This dissertation presents a detailed account of the study undertaken on the subject of heat and mass transfer phenomena in porous media. The current work specifically targets the general reaction-diffusion systems arising in separation processes using porous sorbent particles. These particles are comprised of pore channels spanning length scales over almost three orders of magnitude while involving a variety of physical processes such as mass diffusion, heat transfer and surface adsorption-desorption. A novel methodology is proposed in this work that combines models that account for the multi-scale and multi-physics phenomena involved. Pore-resolving DNS calculations using an immersed boundary method (IBM) framework are used to simulate the macro-scale physics while the phenomena at smaller scales are modeled using a sub-pore modeling technique. The IBM scheme developed as part of this work is applicable to complex geometries on curvilinear grids, while also being very efficient, consuming less than 1% of the total simulation time per time-step. A new method of implementing the conjugate heat transfer (CHT) boundary condition is proposed which is a direct extension of the method used for other boundary conditions and does not involve any complex interpolations like previous CHT implementations using IBM. Detailed code verification and validation studies are carried out to demonstrate the accuracy of the developed method. The developed IBM scheme is used in conjunction with a stochastic reconstruction procedure based on simulated annealing. The developed framework is tested in a two-dimensional channel with two types of porous sections - one created using a random assembly of square blocks and another using the stochastic reconstruction procedure. Numerous simulations are performed to demonstrate the capability of the developed framework. The computed pressure drops across the porous section are compared with predictions from the Darcy-Forchheimer equation for media composed of different structure sizes. The developed methodology is also applied to CO2 diffusion studies in porous spherical particles of varying porosities. For the pore channels that are unresolved by the IBM framework, a sub-pore modeling methodology developed as part of this work which solves a one-dimensional unsteady diffusion equation in a hierarchy of scales represented by a fractal-type geometry. The model includes surface adsorption-desorption, and heat generation and absorption. It is established that the current framework is useful and necessary for reaction-diffusion problems in which the adsorption time scales are very small (diffusion-limited) or comparable to the diffusion time scales. Lastly, parametric studies are conducted for a set of diffusion-limited problems to showcase the powerful capability of the developed methodology. / Ph. D.

No / The transient liquid phase bonding process has long been dealt with as a pure diffusion process at the joint interface, that is, as a mass phenomenon. In spite of the advances in the application of this technique to bond complex engineering alloys, the available models have failed to incorporate the effect of surface phenomena on the joining process. In this work, a new reaction–controlled diffusion formulation model is proposed, and the observation of experimental results of joining Al6061 alloy using thin single (50, 100 micron) and double Cu foils is recorded. This work directly unveils the unique role played by surface reaction–controlled diffusion rather than purely mass diffusion bonding process. Our experimental and modeling results reveal a conceptually new understanding that may well explain the joint formation in TLP bonding process.

Mathematical models are important tools in systems biology, since the regulatory networks in biological cells are too complicated to understand by biological experiments alone. Analytical solutions can be derived only for the simplest models and numerical simulations are necessary in most cases to evaluate the models and their properties and to compare them with measured data. This thesis focuses on the mesoscopic simulation level, which captures both, space dependent behavior by diffusion and the inherent stochasticity of cellular systems. Space is partitioned into compartments by a mesh and the number of molecules of each species in each compartment gives the state of the system. We first examine how to compute the jump coefficients for a discrete stochastic jump process on unstructured meshes from a first exit time approach guaranteeing the correct speed of diffusion. Furthermore, we analyze different methods leading to non-negative coefficients by backward analysis and derive a new method, minimizing both the error in the diffusion coefficient and in the particle distribution. The second part of this thesis investigates macromolecular crowding effects. A high percentage of the cytosol and membranes of cells are occupied by molecules. This impedes the diffusive motion and also affects the reaction rates. Most algorithms for cell simulations are either derived for a dilute medium or become computationally very expensive when applied to a crowded environment. Therefore, we develop a multiscale approach, which takes the microscopic positions of the molecules into account, while still allowing for efficient stochastic simulations on the mesoscopic level. Finally, we compare on- and off-lattice models on the microscopic level when applied to a crowded environment.

Les systèmes complexes propres à la biologie moléculaire sont des sujets d'investigations privilégiés pour la physique statistique hors équilibre. En particulier la dynamique des systèmes d'adhérents qui a déjà été l'objet de description théorique. Ces descriptions sont restreintes au comportement des plaques d'adhérence focales matures, dont la durée caractéristique est la dizaine de minutes et où beaucoup d'acteurs moléculaires différents interviennent, notamment le cortex d'actine. Cependant, la question des mécanismes moléculaires précoces, précédant la mise en place de ces structures, reste entière et ouverte. L'objectif de cette thèse est de proposer un modèle de transduction mécano-chimique bidirectionnelle — de l'intérieur de la cellule vers l'extérieur et inversement — en se basant sur le caractère allostérique de l'interaction entre les intégrines (sensibles aux propriétés des matrices extracellulalires) et un partenaire cytoplasmique activable, la taline. Ce travail se divise en trois parties : i) une modélisation du bord cellulaire qui repose sur le calcul du potentiel chimique du partenaire activable et de son cycle d'activation, ii) la résolution numérique et analytique des équations précédemment définies et iii) une évolution du précédent modèle où les intégrines sont laissés libres de diffuser et qui vont dans ce cas là se regrouper dans les zones de fortes contraintes.

Several types of instability can affect the interface between two fluids. For instance, a Rayleigh-Taylor instability (or density fingering) is encountered when a heavier fluid is placed upon a lighter one in the gravity field and double diffusive instabilities can be triggered by differential diffusivity of the different species present in the fluid. In this context our work aims to understand theoretically in which way a chemical reaction can induce and influence such instabilities in a fluid initially at rest. To understand the dynamics resulting from the coupling between chemical reactions and hydrodynamical instabilities we use chemical fronts as model systems. These fronts result from the coupling between autocatalytical chemical reactions and diffusion and they allow to create a self-organized interface between the products and the reactants. As during a chemical reaction the density may vary due to solutal and thermal effects, the products and the reactants can have different densities which may trigger convection movements leading to the destabilization of the fronts. We have in particular studied the influence of the exothermicity of the reaction on the fingering of chemical fronts, focusing first on the influence of heat losses through the walls of the set-up. These leaks have a marked influence on the dynamics because they affect the temperature profiles and hence the density profiles too. We have also classified the various types of instabilities that may appear dues to solutal and thermal effects. We have found a new type of hydrodynamic instability of statically stable fronts induced by the chemical reaction. We have furthermore analyzed an isothermal model with two chemical species. If they diffuse at different rates the front can be subject to diffusive instabilities as well. We have shown that the coupling between such a diffusive instability and fingering can trigger complex dynamics. We have eventually studied the influence of an external electric field on the diffusive instabilities and on fingering underlying the possibility to destabilize otherwise stable fronts./ Différents types d'instabilités hydrodynamiques peuvent affecter les interfaces entre deux fluides comme par exemple, une instabilité de Rayleigh-Taylor (ou digitation de densité) quand un fluide plus dense se trouve placé au-dessus d'un fluide moins dense dans le champ de gravité ou des instabilités de double diffusion induites par des différences entre les diffusivités d'un soluté et de la chaleur contenus dans les fluides. Dans ce contexte, notre thèse s'attache à comprendre de manière théorique comment une réaction chimique peut influencer ces instabilités voire les générer dans un fluide initialement au repos. Pour étudier les dynamiques résultant du couplage entre réactions chimiques et instabilités hydrodynamiques, nous utilisons des systèmes modèles: les fronts chimiques de conversion résultant de la compétition entre réactions chimiques autocatalytiques et diffusion créant une interface auto-organisée entre les réactifs et les produits. Comme au cours d'une réaction chimique la densité peut varier par des effets solutaux et thermiques, les produits et les réactifs de densités différentes peuvent générer des mouvements de convection qui conduisent à la déstabilisation des fronts. Nous avons en particulier étudié l'influence de l'exothermicité de la réaction sur les instabilités de digitation de fronts chimiques, en nous focalisant dans un premier temps sur l'influence des pertes de chaleur par les parois du réacteur. Ces fuites ont un effet marqué sur les instabilitités car elles affectent les profils de température et donc les profils de densité dans le système. Nous avons également classifié les différentes instabilités qui peuvent apparaître via des changements de densité dûs à des effets thermiques et solutaux et mis en évidence un nouveau type de déstabilisation hydrodynamique de fronts statiquement stables induit par une réaction chimique. Nous avons ensuite analysé un modèle isotherme impliquant deux espèces chimiques. Si ces dernières diffusent a des vitesses différentes le front peut être sujet à une instabilité diffusive. Nous avons montré qu'un couplage entre une telle instabilité diffusive et de la digitation peut être à l'origine de dynamiques complexes. Nous avons ensuite considéré l'influence d'un champ électrique sur les instabilité diffusives et de digitation en soulignant la possibilié de déstabiliser via ce champ des fronts initialement stables.

This thesis is concerned with mathematical modelling of oncolytic virotherapy: the use of genetically modified viruses to selectively spread, replicate and destroy cancerous cells in solid tumours. Traditional spatially-dependent modelling approaches have previously assumed that virus spread is due to viral diffusion in solid tumours, and also neglect the time delay introduced by the lytic cycle for viral replication within host cells. A deterministic, age-structured reaction-diffusion model is developed for the spatially-dependent interactions of uninfected cells, infected cells and virus particles, with the spread of virus particles facilitated by infected cell motility and delay. Evidence of travelling wave behaviour is shown, and an asymptotic approximation for the wave speed is derived as a function of key parameters. Next, the same physical assumptions as in the continuum model are used to develop an equivalent discrete, probabilistic model for that is valid in the limit of low particle concentrations. This mesoscopic, compartment-based model is then validated against known test cases, and it is shown that the localised nature of infected cell bursts leads to inconsistencies between the discrete and continuum models. The qualitative behaviour of this stochastic model is then analysed for a range of key experimentally-controllable parameters. Two-dimensional simulations of in vivo and in vitro therapies are then analysed to determine the effects of virus burst size, length of lytic cycle, infected cell motility, and initial viral distribution on the wave speed, consistency of results and overall success of therapy. Finally, the experimental difficulty of measuring the effective motility of cells is addressed by considering effective medium approximations of diffusion through heterogeneous tumours. Considering an idealised tumour consisting of periodic obstacles in free space, a two-scale homogenisation technique is used to show the effects of obstacle shape on the effective diffusivity. A novel method for calculating the effective continuum behaviour of random walks on lattices is then developed for the limiting case where microscopic interactions are discrete.

The thesis presents a comprehensive study of a posteriori error estimation in the adaptive solution to some classical elliptic partial differential equations. Several new error estimators are proposed for diffusion problems with discontinuous coefficients and for convection-reaction-diffusion problems with dominated convection/reaction. The robustness of the new estimators is justified theoretically. Extensive numerical results demonstrate the robustness of the new estimators for challenging problems and indicate that, compared to the well-known residual-type estimators, the new estimators are much more accurate.

Small devices capable of self-propulsion have potential application in areas of nanoscience where autonomous locomotion and programmability are needed. The specific base-pairing interactions that arise from DNA hybridisation permit the programmed assembly of matter and also the creation of controllable dynamical systems. The aim of this thesis is to use the tools of DNA nanotechnology to design synthetic active matter at the micro and nano scales. In the first section, DNA was used as an active medium capable of transporting information faster than diffusion in the form of chemical waves. DNA waves were generated experimentally using a DNA autocatalytic reaction in a microfluidic channel. The propagation velocity of DNA chemical waves was slowed down by creating concentration gradients that changed the reaction kinetics in space. The second section details the synthesis of chemically-propelled particles and the use of DNA as a 'programmable glue' to mediate their interactions. Janus micromotors were fabricated by physical vapour deposition and a wet-chemical approach was demonstrated to synthesise asymmetrical catalytic Pt-Au nanoparticles that function as nanomotors. Dynamic light scattering measurements showed nanomotor activity that depends on H₂O₂ concentration, consistent with chemical propulsion. Gold nanoparticles/Origami hybrids were assembled in 2D lattices of different symmetries arranged by DNA linkers. The third section details the design process and synthesis of nanomotors using DNA as a structural scaffold. 3D DNA Origami rectangular prisms were functionalised site-specifically with bioconjugated catalysts, i.e. Pt nanoparticles and catalase. Enzymatic nanomotors were also conjugated to various cargoes and their motor activity was demonstrated by Fluorescence Correlation Spectroscopy. In the final section, control mechanisms for autonomous nanomotors are studied, which includes the conformational change of DNA aptamers in response to chemical signals, as well as a design for an adaptive dynamical system based on DNA/enzyme reaction networks.

University of Macau / Faculty of Science and Technology / Department of Mathematics

Se presenta un modelo matemático para el diseño y simulación de un reactor de lecho fijo con enzimas inmovilizadas en partículas esféricas porosas. La ecuación de diseño del reactor se ha resuelto para el caso de un sistema enzimático, con limitaciones difusionales internas, que obedece a una cinética de Michaelis-Menten reversible.La validez del modelo se ha comprobado con el sistema enzimático naringina/naringinasa, aplicable al proceso de desamargado de zumos cítricos. / A mathematical model for design and simulation of a fixed bed reactor with immobilized enzymes in spherical particles is presented. The reactor design equation is solved for an enzymatic system taking into account internal diffusional limitations. Moreover, the enzyme obeys a reversible Michaelis-Menten kinetic. The validity of the model is checked by using the enzymatic system naringine/naringinase, which is used for fruit juice debbitering processes.