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Spatial organization is a core challenge for all large agent-based models with local interactions. In biological tissue models, spatial search and reinsertion are frequently reported as the most expensive steps of the simulation. One of the…
Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g., populations or communities). The analysis of such data often leads to a two-step approach where groups containing similar…
The growth of world population, limitation of resources, economic problems and environmental issues force engineers to develop increasingly efficient solutions for logistic systems. Pure optimization for efficiency, however, has often led…
Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of…
The execution time of programs is a key element in many areas of computer science, mainly those where achieving good performance (e.g., scheduling in cloud computing) or a predictable one (e.g., meeting deadlines in embedded systems) is the…
Probabilistic programming is related to a compositional approach to stochastic modeling by switching from discrete to continuous time dynamics. In continuous time, an operator-algebra semantics is available in which processes proceeding in…
As in the car industry for quite some time, dynamic simulation of complete vehicles is being practiced more and more in the development of off-road machinery. However, specific questions arise due not only to company structure and size, but…
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
The aim of this paper is to propose an alternative behavioural definition of computation (and of a computer) based simply on whether a system is capable of reacting to the environment-the input-as reflected in a measure of programmability.…
Many systems may switch to an undesired state due to internal failures or external perturbations, of which critical transitions toward degraded ecosystem states are a prominent example. Resilience restoration focuses on the ability of…
The simulation of complex stochastic network dynamics arising, for instance, from models of coupled biomolecular processes remains computationally challenging. Often, the necessity to scan a models' dynamics over a large parameter space…
Models that can simulate how environments change in response to actions can be used by agents to plan and act efficiently. We improve on previous environment simulators from high-dimensional pixel observations by introducing recurrent…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
The parameter space of dynamical systems arising in applications is often found to be high-dimensional and difficult to explore. We construct a fast algorithm to numerically analyze "quantitative features" of dynamical systems depending on…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose,…
What determines whether an organism or collective will survive under particular conditions? This question is asked across the life sciences when determining adaptive fit, developing efficacious treatments for diseases, and assessing the…
The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis,…
Build-time configuration and environment assumptions are hampering progress and usability in scientific software. That which would be utterly unacceptable in non-scientific software somehow passes for the norm in scientific packages. The…