Two-dimensional Vertex Model Research Articles

A two-dimensional vertex model for curvy cell-cell interfaces at the subcellular scale.

Cross-sections of cell shapes in a tissue monolayer typically resemble a tiling of convex polygons. Yet, examples exist where the polygons are not convex with curved cell-cell interfaces, as seen in the adaxial epidermis. To date, two-dimensional vertex models predicting the structure and mechanics of cell monolayers have been mostly limited to convex polygons. To overcome this limitation, we introduce a framework to study curvy cell-cell interfaces at the subcellular scale within vertex models by using a parametrized curve between vertices that is expanded in a Fourier series and whose coefficients represent additional degrees of freedom. This extension to non-convex polygons allows for cells with the same shape index, or dimensionless perimeter, to be, for example, either elongated or globular with lobes. In the presence of applied, anisotropic stresses, we find that local, subcellular curvature or buckling can be energetically more favourable than larger scale deformations involving groups of cells. Inspired by recent experiments, we also find that local, subcellular curvature at cell-cell interfaces emerges in a group of cells in response to the swelling of additional cells surrounding the group. Our framework, therefore, can account for a wider array of multicellular responses to constraints in the tissue environment.

Numerical assessment of the applicability of geometry-based force inference on homogeneous and heterogeneous cells.

The measurement of cellular forces, which reflect crucial biological attributes, has the potential to replace conventional cell assessment methods, such as morphology, proliferation, and molecular expression analysis, in medical cell diagnosis and cell culture studies. In medical cell evaluations, force inference techniques have gained prominence due to their non-invasiveness and lack of requirement for specialized equipment. Among those techniques, the method proposed by Ishihara et al., which estimates forces in densely packed cells based only on cell geometry, is a promising method. However, its applicability range of this method has not been fully established. In this study, we employed a two-dimensional vertex model to numerically assess the applicability of this method on homogeneous and heterogeneous cells. Our comparisons between the true values from numerical simulations and the estimated values from the inference method revealed a significant correlation between estimation accuracy and cell roundness in systems of homogeneous cell. Moreover, the method demonstrated efficient force estimations in heterogeneous-cell systems. These findings may be useful when the force inference method is employed to evaluate medical cells.

Chemo-mechanical model of cell polarization initiated by structural polarity.

Cell polarization is crucial in most physiological functions. Living cells at the extracellular matrix (ECM) actively coordinate a polarized morphology to target the preferred signals. In particular, the initial heterogeneity of subcellular components, termed as structural polarity, has been discovered to mediate the early attachment and transmigration of cells in tumour metastasis. However, how heterogeneous cells initiate the early polarization remains incompletely discovered. Here, we establish a multiscale model of a cell to explore the chemo-mechanical mechanisms of cell polarization initiated by structural polarity. The two-dimensional vertex model of the cell is built with the main mechanical components of eukaryotic cells. The initial structural polarity of the modeled cell is introduced by seeding heterogeneous actin filaments at the cell cortex and quantified by the ratio of the filamentous forces at the vertices. Then, the structural polarity is integrated in the reaction-diffusion system of Rho GTPase (Cdc42) at the cell cortex to obtain the traction forces at the leading vertices. Finally, the modeled cell is actuated to spread under the traction forces and discovered to develop into a characteristic polarized morphology. The results indicate that the cell polarization is initiated and dynamically developed by structural polarity through the reaction-diffusion system of Cdc42. In addition, the bistability of Cdc42 activation at the cell cortex is defined and discovered to dominate the polarization status of the cell. Furthermore, biphasic (i.e., positive and negative) durotaxis of the cell is successfully modeled at an ECM with a stiffness gradient, and concluded to be codetermined by the chemo-mechanical coupling of the initial structural polarity and ECM stiffness gradient. The proposed multiscale model provides a quantitative way to probe cell polarization coupled with mechanical stimuli, biochemical reaction and cytoskeletal reorganization, and holds the potential to guide studies of cell polarization under multiple stimuli.

Single and two-cells shape analysis from energy functionals for three-dimensional vertex models.

Vertex models have been extensively used for simulating the evolution of multicellular systems, and have given rise to important global properties concerning their macroscopic rheology or jamming transitions. These models are based on the definition of an energy functional, which fully determines the cellular response and conclusions. While two-dimensional vertex models have been widely employed, three-dimensional models are far more scarce, mainly due to the large amount of configurations that they may adopt and the complex geometrical transitions they undergo. We here investigate the shape of single and two-cells configurations as a function of the energy terms, and we study the dependence of the final shape on the model parameters: namely the exponent of the term penalising cell-cell adhesion and surface contractility. In single cell analysis, we deduce analytically the radius and limit values of the contractility for linear and quadratic surface energy terms, in 2D and 3D. In two-cells systems, symmetrical and asymmetrical, we deduce the evolution of the aspect ratio and the relative radius. While in functionals with linear surface terms yield the same aspect ratio in 2D and 3D, the configurations when using quadratic surface terms are distinct. We relate our results with well-known solutions from capillarity theory, and verify our analytical findings with a three-dimensional vertex model.

Geometrical characterization of active contraction pulses in epithelial cells using the vertex model

Apical constriction is one of the most relevant mechanisms at the cellular level that promotes tissue remodeling, being essential for developmental contexts. Several models have been proposed to describe the dynamics of epithelial tissues under apical constriction pulses, which differ in where the constriction is applied, either at the perimeter or medial regions. To help discriminate between these models, we use the two-dimensional vertex model for epithelial dynamics to analyze the local geometrical impact of where the constriction is applied.

Geometrical characterization of active contraction pulses in epithelial cells using the two-dimensional vertex model.

Several models have been proposed to describe the dynamics of epithelial tissues undergoing morphogenetic changes driven by apical constriction pulses, which differ in where the constriction is applied, either at the perimeter or in the medial regions. To help discriminate between these models, we analyse the impact of where constriction is applied on the final geometry of the active contracted cell, using the two-dimensional vertex model. We find that medial activity, characterized by a reduction in the reference area, generates anisotropic cell shapes, whereas isotropic cell shapes are produced when the reference perimeter is reduced. When plasticity is included, sufficiently slow processes of medial contractile activity, compared with the characteristic times of elasticity and plasticity, cells can achieve less elongated shapes. Similarly, for perimeter activity, the highest level of contraction is achieved. Finally, we apply the model to describe the apical contractile pulses observed within the epithelial enveloping cell layer during the pre-epiboly of the annual killifish Austrolebias nigripinnis. The analysis of the cell shape changes allowed a global fit of all parameters of the vertex model, with the pulses being quantitatively captured using perimeter activity and area plasticity.

Interplay of curvature and rigidity in shape-based models of confluent tissue

Rigidity transitions in simple models of confluent cells have been a powerful organizing principle in understanding the dynamics and mechanics of dense biological tissue. In this work we explore the interplay between geometry and rigidity in two-dimensional vertex models confined to the surface of a sphere. By considering shapes of cells defined by perimeters whose magnitude depends on geodesic distances and areas determined by spherical polygons, the critical shape index in such models is affected by the size of the cell relative to the radius of the sphere on which it is embedded. This implies that cells can collectively rigidify by growing the size of the sphere, i.e. by tuning the curvature of their domain. Finite-temperature studies indicate that cell motility is affected well away from the zero-temperature transition point.

A vertex model of recrystallization with stored energy implemented in GPU

Recrystallization models and simulations have been the subject of much attention in materials community in the past decades due to this process having a significant effect on many technologically important materials characteristics. Statistical analysis performed close to the steady state requires large-scale simulations, which are often prohibitively expensive from computational point of view. Graphical Processing Unit (GPU)-based realizations provide a viable approach to addressing this challenge, yet they remain relatively under-explored in this context.In the present manuscript, we develop a fully-parallelizable matrix-free GPU-based algorithm for implementing a two-dimensional vertex model of recrystallization based on the stored energy formalism. Nucleation is assumed to take place at triple junctions and obeys a Metropolis-type criterion. We include a complete mathematical analysis of the nucleation model deriving conditions under which nucleation is successful. Stability analysis of the dynamics of a triple junction under the presence of bulk energy is provided. On the computational side, we propose a novel polling system for handling topological transitions to ensure robust GPU implementation. Single grain tests are performed for benchmarking purposes. Finally, a set of numerical experiments for large scale systems is presented to explore the effect of initial distributions of stored energy on several statistical characteristics.

Mathematical Modeling of Tissue Folding and Asymmetric Tissue Flow during Epithelial Morphogenesis

Recent studies have revealed that intrinsic, individual cell behavior can provide the driving force for deforming a two-dimensional cell sheet to a three-dimensional tissue without the need for external regulatory elements. However, whether intrinsic, individual cell behavior could actually generate the force to induce tissue deformation was unclear, because there was no experimental method with which to verify it in vivo. In such cases, mathematical modeling can be effective for verifying whether a locally generated force can propagate through an entire tissue and induce deformation. Moreover, the mathematical model sometimes provides potential mechanistic insight beyond the information obtained from biological experimental results. Here, we present two examples of modeling tissue morphogenesis driven by cell deformation or cell interaction. In the first example, a mathematical study on tissue-autonomous folding based on a two-dimensional vertex model revealed that active modulations of cell mechanics along the basal–lateral surface, in addition to the apical side, can induce tissue-fold formation. In the second example, by applying a two-dimensional vertex model in an apical plane, a novel mechanism of tissue flow caused by asymmetric cell interactions was discovered, which explained the mechanics behind the collective cellular movement observed during epithelial morphogenesis.

Mechanical oscillations in biological tissues as a result of delayed rest-length changes

Oscillatory behavior in tissue biology is ubiquitous and may be observed in the form of either chemical or mechanical signals. We present here and solve a mechanical cell model that exhibits oscillations emerging from delayed viscoelastic rheological laws. These include a time delay between the mechanical response and the rest-length changes, which evolve proportionally to the delayed cell deformation and use a remodeling rate parameter. We show that different regimes (no oscillatory response, sustained oscillations, and unstable oscillations) are obtained for different values of the delay or the remodeling rate. The results are analytically demonstrated in a one-dimensional problem with one and two cells that are represented by simple line elements. Oscillations of the cell deformations are obtained whenever different delays coexist, or when the delay is size-dependent. We also extend our results to a multicellular two-dimensional vertex model that includes the same rheological law, and which inherits the presence of critical values of the delay or remodeling rate. We numerically show that indeed the size-dependent rest-length changes induce oscillations in the cell shapes and areas.

Impact of implementation choices on quantitative predictions of cell-based computational models

‘Cell-based’ models provide a powerful computational tool for studying the mechanisms underlying the growth and dynamics of biological tissues in health and disease. An increasing amount of quantitative data with cellular resolution has paved the way for the quantitative parameterisation and validation of such models. However, the numerical implementation of cell-based models remains challenging, and little work has been done to understand to what extent implementation choices may influence model predictions. Here, we consider the numerical implementation of a popular class of cell-based models called vertex models, which are often used to study epithelial tissues. In two-dimensional vertex models, a tissue is approximated as a tessellation of polygons and the vertices of these polygons move due to mechanical forces originating from the cells. Such models have been used extensively to study the mechanical regulation of tissue topology in the literature. Here, we analyse how the model predictions may be affected by numerical parameters, such as the size of the time step, and non-physical model parameters, such as length thresholds for cell rearrangement. We find that vertex positions and summary statistics are sensitive to several of these implementation parameters. For example, the predicted tissue size decreases with decreasing cell cycle durations, and cell rearrangement may be suppressed by large time steps. These findings are counter-intuitive and illustrate that model predictions need to be thoroughly analysed and implementation details carefully considered when applying cell-based computational models in a quantitative setting.

Computational analysis of three-dimensional epithelial morphogenesis using vertex models

The folding of epithelial sheets, accompanied by cell shape changes and rearrangements, gives rise to three-dimensional structures during development. Recently, some aspects of epithelial morphogenesis have been modeled using vertex models, in which each cell is approximated by a polygon; however, these models have been largely confined to two dimensions. Here, we describe an adaptation of these models in which the classical two-dimensional vertex model is embedded in three dimensions. This modification allows for the construction of complex three-dimensional shapes from simple sheets of cells. We describe algorithmic, computational, and biophysical aspects of our model, with the view that it may be useful for formulating and testing hypotheses regarding the mechanical forces underlying a wide range of morphogenetic processes.

Combinatorics of a strongly coupled boson system

We introduce a quantum phase model as a limit for very strong interactions of a strongly correlated q-boson hopping model. We describe the general solution of the phase model and express scalar products of state vectors in determinant form. The representation of state vectors in terms of Schur functions allows obtaining a combinatorial interpretation of the scalar products in terms of nests of self-avoiding lattice paths. We show that under a special parameterization, the scalar products are equal to the generating functions of plane partitions confined in a finite box. We consider the two-dimensional vertex model related to the phase model and express the vertex model partition function with special boundary conditions in terms of the scalar product of the phase model state vectors.

A Classical Background for the Wave Function Prediction in the Infinite System Density Matrix Renormalization Group Method

We report a physical background of the wave function prediction in the infinite system density matrix renormalization group (DMRG) method, from the view point of two-dimensional vertex model, a typical lattice model in statistical mechanics. Singular value decomposition applied to rectangular corner transfer matrices naturally draws matrix product representation for the maximal eigenvector of the row-to-row transfer matrix. The wave function prediction can be expressed as the insertion of an approximate half-column transfer matrix. This insertion process is in accordance with the scheme proposed by McCulloch recently.

On the nucleation of recrystallization by a bulging mechanism: A two-dimensional vertex simulation

Abstract The nucleation of grains by subgrain growth has been investigated using a two-dimensional vertex model. The initial geometry has an on average flat grain boundary, separating two populations of subgrains. The phenomenon has been studied using (i) a constant ratio between the subgrain and the grain boundary mobility or energy and (ii) simple relations for the misorientation dependencies of these two quantities. Bulging of grain boundaries owing to subgrain growth at topologically favoured sites has been observed. A subgrain size gradient at the grain boundary reduces the bulging frequency and leads to a general drift of the grain boundary.

Exact solution of a vertex model with unlimited number of states per bond

The exact solution is obtained for the eigenvalues and eigenvectors of the row-to-row transfer matrix of a two-dimensional vertex model with an unlimited number of states per bond. This model is a classical counterpart of a quantum spin chain with an unlimited value of spin. This quantum chain is studied using general predictions of conformal field theory. The long-distance behaviour of some ground state correlation functions is derived from a finite-size analysis of the gapless excitations.

Exact Solution of a Three-Dimensional Dimer System

We consider a three-dimensional lattice model consisting of layers of vertex models coupled with interlayer interactions. For a particular non-trivial interlayer interaction between charge-conserving vertex models and using a transfer matrix approach, we show that the eigenvalues and eigenvectors of the transfer matrix are related to those of the two-dimensional vertex model. The result is applied to analyze the phase transitions in a realistic three-dimensional dimer system.

Discrete symmetry groups of vertex models in statistical mechanics

We analyze discrete symmetry groups of vertex models in lattice statistical mechanics represented as groups of birational transformations. They can be seen as generated by involutions corresponding respectively to two kinds of transformations onq×q matrices: the inversion of theq×q matrix and an (involutive) permutation of the entries of the matrix. We show that the analysis of the factorizations of the iterations of these transformations is a precious tool in the study of lattice models in statistical mechanics. This approach enables one to analyze two-dimensionalq4-state vertex models as simply as three-dimensional vertex models, or higher-dimensional vertex models. Various examples of birational symmetries of vertex models are analyzed. A particular emphasis is devoted to a three-dimensional vertex model, the 64-state cubic vertex model, which exhibits a polynomial growth of the complexity of the calculations. A subcase of this general model is seen to yield integrable recursion relations. We also concentrate on a specific two-dimensional vertex model to see how the generic exponential growth of the calculations reduces to a polynomial growth when the model becomes Yang-Baxter integrable. It is also underlined that a polynomial growth of the complexity of these iterations can occur even for transformations yielding algebraic surfaces, or higher-dimensional algebraic varieties.

Boundary-induced phase transitions in equilibrium and non-equilibrium systems

Boundary conditions may change the phase diagram of non-equilibrium statistical systems like the one-dimensional asymmetric simple exclusion process with and without particle number conservation. Using the quantum Hamiltonian approach, the model is mapped onto an XXZ quantum chain and solved using the Bethe ansatz. This system is related to a two-dimensional vertex model in thermal equilibrium. The phase transition caused by a point-like boundary defect in the dynamics of the one-dimensional exclusion model is in the same universality class as a continuous (bulk) phase transition of the two-dimensional vertex model caused by a line defect at its boundary.

Quantum-group-invariant integrable n-state vertex models with periodic boundary conditions

An U q (sl( n))-invariant transfer matrix with periodic boundary conditions is analysed by means of the algebraic nested Bethe ansatz for the case of q being a root of unity. The transfer matrix corresponds to a two-dimensional vertex model on a torus with topological interaction with respect to the three-dimensional interior of the torus. By means of finite-size analysis we find the central charge of the corresponding Virasoro algebra as c = (n − 1) [ 1 − n(n + 1) (r(r − 1)) ] .