Related papers: Discrete modelling of bacterial conjugation dynami…
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…
Advances in healthcare and in the quality of life significantly increase human life expectancy. With the ageing of populations, new un-faced challenges are brought to science. The human body is naturally selected to be well-functioning…
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…
Microorganisms employ sophisticated mechanisms for intercellular communication and environmental sensing, with quorum sensing serving as a fundamental regulatory process. Dysregulation of quorum sensing has been implicated in various…
Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…
We present a modeling framework for dynamical and bursty contact networks made of agents in social interaction. We consider agents' behavior at short time scales, in which the contact network is formed by disconnected cliques of different…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Our research is concerned with studying behavioural changes within a dynamic system, i.e. health care, and their effects on the decision-making process. Evolutionary Game theory is applied to investigate the most probable strategy(ies)…
Active swarms, consisting of individual agents which consume energy to move or produce work, are known to generate a diverse range of collective behaviors. Many examples of active swarms are biological in nature (e.g., fish shoals and bird…
As a step towards studying human-agent collectives we conduct an online game with human participants cooperating on a network. The game is presented in the context of achieving group formation through local coordination. The players set…
We discuss the feasibility of predicting, managing and subsequently manipulating, the future evolution of a Complex Adaptive System. Our archetypal system mimics a population of adaptive, interacting objects, such as those arising in the…
We propose an approach of open-ended evolution via the simulation of swarm dynamics. In nature, swarms possess remarkable properties, which allow many organisms, from swarming bacteria to ants and flocking birds, to form higher-order…
The abundance of data affords researchers to pursue more powerful computational tools to learn the dynamics of complex system, such as neural networks, engineered systems and social networks. Traditional machine learning approaches capture…
Collective decision-making arises from individual agents integrating their own personal observations with information obtained from social partners. In many biological systems that exhibit collective decision-making, the process by which…
Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an…
Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…
The nature of distributed computation has often been described in terms of the component operations of universal computation: information storage, transfer and modification. We review the first complete framework that quantifies each of…
Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic…