Hydration Routing Time as a Functional Index in DNA Groove Readability: From Residence Time to N_hydr Maps and a Minimal MD-Only Proof-of-Principle
Year: 2026
Type: preprint
Abstract: Water in biological systems is often described through hydration structure, residence time, hydrogen-bond lifetimes, and local mobility. This work introduces a minimal operational framework in which hydration lifetime is treated as a routing property rather than only as a residence property. The framework defines a dimensionless hydration routing index, N_hydr = N_route = τ_route / τ₀, and distinguishes routing time from residence time. The article proposes that major and minor DNA grooves may possess distinct hydration-routing maps, that ions should be classified not as absolute stabilizers or disruptors but as N_route shifters, and that functional hydration should occupy an intermediate window between noise and rigid barrier regimes. A minimal MD-only proof-of-principle protocol is proposed using a predefined matrix of groove analysis, ion regime, and temperature. The work is intended as a Version 1.0 theoretical and computational proof-of-principle proposal. It does not yet provide MD-derived numerical values or experimental validation. Future revisions may operationalize the MD observable, compare N_route with N_res, and connect routing predictions with NMR, THz, ultrafast spectroscopy, and DNA–protein or DNA–enzyme functional data.
Authors: BALEVSKY, ALEXANDAR, IVANOVA, KRASIMIRA
Institution: Technical University of Sofia
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7164925867