arXiv subjects

Cuncheng Zhu

Publications and source records attributed to Cuncheng Zhu.

4 recordsLinked to original sources

arXiv2026

Mechanics of axis formation in $\textit{Hydra}$

The emergence of a body axis is a fundamental step in the development of multicellular organisms. In simple systems such as $\textit{Hydra}$, growing evidence suggests that mechanical forces generated by collective cellular activity play a central role in this process. Here, we explore a physical mechanism for axis formation based on the coupling between active stresses and tissue elasticity. We analyse the elastic deformation induced by activity-generated stresses and show that, owing to the spherical topology of the tissue, forces globally condense toward configurations in which both elastic strain and nematic defect localise at opposite poles. These mechanically selected states define either a polar or apolar head-food axis. To characterize the condensed regime, we introduce a compact parametrization of of the active force and flux distributions, enabling analytical predictions and direct comparison with experiments. Using this framework, we calculate experimentally relevant observables, including areal strain, lateral pressure, and normal displacements during muscular contraction, as well as the detailed structure of topological defect complexes in head and foot regions. Together, our results identify a mechanical route by which active tissues can spontaneously break symmetry at the organismal scale, suggesting a general physical principle underlying body-axis specification during morphogenesis.

cond-mat.soft↗

arXiv2025

Stokes flow of an evolving fluid film with arbitrary shape and topology

The dynamics of evolving fluid films in the viscous Stokes limit is relevant to various applications, such as the modeling of lipid bilayers in cells. While the governing equations were formulated by Scriven in 1960, solving for the flow of a deformable viscous surface with arbitrary shape and topology has remained a challenge. In this study, we present a straightforward discrete model based on variational principles to address this long-standing problem. We replace the classical equations, which are expressed with tensor calculus in local coordinates, with a simple coordinate-free, differential-geometric formulation. The formulation provides a fundamental understanding of the underlying mechanics and directly translates to discretization. We construct a discrete analogue of the system using the Onsager variational principle, which, in a smooth context, governs the flow of a viscous medium. In the discrete setting, instead of term-wise discretizing the coordinate-based Stokes equations, we construct a discrete Rayleighian for the system and derive the discrete Stokes equations via the variational principle. This approach results in a stable, structure-preserving variational integrator that solves the system on general manifolds.

physics.flu-dyn↗

arXiv2024

Active nematic fluids on Riemannian 2-manifolds

Recent advances in cell biology and experimental techniques using reconstituted cell extracts have generated significant interest in understanding how geometry and topology influence active fluid dynamics. In this work, we present a comprehensive continuous theory and computational method to explore the dynamics of active nematic fluids on arbitrary surfaces without topological constraints. The fluid velocity and nematic order parameter are represented as the sections of the complex line bundle of a 2-manifold. We introduce the Levi-Civita connection and surface curvature form within the framework of complex line bundles. By adopting this geometric approach, we introduce a gauge-invariant discretization method that preserves the continuous local-to-global theorems in differential geometry. We establish a nematic Laplacian on complex functions that can accommodate fractional topological charges through the covariant derivative on the complex nematic representation. We formulate advection of the nematic field based on a unifying definition of the Lie derivative, resulting in a stable geometric semi-Lagrangian discretization scheme for transport by the flow. In general, the proposed surface-based method offers an efficient and stable means to investigate the influence of local curvature and global topology on the 2D hydrodynamics of active nematic systems. Moreover, the complex line representation of the nematic field and the unifying Lie advection present a systematic approach for generalizing our method to active $k$-atic systems.

cond-mat.soft↗

arXiv2021

Mem3DG: Modeling Membrane Mechanochemical Dynamics in 3D using Discrete Differential Geometry

Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared to approximation-based methods (e.g., finite element method), the class of discrete mesh models offers greater flexibility to simulate complex physics and shapes in three dimensions; its formulation produces an efficient algorithm while maintaining coordinate-free geometric descriptions. However, ambiguities in geometric definitions in the discrete context have led to a lack of consensus on which discrete mesh model is theoretically and numerically optimal; a bijective relationship between the terms contributing to both the energy and forces from the discrete and smooth geometric theories remains to be established. We address this and present an extensible framework, $\texttt{Mem3DG}$, for modeling 3D mechanochemical dynamics of membranes based on Discrete Differential Geometry (DDG) on triangulated meshes. The formalism of DDG resolves the inconsistency and provides a unifying perspective on how to relate the smooth and discrete energy and forces. To demonstrate, $\texttt{Mem3DG}$ is used to model a sequence of examples with increasing mechanochemical complexity: recovering classical shape transformations such as 1) biconcave disk, dumbbell, and unduloid and 2) spherical bud on spherical, flat-patch membrane; investigating how the coupling of membrane mechanics with protein mobility jointly affects phase and shape transformation. As high-resolution 3D imaging of membrane ultrastructure becomes more readily available, we envision Mem3DG to be applied as an end-to-end tool to simulate realistic cell geometry under user-specified mechanochemical conditions.

cs.CE↗