Related papers: A Mathematical Theory of Redox Biology
Numerous aqueous systems host elements in multiple redox states, with wide ranging implications such as their influence on the formation/dissolution of minerals, water toxicity, and nutrient cycling. To uncover governing mechanisms and…
Rigidity is an emergent property of materials - it is not a feature of individual components that comprise the structure, but instead arises from interactions between many constituent parts. Recently, it has been recognized that…
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…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
Physics relies on mathematical spaces carefully matched to the phenomena under study. Phase space in classical mechanics, Hilbert space in quantum theory, configuration spaces in field theory all provide representations in which physical…
Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
A notion of biologic system or just a system implies a functional wholeness of comprising system components. Positive and negative feedback are the examples of how the idea to unite anatomical elements in the whole functional structure was…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
Our planet is roughly closed to matter, but open to energy input from the sun. However, to harness this energy, organisms must transform matter from one chemical (redox) state to another. For example, photosynthetic organisms can capture…
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…
The task of modelling and forecasting a dynamical system is one of the oldest problems, and it remains challenging. Broadly, this task has two subtasks - extracting the full dynamical information from a partial observation; and then…
Natural systems are remarkably robust and resilient, maintaining essential functions despite variability, uncertainty, and hostile conditions. Understanding these nonlinear, dynamic behaviours is challenging because such systems involve…
Computation is commonly defined as the execution of abstract algorithms over symbolic representations, with physical systems treated as substrates that realise predefined operations. While effective for engineered machines, this separation…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
The emergence of life from inanimate matter presents a thermodynamic challenge: the Second Law of Thermodynamics dictates a global trend towards disorder, yet life constitutes localized pockets of profound organization. This paper presents…