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Robust biomolecular finite automata
Theoretical Computer Science ( IF 0.9 ) Pub Date : 2020-01-16 , DOI: 10.1016/j.tcs.2020.01.008
Titus H. Klinge , James I. Lathrop , Jack H. Lutz

We present a uniform method for translating an arbitrary nondeterministic finite automaton (NFA) into a deterministic mass action input/output chemical reaction network (I/O CRN) that simulates it. The I/O CRN receives its input as a continuous time signal consisting of concentrations of chemical species that vary to represent the NFA's input string in a natural way. The I/O CRN exploits the inherent parallelism of chemical kinetics to simulate the NFA in real time with a number of chemical species that is linear in the size of the NFA. We prove that the simulation is correct and that it is robust with respect to perturbations of the input signal, the initial concentrations of species, the output (decision), and the rate constants of the reactions of the I/O CRN.



中文翻译:

强大的生物分子有限自动机

我们提出了一种将任意非确定性有限自动机(NFA)转换成模拟它的确定性质量作用输入/输出化学反应网络I / O CRN)的统一方法。I / O CRN接收其输入作为连续时间信号,该信号由化学物质的浓度组成,这些化学物质的浓度变化以自然方式表示NFA的输入字符串。I / O CRN利用化学动力学的内在并行性,以线性的多种化学物质实时模拟NFA。在NFA的大小上。我们证明该模拟是正确的,并且对于输入信号的扰动,物种的初始浓度,输出(决策)和I / O CRN反应的速率常数而言,它是鲁棒的。

更新日期:2020-01-16
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