Related papers: A Dynamic Network Formation Model for Understandin…
Biofilms, bacteria cells surrounded by a self-produced polymeric matrix, are common on medical devices and lead to many hospital infections. The biofilm lifecycle includes disassembly and dispersion, where bacteria clusters detach from the…
Biological pattern formation is one of the most intriguing phenomena in nature. Simplest examples of such patterns are represented by travelling waves and stationary periodic patterns which occur during various biological processes…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
A mathematical model for emerging contaminants sorption in multispecies biofilms, based on a continuum approach and mass conservation principles is presented. Diffusion of contaminants within the biofilm is described using a…
Many networks are complex dynamical systems, where both attributes of nodes and topology of the network (link structure) can change with time. We propose a model of co-evolving networks where both node at- tributes and network structure…
Reconstructing interactions from observational data is a critical need for investigating natural biological networks, wherein network dimensionality (i.e. number of interacting components) is usually high and interactions are time-varying.…
We present a generic mechanism by which reproducing microorganisms, with a diffusivity that depends on the local population density, can form stable patterns. It is known that a decrease of swimming speed with density can promote separation…
Biofilms in porous media critically influence hydraulic properties in environmental and engineered systems. However, a mechanistic understanding of how microbial life controls permeability remains elusive. By combining microfluidics,…
Bacterial biofilms cost an enormous amount of resources in the health, medical, and industrial sectors. To understand early biofilm formation, beginning from planktonic states of active bacterial suspensions (such as Escherichia coli) to…
Antibiotics are a vital class of drugs closely associated with the prevention and treatment of bacterial infections. Accurate prediction of molecular antimicrobial activity remains a key challenge in the pursuit of novel antibiotic…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…
Many scientific collaboration networks exhibit clear community and small world structures. However, the studies on the underlying mechanisms for the formation and evolution of community and small world structures are still insufficient. The…
Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
We propose a modeling approach to study how mature biofilms spread and colonize new surfaces by predicting the formation and growth of satellite colonies generated by dispersing biofilms. This model provides the basis for better…
Cell walls define a cell shape in bacteria. They are rigid to resist large internal pressures, but remarkably plastic to adapt to a wide range of external forces and geometric constraints. Currently, it is unknown how bacteria maintain…
Bayesian network models are finding success in characterizing enzyme-catalyzed reactions, slow conformational changes, predicting enzyme inhibition, and genomics. In this work, we apply them to statistical modeling of peptides by…
The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes is hypothesized to have served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is…
Recently there has been an increasing interest in studying dynamical processes on networks exhibiting higher-order structures, such as simplicial complexes, where the dynamics acts above and beyond dyadic interactions. Using simulations or…
The true slime mold \textit{Physarum polycephalum} has the remarkable capability to perform self-organized activities such as network formation among food sources. Despite well reproducing the emergence of slime networks, existing models…