Mesoscopic Membrane Physics: Concepts, Simulations, and Selected Applications

Abstract

The window of a few tens to a few hundred nanometers in length scale is a booming field in lipid membrane research, owing largely to two reasons. First, many exciting biophysical and cell biological processes take place within it. Second, experimental techniques manage to zoom in on this sub-optical scale, while computer simulations zoom out to system sizes previously unattainable, and both will be meeting soon. This paper reviews a selection of questions and concepts in this field and demonstrates that they can often be favorably addressed with highly simplified simulation models. Among the topics discussed are membrane adhesion to substrates, mixed lipid bilayers, lipid curvature coupling, pore formation by antimicrobial peptides, composition-driven protein aggregation, and curvature driven vesiculation.

Pressure-temperature phase diagram for shapes of vesicles: A coarse-grained molecular dynamics study

“…The CGMD model used here is coarser than that used in previous studies. 12,[18][19][20] In the present model, a membrane particle with a diameter of membrane thickness and described by five degrees of freedom, actually represents a number of lipid molecules. In addition, this model eliminates the explicit consideration of solvent molecules, and their effect is considered by the effective particle interaction potential.…”

“…Since the meso-or macroscopic properties of membranes cannot possibly depend on all the details of the atomic description, coarse-grain atomistic models have been used to study the physical properties of membranes, including formation of membrane structures, 8 membrane elasticity, [8][9][10][11][12][13][14][15][16][17][18] thermal fluctuation, [8][9][10]17 nanoparticle endocytosis, 10,16 composition segregation, 12,[14][15][16] and topological shape changes. [18][19][20] A vesicle may change its shape, volume, or surface area, due to the change in properties of its membrane and/or the presence of external loadings. 21 A phase diagram for vesicle shape transformation at different membrane properties and external loading conditions reveals important thermodynamic behavior of vesicle.…”

“…A modified Lenard-Jones ͑LJ͒ potential was employed to overcome the drawback of the standard LJ 12-6 potential, which was found to be too short to stabilize a liquid phase. 18 The modified pair potential energy between particles i and j is of the following form:…”

Computational ‘microscopy’ of cellular membranes

“…Brownian dynamics or dissipative particle dynamics; see Box 1). Depending on the level of coarse-graining, they can be extremely fast and are able to handle very large systems, but their coarseness often restricts their applicability to address generic problems (Deserno, 2009). However, when carefully parameterized from higher-resolution models, semi-quantitative predictions can be made (Dama et al, 2013).…”

Particle-based membrane model for mesoscopic simulation of cellular dynamics

“…While all-atom molecular simulations are extremely successful for the study of individual macromolecules and small complexes [3][4][5][6][7][8][9] and can reach thermodynamics and kinetics at very long timescales with the aid of enhanced sampling methods and Markov state modeling 7,[10][11][12][13][14][15][16][17][18] , they have severe limitations in terms of system sizes that can be sampled exhaustively 19 . Even for the simple case of equilibrating micron-sized biomembranes, a blind scale up in all-atom molecular dynamics would be out of reach of computational power for a) Corresponding author; Electronic mail: mohsen.sadeghi@fu-berlin.de b) Electronic mail: thomas.weikl@mpikg.mpg.de c) Corresponding author; Electronic mail: frank.noe@fu-berlin.de decades to come 20 . To fill this computational gap, and gain insights into cellular processes, the development and application of coarse-grained models is an important aspect of computer simulation.…”