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Just as a herd of animals relies on its robust social structure to survive in the wild, similarly robustness is a crucial characteristic for the survival of a complex network under attack. The capacity to measure robustness in complex…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
Information flow provides a natural measure for the causal interaction between dynamical events. This study extends our previous rigorous formalism of componentwise information flow to the bulk information flow between two complex…
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
Dynamics of biological-ecological systems is strongly depending on spatial dimensions. Most of powerful simulators in ecology take into account for system spatiality thus embedding stochastic processes. Due to the difficulty of researching…
We address the problem of parameter estimation in models of systems biology from noisy observations. The models we consider are characterized by simultaneous deterministic nonlinear differential equations whose parameters are either taken…
This letter seeks to illuminate the profound connection between complexity, self-organization, emergent behaviour, pattern formation, and entropy concepts that are foundational to understanding our universe. By examining these ideas through…
We present novel analytical results about ecosystem species diversity that stem from a proposed coarse grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The…
A basic model is provided that places active, intentional choices by biological organisms on a solid physical footing. The model is provisionally called "Agent Choice via Quantum Flux." It brings to bear specific physics on living systems…
Discovered by Christopher Alexander, living structure is a physical phenomenon, through which the quality of the built environment or artifacts can be judged objectively. It bears two distinguished properties just like a tree: "far more…
Living systems self-organize in ways that conventional physical frameworks-based on forces, energies, and continuous fields-cannot fully capture. Processes like gene regulation and cellular decision-making involve rule-based logic and…
Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…
Temporal networks are commonly used to model real-life phenomena. When these phenomena represent interactions and are captured at a fine-grained temporal resolution, they are modeled as link streams. Community detection is an essential…
Computer modelling for evolutionary systems consists in: 1) to store in the memory the individual features of each member of a large population; and 2) to update the whole system repeatedly, as time goes by, according to some prescribed…
Economic transformation -- change in what an economy produces -- is foundational to development and rising standards of living. Our understanding of this process has been propelled recently by two branches of work in the field of economic…
The observed architecture of ecological and socio-economic networks differs significantly from that of random networks. From a network science standpoint, non-random structural patterns observed in real networks call for an explanation of…
The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconstructing this tree from genomic sequences is challenging due…
We investigate the self-organising behaviour of Digital Ecosystems, because a primary motivation for our research is to exploit the self-organising properties of biological ecosystems. We extended a definition for the complexity, grounded…