arXiv subjects

Dapeng Bi

Publications and source records attributed to Dapeng Bi.

36 records · Page 2Linked to original sources

arXiv2019

Mechanical heterogeneity in tissues promotes rigidity and controls cellular invasion

We study the influence of cell-level mechanical heterogeneity in epithelial tissues using a vertex-based model. Heterogeneity in single cell stiffness is introduced as a quenched random variable in the preferred shape index($p_0$) for each cell. We uncovered a crossover scaling for the tissue shear modulus, suggesting that tissue collective rigidity is controlled by a single parameter $f_r$, which accounts for the fraction of rigid cells. Interestingly, the rigidity onset occurs at $f_r=0.21$, far below the contact percolation threshold of rigid cells. Due to the separation of rigidity and contact percolations, heterogeneity can enhance tissue rigidity and gives rise to an intermediate solid state. The influence of heterogeneity on tumor invasion dynamics is also investigated. There is an overall impedance of invasion as the tissue becomes more rigid. Invasion can also occur in the intermediate heterogeneous solid state and is characterized by significant spatial-temporal intermittency.

physics.bio-ph↗

arXiv2019

Multicellular rosettes drive fluid-solid transition in epithelial tissues

Models for confluent biological tissues often describe the network formed by cells as a triple-junction network, similar to foams. However, higher order vertices or multicellular rosettes are prevalent in developmental and {\it in vitro} processes and have been recognized as crucial in many important aspects of morphogenesis, disease, and physiology. In this work, we study the influence of rosettes on the mechanics of a confluent tissue. We find that the existence of rosettes in a tissue can greatly influence its rigidity. Using a generalized vertex model and effective medium theory we find a fluid-to-solid transition driven by rosette density and intracellular tensions. This transition exhibits several hallmarks of a second-order phase transition such as a growing correlation length and a universal critical scaling in the vicinity a critical point. Further, we elucidate the nature of rigidity transitions in dense biological tissues and other cellular structures using a generalized Maxwell constraint counting approach. This answers a long-standing puzzle of the origin of solidity in these systems.

physics.bio-ph↗

arXiv2018

Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing

Collective cell migration in cohesive units is vital for tissue morphogenesis, wound repair, and immune response. While the fundamental driving forces for collective cell motion stem from contractile and protrusive activities of individual cells, it remains unknown how their balance is optimized to maintain tissue cohesiveness and the fluidity for motion. Here we present a cell-based computational model for collective cell migration during wound healing that incorporates mechanochemical coupling of cell motion and adhesion kinetics with stochastic transformation of active motility forces. We show that a balance of protrusive motility and actomyosin contractility is optimized for accelerating the rate of wound repair, which is robust to variations in cell and substrate mechanical properties. This balance underlies rapid collective cell motion during wound healing, resulting from a tradeoff between tension mediated collective cell guidance and active stress relaxation in the tissue.

physics.bio-ph↗

arXiv2018

Epithelial Wound Healing Coordinates Distinct Actin Network Architectures to Conserve Mechanical Work and Balance Power

How cells with diverse morphologies and cytoskeletal architectures modulate their mechanical behaviors to drive robust collective motion within tissues is poorly understood. During wound repair within epithelial monolayers in vitro, cells coordinate the assembly of branched and bundled actin networks to regulate the total mechanical work produced by collective cell motion. Using traction force microscopy, we show that the balance of actin network architectures optimizes the wound closure rate and the magnitude of the mechanical work. These values are constrained by the effective power exerted by the monolayer, which is conserved and independent of actin architectures. Using a cell-based physical model, we show that the rate at which mechanical work is done by the monolayer is limited by the transformation between actin network architectures and differential regulation of cell-substrate friction. These results and our proposed molecular mechanisms provide a robust quantitative model for how cells collectively coordinate their non-equilibrium behaviors to dynamically regulate tissue-scale mechanical output.

physics.bio-ph↗

arXiv2018

A biological tissue-inspired tunable photonic fluid

Inspired by how cells pack in dense biological tissues, we design 2D and 3D amorphous materials which possess a complete photonic band gap. A physical parameter based on how cells adhere with one another and regulate their shapes can continuously tune the photonic band gap size as well as the bulk mechanical properties of the material. The material can be tuned to go through a solid-fluid phase transition characterized by a vanishing shear modulus. Remarkably, the photonic band gap persists in the fluid phase, giving rise to a photonic fluid that is robust to flow and rearrangements. Experimentally this design should lead to the engineering of self-assembled non-rigid photonic structures with photonic band gaps that can be controlled in real time via mechanical and thermal tuning.

cond-mat.soft↗

arXiv2017

Hydrodynamics of shape-driven rigidity transitions in motile tissues

In biological tissues, it is now well-understood that mechanical cues are a powerful mechanism for pattern regulation. While much work has focused on interactions between cells and external substrates, recent experiments suggest that cell polarization and motility might be governed by the internal shear stiffness of nearby tissue, deemed "plithotaxis". Meanwhile, other work has demonstrated that there is a direct relationship between cell shapes and tissue shear modulus in confluent tissues. Joining these two ideas, we develop a hydrodynamic model that couples cell shape, and therefore tissue stiffness, to cell motility and polarization. Using linear stability analysis and numerical simulations, we find that tissue behavior can be tuned between largely homogeneous states and patterned states such as asters, controlled by a composite "morphotaxis" parameter that encapsulates the nature of the coupling between shape and polarization. The control parameter is in principle experimentally accessible, and depends both on whether a cell tends to move in the direction of lower or higher shear modulus, and whether sinks or sources of polarization tend to fluidize the system.

cond-mat.soft↗

arXiv2017

Flocking Transition in Confluent Tissues

Collective cell migration underlies important biological processes, such as embryonic development, wound healing and cancer invasion. While many aspects of single cell movements are now well established, the mechanisms leading to displacements of cohesive cell groups are still poorly understood. To elucidate the emergence of collective migration in mechanosensitive cells, we examine a self-propelled Voronoi (SPV) model of confluent tissues with an orientational feedback that aligns a cell's polarization with its local migration velocity. While shape and motility are known to regulate a density-independent liquid-solid transition in tissues, we find that aligning interactions facilitate collective motion and promote solidification. Our model reproduces the behavior observed in jammed epithelial monolayers, which are unjammed by the addition of the endocytic protein RAB5A that promotes cell motility by inducing large scale coherent migratory patterns and local fluidization.

cond-mat.soft↗

arXiv2017

Universal geometric constraints during epithelial jamming

As an injury heals, an embryo develops, or a carcinoma spreads, epithelial cells systematically change their shape. In each of these processes cell shape is studied extensively, whereas variation of shape from cell-to-cell is dismissed most often as biological noise. But where do cell shape and variation of cell shape come from? Here we report that cell shape and shape variation are mutually constrained through a relationship that is purely geometrical. That relationship is shown to govern maturation of the pseudostratified bronchial epithelial layer cultured from both non-asthmatic and asthmatic donors as well as formation of the ventral furrow in the epithelial monolayer of the Drosophila embryo in vivo. Across these and other vastly different epithelial systems, cell shape variation collapses to a family of distributions that is common to all and potentially universal. That distribution, in turn, is accounted for quantitatively by a mechanistic theory of cell-cell interaction showing that cell shape becomes progressively less elongated and less variable as the layer becomes progressively more jammed. These findings thus uncover a connection between jamming and geometry that is generic -spanning jammed living and inert systems alike- and demonstrate that proximity of the cell layer to the jammed state is the principal determinant of the most primitive features of epithelial cell shape and shape variation.

physics.bio-ph↗

arXiv2017

Shear-induced rigidity of frictional particles: Analysis of emergent order in stress space

Solids are distinguished from fluids by their ability to resist shear. In traditional solids, the resistance to shear is associated with the emergence of broken translational symmetry as exhibited by a non-uniform density pattern, which results from either minimizing the energy cost or maximizing the entropy or both. In this work, we focus on a class of systems, where this paradigm is challenged. We show that shear-driven jamming in dry granular materials is a collective process controlled solely by the constraints of mechanical equilibrium. We argue that these constraints lead to a broken translational symmetry in a dual space that encodes the statistics of contact forces and the topology of the contact network. The shear-jamming transition is marked by the appearance of this broken symmetry. We extend our earlier work, by comparing and contrasting real space measures of rheology with those obtained from the dual space. We investigate the structure and behavior of the dual space as the system evolves through the rigidity transition in two different shear protocols. We analyze the robustness of the shear-jamming scenario with respect to protocol and packing fraction, and demonstrate that it is possible to define a protocol-independent order parameter in this dual space, which signals the onset of rigidity.

cond-mat.soft↗

arXiv2017

Correlating Cell Shape and Cellular Stress in Motile Confluent Tissues

Collective cell migration is a highly regulated process involved in wound healing, cancer metastasis and morphogenesis. Mechanical interactions among cells provide an important regulatory mechanism to coordinate such collective motion. Using a Self-Propelled Voronoi (SPV) model that links cell mechanics to cell shape and cell motility, we formulate a generalized mechanical inference method to obtain the spatio-temporal distribution of cellular stresses from measured traction forces in motile tissues and show that such traction-based stresses match those calculated from instantaneous cell shapes. We additionally use stress information to characterize the rheological properties of the tissue. We identify a motility-induced swim stress that adds to the interaction stress to determine the global contractility or extensibility of epithelia. We further show that the temporal correlation of the interaction shear stress determines an effective viscosity of the tissue that diverges at the liquid-solid transition, suggesting the possibility of extracting rheological information directly from traction data.

cond-mat.soft↗

arXiv2016

Motility-driven glass and jamming transitions in biological tissues

Cell motion inside dense tissues governs many biological processes, including embryonic development and cancer metastasis, and recent experiments suggest that these tissues exhibit collective glassy behavior. To make quantitative predictions about glass transitions in tissues, we study a self-propelled Voronoi (SPV) model that simultaneously captures polarized cell motility and multi-body cell-cell interactions in a confluent tissue, where there are no gaps between cells. We demonstrate that the model exhibits a jamming transition from a solid-like state to a fluid-like state that is controlled by three parameters: the single-cell motile speed, the persistence time of single-cell tracks, and a target shape index that characterizes the competition between cell-cell adhesion and cortical tension. In contrast to traditional particulate glasses, we are able to identify an experimentally accessible structural order parameter that specifies the entire jamming surface as a function of model parameters. We demonstrate that a continuum Soft Glassy Rheology model precisely captures this transition in the limit of small persistence times, and explain how it fails in the limit of large persistence times. These results provide a framework for understanding the collective solid-to-liquid transitions that have been observed in embryonic development and cancer progression, which may be associated with Epithelial-to-Mesenchymal transition in these tissues.

physics.bio-ph↗

arXiv2015

A density-independent glass transition in biological tissues

Cell migration is important in many biological processes, including embryonic development, cancer metastasis, and wound healing. In these tissues, a cell's motion is often strongly constrained by its neighbors, leading to glassy dynamics. While self-propelled particle models exhibit a density-driven glass transition, this does not explain liquid-to-solid transitions in confluent tissues, where there are no gaps between cells and therefore the density is constant. Here we demonstrate the existence of a new type of rigidity transition that occurs in the well-studied vertex model for confluent tissue monolayers at constant density. We find the onset of rigidity is governed by a model parameter that encodes single-cell properties such as cell-cell adhesion and cortical tension, providing an explanation for a liquid-to-solid transitions in confluent tissues and making testable predictions about how these transitions differ from those in particulate matter.

physics.bio-ph↗

arXiv2014

The Statistical Physics of Athermal Materials

At the core of equilibrium statistical mechanics lies the notion of statistical ensembles: a collection of microstates, each occurring with a given a priori probability that depends only on a few macroscopic parameters such as temperature, pressure, volume, and energy. In this review article, we discuss recent advances in establishing statistical ensembles for athermal materials. The broad class of granular and particulate materials is immune from the effects of thermal fluctuations because the constituents are macroscopic. In addition, interactions between grains are frictional and dissipative, which invalidates the fundamental postulates of equilibrium statistical mechanics. However, granular materials exhibit distributions of microscopic quantities that are reproducible and often depend on only a few macroscopic parameters. We explore the history of statistical ensemble ideas in the context of granular materials, clarify the nature of such ensembles and their foundational principles, highlight advances in testing key ideas, and discuss applications of ensembles to analyze the collective behavior of granular materials.

cond-mat.stat-mech↗

arXiv2014

Energy barriers govern glassy dynamics in tissues

Recent observations demonstrate that densely packed tissues exhibit features of glassy dynamics, such as caging behavior and dynamical heterogeneities, although it has remained unclear how single-cell properties control this behavior. Here we develop numerical and theoretical models to calculate energy barriers to cell rearrangements, which help govern cell migration in cell monolayers. In contrast to work on sheared foams, we find that energy barrier heights are exponentially distributed and depend systematically on the cell's number of neighbors. Based on these results, we predict glassy two-time correlation functions for cell motion, with a timescale that increases rapidly as cell activity decreases. These correlation functions are used to construct simple random walks that reproduce the caging behavior observed for cell trajectories in experiments. This work provides a theoretical framework for predicting collective motion of cells in wound-healing, embryogenesis and cancer tumorigenesis.

cond-mat.soft↗

arXiv2013

Origin of Rigidity in Dry Granular Solids

Solids are distinguished from fluids by their ability to resist shear. In traditional solids, the resistance to shear is associated with the emergence of broken translational symmetry as exhibited by a non-uniform density pattern. In this work, we focus on the emergence of shear-rigidity in a class of solids where this paradigm is challenged. Dry granular materials have no energetically or entropically preferred density modulations. We show that, in contrast to traditional solids, the emergence of shear rigidity in these granular solids is a collective process, which is controlled solely by boundary forces, the constraints of force and torque balance, and the positivity of the contact forces. We develop a theoretical framework based on these constraints, which connects rigidity to broken translational symmetry in the space of forces, not positions of grains. We apply our theory to experimentally generated shear-jammed (SJ) states and show that these states are indeed characterized by a persistent, non-uniform density modulation in force space, which emerges at the shear-jamming transition.

cond-mat.soft↗

arXiv2013

Fluctuations in Shear-Jammed States: A Statistical Ensemble Approach

Granular matter exists out of thermal equilibrium, i.e. it is athermal. While conventional equilibrium statistical mechanics is not useful for characterizing granular materials, the idea of constructing a statistical ensemble analogous to its equilibrium counterpart to describe static granular matter was proposed by Edwards and Oakshott more than two decades ago. Recent years have seen several implementations of this idea. One of these is the stress ensemble, which is based on properties of the force moment tensor, and applies to frictional and frictionless grains. We demonstrate the full utility of this statistical framework in shear jammed (SJ) experimental states [1,2], a special class of granular solids created by pure shear, which is a strictly non-equilbrium protocol for creating solids. We demonstrate that the stress ensemble provides an excellent quantitative description of fluctuations in experimental SJ states. We show that the stress fluctuations are controlled by a single tensorial quantity: the angoricity of the system, which is a direct analog of the thermodynamic temperature. SJ states exhibit significant correlations in local stresses and are thus inherently different from density-driven, isotropically jammed (IJ) states.

cond-mat.soft↗

arXiv2009

Rheology of Granular Materials: Dynamics in a Stress Landscape

We present a framework for analyzing the rheology of dense driven granular materials, based on a recent proposal of a stress-based ensemble. In this ensemble fluctuations in a granular system near jamming are controlled by a temperature-like parameter, the angoricity, which is conjugate to the stress of the system. In this paper, we develop a model for slowly driven granular materials based on the stress ensemble and the idea of a landscape in stress space. The idea of an activated process driven by the angoricity has been shown by Behringer et al (2008) to describe the logarithmic strengthening of granular materials. Just as in the Soft Glassy Rheology (SGR) picture, our model represents the evolution of a small patch of granular material (a mesoscopic region) in a stress-based trap landscape. The angoricity plays the role of the fluctuation temperature in SGR. We determine (a) the constitutive equation, (b) the yield stress, and (c) the distribution of stress dissipated during granular shearing experiments, and compare these predictions to experiments of Hartley & Behringer (2003).

cond-mat.soft↗

arXiv2008

Why Do Granular Materials Stiffen with Shear Rate? A Test of Novel Stress-Based Statistics

Recent experiments exhibit a rate-dependence for granular shear such that the stress grows linearly in the logarithm of the shear rate, \dotγ. Assuming a generalized activated process mechanism, we show that these observations are consistent with a recent proposal for a stress-based statistical ensemble. By contrast, predictions for rate-dependence using conventional energy-based statistical mechanics to describe activated processes, predicts a rate dependence that of (\ln (\dotγ))^{1/2}.

cond-mat.soft↗