Target-specific multiphysics modeling for thermal medicine applications

Dissertation to obtain the degree of Doctor of Philosophy in Biomedical Engineering

Vasopressin-dependent coupling between sodium transport and water flow in a mouse cortical collecting duct cell line.

Water balance is achieved through the ability of the kidney to control water reabsorption in the connecting tubule and the collecting duct. In a mouse cortical collecting duct cell line (mCCD(c11)), physiological concentrations of arginine vasopressin increased both electrogenic, amiloride-sensitive, epithelial sodium channel (ENaC)-mediated sodium transport measured by the short-circuit current (Isc) method and water flow (Jv apical to basal) measured by gravimetry with similar activation coefficient K(1/2) (6 and 12 pM, respectively). Jv increased linearly according to the osmotic gradient across the monolayer. A small but highly significant Jv was also measured under isoosmotic conditions. To test the coupling between sodium reabsorption and water flow, mCCD(c11) cells were treated for 24 h under isoosmotic condition with either diluent, amiloride, vasopressin or vasopressin and amiloride. Isc, Jv, and net chemical sodium fluxes were measured across the same monolayers. Around 30% of baseline and 50% of vasopressin-induced water flow is coupled to an amiloride-sensitive, ENaC-mediated, electrogenic sodium transport, whereas the remaining flow is coupled to an amiloride-insensitive, nonelectrogenic sodium transport mediated by an unknown electroneutral transporter. The mCCD(c11) cell line is a first example of a mammalian tight epithelium allowing quantitative study of the coupling between sodium and water transport. Our data are consistent with the 'near isoosmotic' fluid transport model.

Modeling of non-isothermalvapor membrane separation with thermodynamic models and generalized mass transfer equations

A rigorous unit operation model is developed for vapor membrane separation. The new model is able to describe temperature, pressure, and concentration dependent permeation as wellreal fluid effects in vapor and gas separation with hydrocarbon selective rubbery polymeric membranes. The permeation through the membrane is described by a separate treatment of sorption and diffusion within the membrane. The chemical engineering thermodynamics is used to describe the equilibrium sorption of vapors and gases in rubbery membranes with equation of state models for polymeric systems. Also a new modification of the UNIFAC model is proposed for this purpose. Various thermodynamic models are extensively compared in order to verify the models' ability to predict and correlate experimental vapor-liquid equilibrium data. The penetrant transport through the selective layer of the membrane is described with the generalized Maxwell-Stefan equations, which are able to account for thebulk flux contribution as well as the diffusive coupling effect. A method is described to compute and correlate binary penetrant¿membrane diffusion coefficients from the experimental permeability coefficients at different temperatures and pressures. A fluid flow model for spiral-wound modules is derived from the conservation equation of mass, momentum, and energy. The conservation equations are presented in a discretized form by using the control volume approach. A combination of the permeation model and the fluid flow model yields the desired rigorous model for vapor membrane separation. The model is implemented into an inhouse process simulator and so vapor membrane separation may be evaluated as an integralpart of a process flowsheet.

Design and implementation of a multipurpose reactor for scale-up studies

In the theoretical part, the different polymerisation catalysts are introduced and the phenomena related to mixing in the stirred tank reactor are presented. Also the advantages and challenges related to scale-up are discussed. The aim of the applied part was to design and implement an intermediate-sized reactor useful for scale-up studies. The reactor setting was tested making one batch of Ziegler–Natta polypropylene catalyst. The catalyst preparation with a designed equipment setting succeeded and the catalyst was analysed. The analyses of the catalyst were done, because the properties of the catalyst were compared to the normal properties of Ziegler–Natta polypropylene catalyst. The total titanium content of the catalyst was slightly higher than in normal Ziegler–Natta polypropylene catalyst, but the magnesium and aluminium content of the catalyst were in the normal level. By adjusting the siphonation tube and adding one washing step the titanium content of the catalyst could be decreased. The particle size of the catalyst was small, but the activity was in a normal range. The size of the catalyst particles could be increased by decreasing the stirring speed. During the test run, it was noticed that some improvements for the designed equipment setting could be done. For example more valves for the chemical feed line need to be added to ensure inert conditions during the catalyst preparation. Also nitrogen for the reactor needs to separate from other nitrogen line. With this change the pressure in the reactor can be kept as desired during the catalyst preparation. The proposals for improvements are presented in the applied part. After these improvements are done, the equipment setting is ready for start-up. The computational fluid dynamics model for the designed reactor was provided by cooperation with Lappeenranta University of Technology. The experiments showed that for adequate mixing with one impeller, stirring speed of 600 rpm is needed. The computational fluid dynamics model with two impellers showed that there was no difference in the mixing efficiency if the upper impeller were pumping downwards or upwards.

Rheological properties of oil-in-water emulsions prepared with oil and protein isolates from sesame (Sesamum Indicum)

In this study, food emulsions of oil in water from sesame (Sesamum indicum) protein isolates and their oil were formulated and standardised. The effect of the concentrations of sesame (Sesamum indicum) protein isolates and base oil and the speed of the emulsification process for the food emulsion stability was studied. The protein isolates were achieved from the defatted sesame flour (DSF), obtaining a percentage of 80% ± 0.05% of protein. Emulsions were formulated through a factorial design 23. The rheological behaviour of sesame (Sesamum indicum) protein isolates-stabilised emulsions and microstructural composition were investigated. Stable emulsions with suitable rheological properties and microstructure were formulated at a concentration of 10% sesame oil and different concentrations of protein isolates, between 1.5% and 2.5%, with the best droplet distribution characteristics being shown for the 2.5% sesame protein isolates. The emulsions showed a non-Newtonian fluid behaviour, adjusting the Sisko model.

Community strategies in England: reshaping spaces of governance?

The preparation of Community Strategies (CS) has been required of LSPs and Local Authorities in England since the passing of the Local Government Act 2000. This paper examines the process and content of two Community Strategies in southern England as part of an ongoing project to understand their impact and explore ways that CSs may be carried through in a meaningful and effective manner. The paper concludes that the two CSs studied illustrate the challenge faced by LSPs in producing Strategies that are meaningful, inclusive and which follow the spirit of the government CS guidance. LAs and LSPs are also posed with a difficult challenge of seeing through an implicitly required transition from a traditional representative democratic structure/process with a more fluid participatory model. Thus we detect that at least two forms of conflict may arise – firstly with elected councillors threatened by a loss of power and secondly between communities and the LAs who are encouraged to problematise local policy and service delivery in the context of limited resource availability.

Modelagem analítica e experimental da filtração em meios porosos

Deep bed filtration occurs in several industrial and environmental processes like water filtration and soil contamination. In petroleum industry, deep bed filtration occurs near to injection wells during water injection, causing injectivity reduction. It also takes place during well drilling, sand production control, produced water disposal in aquifers, etc. The particle capture in porous media can be caused by different physical mechanisms (size exclusion, electrical forces, bridging, gravity, etc). A statistical model for filtration in porous media is proposed and analytical solutions for suspended and retained particles are derived. The model, which incorporates particle retention probability, is compared with the classical deep bed filtration model allowing a physical interpretation of the filtration coefficients. Comparison of the obtained analytical solutions for the proposed model with the classical model solutions allows concluding that the larger the particle capture probability, the larger the discrepancy between the proposed and the classical models

Modelagem e previsão da perda de injetividade em poços canhoneados

Waterflooding is a technique largely applied in the oil industry. The injected water displaces oil to the producer wells and avoid reservoir pressure decline. However, suspended particles in the injected water may cause plugging of pore throats causing formation damage (permeability reduction) and injectivity decline during waterflooding. When injectivity decline occurs it is necessary to increase the injection pressure in order to maintain water flow injection. Therefore, a reliable prediction of injectivity decline is essential in waterflooding projects. In this dissertation, a simulator based on the traditional porous medium filtration model (including deep bed filtration and external filter cake formation) was developed and applied to predict injectivity decline in perforated wells (this prediction was made from history data). Experimental modeling and injectivity decline in open-hole wells is also discussed. The injectivity of modeling showed good agreement with field data, which can be used to support plan stimulation injection wells

Comparability of results from two leakage models

Objective. The goal of this study was to check whether leakage results of the same specimens measured by 2 different leakage models are similar.Study design. Canine root canals were prepared and filled with cold gutta-percha cones and 1 of 4 sealers (20 canals for each sealer). The 80 specimens were first connected to a fluid transport model where air-bubble movement was measured. The same specimens were later connected to a glucose penetration model where the concentration of glucose was measured. In both models, a headspace pressure of 30 kPa was used to accelerate leakage.Results. In both models, 4 sealers ranked the same regarding the leakage they allowed, and a significant correlation between the results of the 2 models was confined (Spearman test coefficient = 0.65; P = .000001).Conclusion. Under the conditions of this study, leakage results of 80 specimens recorded in the fluid transport model and glucose penetration model were similar.

Effect of acid fruit juices combined with electric or sonic toothbrushing on root dentin permeability - An in vitro study

The purpose of this in vitro study was to quantify the alterations on human root dentin permeability after exposure to different acid fruit juices and to evaluate the effect of toothbrushing with electric or sonic toothbrush after acid exposure. The root dentin of 50 extracted third molars was exposed with a high speed bur. Crowns were sectioned above the cementoenamel junction and root fragments were used to prepare dentin specimens. Specimens were randomly assigned to 5 groups according to the fruit juice (kiwifruit, starfruit, green apple, pineapple and acerolla). Each specimen was connected to a hydraulic pressure apparatus to measure root dentin permeability using fluid filtration method after the following sequential steps: I) conditioning with 37% phosphoric acid for 30 s, II) root scaling, III) exposure to acid fruit juices for 5 min and IV) electric or sonic toothbrushing without dentifrice for 3 min. Data were analyzed statistically by the Wilcoxon and Mann-Whitney tests at 5% significance level. All fruit juices promoted a significant increase of dentin permeability while toothbrushing decreased it significantly (p<0.05). It may be concluded that all acid fruit juices increased root dentin permeability, while toothbrushing without dentifrice after acid exposure decreased the permeability. The toothbrush mechanism (electric or sonic) had no influence on the decrease of root dentin permeability.

Differential orthogonality: Laguerre and Hermite cases with applications

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Análise da interface adesiva entre pinos de fibra de vidro e dentina intrarradicular submetida à irrigação com diferentes agentes condicionantes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Plasma environment of a weak comet – Predictions for Comet 67P/Churyumov–Gerasimenko from multifluid-MHD and Hybrid models

The interaction of a comet with the solar wind undergoes various stages as the comet’s activity varies along its orbit. For a comet like 67P/Churyumov–Gerasimenko, the target comet of ESA’s Rosetta mission, the various features include the formation of a Mach cone, the bow shock, and close to perihelion even a diamagnetic cavity. There are different approaches to simulate this complex interplay between the solar wind and the comet’s extended neutral gas coma which include magnetohydrodynamics (MHD) and hybrid-type models. The first treats the plasma as fluids (one fluid in basic single fluid MHD) and the latter treats the ions as individual particles under the influence of the local electric and magnetic fields. The electrons are treated as a charge-neutralizing fluid in both cases. Given the different approaches both models yield different results, in particular for a low production rate comet. In this paper we will show that these differences can be reduced when using a multifluid instead of a single-fluid MHD model and increase the resolution of the Hybrid model. We will show that some major features obtained with a hybrid type approach like the gyration of the cometary heavy ions and the formation of the Mach cone can be partially reproduced with the multifluid-type model.

Sulphate concentrations and sulphur isotopic composition in pore fluids from ODP Leg 168 sites

A numerical model of sulfate reduction and isotopic fractionation has been applied to pore fluid SO4**2- and d34S data from four sites drilled during Ocean Drilling Program (ODP) Leg 168 in the Cascadia Basin at 48°N, where basement temperatures reach up to 62°C. There is a source of sulfate both at the top and the bottom of the sediment column due to the presence of basement fluid flow, which promotes bacterial sulfate reduction below the sulfate minimum zone at elevated temperatures. Pore fluid d34S data show the highest values (135 per mil) yet found in the marine environment. The bacterial sulfur isotopic fractionation factor, a, is severely underestimated if the pore fluids of anoxic marine sediments are assumed to be closed systems and Rayleigh fractionation plots yield erroneous values for a by as much as 15 per mil in diffusive and advective pore fluid regimes. Model results are consistent with a = 1.077+/-0.007 with no temperature effect over the range 1.8 to 62°C and no effect of sulfate reduction rate over the range 2 to 10 pmol/ccm/day. The reason for this large isotopic fractionation is unknown, but one difference with previous studies is the very low sulfate reduction rates recorded, about two orders of magnitude lower than literature values that are in the range of µmol/ccm/day to tens of nmol/ccm/day. In general, the greatest 34S depletions are associated with the lowest sulfate reduction rates and vice versa, and it is possible that such extreme fractionation is a characteristic of open systems with low sulfate reduction rates.

Numerical Error Prediction and its applications in CFD using tau-estimation

Nowadays, Computational Fluid Dynamics (CFD) solvers are widely used within the industry to model fluid flow phenomenons. Several fluid flow model equations have been employed in the last decades to simulate and predict forces acting, for example, on different aircraft configurations. Computational time and accuracy are strongly dependent on the fluid flow model equation and the spatial dimension of the problem considered. While simple models based on perfect flows, like panel methods or potential flow models can be very fast to solve, they usually suffer from a poor accuracy in order to simulate real flows (transonic, viscous). On the other hand, more complex models such as the full Navier- Stokes equations provide high fidelity predictions but at a much higher computational cost. Thus, a good compromise between accuracy and computational time has to be fixed for engineering applications. A discretisation technique widely used within the industry is the so-called Finite Volume approach on unstructured meshes. This technique spatially discretises the flow motion equations onto a set of elements which form a mesh, a discrete representation of the continuous domain. Using this approach, for a given flow model equation, the accuracy and computational time mainly depend on the distribution of nodes forming the mesh. Therefore, a good compromise between accuracy and computational time might be obtained by carefully defining the mesh. However, defining an optimal mesh for complex flows and geometries requires a very high level expertize in fluid mechanics and numerical analysis, and in most cases a simple guess of regions of the computational domain which might affect the most the accuracy is impossible. Thus, it is desirable to have an automatized remeshing tool, which is more flexible with unstructured meshes than its structured counterpart. However, adaptive methods currently in use still have an opened question: how to efficiently drive the adaptation ? Pioneering sensors based on flow features generally suffer from a lack of reliability, so in the last decade more effort has been made in developing numerical error-based sensors, like for instance the adjoint-based adaptation sensors. While very efficient at adapting meshes for a given functional output, the latter method is very expensive as it requires to solve a dual set of equations and computes the sensor on an embedded mesh. Therefore, it would be desirable to develop a more affordable numerical error estimation method. The current work aims at estimating the truncation error, which arises when discretising a partial differential equation. These are the higher order terms neglected in the construction of the numerical scheme. The truncation error provides very useful information as it is strongly related to the flow model equation and its discretisation. On one hand, it is a very reliable measure of the quality of the mesh, therefore very useful in order to drive a mesh adaptation procedure. On the other hand, it is strongly linked to the flow model equation, so that a careful estimation actually gives information on how well a given equation is solved, which may be useful in the context of _ -extrapolation or zonal modelling. The following work is organized as follows: Chap. 1 contains a short review of mesh adaptation techniques as well as numerical error prediction. In the first section, Sec. 1.1, the basic refinement strategies are reviewed and the main contribution to structured and unstructured mesh adaptation are presented. Sec. 1.2 introduces the definitions of errors encountered when solving Computational Fluid Dynamics problems and reviews the most common approaches to predict them. Chap. 2 is devoted to the mathematical formulation of truncation error estimation in the context of finite volume methodology, as well as a complete verification procedure. Several features are studied, such as the influence of grid non-uniformities, non-linearity, boundary conditions and non-converged numerical solutions. This verification part has been submitted and accepted for publication in the Journal of Computational Physics. Chap. 3 presents a mesh adaptation algorithm based on truncation error estimates and compares the results to a feature-based and an adjoint-based sensor (in collaboration with Jorge Ponsín, INTA). Two- and three-dimensional cases relevant for validation in the aeronautical industry are considered. This part has been submitted and accepted in the AIAA Journal. An extension to Reynolds Averaged Navier- Stokes equations is also included, where _ -estimation-based mesh adaptation and _ -extrapolation are applied to viscous wing profiles. The latter has been submitted in the Proceedings of the Institution of Mechanical Engineers, Part G: Journal of Aerospace Engineering. Keywords: mesh adaptation, numerical error prediction, finite volume Hoy en día, la Dinámica de Fluidos Computacional (CFD) es ampliamente utilizada dentro de la industria para obtener información sobre fenómenos fluidos. La Dinámica de Fluidos Computacional considera distintas modelizaciones de las ecuaciones fluidas (Potencial, Euler, Navier-Stokes, etc) para simular y predecir las fuerzas que actúan, por ejemplo, sobre una configuración de aeronave. El tiempo de cálculo y la precisión en la solución depende en gran medida de los modelos utilizados, así como de la dimensión espacial del problema considerado. Mientras que modelos simples basados en flujos perfectos, como modelos de flujos potenciales, se pueden resolver rápidamente, por lo general aducen de una baja precisión a la hora de simular flujos reales (viscosos, transónicos, etc). Por otro lado, modelos más complejos tales como el conjunto de ecuaciones de Navier-Stokes proporcionan predicciones de alta fidelidad, a expensas de un coste computacional mucho más elevado. Por lo tanto, en términos de aplicaciones de ingeniería se debe fijar un buen compromiso entre precisión y tiempo de cálculo. Una técnica de discretización ampliamente utilizada en la industria es el método de los Volúmenes Finitos en mallas no estructuradas. Esta técnica discretiza espacialmente las ecuaciones del movimiento del flujo sobre un conjunto de elementos que forman una malla, una representación discreta del dominio continuo. Utilizando este enfoque, para una ecuación de flujo dado, la precisión y el tiempo computacional dependen principalmente de la distribución de los nodos que forman la malla. Por consiguiente, un buen compromiso entre precisión y tiempo de cálculo se podría obtener definiendo cuidadosamente la malla, concentrando sus elementos en aquellas zonas donde sea estrictamente necesario. Sin embargo, la definición de una malla óptima para corrientes y geometrías complejas requiere un nivel muy alto de experiencia en la mecánica de fluidos y el análisis numérico, así como un conocimiento previo de la solución. Aspecto que en la mayoría de los casos no está disponible. Por tanto, es deseable tener una herramienta que permita adaptar los elementos de malla de forma automática, acorde a la solución fluida (remallado). Esta herramienta es generalmente más flexible en mallas no estructuradas que con su homóloga estructurada. No obstante, los métodos de adaptación actualmente en uso todavía dejan una pregunta abierta: cómo conducir de manera eficiente la adaptación. Sensores pioneros basados en las características del flujo en general, adolecen de una falta de fiabilidad, por lo que en la última década se han realizado grandes esfuerzos en el desarrollo numérico de sensores basados en el error, como por ejemplo los sensores basados en el adjunto. A pesar de ser muy eficientes en la adaptación de mallas para un determinado funcional, este último método resulta muy costoso, pues requiere resolver un doble conjunto de ecuaciones: la solución y su adjunta. Por tanto, es deseable desarrollar un método numérico de estimación de error más asequible. El presente trabajo tiene como objetivo estimar el error local de truncación, que aparece cuando se discretiza una ecuación en derivadas parciales. Estos son los términos de orden superior olvidados en la construcción del esquema numérico. El error de truncación proporciona una información muy útil sobre la solución: es una medida muy fiable de la calidad de la malla, obteniendo información que permite llevar a cabo un procedimiento de adaptación de malla. Está fuertemente relacionado al modelo matemático fluido, de modo que una estimación precisa garantiza la idoneidad de dicho modelo en un campo fluido, lo que puede ser útil en el contexto de modelado zonal. Por último, permite mejorar la precisión de la solución resolviendo un nuevo sistema donde el error local actúa como término fuente (_ -extrapolación). El presenta trabajo se organiza de la siguiente manera: Cap. 1 contiene una breve reseña de las técnicas de adaptación de malla, así como de los métodos de predicción de los errores numéricos. En la primera sección, Sec. 1.1, se examinan las estrategias básicas de refinamiento y se presenta la principal contribución a la adaptación de malla estructurada y no estructurada. Sec 1.2 introduce las definiciones de los errores encontrados en la resolución de problemas de Dinámica Computacional de Fluidos y se examinan los enfoques más comunes para predecirlos. Cap. 2 está dedicado a la formulación matemática de la estimación del error de truncación en el contexto de la metodología de Volúmenes Finitos, así como a un procedimiento de verificación completo. Se estudian varias características que influyen en su estimación: la influencia de la falta de uniformidad de la malla, el efecto de las no linealidades del modelo matemático, diferentes condiciones de contorno y soluciones numéricas no convergidas. Esta parte de verificación ha sido presentada y aceptada para su publicación en el Journal of Computational Physics. Cap. 3 presenta un algoritmo de adaptación de malla basado en la estimación del error de truncación y compara los resultados con sensores de featured-based y adjointbased (en colaboración con Jorge Ponsín del INTA). Se consideran casos en dos y tres dimensiones, relevantes para la validación en la industria aeronáutica. Este trabajo ha sido presentado y aceptado en el AIAA Journal. También se incluye una extensión de estos métodos a las ecuaciones RANS (Reynolds Average Navier- Stokes), en donde adaptación de malla basada en _ y _ -extrapolación son aplicados a perfiles con viscosidad de alas. Este último trabajo se ha presentado en los Actas de la Institución de Ingenieros Mecánicos, Parte G: Journal of Aerospace Engineering. Palabras clave: adaptación de malla, predicción del error numérico, volúmenes finitos