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Humans, domestic animals, orchard crops, and ornamental plants are commonly treated with antibiotics in response to bacterial infection. By curing infectious individuals, antibiotic therapy might limit the spread of contagious disease among…

We present models of dormancy in a planktonic culture and in biofilm, and examine the relative advantage of short dormancy versus long dormancy times in each case. Simulations and analyses indicate that in planktonic batch cultures and in…

Antibiotics resistance has caused much complication in the treatment of diseases, where the pathogen is no longer susceptible to specific antibiotics and the use of such antibiotics are no longer effective for treatment. A recent study that…

Biofilms are microbial collectives that occupy a diverse array of surfaces. The function and evolution of biofilms are strongly influenced by the spatial arrangement of different strains and species within them, but how spatiotemporal…

Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…

Dynamical energy analysis was recently introduced as a new method for determining the distribution of mechanical and acoustic wave energy in complex built up structures. The technique interpolates between standard statistical energy…

Antibiotic resistance presents a growing global health threat by diminishing the effectiveness of treatments and allowing once-manageable bacterial infections to persist. This study develops and analyzes an optimization-based mathematical…

Engineering spatially organized biofilms for creating adaptive and sustainable biomaterials is a forthcoming mission of synthetic biology. Existing technologies of patterning biofilm materials suffer limitations associated with the high…

The goal of this work is to develop a numerical simulation that accurately captures the biomechanical response of bacterial biofilms and their associated extracellular matrix (ECM). In this, the second of a two-part effort, the primary…

We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…

The bacterium {\em Bacilus subtilis} frequently forms biofilms at the interface between the culture medium and the air. We develop a mathematical model that couples a description of bacteria as individual discrete objects to the standard…

We demonstrate 'differential dynamic microscopy' (DDM) for the fast, high throughput characterization of the dynamics of active particles. Specifically, we characterize the swimming speed distribution and the fraction of motile cells in…

We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…

Microscopic organisms, such as bacteria, have the ability of colonizing surfaces and developing biofilms that can determine diseases and infections. Most bacteria secrete a significant amount of extracellular polymer substances that are…

Biofilms pose significant problems for engineers in diverse fields, such as marine science, bioenergy, and biomedicine, where effective biofilm control is a long-term goal. The adhesion and surface mechanics of biofilms play crucial roles…

Microfiltration technology is a widely used engineering strategy for fresh water production and water treatment. The major concern in many applications is the formation of a biological fouling layer leading to increased hydraulic resistance…

The existence of phenotypic heterogeneity in single-species bacterial biofilms is well-established in the published literature. However, the modeling of population dynamics in biofilms from the viewpoint of social interactions, i.e.…

Biofilm growth and transport in confined systems frequently occur in natural and engineered systems. Designing customizable engineered porous materials for controllable biofilm transportation properties could significantly improve the rapid…

Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…

A discrete-to-continuum analysis for free-boundary problems related to crystalline films deposited on substrates is performed by $\Gamma$-convergence. The discrete model here introduced is characterized by an energy with two contributions,…