Lipid membranes with an edge

Mesoscale simulation of biomembranes with FreeDTS

We present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this software, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes at different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.

Pure measures of bending for soft plates

This paper, originally motivated by a question raised by Wood and Hanna [Soft Matter, 2019, 15, 2411], shows that pure measures of bending for soft plates can be defined by introducing the class of bending-neutral deformations, which represent finite incremental changes in the plate's shape that do not induce any additional bending. This class of deformations is subject to a geometric compatibility condition, which is fully characterized. A tensorial pure measure of bending, which is invariant under bending-neutral deformations, is described in detail. As shown by an illustrative class of examples, the general notion of a pure measure of bending could be useful in formulating direct theories for soft plates, where stretching and bending energies are treated separately.

Inhomogeneous Canham-Helfrich Abscission in Catenoid Necks under Critical Membrane Mosaicity

The mechanical effects of membrane compositional inhomogeneities are analyzed in a process analogous to neck formation in cellular membranes. We cast on the Canham-Helfrich model of fluid membranes with both the spontaneous curvature and the surface tension being non-homogeneous functions along the cell membrane. The inhomogeneous distribution of necking forces is determined by the equilibrium mechanical equations and the boundary conditions as considered in the axisymmetric setting compatible with the necking process. To establish the role played by mechanical inhomogeneity, we focus on the catenoid, a surface of zero mean curvature. Analytic solutions are shown to exist for the spontaneous curvature and the constrictive forces in terms of the border radii. Our theoretical analysis shows that the inhomogeneous distribution of spontaneous curvature in a mosaic-like neck constrictional forces potentially contributes to the membrane scission under minimized work in living cells.

Conformal order and Poincaré-Klein mapping underlying electrostatics-driven inhomogeneity in tethered membranes

Understanding the organization of matter under the long-range electrostatic force is a fundamental problem in multiple fields. In this work, based on the electrically charged tethered membrane model, we reveal regular structures underlying the lowest-energy states of inhomogeneously stretched planar lattices by a combination of numerical simulation and analytical geometric analysis. Specifically we show the conformal order characterized by the preserved bond angle in the lattice deformation and reveal the Poincaré-Klein mapping underlying the electrostatics-driven inhomogeneity. The discovery of the Poincaré-Klein mapping, which connects the Poincaré disk and the Klein disk for the hyperbolic plane, implies the connection of long-range electrostatic force and hyperbolic geometry. We also discuss lattices with patterned charges of opposite signs for modulating in-plane inhomogeneity and even creating 3D shapes, which may have a connection to metamaterials design. This work suggests the geometric analysis as a promising approach for elucidating the organization of matter under the long-range force.

A general computational framework for the dynamics of single- and multi-phase vesicles and membranes

The dynamics of thin, membrane-like structures are ubiquitous in nature. They play especially important roles in cell biology. Cell membranes separate the inside of a cell from the outside, and vesicles compartmentalize proteins into functional microregions, such as the lysosome. Proteins and/or lipid molecules also aggregate and deform membranes to carry out cellular functions. For example, some viral particles can induce the membrane to invaginate and form an endocytic vesicle that pulls the virus into the cell. While the physics of membranes has been extensively studied since the pioneering work of Helfrich in the 1970's, simulating the dynamics of large scale deformations remains challenging, especially for cases where the membrane composition is spatially heterogeneous. Here, we develop a general computational framework to simulate the overdamped dynamics of membranes and vesicles. We start by considering a membrane with an energy that is a generalized functional of the shape invariants and also includes line discontinuities that arise due to phase boundaries. Using this energy, we derive the internal restoring forces and construct a level set-based algorithm that can stably simulate the large-scale dynamics of these generalized membranes, including scenarios that lead to membrane fission. This method is applied to solve for shapes of single-phase vesicles using a range of reduced volumes, reduced area differences, and preferred curvatures. Our results match well the experimentally measured shapes of corresponding vesicles. The method is then applied to explore the dynamics of multiphase vesicles, predicting equilibrium shapes and conditions that lead to fission near phase boundaries.

Axisymmetric membranes with edges under external force: buckling, minimal surfaces, and tethers

We use theory and numerical computation to determine the shape of an axisymmetric fluid membrane with a resistance to bending and constant area. The membrane connects two rings in the classic geometry that produces a catenoidal shape in a soap film. In our problem, we find infinitely many branches of solutions for the shape and external force as functions of the separation of the rings, analogous to the infinite family of eigenmodes for the Euler buckling of a slender rod. Special attention is paid to the catenoid, which emerges as the shape of maximal allowable separation when the area is less than a critical area equal to the planar area enclosed by the two rings. A perturbation theory argument directly relates the tension of catenoidal membranes to the stability of catenoidal soap films in this regime. When the membrane area is larger than the critical area, we find additional cylindrical tether solutions to the shape equations at large ring separation, and that arbitrarily large ring separations are possible. These results apply for the case of vanishing Gaussian curvature modulus; when the Gaussian curvature modulus is nonzero and the area is below the critical area, the force and the membrane tension diverge as the ring separation approaches its maximum value. We also examine the stability of our shapes and analytically show that catenoidal membranes have markedly different stability properties than their soap film counterparts.

Nanodissected elastically loaded clathrin lattices relax to increased curvature

Clathrin-mediated endocytosis (CME) is the major endocytosis pathway for the specific internalization of large compounds, growth factors, and receptors. Formation of internalized vesicles from the flat plasma membrane is accompanied by maturation of cytoplasmic clathrin coats. How clathrin coats mature and the mechanistic role of clathrin coats are still largely unknown. Maturation models proposed clathrin coats to mature at constant radius or constant area, driven by molecular actions or elastic energy. Here, combining high-speed atomic force microscopy (HS-AFM) imaging, HS-AFM nanodissection, and elasticity theory, we show that clathrin lattices deviating from the intrinsic curvature of clathrin form elastically loaded assemblies. Upon nanodissection of the clathrin network, the stored elastic energy in these lattices drives lattice relaxation to accommodate an ideal area-curvature ratio toward the formation of closed clathrin-coated vesicles. Our work supports that the release of elastic energy stored in curvature-frustrated clathrin lattices could play a major role in CME.

Pore formation induced by nanoparticles binding to a lipid membrane

Nanoparticles (NPs) enter a cell primarily via endocytosis, during which they are engulfed by the cell and reside in lipid vesicles named endosomes. Apart from when an endosome is pinched off the plasma membrane, structural integrity of its lipid membrane is usually well maintained. Under certain circumstances, however, such structural integrity can be considerably perturbed by a nanoparticle. For instance, recent experiments [Chu et al., Sci. Rep., 2014, 4, 4495] indicate that nanodiamonds with sharp corners can escape from an endosome by piercing its lipid membrane. Nonetheless, the energetics of this behavior and how it may be controlled by membrane adhesion and NP morphology remain unclear. In this work, we employ continuum modeling to investigate membrane pore formation induced by the spontaneous binding of a sharp nanoparticle. Based on two axial-symmetric NP models, we characterize the indispensable role played by curvature heterogeneity, membrane adhesion, and the sharpness as well as the size of a nanoparticle in 'breaking' a lipid membrane. Apart from revealing a general mechanism of NP binding-induced membrane pore formation, our results provide the reference for improving the endosomal escape of nanoparticles through manipulating their morphology, a direction that can be explored either independently or combined with existing strategies targeting NP surface chemistry.

Boundary behaviour of open vesicles in axisymmetric case

A continuous transformation from a closed vesicle to an open vesicle requires that the area of open hole enlarges from zero. Since the shape equation and boundary conditions of lipid open vesicles with free edges have been obtained, we want to know whether this process can be achieved with valid parameters. By studying the boundary conditions in the axisymmetric case, the analytic expression of the boundary edges is obtained generally. It reveals that the radius and line tension of boundary edges are confined strongly by bending moduli. In some cases, there is the minimal nonzero boundary radius and the line tension needs to surmount the maxim following the increase of boundary radius. Without the spontaneous curvature, the line tension will trend to infinite when the boundary radius shrinks to zero. The continuous opening up process requires that the spontaneous curvature is nonzero and the ratio between the bending moduli of Gauss curvature and mean curvature satisfies [Formula: see text], which is smaller than the value [Formula: see text] from experiments and simulations. This result indicates that the opening up process is discontinuous.

Stresses in curved nematic membranes

Ordering configurations of a director field on a curved membrane induces stress. In this work, we present a theoretical framework to calculate the stress tensor and the torque as a consequence of the nematic ordering; we use the variational principle and invariance of the energy under Euclidean motions. Euler-Lagrange equations of the membrane as well as the corresponding boundary conditions also appear as natural results. The stress tensor found includes attraction-repulsion forces between defects; likewise, defects are attracted to patches with the same sign in Gaussian curvature. These forces are mediated by the Green function of the Laplace-Beltrami operator of the surface. In addition, we find nonisotropic forces that involve derivatives of the Green function and the Gaussian curvature, even in the normal direction to the membrane. We examine the case of axial membranes to analyze the spherical one. For spherical vesicles we find the modified Young-Laplace law as a consequence of the nematic texture. In the case of spherical cap with defect at the north pole, we find that the force is repulsive with respect to the north pole, indicating that it is an unstable equilibrium point.

Theory and algorithms to compute Helfrich bending forces: a review

Cell membranes are vital to shield a cell's interior from the environment. At the same time they determine to a large extent the cell's mechanical resistance to external forces. In recent years there has been considerable interest in the accurate computational modeling of such membranes, driven mainly by the amazing variety of shapes that red blood cells and model systems such as vesicles can assume in external flows. Given that the typical height of a membrane is only a few nanometers while the surface of the cell extends over many micrometers, physical modeling approaches mostly consider the interface as a two-dimensional elastic continuum. Here we review recent modeling efforts focusing on one of the computationally most intricate components, namely the membrane's bending resistance. We start with a short background on the most widely used bending model due to Helfrich. While the Helfrich bending energy by itself is an extremely simple model equation, the computation of the resulting forces is far from trivial. At the heart of these difficulties lies the fact that the forces involve second order derivatives of the local surface curvature which by itself is the second derivative of the membrane geometry. We systematically derive and compare the different routes to obtain bending forces from the Helfrich energy, namely the variational approach and the thin-shell theory. While both routes lead to mathematically identical expressions, so-called linear bending models are shown to reproduce only the leading order term while higher orders differ. The main part of the review contains a description of various computational strategies which we classify into three categories: the force, the strong and the weak formulation. We finally give some examples for the application of these strategies in actual simulations.

Equilibrium of fluid membranes endowed with orientational order

Minimization of the low-temperature elastic free-energy functional of orientationlly ordered membranes involves independent variation of the membrane-shape, while keeping the orientational order on it (its texture) fixed. We propose an operational, coordinate-independent method for implementing such a variation. Using the Nelson-Peliti formulation of elasticity that emphasizes the interplay between geometry, topology, and thermal fluctuations of orientationally ordered membranes, we minimize the elastic free energy to obtain equations governing their equilibrium shape, together with associated free boundary conditions. Our results are essential for understanding and predicting equilibrium shapes as well as textures of membranes and vesicles; particularly under conditions in which shape deformations are large.

Free energy of the edge of an open lipid bilayer based on the interactions of its constituent molecules

Lipid-bilayers are the fundamental constituents of the walls of most living cells and lipid vesicles, giving them shape and compartment. The formation and growing of pores in a lipid bilayer have attracted considerable attention from an energetic point of view in recent years. Such pores permit targeted delivery of drugs and genes to the cell, and regulate the concentration of various molecules within the cell. The formation of such pores is caused by various reasons such as changes in cell environment, mechanical stress or thermal fluctuations. Understanding the energy and elastic behaviour of a lipid-bilayer edge is crucial for controlling the formation and growth of such pores. In the present work, the interactions in the molecular level are used to obtain the free energy of the edge of an open lipid bilayer. The resulted free-energy density includes terms associated with flexural and torsional energies of the edge, in addition to a line-tension contribution. The line tension, elastic moduli, and spontaneous normal and geodesic curvatures of the edge are obtained as functions of molecular distribution, molecular dimensions, cutoff distance, and the interaction strength. These parameters are further analyzed by implementing a soft-core interaction potential in the microphysical model. The dependence of the elastic free-energy of the edge to the size of the pore is reinvestigated through an illustrative example, and the results are found to be in agreement with the previous observations.

Anisotropic spontaneous curvatures in lipid membranes

Symmetry restrictions due to fluidity require the strain energy in the Helfrich theory of lipid membranes to be locally isotropic in nature. Although this framework is suitable for modeling the interaction of membranes with proteins that generate spherical curvature such as clathrin, there are other important membrane-bending proteins such as BIN-amphiphysin-Rvs proteins that form a cylindrical coat with different curvatures in the longitudinal and the circumferential directions. In this work, we present a detailed mathematical treatment of the theory of lipid membranes incorporating anisotropic spontaneous curvatures. We derive the associated Euler-Lagrange equations and the edge conditions in a generalized setting that allows spatial heterogeneities in the properties of the membrane-protein system. We employ this theory to model the constriction of a membrane tubule by a cylindrical scaffold. In particular, we highlight the role of the equilibrium equation in the tangential plane in regulating the spatial variation of the surface tension field.

Recent theoretical advances in elasticity of membranes following Helfrich's spontaneous curvature model

Recent theoretical advances in elasticity of membranes following Helfrich's famous spontaneous curvature model are summarized in this review. The governing equations describing equilibrium configurations of lipid vesicles, lipid membranes with free edges, and chiral lipid membranes are presented. Several analytic solutions to these equations and their corresponding configurations are demonstrated.

Emergence and stability of intermediate open vesicles in disk-to-vesicle transitions

The transition between two basic structures, a disk and an enclosed vesicle, of a finite membrane is studied by examining the minimum energy path (MEP) connecting these two states. The MEP is constructed using the string method applied to continuum elastic membrane models. The results reveal that, besides the commonly observed disk and vesicle, open vesicles (bowl-shaped vesicles or vesicles with a pore) can become stable or metastable shapes. The emergence, stability, and probability distribution of these open vesicles are analyzed. It is demonstrated that open vesicles can be stabilized by higher-order elastic energies. The estimated probability distribution of the different structures is in good agreement with available experiments.

Membrane stress tensor in the presence of lipid density and composition inhomogeneities

We derive the expression of the stress tensor for one- and two-component lipid membranes with density and composition inhomogeneities. We first express the membrane stress tensor as a function of the free-energy density by means of the principle of virtual work. We then apply this general result to a monolayer model which is shown to be a local version of the area-difference elasticity (ADE) model. The resulting stress tensor expression generalizes the one associated with the Helfrich model, and can be specialized to obtain the one associated with the ADE model. Our stress tensor directly gives the force exchanged through a boundary in a monolayer with density and composition inhomogeneities. Besides, it yields the force density, which is also directly obtained in covariant formalism. We apply our results to study the forces induced in a membrane by a local perturbation.

Chiral symmetry breaking in crystals of achiral polymers

Many achiral polymers crystallize into spherulites with gigantic chirality, as is evident from spectacular images of periodic banding observed in a polarized optical microscope, arising from the twisting of the lamellae making up the spherulites. We present a new mechanism of the spontaneous chiral symmetry breaking, by accounting for topological defects in finite crystalline ribbons made of achiral molecules in equilibrium. We show that disclinations stabilize a twisted helicoidal ribbon, with spontaneous selection of its width and chiral period, which are proportional to each other, as a universal law.

Equilibrium theory and geometrical constraint equation for two-component lipid bilayer vesicles

This paper aims at the general mathematical framework for the equilibrium theory of two-component lipid bilayer vesicles. To take into account the influences of the local compositions together with the mean curvature and Gaussian curvature of the membrane surface, a general potential functional is constructed. We introduce two kinds of virtual displacement modes: the normal one and the tangential one. By minimizing the potential functional, the equilibrium differential equations and the boundary conditions of two-component lipid vesicles are derived. Additionally, the geometrical constraint equation and geometrically permissible condition for the two-component lipid vesicles are presented. The physical, mathematical, and biological meanings of the equilibrium differential equations and the geometrical constraint equations are discussed. The influences of physical parameters on the geometrically permissible phase diagrams are predicted. Numerical results can be used to explain recent experiments.

Dynamics of vesicle formation from lipid droplets: mechanism and controllability

A coarse-grained model developed by Marrink et al. [J. Phys. Chem. B 111, 7812 (2007)] is applied to investigate vesiculation of lipid [dipalmitoylphosphatidylcholine (DPPC)] droplets in water. Three kinds of morphologies of micelles are found with increasing lipid droplet size. When the initial lipid droplet is smaller, the equilibrium structure of the droplet is a spherical micelle. When the initial lipid droplet is larger, the lipid ball starts to transform into a disk micelle or vesicle. The mechanism of vesicle formation from a lipid ball is analyzed from the self-assembly of DPPC on the molecular level, and the morphological transition from disk to vesicle with increasing droplet size is demonstrated. Importantly, we discover that the transition point is not very sharp, and for a fixed-size lipid ball, the disk and vesicle appear with certain probabilities. The splitting phenomenon, i.e., the formation of a disk/vesicle structure from a lipid droplet, is explained by applying a hybrid model of the Helfrich membrane theory. The elastic module of the DPPC bilayer and the smallest size of a lipid droplet for certain formation of a vesicle are successfully predicted.

Relaxation dynamics of fluid membranes

We study the effect of membrane viscosity in the dynamics of liquid membranes-possibly with free or internal boundaries-driven by conservative forces (curvature elasticity and line tension) and dragged by the bulk dissipation of the ambient fluid and the friction occurring when the amphiphilic molecules move relative to each other. To this end, we formulate a continuum model which includes a form of the governing equations for a two-dimensional viscous fluid moving on a curved, time-evolving surface. The effect of membrane viscosity has received very limited attention in previous continuum studies of the dynamics of fluid membranes, although recent coarse-grained discrete simulations suggest its importance. By applying our model to the study of vesiculation and membrane fusion in a simplified geometry, we conclude that membrane viscosity plays a dominant role in the relaxation dynamics of fluid membranes of sizes comparable to those found in eukaryotic cells, and is not negligible in many large synthetic systems of current interest.

Concise theory of chiral lipid membranes

A theory of chiral lipid membranes is proposed on the basis of a concise free energy density which includes the contributions of the bending and the surface tension of membranes, as well as the chirality and orientational variation of tilting molecules. This theory is consistent with the previous experiments [J.M. Schnur, Science 264, 945 (1994); M.S. Spector, Langmuir 14, 3493 (1998); Y. Zhao,, Proc. Natl. Acad. Sci. USA 102, 7438 (2005)] on self-assembled chiral lipid membranes of DC8,9PC. A torus with the ratio between its two generated radii larger than sqrt[2] is predicted from the Euler-Lagrange equations. It is found that tubules with helically modulated tilting state are not admitted by the Euler-Lagrange equations and that they are less energetically favorable than helical ripples in tubules. The pitch angles of helical ripples are theoretically estimated to be about 0 degrees and 35 degrees, which are close to the most frequent values 5 degrees and 28 degrees observed in the experiment [N. Mahajan, Langmuir 22, 1973 (2006)]. Additionally, the present theory can explain twisted ribbons of achiral cationic amphiphiles interacting with chiral tartrate counterions. The ratio between the width and pitch of twisted ribbons is predicted to be proportional to the relative concentration difference of left- and right-handed enantiomers in the low relative concentration difference region, which is in good agreement with the experiment [R. Oda, Nature (London) 399, 566 (1999)].

Modelling and simulations of multi-component lipid membranes and open membranes via diffuse interface approaches

Diffuse interface (phase field) models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic bending energy and the line tension energy with prescribed volume and surface area constraints. By comparing our numerical simulations with recent biological experiments, it is demonstrated that the diffuse interface models can effectively capture the rich phenomena associated with the multi-component vesicle transformation and thus offering great functionality in their simulation and modelling.

Morphology and phase behavior of two-component lipid membranes

The stability and shapes of domains with different bending rigidities in lipid membranes are investigated. These domains can be formed from the inclusion of an impurity in a lipid membrane or from the phase separation within the membrane. We show that, for weak line tensions, surface tensions and finite spontaneous curvatures, an equilibrium phase of protruding circular domains or striped domains may be obtained. We also predict a possible phase transition between the investigated morphologies.

Theoretical analysis of adhering lipid vesicles with free edges

A theoretical model for describing the adhesion of lipid vesicle with free edges is developed. For adhesion in contact potential or in finite-range potential, the total energy functional is defined as the sum of elastic free energy, the surface energy, the line tension energy and the contact potential or the long-ranged potential. The equilibrium differential equation and boundary conditions for opening-up lipid vesicles are derived through minimizing the total energy functional. Numerical solutions to these equations are obtained under the axial symmetric condition. These numerical solutions can be used to qualitatively explain the influence of the substrate on the open-up lipid vesicles.

General Mathematical Frame for Open or Closed Biomembranes (Part I): Equilibrium Theory and Geometrically Constraint Equation

This paper aims at constructing a general mathematical frame for the equilibrium theory of open or closed biomembranes. Based on the generalized potential functional, the equilibrium differential equation for open biomembrane (with free edge) or closed one (without boundary) is derived. The boundary conditions for open biomembranes are obtained. Besides, the geometrically constraint equation for the existence, formation and disintegration of open or closed biomembranes is revealed. The physical and biological meanings of the equilibrium differential equation and the geometrically constraint equation are discussed. Numerical simulation results for axisymmetric open biomembranes show the effectiveness and convenience of the present theory.

Lipid membranes with free edges

Lipid membrane with freely exposed edge is regarded as smooth surface with curved boundary. Exterior differential forms are introduced to describe the surface and the boundary curve. The total free energy is defined as the sum of Helfrich's free energy and the surface and line tension energy. The equilibrium equation and boundary conditions of the membrane are derived by taking the variation of the total free energy. These equations can also be applied to the membrane with several freely exposed edges. Analytical and numerical solutions to these equations are obtained under the axisymmetric condition. The numerical results can be used to explain recent experimental results obtained by Saitoh et al. [Proc. Natl. Acad. Sci. 95, 1026 (1998)].