Programming and simulating chemical reaction networks on a surface
Programming and simulating chemical reaction networks on a surface
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DOI：
10.1098/rsif.2019.0790
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发表时间：
2020-05-27
影响因子：
3.9
通讯作者：
Winfree, Erik
中科院分区：
文献类型：
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作者：
Clamons, Samuel;Qian, Lulu;Winfree, Erik
混合良好的化学反应网络（CRN）的模型为研究可编程分子系统提供了坚实的基础，但是在这种系统中空间组织的重要性已越来越多地得到认识到。在本文中，我们探讨了Qian＆Winfree在2014年引入的替代化学计算模型，该模型使用了附着在表面上的分子的表面CRN，使每个分子仅与其直接邻居相互作用。在这项工作中扩展的结构，我们首先证明表面CRN可以模仿异步和同步确定性细胞自动机，并实现连续活跃的布尔逻辑电路。我们介绍了三种新技术，用于在地方区域内实施同步，每种技术在空间和化学复杂性方面都有不同的权衡。我们还证明，表面CRN可以从简单的初始条件中制造复杂的空间模式，并使用简单的本地规则实施有趣的群体机器人行为。在表面CRN的所有示例结构中，我们强调了精确放置分子的能力与精确控制分子相互作用的能力之间的权衡。最后，我们为表面CRN提供了一个易于使用的Web界面的Python模拟器，以便读者可以跟随我们的示例或创建自己的表面CRN设计。
Models of well-mixed chemical reaction networks (CRN) have provided a solid foundation for the study of programmable molecular systems, but the importance of spatial organization in such systems has increasingly been recognized. In this paper, we explore an alternative chemical computing model introduced by Qian & Winfree in 2014, the surface CRN, which uses molecules attached to a surface such that each molecule only interacts with its immediate neighbours. Expanding on the constructions in that work, we first demonstrate that surface CRNs can emulate asynchronous and synchronous deterministic cellular automata and implement continuously active Boolean logic circuits. We introduce three new techniques for enforcing synchronization within local regions, each with a different trade-off in spatial and chemical complexity. We also demonstrate that surface CRNs can manufacture complex spatial patterns from simple initial conditions and implement interesting swarm robotic behaviours using simple local rules. Throughout all example constructions of surface CRNs, we highlight the trade-off between the ability to precisely place molecules and the ability to precisely control molecular interactions. Finally, we provide a Python simulator for surface CRNs with an easy-to-use web interface, so that readers may follow along with our examples or create their own surface CRN designs.