The mechanism of fractal-like structure formation by bacterial populations

Simulation of various biofilm fractal morphologies by agent-based model

Biofilms are clusters of bacteria wrapped in extracellular matrix and polymers. The study of biofilm morphological transformation has been around for a long time and has attracted widespread attention. In this paper, we present a model for biofilm growth based on the interaction force, in which bacteria are treated as tiny particles and locations of particles are updated by calculating the repulsive forces among particles. We adapt a continuity equation to indicate nutrient concentration variation in the substrate. Based on the above, we study the morphological transformation of biofilms. We find that nutrient concentration and nutrient diffusion rate dominate different biofilm morphological transition processes, in which biofilms would grow into fractal morphology under the conditions of low nutrient concentration and nutrient diffusivity. At the same time, we expand our model by introducing a second particle to mimic extracellular polymeric substances (EPS) in biofilms. We find that the interaction between different particles can lead to phase separation patterns between cells and EPSs, and the adhesion effect of EPS can attenuate this phenomenon. In contrast to single particle system models, branches are inhibited due to EPS filling in dual particle system models, and this invalidation is boosted by the enhancement of the depletion effect.

Models for Allee effect based on physical principles

We propose some models of single species with Allee effect based on physical principles. A method is used to obtain the expression for the per capita growth rate (a macroscopic information) starting from the characteristics of interactions between the individuals (a microscopic information). We assume that the agents in a model of a single species interact according to the distance between them. Moreover these agents must (i) cooperate with their nearest neighbors, (ii) compete with neighbors at an intermediate distance, and (iii) being indifferent to those who are far away. Using these assumptions and based on fundamental physical principles, we find what appears to be a new way of establishing models of single species with Allee effect.

Rapid prototyping for biomedical engineering: current capabilities and challenges

A new set of manufacturing technologies has emerged in the past decades to address market requirements in a customized way and to provide support for research tasks that require prototypes. These new techniques and technologies are usually referred to as rapid prototyping and manufacturing technologies, and they allow prototypes to be produced in a wide range of materials with remarkable precision in a couple of hours. Although they have been rapidly incorporated into product development methodologies, they are still under development, and their applications in bioengineering are continuously evolving. Rapid prototyping and manufacturing technologies can be of assistance in every stage of the development process of novel biodevices, to address various problems that can arise in the devices' interactions with biological systems and the fact that the design decisions must be tested carefully. This review focuses on the main fields of application for rapid prototyping in biomedical engineering and health sciences, as well as on the most remarkable challenges and research trends.

Swimming patterns and dynamics of simulated Escherichia coli bacteria

A spatially and temporally realistic simulation of Escherichia coli chemotaxis was used to investigate the swimming patterns of wild-type and mutant bacteria within a rectangular arena in response to chemoattractant gradients. Swimming dynamics were analysed during long time series with phase-space trajectories, power spectra and estimations of fractal dimensions (FDs). Cell movement displayed complex trajectories in the phase space owing to interaction of multiple attractors that captured runs and tumbles. Deletion of enzymes responsible for adaptation (CheR and CheB) restricted the pattern of bacterial swimming in the absence of a gradient. In the presence of a gradient, there was a strong increase in trajectories arising from runs and attenuation of those arising from tumbles. Similar dynamics were observed for mutants lacking CheY, which are unable to tumble. The deletion of CheR, CheB and CheY also caused significant shifts in chemotaxis spectral frequencies. Rescaled range analysis and estimation of FD suggest that wild-type bacteria display characteristics of fractional Brownian motion with positive correlation between past and future events. These results reveal an underlying order in bacterial swimming dynamics, which enables a chemotactic search strategy conforming to a fractal walk.

Half-soliton interaction of population taxis waves in predator-prey systems with pursuit and evasion

In this paper, we use numerical simulations to demonstrate a half-soliton interaction of waves in a mathematical model of a "prey-predator" system with taxis when of two colliding waves, one annihilates and the other continues to propagate. We show that this effect depends on the "ages" or, equivalently, "widths" of the colliding waves. In two spatial dimensions we demonstrate that the type of interaction, i.e., annihilation, quasisoliton, or half-soliton, depends not only on curvature and width of the colliding waves, but also on the angle of the collision. When conditions of collision are varying in such a way that only a part of a wave survives the collision, then "taxitons," compact pieces of solitary waves, may form, which can exist for a significant time.