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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…

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…

We consider a simple information-theoretic model of communication, in which two species of bacteria have the option of exchanging information about their environment, thereby improving their chances of survival. For this purpose, we model a…

Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…

Recent measurements of durations of non-equilibrium processes provide valuable information on microscopic mechanisms and energetics. Comprehensive theory for corresponding experiments so far is well developed for single-particle systems…

Translating potential disease biomarkers between multi-species 'omics' experiments is a new direction in biomedical research. The existing methods are limited to simple experimental setups such as basic healthy-diseased comparisons. Most of…

Cell motility is one of the most fundamental phenomena underlying biological processes that maintain living organisms alive. Here we introduce a simple model to describe the motility of cells which include not only time-correlated internal…

Molecular communication is an expanding body of research. Recent advances in biology have encouraged using genetically engineered bacteria as the main component in the molecular communication. This has stimulated a new line of research that…

In recent years it is increasingly being recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that…

Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…

Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…

Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…

Molecular communication, as implied by its name, uses molecules as information carriers for communication between objects. It has an advantage over traditional electromagnetic-wave-based communication in that molecule-based systems could be…

Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…

The ubiquity of information transmission via molecular communication between cells is comprehensively documented on Earth; this phenomenon might even have played a vital role in the origin(s) and early evolution of life. Motivated by these…

Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…

Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…

Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…

We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…

Feedback in sensory biochemical networks can give rise to bifurcations in cells' behavioral response. These bifurcations share many properties with thermodynamic critical points. Evidence suggests that biological systems may operate near…