MEMS and the microbe

Evaluation of Hydrodynamic and Thermal Behaviour of Non-Newtonian-Nanofluid Mixing in a Chaotic Micromixer

Three-dimensional numerical investigations of a novel passive micromixer were carried out to analyze the hydrodynamic and thermal behaviors of Nano-Non-Newtonian fluids. Mass and heat transfer characteristics of two heated fluids have been investigated to understand the quantitative and qualitative fluid faction distributions with temperature homogenization. The effect of fluid behavior and different Al₂O₃ nanoparticles concentrations on the pressure drop and thermal mixing performances were studied for different Reynolds number (from 0.1 to 25). The performance improvement simulation was conducted in intervals of various Nanoparticles concentrations (φ = 0 to 5%) with Power-law index (n) using CFD. The proposed micromixer displayed a mixing energy cost of 50-60 comparable to that achieved for a recent micromixer (2021y) in terms of fluid homogenization. The analysis exhibited that for high nanofluid concentrations, having a strong chaotic flow enhances significantly the hydrodynamic and thermal performances for all Reynolds numbers. The visualization of vortex core region of mass fraction and path lines presents that the proposed design exhibits a rapid thermal mixing rate that tends to 0.99%, and a mass fraction mixing rate of more than 0.93% with very low pressure losses, thus the proposed micromixer can be utilized to enhance homogenization in different Nano-Non-Newtonian mechanism with minimum energy.

Microfluidics for Microswimmers: Engineering Novel Swimmers and Constructing Swimming Lanes on the Microscale, a Tutorial Review

This paper provides an updated review of recent advances in microfluidics applied to artificial and biohybrid microswimmers. Sharing the common regime of low Reynolds number, the two fields have been brought together to take advantage of the fluid characteristics at the microscale, benefitting microswimmer research multifold. First, microfluidics offer simple and relatively low-cost devices for high-fidelity production of microswimmers made of organic and inorganic materials in a variety of shapes and sizes. Microscale confinement and the corresponding fluid properties have demonstrated differential microswimmer behaviors in microchannels or in the presence of various types of physical or chemical stimuli. Custom environments to study these behaviors have been designed in large part with the help of microfluidics. Evaluating microswimmers in increasingly complex lab environments such as microfluidic systems can ensure more effective implementation for in-field applications. The benefits of microfluidics for the fabrication and evaluation of microswimmers are balanced by the potential use of microswimmers for sample manipulation and processing in microfluidic systems, a large obstacle in diagnostic and other testing platforms. In this review various ways in which these two complementary technology fields will enhance microswimmer development and implementation in various fields are introduced.

Enhancement of Mixing Performance of Two-Layer Crossing Micromixer through Surrogate-Based Optimization

Optimum configuration of a micromixer with two-layer crossing microstructure was performed using mixing analysis, surrogate modeling, along with an optimization algorithm. Mixing performance was used to determine the optimum designs at Reynolds number 40. A surrogate modeling method based on a radial basis neural network (RBNN) was used to approximate the value of the objective function. The optimization study was carried out with three design variables; viz., the ratio of the main channel thickness to the pitch length (H/PI), the ratio of the thickness of the diagonal channel to the pitch length (W/PI), and the ratio of the depth of the channel to the pitch length (d/PI). Through a primary parametric study, the design space was constrained. The design points surrounded by the design constraints were chosen using a well-known technique called Latin hypercube sampling (LHS). The optimal design confirmed a 32.0% enhancement of the mixing index as compared to the reference design.

A Review of Passive Micromixers with a Comparative Analysis

A wide range of existing passive micromixers are reviewed, and quantitative analyses of ten typical passive micromixers were performed to compare their mixing indices, pressure drops, and mixing costs under the same axial length and flow conditions across a wide Reynolds number range of 0.01–120. The tested micromixers were selected from five types of micromixer designs. The analyses of flow and mixing were performed using continuity, Navier-Stokes and convection-diffusion equations. The results of the comparative analysis were presented for three different Reynolds number ranges: low-Re (Re ≤ 1), intermediate-Re (1 < Re ≤ 40), and high-Re (Re > 40) ranges, where the mixing mechanisms are different. The results show a two-dimensional micromixer of Tesla structure is recommended in the intermediate- and high-Re ranges, while two three-dimensional micromixers with two layers are recommended in the low-Re range due to their excellent mixing performance.

Artificial Microbial Arenas: Materials for Observing and Manipulating Microbial Consortia

From the smallest ecological niche to global scale, communities of microbial life present a major factor in system regulation and stability. As long as laboratory studies remain restricted to single or few species assemblies, however, very little is known about the interaction patterns and exogenous factors controlling the dynamics of natural microbial communities. In combination with microfluidic technologies, progress in the manufacture of functional and stimuli-responsive materials makes artificial microbial arenas accessible. As habitats for natural or multispecies synthetic consortia, they are expected to not only enable detailed investigations, but also the training and the directed evolution of microbial communities in states of balance and disturbance, or under the effects of modulated stimuli and spontaneous response triggers. Here, a perspective on how materials research will play an essential role in generating answers to the most pertinent questions of microbial engineering is presented, and the concept of adaptive microbial arenas and possibilities for their construction from particulate microniches to 3D habitats is introduced. Materials as active and tunable components at the interface of living and nonliving matter offer exciting opportunities in this field. Beyond forming the physical horizon for microbial cultivates, they will enable dedicated intervention, training, and observation of microbial consortia.

A Novel Microbial Culture Chamber Co-cultivation System to Study Algal-Bacteria Interactions Using Emiliania huxleyi and Phaeobacter inhibens as Model Organisms

Our understanding of microbial natural environments combines in situ experimentation with studies of specific interactions in laboratory-based setups. The purpose of this work was to develop, build and demonstrate the use of a microbial culture chamber enabling both in situ and laboratory-based studies. The design uses an enclosed chamber surrounded by two porous membranes that enables the comparison of growth of two separate microbial populations but allowing free exchange of small molecules. Initially, we tested if the presence of the macroalga Fucus vesiculosus inside the chamber affected colonization of the outer membranes by marine bacteria. The alga did indeed enrich the total population of colonizing bacteria by more than a factor of four. These findings lead us to investigate the effect of the presence of the coccolithophoric alga Emiliania huxleyi on attachment and biofilm formation of the marine bacterium Phaeobacter inhibens DSM17395. These organisms co-exist in the marine environment and have a well-characterized interdependence on secondary metabolites. P. inhibens attached in significantly higher numbers when having access to E. huxleyi as compared to when exposed to sterile media. The experiment was carried out using a wild type (wt) strain as well as a TDA-deficient strain of P. inhibens. The ability of the bacterium to produce the antibacterial compound, tropodithietic acid (TDA) influenced its attachment since the P. inhibens DSM17395 wt strain attached in higher numbers to a surface within the first 48 h of incubation with E. huxleyi as compared to a TDA-negative mutant. Whilst the attachment of the bacterium to a surface was facilitated by presence of the alga, however, we cannot conclude if this was directly affected by the algae or whether biofilm formation was dependent on the production of TDA by P. inhibens, which has been implied by previous studies. In the light of these results, other applications of immersed culture chambers are suggested.

Microfluidics and microbial engineering

The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.

Live cell imaging compatible immobilization of Chlamydomonas reinhardtii in microfluidic platform for biodiesel research

This paper describes a novel surface immobilization method for live-cell imaging of Chlamydomonas reinhardtii for continuous monitoring of lipid droplet accumulation. Microfluidics allows high-throughput manipulation and analysis of single cells in precisely controlled microenvironment. Fluorescence imaging based quantitative measurement of lipid droplet accumulation in microalgae had been difficult due to their intrinsic motile behavior. We present a simple surface immobilization method using gelatin coating as the "biological glue." We take advantage of hydroxyproline (Hyp)-based non-covalent interaction between gelatin and the outer cell wall of microalgae to anchor the cells inside the microfluidic device. We have continuously monitored single microalgal cells for up to 6 days. The immobilized microalgae remain viable (viability was comparable to bulk suspension cultured controls). When exposed to wall shear stress, most of the cells remain attached up to 0.1 dyne/cm(2) . Surface immobilization allowed high-resolution, live-cell imaging of mitotic process in real time-which followed previously reported stages in mitosis of suspension cultured cells. Use of gelatin coated microfluidics devices can result in better methods for microalgae strain screening and culture condition optimization that will help microalgal biodiesel become more economically viable.

Automated single cell microbioreactor for monitoring intracellular dynamics and cell growth in free solution

We report an automated microfluidic-based platform for single cell analysis that allows for cell culture in free solution with the ability to control the cell growth environment. Using this approach, cells are confined by the sole action of gentle fluid flow, thereby enabling non-perturbative analysis of cell growth away from solid boundaries. In addition, the single cell microbioreactor allows for precise and time-dependent control over cell culture media, with the combined ability to observe the dynamics of non-adherent cells over long time scales. As a proof-of-principle demonstration, we used the platform to observe dynamic cell growth, gene expression, and intracellular diffusion of repressor proteins while precisely tuning the cell growth environment. Overall, this microfluidic approach enables the direct observation of cellular dynamics with exquisite control over environmental conditions, which will be useful for quantifying the behaviour of single cells in well-defined media.

Isolation of microorganisms using sub-micrometer constrictions

We present an automated method for isolating pure bacterial cultures from samples containing multiple species that exploits the cell's own physiology to perform the separation. Cells compete to reach a chamber containing nutrients via a constriction whose cross-sectional area only permits a single cell to enter, thereby blocking the opening and preventing other cells from entering. The winning cell divides across the constriction and its progeny populate the chamber. The devices are passive and require no user interaction to perform their function. Device fabrication begins with the creation of a master mold that contains the desired constriction and chamber features. Replica molding is used to create patterned polymer chips from the master, which are bonded to glass microscope cover slips to create the constrictions. We tested constriction geometries ranging from 500 nanometers to 5 micrometers in width, 600 to 950 nanometers in height, and 10 to 40 micrometers in length. The devices were used to successfully isolate a pure Pseudomonas aeruginosa culture from a mixture that also contained Escherichia coli. We demonstrated that individual strains of the same species can be separated out from mixtures using red and green fluorescently-labeled E. coli. We also used the devices to isolate individual environmental species. Roseobacter sp. was separated from another marine species, Psychroserpens sp.

USB-driven microfluidic chips on printed circuit boards

A technology is presented to fabricate a microfluidic chip in which the microchannels and the microelectrodes of sensors are integrated directly into the copper sheet on a printed circuit board. Then, we demonstrate an application of the generation of oil-in-water and water-in-oil emulsion droplets on this microfluidic chip driven by a USB interface, and the droplet size is detected by the microelectrodes on the downstream microchannel. The integration of the microfluidic chip is improved by the direct connection of the channels to the microelectrodes of the driving unit and of the sensors on the same substrate, and it is a promising way to integrate microfluidics into a more complex micro electrical-mechanical system (MEMS).

High throughput screening to investigate the interaction of stem cells with their extracellular microenvironment

Stem cells in vivo are housed within a functional microenvironment termed the "stem cell niche." As the niche components can modulate stem cell behaviors like proliferation, migration and differentiation, evaluating these components would be important to determine the most optimal platform for their maintenance or differentiation. In this review, we have discussed methods and technologies that have aided in the development of high throughput screening assays for stem cell research, including enabling technologies such as the well-established multiwell/microwell plates and robotic spotting, and emerging technologies like microfluidics, micro-contact printing and lithography. We also discuss the studies that utilized high throughput screening platform to investigate stem cell response to extracellular matrix, topography, biomaterials and stiffness gradients in the stem cell niche. The combination of the aforementioned techniques could lay the foundation for new perspectives in further development of high throughput technology and stem cell research.

Advances in microfluidics-based experimental methods for neuroscience research

The application of microfluidics to neuroscience applications has always appealed to neuroscientists because of the capability to control the cellular microenvironment in both a spatial and temporal manner. Recently, there has been rapid development of biological micro-electro-mechanical systems (BioMEMS) for both fundamental and applied neuroscience research. In this review, we will discuss the applications of BioMEMS to various topics in the field of neuroscience. The purpose of this review is to summarise recent advances in the components and design of the BioMEMS devices, in vitro disease models, electrophysiology and neural stem cell research. We envision that microfluidics will play a key role in future neuroscience research, both fundamental and applied research.

Hydrodynamic trapping of Tetrahymena thermophila for the long-term monitoring of cell behaviors

Microfluidic trapping technology has been widely applied for single-cell observation in order to reveal characteristic cell behaviors. However, this strategy has yet to be tested for monitoring highly motile cells, which are often biologically important. In this paper, we seek the conditions that enable effective and long-term trapping of a prominent model ciliate Tetrahymena thermophila within a hydrodynamic microfluidic device. Although motility and flexibility of T. thermophila make it difficult to avoid escaping from the trap, we show that tuning some key parameters in the hydrodynamic circuit was effective to achieve approximately 40 h cell retention, which is long enough to monitor cell behaviors over several generations. Here, we demonstrate the real-time observation of cell division and phagocytic digestion, revealing interesting phenomena such as a wide distribution in doubling time in a poor synthetic medium and heterogeneous time courses in digestion processes. Our results present a strategy for trapping highly motile ciliate cells in order to study the dynamic behaviors of single cells.

Accurate and Effective Live Bacteria Microarray Patterning on Thick Polycationic Polymer Layer Co-Patterned with HMDS

A new bacteria microarray patterning technique is developed by patterning thick polycationic polymers on glass surface, which generates high-coverage and high-precision E. coli cell patterns. Cell immobilization efficiency is greatly improved, compared to conventional monolayer surface patterning approach. Cell viability tests show very low cytotoxicity of polyethyleneimine (PEI). This advancement should further accelerate biomedical and bacteriological researches in the micro scale.

Micromixing within microfluidic devices

Micromixing is a crucial process within microfluidic systems such as micro total analysis systems (μTAS). A state-of-art review on microstructured mixing devices and their mixing phenomena is given. The review first presents an overview of the characteristics of fluidic behavior at the microscale and their implications in microfluidic mixing processes. According to the two basic principles exploited to induce mixing at the microscale, micromixers are generally classified as being passive or active. Passive mixers solely rely on pumping energy, whereas active mixers rely on an external energy source to achieve mixing. Typical types of passive micromixers are discussed, including T- or Y-shaped, parallel lamination, sequential, focusing enhanced mixers, and droplet micromixers. Examples of active mixers using external forces such as pressure field, electrokinetic, dielectrophoretic, electrowetting, magneto-hydrodynamic, and ultrasound to assist mixing are presented. Finally, the advantages and disadvantages of mixing in a microfluidic environment are discussed.

Whole-cell biochips for bio-sensing: integration of live cells and inanimate surfaces

Recent advances in the convergence of the biological, chemical, physical, and engineering sciences have opened new avenues of research into the interfacing of diverse biological moieties with inanimate platforms. A main aspect of this field, the integration of live cells with micro-machined platforms for high throughput and bio-sensing applications, is the subject of the present review. These unique hybrid systems are configured in a manner that ensures positioning of the cells in designated patterns, and enables cellular viability maintenance, and monitoring of cellular functionality. Here we review both animate and inanimate surface properties and how they affect cellular attachment, describe relevant modifications of both types of surfaces, list technologies for platform engineering and for cell deposition in the desired configurations, and discuss the influence of various deposition and immobilization methods on the viability and performance of the immobilized cells.

An agar gel membrane-PDMS hybrid microfluidic device for long term single cell dynamic study

Significance of single cell measurements stems from the substantial temporal fluctuations and cell-cell variability possessed by individual cells. A major difficulty in monitoring surface non-adherent cells such as bacteria and yeast is that these cells tend to aggregate into clumps during growth, obstructing the tracking or identification of single-cells over long time periods. Here, we developed a microfluidic platform for long term single-cell tracking and cultivation with continuous media refreshing and dynamic chemical perturbation capability. The design highlights a simple device-assembly process between PDMS microchannel and agar membrane through conformal contact, and can be easily adapted by microbiologists for their routine laboratory use. The device confines cell growth in monolayer between an agar membrane and a glass surface. Efficient nutrient diffusion through the membrane and reliable temperature maintenance provide optimal growth condition for the cells, which exhibited fast exponential growth and constant distribution of cell sizes. More than 24 h of single-cell tracking was demonstrated on a transcription-metabolism integrated synthetic biological model, the gene-metabolic oscillator. Single cell morphology study under alcohol toxicity allowed us to discover and characterize cell filamentation exhibited by different E. coli isobutanol tolerant strains. We believe this novel device will bring new capabilities to quantitative microbiology, providing a versatile platform for single cell dynamic studies.

High-resolution microcontact printing and transfer of massive arrays of microorganisms on planar and compartmentalized nanoporous aluminium oxide

Handling microorganisms in high throughput and their deployment into miniaturized platforms presents significant challenges. Contact printing can be used to create dense arrays of viable microorganisms. Such "living arrays", potentially with multiple identical replicates, are useful in the selection of improved industrial microorganisms, screening antimicrobials, clinical diagnostics, strain storage, and for research into microbial genetics. A high throughput method to print microorganisms at high density was devised, employing a microscope and a stamp with a massive array of PDMS pins. Viable bacteria (Lactobacillus plantarum, Esherichia coli), yeast (Candida albicans) and fungal spores (Aspergillus fumigatus) were deposited onto porous aluminium oxide (PAO) using arrays of pins with areas from 5 x 5 to 20 x 20 microm. Printing onto PAO with up to 8100 pins of 20 x 20 microm area with 3 replicates was achieved. Printing with up to 200 pins onto PAO culture chips (divided into 40 x 40 microm culture areas) allowed inoculation followed by effective segregation of microcolonies during outgrowth. Additionally, it was possible to print mixtures of C. albicans and spores of A. fumigatus with a degree of selectivity by capture onto a chemically modified PAO surface. High resolution printing of microorganisms within segregated compartments and on functionalized PAO surfaces has significant advantages over what is possible on semi-solid surfaces such as agar.