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In both neuroscience and artificial intelligence, popular functional frameworks and neural network formulations operate by making use of extrinsic error measurements and global learning algorithms. Through a set of conjectures based on…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
The search for universal laws that help establish a relationship between dynamics and computation is driven by recent expansionist initiatives in biologically inspired computing. A general setting to understand both such dynamics and…
This chapter reviews four notions of system structure, three of which are contextual and classic (i.e. the complete computational structure linked to a state space model, the sparsity pattern of a transfer function, and the interconnection…
Human language and its governing rules present a number of analogies with the organization and structure of communication and information management in living organisms. This chapter will provide a short general introduction about grammar,…
For over fifty years, the dynamical systems perspective has had a prominent role in evolutionary biology and economics, through the lens of game theory. In particular, the study of replicator differential equations on the standard…
Impedance Spectroscopy resolves electrical properties into uncorrelated variables, as a function of frequency, with exquisite resolution. Separation is robust and most useful when the system is linear. Impedance spectroscopy combined with…
Information exchange is a critical process in all communication systems, including biological ones. The concept of retroactivity represents the loads that downstream modules apply to their upstream systems in biological circuits. This paper…
Nature uses elongated shapes and filaments to build stable structures, generate motion, and allow complex geometric interactions. In this Review, we examine the role of biological filaments across different length scales. From the molecular…
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…
We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
The infrastructure upon which the functioning of society depends is composed of complex ecosystems of systems. Consequently, we must reason about the properties of such ecosystems, which requires that we construct models of them. There are…
The cells and tissues that make up our body juggle contradictory mechanical demands. It is crucial for their survival to be able to withstand large mechanical loads, but it is equally crucial for them to produce forces and actively change…
Natural organisms can convert environmental stimuli into sensory feedback to regulate their body and realize active adaptivity. However, realizing such a feedback-regulation mechanism in synthetic material systems remains a grand challenge.…
This article frames the relation between biology and physics by characterizing the former as a subdiscipline rather than a special case of the latter. To do this, we posit biological physics as the science of living matter in contrast to…
This work aims at providing a mathematical and numerical framework for the analysis on the effects of pulsed electric fields on biological media. Biological tissues and cell suspensions are described as having a heteregeneous permittivity…
Biological systems produce outputs in response to variable inputs. Input-output relations tend to follow a few regular patterns. For example, many chemical processes follow the S-shaped Hill equation relation between input concentrations…
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,…