Thermodynamics of Computational Copying in Biochemical Systems
Thermodynamics of Computational Copying in Biochemical Systems
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DOI：
10.1103/physrevx.7.021004
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发表时间：
2017-04-07
影响因子：
12.5
通讯作者：
ten Wolde, Pieter Rein
中科院分区：
文献类型：
--
作者：
Ouldridge, Thomas E.;Govern, Christopher C.;ten Wolde, Pieter Rein
活细胞使用读出分子来记录受体蛋白的状态，类似于典型计算设备中的测量或复制。但这种类比严谨吗？细胞能达到最佳效率吗？如果不能，为什么？我们表明，在计算中，一个典型的生化读出网络产生的相关性;提取没有工作从这些相关性设置耗散的下限。对于一般的输入，生化网络无法达到这个界限，即使是任意缓慢的反应或弱热力学驱动。它面临着一个准确性耗散的权衡，这是定性不同的和更糟糕的比所暗示的界限，更复杂的稳态复制过程不能表现得更好。尽管如此，成本仍然接近热力学界限，除非精度非常高。此外，我们表明，生物分子反应可以用于化学燃料的外源性操作下的化学优化设备，这表明了一个实验系统，用于测试计算热力学。
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.