arXiv subjects

M. Lisa Manning

Publications and source records attributed to M. Lisa Manning.

At least 37 records · Page 2Linked to original sources

arXiv2021

Energetic rigidity II: Applications in examples of biological and underconstrained materials

This is the second paper devoted to energetic rigidity, in which we apply our formalism to examples in two dimensions: underconstrained random regular spring networks, vertex models, and jammed packings of soft particles. Spring networks and vertex models are both highly underconstrained, and first-order constraint counting does not predict their rigidity, but second-order rigidity does. In contrast, spherical jammed packings are overconstrained and thus first-order rigid, meaning that constraint counting is equivalent to energetic rigidity as long as prestresses in the system are sufficiently small. Aspherical jammed packings on the other hand have been shown to be jammed at hypostaticity, which we use to argue for a modified constraint counting for systems that are energetically rigid at quartic order.

cond-mat.soft↗

arXiv2021

Bond-space operator disentangles quasi-localized and phononic modes in structural glasses

The origin of several emergent mechanical and dynamical properties of structural glasses is often attributed to populations of localized structural instabilities, coined quasilocalized modes (QLMs). Under a restricted set of circumstances, glassy QLMs can be revealed by analyzing computer glasses' vibrational spectra in the harmonic approximation. However, this analysis has limitations due to system-size effects and hybridization processes with low energy phononic excitations (plane waves) that are omnipresent in elastic solids. Here we overcome these limitations by exploring the spectrum of a linear operator defined on the space of particle interactions (bonds) in a disordered material. We find that this bond-force-response operator offers a unique interpretation of QLMs in glasses, and cleanly recovers some of their important statistical and structural features. The analysis presented here reveals the dependence of the number density (per frequency) and spatial extent of QLMs on material preparation protocol (annealing). Finally, we discuss future research directions and possible extensions of this work.

cond-mat.dis-nn↗

arXiv2021

Effect of cellular rearrangement time delays on the rheology of vertex models for confluent tissues

Large-scale tissue deformation during biological processes such as morphogenesis requires cellular rearrangements. The simplest rearrangement in confluent cellular monolayers involves neighbor exchanges among four cells, called a T1 transition, in analogy to foams. But unlike foams, cells must execute a sequence of molecular processes, such as endocytosis of adhesion molecules, to complete a T1 transition. Such processes could take a long time compared to other timescales in the tissue. In this work, we incorporate this idea by augmenting vertex models to require a fixed, finite time for T1 transitions, which we call the "T1 delay time". We study how variations in T1 delay time affect tissue mechanics, by quantifying the relaxation time of tissues in the presence of T1 delays and comparing that to the cell-shape based timescale that characterizes fluidity in the absence of any T1 delays. We show that the molecular-scale T1 delay timescale dominates over the cell shape-scale collective response timescale when the T1 delay time is the larger of the two. We extend this analysis to tissues that become anisotropic under convergent extension, finding similar results. Moreover, we find that increasing the T1 delay time increases the percentage of higher-fold coordinated vertices and rosettes, and decreases the overall number of successful T1s, contributing to a more elastic-like -- and less fluid-like -- tissue response. Our work suggests that molecular mechanisms that act as a brake on T1 transitions could stiffen global tissue mechanics and enhance rosette formation during morphogenesis.

physics.bio-ph↗

arXiv2021

A simple and broadly-applicable definition of shear transformation zones

Plastic deformation in amorphous solids is known to be carried by stress-induced localized rearrangements of a few tens of particles, accompanied by the conversion of elastic energy to heat. Despite their central role in determining how glasses yield and break, the search for a simple and generally applicable definition of the precursors of those plastic rearrangements -- the so-called shear transformation zones (STZs) -- is still ongoing. Here we present a simple definition of STZs -- based solely on the harmonic approximation of a glass' energy. We explain why and demonstrate directly that our proposed definition of plasticity carriers in amorphous solids is more broadly applicable compared to anharmonic definitions put forward previously. Finally, we offer an open-source library that analyzes low-lying STZs in computer glasses and in laboratory materials such as dense colloidal suspensions for which the harmonic approximation is accessible. Our results constitute a physically motivated methodological advancement towards characterizing mechanical disorder in glasses, and understanding how they yield.

cond-mat.soft↗

arXiv2021

Jamming and arrest of cell motion in biological tissues

Collective cell motility is crucial to many biological processes including morphogenesis, wound healing, and cancer invasion. Recently, the biology and biophysics communities have begun to use the term cell jamming to describe the collective arrest of cell motion in tissues. Although this term is widely used, the underlying mechanisms are varied. In this review, we highlight three independent mechanisms that can potentially drive arrest of cell motion -- crowding, tension-driven rigidity, and reduction of fluctuations -- and propose a speculative phase diagram that includes all three. Since multiple mechanisms may be operating simultaneously, this emphasizes that experiments should strive to identify which mechanism dominates in a given situation. We also discuss how specific cell-scale and molecular-scale biological processes, such as cell-cell and cell-substrate interactions, control aspects of these underlying physical mechanisms.

physics.bio-ph↗

arXiv2021

Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue

In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features.

cond-mat.soft↗

arXiv2020

How does the extracellular matrix affect the rigidity of an embedded spheroid?

Cellularized tissue and polymer networks can both transition from floppy to rigid as a function of their control parameters, and, yet, the two systems often mechanically interact, which may affect their respective rigidities. To study this interaction, we consider a vertex model with interfacial tension (a spheroid) embedded in a spring network in two dimensions. We identify two regimes with different global spheroid shapes, governed by the pressure resulting from competition between interfacial tension and tension in the network. In the first regime, the tissue remains compact, while in the second, a cavitation-like instability leads to the emergence of gaps at the tissue-network interface. Intriguingly, compression of the tissue promotes fluidization, while tension promotes cellular alignment and rigidification, with the mechanisms driving rigidification differing on either side of the instability.

q-bio.CB↗

arXiv2020

Anisotropy links cell shapes to tissue flow during convergent extension

Within developing embryos, tissues flow and reorganize dramatically on timescales as short as minutes. This includes epithelial tissues, which often narrow and elongate in convergent extension movements due to anisotropies in external forces or in internal cell-generated forces. However, the mechanisms that allow or prevent tissue reorganization, especially in the presence of strongly anisotropic forces, remain unclear. We study this question in the converging and extending Drosophila germband epithelium, which displays planar polarized myosin II and experiences anisotropic forces from neighboring tissues, and we show that in contrast to isotropic tissues, cell shape alone is not sufficient to predict the onset of rapid cell rearrangement. From theoretical considerations and vertex model simulations, we predict that in anisotropic tissues two experimentally accessible metrics of cell patterns, the cell shape index and a cell alignment index, are required to determine whether an anisotropic tissue is in a solid-like or fluid-like state. We show that changes in cell shape and alignment over time in the Drosophila germband predict the onset of rapid cell rearrangement in both wild-type and snail twist mutant embryos, where our theoretical prediction is further improved when we also account for cell packing disorder. These findings suggest that convergent extension is associated with a transition to more fluid-like tissue behavior, which may help accommodate tissue shape changes during rapid developmental events.

q-bio.TO↗

arXiv2020

The cell adaptation time sets a minimum length scale for patterned substrates

The structure and dynamics of tissue cultures depend strongly on the physical and chemical properties of the underlying substrate. Inspired by previous advances in the context of inorganic materials, the use of patterned culture surfaces has been proposed as an effective way to induce space-dependent properties in cell tissues. However, cells move and diffuse and the transduction of external stimuli to biological signals is not instantaneous. Here, we show that the fidelity of patterns depends on the relation between the diffusion ($τ_D$) and adaptation ($τ$) times. Numerical results for the self-propelled Voronoi model reveal that the fidelity decreases with $τ/τ_D$, a result that is reproduced by a continuum reaction-diffusion model. We derive a minimum length scale for the patterns that depends on $τ/τ_D$ and can be much larger than the cell size.

cond-mat.soft↗

arXiv2020

Small-scale demixing in confluent biological tissues

Surface tension governed by differential adhesion can drive fluid particle mixtures to sort into separate regions, i.e., demix. Does the same phenomenon occur in confluent biological tissues? We begin to answer this question for epithelial monolayers with a combination of theory via a vertex model and experiments on keratinocyte monolayers. Vertex models are distinct from particle models in that the interactions between the cells are shape-based, as opposed to distance-dependent. We investigate whether a disparity in cell shape or size alone is sufficient to drive demixing in bidisperse vertex model fluid mixtures. Surprisingly, we observe that both types of bidisperse systems robustly mix on large lengthscales. On the other hand, shape disparity generates slight demixing over a few cell diameters, a phenomenon we term micro-demixing. This result can be understood by examining the differential energy barriers for neighbor exchanges (T1 transitions). Experiments with mixtures of wild-type and E-cadherin-deficient keratinocytes on a substrate are consistent with the predicted phenomenon of micro-demixing, which biology may exploit to create subtle patterning. The robustness of mixing at large scales, however, suggests that despite some differences in cell shape and size, progenitor cells can readily mix throughout a developing tissue until acquiring means of recognizing cells of different types.

cond-mat.soft↗

arXiv2019

Two classes of events in sheared particulate matter

Under shear, a system of particles changes its contact network and becomes unstable as it transitions between mechanically stable states. For hard spheres at zero pressure, contact breaking events necessarily generate an instability, but this is not the case at finite pressure, where we identify two types of contact changes: network events that do not correspond to instabilities and rearrangement events that do. The relative fraction of such events is constant as a function of system size, pressure and interaction potential, consistent with our observation that both nonlinearities obey the same finite-size scaling. Thus, the zero-pressure limit of the nonlinear response is highly singular.

cond-mat.soft↗

arXiv2019

Nonlinear analysis of the fluid-solid transition in a model for ordered biological tissues

The rheology of biological tissues is important for their function, and we would like to better understand how single cells control global tissue properties such as tissue fluidity. A confluent tissue can fluidize when cells diffuse by executing a series of cell rearrangements, or T1 transitions. In a disordered 2D vertex model, the tissue fluidizes when the T1 energy barriers disappear as the target shape index approaches a critical value ($s^*_{0} \sim 3.81$), and the shear modulus describing the linear response also vanishes at this same critical point. However, the ordered ground states of 2D vertex models become linearly unstable at a lower value of the target shape index (3.72) [1,2]. We investigate whether the ground states of the 2D vertex model are fluid-like or solid-like between 3.72 and 3.81 $-$ does the "equation of state" for these systems have two branches, like glassy particulate matter, or only one? Using four-cell and many-cell numerical simulations, we demonstrate that for a hexagonal ground state, T1 energy barriers only vanish at $\sim 3.81$, indicating that ordered systems have the same critical point as disordered systems. We also develop a simple geometric argument that correctly predicts how non-linear stabilization disappears at $s^*_{0}$ in ordered systems.

cond-mat.soft↗

arXiv2019

Glassy Dynamics in Models of Confluent Tissue with Mitosis and Apoptosis

Recent work on particle-based models of tissues has suggested that any finite rate of cell division and cell death is sufficient to fluidize an epithelial tissue. At the same time, experimental evidence has indicated the existence of glassy dynamics in some epithelial layers despite continued cell cycling. To address this discrepancy, we quantify the role of cell birth and death on glassy states in confluent tissues using simulations of an active vertex model that includes cell motility, cell division, and cell death. Our simulation data is consistent with a simple ansatz in which the rate of cell-life cycling and the rate of relaxation of the tissue in the absence of cell cycling contribute independently and additively to the overall rate of cell motion. Specifically, we find that a glass-like regime with caging behavior indicated by subdiffusive cell displacements can be achieved in systems with sufficiently low rates of cell cycling.

cond-mat.soft↗

arXiv2019

A minimal-length approach unifies rigidity in under-constrained materials

We present a novel approach to understand geometric-incompatibility-induced rigidity in under-constrained materials, including sub-isostatic 2D spring networks and 2D and 3D vertex models for dense biological tissues. We show that in all these models a geometric criterion, represented by a minimal length $\bar\ell_\mathrm{min}$, determines the onset of prestresses and rigidity. This allows us to predict not only the correct scalings for the elastic material properties, but also the precise {\em magnitudes} for bulk modulus and shear modulus discontinuities at the rigidity transition as well as the magnitude of the Poynting effect. We also predict from first principles that the ratio of the excess shear modulus to the shear stress should be inversely proportional to the critical strain with a prefactor of three, and propose that this factor of three is a general hallmark of geometrically induced rigidity in under-constrained materials and could be used to distinguish this effect from nonlinear mechanics of single components in experiments. Lastly, our results may lay important foundations for ways to estimate $\bar\ell_\mathrm{min}$ from measurements of local geometric structure, and thus help develop methods to characterize large-scale mechanical properties from imaging data.

cond-mat.soft↗

arXiv2018

Tissue flow induces cell shape changes during organogenesis

In embryonic development, programmed cell shape changes are essential for building functional organs, but in many cases the mechanisms that precisely regulate these changes remain unknown. We propose that fluid-like drag forces generated by the motion of an organ through surrounding tissue could generate changes to its structure that are important for its function. To test this hypothesis, we study the zebrafish left-right organizer, Kupffer's vesicle (KV), using experiments and mathematical modeling. During development, monociliated cells that comprise the KV undergo region-specific shape changes along the anterior-posterior axis that are critical for KV function: anterior cells become long and thin, while posterior cells become short and squat. Here, we develop a mathematical vertex-like model for cell shapes, which incorporates both tissue rheology and cell motility, and constrain the model parameters using previously published rheological data for the zebrafish tailbud [Serwane et al.] as well as our own measurements of the KV speed. We find that drag forces due to dynamics of cells surrounding the KV could be sufficient to drive KV cell shape changes during KV development. More broadly, these results suggest that cell shape changes could be driven by dynamic forces not typically considered in models or experiments.

physics.bio-ph↗

arXiv2018

Statistical properties of 3D cell geometry from 2D slices

Although cell shape can reflect the mechanical and biochemical properties of the cell and its environment, quantification of 3D cell shapes within 3D tissues remains difficult, typically requiring digital reconstruction from a stack of 2D images. We investigate a simple alternative technique to extract information about the 3D shapes of cells in a tissue; this technique connects the ensemble of 3D shapes in the tissue with the distribution of 2D shapes observed in independent 2D slices. Using cell vertex model geometries, we find that the distribution of 2D shapes allows clear determination of the mean value of a 3D shape index. We analyze the errors that may arise in practice in the estimation of the mean 3D shape index from 2D imagery and find that typically only a few dozen cells in 2D imagery are required to reduce uncertainty below 2\%. This framework could be naturally extended to estimate additional 3D geometric features and quantify their uncertainty in other materials.

q-bio.QM↗

arXiv2017

Anomalous glassy dynamics in simple models of dense biological tissue

In order to understand the mechanisms for glassy dynamics in biological tissues and shed light on those in non-biological materials, we study the low-temperature disordered phase of 2D vertex-like models. Recently it has been noted that vertex models have quite unusual behavior in the zero-temperature limit, with rigidity transitions that are controlled by residual stresses and therefore exhibit very different scaling and phenomenology compared to particulate systems. Here we investigate the finite-temperature phase of two-dimensional Voronoi and Vertex models, and show that they have highly unusual, sub-Arrhenius scaling of dynamics with temperature. We connect the anomalous glassy dynamics to features of the potential energy landscape associated with zero-temperature inherent states.

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↗