Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of simulation runs. On the one hand, this speeds up the simulation process to obtain multiple runs since we can reuse the segments. On the other hand, questions on diversity and genuineness of our runs arise. However, we ensure that we generate runs close to their true distribution by generating an appropriate abstraction of the original system and utilizing it in the simulation process. Interestingly, as a by-product, we also obtain a yet more efficient simulation scheme, yielding runs over the system's abstraction. These provide a very faithful approximation of concrete runs on the desired level of granularity, at a low cost. Our experiments demonstrate the speedups in the simulations while preserving key dynamical as well as quantitative properties.
翻译:模拟化学反应网络往往在计算上要求很高, 特别是由于僵硬。 我们提出了一个新型的模拟方案, 长期运行不模拟成整体,而是从模拟运行中较短的预计部分组装起来。 一方面, 加速模拟过程以获得多次运行, 因为我们可以再利用这些部分。 另一方面, 产生关于我们运行的多样性和真实性的问题。 然而, 我们通过对原始系统进行适当的抽象化, 并在模拟过程中使用它来保证我们产生接近真实分布。 有趣的是, 作为一个副产品, 我们还得到了一个效率更高的模拟方案, 产生系统抽象的运行。 这些实验以低成本对所期望的颗粒水平的混凝土运行进行非常忠实的近似。 我们的实验在保存关键动态和定量特性的同时, 展示了模拟过程中的加速度。