Macroscopic limits of individual-based models for motile cell populations with volume exclusion

Quantifying tissue growth, shape and collision via continuum models and Bayesian inference

Although tissues are usually studied in isolation, this situation rarely occurs in biology, as cells, tissues and organs coexist and interact across scales to determine both shape and function. Here, we take a quantitative approach combining data from recent experiments, mathematical modelling and Bayesian parameter inference, to describe the self-assembly of multiple epithelial sheets by growth and collision. We use two simple and well-studied continuum models, where cells move either randomly or following population pressure gradients. After suitable calibration, both models prove to be practically identifiable, and can reproduce the main features of single tissue expansions. However, our findings reveal that whenever tissue-tissue interactions become relevant, the random motion assumption can lead to unrealistic behaviour. Under this setting, a model accounting for population pressure from different cell populations is more appropriate and shows a better agreement with experimental measurements. Finally, we discuss how tissue shape and pressure affect multi-tissue collisions. Our work thus provides a systematic approach to quantify and predict complex tissue configurations with applications in the design of tissue composites and more generally in tissue engineering.

From random walks on networks to nonlinear diffusion

Mathematical models of motility are often based on random-walk descriptions of discrete individuals that can move according to certain rules. It is usually the case that large masses concentrated in small regions of space have a great impact on the collective movement of the group. For this reason, many models in mathematical biology have incorporated crowding effects and managed to understand their implications. Here, we build on a previously developed framework for random walks on networks to show that in the continuum limit, the underlying stochastic process can be identified with a diffusion partial differential equation. The diffusion coefficient of the emerging equation is, in general, density dependent, and can be directly related to the transition probabilities of the random walk. Moreover, the relaxation time of the stochastic process is directly linked to the diffusion coefficient and also to the network structure, as it usually happens in the case of linear diffusion. As a specific example, we study the equivalent of a porous-medium-type equation on networks, which shows similar properties to its continuum equivalent. For this equation, self-similar solutions on a lattice and on homogeneous trees can be found, showing finite speed of propagation in contrast to commonly used linear diffusion equations. These findings also provide insights into reaction-diffusion systems with general diffusion operators, which have appeared recently in some applications.

Fock-space methods for diffusion: Capturing volume exclusion via fermionic statistics

Volume exclusion and single-file diffusion play an important role at very small scales, such as those associated with molecular machines, ion channels, and transport in zeolites, while introducing fundamental differences compared to Brownian motion, such as changes to the power-law relation between the mean square displacement and time. In this work we map the chemical master equation for excluded diffusion onto a Schrödinger equation via annihilation and creation ladder operators with fermionic statistics, together with linear and symbolic algebra with the resulting Fock-space representation to describe the effect of volume-exclusion processes in finite one-dimensional chains. We contrast the dynamics with the nonexclusive (bosonic) diffusion for crowded, intermediate, and dilute particle populations. Motivated by shuttling in molecular machines, we proceed to investigate differences in exit time distributions introduced by volume exclusion, incorporating the presence of transport bias. More generally, this study demonstrates how one can analyze volume-excluded transport for small stochastic systems, without the need for stochastic simulation and ensemble averaging, simply by considering anticommutation relations and fermionic statistics in a Fock-space representation of the stochastic dynamics.

From a discrete model of chemotaxis with volume-filling to a generalized Patlak-Keller-Segel model

We present a discrete model of chemotaxis whereby cells responding to a chemoattractant are seen as individual agents whose movement is described through a set of rules that result in a biased random walk. In order to take into account possible alterations in cellular motility observed at high cell densities (i.e. volume-filling), we let the probabilities of cell movement be modulated by a decaying function of the cell density. We formally show that a general form of the celebrated Patlak-Keller-Segel (PKS) model of chemotaxis can be formally derived as the appropriate continuum limit of this discrete model. The family of steady-state solutions of such a generalized PKS model are characterized and the conditions for the emergence of spatial patterns are studied via linear stability analysis. Moreover, we carry out a systematic quantitative comparison between numerical simulations of the discrete model and numerical solutions of the corresponding PKS model, both in one and in two spatial dimensions. The results obtained indicate that there is excellent quantitative agreement between the spatial patterns produced by the two models. Finally, we numerically show that the outcomes of the two models faithfully replicate those of the classical PKS model in a suitable asymptotic regime.

Modelling collective cell migration: neural crest as a model paradigm

A huge variety of mathematical models have been used to investigate collective cell migration. The aim of this brief review is twofold: to present a number of modelling approaches that incorporate the key factors affecting cell migration, including cell-cell and cell-tissue interactions, as well as domain growth, and to showcase their application to model the migration of neural crest cells. We discuss the complementary strengths of microscale and macroscale models, and identify why it can be important to understand how these modelling approaches are related. We consider neural crest cell migration as a model paradigm to illustrate how the application of different mathematical modelling techniques, combined with experimental results, can provide new biological insights. We conclude by highlighting a number of future challenges for the mathematical modelling of neural crest cell migration.

Pulling in models of cell migration

There are numerous biological scenarios in which populations of cells migrate in crowded environments. Typical examples include wound healing, cancer growth, and embryo development. In these crowded environments cells are able to interact with each other in a variety of ways. These include excluded-volume interactions, adhesion, repulsion, cell signaling, pushing, and pulling. One popular way to understand the behavior of a group of interacting cells is through an agent-based mathematical model. A typical aim of modellers using such representations is to elucidate how the microscopic interactions at the cell-level impact on the macroscopic behavior of the population. At the very least, such models typically incorporate volume-exclusion. The more complex cell-cell interactions listed above have also been incorporated into such models; all apart from cell-cell pulling. In this paper we consider this under-represented cell-cell interaction, in which an active cell is able to "pull" a nearby neighbor as it moves. We incorporate a variety of potential cell-cell pulling mechanisms into on- and off-lattice agent-based volume exclusion models of cell movement. For each of these agent-based models we derive a continuum partial differential equation which describes the evolution of the cells at a population level. We study the agreement between the agent-based models and the continuum, population-based models and compare and contrast a range of agent-based models (accounting for the different pulling mechanisms) with each other. We find generally good agreement between the agent-based models and the corresponding continuum models that worsens as the agent-based models become more complex. Interestingly, we observe that the partial differential equations that we derive differ significantly, depending on whether they were derived from on- or off-lattice agent-based models of pulling. This hints that it is important to employ the appropriate agent-based model when representing pulling cell-cell interactions.

The invasion speed of cell migration models with realistic cell cycle time distributions

Cell proliferation is typically incorporated into stochastic mathematical models of cell migration by assuming that cell divisions occur after an exponentially distributed waiting time. Experimental observations, however, show that this assumption is often far from the real cell cycle time distribution (CCTD). Recent studies have suggested an alternative approach to modelling cell proliferation based on a multi-stage representation of the CCTD. In this paper we investigate the connection between the CCTD and the speed of the collective invasion. We first state a result for a general CCTD, which allows the computation of the invasion speed using the Laplace transform of the CCTD. We use this to deduce the range of speeds for the general case. We then focus on the more realistic case of multi-stage models, using both a stochastic agent-based model and a set of reaction-diffusion equations for the cells' average density. By studying the corresponding travelling wave solutions, we obtain an analytical expression for the speed of invasion for a general N-stage model with identical transition rates, in which case the resulting cell cycle times are Erlang distributed. We show that, for a general N-stage model, the Erlang distribution and the exponential distribution lead to the minimum and maximum invasion speed, respectively. This result allows us to determine the range of possible invasion speeds in terms of the average proliferation time for any multi-stage model.

Reactions, diffusion, and volume exclusion in a conserved system of interacting particles

Complex biological and physical transport processes are often described through systems of interacting particles. The effect of excluded volume on these transport processes has been well studied; however, the interplay between volume exclusion and reactions between heterogenous particles is less well studied. In this paper we develop a framework for modeling reaction-diffusion processes which directly incorporates volume exclusion. We consider simple reactions (unimolecular and bimolecular) that conserve the total number of particles. From an off-lattice microscopic individual-based model we use the Fokker-Planck equation and the method of matched asymptotic expansions to derive a low-dimensional macroscopic system of nonlinear partial differential equations describing the evolution of the particles. A biologically motivated, hybrid model of chemotaxis with volume exclusion is explored, where reactions occur at rates dependent upon the chemotactic environment. Further, we show that for reactions that require particle contact the appropriate reaction term in the macroscopic model is of lower order in the asymptotic expansion than the nonlinear diffusion term. However, we find that the next reaction term in the expansion is needed to ensure good agreement with simulations of the microscopic model. Our macroscopic model allows for more direct parametrization to experimental data than existing models.

Multidisciplinary approaches to understanding collective cell migration in developmental biology

Mathematical models are becoming increasingly integrated with experimental efforts in the study of biological systems. Collective cell migration in developmental biology is a particularly fruitful application area for the development of theoretical models to predict the behaviour of complex multicellular systems with many interacting parts. In this context, mathematical models provide a tool to assess the consistency of experimental observations with testable mechanistic hypotheses. In this review, we showcase examples from recent years of multidisciplinary investigations of neural crest cell migration. The neural crest model system has been used to study how collective migration of cell populations is shaped by cell–cell interactions, cell–environmental interactions and heterogeneity between cells. The wide range of emergent behaviours exhibited by neural crest cells in different embryonal locations and in different organisms helps us chart out the spectrum of collective cell migration. At the same time, this diversity in migratory characteristics highlights the need to reconcile or unify the array of currently hypothesized mechanisms through the next generation of experimental data and generalized theoretical descriptions.

Spatial moment dynamics for collective cell movement incorporating a neighbour-dependent directional bias

The ability of cells to undergo collective movement plays a fundamental role in tissue repair, development and cancer. Interactions occurring at the level of individual cells may lead to the development of spatial structure which will affect the dynamics of migrating cells at a population level. Models that try to predict population-level behaviour often take a mean-field approach, which assumes that individuals interact with one another in proportion to their average density and ignores the presence of any small-scale spatial structure. In this work, we develop a lattice-free individual-based model (IBM) that uses random walk theory to model the stochastic interactions occurring at the scale of individual migrating cells. We incorporate a mechanism for local directional bias such that an individual's direction of movement is dependent on the degree of cell crowding in its neighbourhood. As an alternative to the mean-field approach, we also employ spatial moment theory to develop a population-level model which accounts for spatial structure and predicts how these individual-level interactions propagate to the scale of the whole population. The IBM is used to derive an equation for dynamics of the second spatial moment (the average density of pairs of cells) which incorporates the neighbour-dependent directional bias, and we solve this numerically for a spatially homogeneous case.

A cell-centered, agent-based framework that enables flexible environment granularities

BACKGROUND

Mechanistic explanations of cell-level phenomena typically adopt an observer perspective. Explanations developed from a cell's perspective may offer new insights. Agent-based models lend themselves to model from an individual perspective, and existing agent-based models generally utilize a regular lattice-based environment. A framework which utilizes a cell's perspective in an off-lattice environment could improve the overall understanding of biological phenomena.

RESULTS

We present an agent-based, discrete event framework, with a demonstrative focus on biomimetic agents. The framework was first developed in 2-dimensions and then extended, with a subset of behaviors, to 3-dimensions. The framework is expected to facilitate studies of more complex biological phenomena through exploitation of a dynamic Delaunay and Voronoi off-lattice environment. We used the framework to model biological cells and to specifically demonstrate basic biological cell behaviors in two- and three-dimensional space. Potential use cases are highlighted, suggesting the utility of the framework in various scenarios.

CONCLUSIONS

The framework presented in this manuscript expands on existing cell- and agent-centered methods by offering a new perspective in an off-lattice environment. As the demand for biomimetic models grows, the demand for new methods, such as the presented Delaunay and Voronoi framework, is expected to increase.

Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation

In vitro studies and mathematical models are now being widely used to study the underlying mechanisms driving the expansion of cell colonies. This can improve our understanding of cancer formation and progression. Although much progress has been made in terms of developing and analysing mathematical models, far less progress has been made in terms of understanding how to estimate model parameters using experimental in vitro image-based data. To address this issue, a new approximate Bayesian computation (ABC) algorithm is proposed to estimate key parameters governing the expansion of melanoma cell (MM127) colonies, including cell diffusivity, D, cell proliferation rate, λ, and cell-to-cell adhesion, q, in two experimental scenarios, namely with and without a chemical treatment to suppress cell proliferation. Even when little prior biological knowledge about the parameters is assumed, all parameters are precisely inferred with a small posterior coefficient of variation, approximately 2–12%. The ABC analyses reveal that the posterior distributions of D and q depend on the experimental elapsed time, whereas the posterior distribution of λ does not. The posterior mean values of D and q are in the ranges 226–268 µm²h⁻¹, 311–351 µm²h⁻¹ and 0.23–0.39, 0.32–0.61 for the experimental periods of 0–24 h and 24–48 h, respectively. Furthermore, we found that the posterior distribution of q also depends on the initial cell density, whereas the posterior distributions of D and λ do not. The ABC approach also enables information from the two experiments to be combined, resulting in greater precision for all estimates of D and λ.

Quantifying the underlying parameters that drive the expansion of melanoma cell colonies such as the cell diffusivity, cell proliferation rate and cell-to-cell adhesion strength can improve our understanding of melanoma biology and its response to treatment. We combine a simulation-based model of collective cell spreading with a novel Bayesian computational algorithm to estimate these parameters from carefully chosen summaries of collective cell image data and to quantify their associated uncertainty across different experimental conditions. Our summarisation of the image data leads to precise estimates for all parameters. Our analysis reveals that the cell diffusivity and the cell-to-cell adhesion strength estimates depend on experimental elapsed time. Furthermore, the cell-to-cell adhesion strength estimate appears to depend on the initial cell density, whereas the cell proliferation rate estimate is approximately the same over different experimental conditions.

Incorporating pushing in exclusion-process models of cell migration

The macroscale movement behavior of a wide range of isolated migrating cells has been well characterized experimentally. Recently, attention has turned to understanding the behavior of cells in crowded environments. In such scenarios it is possible for cells to interact, inducing neighboring cells to move in order to make room for their own movements or progeny. Although the behavior of interacting cells has been modeled extensively through volume-exclusion processes, few models, thus far, have explicitly accounted for the ability of cells to actively displace each other in order to create space for themselves. In this work we consider both on- and off-lattice volume-exclusion position-jump processes in which cells are explicitly allowed to induce movements in their near neighbors in order to create space for themselves to move or proliferate into. We refer to this behavior as pushing. From these simple individual-level representations we derive continuum partial differential equations for the average occupancy of the domain. We find that, for limited amounts of pushing, comparison between the averaged individual-level simulations and the population-level model is nearly as good as in the scenario without pushing. Interestingly, we find that, in the on-lattice case, the diffusion coefficient of the population-level model is increased by pushing, whereas, for the particular off-lattice model that we investigate, the diffusion coefficient is reduced. We conclude, therefore, that it is important to consider carefully the appropriate individual-level model to use when representing complex cell-cell interactions such as pushing.

Interacting motile agents: taking a mean-field approach beyond monomers and nearest-neighbor steps

We consider a discrete agent-based model on a one-dimensional lattice, where each agent occupies L sites and attempts movements over a distance of d lattice sites. Agents obey a strict simple exclusion rule. A discrete-time master equation is derived using a mean-field approximation and careful probability arguments. In the continuum limit, nonlinear diffusion equations that describe the average agent occupancy are obtained. Averaged discrete simulation data are generated and shown to compare very well with the solution to the derived nonlinear diffusion equations. This framework allows us to approach a lattice-free result using all the advantages of lattice methods. Since different cell types have different shapes and speeds of movement, this work offers insight into population-level behavior of collective cellular motion.

Lattice-free descriptions of collective motion with crowding and adhesion

Cell-to-cell adhesion is an important aspect of malignant spreading that is often observed in images from the experimental cell biology literature. Since cell-to-cell adhesion plays an important role in controlling the movement of individual malignant cells, it is likely that cell-to-cell adhesion also influences the spatial spreading of populations of such cells. Therefore, it is important for us to develop biologically realistic simulation tools that can mimic the key features of such collective spreading processes to improve our understanding of how cell-to-cell adhesion influences the spreading of cell populations. Previous models of collective cell spreading with adhesion have used lattice-based random walk frameworks which may lead to unrealistic results, since the agents in the random walk simulations always move across an artificial underlying lattice structure. This is particularly problematic in high-density regions where it is clear that agents in the random walk align along the underlying lattice, whereas no such regular alignment is ever observed experimentally. To address these limitations, we present a lattice-free model of collective cell migration that explicitly incorporates crowding and adhesion. We derive a partial differential equation description of the discrete process and show that averaged simulation results compare very well with numerical solutions of the partial differential equation.