Fundamental costs in the production and destruction of persistent polymer copies

Abstract

Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that, as in computation, a canonical biochemical readout network generates correlations; extracting no work from these correlations sets a lower bound on dissipation. For general input, the biochemical network cannot reach this bound, even with arbitrarily slow reactions or weak thermodynamic driving. It faces an accuracy-dissipation trade-off that is qualitatively distinct from and worse than implied by the bound, and more complex steady-state copy processes cannot perform better. Nonetheless, the cost remains close to the thermodynamic bound unless accuracy is extremely high. Additionally, we show that biomolecular reactions could be used in thermodynamically optimal devices under exogenous manipulation of chemical fuels, suggesting an experimental system for testing computational thermodynamics.

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• Second law and Landauer principle far from equilibrium
• Reversible self-assembly of patchy particles into monodisperse icosahedral clusters
• Imitating Chemical Motors with Optimal Information Motors
• Kinetic vs. energetic discrimination in biological copying
• Numerical evidence for nucleated self-assembly of DNA brick structures
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• The thermodynamics of computational copying in biochemical systems
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Cited by in corpus (24)

• Stochastic thermodynamics of computation
• The thermodynamic efficiency of computations made in cells across the range of life
• Conservation Laws and Work Fluctuation Relations in Chemical Reaction Networks
• Non-equilibrium correlations in minimal dynamical models of polymer copying
• What we learn from the learning rate
• Role of sufficient statistics in stochastic thermodynamics and its implication to sensory adaptation
• Landauer Principle and Thermodynamics of Computation
• Energetic cost of feedback control
• Length and sequence relaxation of copolymers under recombination reactions
• Biochemical Szilard engines for memory-limited inference
• Designing the Optimal Bit: Balancing Energetic Cost, Speed and Reliability
• Edge-effects dominate copying thermodynamics for finite-length molecular oligomers
• Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions
• Nonequilibrium entropic bounds for Darwinian replicators
• Decomposing information into copying versus transformation
• The polyhedral structure underlying programmable self-assembly
• Thermodynamics of Darwinian selection in molecular replicators
• Generalized Zurek's bound on the cost of an individual classical or quantum computation
• The thermodynamics of quasi-deterministic digital computers
• Non Equilibrium Transitions in a Polymer Replication Ensemble
• A thermodynamically consistent model of finite state machines
• Revisiting thermodynamics in computation and information theory
• Experimental demonstration of kinetic proofreading inherited in ligation-based information replication
• Performance limits and trade-offs in entropy-driven biochemical computers