HAS Theoretical Biology and Ecology Research Group, Department of Plant Taxonomy and Ecology, Eötvös University (ELTE), Budapest, Hungary.
PLoS One. 2011;6(7):e21380. doi: 10.1371/journal.pone.0021380. Epub 2011 Jul 19.
The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix.
模拟由交织子系统组成的复杂生化系统是计算生物学中的一项具有挑战性的任务。由 Gánti 提出的最小细胞模型 chemoton 有效地模拟了细胞复杂的生化组织。由于 chemoton 是一个由大量但固定数量的相互作用分子物种组成的系统，因此它可以有效地用基于进程代数的语言实现，如 BlenX 编程语言。随机模型的行为与 chemoton 的先前连续确定性模型相当。除了众所周知的 chemoton，我们还实现了一个具有两个竞争模板循环的扩展版本。我们研究的新见解是，chemoton 中反应的耦合确保了这些模板共存，为 Eigen 的悖论提供了另一种解决方案。我们的技术创新涉及引入二态开关来控制细胞生长和分裂，从而为 BlenX 中的混合方法提供了一个示例。在附录中提出了对 BlenX 语言的进一步发展建议。
