Mathematical Institute, University of Oxford, Oxford, UK.
J R Soc Interface. 2012 May 7;9(70):859-68. doi: 10.1098/rsif.2011.0574. Epub 2011 Oct 19.
Spatial organization and noise play an important role in molecular systems biology. In recent years, a number of software packages have been developed for stochastic spatio-temporal simulation, ranging from detailed molecular-based approaches to less detailed compartment-based simulations. Compartment-based approaches yield quick and accurate mesoscopic results, but lack the level of detail that is characteristic of the computationally intensive molecular-based models. Often microscopic detail is only required in a small region (e.g. close to the cell membrane). Currently, the best way to achieve microscopic detail is to use a resource-intensive simulation over the whole domain. We develop the two-regime method (TRM) in which a molecular-based algorithm is used where desired and a compartment-based approach is used elsewhere. We present easy-to-implement coupling conditions which ensure that the TRM results have the same accuracy as a detailed molecular-based model in the whole simulation domain. Therefore, the TRM combines strengths of previously developed stochastic reaction-diffusion software to efficiently explore the behaviour of biological models. Illustrative examples and the mathematical justification of the TRM are also presented.
空间组织和噪声在分子系统生物学中起着重要作用。近年来，已经开发了许多用于随机时空模拟的软件包，范围从基于详细分子的方法到不太详细的基于隔室的模拟。基于隔室的方法产生快速而准确的介观结果，但缺乏计算密集型基于分子的模型的特征性细节。通常，只有在小区域（例如靠近细胞膜）才需要微观细节。目前，实现微观细节的最佳方法是在整个区域使用资源密集型模拟。我们开发了两区域方法（TRM），其中在需要的地方使用基于分子的算法，而在其他地方使用基于隔室的方法。我们提出了易于实现的耦合条件，以确保 TRM 结果在整个模拟区域具有与详细基于分子的模型相同的准确性。因此，TRM 结合了先前开发的随机反应扩散软件的优势，可有效地探索生物模型的行为。还介绍了说明性示例和 TRM 的数学证明。
