Phd Defense by Bjarke Frost Nielsen

Title: Self-organizing systems and disease modelling


Part 1: How are organs and complex biological shapes formed by polarized cells? Biological shape formation in the animal kingdom is characterized by enormous diversity and remarkable robustness. We present a computational point-particle model of cells endowed with apical-basal and planar cell polarity and use it to simulate tube-forming processes in vasculogenesis, gastrulation and neurulation. We find that a simple set of dynamically enforced rules can adequately capture these very different processes.

Part 2: How is the crystallization of stripe-forming block copolymers affected by substrate curvature? It is known that pattern formation of lamellar phase smectic block copolymers is sensitive to intrinsic curvature. In our study, we show that the systematic inclusion of finite thickness fundamentally changes this picture, resulting in a coupling between stripe orientation and the extrinsic curvature of the substrate. We simulate the model obtained and show how extrinsic as well as intrinsic curvature can be used to guide pattern formation.

Part 3: How does heterogeneity and superspreading affect the mitigation of infectious diseases? The spread of infectious diseases can be affected by heterogeneities of many different kinds, from differences in the disease progression to social and behavioural differences and heterogenities in infectiousness or susceptibility. Using agent-based models, we focus on two different types of heterogeneity, namely social activity in the form of contact rates and network structure, and transmission overdispersion in the form of superspreading. We find that superspreading has profound implications for the effectiveness of lockdown-like mitigation strategies and that heterogeneous social activity is generally beneficial for contact tracing. Finally, we show that superspreading and non-pharmaceutical interventions may conspire to affect the evolution of a highly overdispersed pathogen such as SARS-CoV-2.