3D Direct Simulation Monte Carlo Modelling of the Inner Gas Coma of Comet 67P/Churyumov-Gerasimenko: A Parameter Study

Direct Simulation Monte Carlo (DSMC) is a powerful numerical method to study rarefied gas flows such as cometary comae and has been used by several authors over the past decade to study cometary outflow. However, the investigation of the parameter space in simulations can be time consuming since 3D DSMC is computationally highly intensive. For the target of ESA's Rosetta mission, comet 67P/Churyumov-Gerasimenko, we have identified to what extent modification of several parameters influence the 3D flow and gas temperature fields and have attempted to establish the reliability of inferences about the initial conditions from in situ and remote sensing measurements. A large number of DSMC runs have been completed with varying input parameters. In this work, we present the simulation results and conclude on the sensitivity of solutions to certain inputs. It is found that among cases of water outgassing, the surface production rate distribution is the most influential variable to the flow field.

Análisis y diseño de multiplicadores y mezcladores mediante el método de Monte Carlo en la banda de THz = Analysis and design of multipliers and mixers via Monte Carlo modelling at THz bands

La región del espectro electromagnético comprendida entre 100 GHz y 10 THz alberga una gran variedad de aplicaciones en campos tan dispares como la radioastronomía, espectroscopíamolecular, medicina, seguridad, radar, etc. Los principales inconvenientes en el desarrollo de estas aplicaciones son los altos costes de producción de los sistemas trabajando a estas frecuencias, su costoso mantenimiento, gran volumen y baja fiabilidad. Entre las diferentes tecnologías a frecuencias de THz, la tecnología de los diodos Schottky juega un importante papel debido a su madurez y a la sencillez de estos dispositivos. Además, los diodos Schottky pueden operar tanto a temperatura ambiente como a temperaturas criogénicas, con altas eficiencias cuando se usan como multiplicadores y con moderadas temperaturas de ruido en mezcladores. El principal objetivo de esta tesis doctoral es analizar los fenómenos físicos responsables de las características eléctricas y del ruido en los diodos Schottky, así como analizar y diseñar circuitos multiplicadores y mezcladores en bandas milimétricas y submilimétricas. La primera parte de la tesis presenta un análisis de los fenómenos físicos que limitan el comportamiento de los diodos Schottky de GaAs y GaN y de las características del espectro de ruido de estos dispositivos. Para llevar a cabo este análisis, un modelo del diodo basado en la técnica de Monte Carlo se ha considerado como referencia debido a la elevada precisión y fiabilidad de este modelo. Además, el modelo de Monte Carlo permite calcular directamente el espectro de ruido de los diodos sin necesidad de utilizar ningún modelo analítico o empírico. Se han analizado fenómenos físicos como saturación de la velocidad, inercia de los portadores, dependencia de la movilidad electrónica con la longitud de la epicapa, resonancias del plasma y efectos no locales y no estacionarios. También se ha presentado un completo análisis del espectro de ruido para diodos Schottky de GaAs y GaN operando tanto en condiciones estáticas como variables con el tiempo. Los resultados obtenidos en esta parte de la tesis contribuyen a mejorar la comprensión de la respuesta eléctrica y del ruido de los diodos Schottky en condiciones de altas frecuencias y/o altos campos eléctricos. También, estos resultados han ayudado a determinar las limitaciones de modelos numéricos y analíticos usados en el análisis de la respuesta eléctrica y del ruido electrónico en los diodos Schottky. La segunda parte de la tesis está dedicada al análisis de multiplicadores y mezcladores mediante una herramienta de simulación de circuitos basada en la técnica de balance armónico. Diferentes modelos basados en circuitos equivalentes del dispositivo, en las ecuaciones de arrastre-difusión y en la técnica de Monte Carlo se han considerado en este análisis. El modelo de Monte Carlo acoplado a la técnica de balance armónico se ha usado como referencia para evaluar las limitaciones y el rango de validez de modelos basados en circuitos equivalentes y en las ecuaciones de arrastredifusión para el diseño de circuitos multiplicadores y mezcladores. Una notable característica de esta herramienta de simulación es que permite diseñar circuitos Schottky teniendo en cuenta tanto la respuesta eléctrica como el ruido generado en los dispositivos. Los resultados de las simulaciones presentados en esta parte de la tesis, tanto paramultiplicadores comomezcladores, se han comparado con resultados experimentales publicados en la literatura. El simulador que integra el modelo de Monte Carlo con la técnica de balance armónico permite analizar y diseñar circuitos a frecuencias superiores a 1 THz. ABSTRACT The terahertz region of the electromagnetic spectrum(100 GHz-10 THz) presents a wide range of applications such as radio-astronomy, molecular spectroscopy, medicine, security and radar, among others. The main obstacles for the development of these applications are the high production cost of the systems working at these frequencies, highmaintenance, high volume and low reliability. Among the different THz technologies, Schottky technology plays an important rule due to its maturity and the inherent simplicity of these devices. Besides, Schottky diodes can operate at both room and cryogenic temperatures, with high efficiency in multipliers and moderate noise temperature in mixers. This PhD. thesis is mainly concerned with the analysis of the physical processes responsible for the characteristics of the electrical response and noise of Schottky diodes, as well as the analysis and design of frequency multipliers and mixers at millimeter and submillimeter wavelengths. The first part of the thesis deals with the analysis of the physical phenomena limiting the electrical performance of GaAs and GaN Schottky diodes and their noise performance. To carry out this analysis, a Monte Carlo model of the diode has been used as a reference due to the high accuracy and reliability of this diode model at millimeter and submillimter wavelengths. Besides, the Monte Carlo model provides a direct description of the noise spectra of the devices without the necessity of any additional analytical or empirical model. Physical phenomena like velocity saturation, carrier inertia, dependence of the electron mobility on the epilayer length, plasma resonance and nonlocal effects in time and space have been analysed. Also, a complete analysis of the current noise spectra of GaAs and GaN Schottky diodes operating under static and time varying conditions is presented in this part of the thesis. The obtained results provide a better understanding of the electrical and the noise responses of Schottky diodes under high frequency and/or high electric field conditions. Also these results have helped to determine the limitations of numerical and analytical models used in the analysis of the electrical and the noise responses of these devices. The second part of the thesis is devoted to the analysis of frequency multipliers and mixers by means of an in-house circuit simulation tool based on the harmonic balance technique. Different lumped equivalent circuits, drift-diffusion and Monte Carlo models have been considered in this analysis. The Monte Carlo model coupled to the harmonic balance technique has been used as a reference to evaluate the limitations and range of validity of lumped equivalent circuit and driftdiffusion models for the design of frequency multipliers and mixers. A remarkable feature of this reference simulation tool is that it enables the design of Schottky circuits from both electrical and noise considerations. The simulation results presented in this part of the thesis for both multipliers and mixers have been compared with measured results available in the literature. In addition, the Monte Carlo simulation tool allows the analysis and design of circuits above 1 THz.

Study of the impact of tissue density heterogeneities on 3-dimensional abdominal dosimetry: comparison between dose kernel convolution and direct monte carlo methods.

Dose kernel convolution (DK) methods have been proposed to speed up absorbed dose calculations in molecular radionuclide therapy. Our aim was to evaluate the impact of tissue density heterogeneities (TDH) on dosimetry when using a DK method and to propose a simple density-correction method. METHODS: This study has been conducted on 3 clinical cases: case 1, non-Hodgkin lymphoma treated with (131)I-tositumomab; case 2, a neuroendocrine tumor treatment simulated with (177)Lu-peptides; and case 3, hepatocellular carcinoma treated with (90)Y-microspheres. Absorbed dose calculations were performed using a direct Monte Carlo approach accounting for TDH (3D-RD), and a DK approach (VoxelDose, or VD). For each individual voxel, the VD absorbed dose, D(VD), calculated assuming uniform density, was corrected for density, giving D(VDd). The average 3D-RD absorbed dose values, D(3DRD), were compared with D(VD) and D(VDd), using the relative difference Δ(VD/3DRD). At the voxel level, density-binned Δ(VD/3DRD) and Δ(VDd/3DRD) were plotted against ρ and fitted with a linear regression. RESULTS: The D(VD) calculations showed a good agreement with D(3DRD). Δ(VD/3DRD) was less than 3.5%, except for the tumor of case 1 (5.9%) and the renal cortex of case 2 (5.6%). At the voxel level, the Δ(VD/3DRD) range was 0%-14% for cases 1 and 2, and -3% to 7% for case 3. All 3 cases showed a linear relationship between voxel bin-averaged Δ(VD/3DRD) and density, ρ: case 1 (Δ = -0.56ρ + 0.62, R(2) = 0.93), case 2 (Δ = -0.91ρ + 0.96, R(2) = 0.99), and case 3 (Δ = -0.69ρ + 0.72, R(2) = 0.91). The density correction improved the agreement of the DK method with the Monte Carlo approach (Δ(VDd/3DRD) < 1.1%), but with a lesser extent for the tumor of case 1 (3.1%). At the voxel level, the Δ(VDd/3DRD) range decreased for the 3 clinical cases (case 1, -1% to 4%; case 2, -0.5% to 1.5%, and -1.5% to 2%). No more linear regression existed for cases 2 and 3, contrary to case 1 (Δ = 0.41ρ - 0.38, R(2) = 0.88) although the slope in case 1 was less pronounced. CONCLUSION: This study shows a small influence of TDH in the abdominal region for 3 representative clinical cases. A simple density-correction method was proposed and improved the comparison in the absorbed dose calculations when using our voxel S value implementation.

Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

The rate at which a given site in a gene sequence alignment evolves over time may vary. This phenomenon-known as heterotachy-can bias or distort phylogenetic trees inferred from models of sequence evolution that assume rates of evolution are constant. Here, we describe a phylogenetic mixture model designed to accommodate heterotachy. The method sums the likelihood of the data at each site over more than one set of branch lengths on the same tree topology. A branch-length set that is best for one site may differ from the branch-length set that is best for some other site, thereby allowing different sites to have different rates of change throughout the tree. Because rate variation may not be present in all branches, we use a reversible-jump Markov chain Monte Carlo algorithm to identify those branches in which reliable amounts of heterotachy occur. We implement the method in combination with our 'pattern-heterogeneity' mixture model, applying it to simulated data and five published datasets. We find that complex evolutionary signals of heterotachy are routinely present over and above variation in the rate or pattern of evolution across sites, that the reversible-jump method requires far fewer parameters than conventional mixture models to describe it, and serves to identify the regions of the tree in which heterotachy is most pronounced. The reversible-jump procedure also removes the need for a posteriori tests of 'significance' such as the Akaike or Bayesian information criterion tests, or Bayes factors. Heterotachy has important consequences for the correct reconstruction of phylogenies as well as for tests of hypotheses that rely on accurate branch-length information. These include molecular clocks, analyses of tempo and mode of evolution, comparative studies and ancestral state reconstruction. The model is available from the authors' website, and can be used for the analysis of both nucleotide and morphological data.

Modelling water adsorption on Au(210) surfaces: II. Monte Carlo simulations

Canonical Monte Carlo simulations for the Au(210)/H(2)O interface, using a force field recently proposed by us, are reported. The results exhibit the main features normally observed in simulations of water molecules in contact with different noble metal surfaces. The calculations also assess the influence of the surface topography on the structural aspects of the adsorbed water and on the distribution of the water molecules in the direction normal to the metal surface plane. The adsorption process is preferential at sites in the first layer of the metal. The analysis of the density profiles and dipole moment distributions points to two predominant orientations. Most of the molecules are adsorbed with the molecular plane parallel to surface, while others adsorb with one of the O-H bonds parallel to the surface and the other bond pointing towards the bulk liquid phase. There is also evidence of hydrogen bond formation between the first and second solvent layers at the interface. (c) 2007 Elsevier B.V. All rights reserved.

Monte Carlo Simulations of Novel Scintillator Detectors and Dosimetry Calculations

Monte Carlo (MC) simulation techniques are becoming very common in the Medical Physicists community. MC can be used for modeling Single Photon Emission Computed Tomography (SPECT) and for dosimetry calculations. 188Re, is a promising candidate for radiotherapeutic production and understanding the mechanisms of the radioresponse of tumor cells "in vitro" is of crucial importance as a first step before "in vivo" studies. The dosimetry of 188Re, used to target different lines of cancer cells, has been evaluated by the MC code GEANT4. The simulations estimate the average energy deposition/per event in the biological samples. The development of prototypes for medical imaging, based on LaBr3:Ce scintillation crystals coupled with a position sensitive photomultiplier, have been studied using GEANT4 simulations. Having tested, in the simulation, surface treatments different from the one applied to the crystal used in our experimental measurements, we found out that the Energy Resolution (ER) and the Spatial Resolution (SR) could be improved, in principle, by machining in a different way the lateral surfaces of the crystal. We have then studied a system able to acquire both echographic and scintigraphic images to let the medical operator obtain the complete anatomic and functional information for tumor diagnosis. The scintigraphic part of the detector is simulated by GEANT4 and first attempts to reconstruct tomographic images have been made using as method of reconstruction a back-projection standard algorithm. The proposed camera is based on slant collimators and LaBr3:Ce crystals. Within the Field of View (FOV) of the camera, it possible to distinguish point sources located in air at a distance of about 2 cm from each other. In particular conditions of uptake, tumor depth and dimension, the preliminary results show that the Signal to Noise Ratio (SNR) values obtained are higher than the standard detection limit.

Calibration of a portal imaging device for high-precision dosimetry: a Monte Carlo study

Today electronic portal imaging devices (EPID's) are used primarily to verify patient positioning. They have, however, also the potential as 2D-dosimeters and could be used as such for transit dosimetry or dose reconstruction. It has been proven that such devices, especially liquid filled ionization chambers, have a stable dose response relationship which can be described in terms of the physical properties of the EPID and the pulsed linac radiation. For absolute dosimetry however, an accurate method of calibration to an absolute dose is needed. In this work, we concentrate on calibration against dose in a homogeneous water phantom. Using a Monte Carlo model of the detector we calculated dose spread kernels in units of absolute dose per incident energy fluence and compared them to calculated dose spread kernels in water at different depths. The energy of the incident pencil beams varied between 0.5 and 18 MeV. At the depth of dose maximum in water for a 6 MV beam (1.5 cm) and for a 18 MV beam (3.0 cm) we observed large absolute differences between water and detector dose above an incident energy of 4 MeV but only small relative differences in the most frequent energy range of the beam energy spectra. It is shown that for a 6 MV beam the absolute reference dose measured at 1.5 cm water depth differs from the absolute detector dose by 3.8%. At depth 1.2 cm in water, however, the relative dose differences are almost constant between 2 and 6 MeV. The effects of changes in the energy spectrum of the beam on the dose responses in water and in the detector are also investigated. We show that differences larger than 2% can occur for different beam qualities of the incident photon beam behind water slabs of different thicknesses. It is therefore concluded that for high-precision dosimetry such effects have to be taken into account. Nevertheless, the precise information about the dose response of the detector provided in this Monte Carlo study forms the basis of extracting directly the basic radiometric quantities photon fluence and photon energy fluence from the detector's signal using a deconvolution algorithm. The results are therefore promising for future application in absolute transit dosimetry and absolute dose reconstruction.

Verification of intensity modulated stereotactic radiotherapy using Monte Carlo calculations and EPID dosimetry

The purpose of this work was to develop a comprehensive IMSRT QA procedure that examined, using EPID dosimetry and Monte Carlo (MC) calculations, each step in the treatment planning and delivery process. These steps included verification of the field shaping, treatment planning system (RTPS) dose calculations, and patient dose delivery. Verification of each step in the treatment process is assumed to result in correct dose delivery to the patient. ^ The accelerator MC model was verified against commissioning data for field sizes from 0.8 × 0.8 cm 2 to 10 × 10 cm 2. Depth doses were within 2% local percent difference (LPD) in low gradient regions and 1 mm distance to agreement (DTA) in high gradient regions. Lateral profiles were within 2% LPD in low gradient regions and 1 mm DTA in high gradient regions. Calculated output factors were within 1% of measurement for field sizes ≥1 × 1 cm2. ^ The measured and calculated pretreatment EPID dose patterns were compared using criteria of 5% LPD, 1 mm DTA, or 2% of central axis pixel value with ≥95% of compared points required to pass for successful verification. Pretreatment field verification resulted in 97% percent of the points passing. ^ The RTPS and Monte Carlo phantom dose calculations were compared using 5% LPD, 2 mm DTA, or 2% of the maximum dose with ≥95% of compared points required passing for successful verification. RTPS calculation verification resulted in 97% percent of the points passing. ^ The measured and calculated EPID exit dose patterns were compared using criteria of 5% LPD, 1 mm DTA, or 2% of central axis pixel value with ≥95% of compared points required to pass for successful verification. Exit dose verification resulted in 97% percent of the points passing. ^ Each of the processes above verified an individual step in the treatment planning and delivery process. The combination of these verification steps ensures accurate treatment delivery to the patient. This work shows that Monte Carlo calculations and EPID dosimetry can be used to quantitatively verify IMSRT treatments resulting in improved patient care and, potentially, improved clinical outcome. ^

Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed to alpha particles

The energy and specific energy absorbed in the main cell compartments (nucleus and cytoplasm) in typical radiobiology experiments are usually estimated by calculations as they are not accessible for a direct measurement. In most of the work, the cell geometry is modelled using the combination of simple mathematical volumes. We propose a method based on high resolution confocal imaging and ion beam analysis (IBA) in order to import realistic cell nuclei geometries in Monte-Carlo simulations and thus take into account the variety of different geometries encountered in a typical cell population. Seventy-six cell nuclei have been imaged using confocal microscopy and their chemical composition has been measured using IBA. A cellular phantom was created from these data using the ImageJ image analysis software and imported in the Geant4 Monte-Carlo simulation toolkit. Total energy and specific energy distributions in the 76 cell nuclei have been calculated for two types of irradiation protocols: a 3 MeV alpha particle microbeam used for targeted irradiation and a 239Pu alpha source used for large angle random irradiation. Qualitative images of the energy deposited along the particle tracks have been produced and show good agreement with images of DNA double strand break signalling proteins obtained experimentally. The methodology presented in this paper provides microdosimetric quantities calculated from realistic cellular volumes. It is based on open-source oriented software that is publicly available.