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A complex system is a system composed of many interacting parts, often called agents, which displays collective behavior that does not follow trivially from the behaviors of the individual parts. Examples include condensed matter systems,…
Harmonic theory provides a mathematical framework to describe the structure, behavior, evolution and emergence of harmonic systems. A harmonic system is context aware, contains elements that manifest characteristics either collaboratively…
Escherichia coli and Bacillus subtilis are two of the best-studied prokaryotic model organisms. Previous analyses of their transcriptional regulatory networks have shown that they exhibit high plasticity during evolution and suggested that…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
A set of general physical principles is proposed as the structural basis for the theory of complex systems. First the concept of harmony is analyzed and its different aspects are uncovered. Then the concept of reflection is defined and…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
A categorical framework for modeling and analyzing systems in a broad sense is proposed. These systems should be thought of as `machines' with inputs and outputs, carrying some sort of signal that occurs through some notion of time. Special…
We construct a stochastic dynamical systems theory in which sustainability is a structural boundary property of a fully coupled Earth--Human--Production system. Each subsystem is modelled as a vector-valued process governed by stochastic…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
In several applications, including in synthetic biology, one often has input/output data on a system composed of many modules, and although the modules' input/output functions and signals may be unknown, knowledge of the composition…
This paper develops a conceptual extension of the Kinetic Theory of Active Particles, building upon the framework introduced in [2]. Living systems cannot be adequately described within classical single-scale paradigms, even when refined.…
A foundation for closing the gap between biometrics in the narrower and the broader perspective is presented trough a conceptualization of biometric systems in both perspectives. A clear distinction between verification, identification and…
This paper proposes a simple model to capture the complexity of multi-layer systems where their constituent layers affect, are affected by, each other. The physical layer is a circuit composed by a power source and resistors in parallel.…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
The concept of boolean autonomous deterministic regular asynchronous system has its origin in switching theory, the theory of modeling the switching circuits from the digital electrical engineering. The attribute boolean vaguely refers to…
Biomolecular feedback systems are now a central application area of interest within control theory. While classical control techniques provide invaluable insight into the function and design of both natural and synthetic biomolecular…
Complementarity among species with different traits is one of the basic processes affecting biodiversity, defined as the number of species in the ecosystem. We present here a soluble model ecosystem in which the species are characterized by…
Dynamics is central to living systems. In the last two decades, experiments have revealed that the dynamics in diverse biological systems - from intracellular cytoplasm to cellular and organismal aggregates - are remarkably similar to that…