Formalizing Modularization and Data Hiding in Synthetic Biology
Formalizing Modularization and Data Hiding in Synthetic Biology
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DOI：
10.1145/2667231
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发表时间：
2014-12-01
影响因子：
2.2
通讯作者：
Krasnogor, Natalio
中科院分区：
文献类型：
--
作者：
Fellermann, Harold;Hadorn, Maik;Krasnogor, Natalio
生物系统采用分区和其他共同定位策略，以便通过同时实现“数据隐藏”和模块化来协调多种生化过程。本文介绍了最近的研究，将分区和协同定位作为合成生物和仿生系统中的一种组织规划原则。在这些系统中，人工囊泡和合成最小细胞被设想为可编程生物化学合成的纳米级反应器和分子信息处理的底盘。我们提出了P系统、膜演算和最近发展的化学容器演算作为形式框架，提供了数据隐藏和模块化，从而使得能够表示高度复杂的分层组织的划分的反应系统。我们展示了分区如何极大地降低实现计算功能所需的复杂性，以及可寻址分区如何允许可编程化学合成的规模扩大。
Biological systems employ compartmentalization and other co-localization strategies in order to orchestrate a multitude of biochemical processes by simultaneously enabling "data hiding" and modularization. This article presents recent research that embraces compartmentalization and co-location as an organizational programmatic principle in synthetic biological and biomimetic systems. In these systems, artificial vesicles and synthetic minimal cells are envisioned as nanoscale reactors for programmable biochemical synthesis and as chassis for molecular information processing. We present P systems, brane calculi, and the recently developed chemtainer calculus as formal frameworks providing data hiding and modularization and thus enabling the representation of highly complicated hierarchically organized compartmentalized reaction systems. We demonstrate how compartmentalization can greatly reduce the complexity required to implement computational functionality, and how addressable compartments permit the scaling-up of programmable chemical synthesis.