arXiv subjects

Tyler N. Shendruk

Publications and source records attributed to Tyler N. Shendruk.

At least 19 recordsLinked to original sources

arXiv2025

Passive polymers in active turbulence undergo a collapse-stretch transition

Active processes in living systems generate nonequilibrium forces that deform embedded passive macromolecules. To understand how such dynamics influence polymer conformation, we study a flexible passive chain in an active nematic fluid. Using hybrid simulations, we uncover a length-dependent transition in polymer behavior: long chains align with and stretch along defect-driven flows, while short chains bend and collapse due to localized stresses. These responses are controlled by a competition between the polymer size and the emergent length scale of the active turbulence. Our results reveal a defect-mediated mechanism for conformational control and point toward general physical principles for designing responsive soft materials that couple passive structure to active dynamics.

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arXiv2025

Topological kicks enhance colloidal diffusivity in topological turbulence

Colloidal inclusions in nematic fluids induce topological defects that govern their dynamics. These defects create well-understood rheological behavior in passive nematics, but the interplay between colloid-associated defects and spontaneously generated activity-induced defects introduces new dynamical regimes in active nematic turbulence. Using mesoscale simulations, we study the motion of colloids with strong anchoring in an active nematic and find effective colloid diffusivity exhibits a striking non-monotonic dependence on activity. At low activities, topological kicks from the motile activity-induced bulk defects drive frequent rearrangements of the colloid-associated defects, enhancing colloidal transport. At high activity, defect interactions become isotropic, decorrelating colloidal motion and reducing the effective diffusivity. Our results reveal how the competition between colloid-associated and activity-induced defects fundamentally shapes transport in active nematics.

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arXiv2025

Scaling laws for passive polymer dynamics in active turbulence

Biological systems commonly combine intrinsically out-of-equilibrium active components with passive polymeric inclusions to produce unique material properties. To explore these composite systems, idealized models - such as polymers in active fluids - are essential to develop a predictive theoretical framework. We simulate a single, freely jointed passive chain in two-dimensional active turbulence. Active flows advect the polymer, producing a substantially enhanced diffusivity. Our results reveal that the dimensionless diffusivity obeys scaling laws governed by the Péclet, Weissenberg, and Ericksen numbers, which paves the way for designing active/polymeric hybrid materials with predictable properties that differ significantly from those of nondeformable inclusions.

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arXiv2025

Multi-Particle Collision Framework for Active Polar Fluids

Sufficiently dense intrinsically out-of-equilibrium suspensions, such as those observed in biological systems, can be modelled as active fluids characterised by their orientational symmetry. While mesoscale numerical approaches to active nematic fluids have been developed, polar fluids are simulated as either ensembles of microscopic self-propelled particles or continuous hydrodynamic-scale equations of motion. To better simulate active polar fluids in complex geometries or as a solvent for suspensions, mesoscale numerical approaches are needed. In this work, the coarse-graining Multi-Particle Collision Dynamics (MPCD) framework is applied to three active particle models to produce mesoscale simulations of polar active fluids. The first active-polar MPCD (AP-MPCD) is a variant of the Vicsek model, while the second and third variants allow the speed of the particles to relax towards a self-propulsion speed subject to Andersen and Langevin thermostats, respectively. Each of these AP-MPCD variants exhibit a flocking transition at a critical activity and banding in the vicinity of the transition point. We leverage the mesoscale nature of AP-MPCD to explore flocking in the presence of external fields, which destroys banding, and anisotropic obstacles, which act as a ratchet that biases the flocking direction. These results demonstrate the capacity of AP-MPCD to capture the known phenomenology of polar active suspensions, and its versatility to study active polar fluids in complex scenarios.

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arXiv2024

Active nematics in corrugated channels

Active nematic fluids exhibit complex dynamics in both bulk and in simple confining geometries. However, complex confining geometries could have substantial impact on active spontaneous flows. Using multiparticle collision dynamics simulations adapted for active nematic particles, we study the dynamic behaviour of an active nematic fluid confined in a corrugated channel. The transition from a quiescent state to a spontaneous flow state occurs from a weak swirling flow to a strong coherent flow due to the presence of curved-wall induced active flows. We show that active nematic fluid flows in corrugated channels can be understood in two different ways: (i) as the result of an early or delayed flow transition when compared with that in a flat-walled channel of appropriate width and (ii) boundary-induced active flows in the corrugations providing an effective slip velocity to the coherent flows in the bulk. Thus, our work illustrates the crucial role of corrugations of the confining boundary in dictating the flow transition and flow states of active fluids.

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arXiv2024

Dynamics of polymers in coarse-grained nematic solvents

Polymers are a primary building block in many biomaterials, often interacting with anisotropic backgrounds. While previous studies have considered polymer dynamics within nematic solvents, rarely are the the effects of anisotropic viscosity and polymer elongation differentiated. Here, we study polymers embedded in nematic liquid crystals with isotropic viscosity via numerical simulations, to explicitly investigate the effect of nematicity on macromolecular conformation and how conformation alone can produce anisotropic dynamics. We employ a hybrid technique that captures nematic orientation, thermal fluctuations and hydrodynamic interactions. The coupling of the polymer backbone to the nematic field elongates the polymer, producing anisotropic diffusion even in nematic solvents with isotropic viscosity. For intermediate coupling, the competition between background anisotropy and macrmolecular entropy leads to hairpins - sudden kinks along the backbone of the polymer. Experiments of DNA embedded in a solution of rod-like fd viruses qualitatively support the role of hairpins in establishing characteristic conformational features that govern polymer dynamics. Hairpin diffusion along the backbone exponentially slows as coupling increases. Better understanding two-way coupling between polymers and their surroundings could allow the creation of more biomimetic composite materials.

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arXiv2024

Entangled nematic disclinations using multi-particle collision dynamics

Colloids dispersed in nematic liquid crystals form topological composites in which colloid-associated defects mediate interactions while adhering to fundamental topological constraints. Better realising the promise of such materials requires numerical methods that model nematic inclusions in dynamic and complex scenarios. We employ a mesoscale approach for simulating colloids as mobile surfaces embedded in a fluctuating nematohydrodynamic medium to study the kinetics of colloidal entanglement. In addition to reproducing far-field interactions, topological properties of disclination loops are resolved to reveal their metastable states and topological transitions during relaxation towards ground state. The intrinsic hydrodynamic fluctuations distinguish formerly unexplored far-from-equilibrium disclination states, including configurations with localised positive winding profiles. The adaptability and precision of this numerical approach offers promising avenues for studying the dynamics of colloids and topological defects in designed and out-of-equilibrium situations.

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arXiv2024

Lock-Key Microfluidics: Simulating Nematic Colloid Advection along Wavy-Walled Channels

Liquid crystalline media mediate interactions between suspended particles and confining geometries, which not only has potential to guide patterning and bottom-up colloidal assembly, but can also control colloidal migration in microfluidic devices. However, simulating such dynamics is challenging because nemato-elasticity, diffusivity and hydrodynamic interactions must all be accounted for within complex boundaries. We model the advection of colloids dispersed in flowing and fluctuating nematic fluids confined within 2D wavy channels. A lock-key mechanism between colloids and troughs is found to be stronger for planar anchoring compared to homeotropic anchoring due to the relative location of the colloid-associated defects. Sufficiently large amplitudes result in stick-slip trajectories and even permanent locking of colloids in place. These results demonstrate that wavy walls not only have potential to direct colloids to specific docking sites but also to control site-specific resting duration and intermittent elution.

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arXiv2024

Active Darcy's Law

While bacterial swarms can exhibit active turbulence in vacant spaces, they naturally inhabit crowded environments. We numerically show that driving disorderly active fluids through porous media enhances Darcy's law. While purely active flows average to zero flux, hybrid active/driven flows display greater drift than pure-driven fluids. This enhancement is non-monotonic with activity, leading to an optimal activity to maximize flow rate. We incorporate the active contribution into an active Darcy's law, which may serve to help understand anomalous transport of swarming in porous media.

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arXiv2024

3D active nematic disclinations behave as Majorana quasiparticles

Quasiparticles are low-energy excitations with important roles in condensed matter physics. An intriguing example is provided by Majorana fermions, quasiparticles which are identical to their antiparticles. Despite being implicated in neutrino oscillations and topological superconductivity, their experimental realisations remain scarce. Here we propose a purely classical realisation of Majorana fermions, in terms of 3-dimensional disclination lines in active nematics. Activity is required to overcome the elastic cost associated with these excitations, so they can appear in steady state. We combine topology and simulations to show that active nematics under confinement spontaneously create in their interior topologically charged disclination lines and loops, akin to Majorana quasiparticles with finite momentum. Within an elongated channel, we find a phenomenology similar to that of the Kitaev chain, as local Majorana-like excitations appear near surfaces, while a non-local system-spanning helical disclination line can arise along the centre. In unconfined active turbulence, Majorana-like charged loops are instead exceedingly rare, suggesting that boundaries are crucial to generate these quasiparticles, as in quantum condensed matter. We suggest that 3-dimensional active disclinations can be used to probe the physics of Majorana spinors at a much larger scale than traditionally considered, potentially facilitating the experimental observation of their dynamics.

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arXiv2024

Controlling flow patterns and topology in active emulsions

Active emulsions and liquid crystalline shells are intriguing and experimentally realisable types of topological matter. Here we numerically study the morphology and spatiotemporal dynamics of a double emulsion, where one or two passive small droplets are embedded in a larger active droplet. We find activity introduces a variety of rich and nontrivial nonequilibrium states in the system. First, a double emulsion with a single active droplet becomes self-motile, and there is a transition between translational and rotational motion: both of these regimes remain defect-free, hence topologically trivial. Second, a pair of particles nucleate one or more disclination loops, with conformational dynamics resembling a rotor or chaotic oscillator, accessed by tuning activity. In the first state a single, topologically charged, disclination loop powers the rotation. In the latter state, this disclination stretches and writhes in 3D, continuously undergoing recombination to yield an example of an active living polymer. These emulsions can be self-assembled in the lab, and provide a pathway to form flow and topology patterns in active matter in a controllable way, as opposed to bulk systems that typically yield active turbulence.

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arXiv2024

Mitigating Density Fluctuations in Particle-based Active Nematic Simulations

Understanding active matter has led to new perspectives on biophysics and non-equilibrium dynamics. However, the development of numerical tools for simulating active fluids capable of incorporating non-trivial boundaries or inclusions has lagged behind. Active particle-based methods, which typically excel at this, suffer from large density fluctuations that affect the dynamics of inclusions. To this end, we advance the Active-Nematic Multi-Particle Collision Dynamics algorithm, a particle-based method for simulating active nematics, by addressing the large density fluctuations that arise from activity. This paper introduces three novel activity formulations that mitigate the coupling between activity and local density. Local density fluctuations are decreased to a level comparable to the passive limit while retaining the phenomenology of active nematics and increasing the active turbulence regime four-fold. These developments extend the technique into a flexible tool for modeling active systems, including solutes and inclusions, with broad applications for the study of biophysical systems.

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arXiv2023

Spontaneous Self-Constraint in Active Nematic Flows

Active processes drive and guide biological dynamics across scales -- from subcellular cytoskeletal remodelling, through tissue development in embryogenesis, to population-level bacterial colonies expansion. In each of these, biological functionality requires collective flows to occur while self-organized structures are protected; however, the mechanisms by which active flows can spontaneously constrain their dynamics to preserve structure have not previously been explained. By studying collective flows and defect dynamics in active nematic films, we demonstrate the existence of a self-constraint -- a two-way, spontaneously arising relationship between activity-driven isosurfaces of flow boundaries and mesoscale nematic structures. Our results show that self-motile defects are tightly constrained to viscometric surfaces -- contours along which vorticity and strain-rate balance. This in turn reveals that self-motile defects break mirror symmetry when they move along a single viscometric surface, in contrast with expectations. This is explained by an interdependence between viscometric surfaces and bend walls -- elongated narrow kinks in the orientation field. Although we focus on extensile nematic films, numerical results show the constraint holds whenever activity leads to motile half-charge defects. This mesoscale cross-field self-constraint offers a new framework for tackling complex 3D active turbulence, designing dynamic control into biomimetic materials, and understanding how biological systems can employ active stress for dynamic self-organization.

cond-mat.soft↗

arXiv2023

Anisotropic run-and-tumble-turn dynamics

Run-and-tumble processes successfully model several living systems. While studies have typically focused on particles with isotropic tumbles, recent examples exhibit "tumble-turns", in which particles undergo 90° tumbles and so possess explicitly anisotropic dynamics. We study the consequences of such tumble-turn anisotropicity at both short and long-time scales. We model run-and-tumble-turn particles as self-propelled particles subjected to an angular potential. Using agent-based simulations, we study the interplay of noise and potential on the particles' trajectories, demonstrating that the long-time effect is to alter the tumble-turn time, which governs the long-time dynamics. In particular, when normalized by this timescale, trajectories become independent of the underlying details of the potential. As such, we develop a simplified continuum theory, which quantitatively agrees with agent simulations. The hydrodynamic limit reveals that the transition to diffusive dynamics precedes the transition to isotropic dynamics as the hydrodynamic limit, while purely diffusive, can drive anisotropicity at intermediate times.

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arXiv2022

Fluctuation-induced dynamics of nematic topological defects

Topological defects are increasingly being identified in various biological systems, where their characteristic flow fields and stress patterns are associated with continuous active stress generation by biological entities. Here, using numerical simulations of continuum fluctuating nematohydrodynamics we show that even in the absence of any specific form of active stresses associated with self-propulsion, mesoscopic fluctuations in either orientational alignment or hydrodynamics can independently result in flow patterns around topological defects that resemble the ones observed in active systems. Our simulations further show the possibility of extensile- and contractile-like motion of fluctuation-induced positive half-integer topological defects. Remarkably, isotropic stress fields also reproduce the experimentally measured stress patterns around topological defects in epithelia. Our findings further reveal that extensile- or contractile-like flow and stress patterns around fluctuation-induced defects are governed by passive elastic stresses and flow-aligning behavior of the nematics.

cond-mat.soft↗

arXiv2022

Smectic Layering: Landau theory for a complex-tensor order parameter

Composed of microscopic layers that stack along one direction while maintaining fluid-like positional disorder within layers, smectics are excellent systems for exploring topology, defects and geometric memory in complex confining geometries. However, the coexistence of crystalline-like characteristics in one direction and fluid-like disorder within layers makes lamellar liquid crystals notoriously difficult to model - especially in the presence of defects and large distortions. Nematic properties of smectics can be comprehensively described by the Q-tensor but to capture the features of the smectic layering alone, we develop a phenomenological Landau theory for a complex-tensor order parameter E, which is capable of describing the local degree of lamellar ordering, layer displacement, and orientation of the layers. This theory can account for both parallel and perpendicular elastic contributions. In addition to resolving the potential ambiguities inherent to complex scalar order parameter models, this model reduces to previous employed models of simple smectics, and opens new possibilities for numerical studies on smectics possessing many defects, within complex geometries and under extreme confinement.

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arXiv2022

Mesoscopic Simulations of Active-Nematics

Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally model passive solvents; however, far-from-equilibrium systems may also be composed of complex solutes suspended in an active fluid. Yet, few coarse-grained simulation methods exist to model an active medium. We introduce an algorithm to simulate active nematics, which builds on multi-particle collision dynamics (MPCD) for passive fluctuating nematohydrodynamics by introducing dipolar activity in the local collision operator. Active-nematic MPCD (AN-MPCD) simulations exhibit the key characteristics of active nematic turbulence but, as a particle-based algorithm, also reproduce crucial attributes of active particle models. Thus, mesoscopic AN-MPCD is an approach that bridges microscopic and continuum descriptions, allowing novel simulations of composite active-passive systems.

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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.

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