arXiv subjects

Tyler N. Shendruk

Publications and source records attributed to Tyler N. Shendruk.

At least 37 records · Page 2Linked to original sources

arXiv2022

Helical Flow States in Active Nematics

We show that confining extensile nematics in 3D channels leads to the emergence of two self-organized flow states with nonzero helicity. The first is a pair of braided anti-parallel streams - this double helix occurs when the activity is moderate, anchoring negligible and reduced temperature high. The second consists of axially aligned counter-rotating vortices - this grinder train arises between spontaneous axial streaming and the vortex lattice. These two unanticipated helical flow states illustrate the potential of active fluids to break symmetries and form complex but organized spatio-temporal structures in 3D fluidic devices.

cond-mat.soft↗

arXiv2022

Complex-tensor theory of simple smectics

Smectic materials represent a unique state between fluids and solids, characterized by orientational and partial positional order, making them notoriously difficult to model, particularly in confining geometries. We propose a complex order parameter tensor to describe the local degree of lamellar ordering, layer displacement and orientation. The theory accounts for both dislocations and disclinations, as well as arrested configurations and colloid-induced local ordering. It considerably simplifies numerics, facilitating studies on the dynamics of topologically complex lamellar systems.

cond-mat.soft↗

arXiv2022

Passive Janus Particles Are Self-propelled in Active Nematics

While active systems possess notable potential to form the foundation of new classes of autonomous materials, designing systems that can extract functional work from active surroundings has proven challenging. In this work, we extend these efforts to the realm of designed active liquid crystal/colloidal composites. We propose suspending colloidal particles with Janus anchoring conditions in an active nematic medium. These passive Janus particles become effectively self-propelled once immersed into an active nematic bath. The self-propulsion of passive Janus particles arises from the effective $+1/2$ topological charge their surface enforces on the surrounding active fluid. We analytically study their dynamics and the orientational dependence on the position of a companion $-1/2$ defect. We predict that at sufficiently small activity, the colloid and companion defect remain bound to each other, with the defect strongly orienting the colloid to propel either parallel or perpendicular to the nematic. At sufficiently high activity, we predict an unbinding of the colloid/defect pair. This work demonstrates how suspending engineered colloids in active liquid crystals may present a path to extracting activity to drive functionality.

cond-mat.soft↗

arXiv2021

Submersed Micropatterned Structures Control Active Nematic Flow, Topology and Concentration

Coupling between flows and material properties imbues rheological matter with its wide-ranging applicability, hence the excitement for harnessing the rheology of active fluids for which internal structure and continuous energy injection lead to spontaneous flows and complex, out-of-equilibrium dynamics. We propose and demonstrate a convenient, highly tuneable method for controlling flow, topology and composition within active films. Our approach establishes rheological coupling via the indirect presence of fully submersed micropatterned structures within a thin, underlying oil layer. Simulations reveal that micropatterned structures produce effective virtual boundaries within the superjacent active nematic film due to differences in viscous dissipation as a function of depth. This accessible method of applying position-dependent, effective dissipation to the active films presents a non-intrusive pathway for engineering active microfluidic systems.

cond-mat.soft↗

arXiv2019

Driven Topological Transitions in Active Nematic Films

The topological properties of many materials are central to their behavior, with the dynamics of topological defects being particularly important to intrinsically out-of-equilibrium, active materials. In this paper, local manipulation of the ordering, dynamics, and topological properties of microtubule-based extensile active nematic films is demonstrated in a joint experimental and simulation study. Hydrodynamic stresses created by magnetically actuated rotation of disk-shaped colloids in proximity to the films compete with internal stresses in the active nematic, enabling local control of the motion of the +1/2 charge topological defects that are intrinsic to spontaneously turbulent active films. Sufficiently large applied stresses drive the formation of +1 charge topological vortices in the director field through the merger of two +1/2 defects. The directed motion of the defects is accompanied by ordering of the vorticity and velocity of the active flows within the film that is qualitatively unlike the response of passive viscous films. Many features of the film's response to the disk are captured by Lattice Boltzmann simulations, leading to insight into the anomalous viscoelastic nature of the active nematic. The topological vortex formation is accompanied by a rheological instability in the film that leads to significant increase in the flow velocities. Comparison of the velocity profile in vicinity of the vortex with fluid-dynamics calculations provides an estimate of film viscosity.

cond-mat.soft↗

arXiv2018

Twist-induced crossover from 2D to 3D turbulence in active nematics

While studies of active nematics in two dimensions have shed light on various aspects of the flow regimes and topology of active matter, three-dimensional properties of topological defects and chaotic flows remain unexplored. By confining a film of active nematics between two parallel plates, we use continuum simulations and analytical arguments to demonstrate that the crossover from quasi-2D to 3D chaotic flows is controlled by the morphology of the disclination lines. For small plate separations, the active nematic behaves as a quasi-2D material, with straight topological disclination lines spanning the height of the channel and exhibiting effectively 2D active turbulence. Upon increasing channel height, we find a crossover to 3D chaotic flows due to the contortion of disclinations above a critical activity. We further show that these contortions are engendered by twist perturbations producing a sharp change in the curvature of disclinations.

cond-mat.soft↗

arXiv2017

Rotation-induced macromolecular spooling of DNA

Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that rotation-induced macromolecular spooling of DNA around a rotating microwire can monotonically order genomic bases, overcoming this challenge. We use single-molecule fluorescence microscopy to directly visualize long DNA strands deforming and elongating in shear flow near a rotating microwire, in agreement with numerical simulations. While untethered DNA is observed to elongate substantially, in agreement with our theory and numerical simulations, strong extension of DNA becomes possible by introducing tethering. For the case of tethered polymers, we show that increasing the rotation rate can deterministically spool a substantial portion of the chain into a fully stretched, single-file conformation. When applied to DNA, the fraction of genetic information sequentially ordered on the microwire surface will increase with the contour length, despite the increased entropy. This ability to handle long strands of DNA is in contrast to modern DNA sample preparation technologies for sequencing and mapping, which are typically restricted to comparatively short strands resulting in challenges in reconstructing the genome. Thus, in addition to discovering new rotation-induced macromolecular dynamics, this work inspires new approaches to handling genomic-length DNA strands.

cond-mat.soft↗

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↗

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

Understanding the Onset of Oscillatory Swimming in Microchannels

Self-propelled colloids (swimmers) in confining geometries follow trajectories determined by hydrodynamic interactions with the bounding surfaces. However, typically these interactions are ignored or truncated to lowest order. We demonstrate that higher-order hydrodynamic moments cause rod-like swimmers to follow oscillatory trajectories in quiescent fluid between two parallel plates, using a combination of lattice-Boltzmann simulations and far-field calculations. This behavior occurs even far from the confining walls and does not require lubrication results. We show that a swimmer's hydrodynamic quadrupole moment is crucial to the onset of the oscillatory trajectories. This insight allows us to develop a simple model for the dynamics near the channel center based on these higher hydrodynamic moments, and suggests opportunities for trajectory-based experimental characterization of swimmers' hydrodynamic properties.

cond-mat.soft↗

arXiv2016

Lattice-Boltzmann Hydrodynamics of Anisotropic Active Matter

A plethora of active matter models exist that describe the behavior of self-propelled particles (or swimmers), both with and without hydrodynamics. However, there are few studies that consider shape-anisotropic swimmers and include hydrodynamic interactions. Here, we introduce a simple method to simulate self-propelled colloids interacting hydrodynamically in a viscous medium using the lattice-Boltzmann technique. Our model is based on raspberry-type viscous coupling and a force/counter-force formalism which ensures that the system is force free. We consider several anisotropic shapes and characterize their hydrodynamic multipolar flow field. We demonstrate that shape-anisotropy can lead to the presence of a strong quadrupole and octupole moments, in addition to the principle dipole moment. The ability to simulate and characterize these higher-order moments will prove crucial for understanding the behavior of model swimmers in confining geometries.

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

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↗

arXiv2015

Electrophoretic Mobility of Polyelectrolytes within a Confining Well

We present a numerical study of polyelectrolytes electrophoresing in free solution while squeezed by an axisymmetric confinement force transverse to their net displacement. Hybrid multi-particle collision dynamics and molecular dynamics simulations with mean-field finite Debye layers show that even though the polyelectrolyte chains remain "free-draining", their electrophoretic mobility increases with confinement in nanoconfining potential wells. The primary mechanism leading to the increase in mobility above the free-solution value, despite long-range hydrodynamic screening by counterion layers, is the orientation of polymer segments within Debye layers. The observed length-dependence of the electrophoretic mobility arises due to secondary effects of counterion condensation related to confinement compactification.

cond-mat.soft↗

arXiv2014

Force-Extension for DNA in a Nanoslit: Using an Effective Dimensionality to Map between the 3D and 2D Limits

The force-extension relation for a semi-flexible polymer such as DNA confined in a nanoslit is investigated and it is found that both the effective persistence length and the form of the force-extension relation change as the chain goes from 3D (very large slit heights) to 2D (very tight confinement). Generalizations of the Marko-Siggia relation appropriate for polymers in nanoconfinement are presented. The forms for both strong and weak confinement regimes are characterized by an \textit{effective dimensionality}. At low forces, the effective dimensionality is given by the correlations along the polymer in the plane of the confining walls. At high forces, the theoretical force must account for reduced conformation space. Together the interpolations give good agreement for all slit heights at all forces. As DNA and other semi-flexible biopolymers are commonly confined \textit{in situ} to various degrees, both the idea of an effective dimensionality and the associated generalized Marko-Siggia interpolations are useful for qualitatively understanding and quantitatively modeling polymers in nanoconfinement.

cond-mat.soft↗

arXiv2014

Simulating the Entropic Collapse of Coarse-Grained Chromosomes

Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition.

cond-mat.soft↗