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A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…

The revival mechanism in dormant bacteria is a puzzling and open issue. We propose a model of information diffusion on a regular grid where agents represent bacteria and their mutual interactions implement quorum sensing. Agents may have…

Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed, diluted cultures routinely used in microbial research, bacteria in a…

This study explores the application of elongated particle interaction models, traditionally used in liquid crystal phase research, in the context of early bacterial biofilm development. Through computer simulations using an agent-based…

Biological functionality of cellular aggregates is largely influenced by the activity and displacements of individual constituent cells. From a theoretical perspective this activity can be characterized by hydrodynamic transport…

We study a generic model for quorum-sensing bacteria in circular confinement. Every bacterium produces signaling molecules, the local concentration of which triggers a response when a certain threshold is reached. If this response lowers…

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…

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…

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…

The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…

There are numerous scenarios in which populations of cells migrate in crowded environments. Typical examples include wound healing, cancer growth and embryo development. In these crowded environments cells are able to interact with each…

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…

Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…

We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. micro-colonies represent the first social step towards the formation of structured multicellular communities…

In vivo, eukaryotic cells are embedded in a matrix environment, where they grow and develop. Generally, this extracellular matrix (ECM) is an anisotropic fibrous structure, through which macromolecules and biochemical signaling molecules at…

Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…

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…

Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network,…

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry…

The spreading of bacterial populations is central to processes in agriculture, the environment, and medicine. However, existing models of spreading typically focus on cells in unconfined settings--despite the fact that many bacteria inhabit…