arXiv subjects

Daniel J. G. Pearce

Publications and source records attributed to Daniel J. G. Pearce.

15 recordsLinked to original sources

arXiv2026

Spatiotemporal Control of Charge +1 Topological Defects in Polar Active Matter

Topological defects are a conspicuous feature of active liquid crystals that have been associated with important morphogenetic transitions in organismal development. Robust development thus requires a tight control of the motion and placement of topological defects. In this manuscript, we study a mechanism to control +1 topological defects in an active polar fluid confined to a disk. If activity is localized in an annulus within the disk, the defect moves on a circular trajectory around the center of the disk. Using an ansatz for the polar field, we determine the dependence of the angular speed and the circle radius on the boundary orientation of the polar field and the active annulus. Using a proportional integral controller, we guide the defect along complex trajectories by changing the active annulus size and the boundary orientation.

cond-mat.soft↗

arXiv2026

Irreversibility and symmetry breaking in the creation and annihilation of defects in active living matter

Active living matter continuously creates and annihilates topological defects in a process that remains poorly understood. Here, we investigate these dynamics in two distinct active living systems: swarming bacteria and human bronchial epithelial cells. Despite their entirely different evolutionary origins, biological functions, and physical scales, both systems exhibit half-integer defects, consistent with the nematic phase. However, in contrast to active nematic theory, we find that defect creation and annihilation undergoes spatial symmetry breaking. We propose that these results stem from a fundamental dualism between nematic structural organization and generated polar forces, which are intrinsic to living systems. Furthermore, estimation of entropy production reveals that creation and annihilation are not reversed processes. Our findings challenge conventional nematic models and emphasize the role of defect-mediated dynamics in non-equilibrium biological systems as a major source of entropy production.

physics.bio-ph↗

arXiv2025

Topological defects lead to energy transfer in active nematics

Active nematics are fluids in which the components have nematic symmetry and are driven out of equilibrium due to the microscopic generation of an active stress. When the active stress is high, it drives flows in the nematic and can lead to the proliferation of topological defects, a state we refer to as defect chaos. Using numerical simulations of active nematics, we observe energy transfer between length scales during defect chaos. We demonstrate that this energy transfer is driven by the exchange between variations in the orientation and degree of order in the nematic that predominantly occur during defect creation and annihilation. We then show that the primary features of energy transfer during defect chaos scale with the active length scale. Finally, we identify a second regime that features few defects, but rather bend walls. Similar to topological defects, these bend walls co-localize variations in the orientation with variations in the scalar order parameter leading to energy transfer.

cond-mat.soft↗

arXiv2025

Actuation of Cell Sheets in 3D

The alignment of fibers and cells in living tissues affect their mechanical properties and functionality. In this context, one can draw an analogy between tissues and nematic liquid crystal elastomers. We explore this analogy by growing fibroblasts on 2D-patterned substrates and observing the contraction of cell sheets upon detachment from the substrates. When fibroblast sheets detach, they undergo an anisotropic contraction, with maximum contraction along the nematic director, like nematic elastomers do during phase transition. We quantify this anisotropy using substrates patterned with stripes to induce alignment, finding that cell sheets resemble nematic elastomers with negative Poisson ratio. Then, we apply design principles used for programming curvature in nematic elastomers to actuate 3D structures in the detached fibroblast layers, demonstrating an application of these principles and we support the results with simulations. This proof of concept shows the ability to control the 3D shape through 2D patterning in cell layers, leading to promising avenues to program tissues.

cond-mat.soft↗

arXiv2024

Optimal self-assembly pathways towards colloidal lattices with tunable flexibility

Flexibility governs the many properties of materials and is crucial for the function of proteins and biopolymers. However, how the self-assembly of flexibly bonded particles can lead to larger structures with global reconfigurability is unexplored. We here use a binary colloidal model system equipped with flexible DNA-based bonds to study how regular structures with tunable flexibility can be created through self-assembly. We find that the reconfigurability during lattice growth leads to lattices with square symmetry which are inherently mechanically unstable and hence thermally floppy. By considering the role of size ratio, number ratio, and directionality induced by particle shape, we identify the optimal pathways that maximize the yield and flexibility of these square lattices using a combination of experiments, analytical calculations, and simulations. Our study highlights the crucial role of reconfigurability in systems that are governed by enthalpic and entropic principles, from synthetic to biological, and might be useful for creating materials with novel or reconfigurable properties.

cond-mat.soft↗

arXiv2024

Topological defects in multi-layered swarming bacteria

Topological defects, which are singular points in a director field, play a major role in shaping active systems. Here, we experimentally study topological defects and the flow patterns around them, that are formed during the highly rapid dynamics of swarming bacteria. The results are compared to the predictions of two-dimensional active nematics. We show that, even though some of the assumptions underlying the theory do not hold, the swarm dynamics is in agreement with two-dimensional nematic theory. In particular, we look into the multi-layered structure of the swarm, which is an important feature of real, natural colonies, and find a strong coupling between layers. Our results suggest that the defect-charge density is hyperuniform, i.e., that long range density-fluctuations are suppressed.

cond-mat.soft↗

arXiv2022

Coupling topological defect phase to extrinsic curvature in nematic shells

In two dimensional nematics, topological defects are point like singularities with both a charge and a phase. We study topological defects within curved nematic textures on the surface of a cylinder. This allows us to isolate the effect of extrinsic curvature on the structure of the topological defect. By minimizing the energy associated with distortions in the nematic director around the core of a defect we show that the phase of the topological defect is coupled to the orientation of the cylinder. This coupling depends on the relative energetic cost associated with splay, bend and twist distortions of the nematic director. We identify a bistability in the phase of the defects when twist deformations dominate. Finally, we show a similar effect for integer charge topological defects.

cond-mat.soft↗

arXiv2021

Self-assembly dynamics of reconfigurable colloidal molecules

Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby restricting their use as model systems. We overcome this limitation by assembling reconfigurable colloidal molecules from silica particles functionalized with mobile DNA linkers in high yields. We achieve this by steering the self-assembly pathway towards the formation of finite-sized clusters by employing high number ratios of particles functionalized with complementary DNA strands. The size ratio of the two species of particles provides control over the overall cluster size, or, "valence", as well as the degree of reconfigurability. The bond flexibility provided by the mobile linkers allows the successful assembly of colloidal clusters with the geometrically expected maximum valence. We quantitatively examine the self-assembly dynamics of these flexible colloidal molecules by a combination of experiments, molecular dynamics simulations, and an analytical model. Our "flexible colloidal molecules" are exciting building blocks for investigating and exploiting the self-assembly of complex hierarchical structures, photonic crystals and colloidal meta-materials.

cond-mat.soft↗

arXiv2021

Properties of twisted topological defects in 2D nematic liquid crystals

Topological defects are one of the most conspicuous features of liquid crystals. In two dimensional nematics, they have been shown to behave effectively as particles with both, charge and orientation, which dictate their interactions. Here, we study "twisted" defects that have a radially dependent orientation. We find that twist can be partially relaxed through the creation and annihilation of defect pairs. By solving the equations for defect motion and calculating the forces on defects, we identify four distinct elements that govern the relative relaxational motion of interacting topological defects, namely attraction, repulsion, co-rotation and co-translation. The interaction of these effects can lead to intricate defect trajectories, which can be controlled by setting relevant timescales.

cond-mat.soft↗

arXiv2021

Mono-to-multilayer transition in growing bacterial colonies

The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial microcolonies comprising a few hundred cells. Using a combination of numerical simulations and analytical modeling, here we demonstrate that this transition originates from the competition between growth-induced in-plane active stresses and vertical restoring forces, due to the cell-substrate interactions. Using a simple chainlike colony of laterally confined cells, we show that the transition sets when individual cells become unstable to rotations, thus it is localized and mechanically deterministic. Asynchronous cell division renders the process stochastic, so that all the critical parameters that control the onset of the transition are continuously distributed random variables. Here we demonstrate that the occurrence of the first division in the colony can be approximated as a Poisson process in the limit of large cells numbers. This allows us to approximately calculate the probability distribution function of the position and time associated with the first extrusion. The rate of such a Poisson process can be identified as the order parameter of the transition, thus highlighting its mixed deterministic-stochastic nature.

cond-mat.soft↗

arXiv2021

Confinement-induced self-organization in growing bacterial colonies

We investigate the emergence of global alignment in colonies of dividing rod-shaped cells under confinement. Using molecular dynamics simulations and continuous modeling, we demonstrate that geometrical anisotropies in the confining environment give rise to imbalance in the normal stresses, which, in turn, drives a collective rearrangement of the cells. This behavior crucially relies on the colony's solid-like mechanical response at short time scales and can be recovered within the framework of active hydrodynamics upon modeling bacterial colonies as growing viscoelastic gels characterized by Maxwell-like stress relaxation.

cond-mat.soft↗

arXiv2018

Geometry and mechanics of microdomains in growing bacterial colonies

Bacterial colonies are abundant on living and nonliving surfaces and are known to mediate a broad range of processes in ecology, medicine, and industry. Although extensively researched, from single cells to demographic scales, a comprehensive biomechanical picture, highlighting the cell-to-colony dynamics, is still lacking. Here, using molecular dynamics simulations and continuous modeling, we investigate the geometrical and mechanical properties of a bacterial colony growing on a substrate with a free boundary and demonstrate that such an expanding colony self-organizes into a "mosaic" of microdomains consisting of highly aligned cells. The emergence of microdomains is mediated by two competing forces: the steric forces between neighboring cells, which favor cell alignment, and the extensile stresses due to cell growth that tend to reduce the local orientational order and thereby distort the system. This interplay results in an exponential distribution of the domain areas and sets a characteristic length scale proportional to the square root of the ratio between the system orientational stiffness and the magnitude of the extensile active stress. Our theoretical predictions are finally compared with experiments with freely growing E. coli microcolonies, finding quantitative agreement.

cond-mat.soft↗

arXiv2014

Differentiating swarming models by mimicking a frustrated anti-Ferromagnet

Self propelled particle (SPP) models are often compared with animal swarms. However, the collective behaviour observed in experiments usually leaves considerable unconstrained freedom in the structure of these models. To tackle this degeneracy, and better distinguish between candidate models, we study swarms of SPPs circulating in channels (like spins) where we permit information to pass through windows between neighbouring channels. Co-alignment between particles then couples the channels (antiferromagnetically) so that they tend to counter-rotate. We study channels arranged to mimic a geometrically frustrated antiferromagnet and show how the effects of this frustration allow us to better distinguish between SPP models. Similar experiments could therefore improve our understanding of collective motion in animals. Finally we discuss how the spin analogy can be exploited to construct universal logic gates and therefore swarming systems that can function as Turing machines.

q-bio.PE↗

arXiv2014

The Role of Projection in the Control of Bird Flocks

Swarming is a conspicuous behavioural trait observed in bird flocks, fish shoals, insect swarms and mammal herds. It is thought to improve collective awareness and offer protection from predators. Many current models involve the hypothesis that information coordinating motion is exchanged between neighbors. We argue that such local interactions alone are insufficient to explain the organization of large flocks of birds and that the mechanism for the exchange of long-ranged information necessary to control their density remains unknown. We show that large flocks self-organize to the maximum density at which a typical individual is still just able to see out of the flock in many directions. Such flocks are marginally opaque - an external observer can also just still see a substantial fraction of sky through the flock. Although seemingly intuitive we show that this need not be the case; flocks could easily be highly diffuse or entirely opaque. The emergence of marginal opacity strongly constrains how individuals interact with each other within large swarms. It also provides a mechanism for global interactions: An individual can respond to the projection of the flock that it sees. This provides for faster information transfer and hence rapid flock dynamics, another advantage over local models. From a behavioural perspective it optimizes the information available to each bird while maintaining the protection of a dense, coherent flock.

q-bio.QM↗

arXiv2014

Density regulation in strictly metric-free swarms

There is now experimental evidence that nearest-neighbour interactions in flocks of birds are metric free, i.e. they have no characteristic interaction length scale. However, models that involve interactions between neighbours that are assigned topologically are naturally invariant under spatial expansion, supporting a continuous reduction in density towards zero, unless additional cohesive interactions are introduced or the density is artificially controlled, e.g. via a finite system size. We propose a solution that involves a metric-free motional bias on those individuals that are topologically identified to be on an edge of the swarm. This model has only two primary control parameters, one controlling the relative strength of stochastic noise to the degree of co-alignment and another controlling the degree of the motional bias for those on the edge, relative to the tendency to co-align. We find a novel power-law scaling of the real-space density with the number of individuals N as well as a familiar order-to-disorder transition.

q-bio.QM↗