Spatial and Stochastic Cellular Modeling with the Smoldyn Simulator
Spatial and Stochastic Cellular Modeling with the Smoldyn Simulator
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DOI：
10.1007/978-1-61779-361-5_26
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发表时间：
2012-01-01
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影响因子：
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通讯作者：
Andrews, Steven S.
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文献类型：
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作者：
Andrews, Steven S.
本章介绍了如何使用Smoldyn，这是一个计算机程序，用于模拟细胞系统的空间和随机细节。Smoldyn将每个感兴趣的分子表示为单个点状颗粒。这些模拟分子扩散，与表面相互作用（例如，生物膜），并经历化学反应，就像它们在真实的生化系统中一样。Smoldyn已被用于模拟细菌细胞内的信号转导、酵母细胞之间的信息素信号传导、细菌羧基体功能、拥挤空间中的扩散以及许多其他系统。一个新的“基于规则的建模”功能自动生成化学物种和反应，因为它们出现在模拟由于蛋白质修饰和络合。Smoldyn易于使用，定量准确，计算效率高。它通常最适合长度尺度在纳米到几微米之间、时间尺度从几十纳秒到几十分钟以及最多约10（5）个单个分子的系统。Smoldyn可以在Macintosh、Linux或Windows系统上运行，是开源的，可以从http://www.smoldyn.org下载。
This chapter describes how to use Smoldyn, which is a computer program for modeling cellular systems with spatial and stochastic detail. Smoldyn represents each molecule of interest as an individual point-like particle. These simulated molecules diffuse, interact with surfaces (e.g., biological membranes), and undergo chemical reactions much as they would in real biochemical systems. Smoldyn has been used to model signal transduction within bacterial cells, pheromone signaling between yeast cells, bacterial carboxysome function, diffusion in crowded spaces, and many other systems. A new "rule-based modeling" feature automatically generates chemical species and reactions as they arise in simulations due to protein modifications and complexation. Smoldyn is easy to use, quantitatively accurate, and computationally efficient. It is generally best for systems with length scales between nanometers and several microns, time scales from tens of nanoseconds to tens of minutes, and up to about 10(5) individual molecules. Smoldyn runs on Macintosh, Linux, or Windows systems, is open source, and can be downloaded from http://www.smoldyn.org.