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Many of the intriguing properties of blood originate from its cellular nature. Bulk effects, such as viscosity, depend on the local shear rates and on the size of the vessels. While empirical descriptions of bulk rheology are available for…
To study implementations and optimisations of interaction net systems we propose a calculus to allow us to reason about nets, a concrete data-structure that is in close correspondence with the calculus, and a low-level language to create…
We advocates here the use of (mathematical) logic for systems biology, as a unified framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The…
Much of the controversy about methods for automated decision making has focused on specific calculi for combining beliefs or propagating uncertainty. We broaden the debate by (1) exploring the constellation of secondary tasks surrounding…
The multi-cellular hydrodynamic interactions play a critical role in the phenomenology of blood flow in the microcirculation. A fast algorithm has been developed to simulate large numbers of cells modeled as elastic thin membranes. For red…
We present an approach for flux analysis in process algebra models of biological systems. We perceive flux as the flow of resources in stochastic simulations. We resort to an established correspondence between event structures, a broadly…
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…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…
For systems that involve particle production through branching processes the concept of chaos is explored. The measures that can describe their behaviors are investigated. Monte Carlo simulation is used to generate events according to…
We present a logical calculus for reasoning about information flow in quantum programs. In particular we introduce a dynamic logic that is capable of dealing with quantum measurements, unitary evolutions and entanglements in compound…
We propose PALPS, a Process Algebra with Locations for Population Systems. PALPS allows us to produce spatially-explicit, individual-based models and to reason about their behavior. Our calculus has two levels: at the first level we may…
We describe here our perception of complex systems, of how we feel the different layers of description are important part of a correct complex system simulation. We describe a rough models categorization between rules based and law based,…
This paper summarizes a research program to express the organization of sensorimotor control by specifying physiological states and the conditions for transitions among them. By a slight change in standard notation, conditional dynamics…
We focus on improving the accuracy of an approximate model of a multiscale dynamical system that uses a set of parameter-dependent terms to account for the effects of unresolved or neglected dynamics on resolved scales. We start by…
Physical mechanisms of phase separation in living systems can play key physiological roles and have recently been the focus of intensive studies. The strongly heterogeneous and disordered nature of such phenomena in the biological domain…
In view of ever-changing conditions both in the external world and in intrinsic brain states, maintaining the robustness of computations poses a challenge, adequate solutions to which we are only beginning to understand. At the level of…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
Many cellular components are present in such low numbers that individual stochastic production and degradation events lead to significant fluctuations in molecular abundances. Although feedback control can, in principle, suppress such…
Changes in an animal's behavioral state, such as arousal and movements, induce {complex modulations of the baseline input currents to sensory areas, eliciting sensory modality-specific effects. A simple computational principle explaining…
We introduce circulance, a scalar measure for classifying time series of dynamical systems. Circulance captures the extent of temporal regularity or irregularity that is encoded in the topology of a directed ordinal pattern transition…