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The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, where a whole macromolecule is represented by a small number of particles, can be of…
Robustness to a wide variety of negative factors and the ability to self-repair is an inherent and natural characteristic of all life forms on earth. As opposed to nature, man-made systems are in most cases not inherently robust and a…
Modellers of complex biological or social systems are often faced with an invidious choice: to use simple models with few mechanisms that can be fully analysed, or to construct complicated models that include all the features which are…
Recent contributions address the problem of language coexistence as that of two species competing to aggregate speakers, thus focusing on the dynamics of linguistic traits across populations. They draw inspiration from physics and biology…
In this paper I present some of the most representative biological models applied to robotics. In particular, this work represents a survey of some models inspired, or making use of concepts, by gene regulatory networks (GRNs): these…
To a good extent, words can be understood as corresponding to patterns or categories that appeared in order to represent concepts and structures that are particularly important or useful in a given time and space. Words are characterized by…
The unprecedented prowess of measurement techniques provides a detailed, multi-scale look into the depths of living systems. Understanding these avalanches of high-dimensional data -- by distilling underlying principles and mechanisms --…
It has been reported that students often leave the introductory physics classroom believing that physics is less connected to the real world than when they entered. In this paper we aim to complicate that narrative by considering students'…
"Mathematicians, like physicists, are pushed by a strong fascination. Research in mathematics is hard, it is intellectually painful even if it is rewarding, and you would not do it without some strong urge." [D. Ruelle]. We shall give some…
The question What is Complexity? has occupied a great deal of time and paper over the last 20 or so years. There are a myriad different perspectives and definitions but still no consensus. In this paper I take a phenomenological approach,…
The complexity of biological systems, and the increasingly large amount of associated experimental data, necessitates that we develop mathematical models to further our understanding of these systems. As biological systems are generally not…
An extrapolation of the genetic complexity of organisms to earlier times suggests that life began before the Earth was formed. Life may have started from systems with single heritable elements that are functionally equivalent to a…
The discipline of `theoretical biology' has been developing from its inception several decades ago almost in parallel with the advances in biology, so much so that the latter is often considered to be almost exclusively an empirical…
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…
The classical "game of life" (GOL) due to Conway is a famous mathematical game constructed as a two-dimensional cellular automaton in which each cell is either alive or dead. A set of evolutionary rules determines whether a cell dies,…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
The standard assumptions that underlie many conceptual and quantitative frameworks do not hold for many complex physical, biological, and social systems. Complex systems science clarifies when and why such assumptions fail and provides…
We pursue research leading towards the nature of causality in the universe. We establish the equation of the universe's evolution from the universe-state function and its series expansion, in which causes and effects connect together to…
This paper presents mathematics as a general science of computation in a way different from the tradition. It is based on the radical philosophical standpoint according to which the content, meaning and justification of experience lies in…
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…