We study diffusion coefficients of liquid domains by explicitly taking into account the two-layered structure called leaflets of the bilayer membrane. In general, the velocity fields associated with each leaflet are different and the layers sliding past each other cause frictional coupling. We obtain analytical results of diffusion coefficients for a circular liquid domain in a leaflet, and quantitatively study their dependence on the inter-leaflet friction. We also show that the diffusion coefficients diverge in the absence of coupling between the bilayer and solvents, even when the inter-leaflet friction is taken into account. In order to corroborate our theory, the effect of the inter-leaflet friction on the correlated diffusion is examined.
We investigate a model of an asymmetric bilayer consisting of sphigomyelin, phosphatidylcholine, and cholesterol in the outer leaflet, and phosphatidyl\-ethanolamine, (PE), phosphatidylserine, and cholesterol in the inner leaflet. Composition fluctuations are coupled to membrane fluctuations via the bending energy which depends upon the local spontaneous curvature dominated by the PE in the inner leaflet. This brings about a microemulsion in that leaflet with a characteristic wavelength of 37 nm as shown by the PE-PE structure function. Thus the inner leaflet will respond to an external pertur…
Shape transformations of flat bilayer membranes and vesicles induced by hydrolysis and condensation reactions of amphiphilic molecules are studied using coarse-grained molecular dynamics simulations. The hydrolysis and condensation reactions result in the formation and dissociation of amphiphilic molecules, respectively. Asymmetric reactions between the inner and outer leaflets of a vesicle can transport amphiphilic molecules between the leaflets. It is found that the resulting area difference between the two leaflets induces bilayer sheet protrusion~(BP) and budding at low reduced volumes of …
Amphiphilic lipid bilayers modify the friction properties of the surfaces on top of which they are deposited. In particular, the measured sliding friction coefficient is significantly reduced compared with the native surface. We investigate in this work the friction properties of a numerical coarse-grained model of DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine) lipid bilayer subject to longitudinal shear. The interleaflet friction coefficient is obtained from out-of-equilibrium pulling and relaxation simulations. In particular, we gain access to the transient viscoelastic response of a shea…
We study the kinetics governing the attainment of inter-leaflet domain symmetry in a phase-separating amphiphilic bilayer. "Indirect" inter-leaflet coupling via hydrophobic mismatch can induce an instability towards a metastable pattern of locally asymmetric domains upon quenching from high temperature. This necessitates a nucleation step to form the conventional symmetric pattern of domains, which are favoured by a "direct" inter-leaflet coupling. We model the energetics for a symmetric domain to nucleate from the metastable state, and find that an interplay between hydrophobic mismatch and t…
We propose a simple mechanism for the self-replication of protocells. Our main hypothesis is that the amphiphilic molecules composing the membrane bilayer are synthesised inside the protocell through globally exothermic chemical reactions. The slow increase of the inner temperature forces the hottest molecules to move from the inner leaflet to the outer leaflet of the bilayer. This asymmetric translocation process makes the outer leaflet grow faster than the inner leaflet. This differential growth increases the mean curvature and amplifies any local shrinking of the protocell until it splits i…
The domain formation of curvature-inducing molecules, such as peripheral or transmembrane proteins and conical surfactants, is studied in thermal equilibrium and nonequilibrium steady states using meshless membrane simulations. These molecules can bind onto both surfaces of a bilayer membrane and also move to the opposite leaflet by a flip-flop. In symmetric conditions for the two leaflets, the membrane domains form checkerboard patterns in addition to stripe and spot patterns. The unbound membrane stabilizes the vertices of the checkerboard. In asymmetric conditions, the domains form kagome-l…
Simulating Curved Lipid Membranes Using Anchored Frozen Patches
Department of Materials Science and Engineering, Grainger College of Engineering, University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校格雷恩工程学院材料科学与工程系）
We discuss the dynamics of a bilayer membrane with partial slip boundary conditions between the monolayers and the bulk fluid. Using Onsager's variational principle to account for the associated dissipations, we derive the coupled dynamic equations for the membrane height and the excess lipid density. The newly introduced friction coefficients appear in the renormalized fluid viscosities. For ordinary lipid bilayer membranes, we find that it is generally justified to ignore the effects of permeation and parallel slip at the membrane surface.
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon nanotubes in membranes. The resulting Oseen correction allows us to extract infinite-system diffusion coefficients and membrane surface viscosities from membrane simulations despite the logarithmic divergence of apparent diffusivities with increasing box width. The hydrodynamic theory of diffusion applies also to membranes with asymmetric leaflets and embed…
We theoretically investigate the dynamics of a floating lipid bilayer membrane coupled with a two-dimensional cytoskeleton network, taking into explicitly account the intermonolayer friction, the discrete lattice structure of the cytoskeleton, and its prestress. The lattice structure breaks lateral continuous translational symmetry and couples Fourier modes with different wavevectors. It is shown that within a short time interval a long-wavelength deformation excites a collection of modes with wavelengths shorter than the lattice spacing. These modes relax slowly with a common renormalized rat…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from cell migration, intercellular transport, and cell communication. Using Onsager's variational principle, we derive the equations that govern the relaxation dynamics of the membrane shape, of the mass densities of the bilayer leaflets, and of the diffusing proteins' concentration. With our generic formalism, we obtain several results on membrane dynamics. We …
We theoretically investigate the relaxation dynamics of a nearly-flat binary lipid bilayer membrane by taking into account the membrane tension, hydrodynamics of the surrounding fluid, inter-monolayer friction and mutual diffusion in each monolayer. We find that two relaxation modes associated with the mutual diffusion appear in addition to the three previously discussed relaxation modes reflecting the bending and compression of the membrane. Because of the symmetry, only one of the two diffusive mode is coupled to the bending mode. The two diffusive modes are much slower than the bending and …
Caffeine (1,3,7-trimethylxanthine), an ingredient of coffee, is used worldwide as a psychostimulant, antioxidant, and adjuvant analgesic. To gain insights into the action mechanism of caffeine, we report on its effects on the phase behaviour and microscopic dynamics of a dioctadecyldimethylammonium bromide (DODAB) lipid membrane, as studied quasielastic neutron scattering (QENS). Tracking the elastic scattering intensity as a function of temperature showed that caffeine does not alter the phase behaviour of the DODAB membrane and that transition temperatures remain almost unaltered. However, Q…
We propose a model that accounts for the budding transition of asymmetric two-component lipid domains, where the two monolayers (leaflets) have different average compositions controlled by independent chemical potentials. Assuming a coupling between the local curvature and local lipid composition in each of the leaflets, we discuss the morphology and thermodynamic behavior of asymmetric lipid domains. The membrane free-energy contains three contributions: the bending energy, the line tension, and a Landau free-energy for a lateral phase separation. Within a mean-field treatment, we obtain vari…
The study of the ability of drug molecules to enter cells through the membrane is of vital importance in the field of drug delivery. In cases where the transport of the drug molecules through the membrane is not easily accomplishable, other carrier molecules are used. Spherical fullerene molecules have been postulated as potential carriers of highly hydrophilic drugs across the plasma membrane. Here we report the coarse-grain molecular dynamics study of the translocation of C60 fullerene and its derivatives across a cell membrane modeled as a 1, 2-distearoyl-sn-glycero-3-phosphocholine (DSPC) …
Membrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be attributed to interactions between proteins and membranes. These interactions include protein diffusion and formation of aggregates due to protein-protein interactions in the plane of the membrane. Recently, we developed a model that couples the in-plane flow of lipids and diffusion of proteins with the out-of-plane bending of the membrane. Building on this work,…
The understanding of the penetration and clusterization of 1-alkanol in bilayer membrane: An open outlook based on atomistic molecular dynamics simulation
Dynamic Permeability in Metastable Droplet Interfacial Bilayers
University of California, Berkeley（加州大学伯克利分校）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）；The Molecular Foundry（分子发现所）；University of Massachusetts, Amherst（马萨诸塞大学阿默斯特分校）
The effect of AC electric fields on the elasticity of supported lipid bilayers has been investigated at the microscopic level using grazing incidence synchrotron x-ray scattering. A strong decrease in the membrane tension up to 1mN/m and a dramatic increase of its effective rigidity up to 300kBT are observed for local electric potentials seen by the membrane < 1V. The experimental results were analyzed using detailed electrokinetic modeling and non-linear Poisson-Boltzmann theory. Based on a modeling of the electromagnetic stress which provides an accurate description of bilayer separation vs …
The prospects of application of graphene and related structures as the membrane mimetic materials, capable of reproducing several biomembrane functions up to the certain limit, are analyzed in the series of our papers. This paper considers the possibility of the ion channel function modeling using graphene and its derivatives. The physical mechanisms providing selective permeability for different membrane mimetic materials, as well as the limits of the adequate simulation of the transport, catalytic, sensing and electrogenic properties of the cell membrane ion channels using bilayered graphene…
Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compressi…
