A new method for simulating the motion of individual ellipsoidal bacteria in microfluidic devices

Microfluidic Sampling and Biosensing Systems for Foodborne Escherichia coli and Salmonella

Developments of portable biosensors for field-deployable detections have been increasingly important to control foodborne pathogens in regulatory environment and in early stage of outbreaks. Conventional cultivation and gene amplification methods require sophisticated instruments and highly skilled professionals; while portable biosensing devices provide more freedom for rapid detections not only in research laboratories but also in the field; however, their sensitivity and specificity are limited. Microfluidic methods have the advantage of miniaturizing instrumental size while integrating multiple functions and high-throughput capability into one streamlined system at low cost. Minimal sample consumption is another advantage to detect samples in different sizes and concentrations, which is important for the close monitoring of pathogens at consumer end. They improve measurement or manipulation of bacteria by increasing the ratio of functional interface of the device to the targeted biospecies and in turn reducing background interference. This article introduces the major active and passive microfluidic devices that have been used for bacteria sampling and biosensing. The emphasis is on particle-based sorting/enrichment methods with or without external physical fields applied to the microfluidic devices and on various biosensing applications reported for bacteria sampling. Three major fabrication methods for microfluidics are briefly discussed with their advantages and limitations. The applications of these active and passive microfluidic sampling methods in the past 5 years have been summarized, with the focus on Escherichia coli and Salmonella. The current challenges to microfluidic bacteria sampling are caused by the small size and nonspherical shape of various bacterial cells, which can induce unpredictable deviations in sampling and biosensing processes. Future studies are needed to develop rapid prototyping methods for device manufacturing, which can facilitate rapid response to various foodborne pathogen outbreaks.

Microfluidic systems for hydrodynamic trapping of cells and clusters

Microfluidic devices have been widely applied to trapping and isolation of cells and clusters for controllable intercellular environments and high-throughput analysis, triggering numerous advances in disease diagnosis and single-cell analysis. Passive hydrodynamic cell trapping is one of the simple and effective methods that has been gaining attention in recent years. Our aim here is to review the existing passive microfluidic trapping approaches, including microposts, microfiltration, microwells, and trapping chambers, with emphasis on design principles and performance. We summarize the remarkable advances that hydrodynamic trapping methods offer, as well as the existing challenges and prospects for development. Finally, we hope that an improved understanding of hydrodynamic trapping approaches can lead to sophisticated and useful platforms to advance medical and biological research.

Modelling bacterial twitching in fluid flows: a CFD-DEM approach

Bacterial habitats are often associated with fluid flow environments. Bacterial twitching is important for initial bacterial colonization and biofilm formation. The existing research about bacteria twitching is largely experimental orientated. There is a lack of models of twitching motility of bacteria in shear flows, which could provide fundamental understanding about how bacterial twitching would be affected by bacteria associated properties such as number of pili and their distribution on the cell body and environmental factors such as flow and surface patterns. In this work, a three-dimensional modelling approach of Computational Fluid Dynamics (CFD) coupled with the Discrete Element Method (DEM) proposed to study bacterial twitching on flat and groove surfaces under shear flow conditions. Rod-shaped bacteria are modelled as groups of spherical particles and Type IV pili attached to bacteria are modelled as dynamic springs which can elongate, retract, attach and detach. The CFD-DEM model of rod-shape bacteria is validated against orbiting of immotile bacteria in shear flows. The effects of fluid flow rate and surface topography on twitching motility are studied. The model can successfully predict upstream twitching motility of rod-shaped bacteria in shear flows. Our model can predict that there would be an optimal range of wall shear stress in which bacterial upstream twitching is most efficient. The results also indicate that when bacteria twitch on groove surfaces, they are likely to accumulate around the downstream side of the groove walls.

Particle shape impacts export and fate in the ocean through interactions with the globally abundant appendicularian Oikopleura dioica

Marine microbes exhibit highly varied, often non-spherical shapes that have functional significance for essential processes, including nutrient acquisition and sinking rates. There is a surprising absence of data, however, on how cell shape affects grazing, which is crucial for predicting the fate of oceanic carbon. We used synthetic spherical and prolate spheroid microbeads to isolate the effect of particle length-to-width ratios on grazing and fate in the ocean. Here we show that the shape of microbe-sized particles affects predation by the appendicularian Oikopleura dioica, a globally abundant marine grazer. Using incubation experiments, we demonstrate that shape affects how particles are retained in the house and that the minimum particle diameter is the key variable determining how particles are ingested. High-speed videography revealed the mechanism behind these results: microbe-sized spheroids oriented with the long axis parallel to fluid streamlines, matching the speed and tortuosity of spheres of equivalent width. Our results suggest that the minimum particle diameter determines how elongated prey interact with the feeding-filters of appendicularians, which may help to explain the prevalence of ellipsoidal cells in the ocean, since a cell’s increased surface-to-volume ratio does not always increase predation. We provide the first evidence that grazing by appendicularians can cause non-uniform export of different shaped particles, thereby influencing particle fate.

Modeling and CFD simulation of nutrient distribution in picoliter bioreactors for bacterial growth studies on single-cell level

A microfluidic device for microbial single-cell cultivation of bacteria was modeled and simulated using COMSOL Multiphysics. The liquid velocity field and the mass transfer within the supply channels and cultivation chambers were calculated to gain insight in the distribution of supplied nutrients and metabolic products secreted by the cultivated bacteria. The goal was to identify potential substrate limitations or product accumulations within the cultivation device. The metabolic uptake and production rates, colony size, and growth medium composition were varied covering a wide range of operating conditions. Simulations with glucose as substrate did not show limitations within the typically used concentration range, but for alternative substrates limitations could not be ruled out. This lays the foundation for further studies and the optimization of existing picoliter bioreactor systems.

Bistability and metabistability scenario in the dynamics of an ellipsoidal particle in a sheared viscoelastic fluid

The motion of an ellipsoidal particle in a viscoelastic liquid subjected to an unconfined shear flow is addressed by numerical simulations. A complex dynamics is found with different transients and long-time regimes depending on the Deborah number De (De is the product of the viscoelastic liquid intrinsic time times the applied shear rate). Spiraling orbits toward a log-rolling motion around the vorticity are observed for low Deborah numbers, whereas the particle aligns with its major axis near to the flow direction at high Deborah numbers. The transition from vorticity to flow alignment is characterized by a periodic regime with small amplitude oscillations around orientations progressively shifting from vorticity to flow direction by increasing De. A range of Deborah numbers is detected such that the periodic solution coexists with the flow alignment regime (bistability). A further range of De is found where flow alignment is attained differently for particles starting far from or next to the shear plane: in the latter case, very long transients are found; hence an effective bistability (metabistability) is predicted to occur in a large time lapse before reaching the fully aligned state. Finally, the computed Deborah number values for flow alignment favorably compare with available experimental data.

Dynamic modeling of cell migration and spreading behaviors on fibronectin coated planar substrates and micropatterned geometries

An integrative cell migration model incorporating focal adhesion (FA) dynamics, cytoskeleton and nucleus remodeling, actin motor activity, and lamellipodia protrusion is developed for predicting cell spreading and migration behaviors. This work is motivated by two experimental works: (1) cell migration on 2-D substrates under various fibronectin concentrations and (2) cell spreading on 2-D micropatterned geometries. These works suggest (1) cell migration speed takes a maximum at a particular ligand density (∼1140 molecules/µm(2)) and (2) that strong traction forces at the corners of the patterns may exist due to combined effects exerted by actin stress fibers (SFs). The integrative model of this paper successfully reproduced these experimental results and indicates the mechanism of cell migration and spreading. In this paper, the mechanical structure of the cell is modeled as having two elastic membranes: an outer cell membrane and an inner nuclear membrane. The two elastic membranes are connected by SFs, which are extended from focal adhesions on the cortical surface to the nuclear membrane. In addition, the model also includes ventral SFs bridging two focal adhesions on the cell surface. The cell deforms and gains traction as transmembrane integrins distributed over the outer cell membrane bond to ligands on the ECM surface, activate SFs, and form focal adhesions. The relationship between the cell migration speed and fibronectin concentration agrees with existing experimental data for Chinese hamster ovary (CHO) cell migrations on fibronectin coated surfaces. In addition, the integrated model is validated by showing persistent high stress concentrations at sharp geometrically patterned edges. This model will be used as a predictive model to assist in design and data processing of upcoming microfluidic cell migration assays.

Geometrical effects in microfluidic-based microarrays for rapid, efficient single-cell capture of mammalian stem cells and plant cells

In this paper, a detailed numerical and experimental investigation into the optimisation of hydrodynamic micro-trapping arrays for high-throughput capture of single polystyrene (PS) microparticles and three different types of live cells at trapping times of 30 min or less is described. Four different trap geometries (triangular, square, conical, and elliptical) were investigated within three different device generations, in which device architecture, channel geometry, inter-trap spacing, trap size, and trap density were varied. Numerical simulation confirmed that (1) the calculated device dimensions permitted partitioned flow between the main channel and the trap channel, and further, preferential flow through the trap channel in the absence of any obstruction; (2) different trap shapes, all having the same dimensional parameters in terms of depth, trapping channel lengths and widths, main channel lengths and widths, produce contrasting streamline plots and that the interaction of the fluid with the different geometries can produce areas of stagnated flow or distorted field lines; and (3) that once trapped, any motion of the trapped particle or cell or a shift in its configuration within the trap can result in significant increases in pressures on the cell surface and variations in the shear stress distribution across the cell's surface. Numerical outcomes were then validated experimentally in terms of the impact of these variations in device design elements on the percent occupancy of the trapping array (with one or more particles or cells) within these targeted short timeframes. Limitations on obtaining high trap occupancies in the devices were shown to be primarily a result of particle aggregation, channel clogging and the trap aperture size. These limitations could be overcome somewhat by optimisation of these device design elements and other operational variables, such as the average carrier fluid velocity. For example, for the 20 μm polystyrene microparticles, the number of filled traps increased from 32% to 42% during 5-10 min experiments in devices with smaller apertures. Similarly, a 40%-60% reduction in trapping channel size resulted in an increase in the amount of filled traps, from 0% to almost 90% in 10 min, for the human bone marrow derived mesenchymal stem cells, and 15%-85% in 15 min for the human embryonic stem cells. Last, a reduction of the average carrier fluid velocity by 50% resulted in an increase from 80% to 92% occupancy of single algae cells in traps. Interestingly, changes in the physical properties of the species being trapped also had a substantial impact, as regardless of the trap shape, higher percent occupancies were observed with cells compared to single PS microparticles in the same device, even though they are of approximately the same size. This investigation showed that in microfluidic single cell capture arrays, the trap shape that maximizes cell viability is not necessarily the most efficient for high-speed single cell capture. However, high-speed trapping configurations for delicate mammalian cells are possible but must be optimised for each cell type and designed principally in accordance with the trap size to cell size ratio.

Primary charge effects on prolate spheroids with moderate aspect ratios

In this article, we investigate the behavior of charged spheroidal colloids with moderate aspect ratios in linear flow fields. We use direct numerical simulation with body-fitted grids for the solution of the Stokes-Poisson-Nernst-Planck system to include all non-linear effects. Therefore, we propose an efficient semi-implicit time discretization based on a splitting of the Stokes equation. We will study the effects of the electric double layer on the forces, torques and on the motion of spheroidal particles. For low Reynolds numbers, we find approximating linear expressions between the ambient fluid flow and the force and torque on the particle. The description of this linear behavior is based on the resistance functions, whose dependencies on the Debye length and the zeta potential are investigated. It is recovered that the resistance functions obey a quadratic dependence on the zeta potential in the small zeta potential regime. For low values of the zeta potential, approximate formulas for the resistance functions are given. The approximation properties are carefully studied by comparing the approximate results with direct numerical simulations. For the case of a shear flow, the approximate formulas can be used to avoid time-consuming direct numerical simulations.

Feedback control system simulator for the control of biological cells in microfluidic cross slots and integrated microfluidic systems

Control systems for lab on chip devices require careful characterisation and design for optimal performance. Traditionally, this involves either extremely computationally expensive simulations or lengthy iteration of laboratory experiments, prototype design, and manufacture. In this paper, an efficient control simulation technique, valid for typical microchannels, Computed Interpolated Flow Hydrodynamics (CIFH), is described that is over 500 times faster than conventional time integration techniques. CIFH is a hybrid approach, utilising a combination of pre-computed flows and hydrodynamic equations and allows the efficient simulation of dynamic control systems for the transport of cells through micro-fluidic devices. The speed-ups achieved by using pre-computed CFD solutions mapped to an n-dimensional control parameter space, significantly accelerate the evaluation and improvement of control strategies and chip design. Here, control strategies for a naturally unstable device geometry, the microfluidic cross-slot, have been simulated and optimal parameters have been found for proposed devices capable of trapping and sorting cells.

Programmed trapping of individual bacteria using micrometre-size sieves

Monitoring the real-time behavior of spatial arrays of single living bacteria cells is only achieved with much experimental difficulty due to the small size and mobility of the cells. To address this problem, we have designed and constructed a simple microfluidic device capable of trapping single bacteria cells in spatially well-defined locations without the use of chemical surface treatments. The device exploits hydrodynamics to slow down and trap cells flowing near a narrow aperture. We have modeled this system numerically by approximating the motion of Escherichia coli cells as rigid 3-D ellipsoids. The numerical predictions for the speed and efficiency of trapping were tested by fabricating the devices and imaging GFP expressing E. coli at a high spatio-temporal resolution. We find that our numerical simulations agree well with the actual cell flow for varying trap geometries. The trapped cells are optically accessible, and combined with our ability to predict their spatial location we demonstrate the ease of this method for monitoring multiple single cells over a time course. The simplicity of the design, inexpensive materials and straightforward fabrication make it an accessible tool for any systems biology laboratory.