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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., Comment: 16 pages, 18 figures more...

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. more...

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., Comment: 13 pages, 7 figures, 2 appendices more...

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., Comment: 17 pages, 11 figures more...

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., Comment: 22 pages, 18 figures more...

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., Comment: 10 pages, 6 figures more...

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. more...

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., Comment: Main text (14 pages, 10 figures), plus SM (8 pages, 8 figures, 3 tables) more...

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. more...

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., Comment: 10 pages, 4 figures more...

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{\deg} 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., Comment: 14 pages, 11 figures more...

Antiferromagnets have recently been propelled to the forefront of spintronics by their high potential for revolutionizing memory technologies. For this, understanding the formation and driving mechanisms of the domain structure is paramount. In this work, we investigate the domain structure in a thin-film canted antiferromagnet $\alpha$-Fe$_2$O$_3$. We find that the internal destressing fields driving the formation of domains do not follow the crystal symmetry of $\alpha$-Fe$_2$O$_3$, but fluctuate due to substrate clamping. This leads to an overall isotropic distribution of the N\'eel order with locally varying effective anisotropy in antiferromagnetic thin films. Furthermore, we show that the weak ferromagnetic nature of $\alpha$-Fe$_2$O$_3$ leads to a qualitatively different dependence on magnetic field compared to collinear antiferromagnets such as NiO. The insights gained from our work serve as a foundation for further studies of electrical and optical manipulation of the domain structure of antiferromagnetic thin films., Comment: 9 pages, 5 figures more...

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., Comment: 23 pages, 3 figures more...

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., Comment: 16 pages, 13 figures more...

Beam-recoil transferred polarizations for the exclusive electroproduction of $K^+\Lambda$ and $K^+\Sigma^0$ final states from an unpolarized proton target have been measured using the CLAS12 spectrometer at Jefferson Laboratory. The measurements at beam energies of 6.535~GeV and 7.546~GeV span the range of four-momentum transfer $Q^2$ from 0.3 to 4.5~GeV$^2$ and invariant energy $W$ from 1.6 to 2.4~GeV, while covering the full center-of-mass angular range of the $K^+$. These new data extend the existing hyperon polarization data from CLAS in a similar kinematic range but from a significantly larger dataset. They represent an important addition to the world data, allowing for better exploration of the reaction mechanism in strangeness production processes, for further understanding of the spectrum and structure of excited nucleon states, and for improved insight into the strong interaction in the regime of non-perturbative dynamics., Comment: 25 pages, 22 figures, 4 tables more...

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., Comment: 6 pages, 3 figures more...

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. more...

Fiber-reinforced composites with nanofiller-modified polymer matrices have immense potential to improve the safety of high-risk engineering structures. These materials are intrinsically self-sensing because their electrical conductivity is affected by deformations and damage. This property, known as piezoresistivity, has been extensively leveraged for conductivity-based damage detection via electrical resistance change methods and tomographic imaging techniques such as electrical impedance tomography (EIT). Although these techniques are very effective at detecting the presence of damage, they suffer from an inability to provide precise information about damage shape, size, or mechanism. This is particularly detrimental for laminated composites which can suffer from complex failure modes, such as delaminations, that are difficult to detect. To that end, we herein propose a new technique for precisely determining damage shape and size in self-sensing composites. Our technique makes use of a genetic algorithm (GA) integrated with realistic physics-based damage models to recover precise damage shape from conductivity changes imaged via EIT. We experimentally validate this technique on carbon nanofiber (CNF)-modified glass fiber-reinforced polymer (GFRP) laminates by considering two specific damage mechanisms: through-holes and delaminations. Our results show that this novel technique can accurately reconstruct multiple through-holes with radii as small as 1.19 mm and delaminations caused by low velocity impacts. These findings illustrate that coupling piezoresistivity with conductivity-based spatial imaging techniques and physics-based inversion strategies can enable damage shaping capabilities in self-sensing composite structures. more...

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., Comment: 4 pages, 4 figures, appendices more...

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., Comment: 14 pages, 9 figures more...

We present the first measurement of the Timelike Compton Scattering process, $\gamma p\to p^\prime \gamma^* (\gamma^*\to e^+e^-) $, obtained with the CLAS12 detector at Jefferson Lab. The photon beam polarization and the decay lepton angular asymmetries are reported in the range of timelike photon virtualities $2.25 more...

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., Comment: 16 pages; 5 main-text-figures; 5-supplemental-figures more...

We report on the measurement of the beam spin asymmetry in the deeply virtual Compton scattering off $^4$He using the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab using a 6 GeV longitudinally polarized electron beam incident on a pressurized $^4$He gaseous target. We detail the method used to ensure the exclusivity of the measured reactions, in particular the upgrade of CLAS with a radial time projection chamber to detect the low-energy recoiling $^4$He nuclei and an inner calorimeter to extend the photon detection acceptance at forward angles. Our results confirm the theoretically predicted enhancement of the coherent ($e^4$He$~\to~e'$$^4$He$'\gamma'$) beam spin asymmetries compared to those observed on the free proton, while the incoherent ($e^4$He$~\to~e'$p$'\gamma'$X$'$) asymmetries exhibit a 30$\%$ suppression. From the coherent data, we were able to extract, in a model-independent way, the real and imaginary parts of the only $^4$He Compton form factor, $\cal H_A$, leading the way toward 3D imaging of the partonic structure of nuclei. more...

Measuring the spin structure of protons and neutrons tests our understanding of how they arise from quarks and gluons, the fundamental building blocks of nuclear matter. At long distances the coupling constant of the strong interaction becomes large, requiring non-perturbative methods to calculate quantum chromodynamics processes, such as lattice gauge theory or effective field theories. Here we report proton spin structure measurements from scattering a polarized electron beam off polarized protons. The spin-dependent cross-sections were measured at large distances, corresponding to the region of low momentum transfer squared between 0.012 and 1.0 GeV$^2$. This kinematic range provides unique tests of chiral effective field theory predictions. Our results show that a complete description of the nucleon spin remains elusive, and call for further theoretical works, e.g. in lattice quantum chromodynamics. Finally, our data extrapolated to the photon point agree with the Gerasimov-Drell-Hearn sum rule, a fundamental prediction of quantum field theory that relates the anomalous magnetic moment of the proton to its integrated spin-dependent cross-sections., Comment: Published version. 10 pages, 5 figures. 20 pages of supplementary material (data tables and a figure) more...

The reaction $\gamma p \rightarrow K^{+} \Lambda(1520)$ using photoproduction data from the CLAS $g12$ experiment at Jefferson Lab is studied. The decay of $\Lambda(1520)$ into two exclusive channels, $\Sigma^{+}\pi^{-}$ and $\Sigma^{-}\pi^{+}$, is studied from the detected $K^{+}$, $\pi^{+}$, and $\pi^{-}$ particles. A good agreement is established for the $\Lambda(1520)$ differential cross sections with the previous CLAS measurements. The differential cross sections as a function of CM angle are extended to higher photon energies. Newly added are the differential cross sections as a function of invariant 4-momentum transfer $t$, which is the natural variable to use for a theoretical model based on a Regge-exchange reaction mechanism. No new $N^*$ resonances decaying into the $K^+\Lambda(1520)$ final state are found., Comment: 16 pages, 12 figures, 2 tables more...