Related papers: Discrete modelling of bacterial conjugation dynami…
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…
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…
Conjugation is a process in which bacteria exchange DNA through a physical connection (conjugative junction) between mating cells. Despite its significance for processes such as the spread of antibiotic resistance, the role of physical…
Bacteria are perhaps the simplest living systems capable of complex behaviour involving sensing and coherent, collective behaviour an example of which is the phenomena of swarming on agar surfaces. Two fundamental questions in bacterial…
We present a proof-of-concept of a model comparison approach for analyzing spatio-temporal observations of interacting populations. Our model variants are a collection of structurally similar Bayesian networks. Their distinct Noisy-Or…
Communication and coordination play a major role in the ability of bacterial cells to adapt to ever changing environments and conditions. Recent work has shown that such coordination underlies several aspects of bacterial responses…
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…
Microbial communities play a significant role in bioremediation,plant growth,human and animal digestion,global elemental cycles including the carbon-cycle,and water treatment.They are also posed to be the engines of renewable energy via…
In many natural synchronization phenomena, communication between individual elements occurs not directly, but rather through the environment. One of these instances is bacterial quorum sensing, where bacteria release signaling molecules in…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Mobile genetic elements like conjugative plasmids play a crucial role in shaping the genetic content and population dynamics of bacterial species. Bacterial populations often contain not one, but multiple co-circulating MGEs, which modify…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Bacterial sensor systems can be used for the detection and measurement of molecular signal concentrations. The dynamics of the sensor directly depend on the biological properties of the bacterial sensor cells; manipulation of these features…
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…
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…
The prospect of new biological and industrial applications that require communication in micro-scale, encourages research on the design of bio-compatible communication networks using networking primitives already available in nature. One of…
With recent and rapid advancements in artificial intelligence (AI), understanding the foundation of purposeful behaviour in autonomous agents is crucial for developing safe and efficient systems. While artificial neural networks have…