In this Doktorarbeit the Lattice Boltzmann scheme, a heuristic method for the simulation of flows in complicated boundaries, is investigated. Its theory is renewed by emphasizing the entropy maximization principle, and new means for the modelling of geometries (including moving boundaries) and the visual representation of evoluting flows are presented. An object oriented implemen- tation is given with communication between objects realized by an interpreter object and communication from outside realized via interprocess communica- tion. Within the new theoretical apprach the applicability of existing Lattice Boltzmann schemes to model thermal flows for arbitrary temperatures is reex- amined. / In dieser Doktorarbeit wird das Gitter-Boltzmann-Schema, eine heuristische Methode fuer die Simulation von Stroemungen innerhalb komplexer Raender, untersucht. Die zugrundeliegende Theorie wird unter neuen Gesichtspunkten, insbesondere dem Prinzip der Entropiemaximierung, betrachtet. Des weiteren werden neuartige Methoden fuer die Modellierung der Geometrie (einschl. beweglicher Raender) und der visuellen Darstellung aufgezeigt. Eine objektorientierte Implementierung wird vorgestellt, wobei die Kommunikation zwischen den Objekten über Interpreter-Objekte und die Kommunikation mit der Aussenwelt ueber Interprozess-Kommunikation gehandhabt wird. Mit dem neuen theoretischen Ansatz wird die Gueltigkeit bestehender Gitter-Boltzmann-Schemata fuer die Anwendung auf Stroemungen mit nicht konstanter Temperatur untersucht.

Many diffusion processes in nature and society were found to be anomalous, in the sense of being fundamentally different from conventional Brownian motion. An important example is the migration of biological cells, which exhibits non-trivial temporal decay of velocity autocorrelation functions. This means that the corresponding dynamics is characterized by memory effects that slowly decay in time. Motivated by this we construct non-Markovian lattice-gas cellular automata models for moving agents with memory. For this purpose the reorientation probabilities are derived from velocity autocorrelation functions that are given a priori; in that respect our approach is “data-driven”. Particular examples we consider are velocity correlations that decay exponentially or as power laws, where the latter functions generate anomalous diffusion. The computational efficiency of cellular automata combined with our analytical results paves the way to explore the relevance of memory and anomalous diffusion for the dynamics of interacting cell populations, like confluent cell monolayers and cell clustering.

Many diffusion processes in nature and society were found to be anomalous, in the sense of being fundamentally different from conventional Brownian motion. An important example is the migration of biological cells, which exhibits non-trivial temporal decay of velocity autocorrelation functions. This means that the corresponding dynamics is characterized by memory effects that slowly decay in time. Motivated by this we construct non-Markovian lattice-gas cellular automata models for moving agents with memory. For this purpose the reorientation probabilities are derived from velocity autocorrelation functions that are given a priori; in that respect our approach is “data-driven”. Particular examples we consider are velocity correlations that decay exponentially or as power laws, where the latter functions generate anomalous diffusion. The computational efficiency of cellular automata combined with our analytical results paves the way to explore the relevance of memory and anomalous diffusion for the dynamics of interacting cell populations, like confluent cell monolayers and cell clustering.

In this Doktorarbeit the Lattice Boltzmann scheme, a heuristic method for the simulation of flows in complicated boundaries, is investigated. Its theory is renewed by emphasizing the entropy maximization principle, and new means for the modelling of geometries (including moving boundaries) and the visual representation of evoluting flows are presented. An object oriented implemen- tation is given with communication between objects realized by an interpreter object and communication from outside realized via interprocess communica- tion. Within the new theoretical apprach the applicability of existing Lattice Boltzmann schemes to model thermal flows for arbitrary temperatures is reex- amined. / In dieser Doktorarbeit wird das Gitter-Boltzmann-Schema, eine heuristische Methode fuer die Simulation von Stroemungen innerhalb komplexer Raender, untersucht. Die zugrundeliegende Theorie wird unter neuen Gesichtspunkten, insbesondere dem Prinzip der Entropiemaximierung, betrachtet. Des weiteren werden neuartige Methoden fuer die Modellierung der Geometrie (einschl. beweglicher Raender) und der visuellen Darstellung aufgezeigt. Eine objektorientierte Implementierung wird vorgestellt, wobei die Kommunikation zwischen den Objekten über Interpreter-Objekte und die Kommunikation mit der Aussenwelt ueber Interprozess-Kommunikation gehandhabt wird. Mit dem neuen theoretischen Ansatz wird die Gueltigkeit bestehender Gitter-Boltzmann-Schemata fuer die Anwendung auf Stroemungen mit nicht konstanter Temperatur untersucht.

Here, we investigate different cell density-dependent migration strategies. In particular, we consider strategies which differ in the precise regulation of transitions between resting and motile phenotypes. We develop a lattice-gas cellular automaton (LGCA) model for each migration strategy. Using a mean-field approximation we quantify the corresponding spreading dynamics at the cell population level. Our results allow for the prediction of cell population spreading based on experimentally accessible single cell migration parameters.

Cancer cells display characteristic traits acquired in a step-wise manner during carcinogenesis. Some of these traits are autonomous growth, induction of angiogenesis, invasion and metastasis. In this thesis, the focus is on one of the latest stages of tumor progression, tumor invasion. Tumor invasion emerges from the combined effect of tumor cell-cell and cell-microenvironment interactions, which can be studied with the help of mathematical analysis. Cellular automata (CA) can be viewed as simple models of self-organizing complex systems in which collective behavior can emerge out of an ensemble of many interacting "simple" components. In particular, we focus on an important class of CA, the so-called lattice-gas cellular automata (LGCA). In contrast to traditional CA, LGCA provide a straightforward and intuitive implementation of particle transport and interactions. Additionally, the structure of LGCA facilitates the mathematical analysis of their behavior. Here, the principal tools of mathematical analysis of LGCA are the mean-field approximation and the corresponding Lattice Boltzmann equation. The main objective of this thesis is to investigate important aspects of tumor invasion, under the microscope of mathematical modeling and analysis: Impact of the tumor environment: We introduce a LGCA as a microscopic model of tumor cell migration together with a mathematical description of different tumor environments. We study the impact of the various tumor environments (such as extracellular matrix) on tumor cell migration by estimating the tumor cell dispersion speed for a given environment. Effect of tumor cell proliferation and migration: We study the effect of tumor cell proliferation and migration on the tumor’s invasive behavior by developing a simplified LGCA model of tumor growth. In particular, we derive the corresponding macroscopic dynamics and we calculate the tumor’s invasion speed in terms of tumor cell proliferation and migration rates. Moreover, we calculate the width of the invasive zone, where the majority of mitotic activity is concentrated, and it is found to be proportional to the invasion speed. Mechanisms of tumor invasion emergence: We investigate the mechanisms for the emergence of tumor invasion in the course of cancer progression. We conclude that the response of a microscopic intracellular mechanism (migration/proliferation dichotomy) to oxygen shortage, i.e. hypoxia, maybe responsible for the transition from a benign (proliferative) to a malignant (invasive) tumor. Computing in vivo tumor invasion: Finally, we propose an evolutionary algorithm that estimates the parameters of a tumor growth LGCA model based on time-series of patient medical data (in particular Magnetic Resonance and Diffusion Tensor Imaging data). These parameters may allow to reproduce clinically relevant tumor growth scenarios for a specific patient, providing a prediction of the tumor growth at a later time stage. / Krebszellen zeigen charakteristische Merkmale, die sie in einem schrittweisen Vorgang während der Karzinogenese erworben haben. Einige dieser Merkmale sind autonomes Wachstum, die Induktion von Angiogenese, Invasion und Metastasis. Der Schwerpunkt dieser Arbeit liegt auf der Tumorinvasion, einer der letzten Phasen der Tumorprogression. Die Tumorinvasion ensteht aus der kombinierten Wirkung von den Wechselwirkungen Tumorzelle-Zelle und Zelle-Mikroumgebung, die mit die Hilfe von mathematischer Analyse untersucht werden können. Zelluläre Automaten (CA) können als einfache Modelle von selbst-organisierenden komplexen Systemen betrachtet werden, in denen kollektives Verhalten aus einer Kombination von vielen interagierenden "einfachen" Komponenten entstehen kann. Insbesondere konzentrieren wir uns auf eine wichtige CA-Klasse, die sogenannten Zelluläre Gitter-Gas Automaten (LGCA). Im Gegensatz zu traditionellen CA bieten LGCA eine einfache und intuitive Umsetzung der Teilchen und Wechselwirkungen. Zusätzlich erleichtert die Struktur der LGCA die mathematische Analyse ihres Verhaltens. Die wichtigsten Werkzeuge der mathematischen Analyse der LGCA sind hier die Mean-field Approximation und die entsprechende Lattice - Boltzmann - Gleichung. Das wichtigste Ziel dieser Arbeit ist es, wichtige Aspekte der Tumorinvasion unter dem Mikroskop der mathematischen Modellierung und Analyse zu erforschen: Auswirkungen der Tumorumgebung: Wir stellen einen LGCA als mikroskopisches Modell der Tumorzellen-Migration in Verbindung mit einer mathematischen Beschreibung der verschiedenen Tumorumgebungen vor. Wir untersuchen die Auswirkungen der verschiedenen Tumorumgebungen (z. B. extrazellulären Matrix) auf die Migration von Tumorzellen dürch Schätzung der Tumorzellen-Dispersionsgeschwindigkeit in einem gegebenen Umfeld. Wirkung von Tumor-Zellenproliferation und Migration: Wir untersuchen die Wirkung von Tumorzellenproliferation und Migration auf das invasive Verhalten der Tumorzellen durch die Entwicklung eines vereinfachten LGCA Tumorwachstumsmodells. Wir leiten die entsprechende makroskopische Dynamik und berechnen die Tumorinvasionsgeschwindigkeit im Hinblick auf die Tumorzellenproliferation- und Migrationswerte. Darüber hinaus berechnen wir die Breite der invasiven Zone, wo die Mehrheit der mitotischer Aktivität konzentriert ist, und es wird festgestellt, dass diese proportional zu den Invasionsgeschwindigkeit ist. Mechanismen der Tumorinvasion Entstehung: Wir untersuchen Mechanismen, die für die Entstehung von Tumorinvasion im Verlauf des Krebs zuständig sind. Wir kommen zu dem Schluss, dass die Reaktion eines mikroskopischen intrazellulären Mechanismus (Migration/Proliferation Dichotomie) zu Sauerstoffmangel, d.h. Hypoxie, möglicheweise für den Übergang von einem gutartigen (proliferative) zu einer bösartigen (invasive) Tumor verantwortlich ist. Berechnung der in-vivo Tumorinvasion: Schließlich schlagen wir einen evolutionären Algorithmus vor, der die Parameter eines LGCA Modells von Tumorwachstum auf der Grundlage von medizinischen Daten des Patienten für mehrere Zeitpunkte (insbesondere die Magnet-Resonanz-und Diffusion Tensor Imaging Daten) ermöglicht. Diese Parameter erlauben Szenarien für einen klinisch relevanten Tumorwachstum für einen bestimmten Patienten zu reproduzieren, die eine Vorhersage des Tumorwachstums zu einem späteren Zeitpunkt möglich machen.

Cellular automata (CA) are fully discrete dynamical systems. Space is represented by a regular lattice while time proceeds in finite steps. Each cell of the lattice is assigned a state, chosen from a finite set of "values". The states of the cells are updated synchronously according to a local interaction rule, whereby each cell obeys the same rule. Formal definitions of deterministic, probabilistic and lattice-gas CA are presented. With the so-called mean-field approximation any CA model can be transformed into a deterministic model with continuous state space. CA rules, which characterise movement, single-component growth and many-component interactions are designed and explored. It is demonstrated that lattice-gas CA offer a suitable tool for modelling such processes and for analysing them by means of the corresponding mean-field approximation. In particular two types of many-component interactions in lattice-gas CA models are introduced and studied. The first CA captures in abstract form the essential ideas of activator-inhibitor interactions of biological systems. Despite of the automaton´s simplicity, self-organised formation of stationary spatial patterns emerging from a randomly perturbed uniform state is observed (Turing pattern). In the second CA, rules are designed to mimick the dynamics of excitable systems. Spatial patterns produced by this automaton are the self-organised formation of spiral waves and target patterns. Properties of both pattern formation processes can be well captured by a linear stability analysis of the corresponding nonlinear mean-field (Boltzmann) equations.

No description available.

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