Dueñas-Díez Marta, Pérez-Mercader Juan
Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University, Cambridge, MA, United States.
Repsol Technology Lab, Madrid, Spain.
Front Chem. 2021 May 11;9:611120. doi: 10.3389/fchem.2021.611120. eCollection 2021.
Computing with molecules is at the center of complex natural phenomena, where the information contained in ordered sequences of molecules is used to implement functionalities of synthesized materials or to interpret the environment, as in Biology. This uses large macromolecules and the hindsight of billions of years of natural evolution. But, can one implement computation with small molecules? If so, at what levels in the hierarchy of computing complexity? We review here recent work in this area establishing that all physically realizable computing automata, from Finite Automata (FA) (such as logic gates) to the Linearly Bound Automaton (LBA, a Turing Machine with a finite tape) can be represented/assembled/built in the laboratory using oscillatory chemical reactions. We examine and discuss in depth the fundamental issues involved in this form of computation exclusively done by molecules. We illustrate their implementation with the example of a programmable finite tape Turing machine which using the Belousov-Zhabotinsky oscillatory chemistry is capable of recognizing words in a Context Sensitive Language and rejecting words outside the language. We offer a new interpretation of the recognition of a sequence of chemicals representing words in the machine's language as an illustration of the "Maximum Entropy Production Principle" and concluding that word recognition by the Belousov-Zhabotinsky Turing machine is equivalent to extremal entropy production by the automaton. We end by offering some suggestions to apply the above to problems in computing, polymerization chemistry, and other fields of science.
分子计算处于复杂自然现象的核心，在生物学中，分子有序序列中包含的信息被用于实现合成材料的功能或解读环境。这利用了大型大分子以及数十亿年自然进化的经验。但是，能否用小分子实现计算呢？如果可以，在计算复杂度层次结构的哪些层面上呢？我们在此回顾该领域的近期工作，这些工作表明，从有限自动机（FA，如逻辑门）到线性有界自动机（LBA，一种磁带有限的图灵机）等所有物理上可实现的计算自动机，都可以在实验室中利用振荡化学反应来表示/组装/构建。我们深入研究并讨论了这种完全由分子进行的计算形式所涉及的基本问题。我们以可编程有限带图灵机为例来说明其实现，该图灵机利用贝洛索夫 - 扎博廷斯基振荡化学能够识别上下文敏感语言中的单词并拒绝该语言之外的单词。我们对机器语言中表示单词的化学序列的识别给出了一种新的解释，以此说明“最大熵产生原理”，并得出结论，贝洛索夫 - 扎博廷斯基图灵机的单词识别等同于自动机的极值熵产生。最后，我们提出一些建议，将上述内容应用于计算、聚合化学及其他科学领域的问题。
