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Eines computacionals avançades per a planificació radioterapèutica mitjançat simulacions Monte CarloOliver Gil, Sandra 27 April 2024 (has links)
Tesis por compendio / [ES] La tesi presentada a aquest document, s'emmarca dins de l'àmbit de la física mèdica. Dins d'aquesta branca de la física, es desenvolupen eines computacionals per oferir millores en la planificació de tractaments que involucren radiació ionitzant. En aquestes planificacions, es calculen factors dosimètrics com la dosi total absorbida tant, a la regió d'interès del tractaments, objectiu del mateix, com a la resta de teixits o òrgans de risc propers a la zona objectiu. Per poder efectuar aquests càlculs, existeixen diferents tècniques, sent les simulacions basades en Monte Carlo les considerades com l'eina més precisa. Aquest tipus de simulacions, permeten modelitzar els dispositius mèdics que emeten el feix de tractament als pacients, de forma detallada. A més, les simulacions Monte Carlo, permeten descriure les fonts de radiació minuciosament i considerar el transport de les partícules involucrades en el problema a través de la geometria considerada.
En els treballs que conformen aquesta tesi, s'han emprat diferents codis Monte Carlo, depenent del problema a dur a terme. S'ha emprat MCNP6 a diferents treballs per la capacitat, i facilitat, de modelar geometries complexes emprant mallats volumètriques, penEasy com a codi per validar algunes de les eines dissenyades i penRed, per les característiques especialitzades en física mèdica, com la lectura i processament automàtic de DICOM i les fonts de braquiteràpia, el que faciliten molt les simulacions en l'entorn mèdic. Degut a estos fets, i a que penRed, és de codi obert i no requereix llicència, com al cas del MCNP, s'ha decidit estendre les capacitats que manquen en este, per poder equiparar el seu ús a la resta de codis en els problemes abordats durant la realització de la tesi doctoral.
Tots aquests treballs contribueixen al desenvolupament d'eines que, mitjançant la simulació Monte Carlo, permeten optimitzar els càlculs en radioteràpia. Més encara, les eines desenvolupades, tenen una aplicabilitat més general i poden emprar-se en altres camps o problemes, com, per exemple, diagnòstic basat en imatge mèdica.
El primer dels treballs, cobreix la necessita del codi MCNP6 de ser capaç de llegir i escriure fitxers d'espai de fase en format estàndard de la IAEA, eina que ja tenen implementadas molts dels codis de simulació Monte Carlo. Per suplir la manca de MCNP6 d'aquesta capacitat, es desenvolupa en aquesta tesi un codi capaç de realitzar aquestes conversions entre format d'espai de fase intern de MCNP6 i formats IAEA i a l'inrevés.
Al segon treball, s'empren simulacions Monte Carlo per tal de dissenyar un filtre que homogeinitze el feix d'electrons de 12 MeV a l'eixida d'un accelerador de radioteràpia intraoperàtoria. El treball proporciona una configuració de filtre, dissenyada amb simulació Monte Carlo i validada amb altre grup d'investigació independent.
El tercer treball, es basa en oferir una millora als elevats temps de computació a l'hora de realitzar planificacions de radioteràpia amb simulacions Monte Carlo per a tractaments amb diferents irradiacions angulars. Amb aquesta eina es pretén agilitzar significativament el procés de càlcul de distribució de dosi en el maniquí o pacient, sense haver de realitzar la simulació a través de tots els components de l'accelerador.
Finalment, arrel d'haver emprat geometries basades en malles en les simulacions realitzades amb MCNP6, s'ha vist la importància d'aquesta capacitat, especialment en simulacions en l'àmbit de la física mèdica. La definició de geometries per descriure el sistema, és una part fonamental de qualsevol simulació, independentment del codi que s'utilitza per a dur-la a terme. És per això que, el quart treball, es centra en el desenvolupament d'un mòdul per a simular sobre geometries mallades en penRed. / [CA] La tesis presentada en este documento se enmarca dentro del ámbito de la física médica. Dentro de esta rama de la física, se desarrollan herramientas computacionales para ofrecer mejoras en la planificación de tratamientos que involucran radiación ionizante. En estas planificaciones, se calculan factores dosimétricos como la dosis total absorbida tanto en la región de interés del tratamiento, objetivo del mismo, como en el resto de tejidos u órganos de riesgo cercanos a la zona objetivo. Para poder llevar a cabo estos cálculos, existen diferentes técnicas, siendo las simulaciones basadas en Monte Carlo consideradas como la herramienta más precisa. Este tipo de simulaciones permiten modelar los dispositivos médicos que emiten el haz de tratamiento a los pacientes de forma detallada. Además, las simulaciones Monte Carlo permiten describir las fuentes de radiación minuciosamente y considerar el transporte de las partículas involucradas en el problema a través de la geometría considerada.
En los trabajos que conforman esta tesis, se han empleado diferentes códigos Monte Carlo, dependiendo del problema a abordar. Se ha utilizado MCNP6 en diferentes trabajos por su capacidad y facilidad para modelar geometrías complejas utilizando mallas volumétricas, penEasy como código para validar algunas de las herramientas diseñadas y penRed, por sus características especializadas en física médica, como la lectura y procesamiento automático de DICOM y las fuentes de braquiterapia, lo que facilita mucho las simulaciones en el entorno médico. Debido a estos hechos, y a que penRed es de código abierto y no requiere licencia, como es el caso de MCNP, se ha decidido ampliar las capacidades que faltan en este, para poder equiparar su uso al resto de códigos en los problemas abordados durante la realización de la tesis doctoral.
Todos estos trabajos contribuyen al desarrollo de herramientas que, mediante la simulación Monte Carlo, permiten optimizar los cálculos en radioterapia. Además, las herramientas desarrolladas tienen una aplicabilidad más general y pueden emplearse en otros campos o problemas, como por ejemplo, el diagnóstico basado en imagen médica.
El primero de los trabajos cubre la necesidad del código MCNP6 de ser capaz de leer y escribir archivos de espacio de fase en formato estándar de la IAEA, herramienta que ya tienen implementadas muchos de los códigos de simulación Monte Carlo. Para suplir la falta de MCNP6 de esta capacidad, se desarrolla en esta tesis un código capaz de realizar estas conversiones entre formato de espacio de fase interno de MCNP6 y formatos IAEA y viceversa.
En el segundo trabajo, se emplean simulaciones Monte Carlo para diseñar un filtro que homogenice el haz de electrones de 12 MeV en la salida de un acelerador de radioterapia intraoperatoria. El trabajo proporciona una configuración de filtro, diseñada con simulación Monte Carlo y validada con otro grupo de investigación independiente.
El tercer trabajo se basa en ofrecer una mejora a los elevados tiempos de computación al realizar planificaciones de radioterapia con simulaciones Monte Carlo para tratamientos con diferentes irradiaciones angulares. Con esta herramienta se pretende agilizar significativamente el proceso de cálculo de distribución de dosis en el maniquí o paciente, sin tener que realizar la simulación a través de todos los componentes del acelerador.
Finalmente, a raíz de haber empleado geometrías basadas en mallas en las simulaciones realizadas con MCNP6, se ha visto la importancia de esta capacidad, especialmente en simulaciones en el ámbito de la física médica. La definición de geometrías para describir el sistema es una parte fundamental de cualquier simulación, independientemente del código que se utilice para llevarla a cabo. Es por ello que el cuarto trabajo se centra en el desarrollo de un módulo para simular sobre geometrías malladas en penRed. / [EN] The thesis presented in this document falls within the scope of medical physics. Within this branch of physics, computational tools are developed to offer improvements in the planning of treatments involving ionizing radiation. In these plans, dosimetric factors are calculated, such as the total absorbed dose both in the region of interest of the treatment, which is the treatment's objective, and in the surrounding tissues or organs at risk near the target area. To perform these calculations, different techniques exist, with Monte Carlo simulations considered the most accurate tool. These simulations allow modeling of medical devices emitting the treatment beam to patients in detail. Furthermore, Monte Carlo simulations enable a detailed description of radiation sources and consider the transport of particles involved in the problem through the considered geometry.
Different Monte Carlo codes have been used in the works comprising this thesis, depending on the problem addressed. MCNP6 has been used in various works for its capacity and ease in modeling complex geometries using volumetric meshes, penEasy as a code to validate some of the designed tools, and penRed for its specialized features in medical physics, such as reading and automatic processing of DICOM and brachytherapy sources, greatly facilitating simulations in the medical environment. Due to these facts, and because penRed is open-source and does not require a license, unlike MCNP, it has been decided to expand its capabilities to match its use with other codes in the problems addressed during the completion of the doctoral thesis.
All of these works contribute to the development of tools that, through Monte Carlo simulation, optimize calculations in radiotherapy. Additionally, the developed tools have broader applicability and can be used in other fields or problems, such as diagnosis based on medical imaging.
The first of the works covers the need for the MCNP6 code to be able to read and write phase space files in the standard IAEA format, a tool that many Monte Carlo simulation codes already have implemented. To address the lack of this capability in MCNP6, a code capable of performing these conversions between the internal phase space format of MCNP6 and IAEA formats, and vice versa, is developed in this thesis.
In the second work, Monte Carlo simulations are used to design a filter that homogenizes the 12 MeV electron beam at the output of an intraoperative radiotherapy accelerator. The work provides a filter configuration, designed with Monte Carlo simulation and validated with another independent research group.
The third work aims to improve the high computation times when performing radiotherapy planning with Monte Carlo simulations for treatments with different angular irradiations. This tool aims to significantly speed up the process of dose distribution calculation in the phantom or patient, without having to simulate through all components of the accelerator.
Finally, due to having employed mesh-based geometries in simulations conducted with MCNP6, the importance of this capability has been recognized, especially in simulations in the field of medical physics. The definition of geometries to describe the system is a fundamental part of any simulation, regardless of the code used to perform it. Therefore, the fourth work focuses on the development of a module to simulate on meshed geometries in penRed. / This study was supported by the program “Ayudas para la promoción de empleo joven e implantación de la Garantía Juvenil en I+D+i, Plan Estatal de Investigación Científica y Técnica e Innovación 2017-2020”
from the “Iniciativa de Empleo Juvenil” (IEJ) and the “Fondo Social Europeo” (FSE) We would like to acknowledge the Spanish “Ministerio de Ciencia e Innovación” (MCIN) grant PID2021-125096NB-I00 funded by MCIN/AEI/10.13039 and the “Generalitat Valenciana” (GVA) grant PROMETEO/2021/064. / Oliver Gil, S. (2024). Eines computacionals avançades per a planificació radioterapèutica mitjançat simulacions Monte Carlo [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/203890 / Compendio
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Computer simulations of electronic energy transfer and a molecular dynamics study of a decapeptideLindberg, Maria January 1991 (has links)
Electronic energy transfer has been investigated in pure donor systems by means of computer simulations. Calculated properties were the probability that the initially excited donor is excited at a time t after the excitation, Gs(t), the mean square displacement of the excitation and different fluorescence observables. For three dimensional systems the results obtained by Monte Carlo simulations were compared to the so-called GAF-theory {Gouchanour,C. R., Andersen, H. C. and Fayer, M. D., J. Chem. Phys. 81, 4380 (1984)}, and the agreement was found to be good. Anisotropic systems, i.e. mono-, bi- and multilayer systems, were compared to the two-particle model {Baumann,J. and Fayer, M. D., J. Chem. Phys. 85, 4087 (1986)}. The agreement between the Gs(t) calculated from the tp- model and the Monte Carlo simulations were good for all systems investigated. However, the agreement between the fluorescence observables obtained by MC and the tp-model were in general poor. A much better agreement was found when a phenomenological approach was used for calculating the fluorescence depolarization ratios. Three dimensional systems where the donors are rotating on the same time scale as the energy transfer takes place have also been studied and compared to analytical theories. The Molecular Dynamics simulations of decapeptide H142 shows that simulations in a continuum with a relative permeability do not provide a reliable alternative to simulations with explicit solvent molecules. / <p>Diss. (sammanfattning) Umeå : Umeå universitet, 1991, härtill 5 uppsatser</p> / digitalisering@umu
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Facility planning and value of information using a tank reservoir model : a case study in reserve uncertaintySingh, Ashutosh 02 November 2010 (has links)
This thesis presents a methodology to incorporate reservoir uncertainties and estimate the loss in project value when facility planning decisions are based on erroneous estimates of input variables. We propose a tank model along with integrated asset development model to simulate the concept selection process. The model endogenizes drilling decisions and includes an option to expand. Key decision variables included in the model are number of pre-drill wells, initial facility capacity and number of well slots. Comparison is made between project value derived under erroneous estimates for reserve size and under an alternate hypothesis. The results suggest loss in project value of up to 40% when reservoir estimates are erroneous. Moreover, both optimistic and pessimistic reserve estimates results in a loss in project value. However, loss in project value is bigger when reserve size is underestimated than when it is overestimated. / text
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Mnohorozměrné testy dobré shody / Multivariate goodness-of-fit testsKuc, Petr January 2016 (has links)
In this thesis we introduce, implement and compare several multivariate goodness-of-fit tests. First of all, we will focus on universal mul- tivariate tests that do not place any assumptions on parametric families of null distributions. Thereafter, we will be concerned with testing of multi- variate normality and, by using Monte Carlo simulations, we will compare power of five different tests of bivariate normality against several alternati- ves. Then we describe multivariate skew-normal distribution and propose a new test of multivariate skew-normality based on empirical moment genera- ting functions. In the final analysis, we compare its power with other tests of multivariate skew-normality. 1
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Modélisation de la topologie des dépôts d’énergie créés par un rayonnement ionisant à l’échelle nanométrique dans les noyaux cellulaires et relation avec les événements précoces radio-induits / Modeling of the topology of energy deposits created by ionizing radiation on a nanometric scale in cell nuclei in relation to radiation-induced early eventsDos Santos, Morgane 02 October 2013 (has links)
Les rayonnements ionisants sont connus pour induire des dommages critiques au sein de la matière biologique et spécialement au sein de l’ADN. Parmi ces dommages, les cassures doubles brins de l’ADN (DSB) sont considérées comme les principales responsables des effets létaux des rayonnements. Comprendre et prédire comment ces cassures sont créées et réparées dans les noyaux cellulaires demeure un défi dans la recherche en radiobiologie. Ce travail s’inscrit dans ce contexte, dans la modélisation des cassures double brin de l’ADN (DSB) à partir des dépôts d’énergie créés par l’irradiation au niveau intracellulaire. Le détail topologique au niveau nanométrique des dépôts d’énergie nécessaire à ce travail est obtenu par modélisation Monte Carlo à l’aide du code Geant4 et, en particulier son extension Geant4-DNA pour des processus à très faible énergie. Les dommages étudiés étant ceux localisés dans l’ADN, le premier objectif de ce travail a été de réaliser une géométrie détaillée de celui-ci afin de l’implémenter dans les calculs Monte Carlo. Deux types de noyaux cellulaires, représentant un fibroblaste et un endothélium, ont été décrits afin d’évaluer l’influence de la densité d’ADN dans les résultats sur la topologie des dépôts pouvant donner lieux à des cassures de la molécule. Cette géométrie nous permet d’effectuer une première sélection des dépôts d’énergie pouvant contribuer aux cassures car situées sur la chaîne sucre-phosphate. Ces dépôts sont ensuite analysés à l’aide d’un algorithme de clustérisation de manière à les regrouper sous forme d’agrégats afin d’étudier leur localisation et complexité. Néanmoins, dans cette étude, seule les interactions physiques entre les rayonnements ionisants et la cible sont modélisées, il n’est donc pas possible d’obtenir un nombre absolu de cassures de brins car cette modélisation n’inclue pas l’étape de création et de transport des radicaux libres pouvant donner lieu à des dommages indirects. Ainsi, le but de ce travail était d’évaluer la dépendance relative des dommages radio-induits directs avec la densité d’ADN, la qualité du rayonnement, la morphologie du noyau ou encore la condensation de la chromatine. Les différentes modélisations réalisées ont permis de quantifier l’influence de ces différents paramètres dans le nombre et la complexité des dommages directs induits dans l’ADN, pouvant ensuite contribuer aux effets tardifs sur le devenir cellulaire. / Ionizing radiations are known to induce critical damages on biological matter and especially on DNA. Among these damages, DNA double strand breaks (DSB) are considered as key precursor of lethal effects of ionizing radiations. Understand and predict how DNA double and simple strand breaks are created by ionising radiation and repaired in cell nucleus is nowadays a major challenge in radiobiology research. This work presents the results on the simulation of the DNA double strand breaks produced from the energy deposited by the irradiation at the intracellular level. At the nanometric scale, the only method to accurately simulate the topological details of energy deposited on the biological matter is the use of Monte Carlo codes. In this work, we used the Geant4 Monte Carlo code and, in particular, the low energy electromagnetic package extensions, referred as Geant4-DNA processes.In order to evaluate DNA radio-induced damages, the first objective of this work consisted in implementing a detailed geometry of the DNA on the Monte Carlo simulations. Two types of cell nuclei, representing a fibroblast and an endothelium, were described in order to evaluate the influence of the DNA density on the topology of the energy deposits contributing to strand breaks. Indeed, the implemented geometry allows the selection of energy transfer points that can lead to strand breaks because they are located on the backbone. Then, these energy transfer points were analysed with a clustering algorithm in order to reveal groups of aggregates and to study their location and complexity.In this work, only the physical interactions of ionizing radiations are simulated. Thus, it is not possible to achieve an absolute number of strand breaks as the creation and transportation of radical species which could lead to indirect DNA damages is not included. Nevertheless, the aim of this work was to evaluate the relative dependence of direct DNA damages with the DNA density, radiation quality, cell nuclei morphology or also chromatin condensation. The results presented in this work have allowed the quantification of the influence of these different parameters in the number and complexity of directs DNA damages which can then contribute to the late effects on cell fate.
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Cost-benefit analysis of mitigation of outages caused by squirrels on the overhead electricity distribution systemsMalve, Priyanka January 1900 (has links)
Master of Science / Department of Electrical and Computer Engineering / Anil Pahwa / Unpredictable power outages due to environmental factors such as lighting, wind, trees, and animals, have always been a concern for utilities because they are often unavoidable. This research aims to study squirrel-related outages by modeling past real-life outage data and provide the optimal result which would assist utilities in increasing electric system reliability. This research is a novel approach to benchmark system performance in order to identify areas and durations with higher than expected outages. The model is illustrated with seven years (2005-2011) of animal-related outage data and 14 years of weather data (1998-2011) for four cities in Kansas, used as training data to predict future outages. The past data indicates that the number of outages on any day varies with the seasons and weather conditions on that day. The prediction is based on a Bayesian Model using conditional probability table, which is calculated based on training data. Since future weather conditions are unknown and random, Monte Carlo Simulation is used with the past 14 years of weather data to create different yearly scenarios. These scenarios are then used with the models to predict expected outages. Multiple runs of Monte Carlo analysis provide a probability distribution of expected outages. Further work discusses about cost-to-benefit analysis of implementation of outage mitigation methods. The analysis is performed by considering different combinations of outage reduction and mitigation levels. In this research, eight cases of outage reduction and nine cases of mitigation levels are defined. The probability of benefit is calculated by a statistical approach for every combination. Several optimal strategies are constructed using the probability values and outage history. The outcomes are compared with each other to propose the most beneficial outage mitigation strategy. This research will immensely assist utilities in reducing the outages due to squirrels more effectively with higher benefits and therefore improve reliability of the electricity supply to consumers.
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Couplage et validation de l'extension GeantA-DNA dans la plateforme de simulation Monte Carlo GATE pour l'irradiation de molécules d'ADN dans un environnement de grille de calcul / Coupling and validation of the Geant4-DNA extension into the Gate Monte Carlo simulation platform for the irradiation of DNA molecules in a grid computing environmentPham, Quang Trung 21 May 2014 (has links)
Les méthodes de simulation Monte-Carlo s’étendent avec succès à différents domaines de la physique médicale mais aussi à différentes échelles, par exemple de la planification des traitements de radiothérapie jusqu’à une prévision des effets des rayonnements au niveau des cellules cancéreuses. La plateforme de simulation Monte-Carlo GATE, basée sur l’outil Geant4, propose des fonctionnalités dédiées aux simulations en physique médicale (médecine nucléaire et radiothérapie). Pour les applications en radiobiologie, les modèles physiques Geant4-DNA implémentés jusqu’à très basse énergie (eV) permettent d’estimer des quantités micro-dosimétriques d’intérêt. Dans le but d’implémenter une plateforme de simulation Monte-Carlo multi-échelles, nous nous sommes d’abord intéressés à la validation des modèles physiques de Geant4-DNA, puis à leur intégration dans la plateforme de simulation GATE et enfin à une validation de cette implémentation dans un contexte de radiothérapie et protonthérapie. De manière à valider les modèles physiques de Geant4-DNA, des points kernels de dose en électrons mono-énergétiques (de 10 keV à 100 keV) ont été simulés en utilisant les modèles physiques de Geant4 et de Geant4-DNA et ils ont comparés au code Monte-Carlo EGSnrc. Les parcours et pouvoirs d’arrêts des électrons (de 7,4 eV à 1 MeV) et des protons (de 1 keV à 100 MeV) calculés avec Geant4-DNA (processus et modèles préalablement intégrés dans GATE) ont ensuite été validés. Nous avons alors proposé de simuler avec la plateforme GATE l’impact de faisceaux cliniques et pré-cliniques sur l’ADN cellulaire. Nous avons ainsi modélisé un faisceau de protonthérapie de 193,1 MeV, un accélérateur linéaire en mode électrons de 6 MeV et un irradiateur RX de 250 kV. Ces simulations ont d’abord été validées en milieu aqueux par une comparaison de la dose macroscopique avec des mesures expérimentales. Les faisceaux ont ensuite été utilisés pour calculer, pour chacun d’entre eux, les fréquences de dépôts d’énergie à l’ADN. La molécule d’ADN a été simulée tout d’abord grâce à des cylindres équivalents en dimension à 10 paires de base (2 nm x 2 nm), équivalents à la taille d’un nucléosome (10 nm x 5 nm) et équivalents à la taille d’une fibre de chromatine (25 nm x 25 nm). Tous ces cylindres ont été placés aléatoirement dans un volume d’eau liquide (de rayon 500 nm). Nous avons ensuite reconstruit la molécule d’ADN dans Geant4 à partir de la lecture de fichiers PDB (Protein Data Bank) représentant douze paires de base de la molécule d’ADN et un dinucléosome (347 paires de base). Enfin, nous avons développé un outil permettant de corréler les positions de dépôts d’énergie directs dans l’eau liquide avec les coordonnées des paires de base de l’ADN, afin de calculer les nombres de cassures simple et double brin de l’ADN. Tous les calculs réalisés au cours de ce travail, ont été déployés sur l’Infrastructure de Grille Européenne ; des tests de performance sont proposés pour mesurer l’intérêt de ce type d’architecture pour les calculs Monte-Carlo. / The Monte Carlo simulation methods are successfully being used in various areas of medical physics but also at different scales, for example, from the radiation therapy treatment planning systems to the prediction of the effects of radiation in cancer cells. The Monte Carlo simulation platform GATE based on the Geant4 toolkit offers features dedicated to simulations in medical physics (nuclear medicine and radiotherapy). For radiobiology applications, the Geant4-DNA physical models are implemented to track particles till very low energy (eV) and are adapted for estimation of micro-dosimetric quantities. In order to implement a multi-scale Monte Carlo platform, we first validated the physical models of Geant4-DNA, and integrated them into GATE. Finally, we validated this implementation in the context of radiation therapy and proton therapy. In order to validate the Geant4-DNA physical models, dose point kernels for monoenergetic electrons (10 keV to 100 keV) were simulated using the physical models of Geant4-DNA and were compared to those simulated with Geant4 Standard physical models and another Monte Carlo code EGSnrc. The range and the stopping powers of electrons (7.4 eV to 1 MeV) and protons (1 keV to 100 MeV) calculated with GATE/Geant4-DNA were then compared with literature. We proposed to simulate with the GATE platform the impact of clinical and preclinical beams on cellular DNA. We modeled a clinical proton beam of 193.1 MeV, 6 MeV clinical electron beam and a X-ray irradiator beam. The beams models were validated by comparing absorbed dose computed and measured in liquid water. Then, the beams were used to calculate the frequency of energy deposits in DNA represented by different geometries. First, the DNA molecule was represented by small cylinders : 2 nm x 2 nm ( 10 bp), 5 nm x 10 nm ( nucleosome) and 25 nm x 25 nm ( chromatin fiber). All these cylinders were placed randomly in a sphere of liquid water (500 nm radius). Then we reconstructed the DNA molecule in Geant4 by reading PDB (Protein Data Bank) files representing twelve base pairs of the DNA molecule and a dinucleosome (347 base pairs). Finally, we developed a tool to correlate the positions of direct energy deposit in liquid water with the coordinates of the base pairs of DNA to calculate the number of single and double strand breaks in DNA. All calculations in this work were perfomed on the European Grid Infrastructure; performance tests are available to estimate the utility of this type of architecture for Monte Carlo calculations.
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Investigation Of Chemical Processes For The Production Of Commercially Viable High Volume Value-Added Products From Bauxite ResidueGostu, Sumedh 12 January 2018 (has links)
Bayer processing of bauxite employed for production of alumina yield a residue red-mud. The worldwide annual-rate of red-mud generation is approximately 120 million tons, and most of this is stockpiled. Red mud is rich in elements like aluminum, titanium and rare earths, in addition to the major iron-bearing constituents. The objective of this research is to explore such a strategy to extract Iron as fine particulate magnetite. Pyrometallurgical reduction experiments using carbon mixtures and a novel hydrometallurgical route are experimented. Reduction experiments performed with petroleum coke as a reductant resulted in incomplete reduction. The ‘optimal conditionsÂ’ for gaseous state reduction are determined to be: a processing temperature of 540oC ± 10oC, partial pressures CO (g) and CO2 (g) each of 0.070atm (bar) ± 0.001atm.(bar)/ inert diluent-gas: N2 (g), for a conversion-time of 30min. A mathematical-model was developed on the basis of unidirectional-diffusion of CO2 (g) within the CO2 (g)–CO (g)–N2 (g) gas-phase of the porous product-layer. Magnetic separation applied to the optimally reduced sample in: obtaining a magnetic portion with high iron and non-magnetic portion containing nonferrous (Al, Ti) is not successful. This finding was subsequently attributed to the nanometer length-scales crystallites of the predominant iron-containing phase, hydrated ferric-oxide(s) as determined by STEM micrographs. In addition, the presence of substitution for Fe3+ by Al3+ and Ti3+/4+ are determined with the help of MÖssbauer spectrograms. A hydrometallurgical route involving selective leaching and precipitation of iron in red-mud is tried. Red-mud is leached in oxalic acid at: 95˚C, 15 % Pulp density, 2.5 h leaching time, 1.5 pH. Kinetic studies yielded the leaching mechanism to be predominantly fluid film control. Ferric oxalate in the leach liquor is reduced to insoluble ferrous oxalate selectively using Iron powder. The ferrous oxalate formed is ~98 % pure. The precipitated ferrous oxalate is magnetically separated and reduced in Nitrogen atmosphere to form fine particulate magnetite. Additionally an economic feasibility study was conducted for the hydro and pyro alternatives to produce magnetite using Monte Carlo Simulations by imparting uncertainties in various input cost components. A traditional process was also compared to the proposed approaches for Total Capital Investment (TCI), Total Product Cost (TPC), Net Present Value (NPV) and sensitivity analysis. ~52 % reduction in Total product cost, 46 % reduction in Total Capital Investment was achieved for the hydrometallurgical process when compared to the traditional approach.
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Estudo de transições de fase em sistemas com simetria \"up-down\" e estados absorventes / Phase transition study in a system with up-down symmetry and symmetrical absorbing statesRodrigues, Áttila Leães 10 March 2014 (has links)
Neste trabalho estudamos um modelo estocástico com simetria Ising e dois estados absorventes em três dimensões com uma rede cúbica e em duas dimensões através de uma rede triangular. O estudo levou em conta cálculos de aproximação de campo médio e simulações de Monte Carlo. Os resultados mostraram que o modelo tem transição de segunda ordem de uma fase paramagnética para uma fase ferromagnética, uma transição da fase ferromagnética para uma fase absorvente, também de segunda ordem, e ainda uma transição de primeira ordem da fase paramagnética para a fase absorvente. No espaço de parâmetros as três linhas de transição se encontram no diagrama de fases em um ponto onde o modelo se comporta como o modelo do votante. / In this work we studied a stochastic model with ising symmetry and two simmetric absorbing configurations in a three-dimensional cubic lattice and in two dimensions using a triangular lattice. The study took into account simple mean-field approximations and Monte Carlo simulations. The results showed that the model has a second-order transition from a paramagnetic phase to a ferromagnetic phase and second-order transition from ferromagnetic phase to the absorbing one. A first-order phase transition from the paramagnetic phase to the absorbing phase is observed too. In the phase diagram the two second-order transition lines aproaches to the point where the model behaves like the voter model.
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Simulations Monte Carlo et mesures de l’émission de gamma prompts appliquées au contrôle en ligne en hadronthérapie / Monte Carlo Simulations and prompt gamma measurement for online control of ion therapyLe Foulher, Fabrice 12 October 2010 (has links)
Au cours du traitement d'une tumeur avec des ions légers, la position du pic de Bragg doit être connue avec précision. Une fraction importante des ions incidents subissent des collisions nucléaires avec les noyaux cibles conduisant à l'émission de particules promptes qui peuvent être porteuses d'informations sur le parcours des ions. Ce travail, qui se concentre sur les gamma prompts, montre que le rendement en profondeur de ces émissions est fortement corrélé au parcours des ions et que les taux de comptage mesurés permettent d'envisager un système d'imagerie réaliste, fonctionnant en temps réel. Dans ce but, nous avons réalisé des expériences au GANIL et au GSI avec un détecteur collimaté placé perpendiculairement à l'axe du faisceau et la technique du temps de vol a été utilisée pour réduire le bruit de fond induit par les neutrons et les particules chargées. Des simulations Geant4 ont été réalisées pour concevoir le dispositif expérimental et interpréter les données. Un accord qualitatif entre les simulations et l'expérience est observé pour la quantité d'énergie déposée dans le détecteur et pour la forme du spectre de temps de vol. Cependant, des divergences apparaissent pour le rendement de gamma prompts et la distribution en profondeur des gamma détectés. Ces divergences sont discutées, principalement en termes de modèles de physique nucléaire qui doivent être améliorés. Après avoir sélectionné les modèles physiques offrant les simulations les plus en accord avec les mesures, des études concernant les lieux d'émissions des gamma prompts et l'influence de la diffusion dans la cible ont été réalisés afin de déterminer l'impact sur la corrélation avec le parcours des ions / During the treatment of a tumor with light ions, the Bragg peak location must be accurately known. A significant fraction of the incident ions undergo nuclear collisions with the target nuclei leading to the prompt emission of particles which may carry information on the ion path. This work, which focuses on prompt gamma, shows that the depth profile of these emissions is highly correlated to the ions path and the measured counting rates allow to consider a realistic imaging system, operating in real time. For that purpose, we performed experiments at GANIL and at GSI with a collimated detector placed perpendicular to the beam axis and the time of flight technique was used in order to reduce the noise induced by neutrons and charged particles. Geant4 simulations were performed for the experimental design and data interpretation. A qualitative agreement between simulations and experiment is observed for the amount of energy deposited in the detector and the shape of the time of flight spectrum. However, discrepancies appear for the prompt gamma yield and the depth distribution of gamma detected. These discrepancies are discussed, mainly in terms of nuclear physics models that must be improved. After selecting the physical models which lead to the best agreement between simulations and measurements, studies on the location of prompt gamma emission and on the influence of diffusion in the target were performed to determine the impact on the correlation with the ion path
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