Dissertations / Theses: 'Bio-modelling'

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Cousin, Thibault. "Synthesis and molecular modelling of bio-based polyamides." Phd thesis, INSA de Lyon, 2013. http://tel.archives-ouvertes.fr/tel-00952848.

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In the current context of oil resources rarefaction, the development of biobased polymers is of major importance. The present work focused on the development of a biobased amorphous polyphthalamide, based on furan-2,5-dicarboxylic acid. The first part of the study was devoted to the development of a molecular modelling protocol that could calculate the glass transition temperature of polyphthalamides with accuracy. In order to do this, model polyphthalamides based on isophthalic, terephthalic acid and hexamethylene diamine were synthesized and characterized as well as simulated. By comparison between simulated and measured Tg, the protocol was validated. In a second part of the study, this protocol was applied to FDCA based polyphthalamides. These PPA were also synthesized. It was found that the PA 6-F undertakes a decarboxylation, preventing it from reaching high a molar mass. It was also found that the mechanical and thermal properties decrease as the amount of FDCA in the copolymers increases.

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Moscardo, Marco <1989&gt. "Modelling trophic network with PEPA and Bio-PEPA." Master's Degree Thesis, Università Ca' Foscari Venezia, 2015. http://hdl.handle.net/10579/5973.

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The thesis focuses on some attemps to model trophic networks using two different stochastic process algebras: PEPA and Bio-PEPA. In the first part we introduce all the main concepts on trophic networks and the process algebras used in the thesis. In the second part we apply PEPA and Bio-PEPA first to a toy example of trophic network and then to a real trophic network. We discuss the problems arised during the modelling and we compare the solutions we obtained. Bio-PEPA seems to permit a better modelling, better analysis of the flow of biomass and better analysis about the variation of the population of the species.

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Dennison, Catherine Lindsay. "Modelling and monitoring of a Herhof bio-degradation system." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape17/PQDD_0007/MQ33218.pdf.

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Bermudez, Contreras Edgar. "Modelling active bio-inspired object recognition in autonomous mobile agents." Thesis, University of Sussex, 2010. http://sro.sussex.ac.uk/id/eprint/2364/.

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Object recognition is arguably one of the main tasks carried out by the visual cortex. This task has been studied for decades and is one of the main topics being investigated in the computer vision field. While vertebrates perform this task with exceptional reliability and in very short amounts of time, the visual processes involved are still not completely understood. Considering the desirable properties of the visual systems in nature, many models have been proposed to not only match their performance in object recognition tasks, but also to study and understand the object recognition processes in the brain. One important point most of the classical models have failed to consider when modelling object recognition is the fact that all the visual systems in nature are active. Active object recognition opens different perspectives in contrast with the classical isolated way of modelling neural processes such as the exploitation of the body to aid the perceptual processes. Biologically inspired models are a good alternative to study embodied object recognition since animals are a working example that demonstrates that object recognition can be performed with great efficiency in an active manner. In this thesis I study biologically inspired models for object recognition from an active perspective. I demonstrate that by considering the problem of object recognition from this perspective, the computational complexity present in some of the classical models of object recognition can be reduced. In particular, chapter 3 compares a simple V1-like model (RBF model) with a complex hierarchical model (HMAX model) under certain conditions which make the RBF model perform as the HMAX model when using a simple attentional mechanism. Additionally, I compare the RBF and HMAX model with some other visual systems using well-known object libraries. This comparison demonstrates that the performance of the implementations of the RBF and HMAX models employed in this thesis is similar to the performance of other state-of-the-art visual systems. In chapter 4, I study the role of sensors in the neural dynamics of controllers and the behaviour of simulated agents. I also show how to employ an Evolutionary Robotics approach to study autonomous mobile agents performing visually guided tasks. In addition, in chapter 5 I investigate whether the variation in the visual information, which is determined by simple movements of an agent, can impact the performance of the RBF and HMAX models. In chapter 6 I investigate the impact of several movement strategies in the recognition performance of the models. In particular I study the impact of the variation in visual information using different movement strategies to collect training views. In addition, I show that temporal information can be exploited to improve the object recognition performance using movement strategies. In chapter 7 experiments to study the exploitation of movement and temporal information are carried out in a real world scenario using a robot. These experiments validate the results obtained in simulations in the previous chapters. Finally, in chapter 8 I show that by exploiting regularities in the visual input imposed by movement in the selection of training views, the complexity of the RBF model can be reduced in a real robot. The approach of this work proposes to gradually increase the complexity of the processes involved in active object recognition, from studying the role of moving the focus of attention while comparing object recognition models in static tasks, to analysing the exploitation of an active approach in the selection of training views for a object recognition task in a real world robot.

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Grimaud, Christel. "Logical modelling of reasoning and learning : a bio-inspired approach." Thesis, Lille 3, 2016. http://www.theses.fr/2016LIL30026/document.

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Dans ce mémoire, on s’inspire des sciences cognitives pour aborder la question de la modélisation logique du raisonnement et de l’apprentissage. Notre principale conviction est qu’il faudrait, pour traiter ce problème, prendre modèle sur la manière dont les agents naturels (c’est à dire les humains et les animaux) procèdent lorsqu’ils raisonnent ou apprennent. Considérant que le raisonnement fait appel à un grand nombre de facultés cognitives distinctes, et qu’il ne serait donc pas raisonnable d’espérer modéliser d’un seul coup l’ensemble du raisonnement humain, on se concentre ici sur un type d’inférences très simples dont on soutient qu’elles constituent le coeur du raisonnement chez tous les animaux à cerveau. On identifie un processus sous-jacent plausible pour ces inférences, d’abord au niveau mental de description, puis au niveau neuronal, et on développe une famille de modèles logiques permettant de le simuler. On s’attache ensuite à produire un ensemble de règles d’inférence caractérisant les relations d’inférence induites par ces modèles. Ces règles résultent du processus suggéré, et doivent donc être vues comme des règles qui, d’après le modèle, émergent fonctionnement des cerveaux. Enfin, on analyse les processus d’apprentissage attachés aux inférences considérées, et on montre comment le formalisme proposé permet de les modéliser. Pour conclure on évoque brièvement les possibles développements futurs du modèle, et notamment on donne quelques indications quant à la manière dont la modélisation d’un certain nombre de facultés additionnelles pourrait être envisagée
In this dissertation, we take inspiration in cognitive sciences to address the issue of the logical modelling of reasoning and learning. Our main thrust is that to address these issues one should take inspiration in the way natural agents (i.e., humans and animals) actually proceed when they draw inferences and learn. Considering that reasoning incorporates a wide range of cognitive abilities, and that it would thus be unreasonable to hope to model the whole of human’s reasoning all at once, we focus here on a very basic kind of inferences that, we argue, can be considered as the primary core of reasoning in all brained animals. We identify a plausible underlying process for these inferences, first at the mental level of description and then at the neural level, and we develop a family of logical models that allow to simulate it. Then we tackle the issue of providing sets of rules to characterise the inference relations induced by these models. These rules are a by-product of the posited process, and should thus be seen as rules that, according to the model, result from the very functioning of brains. Finally we examine the learning processes attached to the considered inferences, and we show how to they can be modelled within our framework. To conclude we briefly discuss possible further developments of the framework, and in particular we give indications about how the modelling of some other cognitive abilities might be envisioned

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Shirinskaya, Anna. "Physical modelling of bio sensors based on Organic Electrochemical Transistors." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX055/document.

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Les Transistors Organiques Electrochimiques (OECT) sont largement utilisés comme les capteurs dans de nombreux appareils bioélectroniques. Bien qu’ils aient été largement étudiés au cours de ces dernières années, il n'y a pas encore de compréhension fondamentale et univoque principe de fonctionnement d'un OECT, notamment en ce qui concerne le mécanisme du dé-dopage.Cette thèse est consacrée à la modélisation des Transistors Organiques Electrochimiques. Tout d'abord, un modèle d'état stationnaire numérique a été établi. Ce modèle utilisant les équations de Poisson-Boltzmann, Nernst-Planck et Nernst, nous permet de décrire finement le processus du dé-dopage dans la couche de PEDOT: PSS ainsi que, la distribution des ions et trous dans le capteur. Il a été prouvé expérimentalement que le modèle numérique dit de « neutralité global » est valable pour expliciter le fonctionnement global du capteur, mais aussi, l'origine et le résultat du processus du dé-dopage. La transition d’un modèle totalement numérique à un modèle analytique a été réalisée en ajustant la fonction analytique logistique paramétrique de Boltzmann au profil de conductivité calculé numériquement.Nous avons pu ainsi extraire, la fonction analytique de la dépendance du courant de drain en Fonction du potentiel local. Cette fonction ajuster sur un profil de courant de drain mesuré expérimentalement en fonction du potentiel appliqué permet d'obtenir la conductivité maximale d'une couche de PEDOT: PSS entièrement dopée. La conductivité maximale était dépendante non seulement du matériau, mais aussi de la taille du canal. Il est possible d'extraire, en utilisant la valeur de conductivité maximale et un modèle de semi-conducteur conventionnel, les autres paramètres pour la description complète d’OECT: densité intrinsèque de charge, densité de trous initiaux, concentration initiale de PSS- et capacité volumétrique de la couche polymère conductrice. Le fait d'avoir un outil permettant d'extraire et de caractériser facilement tous les OECT permet non seulement d'augmenter le niveau de description de compréhension du transistor, mais surtout de mieux maitriser la corrélation entre paramètres internes et externes.Finalement, l’approche que nous avons réalisée, couplant modélisation analytique et numérique, nous a permis de proposer une description complète du fonctionnement physique d’un OECT. En outre nous avons pu valider expérimentalement la pertinence de nos modèles en les comparants avec les caractéristiques obtenues via des mesures réelles
Organic Electrochemical Transistors are widely used as transducers for sensors in bioelectronics devices. Although these devices have been extensively studied in the last years, there is a lack of fundamental understanding of their working mechanism, especially concerning the de-doping mechanism.This thesis is dedicated to Organic Electrochemical Transistors modelling. First of all, a numerical steady state model was established. This model allows implementing the Poisson-Boltzmann, Nernst-Planck and Nernst equations to describe the de-doping process in the conductive PEDOT:PSS layer, and ions and holes distribution in the device. Two numerical models were proposed. In the first, Local Neutrality model, the assumption of electrolyte ions trapping in PEDOT:PSS layer was taken into consideration, thus the local neutrality was preserved. In the second model the ions were allowed to move freely under applied electric field inside conductive polymer layer, thus only global electroneutrality was kept. It was experimentally proven that the Global Neutrality numerical model is valid to explain the global physics of the device, the origin and the result of the de-doping process. The transition from totally numerical model to analytical model was performed by fitting the parametric analytical Boltzmann logistic function to numerically calculated conductivity profiles. As a result, an analytical equation for the Drain current dependence on applied voltage was derived. By fitting this equation to experimentally measured Drain current- applied voltage profiles, we could obtain the maximum conductivity of a fully doped PEDOT:PSS layer. The maximum conductivity is shown to be dependent not only on the material, but also on device channel size. Using the maximum conductivity value together with the Conventional Semiconductor model it is possible to extract the other parameters for the full description of the OECT: intrinsic charge carrier density, initial holes density, initial PSS- concentration and conductive polymer layer volumetric capacitance. Having a tool to make easy parameters extraction and characterization of any OECT, permits not only to increase the level of device description, but most importantly to highlight the correlation between external and internal device parameters.Finally it is shown how to make the whole description of the real OECT device, all the models were validated by fitting the modeled and experimentally measured data profiles.As a result, not only the purely theoretical model was presented in this thesis to describe the device physics, but also the prominent step was made on simple real device characterization

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Smith, David Everett. "Modelling and controlling a bio-inspired flapping-wing micro aerial vehicle." Thesis, Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/43577.

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The objective of this research is to verify the three degree of freedom capabilities of a bio-inspired quad flapping-wing micro aerial vehicle in simulation and in hardware. The simulation employs a nonlinear plant model and input-output feedback linearization controller to verify the three degree of freedom capabilities of the vehicle. The hardware is a carbon fiber test bench with four flapping wings and an embedded avionics system which is controlled via a PD linear controller. Verification of the three degree of freedom capabilities of the quad flapping-wing concept is achieved by analyzing the response of both the simulation and test bench to pitch, roll, and yaw attitude commands.

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Wall, Julie. "Post-cochlear auditory modelling for sound localisation using bio-inspired techniques." Thesis, Ulster University, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.525140.

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This thesis presents spiking neural architectures which simulate the sound localisation capability of the mammalian auditory pathways. This localisation ability is achieved by exploiting important differences in the sound stimulus received by each ear, known as binaural cues. Interaural time difference and interaural intensity difference are the two binaural cues which play the most significant role in mammalian sound localisation. These cues are processed by different regions within the auditory pathways and enable the localisation of sounds at different frequency ranges; interaural time difference is used to localise low frequency sounds whereas interaural intensity difference localises high frequency sounds. Interaural time difference refers to the different points in time at which a sound from a single location arrives at each ear and interaural intensity difference refers to the difference in sound pressure levels of the sound at each ear, measured in decibels. Taking inspiration from the mammalian brain, two spiking neural network topologies were designed to extract each of these cues. The architecture of the spiking neural network designed to process the interaural time difference cue was inspired by the medial superior olive. The lateral superior olive was the inspiration for the architecture designed to process the interaural intensity difference cue. The development of these spiking neural network architectures required the integration of other biological models, such as an auditory periphery (cochlea) model, models of bushy cells and the medial nucleus of the trapezoid body, leaky integrate and fire spiking neurons, facilitating synapses, receptive fields and the appropriate use of excitatory and inhibitory neurons. Two biologically inspired learning algorithms were used to train the architectures to perform sound localisation. Experimentally derived HRTF acoustical data from adult domestic cats was employed to validate the localisation ability of the two architectures. The localisation abilities of the two models are comparable to other computational techniques employed in the literature. The experimental results demonstrate that the two SNN models behave in a similar way to the mammalian auditory system, i.e. the spiking neural network for interaural time difference extraction performs best when it is localising low frequency data, and the interaural intensity difference spiking neuron model performs best when it is localising high frequency data. Thus, the combined models form a duplex system of sound localisation. Additionally, both spiking neural network architectures show a high degree of robustness when the HRTF acoustical data is corrupted by noise.

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Ramraj, Anitha. "Computational modelling of intermolecular interactions in bio, organic and nano molecules." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/computational-modelling-of-intermolecular-interactions-in-bio-organic-and-nano-molecules(7a41f3cd-1847-4ccf-8853-5fd8be2a2c15).html.

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We have investigated the noncovalent interactions in carbohydrate-aromatic interactions which are pivotal to the recognition of carbohydrates in proteins. We have employed quantum mechanical methods to study carbohydrate-aromatic complexes. Due to the importance of dispersion contribution to the interaction energy, we mainly use density functional theory augmented with an empirical correction for the dispersion interactions (DFT-D). We have validated this method with a limited number of high level ab initio calculations. We have also analysed the vibrational and NMR chemical shift characteristics using the DFT-D method. We have mainly studied the complexes involving β-glucose with 3-methylindole and p-hydroxytoluene, which are analogues of tryptophan and tyrosine, respectively. We find that the contribution for interaction energy mainly comes from CH/π and OH/π interactions. We find that the interaction energy of complexes involving CH/π and OH/π interactions is reflected in the associated blue and red shifts of vibrational spectrum. We also find that the interactions involving 3-methylindole are somewhat greater than those for p-hydroxytoluene. The C-H blueshifts are also in parallel with the predicted NMR proton shift. We have also tested different density functionals including both standard density functionals and newly developed M0x functionals and MP2 method for studying carbohydrate-aromatic complexes. The DFT-D method and M06 functionals of the M0x family are found to perform better, while B3LYP and BLYP functionals perform poorly. We find that the inclusion of a dispersion term to BLYP is found to perform better. The dispersion energy dominates over the interaction energy of carbohydrate-aromatic complexes. From the DFT-D calculations, we found that the complexes would be unstable without the contribution from dispersive energy. We have also studied the importance of noncovalent interactions in functionalization of nanotubes by nucleic acid bases and aromatic amino acids by using semi-empirical methods with dispersion term such asPM3-D and PM3-D*. We find that the both semi-empirical schemes give reasonable interaction energies with respect to DFT-D interaction energies. We have also used PM3-D method to study the adsorption of organic pollutants on graphene sheet and on nanotubes. We found that the semi-empirical schemes, which are faster and cheaper, are suitable to study these larger molecules involving noncovalent interactions and can be used as an alternative to DFT-D method. We have also studied the importance of dispersion interaction and the effect of steric hindrance in aggregation of functionalized anthracenes and pentacenes. We have also employed molecular dynamics simulation methods to study the aggregation of anthracene molecules in toluene solution.

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Buoso, Stefano. "High-fidelity modelling and feedback control of bio-inspired membrane wings." Thesis, Imperial College London, 2015. http://hdl.handle.net/10044/1/32832.

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This work is a numerical investigation on the performance of integrally actuated two-dimensional membrane wings made with dielectric elastomers. A high-fidelity model based on the direct numerical integration of the unsteady Navier-Stokes equations is coupled with a geometrically non-linear structural model. The rate-dependent constitutive law for the dielectric elastomer is based on a non-linear formulation, and it has been validated against experimental data. In addition, the implementation of the aeroelastic framework has been verified against the relevant literature for the low-Reynolds number flows investigated in this dissertation. Numerical simulations of the open-loop dynamics of the actuated membrane, in good agreement with experimental observations, show that integral actuation offers enough authority in the control of the wing aerodynamic performance. Dielectric elastomers can then be used as embedded actuators, coupling the advantages of passive membranes with a simple and lightweight control mechanism. Further, this work also proposes a model-reduction methodology for the fully coupled system to aid control system design. The low-order description of the actuated system can capture the main system dynamics, and can be used for the design of the control scheme of the wing. Proportional-Integral-Derivative and Linear Quadratic Gaussian feedback controllers, designed using the reduced-order model, are finally implemented in the high-fidelity model for the rejection of flow disturbances. Results show that the wing aerodynamic performance is noticeably enhanced through the actuation as the disturbances on the lift in case of gusts can be reduced up to 60%.

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Valdés, Amaro Daniel Alejandro. "Statistical shape analysis for bio-structures : local shape modelling, techniques and applications." Thesis, University of Warwick, 2009. http://wrap.warwick.ac.uk/3810/.

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A Statistical Shape Model (SSM) is a statistical representation of a shape obtained from data to study variation in shapes. Work on shape modelling is constrained by many unsolved problems, for instance, difficulties in modelling local versus global variation. SSM have been successfully applied in medical image applications such as the analysis of brain anatomy. Since brain structure is so complex and varies across subjects, methods to identify morphological variability can be useful for diagnosis and treatment. The main objective of this research is to generate and develop a statistical shape model to analyse local variation in shapes. Within this particular context, this work addresses the question of what are the local elements that need to be identified for effective shape analysis. Here, the proposed method is based on a Point Distribution Model and uses a combination of other well known techniques: Fractal analysis; Markov Chain Monte Carlo methods; and the Curvature Scale Space representation for the problem of contour localisation. Similarly, Diffusion Maps are employed as a spectral shape clustering tool to identify sets of local partitions useful in the shape analysis. Additionally, a novel Hierarchical Shape Analysis method based on the Gaussian and Laplacian pyramids is explained and used to compare the featured Local Shape Model. Experimental results on a number of real contours such as animal, leaf and brain white matter outlines have been shown to demonstrate the effectiveness of the proposed model. These results show that local shape models are efficient in modelling the statistical variation of shape of biological structures. Particularly, the development of this model provides an approach to the analysis of brain images and brain morphometrics. Likewise, the model can be adapted to the problem of content based image retrieval, where global and local shape similarity needs to be measured.

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Diamond, Alan. "Bio-inspired approaches to the control and modelling of an anthropomimetic robot." Thesis, University of Sussex, 2013. http://sro.sussex.ac.uk/id/eprint/47191/.

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Introducing robots into human environments requires them to handle settings designed specifically for human size and morphology, however, large, conventional humanoid robots with stiff, high powered joint actuators pose a significant danger to humans. By contrast, “anthropomimetic” robots mimic both human morphology and internal structure; skeleton, muscles, compliance and high redundancy. Although far safer, their resultant compliant structure presents a formidable challenge to conventional control. Here we review, and seek to address, characteristic control issues of this class of robot, whilst exploiting their biomimetic nature by drawing upon biological motor control research. We derive a novel learning controller for discovering effective reaching actions created through sustained activation of one or more muscle synergies, an approach which draws upon strong, recent evidence from animal and humans studies, but is almost unexplored to date in musculoskeletal robot literature. Since the best synergies for a given robot will be unknown, we derive a deliberately simple reinforcement learning approach intended to allow their emergence, in particular those patterns which aid linearization of control. We also draw upon optimal control theories to encourage the emergence of smoother movement by incorporating signal dependent noise and trial repetition. In addition, we argue the utility of developing a detailed dynamic model of a complete robot and present a stable, physics-based model, of the anthropomimetic ECCERobot, running in real time with 55 muscles and 88 degrees of freedom. Using the model, we find that effective reaching actions can be learned which employ only two sequential motor co-activation patterns, each controlled by just a single common driving signal. Factor analysis shows the emergent muscle co-activations can be reconstructed to significant accuracy using weighted combinations of only 13 common fragments, labelled “candidate synergies”. Using these synergies as drivable units the same controller learns the same task both faster and better, however, other reaching tasks perform less well, proportional to dissimilarity; we therefore propose that modifications enabling emergence of a more generic set of synergies are required. Finally, we propose a continuous controller for the robot, based on model predictive control, incorporating our model as a predictive component for state estimation, delay-compensation and planning, including merging of the robot and sensed environment into a single model. We test the delay compensation mechanism by controlling a second copy of the model acting as a proxy for the real robot, finding that performance is significantly improved if a precise degree of compensation is applied and show how rapidly an un-compensated controller fails as the model accuracy degrades.

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Altavilla, Salvatore Flavio <1986&gt. "Modelling Photoinduced Events in Solvated Bio-Cromophores by Hybrid QM/MM Approaches." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amsdottorato.unibo.it/7628/1/Salvatore_Altavilla_XXVII_ciclo_Scienze_Chimiche.pdf.

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The aim of the study has been to provide the rationale underlying the photo-induced processes and dynamics that occur in solvated biological systems such as retinal PSB cromophores and nucleotides. For such purpose, QM/MM setups and computational protocols have been developed and validated on the native and 10-methylated PSB retinal chromophores and on the GMP. COBRAMM has been used for the simulations, and scripts allowing QM/MM IRC calculations and conical intersection optimizations have been developed to tackle the QM/MM study of complex systems. It has been disclosed that the 10-methylation in all-trans RPSB retinal triggers a dramatic change in the excited state subpicosecond dynamics because the methyl group in 10-position stabilizes an excited state minimum with a large charge-transfer character and alternated C-C bonds favoring an efficient photoisomerization. Water-solvated GMP using multireference perturbation theory QM/MM techniques has been studied, disclosing the importance of the environment displaying qualitative differences for the ππ*La and ππ*Lb states whose spectra are shifted compared to their gas-phase counterparts. The ππ*La state is considered the main spectroscopic state driving the ultra-fast deactivation processes that characterize GMP during UV-light irradiation. A shallow stationary point towards the end of the ππ* La MEP has been characterized, with two different CIs with the ground state that account for the two fastest decay times experimentally measured. Upon initial Lb absorption, two CIs between the ππ *Lb and La states have also been located. CIs between the nO π* and the ππ *Lb and La states have also been characterized along its relaxation route, with a minimum in the nO π* state expected to vertically emit at ~2.7eV. Both ππ *Lb and nO π* are suggested to contribute to the longest-lived experimental timescale.

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Mouratiadou, Ioanna. "Assessing agricultural and nitrate pollution control policies with a bio-economic modelling approach." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/28673.

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Agricultural production and sustainable management of water resources are often in conflict. Focusing on the economy-agriculture-water resources links, two major policies are currently in place in the European Union: the Water Framework Directive (WFD) and the Common Agricultural Policy (CAP). Within these two policies, we are dealing with two conflicting goals in relation to agriculture: to minimise the adverse impacts of the sector on the water environment, and to maximise its economic return. Nitrogen fertiliser use is a particularly sensitive issue, given that it is one of the most significant factors determining farm productivity and agricultural diffuse pollution, and its impact on crop yields and pollution losses is determined by complex processes controlled by both natural and man-made factors. Clearly, analysing and modelling such a system requires understanding of both natural and social sciences. This thesis analyses the problem of nitrate water pollution from agricultural sources, with a focus on arable cropping systems. The impact of agricultural and water management policies on farmers' decision making and the resultant economic and nitrate pollution effects are investigated. The Lunan Water catchment in Scotland was used as a case study to i) explore the water quality and economic effects of the 2003 CAP Reform and the CAP Health Check, ii) assess the cost-effectiveness of economic and managerial measures against nitrate pollution, and iii) evaluate the effectiveness of the methodology used. The above goals were achieved by using a bio-economic modelling approach, which combines bio-physical and mathematical programming modelling. The results indicate that the decoupling of subsidies under the CAP reform resulted in minor changes regarding land use and subsequently economic and water quality indicators. The abolition of set-aside under the CAP Health Check increased farm incomes through the substitution of set-aside by profitable winter cereal crops. Even though these changes resulted in increased fertiliser use, the results indicate that this does not necessarily imply increased nitrate leaching due to rotational effects associated to the nature of nitrate losses. An analysis of the relative cost-effectiveness of measures demonstrated that similar leaching reductions can be incentivised through a number of economic instruments, such as per unit taxes on nitrogen fertiliser inputs and nitrate leaching, per hectare nitrate leaching standards and nitrogen fertiliser quotas, and subsidies and cross-compliance measures aiming at the reduction of fertiliser intensity. Taxes impose considerable costs on farmers without resulting in significant nitrate leaching reductions. On the other hand, subsidies impose the costs of environmental protection on the rest of the society, while cross-compliance can deliver water quality improvements at a lower cost compared to taxes. Cross-compliance instruments can either be used for the enforcement of measures at the farm level, such as nitrogen quotas, or measures at the field level, such as crop and soil specific reductions in fertiliser inputs. Further, the results indicate that considerable leaching reductions through changes in inputs can only be achieved at a significant cost. Thus, farm infrastructure measures and training and education of farmers, could further assist in achieving water quality objectives. The bio-economic modelling methodology used provided a consistent framework for water policy assessment in the agricultural sector, as it allowed integrating agronomic, environmental and economic information in a single framework. This was achieved at three spatial scales: the field scale capturing agronomic and environmental diversity, the farm scale that offers a better representation of farmers' actual behaviour, and the catchment scale that allows consideration of the aggregate policy impacts. The thesis also demonstrates the complexity of the issues involved, and highlights the challenges to be overcome.

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Nugrahany, Febryana. "Modelling of Biomass Pyrolysis with Ex-situ Catalytic Upgrading for Bio-crude Production." Thesis, KTH, Materialvetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-231489.

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This study presents a techno-economic assessment of slow pyrolysis of pine sawdust continued by ex-situ catalytic upgrading. The overall process consists of six sections: feed drying, pyrolysis, vapor filtration, ex-situ catalytic upgrading, vapor quenching, and combustion of permanent gas. In the process simulation, biomass is objected to slow pyrolysis at 450ºC in an electrically-heated screw reactor and pyrolysis vapors is upgraded in fixed catalytic bed reactor at 425 ºC (using HZSM-5). The model is then used to investigate effects of feed moisture variation and type of heating source in pyrolysis unit, i.e. thermal vs. electrical heating, to oil energy efficiency. According to the simulation model, the endothermic pyrolysis step requires1.46 MJ/kg dry-feed. On the other hand, ex-situ upgrading is slightly exothermic and releases50kJ/kg dry-feed. Overall, the conversion of biomass to bio-oil demonstrates a mass efficiency of 19.65%wt and an energy efficiency of 29.10%. The energy efficiency raises to 32.81% if a direct thermal source is applied instead of electrical heating. The bio-oil energy efficiency increases by 1.38% if the moisture content of the biomass decreases by 10%wt. In average,bio-oil and char production in ex-situ catalytic upgrading generate profit 1.47 SEK/kg dry feed. The uncertainty of bio-oil price causes the highest profit variation.

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Zhang, Xu. "A new method for generic three dimensional human face modelling for emotional bio-robots." Thesis, University of Gloucestershire, 2012. http://eprints.glos.ac.uk/4592/.

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Existing 3D human face modelling methods are confronted with difficulties in applying flexible control over all facial features and generating a great number of different face models. The gap between the existing methods and the requirements of emotional bio-robots applications urges the creation of a generic 3D human face model. This thesis focuses on proposing and developing two new methods involved in the research of emotional bio-robots: face detection in complex background images based on skin colour model and establishment of a generic 3D human face model based on NURBS. The contributions of this thesis are: A new skin colour based face detection method has been proposed and developed. The new method consists of skin colour model for skin regions detection and geometric rules for distinguishing faces from detected regions. By comparing to other previous methods, the new method achieved better results of detection rate of 86.15% and detection speed of 0.4-1.2 seconds without any training datasets. A generic 3D human face modelling method is proposed and developed. This generic parametric face model has the abilities of flexible control over all facial features and generating various face models for different applications. It includes: The segmentation of a human face of 21 surface features. These surfaces have 34 boundary curves. This feature-based segmentation enables the independent manipulation of different geometrical regions of human face. The NURBS curve face model and NURBS surface face model. These two models are built up based on cubic NURBS reverse computation. The elements of the curve model and surface model can be manipulated to change the appearances of the models by their parameters which are obtained by NURBS reverse computation. A new 3D human face modelling method has been proposed and implemented based on bi-cubic NURBS through analysing the characteristic features and boundary conditions of NURBS techniques. This model can be manipulated through control points on the NURBS facial features to build any specific face models for any kind of appearances and to simulate dynamic facial expressions for various applications such as emotional bio-robots, aesthetic surgery, films and games, and crime investigation and prevention, etc.

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17

Hassani, Ghezelchi Mansoor. "Mathematical Modelling of Bio-oil/Char Slurry Steam Gasification in a Fluidized Bed Reactor." Thesis, Curtin University, 2018. http://hdl.handle.net/20.500.11937/70645.

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This PhD study focuses on gasification of bio-oil/bioslurry in fluidized bed reactor. A methodology was developed for quantifying droplet size distribution from the atomisation of bio-oil or bioslurry. Spray characteristics were then reported for two fast pyrolysis bio-oils and a set of bioslurry samples with different atomizers. Mathematical modelling was then carried out to investigating syngas production from bio-oil/bioslurry gasification, taking into consideration the effect of operating conditions (e.g. droplet size) on syngas production.

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18

Zen, Simone. "Bio-morphodynamics of evolving river meander bends from remote sensing, field observations and mathematical modelling." Thesis, Queen Mary, University of London, 2014. http://qmro.qmul.ac.uk/xmlui/handle/123456789/9081.

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Interactions between fluvial processes and vegetation along the natural channel margins have been shown to be fundamental in determining meandering rivers development. By colonizing exposed sediments, riparian trees increase erosion resistance and stabilize fluvial sediment transport through their root systems, while during a flood event the above-ground biomass interacts with the water flow inducing sediment deposition and altering scour patterns. In turn river dynamics and hydrology influence vegetative biomass growth, affecting the spatial distribution of vegetation. These bio-morphological dynamics have been observed to direct control accretion and degradation rates of the meander bend. In particular, vegetation encroachments within the point bar (i.e. colonizing species and strand wood), initiate pioneeristic landforms that, when evolving, determine the lateral shifting of the margin that separates active channel from river floodplain and thus inner bank aggradation (bar push). This diminishes the portion of the morphologically active channel cross-section, influencing the erosion of the cutting bank and promoting channel widening (bank pull ). As a result of the cyclical occurrence of these erosional and depositional processes, meandering rivers floodplain show a typical ridge and swale pattern characterized by the presence of complex morphological structures, namely, benches, scrolls and chutes within the new-created floodplain. Moreover, difference in migration rate between the two banks have been observed to induce local temporal variations in channel width that affect river channel morphodynamics and its overall planform through their influence on the local flow field and channel bed morphology. Despite enormous advances in field and laboratory techniques and modelling development of the last decades, little is known about the relation between floodplain patterns and their controlling bio-morphological interactions that determine the bank accretion process. This knowledge gap has so far limited the development of physically-based models for the evolution of meandering rivers able to describe the lateral migration of banklines separately. Most existing meander migration models are indeed based on the hypothesis of constant channel width. Starting from this knowledge gap, the present doctoral research has aimed to provide more insight in the mutual interactions among flow, sediment transport and riparian vegetation dynamics in advancing banks of meandering rivers. In order to achieve its aims, the research has been designed as an integration of remote sensing and in-situ field observations with a mathematical modelling approach to i) provide a quantitative description of vegetation and floodplain channel topography patterns in advancing meanders bend and to ii) explore the key control factors and their role in generating the observed patterns. The structure of the present PhD work is based on four main elements. First, two types of airborne historical data (air photographs and Lidar survey) have been investigated, in order to quantify the effects of spatial-temporal evolution of vegetation pattern on meander morphology and to provide evidence for the influence of vegetation within the topography of the present floodplain. Such remote sensing analysis has highlighted a strong correspondence between riparian canopy structure and geomorphological patterns within the floodplain area: this has clearly shown the need to interpret the final river morphology as the result of a two-way interaction between riparian vegetation dynamics and river processes. Second, field measurements have been conducted on a dynamic meander bend of the lower reach of the Tagliamento River, Italy, with the initial aim of checking the outcomes of the remote sensing analysis through ground data. The outcomes of the field measurements have further supported the results, providing ground evidence on the relations between vegetation and topographic patterns within the transition zone that is intermediate between the active channel bed and the vegetated portion of the accreting floodplain. The influence of vegetation on inner bank morphology has also been interpreted in the light of the expected time scales of inundation and geomorphic dynamics that characterize the advancing process of the inner bank. The combined analysis of both remotely sensed data and field measurements associated with the historical hydrological dataset have allowed to quantitatively characterize the biophysical characteristics of the buffer zone, close to the river edge, where the accretion processes take place. The third research element has foreseen the development of a biophysically- based, simplified bio-morphodynamic model for the lateral migration of a meander bend that took advantage of the empirical knowledge gained in the analysis of field data. The model links a minimalist approach that includes biophysically-based relationships to describe the interaction between riparian vegetation and river hydro-morphodynamic processes, and employs a non linear mathematical model to describe the morphodynamics of meander channel bed. Model application has allowed to reproduce the spatial oscillations of vegetation biomass density and ground morphology observed in the previous analyses. Overall, the model allows to understand the role of the main controlling factors for the ground and vegetation patterns that characterize the advancing river bank and to investigate the temporal dynamics of the morphologically active channel width, providing insights into the bank pull and bar push phenomena. The fourth and concluding element of the present PhD research is an analytical investigation of the fundamental role of unsteadiness on the morphodynamic response of the river channel. Results obtained in the previous elements have clearly showed the tendency of a meander bend to develop temporal oscillations of the active channel width during its evolution, but no predictive analytical tool was previously available to investigate the channel bed response to such non-stationary planform dynamics. A non linear model has therefore been proposed to investigate the effect of active channel width unsteadiness on channel bed morphology. The basic case of free bar instability in a straight channel has been used in this first investigation, which has shown the tendency of channel widening to increase river bed instability compared to the steady case, in qualitative agreement with experimental observations. Overall, the research conducted within the present Doctoral Thesis represents a step forward in understanding the bio-morphodynamics of meandering rivers that can help the development of a complete bio-morphodynamic model for meandering rivers evolution, able to provide support for sustainable river management.

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19

Zen, Simone. "Bio-morphodynamics of evolving river meander bends from remote sensing, field observations and mathematical modelling." Doctoral thesis, Università degli studi di Trento, 2014. https://hdl.handle.net/11572/368615.

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Abstract:

Interactions between fluvial processes and vegetation along the natural channel margins have been shown to be fundamental in determining meandering rivers development. By colonizing exposed sediments, riparian trees increase erosion resistance and stabilize fluvial sediment transport through their root systems, while during a flood event the above-ground biomass interacts with the water flow inducing sediment deposition and altering scour patterns. In turn river dynamics and hydrology influence vegetative biomass growth, affecting the spatial distribution of vegetation. These bio-morphological dynamics have been observed to direct control accretion and degradation rates of the meander bend. In particular, vegetation encroachments within the point bar (i.e. colonizing species and strand wood), initiate pioneeristic landforms that, when evolving, determine the lateral shifting of the margin that separates active channel from river floodplain and thus inner bank aggradation (bar push). This diminishes the portion of the morphologically active channel cross-section, influencing the erosion of the cutting bank and promoting channel widen- ing (bank pull ). As a result of the cyclical occurrence of these erosional and depositional processes, meandering rivers floodplain show a typical ridge and swale pattern characterized by the presence of complex morphological structures, namely, benches, scrolls and chutes within the new-created floodplain. Moreover, difference in migration rate between the two banks have been observed to induce local temporal variations in channel width that affect river channel morphodynamics and its overall planform through their influence on the local flow field and channel bed morphology. Despite enormous advances in field and laboratory techniques and modelling development of the last decades, little is known about the relation between floodplain patterns and their controlling bio-morphological interactions that determine the bank accretion process. This knowledge gap has so far limited the development of physically-based models for the evolution of meandering rivers able to describe the lateral migration of banklines separately. Most existing meander migration models are indeed based on the hypothesis of constant channel width. Starting from this knowledge gap, the present doctoral research has aimed to provide more insight in the mutual interactions among flow, sediment transport and riparian vegetation dynamics in advancing banks of meandering rivers. In order to achieve its aims, the research has been designed as an integration of remote sensing and in-situ field observations with a mathematical modelling approach to i) provide a quantitative description of vegetation and floodplain channel topography patterns in advancing meanders bend and to ii) explore the key control factors and their role in generating the observed patterns. The structure of the present PhD work is based on four main elements. First, two types of airborne historical data (air photographs and Lidar survey) have been investigated, in order to quantify the effects of spatial-temporal evolution of vegetation pattern on meander morphology and to provide evidence for the influence of vegetation within the topography of the present floodplain. Such remote sensing analysis has highlighted a strong correspondence between riparian canopy structure and geomorphological patterns within the floodplain area: this has clearly shown the need to interpret the final river morphology as the result of a two-way interaction between riparian vegetation dynamics and river processes. Second, field measurments have been conducted on a dynamic meander bend of the lower reach of the Tagliamento River, Italy, with the initial aim of checking the outcomes of the remote sensing analysis through ground data. The outcomes of the field measurements have further supported the results, providing ground evidence on the relations between vegetation and topographic patterns within the transition zone that is intermediate between the active channel bed and the vegetated portion of the accreting floodplain. The influence of vegetation on inner bank morphology has also been interpreted in the light of the expected time scales of inundation and geomorphic dynamics that characterize the advancing process of the inner bank. The combined analysis of both remotely sensed data and field measurements associated with the historical hydrological dataset have allowed to quantitatively characterize the biophysical characteristics of the buffer zone, close to the river edge, where the accretion processes take place. The third research element has foreseen the development of a biophysically-based, simplified bio-morphodynamic model for the lateral migration of a meander bend that took advantage of the empirical knowledge gained in the analysis of field data. The model links a minimalist approach that includes biophysically-based relationships to describe the interaction between riparian vegetation and river hydromorphodynamic processes, and employs a non linear mathematical model to describe the morphodynamics of meander channel bed. Model application has allowed to reproduce the spatial oscillations of vegetation biomass density and ground morphology observed in the previous analyses. Overall, the model allows to understand the role of the main controlling factors for the ground and vegetation patterns that characterize the advancing river bank and to investigate the temporal dynamics of the morphologically active channel width, providing insights into the bank pull and bar push phenomena. The fourth and concluding element of the present PhD research is a analytical investigation of the fundamental role of unsteadiness on the morphodynamic response of the river channel. Results obtained in the previous elements have clearly showed the tendency of a meander bend to develop temporal oscillations of the active channel width during its evolution, but no predictive analytical tool was previously available to investigate the channel bed response to such non-stationary planform dynamics. A non linear model has therefore been proposed to investigate the effect of active channel width unsteadiness on channel bed morphology. The basic case of free bar instability in a straight channel has been used in this first investigation, which has shown the tendency of channel widening to increase river bed instability compared to the steady case, in qualitative agreement with experimental observations. Overall, the research conducted within the present Doctoral Thesis represents a step forward in understanding the bio-morphodynamics of meandering rivers that can help the development of a complete bio-morphodynamic model for meandering rivers evolution, able to provide support for sustainable river management.

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20

Zen, Simone. "Bio-morphodynamics of evolving river meander bends from remote sensing, field observations and mathematical modelling." Doctoral thesis, University of Trento, 2014. http://eprints-phd.biblio.unitn.it/1378/1/Thesis.pdf.

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Abstract:

Interactions between fluvial processes and vegetation along the natural channel margins have been shown to be fundamental in determining meandering rivers development. By colonizing exposed sediments, riparian trees increase erosion resistance and stabilize fluvial sediment transport through their root systems, while during a flood event the above-ground biomass interacts with the water flow inducing sediment deposition and altering scour patterns. In turn river dynamics and hydrology influence vegetative biomass growth, affecting the spatial distribution of vegetation. These bio-morphological dynamics have been observed to direct control accretion and degradation rates of the meander bend. In particular, vegetation encroachments within the point bar (i.e. colonizing species and strand wood), initiate pioneeristic landforms that, when evolving, determine the lateral shifting of the margin that separates active channel from river floodplain and thus inner bank aggradation (bar push). This diminishes the portion of the morphologically active channel cross-section, influencing the erosion of the cutting bank and promoting channel widen- ing (bank pull ). As a result of the cyclical occurrence of these erosional and depositional processes, meandering rivers floodplain show a typical ridge and swale pattern characterized by the presence of complex morphological structures, namely, benches, scrolls and chutes within the new-created floodplain. Moreover, difference in migration rate between the two banks have been observed to induce local temporal variations in channel width that affect river channel morphodynamics and its overall planform through their influence on the local flow field and channel bed morphology. Despite enormous advances in field and laboratory techniques and modelling development of the last decades, little is known about the relation between floodplain patterns and their controlling bio-morphological interactions that determine the bank accretion process. This knowledge gap has so far limited the development of physically-based models for the evolution of meandering rivers able to describe the lateral migration of banklines separately. Most existing meander migration models are indeed based on the hypothesis of constant channel width. Starting from this knowledge gap, the present doctoral research has aimed to provide more insight in the mutual interactions among flow, sediment transport and riparian vegetation dynamics in advancing banks of meandering rivers. In order to achieve its aims, the research has been designed as an integration of remote sensing and in-situ field observations with a mathematical modelling approach to i) provide a quantitative description of vegetation and floodplain channel topography patterns in advancing meanders bend and to ii) explore the key control factors and their role in generating the observed patterns. The structure of the present PhD work is based on four main elements. First, two types of airborne historical data (air photographs and Lidar survey) have been investigated, in order to quantify the effects of spatial-temporal evolution of vegetation pattern on meander morphology and to provide evidence for the influence of vegetation within the topography of the present floodplain. Such remote sensing analysis has highlighted a strong correspondence between riparian canopy structure and geomorphological patterns within the floodplain area: this has clearly shown the need to interpret the final river morphology as the result of a two-way interaction between riparian vegetation dynamics and river processes. Second, field measurments have been conducted on a dynamic meander bend of the lower reach of the Tagliamento River, Italy, with the initial aim of checking the outcomes of the remote sensing analysis through ground data. The outcomes of the field measurements have further supported the results, providing ground evidence on the relations between vegetation and topographic patterns within the transition zone that is intermediate between the active channel bed and the vegetated portion of the accreting floodplain. The influence of vegetation on inner bank morphology has also been interpreted in the light of the expected time scales of inundation and geomorphic dynamics that characterize the advancing process of the inner bank. The combined analysis of both remotely sensed data and field measurements associated with the historical hydrological dataset have allowed to quantitatively characterize the biophysical characteristics of the buffer zone, close to the river edge, where the accretion processes take place. The third research element has foreseen the development of a biophysically-based, simplified bio-morphodynamic model for the lateral migration of a meander bend that took advantage of the empirical knowledge gained in the analysis of field data. The model links a minimalist approach that includes biophysically-based relationships to describe the interaction between riparian vegetation and river hydromorphodynamic processes, and employs a non linear mathematical model to describe the morphodynamics of meander channel bed. Model application has allowed to reproduce the spatial oscillations of vegetation biomass density and ground morphology observed in the previous analyses. Overall, the model allows to understand the role of the main controlling factors for the ground and vegetation patterns that characterize the advancing river bank and to investigate the temporal dynamics of the morphologically active channel width, providing insights into the bank pull and bar push phenomena. The fourth and concluding element of the present PhD research is a analytical investigation of the fundamental role of unsteadiness on the morphodynamic response of the river channel. Results obtained in the previous elements have clearly showed the tendency of a meander bend to develop temporal oscillations of the active channel width during its evolution, but no predictive analytical tool was previously available to investigate the channel bed response to such non-stationary planform dynamics. A non linear model has therefore been proposed to investigate the effect of active channel width unsteadiness on channel bed morphology. The basic case of free bar instability in a straight channel has been used in this first investigation, which has shown the tendency of channel widening to increase river bed instability compared to the steady case, in qualitative agreement with experimental observations. Overall, the research conducted within the present Doctoral Thesis represents a step forward in understanding the bio-morphodynamics of meandering rivers that can help the development of a complete bio-morphodynamic model for meandering rivers evolution, able to provide support for sustainable river management.

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21

VOLPI, GIORGIO. "Numerical modelling of fluids related thermal anomalies." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2018. http://hdl.handle.net/10281/199141.

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Among the renewable and sustainable energy sources, geothermal energy has been recognized as “the choice” to meet the future electricity demand, economically and environmentally speaking. The increasing threat of a worldwide energy crisis and the growing interest in geothermal systems require further development and application of advanced software and numerical modelling approaches to facilitate geothermal exploration and exploitation. In this regard, the present study is aimed to perform accurate three-dimensional simulations of three high to low-enthalpy type geothermal systems, for which no model was previously available. The selected sites are : i) the Bormio hydrothermal system and ii) the Castel Giorgio – Torre Alfina geothermal reservoir in Italy, and iii) the Tiberian Basin between Israel, Jordan and Syria. The historical Italian thermal site of Bormio (Central Italian Alps) is a typical alpine low enthalpy geothermal site, whose waters are currently exploited by two thermal establishments. Thermal waters from ten springs are heated at a temperature of about 40°C in deep circulation systems and ascend vigorously along the regional permeable Zebrù thrust. A hydrochemical characterization of the discharged thermal waters has been performed to validate the assumptions formulated in the regional numerical model built with the finite element code Feflow®. Results correctly simulate the observed discharge rate of ca. 2400 l/min and the spring temperatures, showing a complete cooling of the aquifer within a period of approximately 50,000 years. Groundwater flow and temperature patterns suggest that thermal water flows through a deep system along a fracture network associated with the thrust system. The Castel Giorgio - Torre Alfina geothermal field (Central Italy) is a promising, early explored and so far not exploited medium enthalpy reservoir. The involved fluids are hosted in a carbonate formation at temperatures ranging between 120-210 °C. Detailed hydro-geothermal data recognized a strong thermal anomaly associated with a vigorous convective regime. The 3D reservoir-scale numerical model has been developed, via the open source finite element code OpenGeoSys, to simulate the undisturbed natural geothermal field and investigate the impacts of a possible exploitation process. The commercial software Feflow® is also used as additional numerical constraint. The analysis of the exploitation process demonstrated the sustainability of a geothermal doublet for the development of a 5 MW pilot plant. The buoyant circulation within the geothermal system allows the reservoir to sustain a 50 years production at a flow rate of 1050 t/h and prevents any thermal breakthrough within the estimated operational lifetime. The Tiberian Basin, within in the Jordan Rift Valley, is characterized by a shallow heat anomaly making that field a potential site for production of electricity through geothermal methods. The Jordan Rift Valley hosts the Lake Tiberias, the main freshwater resource of the entire Middle East. The sustainability of this resource is endangered by the occurrence of clusters of hot (20 - 60 °C) and salty springs, along the lake shore and the Lower Yarmuk Gorge. This deep depression is supposed to act as the mixing zone of different flow paths responsible for the ascent of thermal waters. The first regional 3D model of the Tiberian Basin has been developed with the commercial finite element software Feflow®, accounting for major aquifers, aquicludes and deep-cutting faults. Available water levels for wells at different depths, allowed the correct calibration of the groundwater flow model. Results show that the discharge of thermal waters is tied to the coexistence of free convection in permeable units, and additional advective flow fields induced by topography gradients. These simulations identify the mixed convection as the dominant heat flow process driving thermal waters below the Lower Yarmuk Gorge.
Among the renewable and sustainable energy sources, geothermal energy has been recognized as “the choice” to meet the future electricity demand, economically and environmentally speaking. The increasing threat of a worldwide energy crisis and the growing interest in geothermal systems require further development and application of advanced software and numerical modelling approaches to facilitate geothermal exploration and exploitation. In this regard, the present study is aimed to perform accurate three-dimensional simulations of three high to low-enthalpy type geothermal systems, for which no model was previously available. The selected sites are : i) the Bormio hydrothermal system and ii) the Castel Giorgio – Torre Alfina geothermal reservoir in Italy, and iii) the Tiberian Basin between Israel, Jordan and Syria. The historical Italian thermal site of Bormio (Central Italian Alps) is a typical alpine low enthalpy geothermal site, whose waters are currently exploited by two thermal establishments. Thermal waters from ten springs are heated at a temperature of about 40°C in deep circulation systems and ascend vigorously along the regional permeable Zebrù thrust. A hydrochemical characterization of the discharged thermal waters has been performed to validate the assumptions formulated in the regional numerical model built with the finite element code Feflow®. Results correctly simulate the observed discharge rate of ca. 2400 l/min and the spring temperatures, showing a complete cooling of the aquifer within a period of approximately 50,000 years. Groundwater flow and temperature patterns suggest that thermal water flows through a deep system along a fracture network associated with the thrust system. The Castel Giorgio - Torre Alfina geothermal field (Central Italy) is a promising, early explored and so far not exploited medium enthalpy reservoir. The involved fluids are hosted in a carbonate formation at temperatures ranging between 120-210 °C. Detailed hydro-geothermal data recognized a strong thermal anomaly associated with a vigorous convective regime. The 3D reservoir-scale numerical model has been developed, via the open source finite element code OpenGeoSys, to simulate the undisturbed natural geothermal field and investigate the impacts of a possible exploitation process. The commercial software Feflow® is also used as additional numerical constraint. The analysis of the exploitation process demonstrated the sustainability of a geothermal doublet for the development of a 5 MW pilot plant. The buoyant circulation within the geothermal system allows the reservoir to sustain a 50 years production at a flow rate of 1050 t/h and prevents any thermal breakthrough within the estimated operational lifetime. The Tiberian Basin, within in the Jordan Rift Valley, is characterized by a shallow heat anomaly making that field a potential site for production of electricity through geothermal methods. The Jordan Rift Valley hosts the Lake Tiberias, the main freshwater resource of the entire Middle East. The sustainability of this resource is endangered by the occurrence of clusters of hot (20 - 60 °C) and salty springs, along the lake shore and the Lower Yarmuk Gorge. This deep depression is supposed to act as the mixing zone of different flow paths responsible for the ascent of thermal waters. The first regional 3D model of the Tiberian Basin has been developed with the commercial finite element software Feflow®, accounting for major aquifers, aquicludes and deep-cutting faults. Available water levels for wells at different depths, allowed the correct calibration of the groundwater flow model. Results show that the discharge of thermal waters is tied to the coexistence of free convection in permeable units, and additional advective flow fields induced by topography gradients. These simulations identify the mixed convection as the dominant heat flow process driving thermal waters below the Lower Yarmuk Gorge.

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22

Snyman, Anchen. "Modelling of ecosystem change on rehabilitated ash disposal sites based on selected bio-indicators / A. Snyman." Thesis, North-West University, 2006. http://hdl.handle.net/10394/1185.

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Finding a common language in describing and interpreting multivariate data associated with rehabilitation and disturbance ecology, has became a major challenge. The main objective of this study is to find and evaluate mathematical models to describe ecosystem change based on selected indicators of change. Existing data from a previous rehabilitation project on Hendrina Power Station (Mpumalanga, South Africa) was used as a database for this study and this study aims to report on the development of models concentrating on radar graphs and a model based on matrix mathematics. The main groups of organisms selected for the construction of models, were vegetation, soil mesofauna and ant species. The datasets were limited to some indicative species and their mean abundances were determined. The grids that were used were randomly chosen and the models were constructed. Radar graphs were constructed to model the suite of species identified, through a sensitivity analysis, to indicate possible rehabilitation success over time and was applied to the different rehabilitation ages. The surface areas under the radar graphs were determined and compared for the different rehabilitation ages in the same year of survey. Correlation graphs were drawn between the surface area and the rehabilitation ages. These graphs did not indicate much relevance in indicating rehabilitation success, but the radar graphs proved to be good indicators of change in abundance of the selected species over time. iv The vegetation species, Eragrostis curvula, was the only species that showed a strong significant positive relationship with rehabilitation age and could be considered a good rehabilitation species and indicator of rehabilitation success. After the evaluation of this model, Eragrostis curvula, and two additional ant species, Tetramorium setigerum and Lepisiota laevis, were added. These species that were added, showed an increase in abundance over time, as found in a previous study. These radar graphs also did not indicate much relevance and it can be concluded that the radar graphs can only be used for a visual representation of the changes in abundance of the relevant species over time. This study also refers to a matrix model. This model focused on the interactions between the different variables selected. The percentage carbon in the soil were also added to the list of species. Model fitting graphs were constructed and correlations were drawn between the species that had significant values in the interaction table. This model could be useful for future studies, but more data and replication is necessary, over a longer period of time. This will serve to eliminate possible shortcomings of the model.
Thesis (M. Environmental Science (Biodiversity and Conservation Biology))--North-West University, Potchefstroom Campus, 2007.

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23

Ngo, Anh Cat Le. "Digital system for bio-inspired visual attention processing fast and efficient information theoretic modelling of saliency." Thesis, University of Nottingham, 2015. http://eprints.nottingham.ac.uk/30984/.

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Visual attention is a biological mechanism of human vision systems to cope with rich and fast-changing visual information in surrounding environments. Visual saliency is a strategy, which recommends attentive spots to be visited in descending orders of interest or information amounts. This thesis aims to utilize information theory in computational saliency models, assumed that more attention is drawn toward more informative locations. As visual media, i.e. images and videos, are high-dimensional data, information estimation is often computationally infeasible due to enormous requirement of computation and data samples. This thesis proposes and analyses three different practical and innovative information-based saliency models. The first model, called entropy-based saliency method (ENT), measures salient information with centre-surrounding operation by conditional entropy (ENT-CON) or Kullback-Leibler diver-gence (ENT-KLD). However, ENT only estimates information from local features offixed-size windows, it does not utilize multi-scale and global information of visual media, which are proven to be important in biological visual attention. To utilise multi-scale information, Wavelet-based Scale-Saliency (WSS), the second model, estimates information from power distribution of data across wavelet sub-bands basis descriptors in multiple dyadic scales. Though WSS has benefited from local features at multiple scales, it has not integrated information of global context or statistical characteristics of natural images. Multiscale Discriminant Saliency (MDIS), the third model, adopts Wavelet Hidden Markov Tree (WHMT) to unify both multiple-scale and global information for a comprehensive saliency method. All three models, ENT, WSS and MDIS are evaluated and compared against well-known saliency methods such as PSS, AIM, DIS, etc quantitatively by standard numerical tools (Normalized Scale Saliency (NSS), Linear Correlation Coefficient (LCC), Area Under Curver (AUC)) on N.Bruce’s, Kootstra’s and Judd’s databases with human eye-tracking ground-truth as well as qualitatively by visual examination of individual cases. Performances and comprehen-siveness of three models are reflected through numerical results of an experiment on Bruce’s database. As the latter model is designed in more comprehensive and computationally complex manner than the previous, all three quantitative evaluations (LCC,NSS,AUC) generally and computational time increase in that order. ENT WSS MDIS LCC 0.02263 -0.01731 0.02382 NSS -0.17533 0.31782 0.48019 AUC 0.78167 0.70292 0.88335 TIME(s/frame) 0.87040 1.26889 2.32734 Table 1: ENT,WSS,MDIS’s quantitative results on N.Bruce’s database.

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24

Al, Ketife Ahmed Majeed Daife. "Modelling and Optimization of Combined Wastewater Treatment and CO2 Bio-fixation in a Batch Algal Photobioreactor." Thesis, Curtin University, 2017. http://hdl.handle.net/20.500.11937/59696.

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The research focuses on investigation and optimization (using Box Behnken design) of the key parameters of CO2 gas concentration, light intensity, temperature, feedwater nutrient concentration, and wastewater origin (municipal primary and secondary, and petroleum industry) on photobioreactor algal growth parameters. A mathematical model is provided for predicting algal growth. Finally, the influence of light wavelength on algal growth is investigated. The outcomes can be used to inform design and operation of large-scale algal cultivation systems.

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25

Mengucci, Carlo <1992&gt. "A take on complexity: bio-molecules and human metabolism interaction modelling for health and nutrition with machine learning." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2022. http://amsdottorato.unibo.it/10198/1/PhD_thesis_Carlo_Mengucci_AMS.pdf.

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The advent of omic data production has opened many new perspectives in the quest for modelling complexity in biophysical systems. With the capability of characterizing a complex organism through the patterns of its molecular states, observed at different levels through various omics, a new paradigm of investigation is arising. In this thesis, we investigate the links between perturbations of the human organism, described as the ensemble of crosstalk of its molecular states, and health. Machine learning plays a key role within this picture, both in omic data analysis and model building. We propose and discuss different frameworks developed by the author using machine learning for data reduction, integration, projection on latent features, pattern analysis, classification and clustering of omic data, with a focus on 1H NMR metabolomic spectral data. The aim is to link different levels of omic observations of molecular states, from nanoscale to macroscale, to study perturbations such as diseases and diet interpreted as changes in molecular patterns. The first part of this work focuses on the fingerprinting of diseases, linking cellular and systemic metabolomics with genomic to asses and predict the downstream of perturbations all the way down to the enzymatic network. The second part is a set of frameworks and models, developed with 1H NMR metabolomic at its core, to study the exposure of the human organism to diet and food intake in its full complexity, from epidemiological data analysis to molecular characterization of food structure.

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26

Scales, Kylie Lisa. "The application of ocean front metrics for understanding habitat selection by marine predators." Thesis, University of Plymouth, 2015. http://hdl.handle.net/10026.1/3319.

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Marine predators such as seabirds, cetaceans, turtles, pinnipeds, sharks and large teleost fish are essential components of healthy, biologically diverse marine ecosystems. However, intense anthropogenic pressure on the global ocean is causing rapid and widespread change, and many predator populations are in decline. Conservation solutions are urgently required, yet only recently have we begun to comprehend how these animals interact with the vast and dynamic oceans that they inhabit. A better understanding of the mechanisms that underlie habitat selection at sea is critical to our knowledge of marine ecosystem functioning, and to ecologically-sensitive marine spatial planning. The collection of studies presented in this thesis aims to elucidate the influence of biophysical coupling at oceanographic fronts – physical interfaces at the transitions between water masses – on habitat selection by marine predators. High-resolution composite front mapping via Earth Observation remote sensing is used to provide oceanographic context to several biologging datasets describing the movements and behaviours of animals at sea. A series of species-habitat models reveal the influence of mesoscale (10s to 100s of kilometres) thermal and chlorophyll-a fronts on habitat selection by taxonomically diverse species inhabiting contrasting ocean regions; northern gannets (Morus bassanus; Celtic Sea), basking sharks (Cetorhinus maximus; north-east Atlantic), loggerhead turtles (Caretta caretta; Canary Current), and grey-headed albatrosses (Thalassarche chrysostoma; Southern Ocean). Original aspects of this work include an exploration of quantitative approaches to understanding habitat selection using remotely-sensed front metrics; and explicit investigation of how the biophysical properties of fronts and species-specific foraging ecology interact to influence associations. Main findings indicate that front metrics, particularly seasonal indices, are useful predictors of habitat preference across taxa. Moreover, frontal persistence and spatiotemporal predictability appear to mediate the use of front-associated foraging habitats, both in shelf seas and in the open oceans. These findings have implications for marine spatial planning and the design of protected area networks, and may prove useful in the development of tools supporting spatially dynamic ocean management.

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Liotta, Flavia. "Bio-methanation tests and mathematical modelling to assess the role of moisture content on anaerobic digestion of organic waste." Phd thesis, Université Paris-Est, 2013. http://tel.archives-ouvertes.fr/tel-00967951.

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Dry Anaerobic Digestion (AD) presents different advantages if compared to wet AD, i.e. smaller reactor size, lesser water addition, digestate production and pretreatment needed, although several studies have demonstrated that water promotes substrate hydrolysis and enables the transfer of process intermediates and nutrients to bacterial sites. To better understand the role of water on AD, dry and semidry digestion tests of selected complex organic substrates (food waste, rice straw, carrot waste), with various TS contents of the treated biomass have been carried out in the present study. The results confirm that water plays an essential role on the specific methane production rate, final methane yield and Volatile Solids (VS) degradation. The final methane yield in semi-dry and dry conditions was 51% and 59% lower for rice straw and 4% and 41% lower for food waste, respectively, if compared with wet conditions. Inhibition tests, based on Volatile Fatty Acid (VFA) analysis, were carried out to investigate the specific inhibition processes that take place with the selected substrates at different TS contents. In wet AD of carrot waste no VFA accumulation was found, and all VFA concentrations were lower than the inhibition limits. A direct correlation between TS content and total VFA (TVFA) concentration was noticed for rice straw and food waste AD. For rice straw a maximum TVFA concentration of 2.1 g/kg was found in dry condition, 1 g/kg in semidry conditions and 0.2 g/kg in wet conditions, whereas for food waste the TVFA concentration was 10 g/kg in dry condition, 9 g/kg in semidry conditions and 3 g/kg in wet conditions. A Mathematical model of complex organic substrate AD in dry and semidry conditions has been proposed to simulate the effect of TS content on the process. The data obtained from batch experiments, in terms of methane production and VFA concentrations, were used to calibrate the proposed model. The kinetic parameters of VFA production and degradation, calibrated using the experimental data, resulted highly dependent on the TS content and different from wet AD literature values. This is due to VFA accumulation in dry conditions, which implies higher values of the inhibition factors introduced in the model. Finally, as dry AD takes usually place in Plug Flow (PF) reactors, an historical and critical review on the role of hydrodynamics in PF bioreactors has been carried out

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RIVA, FEDERICO. "DAMAGE-BASED LONG-TERM MODELLING OF PARAGLACIAL TO POSTGLACIAL EVOLUTION OF ALPINE ROCK SLOPES." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2017. http://hdl.handle.net/10281/153286.

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Large mountain slopes in alpine environments undergo a complex long-term evolution from glacial to postglacial environments, through a transient period of paraglacial readjustment. During and after this transition, the interplay among rock strength, topographic relief, and morpho-climatic drivers varying in space and time can lead to the development of different types of slope instability, from sudden catastrophic failures to large, slow, long-lasting yet potentially catastrophic rockslides. Understanding the long-term evolution of large rock slopes requires accounting for the time-dependence of deglaciation unloading, permeability and fluid pressure distribution, displacements and failure mechanisms. In turn, this is related to a convincing description of rock mass damage processes and to their transition from a sub-critical (progressive failure) to a critical (catastrophic failure) character. Although mechanisms of damage occurrence in rocks have been extensively studied in the laboratory, the description of time-dependent damage under gravitational load and variable external actions remains still difficult. This PhD project aims at studying the long-term evolution of alpine rock slopes through their glacial, paraglacial and postglacial stages of evolution. In particular, I investigate the mechanisms driving the transition from a relatively undisturbed, deglaciating slope to a paraglacial rock slope affected by initial development of large slope instabilities, and finally to a mature, hydraulically coupled postglacial rockslide or Deep Seated Gravitational Slope Deformation (DSGSD). To do this, I developed a novel approach able to overcome the limitations of existing numerical modelling techniques and capture the long-term evolution of real, large rock slopes. In this perspective, starting from a time-dependent model conceived to reproduce laboratory rock deformation experiments by combining damage and time-to-failure laws, we pointed at reproducing both diffused and localized damage, meanwhile tracking long-term slope displacements from primary to tertiary creep stages. The adopted approach is completed by taking into account rock mass heterogeneity and property upscaling, time-dependent deglaciation and damage-dependent fluid pressure occurrence.
Large mountain slopes in alpine environments undergo a complex long-term evolution from glacial to postglacial environments, through a transient period of paraglacial readjustment. During and after this transition, the interplay among rock strength, topographic relief, and morpho-climatic drivers varying in space and time can lead to the development of different types of slope instability, from sudden catastrophic failures to large, slow, long-lasting yet potentially catastrophic rockslides. Understanding the long-term evolution of large rock slopes requires accounting for the time-dependence of deglaciation unloading, permeability and fluid pressure distribution, displacements and failure mechanisms. In turn, this is related to a convincing description of rock mass damage processes and to their transition from a sub-critical (progressive failure) to a critical (catastrophic failure) character. Although mechanisms of damage occurrence in rocks have been extensively studied in the laboratory, the description of time-dependent damage under gravitational load and variable external actions remains still difficult. This PhD project aims at studying the long-term evolution of alpine rock slopes through their glacial, paraglacial and postglacial stages of evolution. In particular, I investigate the mechanisms driving the transition from a relatively undisturbed, deglaciating slope to a paraglacial rock slope affected by initial development of large slope instabilities, and finally to a mature, hydraulically coupled postglacial rockslide or Deep Seated Gravitational Slope Deformation (DSGSD). To do this, I developed a novel approach able to overcome the limitations of existing numerical modelling techniques and capture the long-term evolution of real, large rock slopes. In this perspective, starting from a time-dependent model conceived to reproduce laboratory rock deformation experiments by combining damage and time-to-failure laws, we pointed at reproducing both diffused and localized damage, meanwhile tracking long-term slope displacements from primary to tertiary creep stages. The adopted approach is completed by taking into account rock mass heterogeneity and property upscaling, time-dependent deglaciation and damage-dependent fluid pressure occurrence.

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DAVARPANAH, ELAHE. "Investigation and Modelling of Porous Solid Sorbents and Bio-based Ionic Solvents for the Separation of CO2 from Flue gas." Doctoral thesis, Politecnico di Torino, 2020. http://hdl.handle.net/11583/2841182.

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30

Kragt, Marit Ellen. "An integrated assessment approach to linking biophysical modelling and economic valuation." Phd thesis, Canberra, ACT : The Australian National University, 2010. http://hdl.handle.net/1885/8037.

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Changes to land use and land management in Australian catchments have led to pressures on natural resources, and concerns over water quality and ecosystem health in catchment rivers and estuaries. To increase the efficiency of natural resource management (NRM) policies that address these concerns, decision makers require information about the environmental impacts, as well as the marginal costs and benefits associated with policy decisions. Including cost-benefits estimates in NRM policy assessment provides decision makers with economic information about the trade-offs between alternative NRM actions. There are, however, few studies that have assessed the complex environmental and economic trade-offs associated with changes in catchment NRM actions in a single modelling framework. This study uses an integrated assessment (IA) approach to develop a decision support model that incorporates environmental and economic dimensions of catchment NRM, for a case-study of the George catchment in Tasmania. Various (academic and non-academic) stakeholders were consulted during the model development process, to gain an understanding of the wide variety of values that may be impacted by NRM changes. Knowledge from different sources was integrated in a single framework using Bayesian network modelling techniques. The framework incorporates three major sub-models: 1. A physically based water quality model to predict the changes in sediment and nutrient loadings in the George rivers and estuary; 2. Expert opinion and Bayesian network modelling to predict the impacts of catchment NRM changes on three ecosystem attributes: riparian vegetation, rare species and estuary seagrass area; and 3. A choice experiment (CE) survey to estimate the non-market values associated with changes in George catchment ecosystem attributes. The CE study was not only aimed at assessing catchment non-market values, but also addressed methodological challenges associated with attribute level framing and cost anchoring in CE. Rather than coupling existing information and models, synchronous data collection and model development were used to ensure tailored information exchange between the different components. The IA approach to model development highlighted several challenges in synchronizing economic and scientific research. Frequent communication was required between the stakeholders involved in the project to construct a common framework for analysis. The selection of attributes that were relevant for scientists, policy makers, and CE survey respondents was a lengthy process. Agreeing on the level of modelling detail, and predicting attribute levels based on sound scientific information, also posed considerable challenges during the model development process.

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Semaan, Josephine. "Bio-economic modelling for policy analysis of nitrate pollution reduction in irrigated agriculture : the study of a region in Southern Italy /." [Montpellier] : Institut agronomique méditerranéen de Montpellier, 2003. http://catalogue.bnf.fr/ark:/12148/cb391317984.

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Texte remanié de: Th. Master of science--Agron.--Montpellier--Centre international de hautes études agronomiques méditerranéennes, 2001.
Bibliogr. p. 67-70. Résumé en anglais et en français.

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32

Perra, Simone. "The study of Lovastatin production as a benchmark simulation model for bio-manufacturing processes." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2020.

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In this work an end to end bio-pharmaceutical process for the production of lovastatin is implemented into a Matlab/Simulink environment. The simulation is developed with the objective to be a generic reference model, as it captures the typical dynamics of pharmaceutical bio-manufacturing. It can then be used as an open-source test problem to study different process scenarios in dynamic mode. The objective of this work is to propose the benchmark simulation as a testbed for the development and comparison of different control strategies in dynamic mode. To this purpose a highly referenced control framework (the Skogestad method) is adapted and applied to the dynamics of the present model. The implemented framework includes a distributed control system (DCS) as regulatory control layer, and an MPC multiple-input multiple-output application as a supervisory control layer. As an alternative for the supervisory control layer, an override control framework based on process knowledge is developed and validated as a lighter solution. The different control setups are compared from a total productivity and stability point of view in a set of case-studies. As expected, the MPC application is the most stable solution, but in all the case studies the alternative override supervisory control gives comparable API final productivity. Pharmaceutical bio-manufacturing is a highly regulated industry in which the resources and time dedicated to process optimization and control are limited. The development of an end to end reference simulation with a limited number of unit operations is a step towards a smarter resource exploitation in the industry.

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Whitten, Stuart Max Business Australian Defence Force Academy UNSW. "Provision of environmental goods on private land: a case study of Australian wetlands." Awarded by:University of New South Wales - Australian Defence Force Academy. School of Business, 2003. http://handle.unsw.edu.au/1959.4/38661.

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The management of natural resources located on private lands often involves a perceived conflict between the mix of private and public benefit outputs they produce. Governments have tended to respond through legislation to restrict and redirect private decisions about resource management. However, the legislative response faces a lack of information about the costs and benefits of alternative management and policy instruments. A pertinent example of this debate is the management of wetlands on private lands. The goal in this thesis is to advance the design of policy relating to the production of environmental outputs on private lands. This goal is achieved by first estimating the welfare impacts of alternative private land management strategies on the wider community. These estimates are used as inputs into the development of alternative policy instruments that are then evaluated in terms of their potential cost-effectiveness in influencing private management. Two case studies of wetland management on private land in Australia are presented ??? the Upper South East Region of South Australia, and, the Murrumbidgee River Floodplain in New South Wales. The conceptual approach described in the first part of the thesis includes a description of the resource management problem and the strengths and weaknesses of the alternative decision frameworks widely employed in Australia. Identification of the cause and nature of transaction costs in the management process is the focus in this discussion. The welfare impacts of alternative wetland management strategies are investigated through the construction of a bio-economic model for each of the case study areas. The approach integrates biophysical analysis of changing wetland management with the value society places on wetlands. Outputs from this process are used in the development of a range of policy instruments directed towards influencing wetland management. The impact of poorly quantified and uncertain transaction costs on the potential cost-effectiveness of these options is evaluated using threshold policy analysis. The empirical results show that the perception of a conflict between the private and public values generated by resource management is accurate. For example, scenarios changing wetland management in the Upper South East of South Australia on the Murrumbidgee River floodplain in New South Wales were shown to generate net benefits of $5.2m and $5.1m respectively. Hence, changing wetland management could generate increased community welfare. The potential for these findings to be translated into wetland policy is less conclusive. Policies directed towards wetland management (in part or in whole) incur a range of transaction costs and deliver differential wetland protection benefits. Ten ???best bet??? policies are identified, but more information is required to determine conclusively whether a net benefit results to the wider community when transaction costs are included.

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Kowalski, Benjamin [Verfasser]. "Sustainable intensification & agricultural involution in Southern Africa : farming system analysis and bio-economic modelling of smallholder agriculture in the Okavango basin / Benjamin Kowalski." Gießen : Universitätsbibliothek, 2017. http://d-nb.info/1128593769/34.

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MRAK, ELISABETTA. "Analisi strutturale e funzionale di 5 nuove mutazioni del gene CYP21A2 in pazienti affetti da deficit della 21 idrossilasi." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2009. http://hdl.handle.net/2108/986.

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La sindrome adrenogenitale(SAG) è un gruppo di disordini autosomici recessivi dovuti a . deficit enzimatici nella steroidogenesi di cortisolo e aldosterone. Il deficit da 21-idrossilasi (21 OHD) è la forma più comune, interessa circa il 90 95% dei casi. La 21-idrossilasi è un’enzima che appartiene alla famiglia dei citocromi P-450 che catalizza la conversione del 17 idrossiprogesterone in 11 deossicortisolo, un precursore del cortisolo e la conversione del progesterone in deossicorticosterone, un precursore dell’aldosterone. Il fenotipo della sindrome adrenogenitale varia a seconda dell’ attività della 21-idrossilasi. Il gene della 21-idrossilasi (CYP21A2) e` localizzato nel complesso maggiore di istocompatibilita` umano di classe 3 sul cromosoma 6. Sullo stesso locus è presente uno pseudogene (CYP21AP),identico per il 98% al gene, che codifica per una proteina non attiva a causa di numerose mutazioni deleterie; la maggior parte delle mutazioni sono causate da ricombinazioni tra CYP21A2 e CYP21AP: solo il 5% sono nuove mutazioni del gene CYP21A2 che non originano dallo pseudogene , nel quale l’analisi funzionali dell’enzima è stato considerato utile per la correlazione genotipo fenotipo. Quando le sequenze deleterie, normalmente presenti nello pseudogene, sono trasferite al gene attivo, quest’ultimo diventa incapace di codificare per una proteina con attività funzionale, Generalmente, e` stata dimostrata una buona correlazione tra genenotipo-fenotipo e la forma clinica correla con l`allele mutato con attivita` enzimatica piu`alta. Questo ha reso possibile predire un inquadramento clinico in soggetti affetti basandosi sul genotipo. Per le nuove e rare mutazioni, in cui non erano disponibili informazioni cliniche e il fenotipo non coincideva con il genotipo,in particolar modo per i pazienti maschi e doppi eterozigoti, solo studiando le attivita` funzionali degli enzimi, ha reso possibile classificare le mutazioni in base alla severita’ della malattia. Abbiamo trovato 5 nuove mutazioni puntiformi (L122P, M150R, Q481X ,E161X and R366H ) in 5 pazienti italiani con SAG. Per verificare le mutazioni presenti sul gene CYP21A2 e per classificarle in base alla gravità, abbiamo costruito in vitro le mutazioni del CYP21A2 e abbiamo considerato le attività enzimatiche mutanti dopo averle fatte esprimere nelle cellule COS7. Il modelling molecolare suggerisce un impatto maggiore sull’ analisi funzionale e strutturale della 21-idrossilasi dopo l’espressione nelle cellule COS-7 confermando una attività enzimatica ridotta Solo le mutazioni M150R e R366H influenzano in minor modo l’ attività enzimatica probabilmente associata con la forma non classica di SAG.
Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorder caused by the deficiency of a steroidogenic enzyme involved in corstisol or aldosterone biosynthesis. 21-hydroxylase deficiency (21-OHD) is the most common form, accounting for 90-95% of cases. 21-hydroxylase is a cytocrome P-450 enzyme that catalyzes the conversion of 17-hydroxyprogesterone to 11-deoxycortisol, a precursor of cortisol, and the conversion of progesterone to deoxycorticosterone, a precursor of aldosterone. The phenotype of CAH varies greatly, depending of the degree in the impairment of 21-OH activity. The 21-hydroxylase gene (CYP21A”) is a part of a complicated structure located in the human leukocyte antigen class III locus on chromosome 6p21.3. In the same locus, is present a 98% identical pseudogene (CYP21A1P), which does not encode a functionally active protein due to numerous deleterious mutations; most mutations causing 21-OH deficiency arise from recombinations between CYP21A2 and CYP21A1P. When deleterious sequences normally present in the pseudogene are transferred to the active gene, the latter becomes incapable of encoding a normal enzyme: only 5% are novel CYP21A2 mutations, in which functional analysis of mutant enzymes have been helpful to correlate genotype-phenotype. We have found five novel point mutations (L122P, M150R, Q481X ,E161X and R366H ) in five Italian patients with CAH. To verify the status of the point mutations in CYP21A2 gene as disease-causing mutations and to classify them according to severity, we have constructed in vitro the mutations of CYP21A2 and evaluated the activities of the mutant enzymes after expression in COS7 cells. Molecular modeling suggests a major impact on 21-hydroxylase activity and functional analysis after expression in COS-7 cells confirms reduced enzymatic activity of the mutant enzymes. Only the M150R and R366H mutations affected the activity to a minor extent, probably associated with NC CAH.

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Alonzo, Flavien. "Méthodes numériques pour le Glioblastome Multiforme et pour la résolution de problèmes inverses autour des systèmes de réaction-diffusion." Electronic Thesis or Diss., Ecole centrale de Nantes, 2022. http://www.theses.fr/2022ECDN0059.

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Le Glioblastome Multiforme est la tumeur cérébrale gliale la plus fréquente et la plus mortelle chez l’Homme. Les mathématiques ont l’opportunité de pouvoir innover la prise en charge des patients dans la démarche actuelle de médecine personnalisée. Cette thèse propose deux contributions majeures autour de cette thématique. Une premièrecontribution porte sur la modélisation et la simulation la plus réaliste possible de la propagation des cellules tumorales du Glioblastome Multiforme chez un patient après son diagnostic. Ce travail modélise le phénomène d’angiogenèse induite par la tumeur. Un schéma et algorithme numérique sont utilisés pour conserver la positivité des solutions. Enfin, les simulations sont comparées aux connaissances issues de la médecine. Une seconde contribution porte sur l’estimationdes paramètres des modèles de type réactiondiffusion. La méthode développée permet de résoudre des problèmes inverses en résolvant deux systèmes d’équations aux dérivées partielles avec une contrainte fonctionnelle, et non avec des outils statistiques. La résolution numérique d’un tel problème est donnée et évaluée sur deux exemples de modèles avecdes données synthétiques. La méthode permet ainsi de déterminer des paramètres d’un modèle avec des données éparses en temps
Glioblastoma Multiforme is the most frequent and deadliest brain tumour. Mathematics stand as an innovative tool to enhance patient care in the context of personalized medicine. This PhD showcases two major contribution to this theme. A first contribution works on the modelling and simulating of a realistic spreading of the tumour cells in Glioblastoma Multiforme from a patient’s diagnosis. This work models tumour induced angiogenesis. A numerical scheme and algorithmare used to ensure positivity of solutions. Finally, simulations are compared to empirical knowledge from Medicine. A second contribution is on parameter estimation for reaction-diffusion models. The developed method solves inverse problems by solving two partial differential equation systems with a functional constraint, without using statistical tools. Numerical resolution of such problems is given and showcased on two examples of models with synthetic data. This method enables to calibrate parameters from a model using sparse data in time

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Al-Hilo, Naeem A. "Novel Sound Absorbing Materials Made From Elastomeric Waste: Compounding And Structuring Of Elastomeric Waste Crumb And Fibers With Binders Into Innovative Noise Insulation Materials." Thesis, University of Bradford, 2018. http://hdl.handle.net/10454/17383.

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Elastomeric wastes plague our time, polluting our environment and requiring urgent upcycling solutions. This research contributes to this agenda using an important source of waste, car tyre shred fibre residue (TSFR). It is demonstrated how using binders, non-foaming (SBR) and foaming (PU), we can transform these TSFR into structured porous acoustic-thermal insulation materials, suitable as underlay, cavity wall and pipe insulation. These structures were fabricated in purpose designed moulds and characterised for their porosity, tortuosity, flow resistivity and density. Their acoustic absorption performance was measured using industrial standards and the measurement underpinned with the Johnson-Champoux-Allard (JCA) model. With the under-layer materials, thermal insulation was also measured. The results were as follows: (i) 40%/60% SBR/TSFR was an optimal composition for the underlay with the addition of 15% w/w bumper crumb of size > 1mm enhancing both impact sound and thermal insulation, (ii) PU was found to produce well performing wall cavity insulation, particularly when vacuum pressure was applied, allowing micro and macro pores to be formed; (iii) PU applied with controlled amount of water to control foaming CO2 formation produced super-performing (compared with Armacell System B) stratified pipe cladding insulation, optimal at porosity stratification of 90%, 83%, and 70%; (iv) Very good agreement was observed with predictions using JCA model, allowing further research to be carried out with these now well characterised sound insulations. In addition to the developing materials, a novel technique for measuring sound absorption of pipe cladding was developed that could replace the expensive standard using a reverberation chamber.

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Moretto, Marco. "Integrating gene expression data to infer how biological changes drive transcriptional responses." Doctoral thesis, Università degli studi di Padova, 2016. http://hdl.handle.net/11577/3421790.

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The work presented in this Ph.D. thesis is two sided. The first part describes a series of tools to integrate gene expression data, while the second one describes how to mathematically model them. The first part explains the methodology used to integrate publicly available transcriptomic data, the creation of a series of software tools that implement this methodology, and their application to create collections of gene expression data (compendia) for several prokaryote species and one eukaryote (the crop plant Vitis vinifera). Compendia are gene expression matrices in which every row is a gene of the species of interest while columns represent the different conditions in which genes have been measured. They provide a rich source of information for systems biology applications. Besides being the result of the first part of this Ph.D. project, gene expression compendia are the starting point for the second part, with the purpose of facilitating biological knowledge discovery drawing inference from mathematical models. We develop and discuss two complementary models. The first one uses a Bayesian approach, in which we model a probability distribution over an underlying true change in expression for a given gene in response to a given condition. The second one uses Boolean networks to model structural information about the known genetic mechanisms of response to stimuli. Boolean networks are used to fit a distribution over steady-states of cells in measured samples. These models may be used for various types of statistical inference and decision making. They can serve to formulate statistically sound hypothesis about stimuli/signals that better explain observed changes in gene expression, or about the inherent variability of a gene (independently from the conditions in which it is measured), or to find complex patterns of co-expression.
Questa tesi di dottorato tratta principalmente di due argomenti tra loro interconnessi: il primo è lo sviluppo di una serie di tool per l’integrazione di dati di espressione genica. Il secondo è lo sviluppo di metodologie per la modellazione matematica di tali dati. Nella prima parte, quindi, viene descritta la metodologia utilizzata per integrare dati di espressione genica disponibili nei principali database pubblici, la creazione di una serie di strumenti software che implementano tali metodologie e l’applicazione di quest’ultimi al fine di realizzare collezioni di dati di espressione (compendia) per diversi procarioti ed una specie eucariote di interesse agrario (Vitis vinifera). Tali compendia sono particolarmente rilevanti applicate alla systems biology in quanto forniscono una ricca fonte di informazione. Essi sono delle matrici di espressione in cui ogni riga rappresenta un gene della specie di interesse, mentre le colonne rappresentano le diverse condizioni in cui l’espressione genica è stata misurata. Oltre ad essere il risultato della prima parte di questo lavoro di dottorato, i compendia di espressione sono anche il punto di partenza per la seconda parte che ha lo scopo di facilitare l’interpretazione biologica dei dati attraverso inferenza su modelli matematici creati a partire da essi. In particolare vengono discussi e sviluppati due modelli tra loro complementari. Il primo utilizza un approccio Bayesiano modellando una distribuzione di probabilità sul vero cambiamento dell’espressione di un particolare gene in risposta ad una particolare condizione. Il secondo modello sfrutta le reti Booleane per modellare l’informazione strutturale dei meccanismi genetici noti di risposta agli stimoli. Le reti Booleane vengono utilizzate per la creazione di una distribuzione di probabilità sui possibili stati stazionari delle cellule presenti nel campione effettivamente misurato. Utilizzando questi modelli è possibile, ad esempio, formulare ipotesi statisticamente valide sugli stimoli/segnali maggiormente responsabili dell’espressione di alcuni geni, sulla innata variabilità di un determinato gene (indipendentemente dalle condizioni in cui esso è misurato) oppure trovare complessi schemi di co-espressione genica.

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Cherif, Mohamed Amine. "Modélisation dynamique de la (bio)disponibilité des radionucléides dans les sols : approche comparative modèles-expériences appliquée au transfert de césium dans la rhizosphère." Thesis, Aix-Marseille, 2017. http://www.theses.fr/2017AIXM0547/document.

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Ce travail vise à développer un modèle générique capable de mieux rendre compte et de prédire les transferts de radionucléides dans le système sol/solution du sol/plante. La première partie de ce travail a été consacrée à l’analyse critique des modèles disponibles dans la littérature pour décrire l’adsorption du césium par les minéraux argileux (principal processus contrôlant sa disponibilité dans les sols). Cette analyse a débouché sur la formulation d’un nouveau modèle mécaniste combinant deux approches: la complexation de surface et l’échange d’ions. Cette approche, a été testée afin de modéliser l’adsorption du Cs sur plusieurs substrats argileux naturels. Ce travail a permis de valider le modèle proposé et de démontrer qu’il constitue un avantage majeur par rapport aux différents modèles existants. La deuxième partie a été consacrée, à la réalisation d’une série d’expérimentations, conduite en milieux contrôlés sur des systèmes dynamiques, et la modélisation de la (bio)disponibilité du Cs dans ces systèmes. A la suite de ces essais, les interactions entre solide et solution observées ont pu être correctement reproduites à partir du modèle proposé en prenant en compte la fraction argileuse du sol uniquement. Ces simulations ont également été comparées aux simulations obtenues à partir des modèles empirique (Kd) et cinétique (EK). Enfin, le développement d’un outil numérique permettant de coupler la description des interactions géochimiques au transfert vers la plante (approche cinétique) a permis de reproduire correctement les essais réalisés en Rhizotests couplant sol, solution et plante et de mieux caractériser la fraction du Cs disponible pour les plantes
The overall objective of this work is to develop a generic model able to better account and predict the transfer of radionuclides in the soil / soil solution / plant. The first part of the work was devoted to the critical analysis of the models available in the literature to describe the cesium adsorption on clay minerals (the process that mainly controls its availability in the soils). This analysis enabled us to propose a new mechanistic model combining two approaches: surface complexation and cation exchange. Our approach has been tested in order to model the adsorption of Cs on several natural clay substrates, in a wide range of Cs concentrations and physicochemical conditions. This work allowed to validate the proposed mechanistic model and to demonstrate that it constitutes a major advantage over the various existing models. The second part was devoted, to the performing of a series of experiments, carried out in controlled environments on dynamic systems and modeling the (bio)availability of Cs in these systems. Following these tests, the observed interactions between solid and solution could be correctly reproduced with the proposed model taking into account only the clay fraction of the soil. These simulations were also compared with simulations obtained using a empiric (Kd) kinetic models (E-K approach). Finally, the development of a numerical tool for coupling the description of geochemical interactions with transfer to the plant (Michaelis-Menten approach) allowed to reproduce adequately the trials carried out in Rhizotests coupling soil, solution and plant, and to better characterize of the Cs fraction available for plants

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Sim, Darryl Frederick. "Biomechanics of Dysfunction and Injury Management for the Cervical Spine." Thesis, Queensland University of Technology, 2004. https://eprints.qut.edu.au/15852/1/Darryl_Sim_Thesis.pdf.

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The research described in this thesis focuses on the biomechanics of cervical spine injury diagnosis and rehabilitation management. This research is particularly relevant to the diagnosis of minor neck injuries that typically arise from motor vehicle accidents and are classified as "whiplash injuries". The diagnosis and treatment of these chronic neck problems has been particularly difficult and frustrating and these difficulties prompted calls for the objective evaluation of the techniques and procedures used in the measurement and assessment of neck dysfunction. The biomechanical aspects of the clinical diagnosis of minor cervical spine injuries were investigated in this work by reconfiguring an existing detailed biomechanical model of the human neck to simulate injuries to particular structures, and to model abnormal muscle activation. The investigation focused on the range of motion assessment and the methods of testing and rehabilitating the function of the deep neck muscles because the model could be applied to provide further insight into these facets of neck injury diagnosis and management. The de Jager detailed head-neck model, available as a research tool from TNO (The Netherlands), was chosen for this study because it incorporated sufficient anatomical detail, but the model required adaptation because it had been developed for impact and crash test dummy simulations. This adaptation significantly broadened the model's field of application to encompass the clinical domain. The facets of the clinical diagnosis of neck dysfunction investigated in this research were range of motion and deep muscle control testing. Range of motion testing was simulated by applying a force to the head to generate the primary motions of flexion/extension, lateral flexion and axial twisting and parametric changes were made to particular structures to determine the effect on the head-neck movement. The main finding from this study of cervical range of motion testing was that while motion can be accurately measured in three dimensions, consideration of the three dimensional nature of the motion can add little to the clinical diagnosis of neck dysfunctions. Given the non-discriminatory nature of range of motion testing, the scientific collection and interpretation of the three dimensional motion patterns cannot be justified clinically. The de Jager head-neck model was then further adapted to model the cranio-cervical flexion test, which is used clinically to test the function of the deep muscle groups of the neck. This simulation provided confirmation of the efficacy of using a pressure bio-feedback unit to provide visual indication of the activation of the deep flexor muscles in the neck. However, investigation of the properties of the pressure bio-feedback unit identified significant differences in the stiffness of the bag for the different levels of inflation that must be accounted for if comparisons are to be made between subjects. Following the identification of the calibration anomalies associated with the pressure bio-feedback unit, the motion of the point of pressure of the head on the headrest and the force at this point of contact during the activation of the deep flexor muscle group were investigated as an alternative source of feedback. This output, however, was found to be subject specific, depending on the posterior shape of the skull that determined the point of contact during the head rolling action. Clinically, an important outcome of the alternative feedback assessment was that the prescribed action to target the deep flexor muscle group will feel different for each individual, ranging from a slide to a roll of the head on the headrest, and this must be accounted for when explaining the action and during rehabilitation management.

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Sim, Darryl Frederick. "Biomechanics of Dysfunction and Injury Management for the Cervical Spine." Queensland University of Technology, 2004. http://eprints.qut.edu.au/15852/.

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The research described in this thesis focuses on the biomechanics of cervical spine injury diagnosis and rehabilitation management. This research is particularly relevant to the diagnosis of minor neck injuries that typically arise from motor vehicle accidents and are classified as "whiplash injuries". The diagnosis and treatment of these chronic neck problems has been particularly difficult and frustrating and these difficulties prompted calls for the objective evaluation of the techniques and procedures used in the measurement and assessment of neck dysfunction. The biomechanical aspects of the clinical diagnosis of minor cervical spine injuries were investigated in this work by reconfiguring an existing detailed biomechanical model of the human neck to simulate injuries to particular structures, and to model abnormal muscle activation. The investigation focused on the range of motion assessment and the methods of testing and rehabilitating the function of the deep neck muscles because the model could be applied to provide further insight into these facets of neck injury diagnosis and management. The de Jager detailed head-neck model, available as a research tool from TNO (The Netherlands), was chosen for this study because it incorporated sufficient anatomical detail, but the model required adaptation because it had been developed for impact and crash test dummy simulations. This adaptation significantly broadened the model's field of application to encompass the clinical domain. The facets of the clinical diagnosis of neck dysfunction investigated in this research were range of motion and deep muscle control testing. Range of motion testing was simulated by applying a force to the head to generate the primary motions of flexion/extension, lateral flexion and axial twisting and parametric changes were made to particular structures to determine the effect on the head-neck movement. The main finding from this study of cervical range of motion testing was that while motion can be accurately measured in three dimensions, consideration of the three dimensional nature of the motion can add little to the clinical diagnosis of neck dysfunctions. Given the non-discriminatory nature of range of motion testing, the scientific collection and interpretation of the three dimensional motion patterns cannot be justified clinically. The de Jager head-neck model was then further adapted to model the cranio-cervical flexion test, which is used clinically to test the function of the deep muscle groups of the neck. This simulation provided confirmation of the efficacy of using a pressure bio-feedback unit to provide visual indication of the activation of the deep flexor muscles in the neck. However, investigation of the properties of the pressure bio-feedback unit identified significant differences in the stiffness of the bag for the different levels of inflation that must be accounted for if comparisons are to be made between subjects. Following the identification of the calibration anomalies associated with the pressure bio-feedback unit, the motion of the point of pressure of the head on the headrest and the force at this point of contact during the activation of the deep flexor muscle group were investigated as an alternative source of feedback. This output, however, was found to be subject specific, depending on the posterior shape of the skull that determined the point of contact during the head rolling action. Clinically, an important outcome of the alternative feedback assessment was that the prescribed action to target the deep flexor muscle group will feel different for each individual, ranging from a slide to a roll of the head on the headrest, and this must be accounted for when explaining the action and during rehabilitation management.

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TEDONE, FABIO. "The mathematical modeling of plant growth and applications to robotics." Doctoral thesis, Gran Sasso Science Institute, 2020. http://hdl.handle.net/20.500.12571/14997.

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In the thesis, a novel modelling approach to study plant growth is proposed. Motivated by the ability of plants to survive and develop in stressful environments, the analysis here proposed focuses on the efficiency of the plant's growing strategies. Many mathematical models have been proposed in the literature to study plants. Here, most of them are critically reviewed. Among them, it still misses a quantitative definition of what the plant is optimising during the growth. In the thesis, the plant is thought as an active agent able to adapt its growing strategy to optimise something. Both the metabolism and the movements of a plant can be assumed as functions to optimise. Firstly, a mechanistic model of the main signals driving the growth has been developed and a novel definition of the plant efficiency arises based on the metabolic needs of the plant. Then, the optimal control theory has been applied to investigate the efficiency of plant motions. This thesis is the first application of optimal control theory to investigate plant motions while taking care of the quantitative and qualitative validation of the model with biological evidence and laboratory experiments. Such an approach is crucial to characterise the plant behaviour and to improve agricultural and ecological studies in those conditions in which laboratory experiments are difficult or expensive to perform. Furthermore, engineers are developing a new technology of robots able to grow and move like plants. Optimal control theory is a suitable tool to translate the efficiency of plant behaviours in features to design plant-inspired robots. In this thesis, the focus is on a specific movement performed by roots during the soil penetration: the circumnutation. The results presented in the thesis help to better study the root-soil interactions (where data lacks due to the soil complexity) and to support the design of autonomous devices able to explore the soil in the most efficient manner. In particular, the soil-root dynamics leads to a new class of optimal control problems describing phenomena in which a mechanical constrained is concerned. In this case, the investigation of the optimal trajectory does not follow in the standard manner. Then, the thesis concerns the characterisation of the optimal control for this new family of problems.

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Lauria, S. "THE ENDOCANNABINOID ENZYME MONOACYLGLYCEROL LIPASE: DEVELOPMENT OF A NEW FLUORESCENT ASSAY AND NOVEL INHIBITORS." Doctoral thesis, Università degli Studi di Milano, 2015. http://hdl.handle.net/2434/336675.

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The endocannabinoid system (ECS), comprising CB1/CB2 receptors, endocannabinoids (ECs) and their metabolic enzymes, FAAH (fatty acid amide hydrolase) and MAGL (monoacylglycerol lipase), is responsible for maintaining the homeostatic balance, regulating and modulating the physiological responses to improve general well-being [1]. A dysregulation of ECS is connected to pathological conditions such as pain, inflammation, anxiety, and other disorders [2]. Pharmacological blockade of FAAH and MAGL has emerged as a potentially attractive strategy to augment EC signalling and retain the beneficial effects of cannabinoid receptor activation, while avoiding the undesirable side effects, such as impairments in cognition and motor control, observed with direct cannabinoid receptor agonists [3]. The endogenous serine-hydrolase MAGL is the main enzyme responsible for inactivating endocannabinoid agonist 2-arachidonoylglycerol (2-AG) to arachidonic acid and glycerol. Conventional assays for MAGL activity and inhibitors screening utilize radiolabelled substrates [4] or MAGL-catalysed hydrolysis of p-nitrophenyl alkyl esters allowing the liberation of UV-detectable p-nitrophenol [5]. Furthermore, a fluorescence-based assay has been developed applying 7-hydroxycoumarinyl arachidonate (7-HCA) [6] or HPLC method with fluorescence detection using as fluorogenic probe 1,3-dihydroxypropan-2-yl-4-pyren-1-ylbutanoate [7]. The objective of this PhD project was to: - develop a new sensitive MAGL-activity assay simple, sensitive, and suitable for high-throughput screening (HTS) to test potential inhibitors, both in vitro and in cell cultures; - synthesise more potent and selective inhibitors in order to increase the endogenous level of EC prolonging their action. A first part of this project has been focused on the development of a novel fluorescent method for assaying MAGL. Therefore, we designed and synthesized 7-hydroxyresorufinylarachidonate (7-HRA) which is amenable for high-throughput screening (HTS). MAGL catalyses the hydrolysis of 7-HRA to generate arachidonic acid and a highly red fluorescent resorufin. Our new substrate [8] combines high specific reactivity with the enzyme tested with excellent stability against non-specific degradation if stored in the dark and can be a useful tool in further developments of MAGL inhibitors. Moreover, resorufin’s high red absorption and emission wavelengths should be preferred in cell cultures assays to blue emitting molecules in reason of the lower background absorbance and auto fluorescence of tissues in this spectral region [9]. Three known MAGL inhibitors were used to validate the test assay. A second part of the project was the synthesis of reference molecule URB602 [10] and a library of analogues that were tested against MAGL with our new fluorescent method. Some of them showed encouraging results in terms of inhibitory activity, proving to have an increase in the activity compared to reference URB602. A molecular modelling work was made to understand the possible interactions between each compound and the enzyme and to explain the differences among the different structures. Moreover, the fluorescent method was applied to cancer cell lysates to verify its suitability for in vitro experiments - which was confirmed - and a first screening on the new inhibitors was made on these cell lines, finding that their activity is comparable to that of URB602. References [1] P. Pacher et al., Pharmacol. Rev. 58 (2006) 389-462 [2] J.Z. Long et al., Nat. Chem. Biol. 5 (2009) 37–44 [3] J.Z. Long et al., P. Natl. Acad. Sci. USA 106 (2009) 20270-20275 [4] J. Brengdahl et al., Anal. Biochem. 359 (2006) 40-44 [5] G.G. Muccioli et al., ChemBioChem 9 (2008) 2704-2710 [6] Y. Wang et al., Assay Drug Dev. Techn. 6 (2008) 387-393 [7] A. Holtfrerich et al., Anal. Biochem. 399 (2010) 218-224 [8] S. Lauria et al., Anal. Bioanal. Chem. (2015), 407, 8163-8167 DOI 10.1007/s00216-015-8991-9. [9] M. Fritzsche et al., Anal. Bioanal. Chem. 398 (2010) 181-191 [10] M. Szabo et al., Bioorg. Med. Chem. Lett. 21 (2011) 6782-6787

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Zhang, Min [Verfasser]. "Modelling and fabrication of high performance Schottky barrier SOI-MOSFETs with low effective Schottky barriers / Forschungszentrum Jülich in der Helmholtz-Gemeinschaft, Institute of Bio- and Nanosystems. Min Zhang." Jülich : Forschungszentrum, Zentralbibliothek, 2006. http://d-nb.info/987947443/34.

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Dubey, Satya P. "Mathematical modelling and simulation of continuous, highly precise, metal/eco-friendly polymerization of Lactide using alternative energies for reaction extrusion." Thesis, Cranfield University, 2016. http://dspace.lib.cranfield.ac.uk/handle/1826/11253.

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Polylactic acid (PLA) is one of the most promising bio-compostable and biodegradable thermoplastic made from renewable sources. PLA, is typically obtained by polymerising lactide monomer. The technique mainly used for ring opening polymerization (ROP) of Lactide is based on metallic/bimetallic catalyst (Sn, Zn, and Al) or other organic catalysts in suitable solvent. However, the PLA synthesized using such catalysts may contain trace elements of the catalyst, which may be toxic. In this work, reactive extrusion experiments using stannous octoate Sn(Oct)2 and tri-phenyl phosphine (PPh)3 were considered to perform ROP of lactide monomer using ultrasound as an alternative energy (AE) source for activating and/or boosting the polymerization. Mathematical model of ROP of lactide, was developed to estimate the impact of reaction kinetics and AE source on the polymerization process. Ludovic® software, a commercial code was used. It was adopted for the simulation of continuous reactive extrusion of PLA. Results from experiments and simulations were compared to validate the simulation methodology. Results indicate that the application of AE source in reaction process boost the PLA formation rate. Result obtained through Ludovic simulation and experiments were validated. It was shown that there is a case for reducing the residence time distribution (RTD) in Ludovic due to the ‘liquid’ monomer flow in the extruder. This change in the parameters resulted in validation of the simulation. However, it was concluded that the assumption would have to be established by doing further validations. The simulation model includes the details of kinetics of reactions involved with in the process and helps to upscale the reaction output. This work also estimates the usefulness and drawbacks of using different catalysts as well as effect of alternative energies and future aspects for PLA production.

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Litou, Charalampia [Verfasser], Jennifer B. [Akademischer Betreuer] Dressman, Christos [Akademischer Betreuer] Reppas, Jennifer B. [Gutachter] Dressman, and Martin [Gutachter] Kuentz. "Predicting the in vivo performance of bio‐enabling formulations by combining biorelevant in vitro tools with physiologically based absorption modelling / Charalampia Litou ; Gutachter: Jennifer B. Dressman, Martin Kuentz ; Jennifer B. Dressman, Christos Reppas." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2021. http://d-nb.info/1235221210/34.

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Moiroux, Nicolas. "Modélisation du risque d'exposition aux moustiques vecteurs de Plasmodium spp. dans un contexte de lutte anti-vectorielle." Phd thesis, Université Montpellier II - Sciences et Techniques du Languedoc, 2012. http://tel.archives-ouvertes.fr/tel-00812118.

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L'accroissement des résistances aux insecticides chez les anophèles vecteurs de Plasmodium sont mises en cause dans la baisse d'efficacité des principales stratégies de lutte antivectorielle (LAV) en Afrique. Des techniques de combinaisons d'insecticides, évaluées au Bénin, n'ont pas été plus efficaces pour réduire la morbidité palustre et limiter l'extension des résistances que la stratégie préconisée par le Programme National de Lutte contre le Paludisme (moustiquaires imprégnée seules). Dans cette thèse, nous avons cherché à identifier les facteurs opérationnels, biologiques et environnementaux pouvant expliquer cet échec. Nous avons modélisé le risque d'exposition de l'homme aux piqûres de vecteurs en fonction de variables environnementales afin (i) d'identifier les déterminants de la présence et de la densité des vecteurs et (ii) d'analyser l'impact des méthodes de LAV. Nos résultats ont montré à l'échelle des villages une forte hétérogénéité spatio-temporelle de la population vectorielle, caractérisée par des niches écologiques et comportementales différentes qui a ont pu moduler l'efficacité de la LAV. Nous avons mis en évidence le rôle vectoriel majeur de An. funestus qui assurait la transmission en saison sèche tandis que le taux d'utilisation des moustiquaires diminuait en raison des fortes températures et de la baisse de nuisance culicidenne. De plus, nous avons observé des modifications comportementales chez les vecteurs suite à la mise en place de méthodes de LAV. Nous faisons donc des propositions pour l'amélioration des méthodes actuelles de LAV, pour définir les caractéristiques des futures méthodes et pour mieux choisir les méthodes à implémenter en fonction du faciès entomologique.

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Yuan, Haifeng, and Haifeng Yuan. "Degradation modeling of concrete submitted to biogenic acid attack." Phd thesis, Université Paris-Est, 2013. http://pastel.archives-ouvertes.fr/pastel-00985468.

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Bio-deterioration of concrete, which is very common in sewer system and waste water treatment plant, results in significant structure degradation. Normally, the process can be described by the two following parts: 1) Biochemistry reactions producing biogenic aggressive species in biofilms which are spread on the surface of concrete. As one of the most significant biogenic acid in sewer pipes, sulfuric acid (H2SO4) is produced by sulfur oxidizing bacteria (SOB). 2) Chemical reactions between biogenic aggressive species and cement hydration products which is responsible for concrete deterioration. A reactive transport model is proposed to simulate the bio-chemical and chemical deterioration processes of cementitious materials in contact with SOB and H2S or sulfuric acid solution. This model aims at solving simultaneously transport and biochemistry/chemistry in biofilms and cementitious materials by a global coupled approach. To provide an appropriate environment for SOB to grow, the surface neutralization of concrete (i.e., the absorption of H2S and aqueous H2S corrosion) is considered. To obtain the amount of biogenic H2SO4, the bio-oxidation of H2S by the activation of bacteria is simulated via a simplified model. To provide a suitable environment for SOB to grow, the abiotic pH reduction of concrete process is introduced. The production rate of H2SO4 is governed by the pH in the biofilms and the content of H2S in gas.It is assumed that all chemical processes are in thermodynamical equilibrium. The dissolution of portlandite (CH) and calcium silicate hydrates (C-S-H) and the precipitation of gypsum (C¯S H2) and calcium sulfide are described by mass action law and threshold of ion activity products. To take into account the continuous decrease of the Ca/Si ratio during the dissolution of C-S-H a generalization of the mass action law is applied. By simplifying the precipitation process of gypsum, a damage model is introduced to characterize the deterioration of concrete due to the swelling of gypsum. Thus, the porosity evolution and deterioration depth during deterioration process are taken into account. Only diffusion of aqueous species are considered. Different diffusion coefficients are employed for various ions and Nernst-Planck equation was implemented. The effect of the microstructure change during deterioration on transport properties is considered as well. For both biofilms and cementitious materials, the balance equations of total mass of each atom (Ca, Si, S, K, Cl) are used to couple transport equations and (bio-)chemical reactions. The model is implemented within a finite-volume code, Bil. Following the introduction of principle of the finite volume method, the coupling of the bio-chemistry process in biofilms and chemistry process in cementitious materials is illustrated. By this model, some experiments reported in literature, including chemical immersion tests (statical solution condition and flow solution condition) and microbiological simulation tests, are simulated. The numerical results and the experimental observations are compared and discussed. The influence of properties of cementitious materials (initial porosity, carbonated layer, etc.) and environmental factors (concentration of H2SO4, content of H2S, etc.) are investigated by this model as well. Furthermore, a long term predictionis conducted

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Jendoubi, Naoufel. "Mécanismes de transfert des inorganiques dans les procédés de pyrolyse rapide de la biomasse : Impacts de la variabilité des ressources lignocellulosiques sur la qualité des bio-huiles." Thesis, Vandoeuvre-les-Nancy, INPL, 2011. http://www.theses.fr/2011INPL062N/document.

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La pyrolyse rapide de biomasse est un procédé de conversion thermochimique qui permet de produire principalement des huiles de pyrolyse valorisables dans le domaine de l’énergie. Les espèces inorganiques initialement présentes dans la biomasse sont à l’origine de problèmes d’instabilité des huiles, de dépôts et d’encrassement. L’objectif de ce travail consiste à mieux comprendre les mécanismes de transfert des inorganiques depuis la biomasse vers les huiles dans les procédés de pyrolyse rapide.Une méthodologie est mise au point afin de quantifier la répartition des alcalins et alcalino-terreux (K, Ca, Mg et Na), identifiés comme les plus néfastes, dans les produits (charbons et huiles) issus de pyrolyse de bois et de paille de blé. Deux dispositifs complémentaires sont utilisés, pour lesquels les bilans de matière bouclent de façon très satisfaisante: un réacteur pilote de pyrolyse rapide en lit fluidisé et un réacteur laboratoire en four tubulaire. Dans tous les cas, le charbon séquestre 99% des éléments minéraux issus de la biomasse. En outre, grâce à un dispositif original de condensation fractionnée des huiles, on démontre que plus de 60% des inorganiques restants dans les huiles de pyrolyse proviennent des aérosols, ce résultat ouvrant une discussion quant à leur origine. Les teneurs en inorganiques des huiles sont par ailleurs fortement liées à la présence de fines particules de charbon mal séparées dans le procédé. Les possibilités de traitement amont ou aval sont discutées, afin de diminuer ces concentrations.Enfin, des expériences parallèles associées à un modèle permettent de décrire quantitativement les mécanismes de transfert entre les particules de charbon et une phase liquide lors du stockage d’huiles de pyrolyse
Biomass fast pyrolysis is a promising process for the preparation of bio-oils dedicated to energy production. Inorganic species originally present in biomass are known to induce problems such as bio-oil instability, deposits and fouling. The purpose of the present work is to better understand the mechanisms of inorganic species transfer from biomass to bio-oils in fast pyrolysis processes. A methodology is developed for quantifying alkali and alkali-earth species (K, Ca, Mg, Na) distribution in the products (chars and bio-oils) issued from wheat straw and beech wood fast pyrolysis. Two complementary devices are used: a pilot plant fluidized bed reactor, and a horizontal tubular reactor. Mass balances closures are accurately achieved. 99 wt.% of the inorganic species originally contained in biomass are recovered in the chars. Thanks to an original bio-oils fractional condensation device, it is shown that more than 60 wt.% of the inorganic content of overall bio-oil is contained in the aerosols. Different assumptions of possible origins of the aerosols are discussed. Inorganic content of bio-oil is strongly connected to the presence of fine chars particles which are not efficiently separated by the cyclones, and, hence recovered in the bio-oils. The possibilities of upstream or downstream treatments are discussed in order to lower inorganic content of bio-oils. Finally, the mechanisms of inorganics transfers between char particles and a liquid phase, during bio-oil storage, are quantitatively described on the basis of side experiments associated to a model

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Picard, Vincent. "Réseaux de réactions : de l’analyse probabiliste à la réfutation." Thesis, Rennes 1, 2015. http://www.theses.fr/2015REN1S093/document.

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L'étude de la dynamique des réseaux de réactions est un enjeu majeur de la biologie des systèmes. Cela peut-être réalisé de deux manières : soit de manière déterministe à l'aide d'équations différentielles, soit de manière probabiliste à l'aide de chaînes de Markov. Dans les deux cas, un problème majeur est celui de la détermination des lois cinétiques impliquées et l'inférence de paramètres cinétiques associés. Pour cette raison, l'étude directe de grands réseaux de réactions est impossible. Dans le cas de la modélisation déterministe, ce problème peut-être contourné à l'aide d'une analyse stationnaire du réseau. Une méthode connue est celle de l'analyse des flux à l'équilibre (FBA) qui permet d'obtenir des systèmes de contraintes à partir d'informations sur les pentes moyennes des trajectoires. Le but de cette thèse est d'introduire une méthode analogue dans le cas de la modélisation probabiliste. Les résultats de la thèse se divisent en trois parties. Tout d'abord on présente une analyse stationnaire de la modélisation probabiliste reposant sur une approximation de Bernoulli. Dans un deuxième temps, cette dynamique approximée nous permet d'établir des systèmes de contraintes à l'aide d'informations obtenues sur les moyennes, les variances et les co-variances des trajectoires du système. Enfin, on présente plusieurs applications à ces systèmes de contraintes telles que la possibilité de réfuter des réseaux de réactions à l'aide d'informations de variances ou de co-variances et la vérification formelle de propriétés logiques sur le régime stationnaire du système
A major goal in systems biology is to inverstigate the dynamical behavior of reaction networks. There exists two main dynamical frameworks : the first one is the deterministic dynamics where the dynamics is described using odinary differential equations, the second one is probabilistic and relies on Markov chains. In both cases, one major issue is to determine the kinetic laws of the systems together with its kinetic parameters. As a consequence the direct study of large biological reaction networks is impossible. To deal with this issue, stationnary assumptions have been used. A widely used method is flux balance analysis, where systems of constraints are derived from information on the average slopes of the system trajectories. In this thesis, we construct a probabilistic analog of this stationnary analysis. The results are divided into three parts. First, we introduce a stationnary analysis of the probabilistic dynamics which relies on a Bernoulli approximation. Second, this approximated dynamics allows us to derive systems of constraints from information about the means, variances and co-variances of the system trajectories. Third, we present several applications of these systems of constraints such as the possibility to reject reaction networks using information from experimental variances and co-variances and the formal verification of logical properties concerning the stationnary regime of the system

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Dissertations / Theses on the topic 'Bio-modelling'

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