论文标题

限制化学反应网络中的可达性

Reachability in Restricted Chemical Reaction Networks

论文作者

Alaniz, Robert M., Fu, Bin, Gomez, Timothy, Grizzell, Elise, Rodriguez, Andrew, Rodriguez, Marco, Schweller, Robert, Wylie, Tim

论文摘要

分子计算的普及已引起了几种抽象模型,最近的抽象模型是化学反应网络(CRN)。这些等同于其他流行的计算模型,例如矢量增加系统和培养皿,并且有限版本等同于人口协议。本文继续对与化学反应网络有关的Core \ emph {可及性}问题进行工作;给定两种配置,一个可以根据系统的规则到达另一个配置吗?在没有限制的情况下,最近显示出可达性是Ackermann complete,这解决了数十年历史的问题。 在这项工作中,我们完全表征了基于各种限制的单调可及性问题,例如允许的规则大小,可能创建物种的规则数量($ k $ source),可能消耗物种的规则数量($ k $ - 耗尽),卷,规则以及规则是否具有acyclic的生产订单(\ emph {feed-feforwardd {feed-fordorwardd)。我们显示了可及性的PSPACE完整性,仅在两码和两件效果规则中进行双分子反应。这证明了以受限形式的人口协议形式证明可及性的硬度。这是使用运动计划框架内的新技术完成的。 我们为馈送前进的CRN给出了几个重要的结果,其中规则是单源或单扣。我们表明,只要系统不包含特殊\ emph {void}或\ emph {autogenesis}规则,就可以在多项式时间内解决可用性。然后,我们充分表征了这种类型的所有系统,并表明,使用空白/自动化规则,或多个来源和一个消耗,问题变得np complete。最后,我们根据这些限制或轻微的放松来展示几个有趣的CRN特殊案例,并记录了与该分类法有关的未来重大开放问题。

The popularity of molecular computation has given rise to several models of abstraction, one of the more recent ones being Chemical Reaction Networks (CRNs). These are equivalent to other popular computational models, such as Vector Addition Systems and Petri-Nets, and restricted versions are equivalent to Population Protocols. This paper continues the work on core \emph{reachability} questions related to Chemical Reaction Networks; given two configurations, can one reach the other according to the system's rules? With no restrictions, reachability was recently shown to be Ackermann-complete, which resolved a decades-old problem. In this work, we fully characterize monotone reachability problems based on various restrictions such as the allowed rule size, the number of rules that may create a species ($k$-source), the number of rules that may consume a species ($k$-consuming), the volume, and whether the rules have an acyclic production order (\emph{feed-forward}). We show PSPACE-completeness of reachability with only bimolecular reactions in two-source and two-consuming rules. This proves hardness of reachability in a restricted form of Population Protocols. This is accomplished using new techniques within the motion planning framework. We give several important results for feed-forward CRNs, where rules are single-source or single-consuming. We show that reachability is solvable in polynomial time as long as the system does not contain special \emph{void} or \emph{autogenesis} rules. We then fully characterize all systems of this type and show that with void/autogenesis rules, or more than one source and one consuming, the problems become NP-complete. Finally, we show several interesting special cases of CRNs based on these restrictions or slight relaxations and note future significant open questions related to this taxonomy.

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