Biological and synthetic membranes: What can be learned from a coarse-grained description?
arXiv:cond-mat/0609295 · doi:10.1016/j.physrep.2006.08.003
Abstract
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ simple and soft effective potentials, coarse-grained models can provide rather direct insight into collective phenomena in membranes on large time and length scales. We present a summary of recent progress in this rapidly evolving field, and pay special attention to model development and computational techniques. Applications of coarse-grained models to changes of the membrane topology are illustrated with studies of membrane fusion utilizing simulations and self-consistent field theory.
88 pages, 39 figures, accepted to Physics Reports, version with higher resolution figures available at http://www.mrl.ucsb.edu/~katsov/pubs/pub024.pdf
References in corpus (41)
- A nonequilibrium equality for free energy differences
- Equilibrium free energy differences from nonequilibrium measurements: a master equation approach
- Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
- Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly
- Fluid Vesicles in Shear Flow
- Efficient tunable generic model for fluid bilayer membranes
- How to mesh up Ewald sums (II): An accurate error estimate for the P3M algorithm
- Critical Exponents, Hyperscaling and Universal Amplitude Ratios for Two- and Three-Dimensional Self-Avoiding Walks
- Fluid Vesicles with Viscous Membranes in Shear Flow
- Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations
- Integration Schemes for Dissipative Particle Dynamics Simulations: From Softly Interacting Systems Towards Hybrid Models
- "Water-free" computer model for fluid bilayer membranes
- Field theoretic study of bilayer membrane fusion: I. Hemifusion mechanism
- Towards Better Integrators for Dissipative Particle Dynamics Simulations
- A New Mechanism of Model Membrane Fusion Determined from Monte Carlo Simulation
- Local Simulation Algorithms for Coulomb Interaction
- Intrinsic profiles and capillary waves at homopolymer interfaces: a Monte Carlo study
- Anomalous size-dependence of interfacial profiles between coexisting phases of polymer mixtures in thin film geometry: A Monte-Carlo simulation
- Coarse Graining of Nonbonded Inter-particle Potentials Using Automatic Simplex Optimization to Fit Structural Properties
- Flexible Lipid Bilayers in Implicit Solvent
- Automatic Coarse Graining of Polymers
- Field Theoretic Study of Bilayer Membrane Fusion: II. Mechanism of a Stalk-Hole Complex
- Local Molecular Dynamics with Coulombic Interaction
- Wetting and Capillary Condensation in Symmetric Polymer Blends: A comparison between Monte Carlo Simulations and Self-Consistent Field Calculations
- Phase diagram of a ternary mixture of cholesterol and saturated and unsaturated lipids calculated from a microscopic model
- Shape Instabilities in the Dynamics of a Two-component Fluid Membrane
- Molecular Dynamics Study of the Nematic-Isotropic Interface
- Properties of Poly (isoprene) - Model Building in the Melt and in Solution
- Coulomb Interactions via Local Dynamics: A Molecular--Dynamics Algorithm
- A Simple Computer Model for Liquid Lipid Bilayers
- Phase Separation of Saturated and Mono-unsaturated Lipids as determined from a Microscopic Model
- The isotropic-nematic interface in suspensions of hard rods: Mean-field properties and capillary waves
- Theory of Lipid Polymorphism: Application to Phosphatidylethanolamine and Phosphatidylserine
- Meso-scale computer modeling of lipid-DNA complexes for gene therapy
- Pores in Bilayer Membranes of Amphiphilic Molecules: Coarse-Grained Molecular Dynamics Simulations Compared with Simple Mesoscopic Models
- Coupling between membrane tilt-difference and dilation: a new ``ripple'' instability and multiple crystalline inclusions phases
- Calculation of the Phase Behavior of Lipids
- Monte Carlo simulations of copolymers at homopolymer interfaces: Interfacial structure as a function of the copolymer density
- The Shape of Inflated Vesicles
- Local Simulation Algorithms for Coulombic Interactions
- Multiple stalk formation as a pathway of defect-induced membrane fusion
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- Membrane simulation models from nm to m scale
- Main phase transition in lipid bilayers: phase coexistence and line tension in a soft, solvent-free, coarse-grained model
- Density functional theory for soft matter with mesoscopic length scale fluctuations included within field-theoretic formalism
- Measurement of the bending rigidity and spontaneous curvature of fluid membranes in simulations
- Universal formulae for the limiting elastic energy of membrane networks
- Coarse-Grained Simulations of Membranes under Tension
- Solvent-free coarse-grained lipid model for large-scale simulations
- Coarse-Grained Models of Biological Membranes within the Single Chain Mean Field Theory
- Optimal coarse-grained site selection in elastic network models of biomolecules
- On the design space between molecular mechanics and machine learning force fields
- General model of phospholipid bilayers in fluid phase within the single chain mean field theory
- Structure formation in binary mixtures of surfactants: vesicle opening-up to bicelles and octopus-like micelles
- Redox Entropy of Plastocyanin: Developing a Microscopic View of Mesoscopic Polar Solvation
- Shape transition from elliptical to cylindrical membrane tubes induced by chiral crescent-shaped protein rods
- Binding of anisotropic curvature-inducing proteins onto membrane tubes
- Cup-to-vesicle transition of a fluid membrane with spontaneous curvature
- Line tension of branching junctions of bilayer membranes
- Application of Self-Consistent Field Theory to Self-Assembled Bilayer Membranes
- Binding of Curvature-Inducing Proteins onto Biomembranes
- Dependence of the energies of fusion on the intermembrane separation: optimal and constrained
- Structure formation in binary mixtures of lipids and detergents: Self-assembly and vesicle division
- Binding of curvature-inducing proteins onto tethered vesicles
- Nonequilibrium Membrane Dynamics Induced by Active Protein Interactions and Chemical Reactions: A Review
- Detachment of fluid membrane from substrate and vesiculation
- Estimate of entropy generation rate can spatiotemporally resolve the active nature of cell flickering
- GPU implementation of the Rosenbluth generation method for static Monte Carlo simulations
- Curvature-sensing and generation by membrane proteins: a review
- Conformation of ultra-long-chain fatty acid in lipid bilayer: Molecular dynamics study
- Phase separation and near-critical fluctuations in two-component lipid membranes: Monte Carlo simulations on experimentally relevant scales
- Virtual bending method to calculate bending rigidity, saddle-splay modulus, and spontaneous curvature of thin fluid membrane
- The main transition in the Pink membrane model: finite-size scaling and the influence of surface roughness
- Effective potentials and electrostatic interactions in self-assembled molecular bilayers II: the case of biological membranes
- Higher derivative free energy terms and interfacial curvatures
- Modeling Biological Membrane and Red Blood Cells by Coarse- Grained Particle Method
- Forces and fluctuations in planar, spherical and tubular membranes