分子自组装是指组装基元间通过非共价键或弱键相互作用自发地形成具有特定形态和结构的组装体的过程。自组装现象在生物体系中普遍存在，如：蛋白质/多肽和DNA可以分别通过氨基酸残基间和核苷酸碱基间的相互作用形成高度有序的组装体。多肽是一个很好的组装基元且具有良好的生物相容性，通过合理调控其氨基酸序列及外界环境，可使其组装为结构与功能不同的组装体。然而，由于多肽组装过程的复杂性，其自组装微观机制尚不清楚。该项目主要采用多尺度分子模拟方法，即把粗粒化和全原子分子动力学模拟相结合，同时采用抽样效率高的副本交换分子动力学方法，研究多肽浓度、溶液pH值、溶剂效应、及其氨基酸序列对芳香环多肽、表面活性剂多肽、和淀粉样多肽三种不同多肽的组装体结构、组装自由能面、和组装过程的影响。并通过分析多肽-多肽间和多肽-溶剂间的静电、范德华、疏水、氢键、和pi-pi堆积相互作用在组装过程中的作用，揭示多肽自组装本质和规律。

Molecular self-assembly is the autonomous organization of molecules into patterns or structures without human intervention. Self-assembly is a phenomenon which often occurs in biological system. For example, peptide/protein and DNA molecules can self-assemble into well-defined superstructures via non-covalent or weak covalent interactions. Among them, peptide is an ideal biomaterial for its uncomplicated component and excellent biocompatibility. Many factors are involved in the process of peptide self-assembly. By altering the amino acid sequence of peptides and modulating their environment, peptides can assemble into ordered architectures with different shapes and structures. However, due to the complexities of peptide self-assembly, the underlying molecular mechanism is still not well understood. Here, we propose to investigate the self-assembly processes by performing coarse-grained and all-atom (replica-exchange) molecular dynamics simulations in explicit solvent. We will examine the effects of peptide concentration, pH, solvent, and amino acid sequence on the self-assembly processes of three different types of peptides including aromatic peptides, surfactant-like peptides, and hydrophobic amyloid peptides. The structures and the free energy energy landscapes of the supermolecular assemblies will be identified. By analyzing the roles of electrostatic, van der Waals, hydrophobic interactions, hydrogen-bonding interaction, and pi-pi stacking interactions on the assembly process, we aim to reveal the molecular mechanism of peptide self-assembly. The results and the findings would provide theoretical insight into peptide nanostructure formation.