多价生物分子相互作用的无排斥动力学Monte Carlo模拟
Rejection-free kinetic Monte Carlo simulation of multivalent biomolecular interactions
摘要：
多价生物分子相互作用的系统级动力学可以使用基于规则的动力学蒙特卡罗方法来模拟，其中使用拒绝采样策略来生成反应事件。当模拟具有大的生物分子复合物的聚集过程时，该方法变得低效。在这里，我们提出了一个拒绝免费的方法来确定多价生物分子相互作用的动力学，我们应用该方法来模拟简单的配体-受体相互作用的模型。仿真结果表明，在较宽的参数范围内，无拒绝方法的性能与拒绝方法相当或优于拒绝方法，且无拒绝方法更适合于大规模聚集系统的仿真。这里报告的拒绝自由的方法应该是有用的模拟各种系统中，多位点分子相互作用产生大分子聚集体。
英文摘要：
The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient when simulating aggregation processes with large biomolecular complexes. Here, we present a rejection-free method for determining the kinetics of multivalent biomolecular interactions, and we apply the method to simulate simple models for ligand-receptor interactions. Simulation results show that performance of the rejection-free method is equal to or better than that of the rejection method over wide parameter ranges, and the rejection-free method is more efficient for simulating systems in which aggregation is extensive. The rejection-free method reported here should be useful for simulating a variety of systems in which multisite molecular interactions yield large molecular aggregates.
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