论文标题
基于抽象的化学反应网络的分段模拟
Abstraction-Based Segmental Simulation of Chemical Reaction Networks
论文作者
论文摘要
模拟化学反应网络通常在计算上是要求的，特别是由于刚度。我们提出了一种新颖的模拟方案，其中长期不是整体模拟，而是根据较短的预算段组装的模拟运行。一方面，这加快了模拟过程以获得多个运行，因为我们可以重复使用这些段。另一方面，关于我们的多样性和真实性的问题出现了。但是，我们确保通过生成原始系统的适当抽象并在仿真过程中利用它来生成其真实分布。有趣的是，作为副产品，我们还获得了一个更有效的仿真方案，从而在系统的抽象上产生了运行。这些提供了非常忠实的混凝土运行，以低成本的价格在所需的粒度水平上进行。我们的实验证明了模拟中的加速度，同时保留了密钥动力学和定量特性。
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.
