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.

中文翻译：

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模拟多价凝集素-聚糖结合过程的混合 PDE-kMC 建模方法

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。之前提出了动力学蒙特卡罗 (kMC) 模型，以结合聚糖-凝集素相互作用的关键特征，例如多价和聚糖扩散，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，提出了一种将偏微分方程 (PDE) 与 kMC 模型相结合的混合模型，以在保持精度的同时大大降低计算成本。具体来说，由于通过 kMC 执行聚糖扩散在计算上很昂贵，因此 PDE 模拟了聚糖扩散以提高计算效率。混合 PDE-kMC 模型用于模拟霍乱毒素亚基 B​​ 与细胞膜上神经节苷脂之间的结合动力学。通过与唯一的kMC模型进行比较，证明了所提出模型的准确性和效率。