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Contact inhibition refers to a reduction in the rate of cell migration and/or cell proliferation in regions of high cell density. Under normal conditions contact inhibition is associated with the proper functioning tissues, whereas abnormal…

Simulation models often have parameters as input and return outputs to understand the behavior of complex systems. Calibration is the process of estimating the values of the parameters in a simulation model in light of observed data from…

Mesoscale molecular assemblies on the cell surface, such as cilia and filopodia, integrate information, control transport and amplify signals. Synthetic devices mimicking these structures could sensitively monitor these cellular functions…

Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…

Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…

The minimal requirements for life are autopoiesis and cognition. We propose autopoietic models with cognition and perform three classes of evolutionary simulation. In our models the plasticity of the metabolic cycle and the regulation…

Myxococcus xanthus is a unicellular organism whose cells possess the ability to move and communicate, leading to the emergence of complex collective properties and behaviours. This has made it an ideal model system to study the emergence of…

This thesis develops the theory of whispering gallery modes, exploring under what conditions a micro or nanoscale device can sustain these resonances, and for which physical criteria the resonance conditions deteriorate. The study is then…

In vivo wireless medical devices have the potential to play a vital role in future healthcare technologies by improving the quality of human life. In order to fully exploit the capabilities of such devices, it is necessary to characterize…

Cell tracking enables data extraction from time-lapse "cell movies" and promotes modeling biological processes at the single-cell level. We introduce a new fully automated computational strategy to track accurately cells across frames in…

The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…

Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…

Employing an effective cellular automata model, we investigate and analyze the build-up and erosion of soil. Depending on the strategy employed for handling agricultural production, in many cases we find a critical dependence on the…

This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as…

Controlling growth via cell division is crucial in the development of higher organisms, and yet the mechanisms through which this is achieved, e.g., in epithelial tissue, is not yet fully understood. We show that by coupling the cell cycle…

During the morphogenesis of tissues and tumors, cells often interact with neighbors with different mechanical properties, but the understanding of its role is lacking. We use active Brownian Dynamics simulations to study a model co-culture…

This postdoctoral thesis starts by reviewing the historic development of airplane structures and high lift devices from an engineering point of view. However, the main purpose of this document is the development of a novel concept for shape…

The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…

The formation and development of the human person is most influenced by the environment in which it lives, studies, works. Therefore, the problem of the creation of such a high-tech information and communication educational and scientific…

Automatic testing of mobile applications has been a well-researched area in recent years. However, testing in industry is still a very manual practice, as research results have not been fully transferred and adopted. Considering mobile…