细胞贯穿孔洞是一种由细胞膜围成的且跨越整个胞质的通道结构，存在于生 理、病理条件下多种细胞上，并具有重要的生物学功能。例如窗孔（Fenestrae） 结构是肝血窦内皮细胞（LSEC, Liver Sinusoidal Endothelial Cell）发挥其生物学 功能的结构基础，白细胞利用跨内皮细胞大孔（TEM, Trans Endothelial cell Macroaperture）进行迁移进而抵抗病原体的入侵。目前已有研究主要聚焦在该类 贯穿孔洞结构的生物学功能、调控因素及其发生后的演化理论模型等方面，并提 出假设认为该类结构是基于细胞两端膜接触融合而成，但是其从无到有的形成动 力学过程尚不清楚。 基于此，本文将复杂细胞结构简化为仅含有离子和水环境的球形囊泡体系， 采用粗粒化分子动力学（CGMD, Coarse-grained Molecular Dynamics）和调控分 子动力学（SMD, Steered Molecular Dynamics）模拟方法相结合，开展了如下工 作： （1）建立了贯穿孔洞形成动力学模拟方法。借鉴膜融合过程中依次发生的 接触、成茎、半融合横膈膜（HD, Hemifusion Diaphragm）、成孔四个阶段特征， 通过对囊泡体系施加外力，实现了贯穿孔洞的形成，建立了相应模拟方法； （2）考察了脂分和张力对穿孔形成过程的影响。通过比较不同膜脂组分、 不同尺寸大小囊泡体系贯穿孔洞形成过程的孔形态、成茎自由能以及穿孔前后的 张力差异，发现不同脂分在囊泡内贯穿孔形成中表现出不同甚至相反于平板膜融 合的成茎自由能贡献；囊泡穿孔结构的张力分布非常不均匀，特别是在穿孔周围 内膜区域远大于其他区域；并且贯穿孔孔径随内膜孔周张力的增大而增大。 （3）分析了张力对穿孔稳定性的影响。由于囊泡贯穿孔结构并不稳定，在 无约束条件下穿孔结构会迅速消失整体恢复为初始囊泡。本文进一步通过施加约 束进行穿孔结构的稳定模拟，并考察不同约束程度对穿孔结构后续演化和稳定性 的调控。结果发现，约束越大，贯穿孔结构越稳定；而同样约束条件下，不同体 系贯穿孔稳定性随着内膜孔周张力的增大而线性增加；并进一步通过单个体系扩 大贯穿孔或者减少囊泡内水分子的模拟验证了内膜孔周张力与孔稳定性之间的 相关性。 本论文工作成功构建了具有微观结构动力学特征的细胞贯穿孔洞模型，并发 现了穿孔结构不均匀分布的膜张力对孔形态和稳定性的决定性作用，为深入阐释 细胞贯穿孔结构的形成及稳定机制提供基础，为有针对性地调控生物膜孔形成及 相应生物学功能提供思路。

The cell penetration pore is a channel structure crossing the entire cell cytoplasm with enclosed cell membrane, which is presented on many cells under physiological and pathological conditions and plays an important biological function. For example, the fenestrate structure is the structural basis for the biological function of LSEC (Liver Sinusoidal Endothelial Cell), and leukocytes use the TEM (Trans Endothelial cell Macroaperture) to migrate and thus resist to pathogen invasion. Current researches have focused on the biological functions, regulatory factors, and theoretical models for the evolution of already existed penetration pore structures, and a hypothesis is raised that these structures are formed through the membrane contact and fusion between the two sides of the cell, but the dynamics of the formation of these structures from non-existence to existence are not clear. Therefore, in this thesis, the complex cell structure was simplified as a spherical vesicles containing only ions and water molecules. The CGMD (Coarse-Grained Molecular Dynamics) and SMD (Steered Molecular Dynamics) simulation methods were combined, Major works were summarized as follows: (1) Developed a simulation method for the dynamics of penetration pore formation. Based on the features of contact, stalk formation, HD (Hemifusion Diaphragm) and pore formation, which sequentially evolve in the membrane fusion process, the formation of penetration pores was achieved by applying external forces to the vesicle systems, and the simulation method was developed in this way; (2) Investigated the effects of lipid components and tension on the perforation pore formation process. By comparing the differences in pore morphology, the free energy of stalk formation and the membrane tension before and after perforation, it showed that different lipid components display different or even opposite contributions to the free energy of stalk formation in the perforation pore formation within the vesicle than in the planar membrane fusion; the tension distribution of the vesicle perforation structure is very uneven, especially in the inner membrane region around the perforation pore is much larger than the other regions; and the pore size of the penetration pore increases with the increase of inner membrane tension around the pore. (3) Analyzed the effect of tension on the perforation pore stability. Since the vesicle penetration pore structure is not stable, the perforation structure will rapidly disappear and return to the initial vesicle as a whole under unconstrained conditions. The thesis further simulated the stability of the perforation structure by applying constraints, and investigated the regulation of the subsequent evolution and stability of the perforation structure by different levels of constraints. It showed that the stronger the constraint, the more stable the perforation structure is; and the perforation stability of different systems increases linearly with the increase of inner membrane tension around the pore under the same constraint conditions; and the correlation between the inner membrane tension around the pore and the pore stability was further confirmed by those simulations of single system that expands the perforation pore or reduces the water molecules inside the vesicles. In summary, this work successfully developed a model of cell penetration pore with microstructural dynamics and discovered the determining role of unevenly distributed membrane tension of the perforation structure on pore morphology and stability. These results provide a basis for further understanding cell penetration pore formation and stability mechanisms and propose the regulation of membrane pore formation in their corresponding biological functions.