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Quorum sensing (QS) mimickers can be used as an effective tool to disrupt biofilms which consist of communicating bacteria and extracellular polymeric substances. In this paper, a stochastic biofilm disruption model based on the usage of QS…
Bacteria are ubiquitous in our daily lives, either as motile planktonic cells or as immobilized surface-attached biofilms. These different phenotypic states play key roles in agriculture, environment, industry, and medicine; hence, it is…
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
Cooperative effects in neural networks appear because a neuron fires only if a minimal number $m$ of its inputs are excited. The multiple inputs requirement leads to a percolation model termed {\it quorum percolation}. The connectivity…
From pathogens and computer viruses to genes and memes, contagion models have found widespread utility across the natural and social sciences. Despite their success and breadth of adoption, the approach and structure of these models remain…
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…
Recent work suggests that cross-feeding -- the secretion and consumption of metabolic biproducts by microbes -- is essential for understanding microbial ecology. Yet how cross-feeding and competition combine to give rise to ecosystem-level…
Energy-based modelling brings engineering insight to the understanding of biomolecular systems. It is shown how well-established control engineering concepts, such as loop-gain, arise from energy feedback loops and are therefore amenable to…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We…
Microorganisms like bacteria can sense concentration of chemo-attractants in its medium very accurately. They achieve this through interaction between the receptors on their cell surface and the chemo-attractant molecules (like sugar). But…
We introduce a mathematical model of symbiosis between different species by taking into account the influence of each species on the carrying capacities of the others. The modeled entities can pertain to biological and ecological societies…
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular…
Collective decision-making arises from individual agents integrating their own personal observations with information obtained from social partners. In many biological systems that exhibit collective decision-making, the process by which…
Turing patterns play a fundamental role in morphogenesis and population dynamics, encoding key information about the underlying biological mechanisms. Yet, traditional inverse problems have largely relied on non-biological data such as…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
Motile living organisms routinely probe their surroundings to adapt in ever-evolving environments. Although synthetic microswimmers offer surrogates for self-propelled living entities, they often lack the complex feedback mechanisms that…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
Swarming or collective motion of living entities is one of the most common and spectacular manifestations of living systems having been extensively studied in recent years. A number of general principles have been established. The…
Electron transmission through molecules and molecular interfaces has been a subject of intensive research due to recent interest in electron transfer phenomena underlying the operation of the scanning tunneling microscope (STM) on one hand,…