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On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations.

机译:用施加的表面张力模拟脂质双层时:周期性边界条件和起伏。

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摘要

As sketched in Fig. 1, a current molecular dynamics computer simulation of a lipid bilayer fails to capture significant features of the macroscopic system, including long wavelength undulations. Such fluctuations are intrinsically connected to the value of the macroscopic (or thermodynamic) surface tension (cf. Eqs. 1 and 9; for a related treatment, see Brochard et al., 1975, 1976). Consequently, the surface tension that might be evaluated in an MD simulation should not be expected to equal the surface tension obtained from macroscopic measurements. Put another way, the largest of the three simulations presented here contained over 16,000 atoms and required substantial computer time to complete, but modeled a system of only 36 lipids per side. From this perspective it is not surprising that the system is not at the thermodynamic limit. An important practical consequence of this effect is that simulations with fluctuating area should be carried out with a nonzero applied surface tension (gamma 0 of Fig. 2) even when the macroscopic tension is zero, or close to zero. Computer simulations at fixed surface area, which can explicitly determine pressure anisotropy at the molecular level, should ultimately lend insight into the value of gamma 0, including its dependence on lipid composition and other membrane components. As we have noted and will describe further in separate publications (Feller et al., 1996; Feller et al., manuscript in preparation), surface tensions obtained from simulations can be distorted by inadequate initial conditions and convergence, and are sensitive to potential energy functions, force truncation methods, and system size; it is not difficult, in fact, to tune terms in the potential energy function so as to yield surface tensions close to zero. This is why parameters should be tested extensively on simpler systems, for example, monolayers. The estimates of gamma 0 that we have presented here should be regarded as qualitative, and primarily underscore the assertion that the surface tension of a microscopically flat, simulation-sized patch is significantly greater than zero. As the simulation cell length increases, the surface tension that would be evaluated (or should be applied) decreases; in the limit of micrometer-sized simulation cells, gamma would approach zero or its appropriate thermodynamic value. The theories presented here also imply that the estimation of bilayer surface tension from monolayer data should take the degree of flatness into account. These conclusions are independent of the precise values of parameters such as bending constants. In conclusion, from the simulator's perspective, the question "What is the surface tension of a bilayer?" is better phrased as "What is the value of the applied surface tension necessary to simulate a particular experimental system with a given number of lipids?". As we have shown, the answer to the second question varies, but it should not be assumed a priori to equal zero.
机译:如图1所示,目前对脂质双层的分子动力学计算机模拟无法捕获宏观系统的重要特征,包括长波状波动。这种波动本质上与宏观(或热力学)表面张力的值有关(参见方程式1和9;有关处理,请参见Brochard等,1975,1976)。因此,不应期望在MD模拟中评估的表面张力等于从宏观测量获得的表面张力。换句话说,这里提出的三个模拟中最大的一个包含超过16,000个原子,需要大量的计算机时间才能完成,但是对每侧只有36个脂质的系统进行了建模。从这个角度来看,系统没有达到热力学极限也就不足为奇了。这种影响的重要实际结果是,即使宏观张力为零或接近零,也应使用非零的施加表面张力(图2的γ0)进行具有波动区域的模拟。在固定表面积上的计算机模拟可以明确确定分子水平上的压力各向异性,最终应该可以深入了解γ0的值,包括其对脂质成分和其他膜成分的依赖性。正如我们已经注意到的,并将在单独的出版物中进行进一步描述(Feller等,1996; Feller等,准备中的手稿),通过模拟获得的表面张力会因初始条件不足和收敛而变形,并且对势能敏感功能,强制截断方法和系统大小;实际上,调整势能函数中的项以产生接近零的表面张力并不难。这就是为什么应该在较简单的系统(例如单层)上广泛测试参数的原因。我们在这里提出的伽马0的估计值应被视为定性的,并且主要强调这样的主张,即微观平坦,模拟大小的贴片的表面张力明显大于零。随着模拟单元长度的增加,将要评估(或应施加)的表面张力会降低;在微米大小的模拟单元的极限中,γ会接近零或其适当的热力学值。这里介绍的理论还暗示,根据单层数据估算双层表面张力应考虑平坦度。这些结论与诸如弯曲常数之类的参数的精确值无关。总之,从模拟器的角度来看,问题“双层的表面张力是多少?”最好用“用给定数量的脂质模拟特定的实验系统所需要的施加表面张力的值是多少?”更好地表述。如我们所显示的,第二个问题的答案是不同的,但不应假定它先验等于零。

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