Length and sequence relaxation of copolymers under recombination reactions

Abstract

We describe the kinetics and thermodynamics of copolymers undergoing recombination reactions, which are important for prebiotic chemistry. We use two approaches: the first one, based on chemical rate equations and the mass-action law describes the infinite size limit, while the second one, based on the chemical master equation, describes systems of finite size. We compare the predictions of both approaches for the relaxation of thermodynamic quantities towards equilibrium. We find that for some choice of initial conditions, the entropy of the sequence distribution can be lowered at the expense of increasing the entropy of the length distribution. We consider mainly energetically neutral reactions, except for one simple case of non-neutral reactions.

arXiv comment15 pages, 6 figures and 1 table

References in corpus (11)

• Stochastic thermodynamics, fluctuation theorems, and molecular machines
• Ensemble and Trajectory Thermodynamics: A Brief Introduction
• Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics
• Multifarious Assembly Mixtures: Systems Allowing Retrieval of Diverse Stored Structures
• Entropy production for mechanically or chemically driven biomolecules
• Fundamental costs in the production and destruction of persistent polymer copies
• Emergence of information transmission in a prebiotic RNA reactor
• Kinetics and thermodynamics of first-order Markov chain copolymerization
• Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading
• Kinetics and thermodynamics of reversible polymerization in closed systems
• Glucans monomer-exchange dynamics as an open chemical network

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• Multistate reversible copolymerization of nonMarkovian chains under low conversion conditions
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