Related papers: A mass-structured individual-based model of the ch…
We study the formation of spot patterns seen in a variety of bacterial species when the bacteria are subjected to oxidative stress due to hazardous byproducts of respiration. Our approach consists of coupling the cell density field to a…
We present a model for the dynamics of a population of bacteria with a continuum of traits, who compete for resources and exchange horizontally (transfer) an otherwise vertically inherited trait with possible mutations. Competition…
Many processes in chemistry and physics take place on timescales that cannot be explored using standard molecular dynamics simulations. This renders the use of enhanced sampling mandatory. Here we introduce an enhanced sampling method that…
We consider a multiscale stochastic compartmental model with three types of cells (stem cells, immature cells and mature cells) which combines cell proliferation and cell differentiation. We derive a hydrodynamic limit when the number of…
Most conspicuous organisms are multicellular and most multicellular organisms develop somatic cells to perform specific, non-reproductive tasks. The ubiquity of this division of labor suggests that it is highly advantageous. In this paper,…
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…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
Bacteria can chemotactically migrate up attractant gradients by controlling run-and-tumble motility patterns. In addition to this well-known chemotactic behaviour, several soil and marine bacterial species perform chemokinesis: they adjust…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
Cellular aggregates play a significant role in the evolution of biological systems such as tumor growth, tissue spreading, wound healing, and biofilm formation. Analysis of such biological systems, in principle, includes examining the…
We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body…
Bacteria populations rely on mechanisms such as quorum sensing to coordinate complex tasks that cannot be achieved by a single bacterium. Quorum sensing is used to measure the local bacteria population density, and it controls cooperation…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
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…
An individual-based model (IBM) of a spatiotemporal terrestrial ecological population is proposed. This model is spatially explicit and features the position of each individual together with another characteristic, such as the size of the…
We prove a mean-field equation for the dynamics of quorum-sensing microbial populations. In the stochastic many-particle process, individuals of a population produce public good molecules to different degrees. Individual production is…
Colonies of bacteria endowed with a pili-based self-propulsion machinery are ideal models for investigating the structure and dynamics of active many-particle systems. We study Neisseria gonorrhoeae colonies with a molecular-dynamics-based…
We develop a new structured compartmental model for the coevolutionary dynamics between susceptible and infectious individuals in heterogeneous SI epidemiological systems. In this model, the susceptible compartment is structured by a…
We introduce a model of the growth of a single microorganism in a self-cycling fermentor in which an arbitrary number of resources are limiting, and impulses are triggered when the concentration of one specific substrate reaches a…
Several bacteria and bacteria strands form biofilms in different environmental conditions, e.g. pH, temperature, nutrients, etc. Biofilm growth, therefore, is an extremely robust process. Because of this, while biofilm growth is a complex…