arXiv subjects

Julia M. Yeomans

Publications and source records attributed to Julia M. Yeomans.

At least 73 records · Page 4Linked to original sources

arXiv2017

Biopolymer dynamics driven by helical flagella

Microbial flagellates typically inhabit complex suspensions of polymeric material which can impact the swimming speed of motile microbes, filter-feeding of sessile cells, and the generation of biofilms. There is currently a need to better understand how the fundamental dynamics of polymers near active cells or flagella impacts these various phenomena, in particular the hydrodynamic and steric influence of a rotating helical filament on suspended polymers. Our Stokesian dynamics simulations show that as a stationary rotating helix pumps fluid along its long axis, polymers migrate radially inwards while being elongated. We observe that the actuation of the helix tends to increase the probability of finding polymeric material within its pervaded volume. This accumulation of polymers within the vicinity of the helix is stronger for longer polymers. We further analyse the stochastic work performed by the helix on the polymers and show that this quantity is positive on average and increases with polymer contour length.

cond-mat.soft↗

arXiv2017

Multi-scale statistics of turbulence motorized by active matter

A number of micro-scale biological flows are characterized by spatio-temporal chaos. These include dense suspensions of swimming bacteria, microtubule bundles driven by motor proteins, and dividing and migrating confluent layers of cells. A characteristic common to all of these systems is that they are laden with active matter, which transforms free energy in the fluid into kinetic energy. Because of collective effects, the active matter induces multi-scale flow motions that bear strong visual resemblance to turbulence. In this study, multi-scale statistical tools are employed to analyze direct numerical simulations (DNS) of periodic two- (2D) and three-dimensional (3D) active flows and compare them to classic turbulent flows. Statistical descriptions of the flows and their variations with activity levels are provided in physical and spectral spaces. A scale-dependent intermittency analysis is performed using wavelets. The results demonstrate fundamental differences between active and high-Reynolds number turbulence; for instance, the intermittency is smaller and less energetic in active flows, and the work of the active stress is spectrally exerted near the integral scales and dissipated mostly locally by viscosity, with convection playing a minor role in momentum transport across scales.

physics.flu-dyn↗

arXiv2017

Dancing disclinations in confined active nematics

The spontaneous emergence of collective flows is a generic property of active fluids and often leads to chaotic flow patterns characterised by swirls, jets, and topological disclinations in their orientation field. However, the ability to achieve structured flows and ordered disclinations is of particular importance in the design and control of active systems. By confining an active nematic fluid within a channel, we find a regular motion of disclinations, in conjunction with a well defined and dynamic vortex lattice. As pairs of moving disclinations travel through the channel, they continually exchange partners producing a dynamic ordered state, reminiscent of Ceilidh dancing. We anticipate that this biomimetic ability to self-assemble organised topological disclinations and dynamically structured flow fields in engineered geometries will pave the road towards establishing new active topological microfluidic devices.

cond-mat.soft↗

arXiv2017

A solvable model of axisymmetric and non-axisymmetric droplet bouncing

We introduce a solvable Lagrangian model for droplet bouncing. The model predicts that, for an axisymmetric drop, the contact time decreases to a constant value with increasing Weber number, in qualitative agreement with experiments, because the system is well approximated as a simple harmonic oscillator. We introduce asymmetries in the velocity, initial droplet shape, and contact line drag acting on the droplet and show that asymmetry can often lead to a reduced contact time and lift-off in an elongated shape. The model allows us to explain the mechanisms behind non-axisymmetric bouncing in terms of surface tension forces. Once the drop has an elliptical footprint the surface tension force acting on the longer sides is greater. Therefore the shorter axis retracts faster and, due to the incompressibility constraints, pumps fluid along the more extended droplet axis. This leads to a positive feedback, allowing the drop to jump in an elongated configuration, and more quickly.

physics.flu-dyn↗

arXiv2016

The macroscopic pancake bounce

We demonstrate that the so-called pancake bounce of millimetric water droplets on surfaces patterned with hydrophobic posts [Nat. Phys. 10, 515 (2014)] can be reproduced on larger scales. In our experiment, a bed of nails plays the role of the structured surface and a water balloon models the water droplet. The macroscopic version largely reproduces the features of the microscopic experiment, including the Weber number dependence and the reduced contact time for pancake bouncing. The scalability of the experiment confirms the mechanisms of pancake bouncing, and allows us to measure the force exerted on the surface during the bounce. The experiment is simple and inexpensive and is an example where front-line research is accessible to student projects.

cond-mat.soft↗

arXiv2016

Hydrodynamics of Micro-swimmers in Films

One of the principal mechanisms by which surfaces and interfaces affect microbial life is by perturbing the hydrodynamic flows generated by swimming. By summing a recursive series of image systems we derive a numerically tractable approximation to the three-dimensional flow fields of a Stokeslet (point force) within a viscous film between a parallel no-slip surface and no-shear interface and, from this Green's function, we compute the flows produced by a force- and torque-free micro-swimmer. We also extend the exact solution of Liron & Mochon (1976) to the film geometry, which demonstrates that the image series gives a satisfactory approximation to the swimmer flow fields if the film is sufficiently thick compared to the swimmer size, and we derive the swimmer flows in the thin-film limit. Concentrating on the thick film case, we find that the dipole moment induces a bias towards swimmer accumulation at the no-slip wall rather than the water-air interface, but that higher-order multipole moments can oppose this. Based on the analytic predictions we propose an experimental method to find the multipole coefficient that induces circular swimming trajectories, allowing one to analytically determine the swimmer's three-dimensional position under a microscope.

cond-mat.soft↗

arXiv2016

Onset of meso-scale turbulence in living fluids

Meso-scale turbulence is an innate phenomenon, distinct from inertial turbulence, that spontaneously occurs at zero-Reynolds number in fluidized biological systems. This spatio-temporal disordered flow radically changes nutrient and molecular transport in living fluids and can strongly affect the collective behaviour in prominent biological processes, including biofilm formation, morphogenesis and cancer invasion. Despite its crucial role in such physiological processes, understanding meso-scale turbulence and any relation to classical inertial turbulence remains obscure. Here, we show how the motion of active matter along a micro-channel transitions to meso-scale turbulence through the evolution of disordered patches (active puffs) from an absorbing state of flow vortex-lattices. We demonstrate that the critical behaviour of this transition to meso-scale turbulence in a channel belongs to the directed percolation universality class. This finding bridges our understanding of the onset of zero-Reynolds number meso-scale turbulence and traditional scale-invariant turbulence, therefore generalizing theories on the onset of turbulence in confinement to the distinct classes of incoherent flows observed in biological fluids.

physics.flu-dyn↗

arXiv2016

Active micromachines: Microfluidics powered by mesoscale turbulence

Dense active matter, from bacterial suspensions and microtubule bundles driven by motor proteins to cellular monolayers and synthetic Janus particles, is characterised by mesoscale turbulence, the emergence of chaotic flow structures. By immersing an ordered array of symmetric rotors in an active fluid, we introduce a microfluidic system that exploits spontaneous symmetry breaking in mesoscale turbulence to generate work. The lattice of rotors self-organises into a spin-state where neighbouring discs continuously rotate in permanent alternating directions due to combined hydrodynamic and elastic effects. Our virtual prototype demonstrates a new research direction for the design of micromachines powered by the nematohydrodynamic properties of active turbulence.

cond-mat.soft↗

arXiv2016

Active turbulence in active nematics

Dense, active systems show active turbulence, a state characterised by flow fields that are chaotic, with continually changing velocity jets and swirls. Here we review our current understanding of active turbulence. The development is primarily based on the theory and simulations of active liquid crystals, but with accompanying summaries of related literature.

cond-mat.soft↗

arXiv2016

Stabilization of active matter by flow-vortex lattices and defect ordering

Active systems, from bacterial suspensions to cellular monolayers, are continuously driven out of equilibrium by local injection of energy from their constituent elements and exhibit turbulent-like and chaotic patterns. Here we demonstrate both theoretically and through numerical simulations, that the crossover between wet active systems, whose behaviour is dominated by hydrodynamics, and dry active matter where any flow is screened, can be achieved by using friction as a control parameter. Moreover we discover unexpected vortex ordering at this wet-dry crossover. We show that the self organisation of vortices into lattices is accompanied by the spatial ordering of topological defects leading to active crystal-like structures. The emergence of vortex lattices, which leads to the positional ordering of topological defects, suggests potential applications in the design and control of active materials.

cond-mat.soft↗

arXiv2016

Pore emptying transition during nucleation in hydrophobic nanopores

Using the 2D Ising model we study the generic properties of nucleation in hydrophobic nanopores. To explore the pathways to nucleation of a spin-up phase from a metastable spin-down phase we perform umbrella sampling and transition path sampling simulations. We find that for narrow pores the nucleation occurs on the surface outside the pore. For wide pores the nucleation starts in the pore, and continues outside the filled pore. Intriguingly, we observe a pore emptying transition for a range of intermediate pore widths: a pre-critical nucleus fills the pore, continues to expand outside of the filled pore, but then suddenly gets expelled from the pore before reaching its critical size.

cond-mat.soft↗

arXiv2016

Defect-mediated morphologies in growing cell colonies

Morphological trends in growing colonies of living cells are at the core of physiological and evolutionary processes. Using active gel equations, which include cell division, we show that shape changes during the growth can be regulated by the dynamics of topological defects in the orientation of cells. The friction between the dividing cells and underlying substrate drives anisotropic colony shapes toward more isotropic morphologies, by mediating the number density and velocity of topological defects. We show that the defects interact with the interface at a specific interaction range, set by the vorticity length scale of flows within the colony, and that the cells predominantly reorient parallel to the interface due to division-induced active stresses.

cond-mat.soft↗

arXiv2015

Upstream swimming in microbiological flows

Interactions between microorganisms and their complex flowing environments are essential in many biological systems. We develop a model for microswimmer dynamics in non-Newtonian Poiseuille flows. We predict that swimmers in shear-thickening (-thinning) fluids migrate upstream more (less) quickly than in Newtonian fluids and demonstrate that viscoelastic normal stress differences reorient swimmers causing them to migrate upstream at the centreline, in contrast to well-known boundary accumulation in quiescent Newtonian fluids. Based on these observations, we suggest a sorting mechanism to select microbes by swimming speed.

cond-mat.soft↗

arXiv2015

Thermal analogue of gimbal lock in a colloidal ferromagnetic Janus rod

We report an entropy-driven orientational hopping transition in a magnetically confined colloidal Janus rod. In a magnetic field, the sedimented rod randomly hops between horizontal and vertical states: the latter state comes at a substantial gravitational cost at no reduction of magnetic potential energy. The probability distribution over the angles of the rod shows that the presence of an external magnetic field leads to the emergence of a metastable vertical state separated from the ground state by an effective barrier. This barrier does not come from the potential energy but rather from the vast gain in phase space available to the rod as it approaches the vertical state. The loss of rotational degree of freedom that gives rise to this effect is a statistical mechanical analogue of the phenomenon of gimbal lock from classical mechanics.

cond-mat.soft↗

arXiv2015

Intrinsic Free Energy in Active Nematics

Basing our arguments on the theory of active liquid crystals, we demonstrate both analytically and numerically, that the activity can induce an effective free energy which enhances ordering in extensile systems of active rods and in contractile suspensions of active discs. We argue that this occurs because any ordering fluctuation is enhanced by the flow field it produces. A phase-diagram in the temperature-activity plane compares ordering due to a thermodynamic free energy to that resulting from the activity. We also demonstrate that activity can drive variations in concentration, but for a different physical reason that relies on the separation of hydrodynamic and diffusive timescales.

cond-mat.soft↗

arXiv2015

Cell division: a source of active stress in cellular monolayers

We introduce the notion of cell division-induced activity and show that the cell division generates extensile forces and drives dynamical patterns in cell assemblies. Extending the hydrodynamic models of lyotropic active nematics we describe turbulent-like velocity fields that are generated by the cell division in a confluent monolayer of cells. We show that the experimentally measured flow field of dividing Madin-Darby Canine Kidney (MDCK) cells is reproduced by our modeling approach. Division-induced activity acts together with intrinsic activity of the cells in extensile and contractile cell assemblies to change the flow and director patterns and the density of topological defects. Finally we model the evolution of the boundary of a cellular colony and compare the fingering instabilities induced by cell division to experimental observations on the expansion of MDCK cell cultures.

cond-mat.soft↗

arXiv2015

Driven active and passive nematics

We investigate similarities in the micro-structural dynamics between externally driven and actively driven nematics. Walls, lines of strong deformations in the director field, and topological defects are characteristic features of an active nematic. Similar structures form in driven passive nematics when there are inhomogeneities in imposed velocity gradients due to non-linear flow fields or geometrical constraints. Specifically, pressure driven flow of a tumbling passive nematic in an expanding-contracting channel produces walls and defects similar to those seen in active nematics. We also study the response of active nematics to external driving, confirming that imposed shear suppresses the hydrodynamic instabilities. We show that shear fields can lead to wall alignments and the localisation of active turbulence.

cond-mat.soft↗

arXiv2015

Multi-Particle Collision Dynamics Algorithm for Nematic Fluids

Research on transport, self-assembly and defect dynamics within confined, flowing liquid crystals requires versatile and computationally efficient mesoscopic algorithms to account for fluctuating nematohydrodynamic interactions. We present a multi-particle collision dynamics (MPCD) based algorithm to simulate liquid-crystal hydrodynamic and director fields in two and three dimensions. The nematic-MPCD method is shown to successfully reproduce the features of a nematic liquid crystal, including a nematic-isotropic phase transition with hysteresis in 3D, defect dynamics, isotropic Frank elastic coefficients, tumbling and shear alignment regimes and boundary condition dependent order parameter fields.

cond-mat.soft↗