生物系统模拟中的空间因素。
Spatial aspects in biological system simulations.
作者信息
Resat Haluk, Costa Michelle N, Shankaran Harish
机构信息
Pacific Northwest National Laboratory, Computational Biology and Bioinformatics Group, Richland, Washington, USA.
出版信息
Methods Enzymol. 2011;487:485-511. doi: 10.1016/B978-0-12-381270-4.00017-2.
Mathematical models of the dynamical properties of biological systems aim to improve our understanding of the studied system with the ultimate goal of being able to predict system responses in the absence of experimentation. Despite the enormous advances that have been made in biological modeling and simulation, the inherently multiscale character of biological systems and the stochasticity of biological processes continue to present significant computational and conceptual challenges. Biological systems often consist of well-organized structural hierarchies, which inevitably lead to multiscale problems. This chapter introduces and discusses the advantages and shortcomings of several simulation methods that are being used by the scientific community to investigate the spatiotemporal properties of model biological systems. We first describe the foundations of the methods and then describe their relevance and possible application areas with illustrative examples from our own research. Possible ways to address the encountered computational difficulties are also discussed.
生物系统动力学特性的数学模型旨在增进我们对所研究系统的理解，最终目标是在无需实验的情况下预测系统响应。尽管生物建模与模拟已取得巨大进展，但生物系统固有的多尺度特性以及生物过程的随机性，仍然带来了重大的计算和概念挑战。生物系统通常由组织良好的结构层次组成，这不可避免地导致了多尺度问题。本章介绍并讨论了科学界用于研究模型生物系统时空特性的几种模拟方法的优缺点。我们首先描述这些方法的基础，然后通过我们自己研究中的示例说明它们的相关性和可能的应用领域。还讨论了应对所遇到计算困难的可能方法。
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