La hauteur des arbres est un trait écologique majeur représentant l'intensité de la compétition pour la lumière. De plus, la croissance des arbres est le résultat de multiples compromis afin de maintenir leur orientation verticale et leur stabilité mécanique tout en assurant les autres fonctions écophysiologiques. Le contrôle de l'orientation de la croissance est réalisé par deux mécanismes: la croissance différentielle au niveau du méristème apical et la formation de bois de réaction au cours de la croissance secondaire. Cependant, la modélisation simultanée de la croissance et des rétroactions biomécaniques dépasse le cadre classique de la mécanique des structures. En effet, le concept de configuration de référence devient imprécis dû à l'apparition de nouveaux points matériels libres de contraintes sur une surface déformée au cours de la croissance. Dans cette thèse, un nouveau formalisme mathématique est proposé à partir de la théorie des poutres et modélise simultanément les effets de la croissance et de la biomécanique de l'arbre. Afin de résoudre le système d'équations aux dérivées partielles, de nouvelles méthodes numériques sont développées et tiennent compte de la dépendance entre l'espace et le temps. Enfin, deux problèmes de contrôle optimal sont analysés, modélisant les stratégies d'allocation dynamique de la biomasse pour la croissance primaire et secondaire, en fonction de différents contextes écologiques. Ce travail offre de nouvelles perspectives sur les mathématiques de la mécanique de la croissance et ses applications en biologie. / Height is a major ecological trait for growing trees, representing the intensity for light competition. Moreover, tree height results from a trade-off between different functions, including tree mechanical stability. Trees develop growth strategies to maintain their vertical orientation and mechanical stability, in addition to other ecophysiological functions, through differential primary growth near the shoot apical meristem and formation of reaction wood during secondary growth. However, this coupling is a problematic issue since the progressive addition of new material on an existing deformed body makes the definition of a reference configuration unclear. This thesis presents a new mathematical framework for rod theory modelling simultaneously the interactions between the growth process and tree biomechanics. In order to solve the obtained system of partial differential equations, new numerical methods are developed and take into account the dependence between space and time, which is a specific feature of surface growth problems. Finally, the present work addresses the mathematical formulation of two optimal control problems characterising tree's growth strategies. Growth strategies are analysed with respect to the ecological context, through two variables, which are the ratio of biomass allocated to primary growth and the distribution of biomass allocated to secondary growth along the growing stem. This work gives new insights to the mathematical framework of surface growth mechanics and its applications in biology.

The invention of the Glancing Angle Deposition (GLAD) technique a decade ago enabled the fabrication of nanostructured thin films with highly tailorable structural, electrical, optical, and magnetic properties. Here a three-dimensional atomic-scale growth simulator has been developed to model the growth of thin film materials fabricated with the GLAD technique, utilizing the Monte Carlo (MC) and Kinetic Monte Carlo (KMC) methods; the simulator is capable of predicting film structure under a wide range of deposition conditions with a high degree of accuracy as compared to experiment. The stochastic evaporation and transport of atoms from the vapor source to the substrate is modeled as random ballistic deposition, incorporating the dynamic variation in substrate orientation that is central to the GLAD technique, and surface adatom diffusion is modeled as either an activated random walk (MC), or as energy dependent complete system transitions with rates calculated based on site-specific bond counting (KMC). The Sculptured Nanostructured Film Simulator (SNS) provides a three-dimensional physical prediction of film structure given a set of deposition conditions, enabling the calculation of film properties including porosity, roughness, and fractal dimension. Simulations were performed under various growth conditions in order to gain an understanding of the effects of incident angle, substrate rotation, tilt angle, and temperature on the resulting morphology of the thin film. Analysis of the evolution of film porosity during growth suggests a complex growth dynamic with significant variations with changes in tilt or substrate motion, in good agreement with x-ray reflectivity measurements. Future development will merge the physical structure growth simulator, SNS, with Finite-Difference Time-Domain (FDTD) electromagnetics simulation to allow predictive design of nanostructured optical materials. / Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2009-03-31 13:22:11.843

Lattice Monte Carlo methods are used to investigate far from and out-of-equilibrium systems, including surface growth, spin systems and solid mixtures. Applications range from the determination of universal growth or aging behaviors to palpable systems, where coarsening of nanocomposites or self-organization of functional nanostructures are of interest. Such studies require observations of large systems over long times scales, to allow structures to grow over orders of magnitude, which necessitates massively parallel simulations. This work addresses the problem of parallel processing introducing correlations in Monte Carlo updates and proposes a virtually correlation-free domain decomposition scheme to solve it. The effect of correlations on scaling and dynamical properties of surface growth systems and related lattice gases is investigated further by comparing results obtained by correlation-free and intrinsically correlated but highly efficient simulations using a stochastic cellular automaton (SCA). Efficient massively parallel implementations on graphics processing units (GPUs) were developed, which enable large-scale simulations leading to unprecedented precision in the final results. The primary subject of study is the Kardar–Parisi–Zhang (KPZ) surface growth in (2 + 1) dimensions, which is simulated using a dimer lattice gas and the restricted solid-on-solid model (RSOS) model. Using extensive simulations, conjectures regard- ing growth, autocorrelation and autoresponse properties are tested and new precise numerical predictions for several universal parameters are made.:1. Introduction 1.1. Motivations and Goals 1.2. Overview 2. Methods and Models 2.1. Estimation of Scaling Exponents and Error Margins 2.2. From Continuum- to Atomistic Models 2.3. Models for Phase Ordering and Nanostructure Evolution 2.3.1. The Kinetic Metropolis Lattice Monte-Carlo Method 2.3.2. The Potts Model 2.4. The Kardar–Parisi–Zhang and Edwards–Wilkinson Universality Classes 2.4.0.1. Physical Aging 2.4.1. The Octahedron Model 2.4.2. The Restricted Solid on Solid Model 3. Parallel Implementation: Towards Large-Scale Simulations 3.1. Parallel Architectures and Programming Models 3.1.1. CPU 3.1.2. GPU 3.1.3. Heterogeneous Parallelism and MPI 3.1.4. Bit-Coding of Lattice Sites 3.2. Domain Decomposition for Stochastic Lattice Models 3.2.1. DD for Asynchronous Updates 3.2.1.1. Dead border (DB) 3.2.1.2. Double tiling (DT) 3.2.1.3. DT DD with random origin (DTr) 3.2.1.4. Implementation 3.2.2. Second DD Layer on GPUs 3.2.2.1. Single-Hit DT 3.2.2.2. Single-Hit dead border (DB) 3.2.2.3. DD Parameters for the Octahedron Model 3.2.3. Performance 3.3. Lattice Level DD: Stochastic Cellular Automaton 3.3.1. Local Approach for the Octahedron Model 3.3.2. Non-Local Approach for the Octahedron Model 3.3.2.1. Bit-Vectorized GPU Implementation 3.3.3. Performance of SCA Implementations 3.4. The Multi-Surface Coding Approach 3.4.0.1. Vectorization 3.4.0.2. Scalar Updates 3.4.0.3. Domain Decomposition 3.4.1. Implementation: SkyMC 3.4.1.1. 2d Restricted Solid on Solid Model 3.4.1.2. 2d and 3d Potts Model 3.4.1.3. Sequential CPU Reference 3.4.2. SkyMC Benchmarks 3.5. Measurements 3.5.0.1. Measurement Intervals 3.5.0.2. Measuring using Heterogeneous Resources 4. Monte-Carlo Investigation of the Kardar–Parisi–Zhang Universality Class 4.1. Evolution of Surface Roughness 4.1.1. Comparison of Parallel Implementations of the Octahedron Model 4.1.1.1. The Growth Regime 4.1.1.2. Distribution of Interface Heights in the Growth Regime 4.1.1.3. KPZ Ansatz for the Growth Regime 4.1.1.4. The Steady State 4.1.2. Investigations using RSOS 4.1.2.1. The Growth Regime 4.1.2.2. The Steady State 4.1.2.3. Consistency of Fine-Size Scaling with Respect to DD 4.1.3. Results for Growth Phase and Steady State 4.2. Autocorrelation Functions 4.2.1. Comparison of DD Methods for RS Dynamics 4.2.1.1. Device-Layer DD 4.2.1.2. Block-Layer DD 4.2.2. Autocorrelation Properties under RS Dynamics 4.2.3. Autocorrelation Properties under SCA Dynamics 4.2.3.1. Autocorrelation of Heights 4.2.3.2. Autocorrelation of Slopes 4.2.4. Autocorrelation in the SCA Steady State 4.2.5. Autocorrelation in the EW Case under SCA 4.2.5.1. Autocorrelation of Heights 4.2.5.2. Autocorrelations of Slopes 4.3. Autoresponse Functions 4.3.1. Autoresponse Properties 4.3.1.1. Autoresponse of Heights 4.3.1.2. Autoresponse of Slopes 4.3.1.3. Self-Averaging 4.4. Summary 5. Further Topics 5.1. Investigations of the Potts Model 5.1.1. Testing Results from the Parallel Implementations 5.1.2. Domain Growth in Disordered Potts Models 5.2. Local Scale Invariance in KPZ Surface Growth 6. Conclusions and Outlook Acknowledgements A. Coding Details A.1. Bit-Coding A.2. Packing and Unpacking Signed Integers A.3. Random Number Generation / Gitter-Monte-Carlo-Methoden werden zur Untersuchung von Systemen wie Oberflächenwachstum, Spinsystemen oder gemischten Feststoffen verwendet, welche fern eines Gleichgewichtes bleiben oder zu einem streben. Die Anwendungen reichen von der Bestimmung universellen Wachstums- und Alterungsverhaltens hin zu konkreten Systemen, in denen die Reifung von Nanokompositmaterialien oder die Selbstorganisation von funktionalen Nanostrukturen von Interesse sind. In solchen Studien müssen große Systemen über lange Zeiträume betrachtet werden, um Strukturwachstum über mehrere Größenordnungen zu erlauben. Dies erfordert massivparallele Simulationen. Diese Arbeit adressiert das Problem, dass parallele Verarbeitung Korrelationen in Monte-Carlo-Updates verursachen und entwickelt eine praktisch korrelationsfreie Domänenzerlegungsmethode, um es zu lösen. Der Einfluss von Korrelationen auf Skalierungs- und dynamische Eigenschaften von Oberflächenwachtums- sowie verwandten Gittergassystemen wird weitergehend durch den Vergleich von Ergebnissen aus korrelationsfreien und intrinsisch korrelierten Simulationen mit einem stochastischen zellulären Automaten untersucht. Effiziente massiv parallele Implementationen auf Grafikkarten wurden entwickelt, welche großskalige Simulationen und damit präzedenzlos genaue Ergebnisse ermöglichen. Das primäre Studienobjekt ist das (2 + 1)-dimensionale Kardar–Parisi–Zhang- Oberflächenwachstum, welches durch ein Dimer-Gittergas und das Kim-Kosterlitz-Modell simuliert wird. Durch massive Simulationen werden Thesen über Wachstums-, Autokorrelations- und Antworteigenschaften getestet und neue, präzise numerische Vorhersagen zu einigen universellen Parametern getroffen.:1. Introduction 1.1. Motivations and Goals 1.2. Overview 2. Methods and Models 2.1. Estimation of Scaling Exponents and Error Margins 2.2. From Continuum- to Atomistic Models 2.3. Models for Phase Ordering and Nanostructure Evolution 2.3.1. The Kinetic Metropolis Lattice Monte-Carlo Method 2.3.2. The Potts Model 2.4. The Kardar–Parisi–Zhang and Edwards–Wilkinson Universality Classes 2.4.0.1. Physical Aging 2.4.1. The Octahedron Model 2.4.2. The Restricted Solid on Solid Model 3. Parallel Implementation: Towards Large-Scale Simulations 3.1. Parallel Architectures and Programming Models 3.1.1. CPU 3.1.2. GPU 3.1.3. Heterogeneous Parallelism and MPI 3.1.4. Bit-Coding of Lattice Sites 3.2. Domain Decomposition for Stochastic Lattice Models 3.2.1. DD for Asynchronous Updates 3.2.1.1. Dead border (DB) 3.2.1.2. Double tiling (DT) 3.2.1.3. DT DD with random origin (DTr) 3.2.1.4. Implementation 3.2.2. Second DD Layer on GPUs 3.2.2.1. Single-Hit DT 3.2.2.2. Single-Hit dead border (DB) 3.2.2.3. DD Parameters for the Octahedron Model 3.2.3. Performance 3.3. Lattice Level DD: Stochastic Cellular Automaton 3.3.1. Local Approach for the Octahedron Model 3.3.2. Non-Local Approach for the Octahedron Model 3.3.2.1. Bit-Vectorized GPU Implementation 3.3.3. Performance of SCA Implementations 3.4. The Multi-Surface Coding Approach 3.4.0.1. Vectorization 3.4.0.2. Scalar Updates 3.4.0.3. Domain Decomposition 3.4.1. Implementation: SkyMC 3.4.1.1. 2d Restricted Solid on Solid Model 3.4.1.2. 2d and 3d Potts Model 3.4.1.3. Sequential CPU Reference 3.4.2. SkyMC Benchmarks 3.5. Measurements 3.5.0.1. Measurement Intervals 3.5.0.2. Measuring using Heterogeneous Resources 4. Monte-Carlo Investigation of the Kardar–Parisi–Zhang Universality Class 4.1. Evolution of Surface Roughness 4.1.1. Comparison of Parallel Implementations of the Octahedron Model 4.1.1.1. The Growth Regime 4.1.1.2. Distribution of Interface Heights in the Growth Regime 4.1.1.3. KPZ Ansatz for the Growth Regime 4.1.1.4. The Steady State 4.1.2. Investigations using RSOS 4.1.2.1. The Growth Regime 4.1.2.2. The Steady State 4.1.2.3. Consistency of Fine-Size Scaling with Respect to DD 4.1.3. Results for Growth Phase and Steady State 4.2. Autocorrelation Functions 4.2.1. Comparison of DD Methods for RS Dynamics 4.2.1.1. Device-Layer DD 4.2.1.2. Block-Layer DD 4.2.2. Autocorrelation Properties under RS Dynamics 4.2.3. Autocorrelation Properties under SCA Dynamics 4.2.3.1. Autocorrelation of Heights 4.2.3.2. Autocorrelation of Slopes 4.2.4. Autocorrelation in the SCA Steady State 4.2.5. Autocorrelation in the EW Case under SCA 4.2.5.1. Autocorrelation of Heights 4.2.5.2. Autocorrelations of Slopes 4.3. Autoresponse Functions 4.3.1. Autoresponse Properties 4.3.1.1. Autoresponse of Heights 4.3.1.2. Autoresponse of Slopes 4.3.1.3. Self-Averaging 4.4. Summary 5. Further Topics 5.1. Investigations of the Potts Model 5.1.1. Testing Results from the Parallel Implementations 5.1.2. Domain Growth in Disordered Potts Models 5.2. Local Scale Invariance in KPZ Surface Growth 6. Conclusions and Outlook Acknowledgements A. Coding Details A.1. Bit-Coding A.2. Packing and Unpacking Signed Integers A.3. Random Number Generation