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Composable Rate-Independent Computation in Continuous Chemical Reaction Networks

机译:连续化学反应网络中可组合的速率无关计算

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Biological regulatory networks depend upon chemical interactions to process information. Engineering such molecular computing systems is a major challenge for synthetic biology and related fields. The chemical reaction network (CRN) model idealizes chemical interactions, abstracting away specifics of the molecular implementation, and allowing rigorous reasoning about the computational power of chemical kinetics. Here we focus on function computation with CRNs, where we think of the initial concentrations of some species as the input and the eventual steady-state concentration of another species as the output. Specifically, we are concerned with CRNs that are rate-independent (the computation must be correct independent of the reaction rate law) and composable (f ο g can be computed by concatenating the CRNs computing f and g). Rate independence and composability are important engineering desiderata, permitting implementations that violate mass-action kinetics, or even "well-mixedness", and allowing the systematic construction of complex computation via modular design. We show that to construct composable rate-independent CRNs, it is necessary and sufficient to ensure that the output species of a module is not a reactant in any reaction within the module. We then exactly characterize the functions computable by such CRNs as superadditive, positive-continuous, and piece-wise rational linear. Our results show that composability severely limits rate-independent computation unless more sophisticated input/output encodings are used.
机译:生物调节网络依赖于化学相互作用来处理信息。对这样的分子计算系统进行工程设计是合成生物学和相关领域的主要挑战。化学反应网络(CRN)模型理想化了化学相互作用,抽象了分子实现的细节,并允许对化学动力学的计算能力进行严格的推理。在这里,我们专注于使用CRN进行函数计算,其中我们将某些物种的初始浓度视为输入,并将其他物种的最终稳态浓度视为输出。具体来说,我们关注的是CRN,它们与速率无关(计算必须独立于反应速率定律而正确)并且是可组合的(fοg可以通过合并计算f和g的CRN来计算)。速率独立性和可组合性是重要的工程设计,它允许违反质量作用动力学甚至“井井有条”的实现,并允许通过模块化设计来系统地构建复杂的计算。我们表明,构建可组合的速率无关的CRN,有必要且足够的是要确保模块的输出种类在模块内的任何反应中都不是反应物。然后,我们精确地描述了CRN可计算的功能,如超加性,正连续和分段有理线性。我们的结果表明,除非使用更复杂的输入/输出编码,否则可组合性严重限制了速率无关的计算。

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