Calibration and simulations of SIXS-P's response to energetic particles

The Solar Intensity X-ray and particle Spectrometer (SIXS) on board BepiColombo's Mercury Planetary Orbiter (MPO) will study solar energetic particles moving towards Mercury and solar X-rays on the dayside of Mercury. The SIXS instrument consists of two detector sub-systems; X-ray detector SIXS-X and particle detector SIXS-P. The SIXS-P subdetector will detect solar energetic electrons and protons in a broad energy range using a particle telescope approach with five outer Si detectors around a central CsI(Tl) scintillator. The measurements made by the SIXS instrument are necessary for other instruments on board the spacecraft. SIXS data will be used to study the Solar X-ray corona, solar flares, solar energetic particles, the Hermean magnetosphere, and solar eruptions. The SIXS-P detector was calibrated by comparing experimental measurement data from the instrument with Geant4 simulation data. Calibration curves were produced for the different side detectors and the core scintillator for electrons and protons, respectively. The side detector energy response was found to be linear for both electrons and protons. The core scintillator energy response to protons was found to be non-linear. The core scintillator calibration for electrons was omitted due to insufficient experimental data. The electron and proton acceptance of the SIXS-P detector was determined with Geant4 simulations. Electron and proton energy channels are clean in the main energy range of the instrument. At higher energies, protons and electrons produce non-ideal response in the energy channels. Due to the limited bandwidth of the spacecraft's telemetry, the particle measurements made by SIXS-P have to be pre-processed in the data processing unit of the SIXS instrument. A lookup table was created for the pre-processing of data with Geant4 simulations, and the ability of the lookup table to provide spectral information from a simulated electron event was analysed. The lookup table produces clean electron and proton channels and is able to separate protons and electrons. Based on a simulated solar energetic electron event, the incident electron spectrum cannot be determined from channel particle counts with a standard analysis method.

Three-dimensional kinetic simulations of active suspensions: effect of chemotaxis and steric interaction

In this work, the effects of chemotaxis and steric interactions in active suspensions are analyzed by extending the kinetic model proposed by Saintillan and Shelley [1, 2]. In this model, a conservation equation for the active particle configuration is coupled to the Stokes equation for the flow arising from the force dipole exerted by the particles on the fluid. The fluid flow equations are solved spectrally and the conservation equation is solved by second-order finite differencing in space and second-order Adams-Bashforth time marching. First, the dynamics in suspensions of oxytactic run-and-tumble bacteria confined in thin liquid films surrounded by air is investigated. These bacteria modify their tumbling behavior by making temporal comparisons of the oxygen concentration, and, on average, swim towards high concentrations of oxygen. The kinetic model proposed by Saintillan and Shelley [1, 2] is modified to include run-and-tumble effects and oxygentaxis. The spatio-temporal dynamics of the oxygen and bacterial concentration are analyzed. For small film thicknesses, there is a weak migration of bacteria to the boundaries, and the oxygen concentration is high inside the film as a result of diffusion; both bacterial and oxygen concentrations quickly reach steady states. Above a critical film thickness (approximately 200 micron), a transition to chaotic dynamics is observed and is characterized by turbulent-like 3D motion, the formation of bacterial plumes, enhanced oxygen mixing and transport into the film, and hydrodynamic velocities of magnitudes up to 7 times the single bacterial swimming speed. The simulations demonstrate that the combined effects of hydrodynamic interactions and oxygentaxis create collective three-dimensional instabilities which enhances oxygen availability for the bacteria. Our simulation results are consistent with the experimental findings of Sokolov et al. [3], who also observed a similar transition with increasing film thickness. Next, the dynamics in concentrated suspensions of active self-propelled particles in a 3D periodic domain are analyzed. We modify the kinetic model of Saintillan and Shelley [1, 2] by including an additional nematic alignment torque proportional to the local concentration in the equation for the rotational velocity of the particles, causing them to align locally with their neighbors (Doi and Edwards [4]). Large-scale three- dimensional simulations show that, in the presence of such a torque both pusher and puller suspensions are unstable to random fluctuations and are characterized by highly nematic structures. Detailed measures are defined to quantify the degree and direction of alignment, and the effects of steric interactions on pattern formation will be presented. Our analysis shows that steric interactions have a destabilizing effect in active suspensions.

Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc.

INVESTIGATIONS INTO MECHANISMS UNDERLYING EXTREME WAVE FORMATIONS AND COMPUTATIONALLY INTENSIVE SIMULATIONS

Various mechanisms have been proposed to explain extreme waves or rogue waves in an oceanic environment including directional focusing, dispersive focusing, wave-current interaction, and nonlinear modulational instability. The Benjamin-Feir instability (nonlinear modulational instability), however, is considered to be one of the primary mechanisms for rogue-wave occurrence. The nonlinear Schrodinger equation is a well-established approximate model based on the same assumptions as required for the derivation of the Benjamin-Feir theory. Solutions of the nonlinear Schrodinger equation, including new rogue-wave type solutions are presented in the author's dissertation work. The solutions are obtained by using a predictive eigenvalue map based predictor-corrector procedure developed by the author. Features of the predictive map are explored and the influences of certain parameter variations are investigated. The solutions are rescaled to match the length scales of waves generated in a wave tank. Based on the information provided by the map and the details of physical scaling, a framework is developed that can serve as a basis for experimental investigations into a variety of extreme waves as well localizations in wave fields. To derive further fundamental insights into the complexity of extreme wave conditions, Smoothed Particle Hydrodynamics (SPH) simulations are carried out on an advanced Graphic Processing Unit (GPU) based parallel computational platform. Free surface gravity wave simulations have successfully characterized water-wave dispersion in the SPH model while demonstrating extreme energy focusing and wave growth in both linear and nonlinear regimes. A virtual wave tank is simulated wherein wave motions can be excited from either side. Focusing of several wave trains and isolated waves has been simulated. With properly chosen parameters, dispersion effects are observed causing a chirped wave train to focus and exhibit growth. By using the insights derived from the study of the nonlinear Schrodinger equation, modulational instability or self-focusing has been induced in a numerical wave tank and studied through several numerical simulations. Due to the inherent dissipative nature of SPH models, simulating persistent progressive waves can be problematic. This issue has been addressed and an observation-based solution has been provided. The efficacy of SPH in modeling wave focusing can be critical to further our understanding and predicting extreme wave phenomena through simulations. A deeper understanding of the mechanisms underlying extreme energy localization phenomena can help facilitate energy harnessing and serve as a basis to predict and mitigate the impact of energy focusing.

Understanding Co-translational Protein Targeting and Lithium Dendrite Formation through Free Energy Simulations and Coarse-Grained Models

We describe the application of alchemical free energy methods and coarse-grained models to study two key problems: (i) co-translational protein targeting and insertion to direct membrane proteins to the endoplasmic reticulum for proper localization and folding, (ii) lithium dendrite formation during recharging of lithium metal batteries. We show that conformational changes in the signal recognition particle, a central component of the protein targeting machinery, confer additional specificity during the the recognition of signal sequences. We then develop a three-dimensional coarse-grained model to study the long-timescale dynamics of membrane protein integration at the translocon and a framework for the calculation of binding free energies between the ribosome and translocon. Finally, we develop a coarse-grained model to capture the dynamics of lithium deposition and dissolution at the electrode interface with time-dependent voltages to show that pulse plating and reverse pulse plating methods can mitigate dendrite growth.

SIMULATIONS OF NEWTONIAN AND NON-NEWTONIAN FLOWS IN DEFORMABLE TUBES

Computational models for the investigation of flows in deformable tubes are developed and implemented in the open source computing environment OpenFOAM. Various simulations for Newtonian and non-Newtonian fluids under various flow conditions are carried out and analyzed. First, simulations are performed to investigate the flow of a shear-thinning, non-Newtonian fluid in a collapsed elastic tube and comparisons are made with experimental data. The fluid is modeled by means of the Bird-Carreau viscosity law. The computational domain of the deformed tube is constructed from data obtained via computer tomography imaging. Comparison of the computed velocity fields with the ultrasound Doppler velocity profile measurements show good agreement, as does the adjusted pressure drop along the tube's axis. Analysis of the shear rates show that the shear-thinning effect of the fluid becomes relevant in the cross-sections with the biggest deformation. The peristaltic motion is simulated by means of upper and lower rollers squeezing the fluid along a tube. Two frames of reference are considered. In the moving frame the computational domain is fixed and the coordinate system is moving with the roller speed, and in the fixed frame the roller is represented by a deforming mesh. Several two-dimensional simulations are carried out for Newtonian and non-Newtonian fluids. The effect of the shear-thinning behavior of the fluid on the transport efficiency is examined. In addition, the influence of the roller speed and the gap width between the rollers on the xxvii transport efficiency is discussed. Comparison with experimental data is also presented and different types of moving waves are implemented. In addition, the influence of the roller speed and the gap width between the rollers on the transport efficiency is discussed. Comparison with experimental data is also presented and different types of moving waves are implemented.

Power spectrum model of visual masking: simulations and empirical data

In the study of the spatial characteristics of the visual channels, the power spectrum model of visual masking is one of the most widely used. When the task is to detect a signal masked by visual noise, this classical model assumes that the signal and the noise are previously processed by a bank of linear channels and that the power of the signal at threshold is proportional to the power of the noise passing through the visual channel that mediates detection. The model also assumes that this visual channel will have the highest ratio of signal power to noise power at its output. According to this, there are masking conditions where the highest signal-to-noise ratio (SNR) occurs in a channel centered in a spatial frequency different from the spatial frequency of the signal (off-frequency looking). Under these conditions the channel mediating detection could vary with the type of noise used in the masking experiment and this could affect the estimation of the shape and the bandwidth of the visual channels. It is generally believed that notched noise, white noise and double bandpass noise prevent off-frequency looking, and high-pass, low-pass and bandpass noises can promote it independently of the channel's shape. In this study, by means of a procedure that finds the channel that maximizes the SNR at its output, we performed numerical simulations using the power spectrum model to study the characteristics of masking caused by six types of one-dimensional noise (white, high-pass, low-pass, bandpass, notched, and double bandpass) for two types of channel's shape (symmetric and asymmetric). Our simulations confirm that (1) high-pass, low-pass, and bandpass noises do not prevent the off-frequency looking, (2) white noise satisfactorily prevents the off-frequency looking independently of the shape and bandwidth of the visual channel, and interestingly we proved for the first time that (3) notched and double bandpass noises prevent off-frequency looking only when the noise cutoffs around the spatial frequency of the signal match the shape of the visual channel (symmetric or asymmetric) involved in the detection. In order to test the explanatory power of the model with empirical data, we performed six visual masking experiments. We show that this model, with only two free parameters, fits the empirical masking data with high precision. Finally, we provide equations of the power spectrum model for six masking noises used in the simulations and in the experiments.

Subfilter-scale Stress Modelling for Large Eddy Simulations

A subfilter-scale (SFS) stress model is developed for large-eddy simulations (LES) and is tested on various benchmark problems in both wall-resolved and wall-modelled LES. The basic ingredients of the proposed model are the model length-scale, and the model parameter. The model length-scale is defined as a fraction of the integral scale of the flow, decoupled from the grid. The portion of the resolved scales (LES resolution) appears as a user-defined model parameter, an advantage that the user decides the LES resolution. The model parameter is determined based on a measure of LES resolution, the SFS activity. The user decides a value for the SFS activity (based on the affordable computational budget and expected accuracy), and the model parameter is calculated dynamically. Depending on how the SFS activity is enforced, two SFS models are proposed. In one approach the user assigns the global (volume averaged) contribution of SFS to the transport (global model), while in the second model (local model), SFS activity is decided locally (locally averaged). The models are tested on isotropic turbulence, channel flow, backward-facing step and separating boundary layer. In wall-resolved LES, both global and local models perform quite accurately. Due to their near-wall behaviour, they result in accurate prediction of the flow on coarse grids. The backward-facing step also highlights the advantage of decoupling the model length-scale from the mesh. Despite the sharply refined grid near the step, the proposed SFS models yield a smooth, while physically consistent filter-width distribution, which minimizes errors when grid discontinuity is present. Finally the model application is extended to wall-modelled LES and is tested on channel flow and separating boundary layer. Given the coarse resolution used in wall-modelled LES, near the wall most of the eddies become SFS and SFS activity is required to be locally increased. The results are in very good agreement with the data for the channel. Errors in the prediction of separation and reattachment are observed in the separated flow, that are somewhat improved with some modifications to the wall-layer model.

Modelling and simulations of ductile iron solidification-induced variations in mechanical behaviour on component and microstructural level

The mechanical behaviour and performance of a ductile iron component is highly dependent on the local variations in solidification conditions during the casting process. Here we show a framework which combine a previously developed closed chain of simulations for cast components with a micro-scale Finite Element Method (FEM) simulation of the behaviour and performance of the microstructure. A casting process simulation, including modelling of solidification and mechanical material characterization, provides the basis for a macro-scale FEM analysis of the component. A critical region is identified to which the micro-scale FEM simulation of a representative microstructure, generated using X-ray tomography, is applied. The mechanical behaviour of the different microstructural phases are determined using a surrogate model based optimisation routine and experimental data. It is discussed that the approach enables a link between solidification- and microstructure-models and simulations of as well component as microstructural behaviour, and can contribute with new understanding regarding the behaviour and performance of different microstructural phases and morphologies in industrial ductile iron components in service.

Conception et mise à l’essai d’une stratégie pédagogique pour développer la métacognition pendant le processus de débogage de programmes informatiques au collégial

Les étudiantes et étudiants inscrits dans le programme technique Informatique de gestion au collégial ont comme tâche de concevoir, coder et mettre au point divers programmes informatiques. La capacité pour réaliser cette dernière tâche, soit la mise au point de programmes ou débogage de programmes, est très peu développée chez les élèves. Ils ne prennent pas le temps de vérifier si leurs programmes fonctionnent adéquatement. Selon les superviseurs de stage en milieu de travail, ils ne testent pas assez leurs programmes. La procédure pour supprimer les erreurs de programmation qui leur est proposée ne semble pas suffisante en elle-même pour les soutenir dans leur apprentissage. Les ouvrages consultés sur le sujet de la métacognition nous incitent à penser qu’il manque à la procédure de débogage générale une dimension métacognitive qui pourrait leur être enseignée. L’objectif de cette recherche est de développer une stratégie pédagogique socioconstructiviste intervenant sur la métacognition pour soutenir le développement de la capacité à déboguer des programmes informatiques et à améliorer le sentiment d’auto-efficacité des élèves face à cette tâche. L’autoquestionnement semble être une stratégie métacognitive à développer chez les élèves, car il est primordial que les élèves se questionnent avant de débuter et pendant une tâche quelconque, en particulier celle du débogage de programmes. Trop souvent, les élèves escamotent cette étape d’auto-questionnement, ils ont trop hâte de pianoter sur l’ordinateur et voir si cela fonctionne. Notre type d’essai consiste en l’élaboration d’une intervention pédagogique, sa validation et sa mise à l’essai auprès des élèves. Le matériel nécessaire pour l’intervention a été tiré et adapté du livre sur la métacognition de Lafortune et St-Pierre. Plusieurs activités d’apprentissage ont été construites pour ce projet : un exercice de prise de conscience sur des stratégies d’apprentissage efficaces, une activité d’autoévaluation pour vérifier les connaissances des étudiantes et étudiants sur le débogage de programmes et une troisième activité concernant la planification du processus de résolution de problèmes qui a été reprise tout le long de la session. Ces activités ont été mises à l’essai auprès d’un groupe d’étudiants de 2e année en Technique Informatique à la session Hiver 2004. Les résultats de cette mise à l’essai sont intéressants. Dans un premier temps, l’objectif concernant le développement des habiletés métacognitives de planification a été atteint. De même, le développement de la démarche de débogage a été nettement amélioré, car au début, la démarche était très générale et peu efficace tandis qu’à la fin, la démarche était beaucoup plus structurée et détaillée. L’atteinte de l’objectif, concernant le sentiment d’autoefficacité des élèves, est difficile à évaluer car l’objectif semblait être déjà présent au début selon leurs réponses au questionnaire initial. Cela est très surprenant, car les élèves n’ont pas nécessairement une bonne démarche de débogage mais ils pensent que leur démarche est efficace. Les retombées de ce projet ont permis d’approfondir mes connaissances personnelles au sujet de la métacognition, de l’approche socioconstructiviste et du sentiment d’autoefficacité. En ce qui concerne les élèves, ils ont pris conscience de l’importance du débogage de programmes dans leurs fonctions de travail et ils possèdent une procédure efficace de débogage générale qu’ils peuvent utiliser en tout temps. La stratégie pédagogique, les activités prévues et les outils utilisés nécessitent certains ajustements. Entre autres, utiliser davantage la technique du modelage par le professeur en classe et modifier la procédure générale de débogage en la schématisant pour développer davantage l’autoquestionnement chez les élèves.

Understanding significant precipitation in Madeira island using high-resolution numerical simulations of real cases

In order to advance the knowledge about precipitation development over Madeira island, four rainfall patterns are investigated based on high-resolution numerical simulations performed with the MESO-NH model. The main environmental conditions during these precipitation periods are examined, and important factors leading to significant accumulated precipitation in Madeira are shown. We found that the combination of orographic effect and atmospheric conditions is essential for the establishment of each situation. Under a moist and conditionally unstable atmosphere, convection over the island is triggered, and its location was determined mainly by variations of the ambient flow, which was also associated with different moist Froude numbers. Interestingly, our results showed some similarities with situations discussed in idealized studies. However, the real variations of the atmospheric configuration confirm the complexity of significant precipitation development in mountainous regions. In addition, precipitating systems initially formed over the ocean were simulated reaching the island. The four periods were characterised by different time durations, and the local terrain interacting with the mesoscale circulation was decisive in producing a large part of the precipitation, which concentrated in distinct regions of the island induced by the airflow dynamic.

Numerical simulations of significant orographic precipitation in Madeira island

High-resolution simulations of high precipitation events with the MESO-NHmodel are presented, and also used to verify that increasing horizontal resolution in zones of complex orography, such as in Madeira island, improve the simulation of the spatial distribution and total precipitation. The simulations succeeded in reproducing the general structure of the cloudy systems over the ocean in the four periods considered of significant accumulated precipitation. The accumulated precipitation over theMadeirawas better represented with the 0.5 km horizontal resolution and occurred under four distinct synoptic situations. Different spatial patterns of the rainfall distribution over the Madeira have been identified

Numerical Simulations of Fog Events in Southern Portugal

This work aims at improving the knowledge on fog formation and its evolution in the Alentejo region (Portugal). For this purpose, brief regional fog climatology, essentially based on information from the Beja Air Base meteorological station, was produced and several numerical high resolution simulations were performed using the Meso-NH. The ECOCLIMAP database used to generate the model physiography was improved to include the Alqueva reservoir (~250 km2), filled in 2003. The model results were compared with surface and satellite observations, showing good agreement in terms of fog occurrence and persistence. Various forcing mechanisms for formation, development, and dissipation of fog were identified, confirming the influence of two small mountains that block the moist air from the Atlantic Ocean, preventing the fog from reaching innermost regions. The introduction of the Alqueva large reservoir induces changes in the landscape and environment. The effects of the water vapour addition and of the changes in mass and energy surface fluxes on fog formation and evolution were studied. It was found that the reservoir may have a direct impact on fog formation over the lake and its vicinity. Depending on the large scale meteorological conditions, their influence can be both positive and negative, in terms of spatial coverage and temporal persistence.

ISM simulations: an overview of models

Until recently the dynamical evolution of the interstellar medium (ISM) was simu- lated using collisional ionization equilibrium (CIE) conditions. However, the ISM is a dynamical system, in which the plasma is naturally driven out of equilibrium due to atomic and dynamic processes operating on different timescales. A step forward in the field comprises a multi-fluid approach taking into account the joint thermal and dynamical evolutions of the ISM gas.

Large Eddy Simulations applied to wind loading and pollutant dispersion

The application of Computational Fluid Dynamics based on the Reynolds-Averaged Navier-Stokes equations to the simulation of bluff body aerodynamics has been thoroughly investigated in the past. Although a satisfactory accuracy can be obtained for some urban physics problems their predictive capability is limited to the mean flow properties, while the ability to accurately predict turbulent fluctuations is recognized to be of fundamental importance when dealing with wind loading and pollution dispersion problems. The need to correctly take into account the flow dynamics when such problems are faced has led researchers to move towards scale-resolving turbulence models such as Large Eddy Simulations (LES). The development and assessment of LES as a tool for the analysis of these problems is nowadays an active research field and represents a demanding engineering challenge. This research work has two objectives. The first one is focused on wind loads assessment and aims to study the capabilities of LES in reproducing wind load effects in terms of internal forces on structural members. This differs from the majority of the existing research, where performance of LES is evaluated only in terms of surface pressures, and is done with a view of adopting LES as a complementary design tools alongside wind tunnel tests. The second objective is the study of LES capabilities in calculating pollutant dispersion in the built environment. The validation of LES in this field is considered to be of the utmost importance in order to conceive healthier and more sustainable cities. In order to validate the numerical setup adopted, a systematic comparison between numerical and experimental data is performed. The obtained results are intended to be used in the drafting of best practice guidelines for the application of LES in the urban physics field with a particular attention to wind load assessment and pollution dispersion problems.