Abstraction of Graph-Based Models of Bio-molecular Reaction Systems for Efficient Simulation
Abstraction of Graph-Based Models of Bio-molecular Reaction Systems for Efficient Simulation
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DOI：
10.1007/978-3-642-33636-2_12
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发表时间：
2012-10
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影响因子：
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通讯作者：
I. Kawamata;Nathanael Aubert;M. Hamano;M. Hagiya
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文献类型：
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作者：
I. Kawamata;Nathanael Aubert;M. Hamano;M. Hagiya
我们提出了一种通过抽象图模型来高效模拟分子反应系统的技术。图(或网络)及其转换产生了简单但强大的分子及其化学反应模型。根据基于图的模型的目的，图的节点和边可能分别对应于分子单元和化学键。这种模型通过将化学动力学应用于图形转换，提供了对分子反应系统的朴素模拟。然而，这种天真的模型可以立即导致分子物种数量的组合爆炸，因为化学键的结合通常是无界的，这使得模拟变得困难。为了克服这个问题，我们引入了一种抽象技术来将图划分为局部结构。作为案例研究，我们解释了模拟DNA杂交系统和RNA干扰的新抽象模型，以显示我们抽象技术的有效性。然后从结构个数和仿真误差两个方面讨论了抽象模型的效率和准确性之间的权衡。根据对反应的假设，我们将分子反应系统分为三类。第一种方法允许高效而精确的抽象，第二种方法允许有效但近似的抽象，第三种方法不通过抽象来减少结构的数量。我们得出结论，抽象是分析复杂分子反应系统和测量其复杂性的有用工具。
We propose a technique to simulate molecular reaction systems efficiently by abstracting graph models. Graphs (or networks) and their transitions give rise to simple but powerful models for molecules and their chemical reactions. Depending on the purpose of a graph-based model, nodes and edges of a graph may correspond to molecular units and chemical bonds, respectively. This kind of model provides naive simulations of molecular reaction systems by applying chemical kinetics to graph transition. Such naive models, however, can immediately cause a combinatorial explosion of the number of molecular species because combination of chemical bonds is usually unbounded, which makes simulation intractable. To overcome this problem, we introduce an abstraction technique to divide a graph into local structures. New abstracted models for simulating DNA hybridization systems and RNA interference are explained as case studies to show the effectiveness of our abstraction technique. We then discuss the trade-off between the efficiency and exactness of our abstracted models from the aspect of the number of structures and simulation error. We classify molecular reaction systems into three groups according to the assumptions on reactions. The first one allows efficient and exact abstraction, the second one allows efficient but approximate abstraction, and the third one does not reduce the number of structures by abstraction. We conclude that abstraction is a useful tool to analyze complex molecular reaction systems and measure their complexity.