Related papers: A Dynamic Network Formation Model for Understandin…
We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…
Bacterial cells exhibit a diverse array of shapes and sizes, largely governed by their cell walls in conjunction with cytoskeletal proteins and internal turgor pressure. The present study develops a theoretical framework for modeling the…
Models of disease spreading are critical for predicting infection growth in a population and evaluating public health policies. However, standard models typically represent the dynamics of disease transmission between individuals using…
The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform…
The presence of bacterial biofilms in clinical and industrial settings is a major issue worldwide. A biofilm is a viscoelastic matrix, composed of bacteria producing a network of Extracellular Polymeric Substances (EPS) to which bacteria…
The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current…
Controlling bacterial surface adhesion and subsequent biofilm formation in fluid systems is crucial for the safety and efficacy of medical and industrial processes. Here, we theoretically examine the transport of bacteria close to surfaces,…
The study of the interactions of living adherent cells with mechanically stable (visco)elastic materials enables understanding and exploiting physiological phenomena mediated by cell-extracellular communication. However, insight on the…
Monolayers of growing bacteria, confined within channel geometries, exhibit self-organization into a highly aligned laminar state along the axis of the channel. Although this phenomenon has been observed in experiments and simulations under…
We propose and analyze a model for antibiotic resistance transfer in a bacterial biofilm and examine antibiotic dosing strategies that are effective in bacterial elimination. In particular, we consider a 1-D model of a biofilm with…
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…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
In natural environments, solid surfaces present both opportunities and challenges for bacteria. On one hand, they serve as platforms for biofilm formation, crucial for bacterial colonization and resilience in harsh conditions. On the other…
In this work, we propose a dynamical systems perspective on the modeling of sepsis and its organ-damaging consequences. We develop a functional two-layer network model for sepsis based upon the interaction of parenchymal cells and immune…
Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the…
Many social and biological networks consist of communities - groups of nodes within which connections are dense, but between which connections are sparser. Recently, there has been considerable interest in designing algorithms for detecting…
Missing link prediction in indirected and un-weighted network is an open and challenge problem which has been studied intensively in recent years. In this paper, we studied the relationships between community structure and link formation…
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network…
As a granular material is compressed, the particles and forces within the system arrange to form complex heterogeneous structures. Force chains are a prime example and are thought to constrain bulk properties such as mechanical stability…
There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a…