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Hybrid models of chemotaxis combine agent-based models of cells with partial differential equation models of extracellular chemical signals. In this paper, travelling wave properties of hybrid models of bacterial chemotaxis are…
Escherichia coli bacterium is a rod-shaped organism composed of a complex double membrane structure. Knowledge of electric field driven ion transport through both membranes and the evolution of their induced permeabilization has important…
The dynamics of diffusion in complex networks are widely studied to understand how entities, such as information, diseases, or behaviors, spread in an interconnected environment. Complex networks often present community structure, and tools…
The large-scale collective behavior of biological systems can be characterized by macroscopic transport, which arises from the non-equilibrium microscopic interactions among individual constituents. A prominent example is the formation of…
Mathematical models have been widely used to describe the collective movement of bacteria by chemotaxis. In particular, bacterial concentration waves traveling in a narrow channel have been experimentally observed and can be precisely…
Biochemistry, ecology, and neuroscience are examples of prominent fields aiming at describing interacting systems that exhibit non-trivial couplings to complex, ever-changing environments. We have recently shown that linear interactions and…
Collective cell migration is a key driver of embryonic development, wound healing, and some types of cancer invasion. Here we provide a physical perspective of the mechanisms underlying collective cell migration. We begin with a catalogue…
Collision models describe the sequential interactions of a system with independent ancillas. Motivated by recent advances in neutral atom arrays, in this Letter we investigate a model where the ancillas are governed by a classical…
The contact process is a simple infection spreading model showcasing an out-of-equilibrium phase transition between a macroscopically active and an inactive phase. Such absorbing state phase transitions are often sensitive to the presence…
Complex networks have been successfully used to describe the spread of diseases in populations of interacting individuals. Conversely, pairwise interactions are often not enough to characterize social contagion processes such as opinion…
Motility induced phase separation is an efficient aggregation mechanism of active matter, yet biological systems exhibit richer organization through communication among constituents. We investigate suspensions of active particles that…
Various biological cells secrete diffusing chemical compounds into their environment for communication purposes. Secretion usually takes place over the cell membrane in a spatially heterogeneous manner. Mathematical models of these…
Bacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct…
Quantum computers have the potential to simulate chemical systems beyond the capability of classical computers. Recent developments in hybrid quantum-classical approaches enable the determinations of the ground or low energy states of…
Quantifying animal interactions is crucial for understanding various ecological processes, including social community structures, predator-prey dynamics, spreading of pathogens and information. Despite the ubiquity of interaction processes…
Spatio-temporal extensions of familiar compartment models for disease transmission incorporating diffusive behavior, or interactions between individuals at separate locations, are explored. The models considered have the character of…
This paper develops a Bayesian graphical model for fusing disparate types of count data. The motivating application is the study of bacterial communities from diverse high dimensional features, in this case transcripts, collected from…
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…
Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…
Understanding the pattern formation in communities has been at the center of attention in various fields. Here we introduce a novel model, called an "information-particle model," which is based on the reaction-diffusion model and the…