Computer simulations of lipids

生物分子，如蛋白质，DNA，脂质和碳水化合物，存在于微观宇宙中，其时间和长度尺度比我们测量长度和时间的米和秒小6-12个数量级。它们在纳秒的时间尺度上快速移动，并与零点几纳米大小的单个水分子相互作用。与可见光的波长相比，大多数生物分子都非常小。这意味着它们不能用普通的显微镜看到，尽管有许多复杂的实验方法来测量生物分子的行为，形状和相互作用。计算机建模是对这些实验的一种补充方法，无论是通过它们本身还是与实验直接结合，否则无法在分子水平上解释。 使用强大的计算机和原子如何相互作用的描述，可以计算生物分子在时间上如何移动和相互作用的原子细节。近年来，这种分子动力学模拟方法已成为解决涉及所有类型分子的问题的基本方法，在我的研究小组中主要是脂质。 脂质是细胞膜的主要组成部分，细胞膜定义了细胞与其周围环境之间的边界。细胞膜具有显著的机械和电学性质、复杂的化学组成和令人惊讶的复杂物理行为。这些特性主要来自于脂质的分子结构，它有一个喜欢水的头部和一个避免水的尾部。这种结构导致在水中自我聚集成迷人的结构。这些包括基于生物脂质的细胞膜，但也包括由合成脂质和脂质混合物形成的各种其他结构，这些结构在技术和科学应用中既具有根本意义又具有重要意义。 该研究项目旨在开发和应用分子的计算模型，以更好地了解脂质和表面活性剂分子的性质。我们将使用和改进详细的原子模型和一个稍微粗糙的模型，其中一些原子被分组为一个单一的“珠”。虽然我们在这种情况下失去了细节，但探索这种模型的计算成本要低几个数量级。我们的主要兴趣是膜结构域的性质，这些结构域被认为是许多生物学重要过程的基础，表面活性剂和脂质的混合物形成胶束，双胞和纳米盘的性质，以及与实验方法的改进联系，这些实验方法可以洞察脂质结构，包括X射线和中子衍射以及光谱方法。

Biomolecules, such as proteins, DNA, lipids, and carbohydrates, exist in a microscopic universe with time and length scales 6-12 orders of magnitude smaller than the meters and seconds in which we measure length and time. They move rapidly on a time scale of nanoseconds and interact with individual water molecules the size of a few tenths of a nanometer. Most biomolecules are very small compared to the wavelength of visible light. This means they cannot be seen with ordinary microscopes, although there are many sophisticated experimental methods to measure aspects of the behaviour, shape, and interactions of biomolecules. Computer modeling is a complimentary approach to such experiments, both by themselves and in direct combination with experiments that otherwise could not be interpreted at a molecular level. Using powerful computers and a description of how atoms interact with each other, it is possible to calculate in atomic detail how biomolecules move and interact in time. In recent years, this molecular dynamics simulation method has become an essential method to solve problems involving molecules of all types, in my research group primarily lipids.  Lipids are the major building block of cell membranes that define the boundary between a cell and its surroundings. Cell membranes have remarkable mechanical and electrical properties, a complex chemical composition, and a surprisingly complex physical behaviour. These properties are primarily derived from the molecular structure of lipids, which have a water-loving head and a water-avoiding tail. This structure leads to self-aggregation in water into fascinating structures. These include cell membranes based on biological lipids, but also a wide variety of other structures by synthetic lipids and lipid mixtures, which are both of fundamental interest and of interest in technical and scientific applications.  This research project is aimed at developing and applying computational models of molecules to better understand the properties of lipids and surfactant molecules. We will use and improve both detailed atomistic models and a somewhat coarser model in which a few atoms are grouped into a single 'bead'. Although we lose detail in this case, it is computational cheaper by several orders of magnitude to explore such models. Our main interests are the properties of domains in membranes, which are thought to underly many biologically important processes, the properties of mixtures of surfactants and lipids that form micelles, bicelles, and nanodiscs, and an improved link with experimental methods that give insight in lipid structure, including x-ray and neutron diffraction as well as spectroscopic methods.