Abstract：
In this chapter, we present a novel computational framework to study the dynamic behavior of extensive membrane systems, potentially in interaction with peripheral proteins, as an alternative to conventional simulation methods. The framework effectively describes the complex dynamics in protein-membrane systems in a mesoscopic particle-based setup. Furthermore, leveraging the hydrodynamic coupling between the membrane and its surrounding solvent, the coarse-grained model grounds its dynamics in macroscopic kinetic properties such as viscosity and diffusion coefficients, marrying the advantages of continuum- and particle-based approaches. We introduce the theoretical background and the parameter-space optimization method in a step-by-step fashion, present the hydrodynamic coupling method in detail, and demonstrate the application of the model at each stage through illuminating examples. We believe this modeling framework to hold great potential for simulating membrane and protein systems at biological spatiotemporal scales, and offer substantial flexibility for further development and parametrization.
摘要：
在这一章中,我们提出了一个新的计算框架来研究广泛的膜系统的动态行为，可能与外周蛋白相互作用，作为传统模拟方法的替代方法。该框架有效地描述了基于介观粒子的设置中蛋白质-膜系统的复杂动力学。此外，利用膜与其周围溶剂之间的流体动力耦合，粗粒度模型将其动力学基于宏观动力学特性，如粘度和扩散系数，结合基于连续和粒子的方法的优点。我们逐步介绍了理论背景和参数空间优化方法，详细介绍了液力耦合方法，并通过实例说明模型在各个阶段的应用。我们相信这个建模框架在生物时空尺度上模拟膜和蛋白质系统具有巨大的潜力，并为进一步开发和参数化提供了很大的灵活性。
