Information geometric bound on general chemical reaction networks
physics.chem-ph, cond-mat.stat-mech, cs.IT, math.IT, stat.ML
Submitted: 2023-09-19
Updated: 2023-09-19
Comments: 11 pages
Journal ref: Phys. Rev. E 109, 044308 (Published 11 April, 2024)
DOI: 10.1103/PhysRevE.109.044308
License: http://creativecommons.org/licenses/by/4.0/
The gist: We investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates.
Terminology
Abstract
We investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates. This task is challenging due to the nonlinear nature and discrete structure inherent in CRNs. To address this, we employ an information geometric approach, using the natural gradient, to develop a nonlinear system that yields an upper bound for CRN dynamics. We validate our approach through numerical simulations, demonstrating faster convergence in a specific class of CRNs. This class is characterized by the number of chemicals, the maximum value of stoichiometric coefficients of the chemical reactions, and the number of reactions. We also compare our method to a conventional approach, showing that the latter cannot provide an upper bound on reaction rates of CRNs. While our study focuses on CRNs, the ubiquity of hypergraphs in fields from natural sciences to engineering suggests that our method may find broader applications, including in information science.
Sources
- Thermodynamic Bound on the Asymmetry of Cross-Correlations
- Dissipation, quantum coherence, and asymmetry of finite-time cross-correlations
- Thermodynamic bounds on correlation times
- Information Geometry of Dynamics on Graphs and Hypergraphs
- Robust Perfect Adaptation of Reaction Fluxes Ensured by Network Topology
- Bounds on the rates of statistical divergences and mutual information via stochastic thermodynamics
Related papers
- Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamics
- Accelerated "on-the-fly" coupled-cluster path-integral molecular dynamics: Impact of nuclear quantum effects on an asymmetric proton
- Variational Polaron Theory for Ground States of Strongly Coupled Light-Matter and Electron-Phonon Systems
- Pushing the accuracy of on-top functionals with agent-driven supervised learning
- Scaling Machine Learning Interatomic Potentials with Mixtures of Experts
- Localized intrinsic bond orbitals decode correlated charge migration dynamics