Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS

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• 作者：S.-P. Fu^a ; ^{sf47@njit.edu} ; Z. Peng^b ; H. Yuan^c ; R. Kfoury^c ; Y.-N. Young^a
• 关键词：Membranes ; Cell dynamics ; Pair-potential method
• 刊名：Computer Physics Communications
• 出版年：2017
• 出版时间：January 2017
• 年：2017
• 卷：210
• 期：Complete
• 页码：193-203
• 全文大小：3482 K
• 卷排序：210

文摘

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4∼6nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane, such as gel–fluid–gas phase transitions of lipids, diffusion, and bending rigidity Yuan et al. (2010). In this work we implement such an interaction potential in LAMMPS to simulate large-scale lipid systems such as a giant unilamellar vesicle (GUV) and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for RBC dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. To demonstrate that the proposed methods do capture the observed dynamics of vesicles and RBCs, we focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with enclosed volume; 2. RBC shape transitions with different enclosed volume. Finally utilizing the parallel computing capability in LAMMPS, we provide some timing results for parallel coarse-grained simulations to illustrate that it is possible to use LAMMPS to simulate large-scale realistic complex biological membranes for more than 1 ms.Program summaryProgram Title: fluidmembraneProgram Files doi:http://dx.doi.org/10.17632/4v53nkv5hc.1Licensing provisions: GNU GPLv3Programming language: C++.Nature of problem:A pair-potential function for simulating the shape transition of fluid vesicles and the resting shapes of red blood cells.Program Solution method:Nosé-Hoover thermostat and Berendsen pressure coupling algorithms.External routines/libraries: LAMMPSSubprograms used: create_rbc_with_water (MATLAB), bond_harmonic1 (C++), in_example (LAMMPS input script).