Morphogenesis: Bridging Theory and Simulation in Vertebrates Genetic mechanisms of early embryonic development in vertebrates and insights into a novel modelling approach based on smoothedparticle hydrodynamics and GPU-programming

Morphogenesis can be defined as the process by which living organisms build up a functionalanatomical body plan. The concept dates back to Aristotle, but the first empirical studies beganin the late 19th century with observations of embryogenesis. Morphogenesis has been appliedto various scales, yet many of the highly complex and intricate underlying realisations andlevels of emergence still need to be explored.Over the last decades, great progress has been made in the field of developmental biology. Inaddition to the identification of numerous morphogens and effector molecules and theirinteractions, new research methods and tools have been developed, and mathematical andcode-based frameworks have become more practical. This led to a bottom-up and top-downapproach to morphogenesis. Optogenetics, but also organoids, gene editing and bioelectricalrecordings and manipulations, have contributed much to bottom-up research by increasingspatial and temporal resolution and providing unprecedented details of the underlyingmolecular mechanisms. The application of computational models, spatial statistics, informationtheory and dynamical systems theory, is responsible for much of the rise of top-downapproaches in morphogenesis, but also in various other fields such as regeneration, oncology,or psychology, to name a few. Converging bottom-up and top-down approaches will enablefaster and more accurate progress in morphogenesis.This thesis provides an overview of the current state of research and tries to establish a linkbetween practical, computational approaches and neurodevelopmental theory. Starting withthe zygote, it leads through to the structural and functional formation of the earliest, mostimportant morphogenetic processes. It focuses on the underlying principles and applicablemodels of pattern formation of key tissues and organs. It touches on the self-organisinginteractions between the nervous system, the uterine environment, and the later-forming bodyas fundamental properties of the body are dependent on these interactions to develop properly.The discussed mathematical approaches and a simulation program based on smoothedparticle hydrodynamics (SPH), a modelling approach of particular interest, are presented andintegrated into the modelling landscape of tissue mechanics. Three practical examples ofmorphogenetic processes are provided as Python scripts that could serve as a stepping stonein transferring the known theory into the modelling program and could help to gain a betterunderstanding of the goal of modelling embryonic development.