Showing papers by "Julia M. Yeomans published in 2019"
TL;DR: A minimal model of cellular monolayers based on cell deformation and force transmission at the cell-cell interface that explains the formation of topological defects and captures the flow-field and stress patterns around them is presented.
Abstract: There is now growing evidence of the emergence and biological functionality of liquid crystal features, including nematic order and topological defects, in cellular tissues. However, how such features that intrinsically rely on particle elongation emerge in monolayers of cells with isotropic shapes is an outstanding question. In this Letter, we present a minimal model of cellular monolayers based on cell deformation and force transmission at the cell-cell interface that explains the formation of topological defects and captures the flow-field and stress patterns around them. By including mechanical properties at the individual cell level, we further show that the instability that drives the formation of topological defects, and leads to active turbulence, emerges from a feedback between shape deformation and active driving. The model allows us to suggest new explanations for experimental observations in tissue mechanics, and to propose designs for future experiments.
126 citations
TL;DR: This work shows that epithelial cells exhibit large-scale coherent oscillations when constrained within micropatterns of varying shapes and sizes and that their period and amplitude are set by the smallest confinement dimension, and demonstrates that force transmission at cell-cell junctions and its coupling to cell polarity are pivotal for the generation of these collective movements.
103 citations
TL;DR: The field of active matter has been a hot topic in recent years as mentioned in this paper, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents.
Abstract: Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of active matter in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines.
90 citations
TL;DR: In this article, the authors show that the intrinsic active length scale loses its relevance under strong lateral confinement, and they experimentally and numerically study an active nematic system in confinement finding a defect-free regime of shear flow, and defect nucleation under certain boundary conditions, highlighting the importance of topological defects in controlling confined active flows.
Abstract: The physics of active liquid crystals is mostly governed by the interplay between elastic forces that align their constituents, and active stresses that destabilize the order with constant nucleation of topological defects and chaotic flows. The average distance between defects, also called active length scale, depends on the competition between these forces. Here, in experiments with the microtubule/kinesin active nematic system, we show that the intrinsic active length scale loses its relevance under strong lateral confinement. Transitions are observed from chaotic to vortex lattices and defect-free unidirectional flows. Defects, which determine the active flow behaviour, are created and annihilated on the channel walls rather than in the bulk, and acquire a strong orientational order in narrow channels. Their nucleation is governed by an instability whose wavelength is effectively screened by the channel width. These results are recovered in simulations, and the comparison highlights the role of boundary conditions. Active nematics refers to systems made of a collection of elongated units, each of which consumes ambient or stored energy in order to move. The authors experimentally and numerically study an active nematic system in confinement finding a defect-free regime of shear flow, and defect nucleation under certain boundary conditions, highlighting the importance of topological defects in controlling confined active flows.
55 citations
TL;DR: In this paper, the authors demonstrate an increase of up to 60% in swimming speed with polymer density and demonstrate that this is due to a non-uniform distribution of polymers in the vicinity of the bacterium, leading to an apparent slip.
Abstract: The locomotion of swimming bacteria in simple Newtonian fluids can successfully be described within the framework of low-Reynolds-number hydrodynamics1. The presence of polymers in biofluids generally increases the viscosity, which is expected to lead to slower swimming for a constant bacterial motor torque. Surprisingly, however, experiments have shown that bacterial speeds can increase in polymeric fluids2–5. Whereas, for example, artificial helical microswimmers in shear-thinning fluids6 or swimming Caenorhabditis elegans worms in wet granular media7,8 increase their speeds substantially, swimming Escherichia coli bacteria in polymeric fluids show just a small increase in speed at low polymer concentrations, followed by a decrease at higher concentrations2,4. The mechanisms behind this behaviour are currently unclear, and therefore we perform extensive coarse-grained simulations of a bacterium swimming in explicitly modelled solutions of macromolecular polymers of different lengths and densities. We observe an increase of up to 60% in swimming speed with polymer density and demonstrate that this is due to a non-uniform distribution of polymers in the vicinity of the bacterium, leading to an apparent slip. However, this in itself cannot predict the large increase in swimming velocity: coupling to the chirality of the bacterial flagellum is also necessary. Bacteria and other helical microswimmers are known to swim faster in non-Newtonian fluids. Coarse-grained simulations suggest the increase may be due to a polymer depletion effect near the body and flagellum, inducing a slip velocity at the surface.
53 citations
TL;DR: In this paper, a generic framework for modeling three-dimensional deformable shells of active matter is presented, which captures the orientational dynamics of the active particles and hydrodynamic interactions on the shell and with the surrounding environment.
Abstract: We present a generic framework for modeling three-dimensional deformable shells of active matter that captures the orientational dynamics of the active particles and hydrodynamic interactions on the shell and with the surrounding environment. We find that the cross talk between the self-induced flows of active particles and dynamic reshaping of the shell can result in conformations that are tunable by varying the form and magnitude of active stresses. We further demonstrate and explain how self-induced topological defects in the active layer can direct the morphodynamics of the shell. These findings are relevant to understanding morphological changes during organ development and the design of bioinspired materials that are capable of self-organization.
46 citations
TL;DR: In this article, experiments, simulations and theories show how active nematics behave in circular and linear confinement, and in the presence of friction, in each case active turbulence can be suppressed resulting in steady or periodic flows.
Abstract: We discuss experiments, simulations and theories showing how active nematics behave in circular and linear confinement, and in the presence of friction. In each case active turbulence can be suppressed resulting in steady or periodic flows. These have the potential to act as power sources, transforming chemical energy to mechanical work, and we review first steps in this direction.
29 citations
TL;DR: A theoretical model for a magnetically-actuated artificial cilium in a fluid environment and investigate its dynamical behaviour, using both analytical calculations and numerical simulations is proposed.
Abstract: We propose a theoretical model for a magnetically-actuated artificial cilium in a fluid environment and investigate its dynamical behaviour, using both analytical calculations and numerical simulations. The cilium consists of a spherical soft magnet, a spherical hard magnet, and an elastic spring that connects the two magnetic components. Under a rotating magnetic field, the cilium exhibits a transition from phase-locking at low frequencies to phase-slipping at higher frequencies. We study the dynamics of the magnetic cilium in the vicinity of a wall by incorporating its hydrodynamic influence, and examine the efficiency of the actuated cilium in pumping viscous fluids. This cilium model can be helpful in a variety of applications such as transport and mixing of viscous solutions at small scales and fabricating microswimmers.
24 citations
TL;DR: In this article, the authors use continuum simulations to investigate the behavior of active fluids in a two-dimensional channel and identify several different stable flow states, provide a phase diagram and show that the key parameters controlling the flow are the ratio of channel width to the length scale of active flow vortices, and whether the system is flow aligning or flow tumbling.
Abstract: Recent experiments on active materials, such as dense bacterial suspensions and microtubule–kinesin motor mixtures, show a promising potential for achieving self-sustained flows. However, to develop active microfluidics it is necessary to understand the behaviour of active systems confined to channels. Therefore here we use continuum simulations to investigate the behaviour of active fluids in a two-dimensional channel. Motivated by the fact that most experimental systems show no ordering in the absence of activity, we concentrate on temperatures where there is no nematic order in the passive system, so that any nematic order is induced by the active flow. We systematically analyze the results, identify several different stable flow states, provide a phase diagram and show that the key parameters controlling the flow are the ratio of channel width to the length scale of active flow vortices, and whether the system is flow aligning or flow tumbling.
23 citations
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TL;DR: In this article, the authors demonstrate that the active length scale that determines the self-organization of this system in unconstrained geometries loses its relevance under strong lateral confinement, and dramatic transitions are observed from chaotic to vortex lattices and defect-free unidirectional flows.
Abstract: Using novel micro-printing techniques, we develop a versatile experimental setup that allows us to study how lateral confinement tames the active flows and defect properties of the microtubule/kinesin active nematic system. We demonstrate that the active length scale that determines the self-organization of this system in unconstrained geometries loses its relevance under strong lateral confinement. Dramatic transitions are observed from chaotic to vortex lattices and defect-free unidirectional flows. Defects, which determine the active flow behavior, are created and annihilated on the channel walls rather than in the bulk, and acquire a strong orientational order in narrow channels. Their nucleation is governed by an instability whose wavelength is effectively screened by the channel width. All these results are recovered in simulations, and the comparison highlights the role of boundary conditions.
23 citations
TL;DR: In this paper, the dynamics of two-dimensional blue phases in active chiral liquid crystals were numerically studied, and it was shown that introducing contractile activity results in stabilised blue phases, while small extensile activity generates ordered but dynamic blue phases characterised by coherently moving half-skyrmions and disclinations.
Abstract: We numerically study the dynamics of two-dimensional blue phases in active chiral liquid crystals. We show that introducing contractile activity results in stabilised blue phases, while small extensile activity generates ordered but dynamic blue phases characterised by coherently moving half-skyrmions and disclinations. Increasing extensile activity above a threshold leads to the dissociation of the half-skyrmions and active turbulence. We further analyse isolated active half-skyrmions in an isotropic background and compare the activity-induced velocity fields in simulations to an analytical prediction of the flow. Finally, we show that confining an active blue phase can give rise to a system-wide circulation, in which half-skyrmions and disclinations rotate together.
TL;DR: The authors tune the dipolar interactions between rotors to obtain different rotational behaviours when actuated by a magnetic field leading to complex collective dynamics.
Abstract: Magnetic actuation is widely used in engineering specific forms of controlled motion in microfluidic applications. A challenge, however, is how to extract different desired responses from different components in the system using the same external magnetic drive. Using experiments, simulations, and theoretical arguments, we present emergent rotational patterns in an array of identical magnetic rotors under an uniform, oscillating magnetic field. By changing the relative strength of the external field strength versus the dipolar interactions between the rotors, different collective modes are selected by the rotors. When the dipole interaction is dominant the rotors swing upwards or downwards in alternating stripes, reflecting the spin-ice symmetry of the static configuration. For larger spacings, when the external field dominates over the dipolar interactions, the rotors undergo full rotations, with different quarters of the array turning in different directions. Our work sheds light on how collective behaviour can be engineered in magnetic systems.
TL;DR: By constructing the full, three-dimensional, orientation distribution, the orientational dynamics of heavy silica microrods flowing through a microfluidic channel are described and the persistence of Jeffery orbits are quantified using temporal correlation functions of the Jeffery constant.
Abstract: We study the orientational dynamics of heavy silica microrods flowing through a microfluidic channel. Comparing experiments and Brownian dynamics simulations we identify different particle orbits, in particular in-plane tumbling behavior, which cannot be explained by classical Jeffery theory, and we relate this behavior to the rotational diffusion of the rods. By constructing the full, three-dimensional, orientation distribution, we describe the rod trajectories and quantify the persistence of Jeffery orbits using temporal correlation functions of the Jeffery constant. We find that our colloidal rods lose memory of their initial configuration in about a second, corresponding to half a Jeffery period.
TL;DR: In this paper, the authors use linear stability analysis to show that an isotropic phase of elongated particles with dipolar flow fields can develop nematic order as a result of their activity, and that ordering is favored if the particles are flow-aligning and is strongest if the wavevector of the order perturbation is neither parallel nor perpendicular to the nematic director.
Abstract: We use linear stability analysis to show that an isotropic phase of elongated particles with dipolar flow fields can develop nematic order as a result of their activity. We argue that ordering is favoured if the particles are flow-aligning and is strongest if the wavevector of the order perturbation is neither parallel nor perpendicular to the nematic director. Numerical solutions of the hydrodynamic equations of motion of an active nematic confirm the results. The instability is contrasted to the well-known hydrodynamic instability of an ordered active nematic.
TL;DR: It is shown through numerical simulations that confinement can serve as a mechanical guidance to achieve distinct modes of collective invasion when combined with growth dynamics and the intrinsic activity of biological materials.
Abstract: Biologically active materials such as bacterial biofilms and eukaryotic cells thrive in confined micro-spaces. Here, we show through numerical simulations that confinement can serve as a mechanical guidance to achieve distinct modes of collective invasion when combined with growth dynamics and the intrinsic activity of biological materials. We assess the dynamics of the growing interface and classify these collective modes of invasion based on the activity of the constituent particles of the growing matter. While at small and moderate activities the active material grows as a coherent unit, we find that blobs of active material collectively detach from the cohort above a well-defined activity threshold. We further characterise the mechanical mechanisms underlying the crossovers between different modes of invasion and quantify their impact on the overall invasion speed.
TL;DR: In this article, the authors performed hydrodynamic multiparticle collision dynamics simulations of spherical and elongated particles driven through polymeric fluids containing different concentrations of polymers and found that polymer-depleted regions close to the particles are responsible for an apparent tangential slip velocity which accounts for the measured flow fields and transport velocities.
Abstract: Understanding the transport of driven nano- and micro-particles in complex fluids is of relevance for many biological and technological applications. Here we perform hydrodynamic multiparticle collision dynamics simulations of spherical and elongated particles driven through polymeric fluids containing different concentrations of polymers. We determine the mean particle velocities which are larger than expected from Stokes law for all particle shapes and polymer densities. Furthermore we measure the fluid flow fields and local polymer density and polymer conformation around the particles. We find that polymer-depleted regions close to the particles are responsible for an apparent tangential slip velocity which accounts for the measured flow fields and transport velocities. A simple two-layer fluid model gives a good match to the simulation results.
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TL;DR: Continuum simulations are used to investigate the behaviour of active fluids in a two-dimensional channel and show that the key parameters controlling the flow are the ratio of channel width to the length scale of active flow vortices, and whether the system is flow aligning or flow tumbling.
Abstract: Recent experiments on active materials, such as dense bacterial suspensions and microtubule-kinesin motor mixtures, show a promising potential for achieving self-sustained flows. However, to develop active microfluidics it is necessary to understand the behaviour of active systems confined to channels. Therefore here we use continuum simulations to investigate the behaviour of active fluids in a two-dimensional channel. Motivated by the fact that most experimental systems show no ordering in the absence of activity, we concentrate on temperatures where there is no nematic order in the passive system, so that any nematic order is induced by the active flow. We systematically analyze the results, identify several different stable flow states, provide a phase diagram and show that the key parameters controlling the flow are the ratio of channel width to the length scale of active flow vortices, and whether the system is flow aligning or flow tumbling.
TL;DR: In this article, the authors show that confinement can serve as a mechanical guidance to achieve distinct modes of collective invasion when combined with growth dynamics and the intrinsic activity of biological materials, and further characterise the mechanical mechanisms underlying the crossovers between different modes of invasion and quantify their impact on the overall invasion speed.
Abstract: Biological active materials such as bacterial biofilms and eukaryotic cells thrive in confined micro-spaces. Here, we show through numerical simulations that confinement can serve as a mechanical guidance to achieve distinct modes of collective invasion when combined with growth dynamics and the intrinsic activity of biological materials. We assess the dynamics of the growing interface and classify these collective modes of invasion based on the activity of the constituent particles of the growing matter. While at small and moderate activities the active material grows as a coherent unit, we find that blobs of active material collectively detach from the cohort above a well-defined activity threshold. We further characterise the mechanical mechanisms underlying the crossovers between different modes of invasion and quantify their impact on the overall invasion speed.
TL;DR: This work performs hydrodynamic multiparticle collision dynamics simulations of spherical and elongated particles driven through polymeric fluids containing different concentrations of polymers to determine the mean particle velocities which are larger than expected from Stokes law for all particle shapes and polymer densities.
Abstract: Understanding the transport of driven nano- and micro-particles in complex fluids is of relevance for many biological and technological applications. Here we perform hydrodynamic multiparticle collision dynamics simulations of spherical and elongated particles driven through polymeric fluids containing different concentrations of polymers. We determine the mean particle velocities which are larger than expected from Stokes law for all particle shapes and polymer densities. Furthermore we measure the fluid flow fields and local polymer density and polymer conformation around the particles. We find that polymer-depleted regions close to the particles are responsible for an apparent tangential slip velocity which accounts for the measured flow fields and transport velocities. A simple two-layer fluid model gives a good match to the simulation results.
TL;DR: In this article, the authors used mesoscale simulations to gain insight into the digestion of biopolymers by studying the break-up dynamics of polymer aggregates bound by physical cross-links.
Abstract: We use mesoscale simulations to gain insight into the digestion of biopolymers by studying the break-up dynamics of polymer aggregates (boluses) bound by physical cross-links. We investigate aggregate evolution, establishing that the linking bead fraction and the interaction energy are the main parameters controlling stability with respect to diffusion. We show $\textit{via}$ a simplified model that chemical breakdown of the constituent molecules causes aggregates that would otherwise be stable to disperse. We further investigate breakdown of biopolymer aggregates in the presence of fluid flow. Shear flow in the absence of chemical breakdown induces three different regimes depending on the flow Weissenberg number ($Wi$). i) At $Wi \ll 1$, shear flow has a negligible effect on the aggregates. ii) At $Wi \sim 1$, the aggregates behave approximately as solid bodies and move and rotate with the flow. iii) At $Wi \gg 1$, the energy input due to shear overcomes the attractive cross-linking interactions and the boluses are broken up. Finally, we study bolus evolution under the combined action of shear flow and chemical breakdown, demonstrating a synergistic effect between the two at high reaction rates.
TL;DR: In this paper, the orientational dynamics of heavy silica microrods flowing through a microfluidic channel were studied and compared with Brownian dynamics simulations, in particular in-plane tumbling behavior, which cannot be explained by classical Jeffery theory.
Abstract: We study the orientational dynamics of heavy silica microrods flowing through a microfluidic channel. Comparing experiments and Brownian dynamics simulations we identify different particle orbits, in particular in-plane tumbling behavior, which cannot be explained by classical Jeffery theory, and we relate this behavior to the rotational diffusion of the rods. By constructing the full, three-dimensional, orientation distribution, we describe the rod trajectories and quantify the persistence of Jeffery orbits using temporal correlation functions of the Jeffery constant. We find that our colloidal rods lose memory of their initial configuration in about a second, corresponding to half a Jeffery period.
TL;DR: In this article, the impact of anisotropic hydrodynamic friction on the emergent flows of active nematics was studied using continuum simulations, and it was shown that the synergistic effects of friction anisotropy and flow tumbling can lead to the emergence of bound pairs of topological defects that align at an angle to the easy flow direction.
Abstract: We use continuum simulations to study the impact of anisotropic hydrodynamic friction on the emergent flows of active nematics. We show that, depending on whether the active particles align with or tumble in their collectively self-induced flows, anisotropic friction can result in markedly different patterns of motion. In a flow-aligning regime and at high anisotropic friction, the otherwise chaotic flows are streamlined into flow lanes with alternating directions, reproducing the experimental laning state that has been obtained by interfacing microtubule-motor protein mixtures with smectic liquid crystals. Within a flow-tumbling regime, however, we find that no such laning state is possible. Instead, the synergistic effects of friction anisotropy and flow tumbling can lead to the emergence of bound pairs of topological defects that align at an angle to the easy flow direction and navigate together throughout the domain. In addition to confirming the mechanism behind the laning states observed in experiments, our findings emphasise the role of the flow aligning parameter in the dynamics of active nematics.