Bacterial Carpets Research Articles

Optimal Design of Bacterial Carpets for Fluid Pumping

In this work, we outline a methodology for determining optimal helical flagella placement and phase shift that maximize fluid pumping through a rectangular flow meter above a simulated bacterial carpet. This method uses a Genetic Algorithm (GA) combined with a gradient-based method, the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm, to solve the optimization problem and the Method of Regularized Stokeslets (MRS) to simulate the fluid flow. This method is able to produce placements and phase shifts for small carpets and could be adapted for implementation in larger carpets and various fluid tasks. Our results show that given identical helices, optimal pumping configurations are influenced by the size of the flow meter. We also show that intuitive designs, such as uniform placement, do not always lead to a high-performance carpet.

Review on: Elimination of Petroleum Hydrocarbons using Bacteriological Carpets

In this review study, biodegradability of petrol hydrocarbon was premeditated on the petroleum sludge from the chemical industry using bacterial carpet. Bacterial carpet is consisting of biological fiber like jute fiber, coconut fiber. Accidentally, releasing of petroleum products are actual concern in the surroundings. Additionally, one of the main ecological difficulties at the present day is hydrocarbon pollution, which resulting from the activities associated with the chemical and allied industries. Hydrocarbon apparatuses have been known to fit in to the family of carcinogens and neurotoxic organic pollutants. Presently the accepted dumping methods of incineration and landfills are becoming expensive. Chemical and mechanical methods are limited effectiveness and expensive usually used to eradicate hydrocarbons from polluted places. Bioremediation is the hopeful technologies for the treatment of these contaminated sites, since it is cost-effective and lead to complete mineralization. Its functions are basically on biodegradation, which refer to complete mineralization of organic contaminants into carbon dioxide, water, inorganic compounds, and cell protein. Many indigenous microorganisms in water and soil are capable of demeaning hydrocarbon contaminants. This paper presents a review of petroleum hydrocarbon degradation using microorganisms.

Synchronization and Collective Dynamics of Flagella and Cilia as Hydrodynamically Coupled Oscillators

Cooperative motion of flagella and cilia faciliates swimming of microorganisms and material transport in the body of multicellular organisms. Using minimal models, we address the roles of hydrodynamic interaction in synchronization and collective dynamics of flagella and cilia. Collective synchronization of bacterial flagella is studied with a model of bacterial carpets. Cilia and eukaryotic flagella are characterized by periodic modulation of their driving forces, which produces various patterns of two-body synchronization and metachronal waves. Long-range nature of the interaction introduces novel features in the dynamics of these model systems. The flagella of a swimmer synchronize also by a viscous drag force mediated through the swimmer’s body. Recent advance in experimental studies of the collective dynamics of flagella, cilia and related artificial systems are summarized.

Impurity-tuned non-equilibrium phase transition in a bacterial carpet

The effects of impurity on the non-equilibrium phase transition in Vibrio alginolyticus bacterial carpets are investigated through a position-sensitive-diode implemented optical tweezers-microsphere assay. The collective flow increases abruptly as we increase the rotation rate of flagella via Na+ concentration. The effects of impurities on the transition behavior are examined by mixing cells of a wild type strain (VIO5) with cells of a mutant strain (NMB136) in different swimming patterns. For dilute impurities, the transition point is shifted toward higher Na+ concentration. Increasing the impurities' ratio to over 0.25 leads to a significant drop in the collective force, suggesting a partial orientational order with a smaller correlation length.

Electric Field Control of Bacteria-Powered Microrobots Using a Static Obstacle Avoidance Algorithm

A bacteria-powered microrobot (BPM) is a hybrid robotic system consisting of an SU-8 microstructure with active surfaces or bacterial carpets, in which massive arrays of biomolecular flagellar motors work cooperatively. This paper suggests an obstacle-avoidance method based on a BPM's response to electric fields. The negatively charged bacteria enable the BPM to follow electric fields. In our previous demonstration of the single BPM controllability, we observed a vast change in the control dynamics when obstructions distorted the applied electric field and affected BPM steering and control. In this paper, we demonstrate an obstacle avoidance method that takes the electric field distortion into account to navigate a BPM through multiple static obstacles in real time. We used an artificial potential field and configuration space in our algorithm to generate an objective function for the electric field distortion and collision around/with obstacles, respectively. In addition, finite-element modeling through COMSOL Multiphysics engineering software was used to simulate charged-particle trajectories in a distorted electric field. Finally, we describe the feasibility of our proposed obstacle avoidance approach through experiments and compared these data with simulation results.

Hydrodynamics of a self-actuated bacterial carpet using microscale particle image velocimetry.

Microorganisms can effectively generate propulsive force at the microscale where viscous forces overwhelmingly dominate inertia forces; bacteria achieve this task through flagellar motion. When swarming bacteria, cultured on agar plates, are blotted onto the surface of a microfabricated structure, a monolayer of bacteria forms what is termed a "bacterial carpet," which generates strong flows due to the combined motion of their freely rotating flagella. Furthermore, when the bacterial carpet coated microstructure is released into a low Reynolds number fluidic environment, the propulsive force of the bacterial carpet is able to give the microstructure motility. In our previous investigations, we demonstrated motion control of these bacteria powered microbiorobots (MBRs). Without any external stimuli, MBRs display natural rotational and translational movements on their own; this MBR self-actuation is due to the coordination of flagella. Here, we investigate the flow fields generated by bacterial carpets, and compare this flow to the flow fields observed in the bulk fluid at a series of locations above the bacterial carpet. Using microscale particle image velocimetry, we characterize the flow fields generated from the bacterial carpets of MBRs in an effort to understand their propulsive flow, as well as the resulting pattern of flagella driven self-actuated motion. Comparing the velocities between the bacterial carpets on fixed and untethered MBRs, it was found that flow velocities near the surface of the microstructure were strongest, and at distances far above, the surface flow velocities were much smaller.

Collective flow dynamics across a bacterial carpet: Understanding the forces generated

Bacterial carpets consist of randomly anchored uni-polar-flagellated sodium-motive bacterial matrix are prepared by flow deposition. Collective flow dynamics across the bacterial carpets are probed with optical tweezers-microsphere assay. Around the center of a uniform bacterial cluster, collective forces that pull microsphere towards carpet surface are detected at a distance of 10 μm away from carpets. At sodium-motive driving over a critical value, the force magnitudes increase abruptly, suggesting a threshold-like transition of hydrodynamic synchronization across bacterial carpet. The abrupt force increase is explained in term of bifurcation to phase synchronization in a noisy non-linearly coupled rotor array mediated by hydrodynamic interactions.

Collective sub-diffusive dynamics in bacterial carpet microfluidic channel

We experimentally investigate the collective dynamics in bacterial carpet microfluidic channel. The microfluidic channel is composed of single polar flagellated Vibrio alginolyticus deposited glass substrates. The individual flagellum swimming speed is tuned by varying buffer sodium concentration. Hydrodynamic coupling strength is tuned by varying buffer viscosity. The attached bacteria constantly perform two major modes in flagellum motion, namely, the local rotation and large angle flick. Particle tracking statistics shows high flagellum rotational rate and strong hydrodynamic coupling strength lead to collective sub-diffusive dynamics. The observed effect is strongly correlated to hydrodynamic coupling of flick motions between nearby bacteria.

Visualization of flagellar interactions on bacterial carpets

Methods for the in-depth study of the physics of microscale actuation of microfluidics environments by flagellated bacteria 'teamsters' have been developed. These methods, which include single and multi-colour fluorescent labelling and electron microscopy allow for the analysis of the effect that individual flagellar filaments have on bacterially driven microstructures, and allow for the investigation of the interaction and coordination of flagellar filaments of neighbouring bacteria on densely packed monolayers of bacteria, 'bacterial carpets'. We show that the flagella of bacteria that are immobilized on a surface often interact with each other, and that the flagella of these bacteria do not often form multi-flagella bundles that are aligned with the cell body.

Microfluidic Pump Powered by Self‐Organizing Bacteria

Results are presented that demonstrate the successful use of live bacteria as mechanical actuators in microfabricated fluid systems. The flow deposition of bacteria is used to create a motile bacterial carpet that can generate local fluid motion inside a microfabricated system. By tracking the motion of tracer particles, we demonstrate that the bacterial cells that comprise the carpet self-organize, generating a collective fluid motion that can pump fluid autonomously through a microfabricated channel at speeds as high as 25 microm s(-1). The pumping performance of the system can also be augmented by changing the chemical environment. The addition of glucose to the working buffer raises the metabolic activity of the bacterial carpet, resulting in increased pumping performance. The performance of the bacterial pump is also shown to be strongly influenced by the global geometry of the pump, with narrower channels achieving a higher pumping velocity with a faster rise time.

Use of Bacterial Carpets to Enhance Mixing in Microfluidic Systems

We demonstrate that flagellated bacteria can be utilized in surface arrays (carpets) to achieve mixing in a low-Reynolds number fluidic environment. The mixing performance of the system is quantified by measuring the diffusion of small tracer particles. We show that the mixing performance responds to modifications to the chemical and thermal environment of the system, which affects the metabolic activity of the bacteria. Although the mixing performance can be increased by the addition of glucose (food) to the surrounding buffer or by raising the buffer temperature, the initial augmentation is also accompanied by a faster decay in mixing performance, due to falling pH and oxygen starvation, both induced by the higher metabolic activity of the bacterial system.

Moving Fluid with Bacterial Carpets

We activated a solid-fluid interface by attaching flagellated bacteria to a solid surface. We adsorbed swarmer cells of Serratia marcescens to polydimethylsiloxane or polystyrene. The cell bodies formed a densely packed monolayer while their flagella continued to rotate freely. Motion of the fluid close to an extended flat surface, visualized with tracer beads, was dramatically enhanced compared to the motion farther away. The tracer beads revealed complex ever-changing flow patterns, some linear (rivers), others rotational (whirlpools). Typical features of this flow were small (tens of μm) and reasonably stable (many minutes). The surface performed active mixing equivalent to diffusion with a coefficient of 2 × 10 −7 cm 2/s. We call these flat constructs “bacterial carpets”. When attached to polystyrene beads or to fragments of polydimethylsiloxane, the bacteria generated both translation and rotation. We call these constructs “auto-mobile beads” or “auto-mobile chips”. Given the size and strength of the flow patterns near the carpets, the motion must be generated by small numbers of coordinated flagella. We should be able to produce larger and longer-range effects by increasing coordination.