Contributions to mathematical modelling and numerical simulation of biofilms

Programa Oficial de Doutoramento en Métodos Matemáticos e Simulación Numérica en Enxeñaría e Ciencias Aplicadas. 551V01[Abstract]The main goal of this PhD work is the development and numerical resolution of mathematical models that simulate the dynamics of bacterial biofilm systems, paying special attention to those biofilms formed by the Listeria monocytogenes, a pathogen of special relevance in food safety. A biofihn is a layer of microorganisms attached to a surface and protected by a matrix of exopolysaccharides. Biofilm structures difficult the removal of microorganisms, thus the study of the type of structures formed throughout a biofilm life cycle is key to design elimination techniques. In the present work, we develop different models that simulate the dynamics of biofilms formed by different strains of L. monocytogenes. We start with a 1D model that can be used to describe the formation of flat biofilms. Afterwards, we apply the acquired knowledge to develop a 2D model capable of describing more complex structures. All this models are solved with efficient numerical methods and robust numerical techniques, such as the Level Set method, that guarantees the good behaviour of the obtained solutions. Finally, the numerical results are compared with the experimental measurements obtained in the Instituto de Investigaciones Marinas, CSIC (Vigo, Spain), and the Micalis Institute, INRA (Massy, France).[Resumen]El objetivo fundamental de esta tesis consiste en el desarrollo y resolución numérica de modelos matemáticos que reproduzcan la dinámica de biopelículas, en especial, aquellas formadas por Listeria monocytogenes, un patógeno especialmente relevante en la seguridad alimentaria. Una biopelícula es una capa de microorganismos adheridos a una superficie y protegidos por una matriz de expolisacáridos. La estructura de las biopelículas hace difícil la eliminación de los microorganismos, de ahí que sea fillldamental estudiar el tipo de estructuras que se forman durante la vida de una biopelícula para poder diseñar nuevas técnicas de eliminación. En el presente trabajo, desarrollamos modelos que simulan la dinámica de biopelículas de diferentes cepas de L. monocytogenes. Comenzamos estableciendo un modelo 1D capaz de describir la formación de biopelículas planas para, posteriormente, aplicar los conocimientos adquiridos al desarrollo de un modelo 2D capaz de describir estructuras más complejas. Estos modelos se resuelven con métodos numéricos eficientes y técnicas numéricas robustas, como el método Level Set, que garantizan el buen comportamiento de las soluciones. Finalmente, los resultados obtenidos son comparados con las imágenes de microscopía procedentes de experimentos realizados en el Instituto de Investigaciones Marinas, CSIC (Vigo, España) yen el Micalis Institute, INRA (Massy, Francia).[Resumo ] O obxectivo fundamental desta tese é o desenvolvemento e resolución numérica de modelos matemáticos que reproduzan a dinámica de biopelículas, en especial, aquelas formadas por Lisieria monocytogenes, un patóxeno de especial relevancia na seguridade alimentaria. Unha biopelícula é unha capa de microorganismos adheridos a unha superficie e protexidos por unha matriz de expolisacáridos. A estructura das biopelículas fai difícil a eliminación dos microorganismos, de aí que sexa fundamental estudar o tipo de estructuras que se forman ao longo da vida dunha biopelícula para poder deseñar novas técnicas de eliminación. No presente traballo, desenvolvemos modelos que simulan a evolución de diferentes cepas de L. monocytogenes. Comezamos establecendo un modelo 1D capaz de describir a dinámica de cepas chás para, posteriormente, aplicar os coñecementos adquiridos ao desenvolvemento dun modelo 2D capaz de describir estruturas máis complexas. Todos estes modelos resólvense con métodos numéricos eficientes e técnicas numéricas robustas, como o método Level Set, que garanten o bo comportamento das solucións. Finalnlente, os resultados obtidos compáranse coas imáxes de microscopía obtidas en experimentos realizados no Instituto de Investigacions Mariñas, CSIC (Vigo, España) e no Micalis Institute, INRA (Massy, Francia)

A Two-Dimensional Multi-Species Model for Different Listeria Monocytogenes Biofilm Structures and Its Numerical Simulation

[Abstract] In this work we propose a two-dimensional multi-species model to describe the dynamics of biofilms formed by the pathogenic bacteria Listeria monocytogenes. Different Listeria monocytogenes strains produce biofilms with different structures, namely flat, honeycomb and clustered. Previous works showed that glucose impaired uptake and the appearance of damaged or dead cells are critical mechanisms underlying Listeria monocytogenes biofilm dynamics. Here we explicitly propose an extension of the two-dimensional multi-species model proposed by Alpkist and Klapper to account for those mechanisms. The result is a continuous two-dimensional multi-species model with non-linear detachment and mass action nutrient consumption. Moreover, we also propose a set of efficient numerical methods to solve the coupled model and we have developed their computer implementation from scratch in C/C++. Mainly based on finite differences schemes, these numerical techniques include Crank-Nicolson schemes for time discretization, Gibou’s ghost node techniques and level set methods to cope with the free boundary associated to the determination of the time-dependent biofilm domain. To finish with, we compare our simulation results with the dynamics of real biofilms as observed in the laboratory. More precisely, by using model parameters calibrated to experiments, the numerical results clearly illustrate the performance of the proposed model and the numerical methods to reproduce the real dynamics of flat, clustered and honeycomb structures shown by different Listeria monocytogenes strains.ALN and CV acknowledge the funding by MINECO from Spanish Government (Grant MTM2016-76497-R) and by Xunta de Galicia (Grants GRC2014/044 and ED431C2018/033). ALN acknowledges FPU fellowship (FPU13/02191) from the Spanish Government program MECD-FPU. CV and ALN as members of CITIC also akcnowledge the grant ED431G 2019/01, funded by Consellería de Educación, Universidade e Formación Profesional of Xunta de Galicia through FEDER funds with 80%, from FEDER Galicia 2014-2020 Program and 20% from Secretaría Xeral de Universidades. EBC acknowledges funding from Contrato Programa and grant Ref. IN607B 2017/02 from Xunta de Galicia. All grants include FEDER fundsXunta de Galicia; GRC2014/044Xunta de Galicia; ED431C2018/033Xunta de Galicia; ED431G 2019/01Xunta de Galicia; IN607B 2017/0

Elaboración de carpeta técnica para la intervención del Paseo Santa Catarina, Apopa

Como parte de la labor social y en la búsqueda de mejorar la calidad de vida de las personas se elaboró la carpeta técnica con el asesoramiento técnico de INDIGO estudio para la intervención del Paseo Santa Catarina en el municipio de Apopa que sirva como un instrumento integral que brinde a la municipalidad y terceros las herramientas para su ejecució

A novel growth method to improve the quality of GaAs nanowires grown by Ga-assisted chemical beam epitaxy

The successful synthesis of high crystalline quality and high aspect ratio GaAs nanowires (NWs) with a uniform diameter is needed to develop advanced applications beyond the limits established by thin film and bulk material properties. Vertically aligned GaAs NWs have been extensively grown by Ga-assisted vapor–liquid–solid (VLS) mechanism on Si(111) substrates, and they have been used as building blocks in photovoltaics, optoelectronics, electronics, and so forth. However, the nucleation of parasitic species such as traces and nanocrystals on the Si substrate surface during the NW growth could affect significantly the controlled nucleation of those NWs, and therefore the resulting performance of NW-based devices. Preventing the nucleation of parasitic species on the Si substrate is a matter of interest, because they could act as traps for gaseous precursors and/or chemical elements during VLS growth, drastically reducing the maximum length of grown NWs, affecting their morphology and structure, and reducing the NW density along the Si substrate surface. This work presents a novel and easy to develop growth method (i.e., without using advanced nanolithography techniques) to prevent the nucleation of parasitic species, while preserving the quality of GaAs NWs even for long duration growths. GaAs NWs are grown by Ga-assisted chemical beam epitaxy on oxidized Si(111) substrates using triethylgallium and tertiarybutylarsine precursors by a two-step-based growth method presented here; this method includes a growth interruption for an oxidation on air between both steps of growth, reducing the nucleation of parasitic crystals on the thicker SiOx capping layer during the second and longer growth step. VLS conditions are preserved overtime, resulting in a stable NW growth rate of around 6 μm/h for growth times up to 1 h. Resulting GaAs NWs have a high aspect ratio of 85 and average radius of 35 nm. We also report on the existence of characteristic reflection high-energy electron diffraction patterns associated with the epitaxial growth of GaAs NWs on Si(111) substrates, which have been analyzed and compared to the morphological characterization of GaAs NWs grown for different times under different conditions

Gestión para el cambio de la cultura docente a partir del proceso de la planeación didáctica

El presente trabajo es una propuesta de gestión que busca favorecer el cambio de cultura en la función docente, específicamente en relación a la planeación didáctica. El proyecto se orientó a fortalecer el desempeño docente a través de un proceso personal y colaborativo de trabajo colegiado entre los miembros del equipo docente de la institución donde se elaboró. La metodología empleada fue la de intervención educativa, la cual nos permitió reconocer al sujeto en relación con el contexto y la dinámica de la interacción social, de tal modo que desde la perspectiva de la gestión, responda a las necesidades específicas del centro educativo

Stress-assisted atomic diffusion in metastable austenite D03 phase of Cu-Al-Be shape memory alloys

Cu-Al-based shape memory alloys are firm candidates to be used up to 473 K. The main limiting aspect is the activation of diffusion processes in the metastable austenite phase, which drive the alloy decomposition. In the present work the study of short-distance diffusion processes has been approached by internal friction. A relaxation peak has been found in the metastable beta (D0(3)) phase of a Cu-Al-Be shape memory alloy, around 500 K (at 1 Hz), with an activation energy of E-a = 138 +/- 0.05 eV. An atomic mechanism of elastic dipoles Antisite-Vacancy reorientation, involving stress-assisted short distance Cu-atoms diffusion, has been proposed. (C) 2016 Elsevier B.V.This work was supported by the European H2020 Project REACT, Grant No 640241, and the Spanish Ministry MINECO projects, MAT2012-36421 and CONSOLIDER-INGENIO 2010 CSD2009-00013, as well as by the Consolidated Research Group IT-1090-16 from the Education Department and the project ELKARTEK ACTIMAT, KK-2015/0000094, from the Industry Department of the Basque Government

Prescripción de las acciones monitorias y los procesos ordinarios para el cobro de las obligaciones

Introduction: The topic to be investigated is part of the need to know the legal vacuum that exists of the prescription time to collect the obligation by order for payment procedure. These procedures grant the actor the power to exercise the collection action for a monetary, liquid debt, demandable and expired, as stated in article 356 of the COGEP whenever it does not exceed fifty Unified Basic Salaries. Objective: The objective of this investigation has been to analyze the collection of obligations through payment order procedure to establish the need to correct the legal vacuum that exists regarding the prescription time of these. Methodology: The research is part of a systematic method, as well as the analytical - synthetic and deductive - inductive, the approach used is the qualitative one. Thus, an academic work of a historical descriptive and review documentary type has also been prepared. Results: The evidence that proves a previous relationship between creditor and debtor was analyzed when the document -which is intended to be collected- has been created unilaterally by the creditor. Conclusions: Regarding the collection action, COGEP does not establish any time for the prescription, thus generating a structural vacuum that is unavoidable to correct.Introducción: La temática a investigar se enmarca en las necesidades de saber el vacío legal que existe del tiempo de prescripción para cobrar la obligación por procedimiento monitorio, Estos procedimientos otorga al actor la facultad de ejercer la acción de cobro por una deuda dineraria, líquida, exigible y vencida, como consta en el artículo 356 del COGEP toda vez que no exceda de cincuenta Salarios Básicos Unificados. Objetivo: El objetivo de la presente investigación ha sido analizar el cobro de obligaciones a través de procedimiento monitorio a fin de establecer la necesidad de subsanar el vacío legal que existe respecto del tiempo de prescripción de estas. Metodología: La investigación se enmarca en un método sistemático, así como el analítico - sintético y deductivo – inductivo, el enfoque empleado es el cualitativo. Así también se ha elaborado un trabajo académico de tipo documental histórico descriptivo y de revisión. Resultados: Se analizó la prueba que acredita una relación previa entre acreedor y deudor, cuando el documento -que se pretende cobrar- haya sido creado unilateralmente por el acreedor. Conclusiones: Sobre la acción de cobro, el COGEP no estatuye tiempo alguno para la prescripción generando así un vacío estructural que resulta ineludible subsanar. Área de estudio general: Jurisprudencia y Ciencias Sociales. Área de estudio específica: Derecho civil

Post-COVID Patients With New-Onset Chronic Pain 2 Years After Infection: Cross-Sectional Study

Background: Although pain is common in non-hospitalized post-COVID-19 syndrome, only a few studies have provided information on the pain experience of these patients. Aim: To identify the clinical and psychosocial profile associated with pain in non-hospitalized patients with post-COVID-19 syndrome. Method: In this study there were three groups: healthy control group, successfully recovered group, and post-COVID syndrome group. Pain-related clinical profile and pain-related psychosocial variables were collected. Pain-related clinical profile included: pain intensity and interference (Brief Pain Inventory), central sensitization (Central Sensitization Scale), insomnia severity (Insomnia Severity Index), and pain treatment. Pain-related psychosocial variables were: fear of movement and (re)injury (Tampa Scale for Kinesiophobia), catastrophizing (Pain Catastrophizing Scale), depression, anxiety and stress (Depression, Anxiety and Stress Scale), and fear-avoidance beliefs (Fear Avoidance Beliefs Questionnaire). Results: In all, 170 participants were included in the study (healthy control group n = 58, successfully recovered group n = 57, and post-COVID syndrome group n = 55). Post-COVID syndrome group obtained significantly worse punctuation in pain-related clinical profile and psychosocial variables than the other two groups (p < .05). Conclusions: In conclusion, patients with post-COVID-19 syndrome have experienced high pain intensity and interference, central sensitization, increased insomnia severity, fear of movement, catastrophizing, fear-avoidance beliefs, depression, anxiety, and stres

Barriers and applied activity, quality of life and self‑efficacy in prostate cancer survivors 1 year after completing radiotherapy

Purpose The aims of the study were to assess self-reported physical activity (PA) levels, barriers to PA, quality of life and self-efficacy to manage chronic disease of prostate cancer survivor 1 year after radiotherapy treatment. Methods A cross-sectional case–control study was performed. Prostate cancer survivor patients treated with radiotherapy were recruited from the Radiation Oncology Service of the “Complejo Hospitalario Universitario” (Granada) and compared with age-matched healthy men. Outcomes included were perception of benefits for physical activity and potential barriers (Exercise Benefits/Barriers Scale), physical activity levels assessed by the International Physical Activity Questionnaire (IPAQ), quality of life (EuroQol five-dimension three-levels) and self-efficacy (Self-Efficacy to Manage Chronic Disease). Results A total of 120 patients were included in our study. Significant differences were found between groups with worse results for the prostate cancer patient group in the variable perception of the benefit of physical activity, potential barriers, and physical activity. Regarding quality of life and self-efficacy, significant differences were also observed between groups with a greater score in the control group. Conclusion In conclusion, the results of this study reveal that self-reported PA levels, as measured using the IPAQ, were low in prostate cancer survivors after treatment. Results also showed worse perception of benefits for PA and potential barriers by the cancer survivors. Similarly, the quality of life and self-efficacy to manage chronic disease of prostate cancer survivors was lower.Universidad de Granada/ CBUAThe Spanish Ministry of Education (Grant numbers FPU:20/ 01670, FPU:19/02609, FPU:17/00408)

Role of breathing training programs on quality of life in chronic kidney disease patients

Background: Due to its chronic and progressive nature, chronic kidney disease (CKD) affects patients in many spheres including their perception of quality of life (QOL). Breathing training techniques have shown positive effects on health and QOL for different conditions. Objective: The aim of this study was to perform a scoping review to examine the characteristics related to the application of breathing training on patients with CKD, and to identify the relevant outcomes and target group for the application of breathing training. Methods: This scoping review was performed in accordance with PRISMA-SRc guidelines. We systematically searched three electronic databases for articles published before March 2022. The studies included patients with chronic kidney disease that received breathing training programs. The breathing training programs were compared to usual care or no treatment. Results: A total of four studies were included in this scoping review. The four studies had heterogeneous disease stages and breathing training programs. All the studies included reported positive effects of breathing training programs on QOL of CKD patients. Conclusion: The breathing training programs were able to improve the quality of life of patients with CKD undergoing hemodialysis treatment.Spanish Ministry of Education [grant number FPU: 20/0167