Hybrid spatial Gillespie and particle tracking simulation
Hybrid spatial Gillespie and particle tracking simulation
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DOI：
10.1093/bioinformatics/bts384
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发表时间：
2012-09-15
期刊：
影响因子：
5.8
通讯作者：
Koeppl, Heinz
中科院分区：
文献类型：
--
作者：
Klann, Michael;Ganguly, Arnab;Koeppl, Heinz
动机：细胞信号转导涉及时空动力学，并且由于某些分子种类的粒子丰度较低而常常产生随机效应。然而，其他的可能丰度很高。如果空间和随机性很重要，则可以使用空间 Gillespie/随机模拟算法 (SSA) 或布朗/Smoluchowski 动力学来模拟此类系统。为了将基于粒子的方法的准确性与 SSA 的卓越性能结合起来，我们建议采用混合模拟。结果：所提出的模拟允许对细胞中感兴趣的区域或物种进行交互式或自动切换。特别是，如果例如对膜上的受体聚类进行详细建模并且还包括通过细胞质的运输，我们会看到一种应用。结果显示了整体模拟性能的提高，以及如果包含拥挤则该方法的局限性。未来的工作将包括开发 GUI 以改进模拟控制。
Motivation: Cellular signal transduction involves spatial-temporal dynamics and often stochastic effects due to the low particle abundance of some molecular species. Others can, however, be of high abundances. Such a system can be simulated either with the spatial Gillespie/Stochastic Simulation Algorithm (SSA) or Brownian/Smoluchowski dynamics if space and stochasticity are important. To combine the accuracy of particle-based methods with the superior performance of the SSA, we suggest a hybrid simulation.Results: The proposed simulation allows an interactive or automated switching for regions or species of interest in the cell. Especially we see an application if for instance receptor clustering at the membrane is modeled in detail and the transport through the cytoplasm is included as well. The results show the increase in performance of the overall simulation, and the limits of the approach if crowding is included. Future work will include the development of a GUI to improve control of the simulation.