Designing Dynamical Molecular Systems with the PEN Toolbox
Designing Dynamical Molecular Systems with the PEN Toolbox
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DOI：
10.1007/s00354-020-00089-w
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发表时间：
2020-03-19
影响因子：
2.6
通讯作者：
Cazenille, Leo
中科院分区：
文献类型：
--
作者：
Aubert-Kato, Nathanael;Cazenille, Leo
本教程着重于聚合酶-核酸外切酶-切口酶（PEN）工具箱系统的设计、模拟和优化。PEN工具箱是一个分子编程框架，它依赖于DNA分子和酶之间的相互作用来产生高度非线性的动态系统。这种表现力的另一面是，系统的设计严重依赖于试错法，因此需要计算机的帮助。本文包括一个描述的高级应用程序编程接口DACCAD，PEN工具箱系统的主要仿真库，并介绍了方法来扩展现有的软件，以满足设计师的需求。提供了几个例子来说明这种方法。
This tutorial paper focuses on the design, simulation, and optimization of polymerase-exonuclease-nickase (PEN) toolbox systems. The PEN toolbox is a molecular programming framework that relies on the interaction between DNA molecules and enzymes to produce highly non-linear dynamic systems. The flip side of that expressivity is that the design of systems relies heavily on trial-and-error, thus calling for computer assistance. The paper includes a description of the high-level application programming interface of DACCAD, the main simulation library for PEN toolbox systems, and introduces methods to extend the existing software to match the designer's needs. Several examples are provided to illustrate that approach.