Buckling transition of a semiflexible filament in extensional flow

Scaling law for a buckled elastic filament in a shear flow

We analyze the three-dimensional (3D) buckling of an elastic filament in a shear flow of a viscous fluid at low Reynolds number and high Péclet number. We apply the Euler-Bernoulli beam (elastica) theoretical model. We show the universal character of the full 3D spectral problem for a small perturbation of a thin filament from a straight position of arbitrary orientation. We use the eigenvalues and eigenfunctions for the linearized elastica equation in the shear plane, found earlier by Liu et al. [Phys. Rev. Fluids 9, 014101 (2024)2469-990X10.1103/PhysRevFluids.9.014101] with the Chebyshev spectral collocation method, to solve the full 3D eigenproblem. We provide a simple analytic approximation of the eigenfunctions, represented as Gaussian wave packets. As the main result of the paper, we derive the square-root dependence of the eigenfunction wave number on the parameter χ[over ̃]=-ηsin2ϕsin^{2}θ, where η is the elastoviscous number and the filament orientation is determined by the zenith angle θ with respect to the vorticity direction and the azimuthal angle ϕ relative to the flow direction. We also compare the eigenfunctions with shapes of slightly buckled elastic filaments with a non-negligible thickness with the same Young's modulus, using the bead model and performing numerical simulations with the precise hydromultipole numerical codes.

Cross-streamline migration and near-wall depletion of elastic fibers in micro-channel flows

The complex dynamics of elastic fibers in viscous fluids are central to many biological and industrial systems. Fluid-structure interactions underlying these dynamics govern the shape and transport of flexible fibers, and understanding these interactions can help tune flow properties in applications such as microfluidic separation, printing and clogging. In this work, we use slender-body theory to study micromechanical dynamics that arise from the coupling between the elastic backbone of a fiber and the local straining flow that contributes to filament flipping and cross-streamline migration. The resulting transverse drift is unbiased in either direction in simple shear flow. However, a non-uniform shear rate results in bias towards regions of high shear, which we connect to the shape transitions during flips. We discover a depletion layer that forms near the boundaries of pressure-driven channel flow due to the competition between such a cross-streamline drift and steric exclusion from the walls. Finally, we develop scaling laws for the curvature of filaments during flip events, demonstrating the origin of the drift bias in non-uniform flows, and confirm this behavior from our simulations. Put together, these results shed light on the role of a local and dominant coupling between elasticity and viscous resistance in dictating long-term dynamics and transport of elastic fibers in confined flows.

Self-buckling and self-writhing of semi-flexible microorganisms

The twisting and writhing of a cell body and associated mechanical stresses is an underappreciated constraint on microbial self-propulsion. Multi-flagellated bacteria can even buckle and writhe under their own activity as they swim through a viscous fluid. New equilibrium configurations and steady-state dynamics then emerge which depend on the organism's mechanical properties and on the oriented distribution of flagella along its surface. Modeling the cell body as a semi-flexible Kirchhoff rod and coupling the mechanics to a flagellar orientation field, we derive the Euler-Poincaré equations governing the dynamics of the system, and rationalize experimental observations of buckling and writhing of elongated swarmer cells of the bacterium Proteus mirabilis. A sequence of bifurcations is identified as the body is made more compliant, due to both buckling and torsional instabilities. These studies highlight a practical requirement for the stiffness of bacteria below which self-buckling occurs and cell motility becomes ineffective.

Coiling of semiflexible paramagnetic colloidal chains

Semiflexible filaments deform into a variety of configurations that dictate different phenomena manifesting at low Reynolds number. Harnessing the elasticity of these filaments to perform transport-related processes at the microfluidic scale requires structures that can be directly manipulated to attain controllable geometric features during their deformation. The configuration of semiflexible chains assembled from paramagnetic colloids can be readily controlled upon the application of external time-varying magnetic fields. In circularly rotating magnetic fields, these chains undergo coiling dynamics in which their ends close into loops that wrap inward, analogous to the curling of long nylon filaments under shear. The coiling is promising for the precise loading and targeted transport of small materials, however effective implementation requires an understanding of the role that field parameters and chain properties play on the coiling features. Here, we investigate the formation of coils in semiflexible paramagnetic chains using numerical simulations. We demonstrate that the size and shape of the initial coils are governed by the Mason and elastoviscous numbers, related to the field parameters and the chain bending stiffness. The size of the initial coil follows a nonmonotonic behavior with Mason number from which two regions are identified: (1) an elasticity-dependent nonlinear regime in which the coil size decreases with increasing field strength and for which loop shape tends to be circular, and (2) an elasticity-independent linear regime where the size increases with field strength and the shape become more elliptical. From the time scales associated to these regimes, we identify distinct coiling mechanisms for each case that relate the coiling dynamics to two other configurational dynamics of paramagnetic chains: wagging and folding behaviors.

Dynamics of flexible filaments in oscillatory shear flows

The fluid-structure interactions between flexible fibers and viscous flows play an essential role in various biological phenomena, medical problems, and industrial processes. Of particular interest is the case of particles freely transported in time-dependent flows. This work elucidates the dynamics and morphologies of actin filaments under oscillatory shear flows by combining microfluidic experiments, numerical simulations, and theoretical modeling. Our work reveals that, in contrast to steady shear flows, in which small orientational fluctuations from a flow-aligned state initiate tumbling and deformations, the periodic flow reversal allows the filament to explore many different configurations at the beginning of each cycle. Investigation of filament motion during half time periods of oscillation highlights the critical role of the initial filament orientation on the emergent dynamics. This strong coupling between orientation and deformation results in new deformation regimes and novel higher-order buckling modes absent in steady shear flows. The primary outcome of our analysis is the possibility of suppression of buckling instabilities for certain combinations of the oscillation frequency and initial filament orientation, even in very strong flows. We explain this unusual behavior through a weakly nonlinear Landau theory of buckling, in which we treat the filaments as inextensible Brownian Euler-Bernoulli rods whose hydrodynamics are described by local slender-body theory.

Proteinaceous microstructure in a capillary: a study of non-linear bending dynamics

The flap of bendable structures under continuous flow impacts a variety of fields, ranging from energy harvesting to active mixing in microfluidic devices. Similar physical principles determine the flapping dynamics in a variety of systems with different sizes, but a thorough investigation of the bending dynamics at the microscale is still lacking. We employ here two-photon laser polymerization to fabricate elongated proteinaceous flexible microstructures directly within a micro-capillary and we characterize their bending dynamics. The elastic properties of the microstructures with different (circular and square) cross-sections are tested by Atomic Force Microscopy and by studying the deflection-flow dependence in microfluidic experiments at intermediate Reynolds numbers (Re_y ≲ 150). The retrieved Young's modulus of the fabricated matrix (100 kPa ≤ E ≤ 4 MPa) falls in the range of most typical biological tissues and solely depends on the laser fabrication intensity. The elastic constant of the microstructures falls in the range of 0.8 nN μm^-1 ≤ k ≤ 50 nN μm^-1, and fully agrees with the macroscopic Euler Bernoulli theory. For soft microstructures (0.8 nN μm^-1 ≤ k ≤ 8 nN μm^-1) we reveal undamped bending oscillations under continuous microfluidic flow, corresponding to ∼10% of the total structure deflection. This behavior is ascribed to the coupling of the viscoelasticity and non-linear elasticity of the polymer matrix with non-linear dynamics arising from the time-dependent friction coefficient of the bendable microstructures. We envision that similar instabilities may lead to the development of promising energy conversion nanoplatforms.

Compression-induced buckling of a semiflexible filament in two and three dimensions

The ability of biomolecules to exert forces on their surroundings or resist compression from the environment is essential in a variety of biologically relevant contexts. For filaments in the low-temperature limit and under a constant compressive force, Euler buckling theory predicts a sudden transition from a compressed to a bent state in these slender rods. In this paper, we use a mean-field theory to show that if a semiflexible chain is compressed at a finite temperature with a fixed end-to-end distance (permitting fluctuations in the compressive forces), it exhibits a continuous phase transition to a buckled state at a critical level of compression. We determine a quantitatively accurate prediction of the transverse position distribution function of the midpoint of the chain that indicates this transition. We find the mean compressive forces are non-monotonic as the extension of the filament varies, consistent with the observation that strongly buckled filaments are less able to bear an external load. We also find that for the fixed extension (isometric) ensemble, the buckling transition does not coincide with the local minimum of the mean force (in contrast to Euler buckling). We also show the theory is highly sensitive to fluctuations in length in two dimensions, and that the buckling transition can still be accurately recovered by accounting for those fluctuations. These predictions may be useful in understanding the behavior of filamentous biomolecules compressed by fluctuating forces, relevant in a variety of biological contexts.

Fiber Buckling in Confined Viscous Flows: An Absolute Instability Described by the Linear Ginzburg-Landau Equation

We explore the dynamics of a flexible fiber transported by a viscous flow in a Hele-Shaw cell of height comparable to the fiber height. We show that long fibers aligned with the flow experience a buckling instability. Competition between viscous and elastic forces leads to the deformation of the fiber into a wavy shape convolved by a Bell-shaped envelope. We characterize the wavelength and phase velocity of the deformation as well as the growth and spreading of the envelope. Our study of the spatiotemporal evolution of the deformation reveals a linear and absolute instability arising from a local mechanism well described by the Ginzburg-Landau equation.

Thermally fluctuating, semiflexible sheets in simple shear flow

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 different dynamical conformations on rheological properties such as viscosity and normal stress differences are also quantified. Namely, the viscosity in a dilute dispersion of sheets is found to decrease with increasing shear rate (shear-thinning) up until the dynamical crumpling transition, at which point it increases again (shear-thickening), and non-zero first normal stress differences are found that exhibit a local maximum with respect to temperature at large S (small shear rate). These results shed light on the dynamical behavior of fluctuating 2D materials dispersed in fluids and should greatly inform the design of associated solution processing methods.

Generation of buckling and wrinkling in elastic films: The effect of initial imperfection

The symmetry breaking that is induced by initial imperfection (e.g., geometry or material inhomogeneity and out-of-plane disturbance) is a necessary condition for film buckling. However, the effect of initial imperfection on the buckling behavior is still not clear cut. Herein, given an elastic substrate-free circular film subjected to in-plane compressive stress and arbitrary initial imperfection, evolution of the deflection morphology is numerically studied and theoretically analyzed. Specifically, a two-dimensional spatial spectrum analysis is adopted to acquire the deflection morphology's dominant wavelength, which is combined with the maximum absolute deflection to characterize the deflection patterns. Before the so-called critical instability, the film under compression is found to go through a transition stage. Overall, the deflection increment in this stage is negligible except approaching the critical state. However, the dominant wavelength is found to be continuously growing (or decreasing) rather than suddenly appears upon reaching the so-called critical state, and, interestingly, such growth is found to be independent of the intensity and pattern of the initial imperfection if the same initial dominant wavelength is guaranteed. In the discussion, for both the transition and buckling stages, evolution laws of the deflection amplitude and wavelength are established analytically and found to agree well with the numerical results. This research clearly presents the actual evolution process of wrinkling morphology from linear in-plane deformation with small stable deflection to out-of-plane instability with large deflection, which deepens the cognition of instability behavior of films and provides a basis for related applications such as high-precision mechanical characterization.

Trapping, gliding, vaulting: transport of semiflexible polymers in periodic post arrays

The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the dynamics of semiflexible polymers under the influence of an imposed flow in a structured two-dimensional lattice serving as an idealization of a porous medium. This problem has received much attention in the limit of reptation and for long-chain polymer molecules such as DNA that are transported through micropost arrays for electrophoretic chromatographic separation. In contrast to long entropic molecules, the dynamics of elastic polymers results from a combination of scattering with the obstacles and flow-induced buckling instabilities. We identify three dominant modes of transport that involve trapping, gliding and vaulting of the polymers around the obstacles, and we reveal their essential features using tools from dynamical systems theory. The interplay of these scattering dynamics with transport and deformations in the imposed flow results in the long-time asymptotic dispersion of the center of mass, which we quantify in terms of a hydrodynamic dispersion tensor. We then discuss a simple yet efficient chromatographic device that exploits the competition between different modes of transport to sort filaments in a dilute suspension according to their lengths.

Morphological transitions of elastic filaments in shear flow

The morphological dynamics, instabilities, and transitions of elastic filaments in viscous flows underlie a wealth of biophysical processes from flagellar propulsion to intracellular streaming and are also key to deciphering the rheological behavior of many complex fluids and soft materials. Here, we combine experiments and computational modeling to elucidate the dynamical regimes and morphological transitions of elastic Brownian filaments in a simple shear flow. Actin filaments are used as an experimental model system and their conformations are investigated through fluorescence microscopy in microfluidic channels. Simulations matching the experimental conditions are also performed using inextensible Euler-Bernoulli beam theory and nonlocal slender-body hydrodynamics in the presence of thermal fluctuations and agree quantitatively with observations. We demonstrate that filament dynamics in this system are primarily governed by a dimensionless elasto-viscous number comparing viscous drag forces to elastic bending forces, with thermal fluctuations playing only a secondary role. While short and rigid filaments perform quasi-periodic tumbling motions, a buckling instability arises above a critical flow strength. A second transition to strongly deformed shapes occurs at a yet larger value of the elasto-viscous number and is characterized by the appearance of localized high-curvature bends that propagate along the filaments in apparent "snaking" motions. A theoretical model for the as yet unexplored onset of snaking accurately predicts the transition and explains the observed dynamics. We present a complete characterization of filament morphologies and transitions as a function of elasto-viscous number and scaled persistence length and demonstrate excellent agreement between theory, experiments, and simulations.

Unfolding Kinetics of a Wormlike Chain under Elongational Flow

A simple theory of the unfolding kinetics of a semi-flexible polymer chain is presented in terms of a Kramers type picture for the energy of elongation. The hydrodynamic interactions are discussed in terms of slender body theory. It turns out that the elongation of the chain is basically linear in time and independent of the viscosity. The former prediction agrees with experiments on the stretching dynamics of DNA under planar elongational flow. Nevertheless, the theory overestimates the experimental rate by a significant amount for reasons that are unclear.

A dissipative particle dynamics study of a flexible filament in confined shear flow

In this paper, we investigate the dynamics of a tethered flexible filament due to fluid flow inside a microchannel. We use the finite sized dissipative particle dynamics (FDPD) approach to model this problem. The flexible filament is modeled as a bead-spring system with both extensional and flexural rigidity. The influence of flow rate and bending stiffness on the filament dynamics is studied in terms of the different conformational modes obtained. The competing effects of the hydrodynamic force and elastic force in the presence of Brownian thermal effects of comparable order influence the mode shapes of the filament. The dynamics of the filament motions are further analyzed using proper orthogonal decomposition. An important consequence of the dynamics of the filament is that it causes cross-flow in the micro-channel, which could potentially be exploited in micro-mixing and pumping applications. The cross stream fluid transport is observed to be more pronounced for higher bending stiffness.