To mimic the mechanical response of passive biological cilia in complex fluids, we study the bending dynamics of an anchored elastic fiber submitted to a dilute granular suspension under shear. We show that the bending fluctuations of the fiber accurately encode minute variations of the granular suspension concentration. Indeed, besides the stationary bending induced by the continuous phase flow, the passage of each single particle induces an additional deflection. We demonstrate that the dominant particle/fiber interaction arises from direct contacts of the particles with the fiber and we propose a simple elastohydrodynamics model to predict their amplitude. Our results shed light on the extreme mechanical sensitivity of biological cilia to detect the presence of solid particles in their vicinity and bring a physical framework to describe their dynamics in particulate flows.
Long-scale dynamic fluctuation phenomena in freely suspended films is analyzed. We consider isotropic films that, say, can be pulled from bulk smectic A liquid crystals. The key feature of such objects is possibility of bending deformations of the film. The bending (also known as flexular) mode turns out to be anomalously weakly attenuated. In the harmonic approximation there is no viscous-like damping of the bending mode, proportional to q^2 (q is the wave vector of the mode), since it is forbidden by the rotational symmetry. Therefore the bending mode is strongly affected by non-linear dynam…
In this Letter, we consider a neutral system of mobile positive and negative charges confined on the surface of curved films. This may be an appropriate model for: i) a highly charged membrane whose counterions are confined to a sheath near its surface; ii) a membrane composed of an equimolar mixture of anionic and cationic surfactants in aqueous solution. We find that the charge fluctuations contribute a non-analytic term to the bending rigidity that varies logarithmically with the radius of curvature. This may lead to spontaneous vesicle formation, which is indeed observed in similar systems…
A widely used method to measure the bending rigidity of bilayer membranes is fluctuation spectroscopy, which analyses the thermally-driven membrane undulations of giant unilamellar vesicles recorded with either phase-contrast or confocal microscopy. Here, we analyze the fluctuations of the same vesicle using both techniques and obtain consistent values for the bending modulus. We discuss the factors that may lead to discrepancies.
We study the effects of thermal fluctuations on symmetric tensionless heterogeneous (two-component) fluid membranes in a simple minimal model. Close to the critical point $T_c$ of the associated miscibility phase transition of the composition and for sufficiently strong curvature-composition interactions, mediated through a composition-dependent bending modulus, thermal fluctuations lead to enhancement of the effective bending modulus. Thus, the membrane conformation fluctuations will be {\em suppressed} near $T_c$, in comparison with a pure fluid membrane, for which thermal fluctuations are k…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory focuses on two competing effects: polymer shape fluctuations, which speed up association, and the hydrodynamic coupling between the diffusing particle and the chain, which slows down association. Polymer bending fluctuations are described using a mean field dynamical theory, while the hydrodynamic coupling between polymer and particle is incorporated through a si…
We investigate the effect of an applied electric potential on the mechanics of a coarse grained POPC bilayer under tension. The size and duration of our simulations allow for a detailed and accurate study of the fluctuations. Effects on the fluctuation spectrum, tension, bending rigidity, and bilayer thickness are investigated in detail. In particular, the least square fitting technique is used to calculate the fluctuation spectra. The simulations confirm a recently proposed theory that the effect of an applied electric potential on the membrane will be moderated by the elastic properties of t…
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the fraction of denaturation bubbles and their correlation length is deduced. The thermal denaturation transition emerges naturally when the chain fluctuations are integrated out and is driven by the difference in bending (entropy dominated) free energy between broken and unbroken segments. Conformational properties of DNA, such as persistence length and mean-s…
We amplify previous arguments why mean curvature should be used as measure of integration in calculating the effective bending rigidity of fluid membranes subjected to a weak background curvature. The stiffening of the membrane by its fluctuations, recently derived for spherical shapes, is recovered for cylindrical curvature. Employing curvilinear coordinates, we then discuss stiffening for arbitrary shapes, confirm that the elastic modulus of Gaussian curvature is not renormalized in the presence of fluctuations, and show for the first time that any spontaneous curvature also remains unchange…
We show that to account for the full spectrum of surface fluctuations from low scattering vector qd << 1 (classical capillary wave theory) to high qd > 1 (bulk-like fluctuations), one must take account of the interface's bending rigidity at intermediate scattering vector qd = 1, where d is the molecular diameter. A molecular model is presented to describe the bending correction to the capillary wave model for short-ranged and long-ranged interactions between molecules. We find that the bending rigidity is negative when the Gibbs equimolar surface is used to define the location of the fluctuati…
Biological activity gives rise to non-equilibrium fluctuations in the cytoplasm of cells; however, there are few methods to directly measure these fluctuations. Using a reconstituted actin cytoskeleton, we show that the bending dynamics of embedded microtubules can be used to probe local stress fluctuations. We add myosin motors that drive the network out of equilibrium, resulting in an increased amplitude and modified time-dependence of microtubule bending fluctuations. We show that this behavior results from step-like forces on the order of 10 pN driven by collective motor dynamics.
The cytoskeleton is an inhomogeneous network of semi-flexible filaments, which are involved in a wide variety of active biological processes. Although the cytoskeletal filaments can be very stiff and embedded in a dense and cross-linked network, it has been shown that, in cells, they typically exhibit significant bending on all length scales. In this work we propose a model of a semi-flexible filament deformed by different types of cross-linkers for which one can compute and investigate the bending spectrum. Our model allows to couple the evolution of the deformation of the semi-flexible polym…
Theoretical studies of nearly spherical vesicles and microemulsion droplets, that present typical examples for thermally-excited systems that are subject to constraints, are reviewed. We consider the shape fluctuations of such systems constrained by fixed area $A$ and fixed volume $V$, whose geometry is presented in terms of scalar spherical harmonics. These constraints can be incorporated in the theory in different ways. After an introductory review of the two approaches: with an exactly fixed by delta-function membrane area $A$ [Seifert, Z. Phys. B, 97, 299, (1995)] or approximatively by mea…
The elastic properties of two-component bilayer membranes are studied using a coarse grain model for amphiphilic molecules. The two species of amphiphiles considered here differ only in their length. Molecular Dynamics simulations are performed in order to analyze the shape fluctuations of the two-component bilayer membranes and to determine their bending rigidity. Both the bending rigidity and its inverse are found to be nonmonotonic functions of the mole fraction $x_{\rm B}$ of the shorter B-amphiphiles and, thus, do not satisfy a simple lever rule. The intrinsic area of the bilayer also exh…
To describe the full spectrum of surface fluctuations of the interface between phase-separated colloid-polymer mixtures from low scattering vector q (classical capillary wave theory) to high q (bulk-like fluctuations), one must take account of the interface's bending rigidity. We find that the bending rigidity is negative and that on approach to the critical point it vanishes proportionally to the interfacial tension. Both features are in agreement with Monte Carlo simulations.
Two-dimensional crystalline membranes have recently been realized experimentally in such systems as graphene and molybdenum disulfide, sparking a resurgence in interest in their statistical properties. Thermal fluctuations can significantly affect the effective mechanical properties of properly thermalized membranes, renormalizing both bending rigidity and elastic moduli so that in particular they become stiffer to bending than their bare bending rigidity would suggest. We use molecular dynamics simulations to examine how the mechanical behavior of thermalized two-dimensional clamped ribbons (…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces is obtained by computing the average bending angles between adjacent base pairs along the molecule axis. The ensemble averages are performed over a room temperature equilibrium distribution of base pair separations and bending fluctuations. The analysis of the end-to-end distances and persistence lengths shows that even short sequences with less than $100$ b…
We study the quasi-static penetration of a flexible beam in a two-dimensional dense granular medium lying on an horizontal plate. Rather than a buckling-like behavior we observe a transition between a regime of crack-like penetration in which the fiber only shows small fluctuations around a stable straight geometry and a bending regime in which the fiber fully bends and advances through series of loading/unloading steps. We show that the shape reconfiguration of the fiber is controlled by a single non dimensional parameter: L/Lc, the ratio of the length of the flexible beam L to Lc, a bending …
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and twist persistence lengths, and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a worm-like chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA an…
A self-consistent theory is proposed for the general problem of interacting undulating fluid membranes subject to the constraint that they do not interpenetrate. We implement the steric constraint via an exact functional integral representation, and through the use of a saddle-point approximation transform it into a novel effective steric potential. The steric potential is found to consist of two contributions: one generated by zero mode fluctuations of the membranes, and the other by thermal bending fluctuations. For membranes of cross-sectional area $S$, we find that the bending fluctuation …
An elastic surface model is investigated by using the canonical Monte Carlo simulation technique on triangulated spherical meshes. The model undergoes a first-order collapsing transition and a continuous surface fluctuation transition. The shape of surfaces is maintained by a one-dimensional bending energy, which is defined on the mesh, and no two-dimensional bending energy is included in the Hamiltonian.
The rigidity of elastic networks depends sensitively on their internal connectivity and the nature of the interactions between constituents. Particles interacting via central forces undergo a zero-temperature rigidity-percolation transition near the isostatic threshold, where the constraints and internal degrees of freedom are equal in number. Fibrous networks, such as those that form the cellular cytoskeleton, become rigid at a lower threshold due to additional bending constraints. However, the degree to which bending governs network mechanics remains a subject of considerable debate. We stud…
It has been known for long that the fluctuation surface tension of membranes $r$, computed from the height fluctuation spectrum, is not equal to the bare surface tension $σ$ introduced in the Helfrich theory. In this work we relate these two surface tensions both analytically and numerically and compare them to the Laplace tension $γ$, and the mechanical frame tension $τ$. Using one-loop renormalisation calculations, we obtain, in addition to the effective bending modulus $κ_{\rm eff}$, a new expression for the effective surface tension $σ_{\rm eff}=σ- εk_{\rm B}T/(2a_p)$ where $a_p$ the proje…
The eukaryotic flagellum beats periodically, driven by the oscillatory dynamics of molecular motors, to propel cells and pump fluids. Small, but perceivable fluctuations in the beat of individual flagella have physiological implications for synchronization in collections of flagella as well as for hydrodynamic interactions between flagellated swimmers. Here, we characterize phase and amplitude fluctuations of flagellar bending waves using shape mode analysis and limit cycle reconstruction. We report a quality factor of flagellar oscillations, $Q=38.0\pm 16.7$ (mean$\pm$s.e.). Our analysis show…
Using x-ray photon correlation spectroscopy, we studied the layer fluctuations in the lamellar phase of an ionic lyotropic system. We measured the relaxation rate of in-plane (undulation) fluctuations as a function of the wave vector. Static and dynamic results obtained during the same experiment were combined to yield the values of both elastic constants of the lamellar phase (compression and bending moduli) as well as that of the sliding viscosity. The results are in very good agreement with dynamic light-scattering data, validating the use of the technique in ordered phases.
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a double stranded DNA oligomer (shorter than its thermal persistence length) whose free ends are linked by a single standed DNA chain. This construct, studied by Qu et al. [Europhys. Lett., $\bf{94}$, 18003, 2011], displays nonlinear strain softening associated with the local melting of the double stranded DNA under applied torque and serves as a model system with…
In this theoretical and numerical study, we show how spatially extended fluctuations can influence and dominate the dynamics of a fluid filled elastic blister as is deforms onto a pre-wetted solid substrate. To describe the blister dynamics, we develop a stochastic elastohydrodynamic framework that couples the viscous flow, the elastic bending of the interface and the noise from the environment. We deploy a scaling analysis to find the elastohydrodynamic spreading law $\hat R\sim {\hat t}^{1/11}$ a direct analogue to the capillary spreading of drops, while the inclusion of noise in our model h…
We study the dynamics of a single semiflexible filament coupled to a Hookean spring at its boundary. The spring produces a fluctuating tensile force on the filament, whose value depends on the filament's instantaneous end-to-end length. The spring thereby introduces a nonlinearity, which mixes the undulatory normal modes of the filament and changes their dynamics. We study these dynamics using the Martin-Siggia-Rose-Janssen-de-Domincis formalism, and compute the time-dependent correlation functions of transverse undulations and of the filament's end-to-end distance. The relaxational dynamics o…
We perform Brownian dynamics simulations of semiflexible colloidal sheets with hydrodynamic interactions and thermal fluctuations in shear flow. As a function of the ratio of bending rigidity to shear energy (a dimensionless quantity we denote $S$) and the ratio of bending rigidity to thermal energy, we observe a dynamical transition from stochastic flipping to crumpling and continuous tumbling. This dynamical transition is broadened by thermal fluctuations, and the value of $S$ at which it occurs is consistent with the onset of chaotic dynamics found for athermal sheets. The effects of differ…
We investigate thermal fluctuations in a smectic A phase of an amphiphile-solvent mixture with molecular dynamics simulations. We use an idealized model system, where solvent particles are represented by simple beads, and amphiphiles by bead-and-spring tetramers. At a solvent bead fraction of 20 % and sufficiently low temperature, the amphiphiles self-assemble into a highly oriented lamellar phase. Our study aims at comparing the structure of this phase with the predictions of the elastic theory of thermally fluctuating fluid membrane stacks [Lei et al., J. Phys. II 5, 1155 (1995)]. We suggest…
The mechanical properties of biological membranes play an important role in the structure and the functioning of living organisms. One of the most widely used methods for determination of the bending elasticity modulus of the model lipid membranes (simplified models of the biomembranes with similar mechanical properties) is analysis of the shape fluctuations of the nearly spherical lipid vesicles. A theoretical basis of such an analysis is developed by Milner and Safran. In the present studies we analyze their results using an approach based on the Bogoljubov inequalities and the approximating…
Normal thermal fluctuations of the cell membrane have been studied extensively using high resolution microscopy and focused light, particularly at the peripheral regions of a cell. We use a single probe particle attached non-specifically to the cell-membrane to determine that the power spectral density is proportional to (frequency)^(-1.66) in the range of 5 Hz to 1 kHz. We also use a new technique to simultaneously ascertain the slope fluctuations of the membrane by relying upon the determination of pitch motion of the birefringent probe particle trapped in linearly polarized optical tweezers…
We study the motion of a solid particle immersed in a Newtonian fluid and confined between two parallel elastic membranes possessing shear and bending rigidity. The hydrodynamic mobility depends on the frequency of the particle motion due to the elastic energy stored in the membrane. Unlike the single-membrane case, a coupling between shearing and bending exists. The commonly used approximation of superposing two single-membrane contributions is found to give reasonable results only for motions in the parallel, but not in the perpendicular direction. We also compute analytically the membrane d…
Myosin motor proteins drive vigorous steady-state fluctuations in the actin cytoskeleton of cells. Endogenous embedded semiflexible filaments such as microtubules, or added filaments such as single-walled carbon nanotubes are used as novel tools to non-invasively track equilibrium and non-equilibrium fluctuations in such biopolymer networks. Here we analytically calculate shape fluctuations of semiflexible probe filaments in a viscoelastic environment, driven out of equilibrium by motor activity. Transverse bending fluctuations of the probe filaments can be decomposed into dynamic normal modes…
The macroscopic properties, the properties of individual components and how those components interact with each other are three important aspects of a composited structure. An understanding of the interplay between them is essential in the study of complex systems. Using axonal cytoskeleton as an example system, here we perform a theoretical study of slender structures that can be coarse-grained as a simple smooth 3-dimensional curve. We first present a generic model for such systems based on the fundamental theorem of curves. We use this generic model to demonstrate the applicability of the w…
