Simulations of Computing by Self-Assembly
Simulations of Computing by Self-Assembly
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发表时间：
1998-05
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通讯作者：
E. Winfree
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作者：
E. Winfree
Winfree（1996）提出了DNA自组装的图灵普适模型。在这个抽象模型中，DNA双交叉分子自组装形成算法模式化的二维晶格。在这里，我们开发了一个更现实的模型的基础上的热力学和动力学的寡核苷酸双链化。使用计算机模拟，我们研究了哪些物理因素影响错误率，即，当更现实的模型偏离抽象模型的理想时。我们发现，在协议与晶体生长的经验法则，最低的错误率发生在熔化温度时，晶体生长最慢，并且可以通过降低浓度和增加结合强度的错误率任意低。
Winfree (1996) proposed a Turing-universal model of DNA self-assembly. In this abstract model, DNA double-crossover molecules self-assemble to form an algorithmically-patterned two-dimensional lattice. Here, we develop a more realistic model based on the thermodynamics and kinetics of oligonucleotide hydridization. Using a computer simulation, we investigate what physical factors influence the error rates, i.e., when the more realistic model deviates from the ideal of the abstract model. We find, in agreement with rules of thumb for crystal growth, that the lowest error rates occur at the melting temperature when crystal growth is slowest, and that error rates can be made arbitrarily low by decreasing concentration and increasing binding strengths.