5 papers
A Mathematical Theory of Redox Biology
James N. Cobley, Michalis G. Nikolaidis
Redox biology underpins signalling, metabolism, immunity, and adaptation, yet lacks a unifying theoretical framework capable of formalising structure, function, and dynamics. Curre…
Oxi-Shapes: Tropical geometric analysis of bounded redox proteomic state spaces
James N. Cobley
Redox proteomics generates bounded biochemical measurements that are categorically mismatched to conventional linear algebraic formalisms. This work introduces Oxi-Shapes, a tropic…
A tropical geometry for bounded biochemical state spaces
James N. Cobley
Many biochemical measurements define state spaces that are bounded, absorbing, and physically irreversible, yet are routinely analysed using linear and Euclidean frameworks that as…
Local Electromagnetic Fields Enable Fast Redox Sensing by Physically Accelerating Cysteine Oxidation
James N. Cobley
Hydrogen peroxide oxidises cysteine residues to control protein function, yet bulk rate constants predict hours for changes that occur in cells in seconds. Here, this work shows th…
Modal Geometry Governs Proteoform Dynamics
James N. Cobley
The fundamental laws governing proteoform dynamics have yet to be formulated. As a result, it is unclear how a specific proteoform, a distinct molecular variant of a protein, dynam…