Related papers: Inferring models of bacterial dynamics toward poin…
We use the mean-bacterial-velocity model to investigate the \textit{irreversibility} of two-dimensional (2D) \textit{bacterial turbulence} and to compare it with its 2D fluid-turbulence counterpart. We carry out extensive direct numerical…
This paper studies a chemotaxis system where cells move in response to a chemical signal within a confined habitat. The model includes external source terms that combine local and nonlocal growth with dampening effects. The main focus is on…
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…
Periodic reversals of the direction of motion in systems of self-propelled rod shaped bacteria enable them to effectively resolve traffic jams formed during swarming and maximize their swarming rate. In this paper, a connection is found…
In an act of sabotage or terrorism, hazardous material might be released deliberately into the atmosphere to threaten individuals, e.g., those operating critical infrastructure. Hazardous materials in such a scenario include toxic…
Microorganisms are found in almost every environment, including the soil, water, air, and inside other organisms, like animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as…
Protein variability in single cells has been studied extensively in populations, but little is known about temporal protein fluctuations in a single cell over extended times. We present here traces of protein copy number measured in…
Bacteria typically reside in heterogeneous environments with various chemogradients where motile cells can gain an advantage over non-motile cells. Since motility is energetically costly, cells must optimize their swimming speed and…
Invasion of new territories by alien organisms is of primary concern for environmental and health agencies and has been a core topic in mathematical modeling, in particular in the intents of reconstructing the past dynamics of the alien…
Motile cells often explore natural environments characterized by a high degree of structural complexity. Moreover cell motility is also intrinsically noisy due to spontaneous random reorientation and speed fluctuations. This interplay of…
We present a model for a biological reactor in which bacteria tend to aggregate in flocs, as encountered in wastewater treatment plants. The influence of this flocculation on the growth dynamics of the bacteria is studied. We argue that a…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
Causal discovery is at the core of human cognition. It enables us to reason about the environment and make counterfactual predictions about unseen scenarios that can vastly differ from our previous experiences. We consider the task of…
Linear structural causal models (SCMs) -- in which each observed variable is generated by a subset of the other observed variables as well as a subset of the exogenous sources -- are pervasive in causal inference and casual discovery.…
Individual-based models of contagious processes are useful for predicting epidemic trajectories and informing intervention strategies. In such models, the incorporation of contact network information can capture the non-randomness and…
How is the progression of a virus influenced by properties intrinsic to individual cells? We address this question by studying the susceptibility of cells infected with two strains of the human respiratory syncytial virus (RSV-A and RSV-B)…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
Cell migration often exhibits long-range temporal correlations and anomalous diffusion, even in the absence of external guidance cues such as chemical gradients or topographical constraints. These observations raise a fundamental question:…
Model checking is usually based on a comprehensive traversal of the state space. Causality-based model checking is a radically different approach that instead analyzes the cause-effect relationships in a program. We give an overview on a…
{\it E. coli} bacteria swim in straight runs interrupted by sudden reorientation events called tumbles. The resulting random walks give rise to density fluctuations that can be derived analytically in the limit of non interacting particles…