and the characteristics of the resulting dataset. We produce a set of recommendations that can be used to inform sample preparation that is the most useful the particular study. The AMP trial infuses HIV-negative patients with the VRC01 antibody and monitors for HIV infections. Accurately timing the infection event and reconstructing the founder viruses of these infections are critical for relating infection risk to antibody titer and homology between the founder virus and antibody binding sites. Dr. Paul Edlefsen at the Fred Hutch Cancer Research Institute developed a pipeline that performs infection timing and founder reconstruction. Here, we document a portion of the pipeline, produce detailed tests for that portion of the pipeline and investigate the robustness of some of the tools used in the pipeline to violations of their assumptions.

Submitted by Cátia Araújo (catia.araujo@unipampa.edu.br) on 2017-09-29T13:05:00Z No. of bitstreams: 1 Mariovane Sabino Donini - 2017.pdf: 4347435 bytes, checksum: b83edb6c2d0b7868757722dc435be9fa (MD5) / Approved for entry into archive by Marlucy Farias Medeiros (marlucy.farias@unipampa.edu.br) on 2017-09-29T16:25:43Z (GMT) No. of bitstreams: 1 Mariovane Sabino Donini - 2017.pdf: 4347435 bytes, checksum: b83edb6c2d0b7868757722dc435be9fa (MD5) / Made available in DSpace on 2017-09-29T16:25:43Z (GMT). No. of bitstreams: 1 Mariovane Sabino Donini - 2017.pdf: 4347435 bytes, checksum: b83edb6c2d0b7868757722dc435be9fa (MD5) Previous issue date: 2017 / In the present work, vaporization and combustion of an isolated fuel droplet at diferente ambient temperatures are examined numerically in order to analyze the effect of buoyancy force on the flame. Generally, fuel droplets in combustion devices are so small that the influence of buoyancy force on vaporization and combustion of droplets is negligible. On the other hand, fuel droplets in experimental devices are affected by the buoyancy force due to their diameters being around or more than 1 mm. To reduce the buoyancy effects, expensive experimental studies are performed in microgravity ambient (drop-tower or out of space). In normal-gravity conditions, the buoyancy force is induced by temperature gradient on ambient atmosphere. The buoyancy is positive in regions of hot gases and negative in regions of cold gases compared with the ambient atmosphere gas. Hot gases move upward and cold gases downward. Playing with the positive buoyancy force of hot gases around the flame and with the negative (cold) buoyancy force of cold gases around the droplet via ambient atmosphere temperature, it is possible to modify the flame shape. In the numerical simulations, incompressible Navier–Stokes equations along with mixture fraction and excess enthalpy conservation equations are solved using a finite volume technique with a uniform structured grid. An artificial compressibility method was applied to reach steady state solutions. The numerical predictions have been compared with analytical results for a zero gravity condition, showing good agreement. For normal gravity condition the numerical results showed that when the ambient temperature increases, the velocity gradient and buoyancy source term decreases. Despite that, the flame increased in all directions. The results have also shown that increasing the ambient temperature, decreases the temperature gradient in the flame, which ends up affecting the flame position. / No presente trabalho, a vaporização e a combustão de uma gota de combustível isolada a diferentes temperaturas ambiente são examinadas numericamente para analisar o efeito da força de flutuação na chama. Geralmente, as gotículas de combustível em dispositivos de combustão são tão pequenas que a influência da força de flutuação na vaporização e na combustão de gotículas é insignificante. Por outro lado, as gotículas de combustível em dispositivos experimentais são afetadas pela força de flutuabilidade devido ao seu diâmetro em torno de ou mais de 1 mm. Para reduzir os efeitos de flutuabilidade, estudos experimentais caros são realizados em ambiente de microgravidade (drop-tower ou fora do espaço). Em condições de gravidade normal, a força de flutuação é induzida por gradiente de temperatura na atmosfera ambiente. A flutuabilidade é positiva em regiões de gases quentes e negativas em regiões de gases frios em comparação com o gás atmosférico ambiente. Os gases quentes movem-se para cima e os gases frios para baixo. Jogando com a força de flutuação positiva dos gases quentes ao redor da chama e com a força de flutuação negativa (fria) dos gases frios ao redor da gota através da temperatura da atmosfera ambiente, é possível modificar a forma da chama. Nas simulações numéricas, as equações de Navier-Stokes incompressíveis juntamente com a fração de mistura e as equações de conservação de entalpia em excesso são resolvidas usando uma técnica de volume finito com uma grade estruturada uniforme. Foi aplicado um método de compressibilidade artificial para alcançar soluções de estado estacionário. As previsões numéricas foram comparadas com resultados analíticos para uma condição de gravidade zero, mostrando boa concordância. Para a condição de gravidade normal, os resultados numéricos mostraram que, quando a temperatura ambiente aumenta, o gradiente de velocidade e o termo da fonte de flutuação diminuem. Apesar disso, a chama aumentou em todas as direções. Os resultados também mostraram que aumentar a temperatura ambiente, diminui o gradiente de temperatura na chama, o que acaba afetando a posição da chama.

Dans cette thèse, la dynamique d'évaporation de gouttes sessiles de solutions salines sur des surfaces planes inertes et métalliques a été étudiée et le phénomène de corrosion pour les surfaces ferriques caractérisé. En premier lieu, nous nous sommes intéressés à la dynamique d'évaporation de gouttes sessiles salées sur des surfaces inertes pour une large gamme de concentrations en sel, d'humidité relatives, de tailles de goutte et d'angles de contact. Notre étude révèle les domaines de validité du modèle classique d'évaporation, processus contrôlé par la diffusion de la vapeur dans l'air et met en évidence l'impact de flux (de Marangoni) induits par des gradients de concentration (tension de surface) en sel sur la dynamique d'évaporation et les dépôts salins obtenus après évaporation de la goutte. De plus, nous nous sommes consacrés à l'évolution spatio-temporelle de gouttes sessiles de solutions salines sur des surfaces métalliques. Contrairement au modèle simplifié de la goutte d'Evans, nous avons montré que le processus de corrosion s'étend aux abords de la ligne de contact, avec la formation d'un film périphérique. La ligne triple est déstabilisée par des gradients de tension de surface induits par des variations de composition ionique au cours du processus de corrosion et la migration des cations vers la périphérie de la goutte. Enfin nous avons étudié le phénomène de corrosion du métal induit par l'évaporation de gouttes sessiles salées. Le processus de corrosion, en particulier la localisation des réactions anodiques et cathodiques sur la surface métallique en contact avec la goutte est corrélée à la distribution spatiale du sel au sein de la goutte s'évaporant. / In this thesis we investigate the evaporation behaviour of sessile droplets of aqueous saline solutions on planar inert and metallic surfaces and characterise the corrosion phenomenon for iron surfaces. First we study the evaporation behaviour of sessile salty droplets on inert surfaces for a wide range of salt concentrations, relative humidities, droplet sizes and contact angles. Our study reveals the range of validity of the well-accepted diffusion-controlled evaporation model and highlights the impact of salt concentration (surface tension) gradients driven Marangoni flows on the evaporation behaviour and the subsequent salt deposit patterns. Furthermore we study the spatial-temporal evolution of sessile droplets from saline solutions on metallic surfaces. In contrast to the simple, generally accepted Evans droplet model, we show that the corrosion spreads ahead of the macroscopic contact line with a peripheral film. The three-phase contact line is destabilized by surface tension gradients induced by ionic composition change during the course of the corrosion process and migrations of cations towards the droplet perimeter. Finally we investigate the corrosion behaviour under drying salty sessile droplets on metallic surfaces. The corrosion process, in particular the location of anodic and cathodic activities over the footprint droplet area is correlated to the spatial distribution of the salt inside the drying droplet.

In spite of recent attention to renewable sources of energy, liquid hydrocarbon fuels are still the main source of energy for industrial and transportation systems. Manufactures and consumers are consistently looking for ways to optimize the efficiency of fuel combustion in terms of cost, emissions and consumer safety. In this regard, increasing burning rate of liquid fuels has been of special interest in both industrial and transportation systems. Recent studies have shown that adding combustible nano-particles could have promising effects on improving combustion performance of liquid fuels. Combustible nano-particles could enhance radiative and conductive heat transfer and also mixing within the droplet. Polymeric additive have also shown promising effect on improving fire safety by suppressing spreading behavior and splatter formation in case of crash scenario. Polymers are also known to have higher burning rate than regular hydrocarbon fuels. Therefore adding polymeric additive could have the potential to increase the burning rate. In this work, combustion dynamics of liquid fuel droplets with both polymeric and nanoparticle additives is studied in normal gravity. High speed photography is employed and the effect of additive concentration on droplet burning rate, burning time, extinction and soot morphology is investigated. Polymer added fuel was found to have a volatility controlled combustion with four distinct regimes. The first three zones are associated with combustion of base fuel while the polymer burns last and after a heating zone because of its higher boiling point. Polymer addition reduces the burning rate of the base fuel in the first zone by means of increasing viscosity and results in nucleate boiling and increased burning rates in the second and third stages. Overall, polymer addition resulted in a higher burning rate and shorter burning time in most of the scenarios. Colloidal suspensions of carbon-based nanomaterials in liquid fuels were also tested at different particle loadings. It was found that dispersing nanoparticles results in higher burning rate by means of enhanced radiative heat absorption and thermal conductivity. An optimum particle loading was found for each particle type at which the maximum burning rate was achieved. It was observed that the burning rate again starts to reduce after this optimum point most likely due to the formation of large aggregates that reduce thermal conductivity and suppress the diffusion of species.

This article reports the recent progress of re-search made in the Droplet-Based Manufacturing Laboratory at MIT. The study has been focused on obtaining a fundamental understanding of microdroplet deposition and applying the technology to various practical applications. Specific scientific contributions include the development of an analytical model for droplet splashing/recoiling, an in situ droplet size control methodology, and a study of microstructure design for spray forming. The research per-formed in the lab provides both fundamental knowledge base and practical process developments for a range of manufacturing applications, including electronics packaging, spray forming and freeform fabrication. / Singapore-MIT Alliance (SMA)

In this thesis, we discuss some physical phenomena related to the manipulation of droplets, and their possible use as alternatives for digital microfluidics. In a first part, the behavior of droplets in the vicinity of another liquid interface is explored. We have shown that droplets can be kept bouncing onto a liquid interface, provided this latter is vertically vibrated. The bouncing mechanisms are investigated in several configurations. Bouncing droplets may also experience self-propulsion and partial coalescence. The second part of this thesis is dedicated to the study of droplets sliding down fibers. The basic microfluidic operations are advantageously implemented with simple fiber networks. Dans cette thèse, nous discutons plusieurs phénomènes physiques liés à la manipulation des gouttes et à leur application possible en temps qu'alternatives à la microfluidique digitale actuelle. La première partie est consacrée au comportement de gouttes au voisinage d'une autre interface liquide. Nous avons prouvé qu'une goutte peut rebondir indéfiniment sur une interface liquide vibrée verticalement. Les mécanismes du rebond sont analysés en détail pour plusieurs configurations. Sous certaines conditions, les gouttes rebondissantes peuvent également s'auto-propulser ou coalescer partiellement. Dans une seconde partie, nous étudions le glissement des gouttes sur des fibres. Les opérations microfluidiques de base sont avantageusement réalisées sur de simples réseaux de fibres.

<p>This thesis addresses mass transfer in multi-phase single particle systems. By using a novel technique based upon the micropipette, the dissolution of liquid and gas droplets in a liquid medium can be observed. Three classes of experimental systems are observed: pure liquid droplet dissolution in a pure liquid environment, miscible mixture liquid droplet dissolution in a pure liquid environment, and solute-containing liquid droplet dissolution in a pure liquid environment. Experiments on the dissolution of pure droplets of water in n-alcohols and n-alkanes showed that water droplets dissolved ten times faster in the alcohols as compared to in the alkanes. When solubility was taken into account, however, and diffusion coefficients calculated using the Epstein-Plesset equation, diffusion constants for alkanes were twenty five times higher in alkanes than for the corresponding alcohol (for example 12.5 vs 0.5 x 10-8 cm2/s for pentane and pentanol). This difference in rates of diffusion of the single molecules reflects the effect of hydrogen bonding on small solute diffusion, which is expounded upon in Chapter 2.</p><p> A model for the dissolution of a droplet containing a mixture, each component of which is soluble in the surrounding liquid medium is presented in Chapter 3. The model is based upon a reduced surface area approximation and the assumption of ideal homogenous mixing : Mass flux (dm_i)/dt=&#12310;Afrac&#12311;_i D_i (c_i-c_s){1/R+1/&#8730;(&#960;D_i t)}, where Afraci is the area fraction of component i, ci and cs are the initial and saturation concentrations of the droplet material in the surrounding medium, respectively, R is the radius of the droplet, t is time, and Di is the coefficient of diffusion of component i in the surrounding medium. This model was tested for the dissolution of ethyl acetate and butyl acetate in water and the dissolution of butyl acetate and amyl acetate in water, and was found to provide a good fit. In Chapter 4, a partial differential equation, R^2/D &#9500; &#8706;c/&#8706;t&#9508;|_&#951;=(&#8733;&#951;)/D &#8706;c/&#8706;&#951;+(&#8706;^2 c)/&#12310;&#8706;&#951;&#12311;^2 +2/&#951; &#8706;c/&#8706;&#951;, is presented for the dissolution of a solute containing droplet in a liquid medium, and shell or bead formation is predicted. In Chapter 5, an application of the solute containing droplet dissolution is presented in which suspensions of glassified protein microspehres are used to improve the injectability of protein based pharmaceuticals. Injectability is related to viscosity, and the viscosity of a suspension may be predicted to follow the Krieger Dougherty equation: (&#951;(&#934;))/&#951;_0 =(1-&#934;/&#934;_m )^(-2.5&#934;_m ) , where &#934; is the volume fraction of the suspensate, &#951; is the viscosity of the overall suspension, &#951;0 is the viscosity of the suspending fluid, and &#934;m is the maximum possible volume fraction. Finally, in Chapter 6, various experimental methods used to generate droplets are addressed.</p> / Dissertation