Modeling flexible amphiphilic bilayers: A solvent-free off-lattice Monte Carlo study

Wang, Zun-Jing; Frenkel, Daan

doi:10.1063/1.1927509

Cited by 72 publications

(75 citation statements)

References 38 publications

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“….5 were found. 202 A few years later Wang and Frenkel proposed a variant of this model, 203 in which the lipids had an additional bending degree of freedom and the density dependence of the hydrophobic interactions was parametrized slightly differently, in particular by evaluating the average density of hydrophobic units inside a slightly prolate ellipsoid, oriented along the direction of the average bilayer normal. Within their parametrization these authors obtained a physically more realistic bending rigidity of k/k B T E 13, as measured via a fluctuation analysis.…”

Section: B Basic Ideas and Specific Implementationsmentioning

confidence: 99%

Multiscale modeling of emergent materials: biological and soft matter

Murtola

Bunker

Vattulainen

et al. 2009

Phys. Chem. Chem. Phys.

260

234

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On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models Moritz Winger, Daniel Trzesniak, Riccardo Baron and Wilfred F. In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed in the context of the so-called Henderson theorem and the inverse Monte Carlo method of Lyubartsev and Laaksonen. In the second part, we take a different look at coarse graining by analyzing conformations of molecules. This is done by the application of self-organizing maps, i.e., a neural network type approach. Such an approach can be used to guide the selection of the relevant degrees of freedom. Then, we discuss technical issues related to the popular dissipative particle dynamics (DPD) method. Importantly, the potentials derived using the inverse Monte Carlo method can be used together with the DPD thermostat. In the final part we focus on solvent-free modeling which offers a different route to coarse graining by integrating out the degrees of freedom associated with solvent.

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Section: B Basic Ideas and Specific Implementationsmentioning

confidence: 99%

Multiscale modeling of emergent materials: biological and soft matter

Murtola

Bunker

Vattulainen

et al. 2009

Phys. Chem. Chem. Phys.

260

234

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“…Simple Lennard-Jones ͑LJ͒ interactions for the tail-tail interactions do not appear to adequately stabilize the biologically relevant fluid phase, leading to models that crystallize or do not form stable bilayers, and alternative efforts employing many-body potentials [23][24][25] or anisotropic interactions 26 did not fundamentally overcome this problem. However, in 2003 Farago 27 employed a simple three-site lipid model with six interaction types, and was able to obtain a fluid bilayer.…”

Section: Introductionmentioning

confidence: 99%

An implicit solvent coarse-grained lipid model with correct stress profile

Sodt

Head‐Gordon

2010

The Journal of Chemical Physics

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We develop a coarse-grained parametrization strategy for lipid membranes that we illustrate for a dipalmitoylphosphatidylcholine bilayer. Our coarse-graining approach eliminates the high cost of explicit solvent but maintains more lipid interaction sites. We use a broad attractive tail-tail potential and extract realistic bonded potentials of mean force from all-atom simulations, resulting in a model with a sharp gel to fluid transition, a correct bending modulus, and overall very reasonable dynamics when compared with experiment. We also determine a quantitative stress profile and correct breakdown of contributions from lipid components when compared with detailed all-atom simulation benchmarks, which has been difficult to achieve for implicit membrane models. Such a coarse-grained lipid model will be necessary for efficiently simulating complex constructs of the membrane, such as protein assembly and lipid raft formation, within these nonaqueous chemical environments.

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“…21 This discrepancy is not surprising in view of the special condition of the modeled membrane, even though this solventfree model can reproduce elastic properties of biological membranes roughly within experimental range. 17 Suppose the theoretical analysis of experimental data is correct, there are still many factors which could lead to the quantitative difference of the free-energy barriers between simulations and experiments., e.g., the effect of impurities in experiments, the variations of solvent hydrophobicity and amphiphile molecular flexibility, the finite size of simulated membranes, etc.…”

Section: -3mentioning

confidence: 99%

“…To limit the computational cost, we made use of a solvent-free coarse-grained membrane model that we had tested previously. 17 In the present study, we consider bilayer membranes consisting of 1152 lipid molecules.As pore nucleation is an activated process, the spontaneous formation of pore nuclei in a moderately stretched membrane is infrequent. It can be invoked by a very high tension, but in this case, once a pore occurs, membrane rupture follows quickly.…”

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confidence: 99%

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Pore nucleation in mechanically stretched bilayer membranes

Wang

Frenkel

2005

The Journal of Chemical Physics

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We report a computer-simulation study of the free-energy barrier for the nucleation of pores in the bilayer membrane under constant stretching lateral pressure. We find that incipient pores are hydrophobic but as the lateral size of the pore nucleus becomes comparable with the molecular length, the pore becomes hydrophilic. In agreement with previous investigations, we find that the dynamical process of growth and closure of hydrophilic pores is controlled by the competition between the surface tension of the membrane and the line tension associated with the rim of the pore. We estimate the line tension of a hydrophilic pore from the shape of the computed free-energy barriers. The line tension thus computed is in a good agreement with available experimental data. We also estimate the line tension of hydrophobic pores at both macroscopic and microscopic levels. The comparison of line tensions at these two different levels indicates that the "microscopic" line tension should be carefully distinguished from the "macroscopic" effiective line tension used in the theoretical analysis of pore nucleation. The overall shape of the free-energy barrier for pore nucleation shows no indication for the existence of a metastable intermediate during pore The formation of pores in bilayer membranes plays a role in many biological and biomimetic systems. [1][2][3] The simplest model for pore formation in membranes is based on classical nucleation theory ͑CNT͒. 4 In this picture, the formation of pores in membranes is an activated process that is controlled by the competition between the surface tension of the membrane and the line tension associated with the rim of the pore. Based on this model, several theoretical investigations have been carried out to analyze the structural and dynamical properties of pores in membranes. [5][6][7][8][9][10] In order to observe pore formation in realistic models for phospholipid bilayers 11 on the time scale of a simulation ͑nanoseconds͒, very large stresses ͑or very large electric fields͒ are required. Coarse-grained simulations offer the possibility to perform a systematic study of the size and shape distribution of pores that appear spontaneously in a membrane at thermal equilibrium. 12 Using such studies, it is possible to estimate the line tension associated with the rim of the pore, 13 and the free-energy profile of pore formation in a membrane at constant surface area. 14 In parallel, there has been much progress in the development of experimental techniques to probe the dynamical features of pore formation in membranes. 15,16 In spite of these efforts, our knowledge about the early stages of pore nucleation is still limited. Yet, experiments by Evans et al. 16 suggest that, precisely in this regime, something interesting happens. In Ref. 16, the rupture rate of spherical vesicles is probed as a function of the rate at which the tension is increased. These experiments suggest that pore nucleation is a two-stage process: presumably, in the early stages a molecular-size metastable defect f...

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Modeling flexible amphiphilic bilayers: A solvent-free off-lattice Monte Carlo study

Cited by 72 publications

References 38 publications

Multiscale modeling of emergent materials: biological and soft matter

Multiscale modeling of emergent materials: biological and soft matter

An implicit solvent coarse-grained lipid model with correct stress profile

Pore nucleation in mechanically stretched bilayer membranes

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