Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion

Jakob Wohlert, Olle Edholm

Abstract:

It is shown that a long, near microsecond, atomistic simulation can shed some light upon the dynamical processes occurring in a lipid bilayer. The analysis focuses on reorientational dynamics of the chains and lateral diffusion of lipids. It is shown that the reorientational correlation functions exhibits an algebraic decay (rather than exponential) for several orders of magnitude in time. The calculated nuclear magnetic resonance relaxation rates agree with experiments for carbons at the C7 position while there are some differences for C3. Lateral diffusion can be divided into two stages. In a first stage occurring at short times, t<5 ns, the center of mass of the lipid moves due to conformational changes of the chains while the headgroup position remains relatively fixed. In this stage, the center of mass can move up to approximately 0.8 nm. The fitted short-time diffusion coefficient is D(1)=13 x 10(-7) cm(2) s(-1) On a longer time scale, the diffusion coefficient becomes D(2)=0.79 x 10(-7) cm(2) s(-1).

2022-04-28 21:30:00

李翛然:

#paper Wohlert and Edholm (2006) J. Chem. Phys. 125: 204703
Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion 本论文提出了不同脂分子的面积，相转变温度，等各种参数的得出方法，并列举出了模拟当中的一些参数选择背后的原因。最近正在深耕细挖分子动力学，因为接下来要和量子计算进行合作了，需要充分理解目前的原理及参数选择，以便找到一个最适合用量子计算的场景。