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The phase transition kinetics in three phase systems was investigated using the numerically efficient cell dynamics method. A phasefield model with a simple analytical free energy and single order parameter was used to study the kinetics…
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…
Stick-slip motion, a common phenomenon observed during crawling of cells, is found to be strongly sensitive to the substrate stiffness. Stick-slip behaviours have previously been investigated typically using purely elastic substrates. For a…
The local balance equations for the density, momentum, and energy of a dilute gas of elastic or inelastic hard spheres, strongly confined between two parallel hard plates are obtained. The starting point is a Boltzmann-like kinetic…
Biological systems excel at building spatial structures on scales ranging from nanometers to kilometers and exhibit temporal patterning from milliseconds to years. One approach that nature has taken to accomplish this relies on the…
High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…
This work presents a mathematical model which describes both the genesis and growth of oxygenic photogranules (OPGs) and the related treatment process. The photogranule has been modelled as a free boundary domain with radial symmetry, which…
This chapter is an overview of foundational results in the mathematical theory of replicator systems. Its primary aim is to provide a unified framework for the mathematical formalisation of evolutionary processes in the spirit of…
An adequate control of cell response in tissue engineering applications is of utmost importance to obtain products suitable to clinical practice. This paper is the first part of a series of two connected publications in which we study via…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…
We study non-equilibrium bacterial colony growth using a geometry-first, time-resolved analysis of morphology. From time-lapse microscopy data, we track the coupled evolution of area, perimeter, and boundary-sensitive shape descriptors…
Mechanical cues like the rigidity of the substrate are main determinants for the decision making of adherent cells. Here we use a mechano-chemical model to predict the cellular response to varying substrate stiffness. The model equations…
We present a rotationally invariant viscous vertex model that accounts for both cortical and bulk dissipation of cells. The vanishing substrate-friction limit is enforced via Lagrange multipliers, which also provides a framework for…
We investigate growth on vicinal surfaces by molecular beam epitaxy making use of a generalized Burton--Cabrera--Frank model. Our primary aim is to propose and implement a novel analytical program based on a perturbative solution of the…
Microbial interactions regulate their spread and survival in competitive environments. It is not clear if the physical parameters of the environment regulate the outcome of these interactions. In this work, we show that the opportunistic…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…
Experiments show that the movement of eukaryotic cells is regulated by a process of phase separation of two competing enzymes on the cell membrane, that effectively amplifies shallow external gradients of chemical attractant. Notably, the…
Active nematics are the nonequilibrium analog of passive liquid crystals in which anisotropic units consume free energy to drive emergent behavior. Similar to liquid crystal (LC) molecules in displays, ordering and dynamics in active…
A dynamic model for failures in biological organisms is proposed and studied both analytically and numerically. Each cell in the organism becomes dead under sufficiently strong stress, and is then allowed to be healed with some probability.…