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Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
The quantitative description of marine systems is constrained by a major issue of scale separation: most marine biochemical processes occur at sub-centimeter scales, while the contribution to the Earth's biogeochemical cycles is expressed…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Proliferating cell collectives often develop an active growth layer near their boundary that regulates expansion and morphology, as observed in systems ranging from bacterial biofilms to epithelial tissues and tumor spheroids. While such…
A connection is established between discrete stochastic model describing microscopic motion of fluctuating cells, and macroscopic equations describing dynamics of cellular density. Cells move towards chemical gradient (process called…
Various bacterial strains exhibit colonial branching patterns during growth on poor substrates. These patterns reflect bacterial cooperative self-organization and cybernetic processes of communication, regulation and control employed during…
Many mathematical models for biological phenomena, such as the spread of diseases, are based on reaction-diffusion equations for densities of interacting cell populations. We present a consistent derivation of reaction-diffusion equations…
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…
A diffusion-reaction model for the growth of bacterial colonies is presented. The often observed cooperative behavior developed by bacteria which increases their motility in adverse growth conditions is here introduced as a nonlinear…
We study the dynamics of proliferating cell collectives whose microscopic constituents' growth is inhibited by macroscopic growth-induced stress. Discrete particle simulations of a growing collective show the emergence of concentric-ring…
The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses,…
Many active systems are capable of forming intriguing patterns at scales significantly larger than the size of their individual constituents. Cyanobacteria are one of the most ancient and important phyla of organisms that has allowed the…
Cell proliferation and cell movement are fundamentally stochastic processes which lead to variability in the growth and spatial structure of cell populations in many biological settings, such as cell invasion, wound healing, and tumour…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…