Recent clinical findings in chronic myeloid leukemia (CML) patients suggest that the risk of molecular recurrence after stopping tyrosine kinase inhibitor (TKI) treatment substantially depends on an individual’s leukemia-specific immune response. However, it is still not possible to prospectively identify patients that will remain in treatment-free remission (TFR). Here, we used an ordinary differential equation (ODE) model for CML, which explicitly includes an anti-leukemic immunological effect and applied it to 21 CML patients for whom BCR-ABL1/ABL1 time courses had been quantified before and after TKI cessation. Immunological control was conceptually necessary to explain TFR as observed in about half of the patients. Fitting the model simulations to data, we identified patient-specific parameters and classified patients into three different groups according to their predicted immune system configuration ('immunological landscapes”). While one class of patients required complete CML eradication to achieve TFR, other patients were able to control residual leukemia levels after treatment cessation. Among them were a third class of patients, that maintained TFR only if an optimal balance between leukemia abundance and immunological activation was achieved before treatment cessation. Model simulations further suggested that changes in the BCR-ABL1 dynamics resulting from TKI dose reduction convey information about the patient-specific immune system and allow prediction of outcome after treatment cessation. This inference of individual immunological configurations based on treatment alterations can also be applied to other cancer types in which the endogenous immune system supports maintenance therapy, long-term disease control or even cure.

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No description available.

In vitro tissue engineering is a method for developing living and functional tissues external to the body, often within a device called a bioreactor to control the chemical and mechanical environment. However, the quality of bone tissue engineered products is currently inadequate for clinical use as the implant cannot bear weight. In an effort to improve the quality of the construct, hydrostatic pressure, the pressure in a fluid at equilibrium that is required to balance the force exerted by the weight of the fluid above, has been investigated as a mechanical stimulus for promoting extracellular matrix deposition and mineralisation within bone tissue. Thus far, little research has been performed into understanding the response of bone tissue cells to mechanical stimulation. In this thesis we investigate an in vitro bone tissue engineering experimental setup, whereby human mesenchymal stem cells are seeded within a collagen gel and cultured in a hydrostatic pressure bioreactor. In collaboration with experimentalists a suite of mathematical models of increasing complexity is developed and appropriate numerical methods are used to simulate these models. Each of the models investigates different aspects of the experimental setup, from focusing on global quantities of interest through to investigating their detailed local spatial distribution. The aim of this work is to increase understanding of the underlying physical processes which drive the growth and development of the construct, and identify which factors contribute to the highly heterogeneous spatial distribution of the mineralised extracellular matrix seen experimentally. The first model considered is a purely temporal model, where the evolution of cells, solid substrate, which accounts for the initial collagen scaffold and deposited extracellular matrix along with attendant mineralisation, and fluid in response to the applied pressure are examined. We demonstrate that including the history of the mechanical loading of cells is important in determining the quantity of deposited substrate. The second and third models extend this non-spatial model, and examine biochemically and biomechanically-induced spatial patterning separately. The first of these spatial models demonstrates that nutrient diffusion along with nutrient-dependent mass transfer terms qualitatively reproduces the heterogeneous spatial effects seen experimentally. The second multiphase model is used to investigate whether the magnitude of the shear stresses generated by fluid flow, can qualitatively explain the heterogeneous mineralisation seen in the experiments. Numerical simulations reveal that the spatial distribution of the fluid shear stress magnitude is highly heterogeneous, which could be related to the spatial heterogeneity in the mineralisation seen experimentally.

A produção de petróleo no pré-sal pode ser associada a contaminantes como o CO2. As plataformas instaladas neste polo possuem o sistema de remoção de CO2 usando permeação em membrana polimérica, que separa a corrente de gás em uma pobre em CO2 e outra rica neste. Este trabalho propõe um modelo para simulação da separação de gases utilizando permeador de gases do tipo espiral em contra-corrente. Este modelo utiliza equações baseadas em fenômenos de transporte e termodinâmica, tais como: comportamento real dos gases, variação da permeância com temperatura, transferência de calor dentro do equipamento e efeito Joule-Thomson. A validação foi feita utilizando dados da literatura para separações isotérmicas e dados obtidos em permeador instalado em plataforma de petróleo. Utilizou-se metodologia de reconciliação de dados e agrupamento para tratamento dos dados industriais, o que permitiu maior eficiência na reconciliação dos parâmetros do modelo. A partir da modelagem proposta determinaram-se os parâmetros de processos mais relevantes, permitindo a simulação de condições operacionais diferentes das utilizadas na regressão e a verificação da influência da variação de cada uma das condições operacionais. / The production of oil in pre-salt field is associated with contaminants such as CO2. The rigs installed in this field have a CO2 removal system using permeation on polymer membrane, which separates the gas stream in a stream with low CO2 content and another one with high CO2 content. This paper proposes a model for simulation of gas separation using spiral type permeator of gases in countercurrent flow. This model uses equations based on transport and thermodynamic phenomena such as: real behavior of gases, permeance dependence with temperature, heat transfer inside the equipment and Joule-Thomson effect. The validation was performed using literature data for isothermal separations and data from permeator installed on the oil rig. Was used data reconciliation methodology and clusterization for treatment of industrial data, allowing more efficient reconciliation of the model parameters. From the proposed model were determined the most relevant process parameters, allowing the simulation of operating conditions different than those used in the regression and verification of the influence of the change of each of the operating conditions.

Limitation of conventional machining equipment has become a growing concern over the past two decades due to the demands for greater machining accuracy in today’s manufacturing. The development of micro-machining has therefore attracted significant attention; it signifies the advancement of national economy as well as the level of accuracy manufacturing industry could achieve. While the connection between tool lifespan, cost of machining and throughput is well established, the factor of tool lifespan appears to have more significance since the miniaturization of tool could lead to further performance concerns such as its lack of strength and durability. On the other hand, raising feed rate and spindle rotation speed are the two common approaches for increasing manufacturing throughput. Such approaches tend to cause an increase in the thrust force subjecting the tool to greater stress, which is the main cause of tool wear and even tool failure. Through literature review and preliminary experiments, it was found that spot-drill is often done prior to micro-drilling since it prepares a pre-drill countersunk hole that helps the alignment of tool for subsequent micro-drilling. Although such pre-drill step does improve the micro-drilling operation, the fundamental issue of tool diameter difference still remains. Often the tool used for pre-drill has a bigger diameter than the one for micro-drilling although a significant difference is always something to be avoided. This is because the difference has to be picked up by the tool used for micro-drilling and is directly linked to the wear caused by increased thrust force. In this research the operation of micro-drilling is investigated via mathematical models. Such operation is further broken down into various steps and stages so more detailed description can be achieved. The findings are then further enhanced by simulation based on the 3D model of micro-drilling. Three materials were selected for this research: Al 6061T, Al/Cu metal alloy panel and Carbon fibre reinforced composites. Such a selection enables the study of individual characteristics of different materials and the variation in respective thrust forces. Finally, Conclusions present the summary of the main findings from micro-drilling process analysis based on research and investigation shown in earlier chapters. By combining actual measurements on micro-drilling and mathematic model this research hopefully would improve the understanding towards micro-drilling processes.

Cerebrovascular diseases are by far the largest causes of death in the UK, as well as one of the leading causes of adult disability. The brain's healthy function depends on a steady supply of oxygen, delivered through the microvasculature. Cerebrovascular diseases, such as stroke and dementia, can interrupt the transport of blood (and hence oxygen) rapidly, or over a prolonged period of time. An interruption in flow can lead to ischaemia, with prolonged interruptions leading to tissue death and eventual brain damage. The microvasculature plays a key role in the transport of oxygen and nutrients to brain tissue; however, its role in diseases such as dementia is poorly understood, primarily due to the inability of current clinical imaging techniques to resolve microvessels, and due to the complexity of the underlying microvasculature. Therefore, in order to understand cerebrovascular diseases, it is necessary to be able to resolve and understand the microvasculature. In particular, generating large-scale models of the human microvasculature that can be linked back to contemporary clinical imaging is important in helping plug the current imaging gap that exists. A novel statistical model is proposed here that generates such large-scale models efficiently. Homogenization theory is used to generate a porous continuum capillary bed (characterised by its permeability) that allows for the efficient scaling up of the microvasculature. A novel order-based density-filling algorithm is then developed which generates morphologically accurate penetrating arterioles and venules, also demonstrating that the topology of the vessels only has a minor influence on CBF compared to diameter. Finally, the capillary bed and penetrating vessels are coupled into a large voxel-sized model of the microvasculature from which pressure and flux variations through the voxel can be analysed. A decoupling of the pressure and flux, as well as a layering of flow, was observed within the voxel, driven by the topology of the penetrating vessels. Micro-infarctions were also simulated, demonstrating the large local effects they have on the pressure and flux, whilst only causing a minor drop in CBF within the voxel.

Living cells are made up of networks of interacting genes, proteins and other bio-molecules. Simple interactions between network components in forms of feedback regulations can lead to complex collective dynamics. A key task in cell biology is to gain a thorough understanding of the dynamics of intracellular systems and processes. In this thesis, a combined approach of mathematical modelling, computational simulation and analytical techniques, has been used to obtain a deeper insight into the dynamical aspects of a variety of feedback systems commonly encountered in cells. These systems range from model system with detailed available molecular knowledge to general regulatory motifs with varying network structures. Deterministic as well as stochastic modelling techniques have been employed, depending primarily on the specific questions asked. The first part of the thesis focuses on dissecting the principles behind the regulatory design of the Tryptophan Operon system in Escherichia coli. It has evolved three negative feedback loops, namely repression, attenuation and enzyme inhibition, as core regulator mechanisms to control the intracellular level of tryptophan amino acid, which is taken up for protein synthesis. Despite extensive experimental knowledge, the roles of these seemingly redundant loops remain unclear from a dynamical point of view. We aim to understand why three loops, rather than one, have evolved. Using a large-scale perturbation/response analysis through modelling and simulations and novel metrics for transient dynamics quantification, it has been revealed that the multiple negative feedback loops employed by the tryptophan operon are not redundant. In fact, they have evolved to concertedly give rise to a much more efficient, adaptive and stable system, than any single mechanism would provide. Since even the full topology of feedback interactions within a network is insufficient to determine its behavioural dynamics, other factors underlying feedback loops must be characterised to better predict system dynamics. In the second part of the thesis, we aim to derive these factors and explore how they shape system dynamics. We develop an analytical approach for stability and bifurcation analysis and apply it to class of feedback systems commonly encountered in cells. Our analysis showed that the strength and the Hill coefficient of a feedback loop play key role in determining the dynamics of the system carrying the loop. Not only that, the position of the loop was also found to be crucial in this decision. The analytical method we developed also facilitates parameter sensitivity analysis in which we investigate how the production and degradation rates affect system dynamics. We find that these rates are quite different in the way they shape up system behaviour, with the degradation rates exhibiting a more intricate manner. We demonstrated that coupled-loop systems display greater complexity and a richer repertoire of behaviours in comparison with single-loop ones. Different combinations of the feedback strengths of individual loops give rise to different dynamical regimes. The final part of the thesis aims to understand the effects of molecular noise on dynamics of specific systems, in this case the Tryptophan Operon. We developed two stochastic models for the system and compared their predictions to those given by the deterministic model. By means of simulations, we have shown that noise can induce oscillatory behaviour. On the other hand, incorporating noise in an oscillatory system can alter the characteristics of oscillation by shifting the bifurcation point of certain parameters by a substantial amount. Measurement of fluctuations reveals that that noise at the transcript level is most significant while noise at the enzyme level is smallest. This study highlights that noise should not be neglected if we want to obtain a complete understanding of the dynamic behaviour of cells.

A goal of the Swedish government is to increase the usage of renewable fuels and biomass-based fuels. Fuel cells, and especially the MCFC, are useful for these types of fuels. The Swedish market may benefit from the MCFC in two ways: increased efficiency of the biofuels and also utilisation of produced heat in district heating. Most of the commercial MCFC systems today are optimised for use with methane. The possibility to utilise biomass in Sweden makes it important to study how the MCFC may be adapted or optimised for good performance and low degradation with gas produced from biomass or other renewable fuels. This thesis is focused on methods that may be used to investigate and evaluate MCFC electrodes and electrolytes with renewable fuels i.e. CO2-containing gases. The methods and results are both experimental and mathematically modelled. The objectives of this thesis are to better understand how the performance of the anode is dependent on different fuels. Anode kinetics and the water-gas shift reaction have been investigated as well as the possibility to increase cell lifetime by increasing the initial electrolyte amount by having the anode as a reservoir. The effect of segregation of cations in the electrolyte during operation has also been studied. It was found that if the gas composition at the current collector inlet is in equilibrium according to the water gas-shift reaction the gas composition inside the electrode is almost uniform. However, if the gas is not in equilibrium then the concentration gradients inside the current collector have a large effect on the gas composition inside the electrode. The conversion of the gas in the gas flow channels according to the water-gas shift reaction depends on the gas flow rate. For an anode used in a gas mixture of humidified hydrogen and carbon dioxide that are not in equilibrium some solubility of Ni in a (Li/Na)2CO3 mixture was found. To have the anode act as an electrolyte reservoir to prolong cell lifetime the anode pore size should be carefully matched with that of the cathode and a bimodal pore-size distribution for the anode is preferable to have as good performance as possible for as large electrolyte filling degree interval as possible. Modelling results of segregation of cations in the electrolyte during operation indicate that the electrolyte composition changes during operation and that the lithium ions are enriched at the anode for both types of electrolyte used for the MCFC. The electrolyte composition changes are small but might have to be considered in long-time operation. The results from this thesis may be used to better understand how the MCFC may be used for operation with renewable fuels and how electrodes may be designed to prolong cell lifetime. / Ett av den svenska regeringens mål är att öka användandet av förnyelsebara bränslen och bränslen från biomassa. Bränsleceller och framförallt MCFC är användbara för dessa typer av bränslen. Den svenska marknaden kan dra fördelar av MCFC på två sätt; ökad bränsleutnyttjandegrad och utnyttjande av producerad värme för fjärrvärme. De flesta kommersiella MCFC-systemen idag är optimerade för användning av metan. Möjligheten att använda biomassa på den svenska marknaden gör det viktigt att studera hur MCFC kan anpassas eller optimeras för bra prestanda och låg degradering för användning med gas från biomassa eller andra förnyelsebara bränslen. Fokus i denna avhandling är på metoder som kan användas för att undersöka och utvärdera MCFC-elektroder och -elektrolyter med förnyelsebara bränslen, dvs. gaser innehållande CO2. Metoderna och resultaten är både experimentella och matematiskt modellerade. Målet med denna avhandling är att bättre förstå hur anodens prestanda beror på användningen av olika bränslen. Anodens kinetik och vattengasskiftreaktionen har studerats liksom möjligheten att förlänga cellens livstid genom att öka den initiala mängden elektrolyt medelst användning av anoden som reservoar. Effekten av segregation av katjoner i elektrolyten under last har också undersökts. Om gassammansättningen är i jämvikt enligt vattengasskiftreaktionen vid inloppet till strömtilledaren kommer gassammansättningen att vara nära uniform inuti elektroden. Om ingående gas inte är i jämvikt kommer stora koncentrationsgradienter uppkomma i strömtilledaren och påverka gassammansättningen i elektroden. Omsättningen med avseende på vattenskiftreaktionen av gasen i flödeskanalen verkar vara beroende av gasens flödeshastighet. För en anod som används i en uppfuktad blandning av vätgas och koldioxid som inte är i jämvikt befanns det att Ni har en viss löslighet i (Li/Na)2CO3. För att kunna använda anoden som reservoar för elektrolyt för att förlänga livstiden för MCFC skall anodens porstorleksfördelning överensstämma med katodens och ha en bimodal porstorleksfördelning för att ge en tillräckligt god prestanda i ett så stort elektrolytfyllnadsgradsintervall som möjligt. Modelleringsresultat för segregering av katjoner i elektrolyten under drift visar att litiumjoner anrikas i anoden för båda typerna av elektrolyt som används i MCFC. Elektrolytkoncentrationsförändringarna är små men kan behövas tas i beaktande vid långa driftstider. Denna avhandlings resultat kan användas för att bättre förstå hur MCFC skall anpassas för drift med förnyelsebara bränslen och hur elektroder kan utformas för att förlänga livstiden. / QC 20100630

The primary focus of the present work is the development of macro-models for numerical simulation of binary alloy solidification processes, consistent with microscopic phase-change considerations, with a particular emphasis on capturing the effects of non-equilibrium species redistribution on overall macrosegregation behaviour. As a first step, a generalised macroscopic framework is developed for mathematical modelling of the process. The complete set of equivalent single-phase governing equations (mass, momentum, energy and species conservation) are solved following a pressure-based Finite Volume Method according to the SIMPLER algorithm. An algorithm is also developed for the prescription of the coupling between temperature and the melt-fraction. Based on the above unified approach of solidification modelling, a macroscopic numerical model is devised that is capable of capturing the interaction between the double-diffusive convective field and a localised fluid flow on account of solutal undercooling during non-equilibrium solidification of binary alloys. Numerical simulations are performed for the case of two-dimensional transient solidification of Pb-Sn alloys, and the simulation results are also compared with the corresponding experimental results quoted in the literature. It is observed that non-equilibrium effects on account of solutal undercooling result in an enhanced macrosegregation. Next, the model is extended to capture the effects of dendritic arm coarsening on the macroscopic transport phenomena occurring during a binary alloy solidification process. The numerical results are first tested against experimental results quoted in the literature, corresponding to the solidification of an Al-Cu alloy in a bottom-cooled cavity. It is concluded that dendritic arm coarsening leads to an increased effective permeability of the mushy region as well as an enhanced eutectic fraction of the solidified ingot. Consequently, an enhanced macrosegregation can be predicted as compared to that dictated by shrinkage-induced fluid flow alone. For an order-of-magnitude assessment of predictions from the numerical models, a systematic approach is subsequently developed for scaling analysis of momentum, heat and species conservation equations pertaining to the case of solidification of a binary mixture. A characteristic velocity scale inside the mushy region is derived, in terms of the morphological parameters of the two-phase region. A subsequent analysis of the energy equation results in an estimation of the solid layer thickness. It is also shown from scaling principles that non-equilibrium effects result in an enhanced macro-segregation compared to the case of an equilibrium model For the sake of assessment of the scaling analysis, the predictions are validated against computational results corresponding to the simulation of a full set of governing equations, thus confirming the trends suggested by the scale analysis. In order to analytically investigate certain limiting cases of unidirectional alloy solidification, a fully analytical solution technique is established for the solution of unidirectional, conduction-dominated, alloy solidification problems. The results are tested for the problem of solidification of an ammonium chloride-water solution, and are compared with those from existing analytical models as well as with the corresponding results from a fully numerical simulation. The effects of different microscopic models on solidification behaviour are illustrated, and transients in temperature and heat flux distribution are also analysed. An excellent agreement between the present solutions and results from the computational simulation can be observed. The generalised numerical model is subsequently utilised to investigate the effects of laminar double-diffusive Rayleigh-Benard convection on directional solidification of binary fluids, when cooled and solidified from the top. A series of experiments is also performed with ammonium chloride-water solutions of hypoeutectic and hypereutectic composition, so as to facilitate comparisons with numerical predictions. While excellent agreements can be obtained for the first case, the second case results in a peculiar situation, where crystals nucleated on the inner roof of the cavity start descending through the bulk fluid, and finally settle down at the bottom of the cavity in the form of a sedimented solid layer. An eutectic solidification front subsequently progresses from the top surface vertically downwards, and eventually meets the heap of solid crystals collected on the floor of the cavity. However, comparison of experimental observations with corresponding numerical results from the present model is not possible under this situation, since the associated transport process involves a complex combination of a number of closely interconnected physical mechanisms, many of which are yet to be resolved. Subsequent to the development of the mathematical model and experimental arrangements for macroscopic transport processes during an alloy solidification process, some of the important modes of double-diffusive instability are analytically investigated, as a binary alloy of any specified initial composition is directionally solidified from the top. By employing a close-formed solution technique, the critical liquid layer heights corresponding to the onset of direct mode of instability are identified, corresponding two a binary alloy with three different initial compositions. In order to simulate turbulent transport during non-equilibrium solidification processes of binary alloys, a modified k-8 model is subsequently developed. Particular emphasis is given for appropriate modelling of turbulence parameters, so that the model merges with single-phase turbulence closure equations in the pure liquid region in a smooth manner. Laboratory experiments are performed using an ammonium chloride-water solution that is solidified by cooling from the top of a rectangular cavity. A good agreement between numerical and experimental results is observed. Finally, in order to study the effects of three-dimensionality in fluid flow on overall macrosegregation behaviour, the interaction between double-diffusive convection and non-equilibrium solidification of a binary mixture in a cubic enclosure (cooled from a side) is numerically investigated using a three-dimensional transient mathematical model. Investigations are carried out for two separate model systems, one corresponding to a typical metal-ally analogue system and other corresponding to an actual metal-alloy system. As a result of three-dimensional convective flow-patterns, a significant solute macrosegregation is observed in the transverse sections of the cavity, which cannot be captured by two-dimensional simulations.