Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology.
Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology.
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DOI：
10.1007/s12021-010-9066-x
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发表时间：
2010-06
期刊：
影响因子：
3
通讯作者：
Kubota Y
中科院分区：
文献类型：
--
作者：
Byrne MJ;Waxham MN;Kubota Y
本文介绍了用于模拟拥挤分子环境中扩散和化学反应的细胞动力学模拟器(CDS)。CDS基于一种新的事件驱动算法，专门为精确计算环境中每个单独分子的碰撞、反应和其他事件的时间而设计。基于普通网格的隔室允许创建/导入存在于3D环境中的非常简单或详细的蜂窝结构。多层隔间和静态障碍物可以用来创造一个密集的环境，以模拟细胞边界和细胞内空间。CDS算法考虑了体积排斥和分子拥挤，这可能会影响树突等小亚细胞隔间的信号级联。使用CDS，我们可以模拟简单的酶反应；自由扩散和膜结合的多蛋白质复合体的聚集、通道传输以及高度复杂的化学反应网络。CDS的组件通常被定义为使得模拟器可以在规模和细节级别方面应用于广泛的环境。通过初始化图形用户界面，可以在几分钟内创建和填充一个简单的模拟环境，而且功能强大，足以设计复杂的3D蜂窝架构。初始化工具允许在模拟器执行之前对环境构造进行可视确认。本文描述了CDS算法、设计实现，并概述了可用的功能类型，并在演示中重点介绍了这些功能的用途。
In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations.
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影响因子：
--
作者：
MULLER, ME
通讯作者：
MULLER, ME
DOI：
10.1098/rspa.1952.0051
发表时间：
1952-01-01
影响因子：
--
作者：
KLEIN, G
通讯作者：
KLEIN, G
影响因子：
2
作者：
Andrews, SS;Bray, D
通讯作者：
Bray, D
影响因子：
2.5
作者：
Kubota, Yoshihisa;Putkey, John A.;Waxham, M. Neal
通讯作者：
Waxham, M. Neal
影响因子：
16.2
作者：
Santamaria, Fidel;Wils, Stefan;Augustine, George J.
通讯作者：
Augustine, George J.