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Motivated by recent research of aging in E. coli, we explore the effects of aging on bacterial fitness. The disposable soma theory of aging was developed to explain how differences in lifespans and aging rates could be linked to life…
We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body…
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…
Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…
GreenLab Model is a functional-structural plant growth model that combines both organogenesis (at each cycle, new organs are created with respect to genetic rules) and photosynthesis (organs are filled with the biomass produced by the…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
The Lotka-Volterra system is a set of ordinary differential equations describing growth of interacting ecological species. This model has gained renewed interest in the context of random interaction networks. One of the debated questions is…
Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in…
Microbial networks, representing microbes as nodes and their interactions as edges, are crucial for understanding community dynamics in various environments. Analyzing microbiome networks is crucial for identifying keystone taxa that play…
Spatial evolution is investigated in a simulated system of nine competing and mutating bacterium strains, which mimics the biochemical war among bacteria capable of producing two different bacteriocins (toxins) at most. Random sequential…
Genetic algorithms have played an important role in engineering optimization. Traditional GAs treat each gene separately. However, biophysical studies of gene regulatory networks revealed direct associations between different genes. It…
In many social mammals, early life social adversity and social integration largely predict individual health, lifespan and reproductive success. Efforts in identifying the physiological mechanisms mediating the relationship between the…
Systems of interacting species, such as biological environments or chemical reactions, are often described mathematically by sets of coupled ordinary differential equations. While a large number $\beta$ of species may be involved in the…
Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…
Lately, experimental research on microbial symbioses based on nutrient exchange and interdependence has yielded a number of interesting findings, however an in-depth mathematical description of the exact underlying dynamics of such…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
We use generating functionals to derive a dynamic mean-field description for generalised Lotka-Volterra systems with higher-order quenched random interactions. We use the resulting single effective species process to determine the stability…
The aim of this study is to analyze the integrability problem of Lotka--Volterra three species biological system. The system which considered in this work is a biological plausibility or a chemical model. The system has a complex dynamical…
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…
Mixed-membership (MM) models such as Latent Dirichlet Allocation (LDA) have been applied to microbiome compositional data to identify latent subcommunities of microbial species. These subcommunities are informative for understanding the…