Thermodynamic Space of Chemical Reaction Networks

arXiv:2407.11498 · cond-mat.stat-mech, q-bio.MN · Submitted 2024-07-16 · Read on arXiv

cond-mat.stat-mech, q-bio.MN

Submitted: 2024-07-16

Updated: 2026-09-16

Code: https://github.com/Shiling42/TACOS

Terminology

• Conservation Laws — 18× in this paper · explained in 3 episodes
• Hypergraph — 16× in this paper · explained in 2 episodes
• Chemical Reaction Network — 12× in this paper
• Symmetry Breaking — 8× in this paper · explained in 3 episodes
• Native Dimer — 4× in this paper
• Abundance — 3× in this paper · explained in 1 episode
• Alignment — 3× in this paper · explained in 1 episode
• Computational Biology — 3× in this paper · explained in 2 episodes
• Consistency — 3× in this paper · explained in 3 episodes
• Limit Cycles — 3× in this paper · explained in 2 episodes
• Native Monomer — 3× in this paper
• Robustness — 2× in this paper · explained in 5 episodes
• Verification — 2× in this paper · explained in 2 episodes
• Abstraction — 1× in this paper · explained in 1 episode
• Accuracy — 1× in this paper · explained in 1 episode
• Aggregation — 1× in this paper · explained in 1 episode
• Benchmark — 1× in this paper · explained in 2 episodes
• Calibration — 1× in this paper · explained in 7 episodes
• Dynamics and Local Detailed Balance — 1× in this paper
• Generalization — 1× in this paper · explained in 13 episodes
• Information Gain — 1× in this paper · explained in 2 episodes
• Redundancy — 1× in this paper · explained in 2 episodes
• alpha — 1× in this paper · explained in 1 episode

Sources

• Nonequilibrium Thermodynamic Formalism of Nonlinear Chemical Reaction Systems with Waage-Guldberg's Law of Mass Action
• Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics
• Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws
• The information gain limit of molecular computation
• A minimal scenario for the origin of non-equilibrium order
• The Parma Polyhedra Library: Toward a Complete Set of Numerical Abstractions for the Analysis and Verification of Hardware and Software Systems

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