Related papers: Selective sweeps in growing microbial colonies
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…
How adaptive evolution to one environmental stress improves or suppresses adaptation to another is an important problem in evolutionary biology. For instance, in microbiology, the evolution of bacteria to be resistant to different…
We study colonies of non-motile, rod-shaped bacteria growing on solid substrates. In our model, bacteria interact purely mechanically, by pushing each other away as they grow, and consume a diffusing nutrient. We show that mechanical…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
A pore-scale model is introduced for two-phase flow in dense packings of polydisperse spheres. The model is developed as a component of a more general hydromechanical coupling framework based on the discrete element method, which will be…
The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages like facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by…
Statistical models used to estimate the spatio-temporal pattern in disease risk from areal unit data represent the risk surface for each time period with known covariates and a set of spatially smooth random effects. The latter act as a…
Diffusion models have achieved remarkable success in high-fidelity image generation but remain computationally demanding due to their multi-step denoising process and large model sizes. Although prior work improves efficiency either by…
To explore the coupling between a growing population of microorganisms such as E. coli and a nonuniform nutrient distribution, we formulate a minimalistic model. It consists of active Brownian particles that divide and grow at a…
Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell…
With the development of next generation sequencing technology, researchers have now been able to study the microbiome composition using direct sequencing, whose output are bacterial taxa counts for each microbiome sample. One goal of…
A simulation approach to the stochastic growth of bacterial towers is presented, in which a non-uniform and finite nutrient supply essentially determines the emerging structure through elementary chemotaxis. The method is based on cellular…
Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and the diversity within these colonies, various numerical…
We propose a modeling approach to study how mature biofilms spread and colonize new surfaces by predicting the formation and growth of satellite colonies generated by dispersing biofilms. This model provides the basis for better…
We model an enclosed system of bacteria, whose motility-induced phase separation is coupled to slow population dynamics. Without noise, the system shows both static phase separation and a limit cycle, in which a rising global population…
We consider a system of two competing populations in two-dimensional heterogeneous environments. The populations are assumed to move horizontally and vertically with different probabilities, but are otherwise identical. We regard these…
Swimming microbes, such as bacteria and algae, live in diverse habitats including soil, ocean and human body which are characterized by structural boundaries and heterogeneous fluid flows. Although much progress has been made in…
Here, we study the evolution of specialization using realistic computer simulations of bacteria that secrete two public goods in a dynamic fluid. Through this first principles approach, we find physical factors such as diffusion, flow…
Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the…
One of the central themes in modern ecology is the enduring debate on whether there is a relationship between the complexity of a biological community and its stability. In this paper, we focus on the role of detritus and spatial dispersion…