Sadeghi, M. and Weikl, T. and Noé, F. (2018) Particlebased membrane model for mesoscopic simulation of cellular dynamics. J. Chem. Phys., 148 (4). 044901.

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Official URL: http://dx.doi.org/10.1063/1.5009107
Abstract
We present a simple and computationally efficient coarsegrained and solventfree model for simulating lipid bilayer membranes. In order to be used in concert with particlebased reactiondiffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearestneighbor bondstretching and anglebending, and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. Inplane fluidity is implemented with Monte Carlo bondflipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particlebased representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of twodimensional shear flow under a gravity force is employed to measure the effective inplane viscosity of the membrane model, and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarsegrained molecular dynamics or particlebased reactiondiffusion simulations of biological systems.
Item Type:  Article 

Additional Information:  SFB 1114 preprint in arXiv:1710.06907 
Subjects:  Biological Sciences Physical Sciences 
Divisions:  Department of Mathematics and Computer Science > Institute of Mathematics > Comp. Molecular Biology 
ID Code:  2121 
Deposited By:  BioComp Admin 
Deposited On:  23 Oct 2017 13:58 
Last Modified:  16 Feb 2018 13:41 
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