A hydration-scaffold framework for phase-sensitive coupling and collective organization in biomolecular water

Abstract

We propose a theoretical and computational framework in which ordered hydration layers at biomolecular interfaces act as multi-scale coupled, phase-sensitive degrees of freedom that self-organize biological information processing at all scales. When biomolecular surfaces approach nanometer-to-subnanometer separations, overlapping hydration structures are represented by a shared-water coupling Hamiltonian incorporating evanescent and protonic channels. Coarse-graining yields a nonlocal complex-field description for locally connected hydration regions, while slow conformational variation introduces geometric-phase terms define vortex-like phase textures and routing-like correlation patterns. We further use a driven-dissipative Gross-Pitaevskii-type model as a phenomenological, not definitive, description of nonlinear hydration-sensitive collective modes. The model generates testable observables, including step-like phase responses, band-limited correlation windows, multi-timescale pump-probe relaxation, and sensitivity to temperature, osmolytes, and hydration state. We outline a GHz vector-network-analyzer and near-infrared pump-probe validation protocol on hydrated biomolecular films, together with negative controls for phase wrapping, RF leakage, standing waves, ionic conduction, and thermal drift. The framework is built as systems-level modeling that links hydration structure at atomic scale to macroscale, translating molecular recognition at the highest scales with information-like phase organization where continuity of water channels alone spontaneously emerges quantization and fractal-like phase conservation. Water as a singular unifying entity governing a bio-system has been neglected thus far.