Literature DB >> 8874010

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

S E Feller1, R W Pastor.   

Abstract

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.

Entities:  

Mesh:

Substances:

Year:  1996        PMID: 8874010      PMCID: PMC1233603          DOI: 10.1016/S0006-3495(96)79337-2

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  12 in total

1.  Entropy-driven tension and bending elasticity in condensed-fluid membranes.

Authors: 
Journal:  Phys Rev Lett       Date:  1990-04-23       Impact factor: 9.161

2.  Hydrostatic pressure in small phospholipid vesicles.

Authors:  C Tanford
Journal:  Proc Natl Acad Sci U S A       Date:  1979-07       Impact factor: 11.205

3.  What is the surface tension of a lipid bilayer membrane?

Authors:  F Jähnig
Journal:  Biophys J       Date:  1996-09       Impact factor: 4.033

4.  X-ray structure determination of fully hydrated L alpha phase dipalmitoylphosphatidylcholine bilayers.

Authors:  J F Nagle; R Zhang; S Tristram-Nagle; W Sun; H I Petrache; R M Suter
Journal:  Biophys J       Date:  1996-03       Impact factor: 4.033

5.  Small phospholipid vesicles: internal pressure, surface tension, and surface free energy.

Authors:  S H White
Journal:  Proc Natl Acad Sci U S A       Date:  1980-07       Impact factor: 11.205

6.  Thermoelasticity of large lecithin bilayer vesicles.

Authors:  R Kwok; E Evans
Journal:  Biophys J       Date:  1981-09       Impact factor: 4.033

7.  Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer.

Authors:  K Tu; D J Tobias; J K Blasie; M L Klein
Journal:  Biophys J       Date:  1996-02       Impact factor: 4.033

8.  Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane.

Authors:  S W Chiu; M Clark; V Balaji; S Subramaniam; H L Scott; E Jakobsson
Journal:  Biophys J       Date:  1995-10       Impact factor: 4.033

9.  Interactions between neutral phospholipid bilayer membranes.

Authors:  L J Lis; M McAlister; N Fuller; R P Rand; V A Parsegian
Journal:  Biophys J       Date:  1982-03       Impact factor: 4.033

10.  1-Palmitoyl-2-pyrenedecanoyl glycerophospholipids as membrane probes: evidence for regular distribution in liquid-crystalline phosphatidylcholine bilayers.

Authors:  P J Somerharju; J A Virtanen; K K Eklund; P Vainio; P K Kinnunen
Journal:  Biochemistry       Date:  1985-05-21       Impact factor: 3.162

View more
  62 in total

1.  Effect of pH on the interfacial tension of lipid bilayer membrane.

Authors:  A D Petelska; Z A Figaszewski
Journal:  Biophys J       Date:  2000-02       Impact factor: 4.033

2.  Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants.

Authors:  R D Groot; K L Rabone
Journal:  Biophys J       Date:  2001-08       Impact factor: 4.033

3.  Calculating the bulk modulus for a lipid bilayer with nonequilibrium molecular dynamics simulation.

Authors:  Gary Ayton; Alexander M Smondyrev; Scott G Bardenhagen; Patrick McMurtry; Gregory A Voth
Journal:  Biophys J       Date:  2002-03       Impact factor: 4.033

4.  Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions.

Authors:  Elizabeth A Dolan; Richard M Venable; Richard W Pastor; Bernard R Brooks
Journal:  Biophys J       Date:  2002-05       Impact factor: 4.033

5.  Atomic detail peptide-membrane interactions: molecular dynamics simulation of gramicidin S in a DMPC bilayer.

Authors:  D Mihailescu; J C Smith
Journal:  Biophys J       Date:  2000-10       Impact factor: 4.033

6.  Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations.

Authors:  Kevin C Song; Philip W Livanec; Jeffery B Klauda; Krzysztof Kuczera; Robert C Dunn; Wonpil Im
Journal:  J Phys Chem B       Date:  2011-04-22       Impact factor: 2.991

7.  Computer simulation of small molecule permeation across a lipid bilayer: dependence on bilayer properties and solute volume, size, and cross-sectional area.

Authors:  D Bemporad; C Luttmann; J W Essex
Journal:  Biophys J       Date:  2004-07       Impact factor: 4.033

8.  The effect of thermal fluctuations on Schulman area elasticity.

Authors:  O Farago; P Pincus
Journal:  Eur Phys J E Soft Matter       Date:  2003-08       Impact factor: 1.890

9.  Hydrodynamic flow in a synaptic cleft during exocytosis.

Authors:  M N Shneider; R S Gimatdinov; A I Skorinkin; I V Kovyazina; E E Nikolsky
Journal:  Eur Biophys J       Date:  2011-11-01       Impact factor: 1.733

10.  Molecular dynamics simulations of homo-oligomeric bundles embedded within a lipid bilayer.

Authors:  Thuy Hien T Nguyen; Zhiwei Liu; Preston B Moore
Journal:  Biophys J       Date:  2013-10-01       Impact factor: 4.033

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.