Neurite, a finite difference large scale parallel program for the simulation of the electrical signal propagation in neurites under mechanical loading

With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, function of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells has only very recently been proposed (Jerusalem et al., 2013). In this paper, we present the implementation details of Neurite: the finite difference parallel program used in this reference. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to simulate the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The simulation of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the simulated cells grows. The solvers implemented in Neurite-explicit and implicit-were therefore parallelized using graphics processing units in order to reduce the burden of the simulation costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between lectrophysiology and mechanics (Jerusalem et al., 2013). This paper provides the details of the parallel implementation of Neurite, along with three different application examples: a long myelinated axon, a segmented dendritic tree, and a damaged axon. The capabilities of the program to deal with large scale scenarios, segmented neuronal structures, and functional deficits under mechanical loading are specifically highlighted.

Computer simulation of random parckings for self-similar particle size distributions in soil and granular materials: porosity and pore size distribution

A 2D computer simulation method of random packings is applied to sets of particles generated by a self-similar uniparametric model for particle size distributions (PSDs) in granular media. The parameter p which controls the model is the proportion of mass of particles corresponding to the left half of the normalized size interval [0,1]. First the influence on the total porosity of the parameter p is analyzed and interpreted. It is shown that such parameter, and the fractal exponent of the associated power scaling, are efficient packing parameters, but this last one is not in the way predicted in a former published work addressing an analogous research in artificial granular materials. The total porosity reaches the minimum value for p = 0.6. Limited information on the pore size distribution is obtained from the packing simulations and by means of morphological analysis methods. Results show that the range of pore sizes increases for decreasing values of p showing also different shape in the volume pore size distribution. Further research including simulations with a greater number of particles and image resolution are required to obtain finer results on the hierarchical structure of pore space.

Time-multiscale methods for the simulation of slow transport problems in atomistic systems

En esta tesis presentamos una teoría adaptada a la simulación de fenómenos lentos de transporte en sistemas atomísticos. En primer lugar, desarrollamos el marco teórico para modelizar colectividades estadísticas de equilibrio. A continuación, lo adaptamos para construir modelos de colectividades estadísticas fuera de equilibrio. Esta teoría reposa sobre los principios de la mecánica estadística, en particular el principio de máxima entropía de Jaynes, utilizado tanto para sistemas en equilibrio como fuera de equilibrio, y la teoría de las aproximaciones del campo medio. Expresamos matemáticamente el problema como un principio variacional en el que maximizamos una entropía libre, en lugar de una energía libre. La formulación propuesta permite definir equivalentes atomísticos de variables macroscópicas como la temperatura y la fracción molar. De esta forma podemos considerar campos macroscópicos no uniformes. Completamos el marco teórico con reglas de cuadratura de Monte Carlo, gracias a las cuales obtenemos modelos computables. A continuación, desarrollamos el conjunto completo de ecuaciones que gobiernan procesos de transporte. Deducimos la desigualdad de disipación entrópica a partir de fuerzas y flujos termodinámicos discretos. Esta desigualdad nos permite identificar la estructura que deben cumplir los potenciales cinéticos discretos. Dichos potenciales acoplan las tasas de variación en el tiempo de las variables microscópicas con las fuerzas correspondientes. Estos potenciales cinéticos deben ser completados con una relación fenomenológica, del tipo definido por la teoría de Onsanger. Por último, aportamos validaciones numéricas. Con ellas ilustramos la capacidad de la teoría presentada para simular propiedades de equilibrio y segregación superficial en aleaciones metálicas. Primero, simulamos propiedades termodinámicas de equilibrio en el sistema atomístico. A continuación evaluamos la habilidad del modelo para reproducir procesos de transporte en sistemas complejos que duran tiempos largos con respecto a los tiempos característicos a escala atómica. ABSTRACT In this work, we formulate a theory to address simulations of slow time transport effects in atomic systems. We first develop this theoretical framework in the context of equilibrium of atomic ensembles, based on statistical mechanics. We then adapt it to model ensembles away from equilibrium. The theory stands on Jaynes' maximum entropy principle, valid for the treatment of both, systems in equilibrium and away from equilibrium and on meanfield approximation theory. It is expressed in the entropy formulation as a variational principle. We interpret atomistic equivalents of macroscopic variables such as the temperature and the molar fractions, wich are not required to be uniform, but can vary from particle to particle. We complement this theory with Monte Carlo summation rules for further approximation. In addition, we provide a framework for studying transport processes with the full set of equations driving the evolution of the system. We first derive a dissipation inequality for the entropic production involving discrete thermodynamic forces and fluxes. This discrete dissipation inequality identifies the adequate structure for discrete kinetic potentials which couple the microscopic field rates to the corresponding driving forces. Those kinetic potentials must finally be expressed as a phenomenological rule of the Onsanger Type. We present several validation cases, illustrating equilibrium properties and surface segregation of metallic alloys. We first assess the ability of a simple meanfield model to reproduce thermodynamic equilibrium properties in systems with atomic resolution. Then, we evaluate the ability of the model to reproduce a long-term transport process in complex systems.

A code for direct numerical simulation of turbulent boundary layers at high Reynolds numbers in BG/P supercomputers

A new high-resolution code for the direct numerical simulation of a zero pressure gradient turbulent boundary layers over a flat plate has been developed. Its purpose is to simulate a wide range of Reynolds numbers from Reθ = 300 to 6800 while showing a linear weak scaling up to 32,768 cores in the BG/P architecture. Special attention has been paid to the generation of proper inflow boundary conditions. The results are in good agreement with existing numerical and experimental data sets.

Simulation of scheduling gains in LTE

This paper describes the implementation of an LTE downlink simulator that is able to precisely model the fast time and frequency variations existing in a multipath channel. This is decisive to properly simulate the gains achievable by the channeldependent scheduling LTE is capable of. The aim of this study is to investigate the relationship between the throughput achieved by a base station and parameters of active users in the cell (such as SINR or speed). The ultimate goal is to obtain a model that can predict throughput as a function of a few selected parameters that characterize users’ conditions. A proportional fair scheduler is used because of its ability to maximize the BS throughput while preventing user starvation. Some conclusions are drawn on the main parameters affecting the BS throughput based on results obtained so far.

Simulation of thermal performance of glazing in architecture using scale models = Simulación del comportamiento térmico de los acristalamientos en la arquitectura mediante modelos a escala

El propósito de esta tesis es estudiar la aproximación a los fenómenos de transporte térmico en edificación acristalada a través de sus réplicas a escala. La tarea central de esta tesis es, por lo tanto, la comparación del comportamiento térmico de modelos a escala con el correspondiente comportamiento térmico del prototipo a escala real. Los datos principales de comparación entre modelo y prototipo serán las temperaturas. En el primer capítulo del Estado del Arte de esta tesis se hará un recorrido histórico por los usos de los modelos a escala desde la antigüedad hasta nuestro días. Dentro de éste, en el Estado de la Técnica, se expondrán los beneficios que tiene su empleo y las dificultades que conllevan. A continuación, en el Estado de la Investigación de los modelos a escala, se analizarán artículos científicos y tesis. Precisamente, nos centraremos en aquellos modelos a escala que son funcionales. Los modelos a escala funcionales son modelos a escala que replican, además, una o algunas de las funciones de sus prototipos. Los modelos a escala pueden estar distorsionados o no. Los modelos a escala distorsionados son aquellos con cambios intencionados en las dimensiones o en las características constructivas para la obtención de una respuesta específica por ejemplo, replicar el comportamiento térmico. Los modelos a escala sin distorsión, o no distorsionados, son aquellos que mantienen, en la medida de lo posible, las proporciones dimensionales y características constructivas de sus prototipos de referencia. Estos modelos a escala funcionales y no distorsionados son especialmente útiles para los arquitectos ya que permiten a la vez ser empleados como elementos funcionales de análisis y como elementos de toma de decisiones en el diseño constructivo. A pesar de su versatilidad, en general, se observará que se han utilizado muy poco estos modelos a escala funcionales sin distorsión para el estudio del comportamiento térmico de la edificación. Posteriormente, se expondrán las teorías para el análisis de los datos térmicos recogidos de los modelos a escala y su aplicabilidad a los correspondientes prototipos a escala real. Se explicarán los experimentos llevados a cabo, tanto en laboratorio como a intemperie. Se han realizado experimentos con modelos sencillos cúbicos a diferentes escalas y sometidos a las mismas condiciones ambientales. De estos modelos sencillos hemos dado el salto a un modelo reducido de una edificación acristalada relativamente sencilla. Los experimentos consisten en ensayos simultáneos a intemperie del prototipo a escala real y su modelo reducido del Taller de Prototipos de la Escuela Técnica Superior de Arquitectura de Madrid (ETSAM). Para el análisis de los datos experimentales hemos aplicado las teorías conocidas, tanto comparaciones directas como el empleo del análisis dimensional. Finalmente, las simulaciones nos permiten comparaciones flexibles con los datos experimentales, por ese motivo, hemos utilizado tanto programas comerciales como un algoritmo de simulación desarrollado ad hoc para esta investigación. Finalmente, exponemos la discusión y las conclusiones de esta investigación. Abstract The purpose of this thesis is to study the approximation to phenomena of heat transfer in glazed buildings through their scale replicas. The central task of this thesis is, therefore, the comparison of the thermal performance of scale models without distortion with the corresponding thermal performance of their full-scale prototypes. Indoor air temperatures of the scale model and the corresponding prototype are the data to be compared. In the first chapter on the State of the Art, it will be shown a broad vision, consisting of a historic review of uses of scale models, from antiquity to our days. In the section State of the Technique, the benefits and difficulties associated with their implementation are presented. Additionally, in the section State of the Research, current scientific papers and theses on scale models are reviewed. Specifically, we focus on functional scale models. Functional scale models are scale models that replicate, additionally, one or some of the functions of their corresponding prototypes. Scale models can be distorted or not. Scale models with distortion are considered scale models with intentional changes, on one hand, in dimensions scaled unevenly and, on the other hand, in constructive characteristics or materials, in order to get a specific performance for instance, a specific thermal performance. Consequently, scale models without distortion, or undistorted scale models scaled evenly, are those replicating, to the extent possible, without distortion, the dimensional proportions and constructive configurations of their prototypes of reference. These undistorted and functional scale models are especially useful for architects because they can be used, simultaneously, as functional elements of analysis and as decision-making elements during the design. Although they are versatile, in general, it is remarkable that these types of models are used very little for the study of the thermal performance of buildings. Subsequently, the theories related to the analysis of the experimental thermal data collected from the scale models and their applicability to the corresponding full-scale prototypes, will be explained. Thereafter, the experiments in laboratory and at outdoor conditions are detailed. Firstly, experiments carried out with simple cube models at different scales are explained. The prototype larger in size and the corresponding undistorted scale model have been subjected to same environmental conditions in every experimental test. Secondly, a step forward is taken carrying out some simultaneous experimental tests of an undistorted scale model, replica of a relatively simple lightweight and glazed building construction. This experiment consists of monitoring the undistorted scale model of the prototype workshop located in the School of Architecture (ETSAM) of the Technical University of Madrid (UPM). For the analysis of experimental data, known related theories and resources are applied, such as, direct comparisons, statistical analyses, Dimensional Analysis and last, but not least important, simulations. Simulations allow us, specifically, flexible comparisons with experimental data. Here, apart the use of the simulation software EnergyPlus, a simulation algorithm is developed ad hoc for this research. Finally, the discussion and conclusions of this research are exposed.