相关论文: A mass-structured individual-based model of the ch…
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…
In this paper, experimental data is presented and a simple model is developed for the time evolution of a F-amp \textit{E. Coli} culture population. In general, the bacteria life cycle as revealed by monitoring a culture's population…
The transition from localized to systemic spreading of bacteria, viruses and other agents is a fundamental problem that spans medicine, ecology, biology and agriculture science. We have conducted experiments and simulations in a simple…
The ubiquitous existence of microbial communities marks the importance of understanding how species interact within the community to coexist and their spatial organization. We study a two-species mutualistic cross-feeding model through a…
Microbial growth and division are fundamental processes relevant to many areas of life science. Of particular interest are homeostasis mechanisms, which buffer growth and division from accumulating fluctuations over multiple cycles. These…
Chemotaxis in bacteria such as \textit{E.\ coli} is controlled by the slow methylation of chemoreceptors. As a consequence, intrinsic time and length scales of tens of seconds and hundreds of micrometers emerge, making the Keller--Segel…
Motivated by observations of the dynamics of {\it Myxococcus xanthus}, we present a self-interacting random walk model that describes the competition between chemokinesis and chemotaxis. Cells are constrained to move in one dimension, but…
We propose a computational framework to study the growth and spread of bacterial biofilms on interfaces, as well as the action of antibiotics on them. Bacterial membranes are represented by boundaries immersed in a fluid matrix and subject…
A key problem toward the use of microorganisms as bio-factories is reaching and maintaining cellular communities at a desired density and composition so that they can efficiently convert their biomass into useful compounds. Promising…
The Cellular Potts Model (CPM) has been used for simulating various biological phenomena such as differential adhesion, fruiting body formation of the slime mold Dictyostelium discoideum, angiogenesis, cancer invasion, chondrogenesis in…
Bacterial populations in natural conditions are expected to experience stochastic environmental fluctuations, and in addition, environments are affected by bacterial activities since they consume substrates and excrete various chemicals. We…
Bacteria can spontaneously develop collective motions by aligning their motions in dense systems. Here, we show that bacteria can also respond collectively to an alternating electrical field and form dynamic clusters oscillating at the same…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
We study the mathematical properties of a model of cell division structured by two variables, the size and the size increment, in the case of a linear growth rate and a self-similar fragmentation kernel. We first show that one can construct…
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 investigate the propagating profiles of a degenerate chemotaxis model describing the bacteria chemotaxis and consumption of oxygen by aerobic bacteria, in particular, the effect of the initial attractant distribution on bacterial…
We present a mathematical model based on a system of partial differential equations (PDEs) with cross-diffusion and reaction terms to describe ecological interactions between multiple bacterial species and substrates within microaggregates,…
How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a…
We present a flexible branching process model for cell population dynamics in synchrony/time-series experiments used to study important cellular processes. Its formulation is constructive, based on an accounting of the unique cohorts in the…
We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division…