More is Different: Modern Computational Modeling for Heterogeneous Catalysis

La combinació d'observacions experimentals i estudis de la Density Functional Theory (DFT) és un dels pilars de la investigació química moderna. Atès que permeten recopilar informació física addicional d'un sistema químic, difícilment accessible a través de l'entorn experimental, aquests estudis es fan servir àmpliament per modelar i predir el comportament d'una gran varietat de compostos químics en entorns únics. A la catàlisi heterogènia, els models DFT s'utilitzen habitualment per avaluar la interacció entre els compostos moleculars i els catalitzadors, vinculant aquestes interpretacions amb els resultats experimentals. Tanmateix, l'alta complexitat trobada tant als escenaris catalítics com a la reactivitat, implica la necessitat de metodologies sofisticades que requereixen automatització, emmagatzematge i anàlisi per estudiar correctament aquests sistemes. Aquest treball presenta el desenvolupament i la combinació de múltiples metodologies per avaluar correctament la complexitat d'aquests sistemes químics. A més, aquest treball mostra com s'han utilitzat les tècniques proporcionades per estudiar noves configuracions catalítiques d'interès acadèmic i industrial.La combinación de observaciones experimentales y estudios de la Density Functional Theory (DFT) es uno de los pilares de la investigación química moderna. Dado que permiten recopilar información física adicional de un sistema químico, difícilmente accesible a través del entorno experimental, estos estudios se emplean ampliamente para modelar y predecir el comportamiento de una gran variedad de compuestos químicos en entornos únicos. En la catálisis heterogénea, los modelos DFT se emplean habitualmente para evaluar la interacción entre los compuestos moleculares y los catalizadores, vinculando estas interpretaciones con los resultados experimentales. Sin embargo, la alta complejidad encontrada tanto en los escenarios catalíticos como en la reactividad, implica la necesidad de metodologías sofisticadas que requieren de automatización, almacenamiento y análisis para estudiar correctamente estos sistemas. Este trabajo presenta el desarrollo y la combinación de múltiples metodologías con el objetivo de evaluar correctamente la complejidad de estos sistemas químicos. Además, este trabajo muestra cómo las técnicas proporcionadas se han utilizado para estudiar nuevas configuraciones catalíticas de interés académico e industrial.The combination of Experimental observations and Density Functional Theory studies is one of the pillars of modern chemical research. As they enable the collection of additional physical information of a chemical system, hardly accessible via the experimental setting, Density Functional Theory studies are widely employed to model and predict the behavior of a diverse variety of chemical compounds under unique environments. Particularly, in heterogeneous catalysis, Density Functional Theory models are commonly employed to evaluate the interaction between molecular compounds and catalysts, lately linking these interpretations with experimental results. However, high complexity found in both, catalytic settings and reactivity, implies the need of sophisticated methodologies involving automation, storage and analysis to correctly study these systems. Here, I present the development and combination of multiple methodologies, aiming at correctly asses complexity. Also, this work shows how the provided techniques have been actively used to study novel catalytic settings of academic and industrial interest

A Farewell to Flat Biology. Three-dimensional Cell Culture Models in Cancer Drug Target Identification and Validation

Cells of epithelial origin, e.g. from breast and prostate cancers, effectively differentiate into complex multicellular structures when cultured in three-dimensions (3D) instead of conventional two-dimensional (2D) adherent surfaces. The spectrum of different organotypic morphologies is highly dependent on the culture environment that can be either non-adherent or scaffold-based. When embedded in physiological extracellular matrices (ECMs), such as laminin-rich basement membrane extracts, normal epithelial cells differentiate into acinar spheroids reminiscent of glandular ductal structures. Transformed cancer cells, in contrast, typically fail to undergo acinar morphogenic patterns, forming poorly differentiated or invasive multicellular structures. The 3D cancer spheroids are widely accepted to better recapitulate various tumorigenic processes and drug responses. So far, however, 3D models have been employed predominantly in the Academia, whereas the pharmaceutical industry has yet to adopt a more widely and routine use. This is mainly due to poor characterisation of cell models, lack of standardised workflows and high throughput cell culture platforms, and the availability of proper readout and quantification tools. In this thesis, a complete workflow has been established entailing well-characterised 3D cell culture models for prostate cancer, a standardised 3D cell culture routine based on high-throughput-ready platform, automated image acquisition with concomitant morphometric image analysis, and data visualisation, in order to enable large-scale high-content screens. Our integrated suite of software and statistical analysis tools were optimised and validated using a comprehensive panel of prostate cancer cell lines and 3D models. The tools quantify multiple key cancer-relevant morphological features, ranging from cancer cell invasion through multicellular differentiation to growth, and detect dynamic changes both in morphology and function, such as cell death and apoptosis, in response to experimental perturbations including RNA interference and small molecule inhibitors. Our panel of cell lines included many non-transformed and most currently available classic prostate cancer cell lines, which were characterised for their morphogenetic properties in 3D laminin-rich ECM. The phenotypes and gene expression profiles were evaluated concerning their relevance for pre-clinical drug discovery, disease modelling and basic research. In addition, a spontaneous model for invasive transformation was discovered, displaying a highdegree of epithelial plasticity. This plasticity is mediated by an abundant bioactive serum lipid, lysophosphatidic acid (LPA), and its receptor LPAR1. The invasive transformation was caused by abrupt cytoskeletal rearrangement through impaired G protein alpha 12/13 and RhoA/ROCK, and mediated by upregulated adenylyl cyclase/cyclic AMP (cAMP)/protein kinase A, and Rac/ PAK pathways. The spontaneous invasion model tangibly exemplifies the biological relevance of organotypic cell culture models. Overall, this thesis work underlines the power of novel morphometric screening tools in drug discovery.Siirretty Doriast

Multi-scale Modelling of Allostery in Protein Homodimers

Allostery is a form of signalling within biomolecules such that ligand binding to a protein affects its activity at a second site. Allostery was described by early models to be driven by structural changes in the protein. However, more recently there has been increasing evidence that dynamics can contribute to or even drive allostery. The protein studied in this thesis, the Catabolite Activator Protein (CAP), is an allosteric protein homodimer that has been shown to exhibit negatively cooperative binding of the ligand cyclic Adenosine Monophosphate (cAMP) to each of its monomers. Interestingly, CAP is a protein whose allostery is believed to be driven by dynamics rather than a conformational change. In this thesis, a number of coarse grained models are employed to investigate this dynamic allostery in CAP. One family of models, termed Super Coarse Grained (SCG) models explore the global properties of the dynamics of the CAP dimer that cause it to exhibit negatively cooperative allostery. It is shown through these models that changes in protein interactions can provide a basis for changing cooperativity. A second family of coarse grained models called Elastic Network Models (ENM) are studied. These are used to show that adjusting the interactions between specific residues can affect cooperative binding of cAMP to CAP. A number of atomistic approaches are also used to study the cAMP-CAP system, including Molecular Dynamics (MD) and Normal Mode Analysis (NMA). The efficacy of using such approaches for studying the thermodynamics of the allostery in CAP is investigated. The motion observed within the protein is also studied closely to identify potential allosteric pathways. X-ray crystallography and Isothermal Titration Calorimetry (ITC) are finally used to investigate how accurately computational methods can describe the cooperative binding of cAMP to CAP. They are also used to try and determine whether the allostery in CAP can be manipulated experimentally without any observed changes to its structure

Uniscale and multiscale gait recognition in realistic scenario

The performance of a gait recognition method is affected by numerous challenging factors that degrade its reliability as a behavioural biometrics for subject identification in realistic scenario. Thus for effective visual surveillance, this thesis presents five gait recog- nition methods that address various challenging factors to reliably identify a subject in realistic scenario with low computational complexity. It presents a gait recognition method that analyses spatio-temporal motion of a subject with statistical and physical parameters using Procrustes shape analysis and elliptic Fourier descriptors (EFD). It introduces a part- based EFD analysis to achieve invariance to carrying conditions, and the use of physical parameters enables it to achieve invariance to across-day gait variation. Although spatio- temporal deformation of a subject’s shape in gait sequences provides better discriminative power than its kinematics, inclusion of dynamical motion characteristics improves the iden- tification rate. Therefore, the thesis presents a gait recognition method which combines spatio-temporal shape and dynamic motion characteristics of a subject to achieve robust- ness against the maximum number of challenging factors compared to related state-of-the- art methods. A region-based gait recognition method that analyses a subject’s shape in image and feature spaces is presented to achieve invariance to clothing variation and carry- ing conditions. To take into account of arbitrary moving directions of a subject in realistic scenario, a gait recognition method must be robust against variation in view. Hence, the the- sis presents a robust view-invariant multiscale gait recognition method. Finally, the thesis proposes a gait recognition method based on low spatial and low temporal resolution video sequences captured by a CCTV. The computational complexity of each method is analysed. Experimental analyses on public datasets demonstrate the efficacy of the proposed methods

Advances in Image Processing, Analysis and Recognition Technology

For many decades, researchers have been trying to make computers’ analysis of images as effective as the system of human vision is. For this purpose, many algorithms and systems have previously been created. The whole process covers various stages, including image processing, representation and recognition. The results of this work can be applied to many computer-assisted areas of everyday life. They improve particular activities and provide handy tools, which are sometimes only for entertainment, but quite often, they significantly increase our safety. In fact, the practical implementation of image processing algorithms is particularly wide. Moreover, the rapid growth of computational complexity and computer efficiency has allowed for the development of more sophisticated and effective algorithms and tools. Although significant progress has been made so far, many issues still remain, resulting in the need for the development of novel approaches

Face pose estimation with automatic 3D model creation for a driver inattention monitoring application

Texto en inglés y resumen en inglés y españolRecent studies have identified inattention (including distraction and drowsiness) as the main cause of accidents, being responsible of at least 25% of them. Driving distraction has been less studied, since it is more diverse and exhibits a higher risk factor than fatigue. In addition, it is present over half of the inattention involved crashes. The increased presence of In Vehicle Information Systems (IVIS) adds to the potential distraction risk and modifies driving behaviour, and thus research on this issue is of vital importance. Many researchers have been working on different approaches to deal with distraction during driving. Among them, Computer Vision is one of the most common, because it allows for a cost effective and non-invasive driver monitoring and sensing. Using Computer Vision techniques it is possible to evaluate some facial movements that characterise the state of attention of a driver. This thesis presents methods to estimate the face pose and gaze direction of a person in real-time, using a stereo camera as a basic for assessing driver distractions. The methods are completely automatic and user-independent. A set of features in the face are identified at initialisation, and used to create a sparse 3D model of the face. These features are tracked from frame to frame, and the model is augmented to cover parts of the face that may have been occluded before. The algorithm is designed to work in a naturalistic driving simulator, which presents challenging low light conditions. We evaluate several techniques to detect features on the face that can be matched between cameras and tracked with success. Well-known methods such as SURF do not return good results, due to the lack of salient points in the face, as well as the low illumination of the images. We introduce a novel multisize technique, based on Harris corner detector and patch correlation. This technique benefits from the better performance of small patches under rotations and illumination changes, and the more robust correlation of the bigger patches under motion blur. The head rotates in a range of ±90º in the yaw angle, and the appearance of the features change noticeably. To deal with these changes, we implement a new re-registering technique that captures new textures of the features as the face rotates. These new textures are incorporated to the model, which mixes the views of both cameras. The captures are taken at regular angle intervals for rotations in yaw, so that each texture is only used in a range of ±7.5º around the capture angle. Rotations in pitch and roll are handled using affine patch warping. The 3D model created at initialisation can only take features in the frontal part of the face, and some of these may occlude during rotations. The accuracy and robustness of the face tracking depends on the number of visible points, so new points are added to the 3D model when new parts of the face are visible from both cameras. Bundle adjustment is used to reduce the accumulated drift of the 3D reconstruction. We estimate the pose from the position of the features in the images and the 3D model using POSIT or Levenberg-Marquardt. A RANSAC process detects incorrectly tracked points, which are not considered for pose estimation. POSIT is faster, while LM obtains more accurate results. Using the model extension and the re-registering technique, we can accurately estimate the pose in the full head rotation range, with error levels that improve the state of the art. A coarse eye direction is composed with the face pose estimation to obtain the gaze and driver's fixation area, parameter which gives much information about the distraction pattern of the driver. The resulting gaze estimation algorithm proposed in this thesis has been tested on a set of driving experiments directed by a team of psychologists in a naturalistic driving simulator. This simulator mimics conditions present in real driving, including weather changes, manoeuvring and distractions due to IVIS. Professional drivers participated in the tests. The driver?s fixation statistics obtained with the proposed system show how the utilisation of IVIS influences the distraction pattern of the drivers, increasing reaction times and affecting the fixation of attention on the road and the surroundings

Face pose estimation with automatic 3D model creation for a driver inattention monitoring application

Texto en inglés y resumen en inglés y españolRecent studies have identified inattention (including distraction and drowsiness) as the main cause of accidents, being responsible of at least 25% of them. Driving distraction has been less studied, since it is more diverse and exhibits a higher risk factor than fatigue. In addition, it is present over half of the inattention involved crashes. The increased presence of In Vehicle Information Systems (IVIS) adds to the potential distraction risk and modifies driving behaviour, and thus research on this issue is of vital importance. Many researchers have been working on different approaches to deal with distraction during driving. Among them, Computer Vision is one of the most common, because it allows for a cost effective and non-invasive driver monitoring and sensing. Using Computer Vision techniques it is possible to evaluate some facial movements that characterise the state of attention of a driver. This thesis presents methods to estimate the face pose and gaze direction of a person in real-time, using a stereo camera as a basic for assessing driver distractions. The methods are completely automatic and user-independent. A set of features in the face are identified at initialisation, and used to create a sparse 3D model of the face. These features are tracked from frame to frame, and the model is augmented to cover parts of the face that may have been occluded before. The algorithm is designed to work in a naturalistic driving simulator, which presents challenging low light conditions. We evaluate several techniques to detect features on the face that can be matched between cameras and tracked with success. Well-known methods such as SURF do not return good results, due to the lack of salient points in the face, as well as the low illumination of the images. We introduce a novel multisize technique, based on Harris corner detector and patch correlation. This technique benefits from the better performance of small patches under rotations and illumination changes, and the more robust correlation of the bigger patches under motion blur. The head rotates in a range of ±90º in the yaw angle, and the appearance of the features change noticeably. To deal with these changes, we implement a new re-registering technique that captures new textures of the features as the face rotates. These new textures are incorporated to the model, which mixes the views of both cameras. The captures are taken at regular angle intervals for rotations in yaw, so that each texture is only used in a range of ±7.5º around the capture angle. Rotations in pitch and roll are handled using affine patch warping. The 3D model created at initialisation can only take features in the frontal part of the face, and some of these may occlude during rotations. The accuracy and robustness of the face tracking depends on the number of visible points, so new points are added to the 3D model when new parts of the face are visible from both cameras. Bundle adjustment is used to reduce the accumulated drift of the 3D reconstruction. We estimate the pose from the position of the features in the images and the 3D model using POSIT or Levenberg-Marquardt. A RANSAC process detects incorrectly tracked points, which are not considered for pose estimation. POSIT is faster, while LM obtains more accurate results. Using the model extension and the re-registering technique, we can accurately estimate the pose in the full head rotation range, with error levels that improve the state of the art. A coarse eye direction is composed with the face pose estimation to obtain the gaze and driver's fixation area, parameter which gives much information about the distraction pattern of the driver. The resulting gaze estimation algorithm proposed in this thesis has been tested on a set of driving experiments directed by a team of psychologists in a naturalistic driving simulator. This simulator mimics conditions present in real driving, including weather changes, manoeuvring and distractions due to IVIS. Professional drivers participated in the tests. The driver?s fixation statistics obtained with the proposed system show how the utilisation of IVIS influences the distraction pattern of the drivers, increasing reaction times and affecting the fixation of attention on the road and the surroundings