arXiv subjects

Md Mainul Hasan Sabbir

Publications and source records attributed to Md Mainul Hasan Sabbir.

6 recordsLinked to original sources

arXiv2026

Measures of Chaotic Advection in Simulations of Active Nematics

Active nematics are non-equilibrium fluids composed of rod-like self-propelled units that collectively generate large-scale coherent flows. Here, we focus on a canonical experimental system: an active nematic fluid in $2D$ driven by ATP, composed of densely packed, extended microtubule (MT) bundles cross-linked by kinesin motors. An intriguing feature of this system is the creation and annihilation of topological defects with topological charge $\pm1/2$, due to the fracturing of the material. Experiments confirm that the positive ($+1/2$) defects serve as "virtual stirring rods" that move around each other in a complex braiding pattern. This collective braiding motion of positive defects stretches and folds the fluid itself, i.e., produces macroscale chaotic advection. The degree of self-mixing due to the chaotic advection can be measured using topological entropy and the Lyapunov exponent. Our goal is to determine whether continuum models of MT-based active nematic fluid can reproduce these measurements. To this end, we use two continuum models: the traditional Beris-Edwards (BE) model and the more recently developed Beris-Edwards model with enhanced nematic locking (BENL). The difference between the two models is the adoption of the "nematic locking principle", which states that an individual MT bundle cannot rotate independently of its neighbors due to steric interactions among elongated dense MT bundles. This principle holds in the BENL model except in small localized areas of the material domain where the material fractures, specifically near the creation and annihilation of topological defects. We employ several numerical methods to estimate measures of chaotic advection using both models. Our study shows that the BENL model more accurately reproduces experimental measures of self-mixing driven by chaotic advection in MT-based active nematic fluids.

cond-mat.soft↗

arXiv2026

Modeling density variations in two-dimensional microtubule-based active nematics

A dense two-dimensional layer of aligned microtubules (MTs), powered by molecular motors, is a canonical laboratory model of active materials and a synthetic analog of biological systems such as bacterial turbulence, mitotic spindles, and morphogenesis. This material exhibits nematic ordering and associated topological defects, which display complex emergent dynamics, including the creation and annihilation of defects and the braiding of defects around one another in a complicated chaotic dance. Despite its prominent role in research, the MT-based active nematic material lacks a well established theoretical model that accurately captures the rich density variations prominently seen in experiments---density variations that are, in fact, the experimental signature of the nematic structure itself. The MT-system is typically modeled using two fields: the Q-tensor (encoding the order and orientation of the nematic phase) and the fluid velocity; critically, the microtubule density is assumed to be constant. This traditional model is adopted from classical Landau-de Gennes liquid crystal theory. Here, we present a fundamentally different approach to modeling MT-based active nematics that explicitly incorporates density variations, producing simulations that strongly resemble experimental videos, including the characteristic striation patterns. It also reproduces important behavior of the system confined to a circular well---behavior seen experimentally, but not captured by current theory. In crafting our model, we present an alternative to Landau-de Gennes theory for the creation and annihilation of topological defects that does not rely on the classic isotropic-nematic phase transition.

cond-mat.soft↗

arXiv2026

Chaos-generating periodic orbits of topological defects in confined active nematics

Active nematics in two dimensions stir themselves efficiently through internally generated chaotic flows, largely driven by motile $+1/2$ disclinations. We investigate how this tendency toward chaotic fluid stirring can, counterintuitively, produce certain ordered, periodic flows in confinement, characterized by stable periodic orbits of $+1/2$ disclinations. We computationally study two-dimensional active nematics in systems with boundary conditions requiring a prescribed number $n$ of excess $+1/2$ disclinations, using Beris-Edwards nematohydrodynamics simulations alongside an agent-based simulation approach. We find that when confinement is sufficiently strong to prevent defect pair-nucleation, but not strong enough to arrest all flow, then $n=3$ defects generically follow a "golden braid" orbit as observed recently in experiments, and we predict a "silver braid" orbit of $n=4$ defects. For these results and for greater numbers of defects, we show that the periodic or chaotic nature of the dynamics is determined by a balance between the number of defects and the number of vortices in the flow field, suggesting a new design criterion for ordered flows in active nematics.

cond-mat.soft↗

arXiv2025

Modeling active nematics via the nematic locking principle

Active nematic systems consist of rod-like internally driven subunits that interact with one another to form large-scale coherent flows. They are important examples of far-from-equilibrium fluids, which exhibit a wealth of nonlinear behavior. This includes active turbulence, in which topological defects braid around one another in a chaotic fashion. One of the most studied examples of active nematics is a dense two-dimensional layer of microtubules, crosslinked by kinesin molecular motors that inject extensile deformations into the fluid. Though numerous studies have modeled microtubule-based active nematics, no consensus has emerged on how to fully capture the features of the experimental system. To better understand the foundations for modeling this system, we propose a fundamental principle we call the nematic locking principle: individual microtubules cannot rotate without all neighboring microtubules also rotating. Physically, this is justified by the high density of the microtubules, their elongated nature, and their corresponding steric interactions. We assert that nematic locking holds throughout the majority of the material but breaks down in the neighborhood of topological defects and other regions of low density. We derive the most general nematic transport equation consistent with this principle and also derive the most general term that violates it. We examine the standard Beris-Edwards approach used to model this system and show that it violates nematic locking throughout the majority of the material. We then propose a modification to the Beris-Edwards model that enforces nematic locking nearly everywhere. This modification shuts off fracturing except in regions where the order parameter is reduced. The resulting simulations show strong nematic locking throughout the bulk of the material, consistent with experimental observation.

cond-mat.soft↗

arXiv2024

Controlling chaos: Periodic defect braiding in active nematics confined to a cardioid

This work examines self-mixing in active nematics, a class of fluids in which mobile topological defects drive chaotic flows in a system comprised of biological filaments and molecular motors. We present experiments that demonstrate how geometrical confinement can influence the braiding dynamics of the defects. Notably, we show that confinement in cardioid-shaped wells leads to realization of the golden braid, a maximally efficient mixing state of exactly three defects with no defect creation or annihilation. We characterize the golden braid state using different measures of topological entropy and the Lyapunov exponent. In particular, topological entropy measured from the stretching rate of material lines agrees well with an analytical computation from braid theory. Increasing the size of the confining cardioid produces a transition from the golden braid, to the fully chaotic active turbulent state.

cond-mat.soft↗

arXiv2023

Maximally mixing active nematics

Active nematics are an important new paradigm in soft condensed matter systems. They consist of rod-like components with an internal driving force pushing them out of equilibrium. The resulting fluid motion exhibits chaotic advection, in which a small patch of fluid is stretched exponentially in length. Using simulation, this Letter shows that this system can exhibit stable periodic motion when sufficiently confined to a square with periodic boundary conditions. Moreover, employing tools from braid theory, we show that this motion is maximally mixing, in that it optimizes the (dimensionless) ``topological entropy'' -- the exponential stretching rate of a material line advected by the fluid. That is, this periodic motion of the defects, counterintuitively, produces more chaotic mixing than chaotic motion of the defects. We also explore the stability of the periodic state. Importantly, we show how to stabilize this orbit into a larger periodic tiling, a critical necessity for it to be seen in future experiments.

cond-mat.soft↗