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Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
In its broadest definition, systems biology is the application of a `systems' way of thinking about and doing cell biology. By implication, this also invites us to consider a systems approach in the context of medicine and the treatment of…
Monotone systems constitute one of the most important classes of dynamical systems used in mathematical biology modeling. The objective of this paper is to extend the notion of monotonicity to systems with inputs and outputs, a necessary…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach…
Feedback loops are major components of biochemical systems. Many systems show multiple such (positive or negative) feedback loops. Nevertheless, very few quantitative analyses address the question how such multiple feedback loops evolved.…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Monotone systems constitute one of the most important classes of dynamical systems used in mathematical biology modeling. The objective of this paper is to extend the notion of monotonicity to systems with inputs and outputs, a necessary…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
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…
In the study of the basic properties observed in the immune system and, in a broader view, in biological systems, several concepts have already been mathematically formulated or treated in an analytical perspective, such as degeneracy,…
Control theory arose from a need to control synthetic systems. From regulating steam engines to tuning radios to devices capable of autonomous movement, it provided a formal mathematical basis for understanding the role of feedback in the…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
Redox biology underpins signalling, metabolism, immunity, and adaptation, yet lacks a unifying theoretical framework capable of formalising structure, function, and dynamics. Current interpretations rely on descriptive catalogues of…
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…
At its core, the physics paradigm adopts a reductionist approach, aiming to understand fundamental phenomena by decomposing them into simpler, elementary processes. While this strategy has been tremendously successful in physics, it has…
Living systems exhibit a range of fundamental characteristics: they are active, self-referential, self-modifying systems. This paper explores how these characteristics create challenges for conventional scientific approaches and why they…