Hybrid PDE‐kMC modeling approach to simulate multivalent lectin‐glycan binding process
Hybrid PDE‐kMC modeling approach to simulate multivalent lectin‐glycan binding process
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DOI：
10.1002/aic.17453
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发表时间：
2021-09
期刊：
影响因子：
3.7
通讯作者：
Dongheon Lee;Aaron Green;Hung‐Jen Wu;J. Kwon
中科院分区：
文献类型：
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作者：
Dongheon Lee;Aaron Green;Hung‐Jen Wu;J. Kwon
聚糖是细胞膜的主要成分，通过与凝集素的相互作用介导许多细胞过程。之前提出了一种动力学蒙特卡罗（kMC）模型，以纳入聚糖凝集素相互作用的关键特征，如多价性和聚糖扩散，其准确性已通过实验验证。然而，kMC模型的计算成本是其主要瓶颈。在这项研究中，一个混合模型结合偏微分方程（PDE）与kMC模型，提出了大大减少计算成本，同时保持精度。具体地，由于通过kMC执行聚糖扩散在计算上是昂贵的，因此通过PDE模拟聚糖扩散以提高计算效率。采用混合PDE‐kMC模型模拟霍乱毒素亚基B与细胞膜上神经节苷脂的结合动力学。通过与单一kMC模型的比较，验证了该模型的准确性和有效性。
Glycans are the major components of the cellular membranes and mediate many cellular processes via their interactions with lectins. A kinetic Monte Carlo (kMC) model was proposed previously to incorporate the key features of glycan‐lectin interactions such as multivalency and glycan diffusion, and its accuracy has been validated by experiments. However, computational cost of the kMC model is its major bottleneck. In this study, a hybrid model combining a partial differential equation (PDE) with the kMC model is proposed to greatly reduce the computational cost while preserving the accuracy. Specifically, glycan diffusion is simulated by the PDE for improving computational efficiency since the glycan diffusion execution through the kMC is computationally expensive. The hybrid PDE‐kMC model is employed to simulate the binding dynamics between cholera toxin subunit B and gangliosides on cellular membranes. The accuracy and efficiency of the proposed model was demonstrated by comparing with the sole kMC model.