化学反应网络的热力学空间

Shiling Liang, Paolo De Los Rios, Daniel Maria Busiello
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引用次数: 0

摘要

生命系统通常维持在非平衡状态,并表现出复杂的动力学行为。外部能量供应通常来自化学流动,化学流动可使某些物种的浓度保持恒定。此外,底层化学反应网络(CRN)的特性也是建立稳健生物功能的关键。因此,捕捉生命系统的突发复杂性及其非平衡性的作用,对于揭示支撑其功能的化学反应网络的制约因素和特性至关重要。特别是,虽然动力学在塑造详细的动力学现象中起着关键作用,但任何有源化学网络的运行范围都必须从根本上受到热力学的制约,因为它们必须在给定的能量预算下运行。在这里,我们推导出了通用 CRN 中物种浓度可访问空间的通用热力学上限和下限。由此得出的区域决定了 CRN 的 "热力学空间",这是我们在这项工作中引入的一个概念。此外,我们还获得了亲和力的类似边界,从而揭示了全局热力学特性如何限制局部非平衡量。我们用两个典型的例子--双稳态的 Schl\"ogl 模型和最小自组装过程--来说明我们的结果,证明了复杂行为的发生如何与非平衡驱动的存在密切相关。总之,我们的工作揭示了 CRN 必须在其能量预算函数作用下工作的可访问空间的精确形式,揭示了从放大到模式形成等各种现象的非平衡起源。最终,通过提供分析 CRN 的通用工具,所提出的框架成为我们深化预测复杂的非平衡行为和设计人工化学反应系统能力的基石。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Thermodynamic Space of Chemical Reaction Networks
Living systems are usually maintained out of equilibrium and exhibit complex dynamical behaviors. The external energy supply often comes from chemical fluxes that can keep some species concentrations constant. Furthermore, the properties of the underlying chemical reaction networks (CRNs) are also instrumental in establishing robust biological functioning. Hence, capturing the emergent complexity of living systems and the role of their non-equilibrium nature is fundamental to uncover constraints and properties of the CRNs underpinning their functions. In particular, while kinetics plays a key role in shaping detailed dynamical phenomena, the range of operations of any CRN must be fundamentally constrained by thermodynamics, as they necessarily operate with a given energy budget. Here, we derive universal thermodynamic upper and lower bounds for the accessible space of species concentrations in a generic CRN. The resulting region determines the "thermodynamic space" of the CRN, a concept we introduce in this work. Moreover, we obtain similar bounds also for the affinities, shedding light on how global thermodynamic properties can limit local non-equilibrium quantities. We illustrate our results in two paradigmatic examples, the Schl\"ogl model for bistability and a minimal self-assembly process, demonstrating how the onset of complex behaviors is intimately tangled with the presence of non-equilibrium driving. In summary, our work unveils the exact form of the accessible space in which a CRN must work as a function of its energy budget, shedding light on the non-equilibrium origin of a variety of phenomena, from amplification to pattern formation. Ultimately, by providing a general tool for analyzing CRNs, the presented framework constitutes a stepping stone to deepen our ability to predict complex out-of-equilibrium behaviors and design artificial chemical reaction systems.
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