arXiv subjects

Dapeng Bi

Publications and source records attributed to Dapeng Bi.

At least 19 recordsLinked to original sources

arXiv2026

Shape-Independent Fluidity in Epithelial Cell Monolayers

Tissue fluidity regulates biological processes such as embryonic development, wound healing, and cancer metastasis. In confluent epithelia, where cell packing fraction is effectively fixed, the prevailing paradigm postulates that fluidity is governed by a geometric shape index determined by the balance of cortical tension and intercellular adhesion. Here, we report that reducing cell-cell adhesion triggers an increase in fluidity with no change in cell shape index, cell density, substrate traction, or junctional line tension. The observed decoupling of shape and fluidity reveals that current vertex models, which treat adhesion as contributing solely to interfacial tension, are incomplete. To reconcile these findings, we extend the theoretical framework to account for the dual nature of adhesion---its thermodynamic role in setting interfacial adhesion energy at the cell-cell junctions and its kinetic role in generating viscous drag due to relative motion between adjacent cells. This generalized model quantitatively captures the experimental data, demonstrating that the interplay between adhesive energy and dissipative friction is essential for epithelial fluidity.

physics.bio-ph↗

arXiv2026

Cell-Cell Adhesion as a Double-Edged Sword in Tissue Fluidity

Cell migration plays a fundamental role in numerous physiological processes, including embryonic development, wound healing, and cancer metastasis. While cell-cell adhesion is known to regulate motion by shaping cell morphology and intercellular force balance, its dynamic, rate-dependent contributions to tissue behavior remain poorly understood. In this study, we examine how the dissipative nature of cell-cell adhesion influences tissue dynamics and collective migration using an extended vertex model with explicit junctional viscosity. Our findings reveal a nontrivial interplay between two distinct components of adhesion: an interfacial adhesion energy (energetic, rate-independent) contribution, which sets the effective junctional tension, and a dissipative (rate-dependent) contribution, which controls resistance to relative motion during cell rearrangements. We show that increasing the energetic component promotes migration by modifying cell shape and lowering the barrier to neighbor exchanges, whereas strengthening the dissipative component induces jamming and suppresses cell motion. Linear rheological analysis further demonstrates that, in the unjammed regime, vertex-model tissues exhibit power-law viscoelastic behavior, with adhesion modulating the power-law exponent and thereby controlling the spread of relaxation timescales. Together, these findings clarify the dual role of adhesion in governing tissue mechanics and rheology and provide a mechanistic framework for understanding the balance between fluidity and rigidity in epithelial monolayers.

physics.bio-ph↗

arXiv2024

Origin of yield stress and mechanical plasticity in model biological tissues

During development and under normal physiological conditions, biological tissues are continuously subjected to substantial mechanical stresses. In response to large deformations cells in a tissue must undergo multicellular rearrangements in order to maintain integrity and robustness. However, how these events are connected in time and space remains unknown. Here, using computational and theoretical modeling, we studied the mechanical plasticity of epithelial monolayers under large deformations. Our results demonstrate that the jamming-unjamming (solid-fluid) transition in tissues can vary significantly depending on the degree of deformation, implying that tissues are highly unconventional materials. Using analytical modeling, we elucidate the origins of this behavior. We also demonstrate how a tissue accommodates large deformations through a collective series of rearrangements, which behave similarly to avalanches in non-living materials. We find that these tissue avalanches are governed by stress redistribution and the spatial distribution of vulnerable spots. Finally, we propose a simple and experimentally accessible framework to predict avalanches and infer tissue mechanical stress based on static images.

physics.bio-ph↗

arXiv2024

Tunable Hyperuniformity and Hidden Information in Random Cellular Structures

Hyperuniform systems possess the isotropic microstructure of liquids while suppressing large-scale density fluctuations with crystal-like precision, endowing them with exotic optical and transport properties. However, generating these states typically relies on top-down algorithmic optimizations that lack physical realism, leaving the fundamental mechanical and thermodynamic limits of such disordered order largely unexplored. Here, we utilize a mechanical vertex model to explore physical conditions that drive self-organized hyperuniformity in this model. By tuning cortical elasticity and interfacial tension, we engineer a continuous spectrum of effectively hyperuniform states. Crucially, hyperuniformity and rigidity are independently tunable in this system: hyperuniform states occur on both sides of the solid--fluid transition, and the degree of hyperuniformity is set by cell mechanics rather than by the onset of rigidity. Building on these states, we introduce the Hyperuniform Poisson Ensemble (HyPE), constructed by overlaying independent hyperuniform subsets. HyPE states preserve long-range hidden order while asymptotically approaching Poissonian randomness at short length scales, establishing universal scaling relations for density fluctuations. As the most disordered hyperuniform systems reported, HyPEs exhibit vanishing configurational entropy, establishing a fundamental thermodynamic lower bound for the information content of hyperuniform matter. By bridging cellular mechanics with the statistical physics of hidden information, this framework provides a universal blueprint for designing multifunctional metamaterials, with direct applications in photonic bandgap engineering, phononic control, and stress-responsive composites.

cond-mat.dis-nn↗

arXiv2024

Multicell-Fold: geometric learning in folding multicellular life

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how every single cell decides to position itself relative to its neighboring cells. Despite its importance, it remains a major challenge to understand and predict the behavior of every cell within the living tissue over time during such intricate processes. To tackle this question, we propose a geometric deep learning model that can predict multicellular folding and embryogenesis, accurately capturing the highly convoluted spatial interactions among cells. We demonstrate that multicellular data can be represented with both granular and foam-like physical pictures through a unified graph data structure, considering both cellular interactions and cell junction networks. We successfully use our model to achieve two important tasks, interpretable 4-D morphological sequence alignment, and predicting local cell rearrangements before they occur at single-cell resolution. Furthermore, using an activation map and ablation studies, we demonstrate that cell geometries and cell junction networks together regulate local cell rearrangement which is critical for embryo morphogenesis. This approach provides a novel paradigm to study morphogenesis, highlighting a unified data structure and harnessing the power of geometric deep learning to accurately model the mechanisms and behaviors of cells during development. It offers a pathway toward creating a unified dynamic morphological atlas for a variety of developmental processes such as embryogenesis.

cond-mat.soft↗

arXiv2024

A shape-driven reentrant jamming transition in confluent monolayers of synthetic cell-mimics

Many critical biological processes, like wound healing, require confluent cell monolayers/bulk tissues to transition from a jammed solid-like to a fluid-like state. Although numerical studies anticipate changes in the cell shape alone can lead to unjamming, experimental support for this prediction is not definitive because, in living systems, fluidization due to density changes cannot be ruled out. Additionally, a cell's ability to modulate its motility only compounds difficulties since even in assemblies of rigid active particles, changing the nature of self-propulsion has non-trivial effects on the dynamics. Here, we design and assemble a monolayer of synthetic cell-mimics and examine their collective behaviour. By systematically increasing the persistence time of self-propulsion, we discovered a cell shape-driven, density-independent, re-entrant jamming transition. Notably, we observed cell shape and shape variability were mutually constrained in the confluent limit and followed the same universal scaling as that observed in confluent epithelia. Dynamical heterogeneities, however, did not conform to this scaling, with the fast cells showing suppressed shape variability, which our simulations revealed is due to a transient confinement effect of these cells by their slower neighbors. Our experiments unequivocally establish a morphodynamic link, demonstrating that geometric constraints alone can dictate epithelial jamming/unjamming.

cond-mat.soft↗

arXiv2023

Ductile-to-brittle transition and yielding in soft amorphous materials: perspectives and open questions

Soft amorphous materials are viscoelastic solids ubiquitously found around us, from clays and cementitious pastes to emulsions and physical gels encountered in food or biomedical engineering. Under an external deformation, these materials undergo a noteworthy transition from a solid to a liquid state that reshapes the material microstructure. This yielding transition was the main theme of a workshop held from January 9 to 13, 2023 at the Lorentz Center in Leiden. The manuscript presented here offers a critical perspective on the subject, synthesizing insights from the various brainstorming sessions and informal discussions that unfolded during this week of vibrant exchange of ideas. The result of these exchanges takes the form of a series of open questions that represent outstanding experimental, numerical, and theoretical challenges to be tackled in the near future.

cond-mat.soft↗

arXiv2023

Spatial Confinement Affects the Heterogeneity and Interactions Between Shoaling Fish

Living objects are able to consume chemical energy and process information independently from others. However, living objects can coordinate to form ordered groups such as schools of fish. This work considers these complex groups as living materials and presents imaging-based experiments of laboratory schools of fish to understand how this non-equilibrium activity affects the mechanical properties of a group. We use spatial confinement to control the motion and structure of fish within quasi-2D shoals of fish. Using image analysis techniques, we make quantitative observations of the structures, their spatial heterogeneity, and their temporal fluctuations. Furthermore, we utilize Monte Carlo simulations to replicate the experimentally observed area distribution patterns which provide insight into the effective interactions between fish and confirm the presence of a confinement-based behavioral preference transition. In addition, unlike in short-range interacting systems, here structural heterogeneity and dynamic activities are positively correlated as a result of complex interplay between spatial arrangement and behavioral dynamics in fish collectives.

cond-mat.soft↗

arXiv2023

Epithelial layer fluidization by curvature-induced unjamming

The transition of an epithelial layer from a stationary, quiescent state to a highly migratory, dynamic state is required for wound healing, development, and regeneration. This transition, known as the unjamming transition (UJT), is responsible for epithelial fluidization and collective migration. Previous theoretical models have primarily focused on the UJT in flat epithelial layers, neglecting the effects of strong surface curvature characteristic of the epithelium \textit{in vivo}. In this study, we investigate the role of surface curvature on tissue plasticity and cellular migration using a vertex model embedded on a spherical surface. Our findings reveal that increasing curvature promotes the UJT by reducing the energy barriers to cellular rearrangements. Higher curvature favors cell intercalation, mobility, and self-diffusivity, resulting in epithelial structures that are malleable and migratory when small, but become more rigid and stationary as they grow. Together, these results provide a conceptual framework to better understand how cell shape, cell propulsion, and tissue geometry contribute to tissue malleability, remodeling, and stabilization.

physics.bio-ph↗

arXiv2023

A Mechanistic Model of the Organization of Cell Shapes in Epithelial Tissues

The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our study, we explore a mechanistic model of cellular organization that represents cells as force dipoles that interact with each other via the tissue, which we model as an elastic medium. By conducting numerical simulations using this model, we are able to observe organizational features that are consistent with those obtained from vertex model simulations. This approach provides valuable insights into the underlying mechanisms that govern cellular organization within tissues, which can help us better understand the processes involved in development and disease.

cond-mat.soft↗

arXiv2023

Bridging the Gap Between Collective Motility and Epithelial-Mesenchymal Transitions through the Active Finite Voronoi Model

We introduce an active version of the recently proposed finite Voronoi model of epithelial tissue. The resultant Active Finite Voronoi (AFV) model enables the study of both confluent and non-confluent geometries and transitions between them, in the presence of active cells. Our study identifies six distinct phases, characterized by aggregation-segregation, dynamical jamming-unjamming, and epithelial-mesenchymal transitions (EMT), thereby extending the behavior beyond that observed in previously studied vertex-based models. The AFV model with rich phase diagram provides a cohesive framework that unifies the well-observed progression to collective motility via unjamming with the intricate dynamics enabled by EMT. This approach should prove useful for challenges in developmental biology systems as well as the complex context of cancer metastasis. The simulation code is also provided at https://github.com/jxhuangphys/Active_Finite_Voronoi_simulation.

cond-mat.soft↗

arXiv2023

Cell Division and Motility Enable Hexatic Order in Biological Tissues

Biological tissues transform between solid-like and liquid-like states in many fundamental physiological events. Recent experimental observations further suggest that in two-dimensional epithelial tissues these solid-liquid transformations can happen via intermediate states akin to the intermediate hexatic phases observed in equilibrium two-dimensional melting. The hexatic phase is characterized by quasi-long-range (power-law) orientational order but no translational order, thus endowing some structure to an otherwise structureless fluid. While it has been shown that hexatic order in tissue models can be induced by motility and thermal fluctuations, the role of cell division and apoptosis (birth and death) has remained poorly understood, despite its fundamental biological role. Here we study the effect of cell division and apoptosis on global hexatic order within the framework of the self-propelled Voronoi model of tissue. Although cell division naively destroys order and active motility facilitates deformations, we show that their combined action drives a liquid-hexatic-liquid transformation as the motility increases. The hexatic phase is accessed by the delicate balance of dislocation defect generation from cell division and the active binding of disclination-antidisclination pairs from motility. We formulate a mean-field model to elucidate this competition between cell division and motility and the consequent development of hexatic order.

cond-mat.soft↗

arXiv2023

Network physics of attractive colloidal gels: Resilience, Rigidity, and Phase Diagram

Attractive colloidal gels exhibit solid-like behavior at vanishingly small fractions of solids, owing to ramified space-spanning networks that form due to particle-particle interactions. These networks give the gel its rigidity, and as the attraction between the particles grows, so does the elasticity of the colloidal network formed. The emergence of this rigidity can be described through a mean field approach; nonetheless, fundamental understanding of how rigidity varies in gels of different attraction strengths is lacking. Moreover, recovering an accurate gelation phase diagram based on the system's variables have been an extremely challenging task. Understanding the nature of these fractal clusters, and how rigidity emerges from their connections is key to controlling and designing gels with desirable properties. Here, we employ well-established concepts of network science to interrogate and characterize the network of colloidal gels. We construct a particle-level network, having all the spatial coordinates of colloids with different attraction levels, and also identify polydisperse rigid fractal clusters using a Gaussian Mixture Model, to form a coarse-grained cluster network that distinctly shows main physical features of the colloidal gels. A simple mass-spring model then is used to recover quantitatively the elasticity of colloidal gels from these cluster networks. Interrogating the resilience of these gel networks show that the elasticity of a gel (a dynamic property) is directly correlated to its cluster network's resilience (a static measure). Finally, we use the resilience investigations to devise [and experimentally validate] a fully resolved phase diagram for colloidal gelation, with a clear solid-liquid phase boundary using a single volume fraction of particles well beyond this phase boundary.

cond-mat.soft↗

arXiv2023

Discontinuous rigidity transition associated with shear jamming in granular simulations

We investigate the rigidity transition associated with shear jamming in frictionless, as well as frictional, disk packings in the quasi-static regime and at low shear rates. For frictionless disks, the transition is under quasistatic shear is discontinuous, with an instantaneous emergence of a system spanning rigid cluster at the jamming transition. For frictional systems, the transition appears continuous for finite shear rates, but becomes sharper for lower shear rates. In the quasi-static limit, it is discontinuous as in the frictionless case. Thus, our results show that the rigidity transition associated with shear jamming is discontinuous, as demonstrated in a past for isotropic jamming of frictionless particles, and therefore a unifying feature of the jamming transition in general.

cond-mat.soft↗

arXiv2022

Discontinuous shear thickening in biological tissue rheology

During embryonic morphogenesis, tissues undergo dramatic deformations in order to form functional organs. Similarly, in adult animals, living cells and tissues are continually subjected to forces and deformations. Therefore, the success of embryonic development and the proper maintenance of physiological functions rely on the ability of cells to withstand mechanical stresses as well as their ability to flow in a collective manner. During these events, mechanical perturbations can originate from active processes at the single cell level, competing with external stresses exerted by surrounding tissues and organs. However, the study of tissue mechanics has been somewhat limited to either the response to external forces or to intrinsic ones. In this work, we use an active vertex model of a 2D confluent tissue to study the interplay of external deformations that are applied globally to a tissue with internal active stresses that arise locally at the cellular level due to cell motility. We elucidate in particular the way in which this interplay between globally external and locally internal active driving determines the emergent mechanical properties of the tissue as a whole. For a tissue in the vicinity of a solid-fluid jamming/unjamming transition, we uncover a host of fascinating rheological phenomena, including yielding, shear thinning, continuous shear thickening (CST) and discontinuous shear thickening (DST). These model predictions provide a framework for understanding the recently observed nonlinear rheological behaviors {\it in vivo}.

cond-mat.soft↗

arXiv2022

Constitutive model for the rheology of biological tissue

The rheology of biological tissue is key to processes such as embryo development, wound healing and cancer metastasis. Vertex models of confluent tissue monolayers have uncovered a spontaneous liquid-solid transition tuned by cell shape; and a shear-induced solidification transition of an initially liquid-like tissue. Alongside this jamming/unjamming behaviour, biological tissue also displays an inherent viscoelasticity, with a slow time and rate dependent mechanics. With this motivation, we combine simulations and continuum theory to examine the rheology of the vertex model in nonlinear shear across a full range of shear rates from quastistatic to fast, elucidating its nonlinear stress-strain curves after the inception of shear of finite rate, and its steady state flow curves of stress as a function of strain rate. We formulate a rheological constitutive model that couples cell shape to flow and captures both the tissue solid-liquid transition and its rich linear and nonlinear rheology.

cond-mat.soft↗

arXiv2021

Shear-driven solidification and nonlinear elasticity in epithelial tissues

Biological processes, from morphogenesis to tumor invasion, spontaneously generate shear stresses inside living tissue. The mechanisms that govern the transmission of mechanical forces in epithelia and the collective response of the tissue to bulk shear deformations remain, however, poorly understood. Using a minimal cell-based computational model, we investigate the constitutive relation of confluent tissues under simple shear deformation. We show that an initially undeformed fluidlike tissue acquires finite rigidity above a critical applied strain. This is akin to the shear-driven rigidity observed in other soft matter systems. Interestingly, shear-driven rigidity can be understood by a critical scaling analysis in the vicinity of the second order critical point that governs the liquid-solid transition of the undeformed system. We further show that a solidlike tissue responds linearly only to small strains and but then switches to a nonlinear response at larger stains, with substantial stiffening. Finally, we propose a mean-field formulation for cells under shear that offers a simple physical explanation of shear-driven rigidity and nonlinear response in a tissue.

cond-mat.soft↗

arXiv2020

Controlled neighbor exchanges drive glassy behavior, intermittency and cell streaming in epithelial tissues

Cell neighbor exchanges are integral to tissue rearrangements in biology, including development and repair. Often these processes occur via topological T1 transitions analogous to those observed in foams, grains and colloids. However, in contrast to in non-living materials the T1 transitions in biological tissues are rate-limited and cannot occur instantaneously due to the finite time required to remodel complex structures at cell-cell junctions. Here we study how this rate-limiting process affects the mechanics and collective behavior of cells in a tissue by introducing this important biological constraint in a theoretical vertex-based model as an intrinsic single-cell property. We report in the absence of this time constraint, the tissue undergoes a motility-driven glass transition characterized by a sharp increase in the intermittency of cell-cell rearrangements. Remarkably, this glass transition disappears as T1 transitions are temporally limited. As a unique consequence of limited rearrangements, we also find that the tissue develops spatially correlated streams of fast and slow cells, in which the fast cells organize into stream-like patterns with leader-follower interactions, and maintain optimally stable cell-cell contacts. The predictions of this work is compared with existing in-vivo experiments in Drosophila pupal development.

cond-mat.soft↗