Related papers: Complex versus Complicated Systems Biology, Univer…
This document is both a synthesis of current notions about complex systems, and a practical approach description. A disambiguation is proposed and exposes possible reasons for controversies related to causation and emergence. Theoretical…
Recommender systems support decisions in various domains ranging from simple items such as books and movies to more complex items such as financial services, telecommunication equipment, and software systems. In this context,…
Nature's many varied complex systems (including galaxies, stars, planets, life, and society) are islands of order within the increasingly disordered universe. All organized systems are subject to physical, biological or cultural evolution,…
It is argued that the two problems of choosing characterizations and models of complex systems should not be considered independently. A particular criterion for these choices, oriented on the potential usefulness of the results, is…
Biological and robotic grasp and manipulation are undeniably similar at the level of mechanical task performance. However, their underlying fundamental biological vs. engineering mechanisms are, by definition, dramatically different and can…
This paper discusses the meaning and scope of biological hypercomputation (BH). The framework here is computational, and from the outset it should be clear that life is not a standard Turing Machine. Living systems hypercompute, but the…
Understanding realistic complex systems requires confronting significant conceptual, theoretical and experimental limitations rooted in the persistence of views that originated in the mechanics of simple moving bodies. We define the…
Modeling social-ecological systems is difficult due to the complexity of ecosystems and of individual and collective human behavior. Key components of the social-ecological system are often over-simplified or omitted. Generalized modeling…
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…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
In this paper we will try to provide a formalization of some characteristics of the development of biological systems aiming at the highest level of adequacy: justificative adequacy, that is, not only what we observe (descriptive adequacy)…
The spatial character of territorial systems plays a crucial role in the emergence of their complexities. This contribution aims at illustrating to what extent different types of complexities can be exhibited in models of such systems. We…
All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments…
A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
Biological systems perform an astonishing array of dynamical processes -- including development and repair, regulation, behavior and motor control, sensing and signaling, and adaptation, among others. Powered by the transduction of stored…
Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to…
The determination of environmentally- and economically-optimal energy system designs and operations is complex. In particular, the integration of weather-dependent renewable energy technologies into energy system optimization models…
The diversity of patterns that emerge from complex systems motivates their use for scientific or artistic purposes. When exploring these systems, the challenges faced are the size of the parameter space and the strongly non-linear mapping…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…