计算系统化学的中级抽象
An Intermediate Level of Abstraction for Computational Systems Chemistry
摘要：
需要计算技术来缩小可能性的巨大空间，以合理的前生物情景，因为关于分子组成，主要反应化学和那个时代的条件的精确信息是稀缺的。探索大型化学反应网络是这一努力的一个中心方面。虽然量子化学方法可以准确预测小分子的结构和反应性，但它们的效率不足以应对大规模的反应系统。将化学反应形式化为图形语法提供了一个生成系统，该系统以范畴论为基础，在正确的抽象层次上分析大型复杂的反应网络。将基本形式主义扩展到整数超流领域，可以使用优化技术识别大型反应网络中的复杂反应模式，例如自催化。
英文摘要：
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that era are scarce. The exploration of large chemical reaction networks is a central aspect in this endeavour. While quantum chemical methods can accurately predict the structures and reactivities of small molecules, they are not efficient enough to cope with large-scale reaction systems. The formalization of chemical reactions as graph grammars provides a generative system, well grounded in category theory, at the right level of abstraction for the analysis of large and complex reaction networks. An extension of the basic formalism into the realm of integer hyperflows allows for the identification of complex reaction patterns, such as auto-catalysis, in large reaction networks using optimization techniques.
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