Muzika František, Schreiberová Lenka, Schreiber Igor
Department of Chemical Engineering, University of Chemistry and Technology, Prague, Czechia.
Front Chem. 2020 Oct 29;8:559650. doi: 10.3389/fchem.2020.559650. eCollection 2020.
We examine dynamical switching among discrete Turing patterns that enable chemical computing performed by mass-coupled reaction cells arranged as arrays with various topological configurations: three coupled cells in a cyclic array, four coupled cells in a linear array, four coupled cells in a cyclic array, and four coupled cells in a branched array. Each cell is operating as a continuous stirred tank reactor, within which the glycolytic reaction takes place, represented by a skeleton inhibitor-activator model where ADP plays the role of activator and ATP is the inhibitor. The mass coupling between cells is assumed to be operating in three possible transport regimes: (i) equal transport coefficients of the inhibitor and activator (ii) slightly faster transport of the activator, and (iii) strongly faster transport of the inhibitor. Each cellular array is characterized by two pairs of tunable parameters, the rate coefficients of the autocatalytic and inhibitory steps, and the transport coefficients of the coupling. Using stability and bifurcation analysis we identified conditions for occurrence of discrete Turing patterns associated with non-uniform stationary states. We found stable symmetric and/or asymmetric discrete Turing patterns coexisting with stable uniform periodic oscillations. To switch from one of the coexisting stable regimes to another we use carefully targeted perturbations, which allows us to build systems of logic gates specific to each topological type of the array, which in turn enables to perform advanced modes of chemical computing. By combining chemical computing techniques in the arrays with glycolytic excitable channels, we propose a cellular assemblage design for advanced chemical computing.
我们研究了离散图灵模式之间的动态切换，这种切换能够使由质量耦合反应池进行的化学计算得以实现，这些反应池排列成具有各种拓扑结构的阵列：循环阵列中的三个耦合反应池、线性阵列中的四个耦合反应池、循环阵列中的四个耦合反应池以及分支阵列中的四个耦合反应池。每个反应池都作为一个连续搅拌釜式反应器运行，糖酵解反应在其中发生，由一个骨架抑制剂 - 激活剂模型表示，其中二磷酸腺苷（ADP）起激活剂的作用，三磷酸腺苷（ATP）是抑制剂。假设反应池之间的质量耦合在三种可能的传输模式下运行：（i）抑制剂和激活剂的传输系数相等；（ii）激活剂的传输稍快；（iii）抑制剂的传输快得多。每个细胞阵列由两对可调参数表征，即自催化和抑制步骤的速率系数以及耦合的传输系数。通过稳定性和分岔分析，我们确定了与非均匀稳态相关的离散图灵模式出现的条件。我们发现稳定的对称和/或不对称离散图灵模式与稳定的均匀周期振荡共存。为了从一种共存的稳定状态切换到另一种状态，我们使用精心设计的有针对性的扰动，这使我们能够构建特定于阵列每种拓扑类型的逻辑门系统，进而实现高级化学计算模式。通过将阵列中的化学计算技术与糖酵解可兴奋通道相结合，我们提出了一种用于高级化学计算的细胞组合设计。
