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Layered Cellular Automata (LCA) extends the concept of traditional cellular automata (CA) to model complex systems and phenomena. In LCA, each cell's next state is determined by the interaction of two layers of computation, allowing for…
Understanding the dissemination of diseases, information, and behavior stands as a paramount research challenge in contemporary network and complex systems science. The COVID-19 pandemic and the proliferation of misinformation are relevant…
We investigate methods for modelling metabolism within populations of cells. Typically one represents the interaction of a cloned population of cells with their environment as though it were one large cell. The question is as to whether any…
We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…
The metabolic network plays a crucial role in regulating bacterial metabolism and growth, but it is subject to inherent molecular stochasticity. Previous studies have utilized flux balance analysis and the maximum entropy method to predict…
This study explores the emergence of life through a simulation model approach. The model "Multi-set chemical lattice model" is a model that allows virtual molecules of multiple types to be placed in each lattice cell on a two-dimensional…
We introduce a new methodology to analyze the evolution of epidemic time series, which is based on the construction of epidemic networks. First, we translate the time series into ordinal patterns containing information about local…
The fundamental concept of applying the system methodology to network analysis declares that network architecture should take into account services and applications which this network provides and supports. This work introduces a formal…
Representation of cities as organisms with metabolic processes is a useful analogy for urban design, development and sustainability. Urban metabolism can be modeled by representing urban systems as networks. The various networks included in…
There are many systems in different subjects such as industry, medicine, transport, social and others, can be discribed on their dynamic of flows. Nowadays models of flows consist of micro- and macro-models. In practice there is a problem…
The emergence and evolution of real-world systems have been extensively studied in the last few years. However, equally important phenomena are related to the dynamics of systems' collapse, which has been less explored, especially when they…
Complex systems are characterized by many interacting units that give rise to emergent behavior. A particularly advantageous way to study these systems is through the analysis of the networks that encode the interactions among the system's…
Molecular chaperones play a prominent role in signaling and transcriptional regulatory networks of the cell. Recent advances uncovered that chaperones act as genetic buffers stabilizing the phenotype of various cells and organisms and may…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Complex networks have recently attracted much interest due to their prevalence in nature and our daily lives [1, 2]. A critical property of a network is its resilience to random breakdown and failure [3-6], typically studied as a…
This paper presents a novel framework for the modeling of biological networks. It makes use of recent tools analyzing the robust satisfaction of properties of (hybrid) dynamical systems. The main challenge of this approach as applied to…
This chapter reviews the purpose and use of models from the field of complex systems and, in particular, the implications of trying to use models to understand or make decisions within complex situations, such as policy makers usually face.…
Vascular networks play a key role in the development, function, and survival of many organisms, facilitating transport of nutrients and other critical factors within and between systems. The development of these vessel networks has been…
Transformations to create more sustainable social-ecological systems are urgently needed. Structural change is a feature of transformations of social-ecological systems that is of critical importance but is little understood. Here, we…
A cell can be seen as an adaptive autonomous agent or as a society of adaptive autonomous agents, where each can exhibit a particular behaviour depending on its cognitive capabilities. We present an intracellular signalling model obtained…