Rule-based spatial modeling with diffusing, geometrically constrained molecules.
Rule-based spatial modeling with diffusing, geometrically constrained molecules.
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DOI：
10.1186/1471-2105-11-307
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发表时间：
2010-06-07
影响因子：
3
通讯作者：
Dittrich P
中科院分区：
文献类型：
--
作者：
Gruenert G;Ibrahim B;Lenser T;Lohel M;Hinze T;Dittrich P
我们提出了一种新的建模方法，用于组合复杂化学反应系统的粗粒度、基于粒子的空间模拟。在我们的方法中，分子在反应器中具有一个位置，以及一个方向和几何形状，而反应是根据一系列隐式指定的反应规则进行的。由于反应规则可以包含分子的模式，因此可以定义组合复杂甚至无限大小的反应网络。对于我们的实现（基于LAMMPS），我们选择了一个已经存在的形式（BioNetGen）来隐式规范反应网络。这种兼容性允许很容易地导入现有模型，也就是说，只需要提供额外的几何数据文件。我们的模拟表明，获得的动力学可以从根本上不同于那些使用经典的反应扩散方法的模拟，如偏微分方程或吉莱斯皮型空间随机模拟。例如，我们表明，组合复杂性和几何效应的结合导致复杂的自组装和运输现象的出现，其发生速度快于扩散（使用微管上的分子行走器模型）。当应用上述经典模拟方法时，如果不进行特殊处理，就无法观察到建模系统的这些方面。此外，我们还发现几何信息甚至可以改变反应体系的组织结构。也就是说，一组化学物质原则上可以在微分方程的形式中形成一个稳定的状态，当考虑几何时，它可能是不稳定的，反之亦然。我们的结论是，我们的方法提供了一个新的通用框架，填补了没有或刚性空间表示的方法（如偏微分方程）和专门的粗粒度空间模拟系统（如DNA或病毒衣壳自组装）之间的空白。
We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly.