Simulation of the spatial structure and cellular organization evolution of cell aggregates arranged in various simple geometries, using a kinetic monte carlo method applied to a lattice model

ilustraciones, graficasEsta tesis trata los modelos de morfogénesis, en particular los modelos de evolución guiada por contacto que son coherentes con la hipótesis de la adhesión diferencial. Se presenta una revisión de algunos modelos, sus principios biológicos subyacentes, la relevancia y aplicaciones en el marco de la bioimpresión, la ingeniería de tejidos y la bioconvergencia. Luego, se presentan los detalles de los modelos basados en métodos de Monte Carlo para profundizar más adelante en el modelo basados en algoritmos Kinetic Monte Carlo (KMC) , más específicamente, se describe en detalle un modelo KMC de autoaprendizaje (SL-KMC). Se presenta y explica la estructura algorítmica del código implementado, se evalúa el rendimiento del modelo y se compara con un modelo KMC tradicional. Finalmente, se realizan los procesos de calibración y validación, se observó que el modelo es capaz de replicar la evolución del sistema multicelular cuando las condiciones de energía interfacial del sistema simulado son similares a las del sistema de calibraciones. (Texto tomado de la fuente)This thesis treats the models for morphogenesis, in particular the contact-guided evolution models that are coherent with the differential adhesion hypothesis. A review of some models, their biological underpinning principles, the relevance and applications in the framework of bioprinting, tissue engineering and bioconvergence are presented. Then the details for the Monte Carlo methods-based models are presented to later deep dive into the Kinetic Monte Carlo (KMC) based model, and more specifically a Self-Learning KMC (SL-KMC) model is described to detail. The algorithmic structure of the implemented code is presented and explained, the model performance is assessed and compared with a traditional KMC model. Finally, the calibration and validation processes have been carried out, it was observed that the model is able to replicate the multicellular system evolution when the interfacial energy conditions of the simulated system are similar to those of the calibrations system.MaestríaMagíster en Ingeniería - Ingeniería Químic

The emergence of biofilms:Computational and experimental studies

The response of biofilms to any external stimuli is a cumulative response aggregated from individual bacteria residing within the biofilm. The organizational complexity of biofilm can be studied effectively by understanding bacterial interactions at cell level. The overall aim of the thesis is to explore the complex evolutionary behaviour of bacterial biofilms. This thesis is divided into three major studies based on the type of perturbation analysed in the study. The first study analyses the physics behind the development of mushroom-shaped structures from the influence of nutrient cues in biofilms. Glazier-Graner-Hogeweg model is used to simulate the cell characteristics. From the study, it is observed that chemotaxis of bacterial cells towards nutrient source is one of the major precursors for formation of mushroom-shaped structures. The objective of the second study is to analyse the impact of environmental conditions on the inter-biofilm quorum sensing (QS) signalling. Using a hybrid convection-diffusion-reaction model, the simulations predict the diffusivity of QS molecules, the spatiotemporal variations of QS signal concentrations and the competition outcome between QS and quorum quenching mutant bacterial communities. The mechanical effects associated with the fluid-biofilm interaction is addressed in the third study. A novel fluid-structure interaction model based on fluid dynamics and structural energy minimization is developed in the study. Model simulations are used to analyse the detachment and surface effects of the fluid stresses on the biofilm. In addition to the mechanistic models described, a separate study is carried out to estimate the computational efficiency of the biofilm simulation models

LHCb distributed data analysis on the computing grid

LHCb is one of the four Large Hadron Collider (LHC) experiments based at CERN, the European Organisation for Nuclear Research. The LHC experiments will start taking an unprecedented amount of data when they come online in 2007. Since no single institute has the compute resources to handle this data, resources must be pooled to form the Grid. Where the Internet has made it possible to share information stored on computers across the world, Grid computing aims to provide access to computing power and storage capacity on geographically distributed systems. LHCb software applications must work seamlessly on the Grid allowing users to efficiently access distributed compute resources. It is essential to the success of the LHCb experiment that physicists can access data from the detector, stored in many heterogeneous systems, to perform distributed data analysis. This thesis describes the work performed to enable distributed data analysis for the LHCb experiment on the LHC Computing Grid

Influência do surfactante na evolução de espumas molhadas e definição dos graus de liberdade do Modelo de Potts Celular

A dinâmica de crescimento de espumas depende da fração de líquido, , que elas possuem. A dinâmica nos casos limites ! 0% (espuma seca) e > 40% (líquido com bolhas) estão bem definidos. Entretanto, a região de transição entre eles ainda carece de explicação. Neste trabalho vamos investigar, através de simulações computacionais tridimensionais, a influência do surfactante na evolução da espuma quando a fração líquida dela é intermediária. As simulações serão feitas no ambiente computacional Compucell3D, que se baseia no modelo de Potts Celular, uma generalização do modelo de Potts. Parte da investigação será justamente sobre características do modelo de Potts Celular. A saber, o que são os graus de liberdade de sistemas que utilizam esse modelo e como a energia do sistema se altera conforme se muda o volume alvo para células do mesmo.Foam growth dynamics depend on its liquid fraction, . The dynamics in the limits of ! 0% (dry foams) and > 40% (bubbly liquid) are well defined. However, the transition region between them still lacks explanation. In this work we will investigate, through three-dimensional computational simulations, the surfactant’s influence on the evolution of a foam when its liquid fraction is intermediate. The computational simulations will be done in the computational environment Compucell3D, which is based on the Celular Potts Model, a generalization of the Potts model. Part of the investigation will be about characteristics of Celular Potts Model. Namely, what are the degrees of freedom of systems that use this model and how the system’s energy changes with the cells’ target volume

Solid tumour growth: a comparison of mathematical models and computer simulations

SIGLEAvailable from British Library Document Supply Centre-DSC:DXN025363 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Morphological characterization of soft matter systems using advanced 3-dimensional imaging

Soft matter systems, such as foams and emulsions, play a central role in numerous applications for consumer goods, mineral beneficiation, and enhanced oil recovery. Detailed microstructural information of the soft matter system enables accurate modeling of its aging mechanisms and bulk mechanical properties. Foams and emulsions are traditionally characterized in 2D using microscopy or evaluating bulk properties, which lack the full 3D vision of the internal structure of the system. Herein, X-ray computed microtomography (µ-CT) coupled with advanced image processing tools is used for extracting detailed microstructural information of foams and emulsions. The derived morphological information is used for evaluating the aging mechanisms of liquid foams, and the arrested coalescence of oil-in-water emulsions. Firstly, a workflow for 3D µ-CT imaging and pore network modeling (PNM) is developed to characterize drainage, coalescence, and diffusive-coarsening in liquid foams. PNM is useful for decomposition of the Plateau borders and nodes within the liquid structure of the foams, while µ-CT provides time-lapsed spatial information. Foam permeability (ĸ) simulations conducted on the extracted PNM are shown to aid foam drainage modeling by the extraction of ĸ versus liquid fraction relationships. Secondly, challenges in using laboratory µ-CT systems are dealt with by the implementation of deep learning. It is demonstrated that deep learning can reduce scan times to only 5 minutes, thus, allowing high temporal resolution for the study of fast-aging liquid foams. These developments are achieved using a laboratory µ-CT system that is traditionally used for imaging static systems over hour-long scan time. Thirdly, novel measurements for droplet networks of oil-in-water emulsions formed via arrested coalescence are presented. Combination of topological and geometrical measurements is demonstrated as effective means for evaluating the stabilizing forces present in the arrested system. Particularly, linear strain measurements of the 3D droplet network elucidate the distribution of strain and stresses within the network, which is not possible to observe in 2D studies. Overall, the dissertation is a step forward in advancing 3D µ-CT imaging for characterizing and modeling soft matter systems

Modelos formales para la simulación de la epidermis humana

Tesis doctoral inédita léida en la Universidad Autónoma de Madrid, Escuela Politécnica Superior, Departamento de Ingeniería Informática. Fecha de lectura: enero del 2014La epidermis humana es un ejemplo de sistema complejo. Está compuesto por multitud de copias de diferentes tipos de células. El comportamiento del sistema completo emerge de las conductas individuales de sus células. Se han desarrollado muchos modelos que describen la conducta individual de las células. En muchas ocasiones, el conocimiento que se tiene de la aportación de la conducta de cada célula a la conducta del tejido completo es de alto grado de abstracción y la poseen los expertos de este dominio. Estas conduc-tas individuales son bien conocidas. Son muchas las razones por las que pue-de resultar de interés la simulación de este órgano. Por todo esto, estamos ante las características que habitualmente hacen provechoso un enfoque ba-sado en modelos de cómputo bioinspirados. Los autómatas celulares serían uno de los sistemas que, por su definición, podrían considerarse ideales para abordar la simulación de la epidermis. Sin embargo, una característica fun-damental tiene que ser incorporada a cualquier simulador de la epidermis: mantener una configuración de mínima energía en cada instante. Los mode-los matemáticos más prometedores en la simulación de tejidos y que, por tanto, incorporan esta característica, son la familia de modelos que parte del modelo de Ising, sigue por el modelo de Potts y el modelo extendido a células de Potts y termina con el modelo CPM-GGH. Una de las principales limitacio-nes para la aplicación de este modelo para problemas reales relacionados con la epidermis es el rendimiento. Una vía tradicional para subsanar esta limita-ción es el acceso a recursos masivamente paralelos mediante versiones para-lelas, concurrentes y distribuidas de los algoritmos de simulación iii La presente tesis doctoral utiliza una implementación del modelo CPM-GGH para definir un modelo básico de epidermis que simula con éxito el proceso de homeostasis y regeneración de pérdida de capas celulares en rasguños. Este modelo permitirá, en líneas futuras abordar la simulación de fenómenos más complejos. También se han abordado dos posibles aproximaciones a la ejecución me-diante hardware paralelo de versiones de los algoritmos que simulan los mo-delos básicos que subyacen al CPM-GGH. Estas aproximaciones permitirán en el futuro proporcionar versiones paralelas y más eficientes que permitan abordar la simulación de fragmentos grandes de epidermis.Human skin is an example of a complex system. It is made of several copies of different cell types. The behavior of the complete system emerges from the individual behaviors of its cells. Many models have been developed that describe the behavior of individual cells. The knowledge about the contribu-tion of each cell to the behavior of the complete tissue is usually quite com-plicated and only known by the experts on the field. The behavior of individu-al cells is, however, quite well known. The simulation of skin tissue is interesting for many reasons. The system to be simulated is very appropriate for the use of bioinspired computational models such as cellular automata, which can be considered ideal for the simulation of the epidermis because they can assure at every instant the maintenance of a minimum energy situation. The most promising family of mathematical models in tissue simulation are those based on the Ising mod-el, the Potts model and the CPM-GGH model. Performance is one of the main limitations posed by this family of models. A possible way to solve it is the access to massively parallel resources by means of parallel, concurrent and distributed versions of the simulation algo-rithms. This doctoral thesis implements the CPM-GGH model and successfully repre-sents the processes of homeostasis and regeneration after the loss of cell layers in small wounds and scratches. This model will make it possible to tackle the simulation of more complex phenomena in the future. Two different ways to implement it by means of parallel hardware have been envisaged, which in the future should make it possible to address the simula-tion of bigger fragments of epidermis

Processing of Heavy Crude Oils

Unconventional heavy crude oils are replacing the conventional light crude oils slowly but steadily as a major energy source. Heavy crude oils are cheaper and present an opportunity to the refiners to process them with higher profit margins. However, the unfavourable characteristics of heavy crude oils such as high viscosity, low API gravity, low H/C ratio, chemical complexity with high asphaltenes content, high acidity, high sulfur and increased level of metal and heteroatom impurities impede extraction, pumping, transportation and processing. Very poor mobility of the heavy oils, due to very high viscosities, significantly affects production and transportation. Techniques for viscosity reduction, drag reduction and in-situ upgrading of the crude oil to improve the flow characteristics in pipelines are presented in this book. The heavier and complex molecules of asphaltenes with low H/C ratios present many technological challenges during the refining of the crude oil