Noise control for molecular computing
Noise control for molecular computing
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DOI：
10.1098/rsif.2018.0199
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发表时间：
2018-07-01
影响因子：
3.9
通讯作者：
Erban, Radek
中科院分区：
文献类型：
--
作者：
Plesa, Tomislav;Zygalakis, Konstantinos C.;Erban, Radek
合成生物学是一个不断发展的跨学科领域，具有深远的应用，旨在设计以所需方式运行的生化系统。随着基于核酸的技术的进步，特别是链置换DNA计算的进步，一大类抽象的生化网络可以使用核酸在物理上实现。具有规定行为的抽象系统的系统设计方法主要是在（不太详细的）确定性级别上开发的。然而，在确定性水平上被忽视的随机效应越来越多地被发现在生物化学中发挥着重要作用。在这种情况下，控制系统中固有噪声的方法对于在（更详细的）随机级别成功进行网络设计是必要的。为了弥补这一差距，本文开发了用于设计生化网络的噪声控制算法。该算法在结构上修改了质量作用动力学下的任何给定反应网络，从而 (i) 将可控状态相关噪声引入随机动力学，同时 (ii) 保留确定性动力学。该算法的功能在生产衰变反应系统和显示双稳态的奇异系统上得到了证明。对于产生式衰减系统，结果表明该算法可用于重新设计网络以实现噪声引起的多稳态。对于奇异系统，利用该算法重新设计网络来控制随机切换，实现噪声引起的振荡。
Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement in nucleic-acid-based technology in general, and strand-displacement DNA computing in particular, a large class of abstract biochemical networks may be physically realized using nucleic acids. Methods for systematic design of the abstract systems with prescribed behaviours have been predominantly developed at the (less-detailed) deterministic level. However, stochastic effects, neglected at the deterministic level, are increasingly found to play an important role in biochemistry. In such circumstances, methods for controlling the intrinsic noise in the system are necessary for a successful network design at the (more-detailed) stochastic level. To bridge the gap, the noise-control algorithm for designing biochemical networks is developed in this paper. The algorithm structurally modifies any given reaction network under mass-action kinetics, in such a way that (i) controllable state-dependent noise is introduced into the stochastic dynamics, while (ii) the deterministic dynamics are preserved. The capabilities of the algorithm are demonstrated on a production-decay reaction system, and on an exotic system displaying bistability. For the production-decay system, it is shown that the algorithm may be used to redesign the network to achieve noise-induced multistability. For the exotic system, the algorithm is used to redesign the network to control the stochastic switching, and achieve noise-induced oscillations.