arXiv subjects

Amin Doostmohammadi

Publications and source records attributed to Amin Doostmohammadi.

At least 19 recordsLinked to original sources

arXiv2026

Spontaneous filament formation and network self-assembly via active phase separation

We introduce Active Model H$^{-}$, a scalar phase-field model of non-equilibrium phase separation in the overdamped hydrodynamic limit, and show that it produces filamentous networks with enhanced connections and arrested coarsening, a morphology not observed in existing scalar active field theories. Isolated filaments are unstable to spontaneous bending, and the resulting curvature drives self-propulsion towards the convex side, causing them to collide and assemble into a percolating network. The networks are locally non-equilibrium, with anomalously curved edges, disordered vertex angles and heterogeneous topological charge, yet recover Lewis's law macroscopically. Under noise they show balanced break and reform dynamics.

cond-mat.soft↗

arXiv2026

Spontaneous Vortex Instability in Active Nematics

One of the defining results in the study of active matter is the spontaneous flow instability, through which a homogeneous, uniformly aligned state breaks translational symmetry along a single direction and develops sustained flow. The vortex state that emerges at higher activity has instead been attributed to nonlinear dynamics. Using a Floquet-type linear stability analysis, we show that no such mechanism is required: the flowing state undergoes a secondary, zigzag instability that breaks the remaining translational symmetry and produces the vortex state. We further identify a regime in which the flowing state ceases to exist and vortices emerge directly from the uniformly aligned state. Under channel confinement, the instability selects a length scale that differs from the establishedactivelengthscale, andsetsthenumberofvorticesthatappear, leadingtoaconfinement- selected pattern reminiscent of a vortex lattice, opening a route toward direct experimental tests of this instability. Full nonlinear simulations reproduce the predicted onset activities and the selected vortex number.

cond-mat.soft↗

arXiv2026

Epithelia Realize Nematopolar Topological Defect Structures

We introduce a shape-based polar order parameter that captures the structural asymmetry of cells within epithelial monolayers. By combining bright-field imaging and traction force microscopy, we demonstrate that shape polarity serves as a unifying biomechanical metric, integrating the physical information encoded by nematic directors, principal stresses, and cellular motion. Furthermore, we show that the tissue organizes into a mixed polar-nematic phase, characterized by the coexistence of integer ($\pm 1$) and half-integer ($\pm 1/2$) defects. Through mechanical perturbations, we demonstrate that both substrate stiffness and cell-cell adhesion modulate the density of these excitations and the length of domain walls binding like-signed positive half-integer defects. Using a minimal continuum model of polar-nematic active matter, we establish that this mixed phase is fundamentally driven by the interplay of active stresses and polar-nematic elasticity. These findings provide a direct experimental evidence that epithelial monolayers behave as nematopolar matter, in which coupled polar and nematic elastic interactions jointly shape the active state

cond-mat.soft↗

arXiv2026

Activity driven buckling and pattern formation in shells of oriented solids

We investigate shells of active oriented solid, materials in which orientationally ordered active particles are embedded in a deformable elastic surface. Focusing on cylindrical geometries, we show that active stresses drive a new class of buckling instabilities and nonlinear patterns absent in passive shells. Linear stability analysis reveals that the unstable buckling mode is selected by the nematic orientation and activity sign, leading to axial, circumferential, and helical deformations. Remarkably, circumferential modes become unstable at arbitrarily small activity due to the absence of stretching costs. The results of the linear stability analysis are corroborated by full nonlinear simulations, which further uncover steady diamond shaped patterns and persistent dynamical states including oscillations, traveling domain walls, and propagating waves. Our results establish fundamental buckling modes and emergent patterns in shells of active oriented solid materials, with potential relevance to active biological tissues and engineered responsive materials.

cond-mat.soft↗

arXiv2026

Flow Coupling Alters Topological Phase Transition in Nematic Liquid Crystals

We investigate how coupling to fluid flow influences defect-mediated transitions in two-dimensional passive nematic fluids using fluctuating nematohydrodynamic simulations. The system is driven by tuning the fluctuation strength, with increasing (decreasing) fluctuations defining the forward (backward) protocol. In the absence of flow coupling, the transition follows the Berezinskii--Kosterlitz--Thouless (BKT) scenario, governed by reversible binding and unbinding of $\pm 1/2$ defect pairs. When hydrodynamics is included, the outcome is controlled by the flow--alignment parameter. For non-aligning nematics ($λ=0$), the transition remains consistent with BKT. By contrast, for strain-rate--aligning nematics ($λ\neq 0$), bend--splay walls emerge, lowering the defect nucleation threshold and preventing sustained recombination: once created, defects remain unbound across the full range of fluctuation strengths in both forward and backward protocols. These results identify flow alignment as a fundamental control parameter for topological phase behavior and suggest that the canonical BKT transition emerges only in the absence of flow alignment.

cond-mat.soft↗

arXiv2026

Cell-induced wrinkling patterns on soft substrates

Cells exert traction forces on compliant substrates and can induce surface instabilities that appear as characteristic wrinkling patterns. Here, we develop a mechanical description of cell-induced wrinkling on soft substrates using a thin film elastic framework based on the Föppl-von Kármán equations coupled to a phase-field model of a single cell. We model in-plane contractile stresses driven by cellular activity and study how their magnitude, spatial distribution, and symmetry determine the onset of wrinkling and the resulting pattern selection. The theory predicts transitions between distinct morphologies, such as radial, circumferential, and anisotropic wrinkle arrangements, and provides scaling relations for wrinkle wavelength and amplitude as functions of elastic parameters and imposed cellular forcing. We compare these predictions with available experimental observations of cell-driven wrinkling on compliant gels and find good agreement for both qualitative pattern classes and quantitative wavelength trends. Our results offer a minimal modelling framework to interpret wrinkling assays and connect observed surface patterns to underlying cellular forces.

cond-mat.soft↗

arXiv2026

Non-equilibrium geometric forces steer spiral waves on folded surfaces

Spiral waves are ubiquitous signatures of non equilibrium dynamics, appearing across chemical, biological, and active systems. Yet, in many living systems these waves unfold on curved and folded surfaces whose geometry has rarely been treated as a dynamical factor. Here we show that surface curvature fundamentally shapes spiral wave behavior and can contribute to the organization of neural activity in the brain. Via analytical theory and simulations of the complex Ginzburg Landau equation (CGLE) on curved surfaces, we demonstrate that curvature enters through the Laplace Beltrami operator as a spatial modulation of effective diffusion. Gradients of this effective diffusion generate a geometric force on spiral defects, and the complex nature of the CGLE produces a complex mobility that leads to non central and non reciprocal responses. Applied to realistic cortical surfaces of the human brain, the model predicts that the pattern of cortical folding stabilizes and localizes spiral waves, while progressive smoothing of the surface erases these non equilibrium structures. This reveals that brain geometry is not a passive scaffold but an active physical constraint that shapes neural dynamics. More broadly, the same geometric mechanism provides a universal route by which curvature and topology control pattern formation across oscillatory, chemical, and active matter systems.

cond-mat.soft↗

arXiv2026

Nematic ordering in active fluids driven by substrate deformations: Mechanisms and patterning regimes

The interplay between active matter and its environment is central to understanding emergent behavior in biological and synthetic systems. Here, we show that coupling active nematic flows to small-amplitude deformations of a compliant substrate can fundamentally reorganize the system's dynamics. Using a model that combines active nematohydrodynamics with substrate mechanics, we find that contractile active nematics-normally disordered in flat geometries-undergo a sharp transition to long-range orientational order when the environment is deformable. This environmentally induced ordering is robust and enables distinct patterning regimes, with wrinkle morphologies reflecting the nature of the active stresses. Our results reveal a generic mechanism by which mechanical feedback from soft environments can lead to ordering in active systems.

cond-mat.soft↗

arXiv2025

Hydrodynamic bend instability of motile particles on a substrate

The emergence of hydrodynamic bend instabilities in ordered suspensions of active particles is widely observed across diverse living and synthetic systems, and is considered to be governed by dipolar active stresses generated by the self-propelled particles. Here, using linear stability analyses and numerical simulations, we show that a hydrodynamic bend instability can emerge in the absence of any dipolar active stress and solely due to the self-propulsion force acting on polar active units suspended in an incompressible fluid confined to a substrate. Specifically, we show analytically, and confirm in simulations, that a uniformly ordered state develops bend instability above a critical self-propulsion force. Numerical simulations show that a further increase in the self-propulsion strength leads the system towards a disorderly flow state. The results offer a new route for development of hydrodynamic instabilities in two-dimensional self-propelled materials that are in contact with a substrate, with wide implications in layers of orientationally ordered cells and synthetic active particles.

cond-mat.soft↗

arXiv2025

Identifying non-equilibrium fluctuations in Intracellular Motion Using Recurrent Neural Networks

Distinguishing active from passive dynamics is a fundamental challenge in understanding the motion of living cells and other active matter systems. Here, we introduce a framework that combines physical modeling, analytical theory, and machine learning to identify and characterize active fluctuations from trajectory data. We train a long short-term memory (LSTM) neural network on synthetic trajectories generated from well-defined stochastic models of active particles, enabling it to classify motion as passive or active and to infer the underlying active process. Applied to experimental trajectories of a tracer in the cytoplasm of a living cell, the method robustly identifies actively driven motion and selects an Ornstein-Uhlenbeck active noise model as the best description. Crucially, the classifier's performance on simulated data approaches the theoretical optimum that we derive, and it also yields accurate estimates of the active diffusion coefficient. This integrated approach opens a powerful route to quantify non-equilibrium fluctuations in complex biological systems from limited data.

cond-mat.stat-mech↗

arXiv2025

A spectrum of p-atic symmetries and defects in confluent epithelia

Topological defects provide a unifying language to describe how orientational order breaks down in active and living matter. Considering cells as elongated particles confluent, epithelial tissues can be interpreted as nematic fields and its defects have been linked to extrusion, migration, and morphogenetic transformations. Yet, epithelial cells are not restricted to nematic order: their irregular shapes can express higher rotational symmetries, giving rise to p-atic order. Here we introduce a framework to extract p-atic fields and their defects directly from experimental images. Applying this method to MDCK cells, we find that all symmetries generate defects.No strong positional or orientational correlations are found between nematic and hexatic defects, suggesting that different symmetries coexist largely independently. These results demonstrate that epithelial tissues should not be described by nematic order alone, but instead host a spectrum of p-atic symmetries. Our work provides the first direct experimental evidence for this multivalency of order and offers a route to test and refine emerging p-atic liquid crystal theories of living matter.

cond-mat.soft↗

arXiv2025

Anti-hyperuniform Critical States of Active Topological Defects

Topological defects are fundamental to the collective dynamics of non-equilibrium systems and in active matter, mediating spontaneous flows, dynamic self-organization, and emergent pattern formation. Here, we reveal critical states in active nematics, marked by slowed defect density relaxation, amplified fluctuations, and heightened sensitivity to activity. Near criticality, defect interactions become long-ranged, scaling with system size, and the system enters an anti-hyperuniform regime with giant number fluctuations of topological defects and defect clustering. This transition reflects a dual scaling behavior: fluctuations are uniform at small scales but become anti-hyperuniform at larger scales, \tm{as supported by experimental measurements on large-field-of-view endothelial monolayers. We find that these anti-hyperuniform states with multiscale defect density fluctuations are robust to varying parameters, introducing frictional damping, and changing boundary conditions.} Finally, we show that the observed anti-hyperuniformity originates from defect clustering, distinguishing this transition from defect-unbinding or phase separation processes. Beyond fundamental implications for non-equilibrium systems, these results may inform biological contexts where topological defects are integral to processes such as morphogenesis and collective cellular self-organization.

cond-mat.soft↗

arXiv2025

Self-propulsive active nematics

Increasing evidence suggests that active matter exhibits instances of mixed symmetry that cannot be fully described by either polar or nematic formalism. Here, we introduce a minimal model that integrates self-propulsion into the active nematic framework. Our linear stability analyses reveal how self-propulsion shifts the onset of instability, fundamentally altering the dynamical landscape. Numerical simulations confirm these predictions, showing that self-propulsion induces anti-hyperuniform fluctuations, anomalous long-range order in vorticity, and non-universal self-similar energy cascades. Notably, these long-range ordered states emerge within the active turbulence regime well before the transition to a flocking state. Additionally, our analyses highlight a non-monotonic dependence of self-organization on self-propulsion, with optimal states characterized by a peak in correlation length. These findings are relevant for understanding of active nematic systems that self-propel, such as migrating cell layers or swarming bacteria, and offer new avenues for designing synthetic systems with tailored collective behaviours, bridging the gap between active nematics and self-propulsive systems.

cond-mat.soft↗

arXiv2025

Density-Velocity Relation Is Scale-Dependent in Epithelial Monolayers

The relationship between cell density and velocity is often assumed to be negative, reflecting crowding-induced suppression of movement. However, observations across systems reveal a more nuanced picture: while some emphasize contact inhibition of locomotion, others suggest that dense regions exhibit enhanced activity due to force generation and stress buildup. Here, using experimental measurements we show that density-velocity relations in epithelial monolayers are inherently scale dependent. By coarse-graining cell trajectories over multiple spatial windows, we find that cell velocity correlates positively with local density at small scales, but negatively at large scales. Employing traction force measurements, we find that this crossover coincides with the emergence of mechanical pressure segregation, defining a characteristic length scale beyond which crowding dominates. A minimal model incorporating activity-induced shape changes reproduces this crossover and identifies the competition between active force generation and mechanical confinement as the underlying mechanism. Our results reconcile conflicting views of density-regulated migration and highlight an emergent length scale as a key factor in interpreting collective cell dynamics.

cond-mat.soft↗

arXiv2025

Cellular Flow Architecture Exposes the Hidden Mechanics of Biological Matter

Understanding how biomechanical reorganization governs key biological processes, such as morphogenesis and development, requires predictive insights into stress distributions and cellular behavior. While traditional approaches focused on cell motion as a response to stress, we demonstrate that Lagrangian coherent structures (LCSs) -- robust attractors and repellers in cellular flows -- precede and drive long-term intercellular stress reorganization, physically governed by the mechanical properties of intercellular junctions. We show that this hidden flow skeleton correlates strongly with biomechanical metrics, bridging microscopic cell motion with mesoscopic biomechanics. Specifically, attractors and repellers mark hotspots of compressive and tensile stress enrichment (exceeding tenfold), alongside heterogeneities in cell packing. Notably, these connections remain robust across varying strengths of cell-cell and cell-substrate force transmission. Finally, by linking the attracting regions in the flow skeleton to future cell extrusion spots, we establish a direct link between cell motion and biologically significant outcomes. Together, these findings establish a framework for using cell motion to independently infer biomechanical metrics and bridge the scale mismatch between cell motion and biomechanics, potentially offering a new route to interpret mechanosensitive biological processes directly from cell trajectories.

physics.bio-ph↗

arXiv2025

The Interplay of Polar and Nematic Order in Active Matter: Implications for Non-Equilibrium Physics and Biology

Active matter has played a pivotal role in advancing our understanding of non-equilibrium systems, leading to a fundamental shift in the study of biophysical phenomena. The foundation of active matter research is built on assumptions regarding the symmetry of microscopic constituents. While these assumptions have been validated extensively, instances of mixed or joint symmetries are prevalent in biological systems. This review explores the coexistence of polar and nematic order in active matter, emphasizing the theoretical and experimental challenges associated with these systems. By integrating insights from recent studies, we highlight the importance of considering mixed symmetries to accurately describe biological processes. This exploration not only benefits the field of biology but could also open new horizons for non-equilibrium physics, offering a comprehensive framework for understanding complex behavior in active matter.

cond-mat.soft↗

arXiv2025

Multi-phase-field Models of Biological Tissues

The development of complex multicellular organisms from a single parent cell is a highly orchestrated process that cells conduct collectively without central guidance, creating intricate dynamic patterns essential for development and regeneration. Despite significant advances in imaging spatiotemporal dynamics of cell collectives and mechanical characterization techniques, the role of physical forces in biological functions remains poorly understood. Physics-based models are crucial in complementing experiments, providing high-resolution spatiotemporal fields in three dimensions. This review focuses on dense, soft multicellular systems, such as tissues, where mechanical deformation of one cell necessitates the re-organization of neighboring cells. The multi-phase-field model offers a rich physics-based framework to advance our understanding of biological systems and provides a robust playground for non-equilibrium physics of active matter. We discuss the foundational aspects of the multi-phase-field model and their applications in understanding physics of active matter. We also explore the integration of biological physics with experimental data, covering cell migration, heterogeneous cell populations, and confined systems. Finally, we highlight current trends, the importance of multi-phase-field models in biological and physics research, and future challenges.

cond-mat.soft↗

arXiv2025

Beyond Dipolar Activity: Quadrupolar Stress Drives Collapse of Nematic Order on Frictional Substrates

The field of active nematics has traditionally employed descriptions based on dipolar activity, with interactions that align along a single axis. However, it has been theoretically predicted that interactions with a substrate, prevalent in most biological systems, would require novel forms of activity, such as quadrupolar activity, that are governed by hydrodynamic screening. Here, by combining experiments and numerical simulations, we show that upon light-induced solidification of the underlying medium, microtubule-kinesin mixtures undergo a transformation that leads to a biphasic active suspension. Using an active lyotropic model, we prove that the transition is governed by screening effects that alter the dominant form of active stress. Specifically, the combined effect of friction and quadrupolar activity leads to a hierarchical folding that follows the intrinsic bend instability of the active nematic layer. Our results demonstrate the dynamics of the collapse of orientational order in active nematics and present a new route for controlling active matter by modifying the activity through changing the surrounding environment.

cond-mat.soft↗