Mass transport and surface reactions in microfluidic systems

Design of a prototype flow microreactor for synthetic biology in vitro

As a reference platform for in vitro synthetic biology, we have developed a prototype flow microreactor for enzymatic biosynthesis. We report the design, implementation, and computer-aided optimisation of a three-step model pathway within a microfluidic reactor. A packed bed format was shown to be optimal for enzyme compartmentalisation after experimental evaluation of several approaches. The specific substrate conversion efficiency could significantly be improved by an optimised parameter set obtained by computational modelling. Our microreactor design provides a platform to explore new in vitro synthetic biology solutions for industrial biosynthesis.

Enhancement of affinity-based biosensors: effect of sensing chamber geometry on sensitivity

Affinity-based biosensing systems have become an important analytical tool for the detection and study of numerous biomolecules. The merging of these sensing technologies with microfluidic flow cells allows for faster detection times, increased sensitivities, and lower required sample volumes. In order to obtain a higher degree of performance from the sensor, it is important to know the effects of the flow cell geometry on the sensor sensitivity. In these sensors, the sensor sensitivity is related to the overall diffusive flux of analyte to the sensing surface; therefore increases in the analyte flux will be manifested as an increase in sensitivity, resulting in a lower limit of detection (LOD). Here we present a study pertaining to the effects of the flow cell height H on the analyte flux J, where for a common biosensor design we predict that the analyte flux will scale as J ≈ H(-2/3). We verify this scaling behavior via both numerical simulations as well as an experimental surface plasmon resonance (SPR) biosensor. We show the reduction of the flow cell height can have drastic effects on the sensor performance, where the LOD of our experimental system concerning the detection of ssDNA decreases by a factor of 4 when H is reduced from 47 μm to 7 μm. We utilize these results to discuss the applicability of this scaling behavior with respect to a generalized affinity-based biosensor.

Porous bead-based diagnostic platforms: bridging the gaps in healthcare

Advances in lab-on-a-chip systems have strong potential for multiplexed detection of a wide range of analytes with reduced sample and reagent volume; lower costs and shorter analysis times. The completion of high-fidelity multiplexed and multiclass assays remains a challenge for the medical microdevice field; as it struggles to achieve and expand upon at the point-of-care the quality of results that are achieved now routinely in remote laboratory settings. This review article serves to explore for the first time the key intersection of multiplexed bead-based detection systems with integrated microfluidic structures alongside porous capture elements together with biomarker validation studies. These strategically important elements are evaluated here in the context of platform generation as suitable for near-patient testing. Essential issues related to the scalability of these modular sensor ensembles are explored as are attempts to move such multiplexed and multiclass platforms into large-scale clinical trials. Recent efforts in these bead sensors have shown advantages over planar microarrays in terms of their capacity to generate multiplexed test results with shorter analysis times. Through high surface-to-volume ratios and encoding capabilities; porous bead-based ensembles; when combined with microfluidic elements; allow for high-throughput testing for enzymatic assays; general chemistries; protein; antibody and oligonucleotide applications.

Mass transport effects in suspended waveguide biosensors integrated in microfluidic channels

Label-free optical biosensors based on integrated photonic devices have demonstrated sensitive and selective detection of biological analytes. Integrating these sensor platforms into microfluidic devices reduces the required sample volume and enables rapid delivery of sample to the sensor surface, thereby improving response times. Conventionally, these devices are embedded in or adjacent to the substrate; therefore, the effective sensing area lies within the slow-flow region at the floor of the channel, reducing the efficiency of sample delivery. Recently, a suspended waveguide sensor was developed in which the device is elevated off of the substrate and the sensing region does not rest on the substrate. This geometry places the sensing region in the middle of the parabolic velocity profile, reduces the distance that a particle must travel by diffusion to be detected, and allows binding to both surfaces of the sensor. We use a finite element model to simulate advection, diffusion, and specific binding of interleukin 6, a signaling protein, to this waveguide-based biosensor at a range of elevations within a microfluidic channel. We compare the transient performance of these suspended waveguide sensors with that of traditional planar devices, studying both the detection threshold response time and the time to reach equilibrium. We also develop a theoretical framework for predicting the behavior of these suspended sensors. These simulation and theoretical results provide a roadmap for improving sensor performance and minimizing the amount of sample required to make measurements.

High throughput fabrication of plasmonic nanostructures in nanofluidic pores for biosensing applications

One of the primary advantages of nanoscale sensors is that they often can provide conceptually new ways of performing sensing that are not feasible with their large-scale analogs. For example, the small size of nanoscale sensor elements, such as plasmonic metal nanoparticles, allows them to be combined with nanofluidic systems. Among the potential applications of such a combination is the efficient delivery of analyte to the sensor surface. With this in mind, in this work we look to address the challenge of creating and positioning nanoplasmonic sensor elements within nanofluidic pores. A scheme is presented that allows for the production of arrays of pores in a thin (220 nm) silicon nitride membrane with one plasmonic nanoparticle sensor element in each pore. The high throughput fabrication protocol is parallel and enables multiple sensor chips to be produced simultaneously, yet with accurate tuning of the dimension and shape of the nanoparticles. The presented system is shown to possess polarization-sensitive plasmonic resonances that can be tuned significantly in the visible wavelength range by just varying one process parameter. The thickness of the membrane could be optimized to minimize the influence of the optical membrane interference on the plasmonic readout. The sensitivity of the plasmon resonances to changes in refractive index, which forms the basis for using the system for biosensing, was found to be competitive with other nanoplasmonic sensors.

Joining plasmonics with microfluidics: from convenience to inevitability

Along the advances in optofluidics, functionalities based on the surface plasmon-polariton have also been finding an increasing level of involvement within micro/nano-fluidic systems, gradually forming a new field of plasmo-fluidics. This survey of the burgeoning field reveals that judicious selection and combination of plasmonic and micro/nano-fluidic features render the plasmo-fluidic integration useful and mutually beneficial to the point of inevitability. We establish categories for the level of integration and utilize them as a framework for surveying existing work and extracting future perspectives.

Massively parallel measurements of molecular interaction kinetics on a microfluidic platform

Quantitative biology requires quantitative data. No high-throughput technologies exist capable of obtaining several hundred independent kinetic binding measurements in a single experiment. We present an integrated microfluidic device (k-MITOMI) for the simultaneous kinetic characterization of 768 biomolecular interactions. We applied k-MITOMI to the kinetic analysis of transcription factor (TF)-DNA interactions, measuring the detailed kinetic landscapes of the mouse TF Zif268, and the yeast TFs Tye7p, Yox1p, and Tbf1p. We demonstrated the integrated nature of k-MITOMI by expressing, purifying, and characterizing 27 additional yeast transcription factors in parallel on a single device. Overall, we obtained 2,388 association and dissociation curves of 223 unique molecular interactions with equilibrium dissociation constants ranging from 2 × 10(-6) M to 2 × 10(-9) M, and dissociation rate constants of approximately 6 s(-1) to 8.5 × 10(-3) s(-1). Association rate constants were uniform across 3 TF families, ranging from 3.7 × 10(6) M(-1) s(-1) to 9.6 × 10(7) M(-1) s(-1), and are well below the diffusion limit. We expect that k-MITOMI will contribute to our quantitative understanding of biological systems and accelerate the development and characterization of engineered systems.

Transient convection, diffusion, and adsorption in surface-based biosensors

This paper presents a theoretical and computational investigation of convection, diffusion, and adsorption in surface-based biosensors. In particular, we study the transport dynamics in a model geometry of a surface plasmon resonance (SPR) sensor. The work, however, is equally relevant for other microfluidic surface-based biosensors, operating under flow conditions. A widely adopted approximate quasi-steady theory to capture convective and diffusive mass transport is reviewed, and an analytical solution is presented. An expression of the Damköhler number is derived in terms of the nondimensional adsorption coefficient (Biot number), the nondimensional flow rate (Péclet number), and the model geometry. Transient dynamics is investigated, and we quantify the error of using the quasi-steady-state assumption for experimental data fitting in both kinetically limited and convection-diffusion-limited regimes for irreversible adsorption, in specific. The results clarify the conditions under which the quasi-steady theory is reliable or not. In extension to the well-known fact that the range of validity is altered under convection-diffusion-limited conditions, we show how also the ratio of the inlet concentration to the maximum surface capacity is critical for reliable use of the quasi-steady theory. Finally, our results provide users of surface-based biosensors with a tool for correcting experimentally obtained adsorption rate constants.

Optofluidic concentration: plasmonic nanostructure as concentrator and sensor

The integration of fluidics and optics, as in flow-through nanohole arrays, has enabled increased transport of analytes to sensing surfaces. Limits of detection, however, are fundamentally limited by local analyte concentration. We employ the nanohole array geometry and the conducting nature of the film to actively concentrate analyte within the sensor. We achieve 180-fold enrichment of a dye, and 100-fold enrichment and simultaneous sensing of a protein in less than 1 min. The method presents opportunities for an order of magnitude increase in sensing speed and 2 orders of magnitude improvement in limit of detection.

Michaelis-Menten kinetics in shear flow: Similarity solutions for multi-step reactions

Models for chemical reaction kinetics typically assume well-mixed conditions, in which chemical compositions change in time but are uniform in space. In contrast, many biological and microfluidic systems of interest involve non-uniform flows where gradients in flow velocity dynamically alter the effective reaction volume. Here, we present a theoretical framework for characterizing multi-step reactions that occur when an enzyme or enzymatic substrate is released from a flat solid surface into a linear shear flow. Similarity solutions are developed for situations where the reactions are sufficiently slow compared to a convective time scale, allowing a regular perturbation approach to be employed. For the specific case of Michaelis-Menten reactions, we establish that the transversally averaged concentration of product scales with the distance x downstream as x(5/3). We generalize the analysis to n-step reactions, and we discuss the implications for designing new microfluidic kinetic assays to probe the effect of flow on biochemical processes.

Antibody-functionalized fluid-permeable surfaces for rolling cell capture at high flow rates

Adhesion-based cell capture on surfaces in microfluidic devices forms the basis of numerous biomedical diagnostics and in vitro assays. However, the performance of these platforms is partly limited by interfacial phenomena that occur at low Reynolds numbers. In contrast, cell homing to porous vasculature is highly effective in vivo during inflammation, stem cell trafficking, and cancer metastasis. Here, we show that a porous, fluid-permeable surface functionalized with cell-specific antibodies promotes efficient and selective cell capture in vitro. This architecture is advantageous due to enhanced transport as streamlines are diverted toward the surface. Moreover, specific cell-surface interactions are promoted due to reduced shear, allowing gentle cell rolling and arrest. Together, these synergistic effects enable highly effective cell capture at flow rates more than an order of magnitude larger than those provided by existing devices with solid surfaces.

Modeling Taylor dispersion injections: determination of kinetic/affinity interaction constants and diffusion coefficients in label-free biosensing

A new method based on Taylor dispersion has been developed that enables an analyte gradient to be titrated over a ligand-coated surface for kinetic/affinity analysis of interactions from a minimal number of injections. Taylor dispersion injections generate concentration ranges in excess of four orders of magnitude and enable the analyte diffusion coefficient to be reliably estimated as a fitted parameter when fitting binding interaction models. A numerical model based on finite element analysis, Monte Carlo simulations, and statistical profiling were used to compare the Taylor dispersion method with standard fixed concentration injections in terms of parameter correlation, linearity of parameter error space, and global versus local model fitting. A dramatic decrease in parameter correlations was observed for TDi curves relative to curves from standard fixed concentration injections when surface saturation was achieved. In FCI the binding progress is recorded with respect to injection time, whereas in TDi the second time dependency encoded in the analyte gradient increases resolving power. This greatly lowers the dependence of all parameters on each other and on experimental interferences. When model parameters were fitted locally, the performance of TDis remained comparable to global model fitting, whereas fixed concentration binding response curves yielded unreliable parameter estimates.

Biosensing with quantum dots: a microfluidic approach

Semiconductor quantum dots (QDs) have served as the basis for signal development in a variety of biosensing technologies and in applications using bioprobes. The use of QDs as physical platforms to develop biosensors and bioprobes has attracted considerable interest. This is largely due to the unique optical properties of QDs that make them excellent choices as donors in fluorescence resonance energy transfer (FRET) and well suited for optical multiplexing. The large majority of QD-based bioprobe and biosensing technologies that have been described operate in bulk solution environments, where selective binding events at the surface of QDs are often associated with relatively long periods to reach a steady-state signal. An alternative approach to the design of biosensor architectures may be provided by a microfluidic system (MFS). A MFS is able to integrate chemical and biological processes into a single platform and allows for manipulation of flow conditions to achieve, by sample transport and mixing, reaction rates that are not entirely diffusion controlled. Integrating assays in a MFS provides numerous additional advantages, which include the use of very small amounts of reagents and samples, possible sample processing before detection, ultra-high sensitivity, high throughput, short analysis time, and in situ monitoring. Herein, a comprehensive review is provided that addresses the key concepts and applications of QD-based microfluidic biosensors with an added emphasis on how this combination of technologies provides for innovations in bioassay designs. Examples from the literature are used to highlight the many advantages of biosensing in a MFS and illustrate the versatility that such a platform offers in the design strategy.

Effect of fluidic transport on the reaction kinetics in lectin microarrays

Lectins are the proteins which can distinguish glycosylation patterns. They are frequently used as biomarkers for progressions of several diseases including cancer. As the lectin microarray based prognosis devices miniaturize the process of glycoprofiling, it is anticipated that their performance can be augmented by integration with microfluidic framework. This is analogous to microfluidics based DNA arrays. However, unlike small oligonucleotide microarrays, it remains uncertain whether the binding reaction-kinetic parameters can be considered invariant of imposed hydrodynamics, for relatively larger and structure sensitive molecules such as lectins. Here we show, using two standard lectins namely Concanavalin A and Abrus Agglutinin, that the steady state binding efficiency unexpectedly declines beyond a critical shear rate magnitude. This observation can be explained only if the associated reaction constants are presumed to be functions of hydrodynamic parameters. We methodically deduce the shear rate dependence of association and dissociation constants from the comparison of experimental and model-simulation trends. The aforementioned phenomena are perceived to be the consequences of strong hydrodynamic perturbations, culminating into molecular structural distortion. The exploration, therefore, reveals a unique coupling between reaction kinetics and hydrodynamics for biomacromolecules and provides a generic scheme towards futuristic microfluidics-coupled biomedical assays.

Integration of fiber optic-particle plasmon resonance biosensor with microfluidic chip

This article reports the integration of the fiber optic-particle plasmon resonance (FO-PPR) biosensor with a microfluidic chip to reduce response time and improve detection limit. The microfluidic chip made of poly(methyl methacrylate) had a flow-channel of dimensions 4.0 cm × 900 μm × 900 μm. A partially unclad optical fiber with gold or silver nanoparticles on the core surface was placed within the flow-channel, where the volume of the flow space was about 14 μL. Results using sucrose solutions of various refractive indexes show that the refractive index resolution improves by 2.4-fold in the microfluidic system. The microfluidic chip is capable of delivering a precise amount of biological samples to the detection area without sample dilution. Several receptor/analyte pairs were chosen to examine the biosensing capability of the integrated platform: biotin/streptavidin, biotin/anti-biotin, DNP/anti-DNP, OVA/anti-OVA, and anti-MMP-3/MMP-3. Results show that the response time to achieve equilibrium can be shortened from several thousand seconds in a conventional liquid cell to several hundred seconds in a microfluidic flow-cell. In addition, the detection limit also improves by about one order of magnitude. Furthermore, the normalization by using the relative change of transmission response as the sensor output alleviate the demand on precise optical alignment, resulting in reasonably good chip-to-chip measurement reproducibility.

Flow-through vs flow-over: analysis of transport and binding in nanohole array plasmonic biosensors

We quantify the efficacy of flow-through nanohole sensing, as compared to the established flow-over format, through scaling analysis and numerical simulation. Nanohole arrays represent a growing niche within surface plasmon resonance-based sensing methods, and employing the nanoholes as nanochannels can enhance transport and analytical response. The additional benefit offered by flow-through operation is, however, a complex function of operating parameters and application-specific binding chemistry. Compared here are flow-over sensors and flow-through nanohole array sensors with equivalent sensing area, where the nanohole array sensing area is taken as the inner-walls of the nanoholes. The footprints of the sensors are similar (e.g., a square 20 μm wide flow-over sensor has an equivalent sensing area as a square 30 μm wide array of 300 nm diameter nanoholes with 450 nm periodicity in a 100 nm thick gold film). Considering transport alone, an analysis here shows that given equivalent sensing area and flow rate the flow-through nanohole format enables greatly increased flux of analytes to the sensing surface (e.g., 40-fold for the case of Q = 10 nL/min). Including both transport and binding kinetics, a computational model, validated by experimental data, provides guidelines for performance as a function of binding time constant, analyte diffusivity, and running parameters. For common binding kinetics and analytes, flow-through nanohole arrays offer ∼10-fold improvement in response time, with a maximum of 20-fold improvement for small biomolecules with rapid kinetics.

Numerical study of in situ preconcentration for rapid and sensitive nanoparticle detection

This paper presents a numerical study of a preconcentrator design that can effectively increase the binding rate at the sensor in a real time manner. The particle enrichment is realized by the ac electrothermal (ACET) effect, which induces fluid movement to carry nanoparticles toward the sensor. The ACET is the only electrical method to manipulate a biological sample of medium to high ionic strength (>0.1 Sm, e.g., 0.06x phosphate buffered saline). The preconcentrator consists of a pair of electrodes striding over the sensor, simple to implement as it is electrically controlled. This preconcentrator design is compatible and can be readily integrated with many types of micro- to nanosensors. By applying an ac signal over the electrodes, local vortices will generate a large velocity perpendicular to the reaction surface, which enhances transport of analytes toward the sensor. Our simulation shows that the binding rate at the sensor surface is greatly enhanced. Our study also shows that the collection of analytes will be affected by various parameters such as channel height, inlet velocity, and sensor size, and our results will provide guidance in optimization of the preconcentrator design.

Integrated electrokinetic sample focusing and surface plasmon resonance imaging system for measuring biomolecular interactions

Label-free biomolecular binding measurement methods, such as surface plasmon resonance (SPR), are becoming increasingly more important for the estimation of real-time binding kinetics. Recent advances in surface plasmon resonance imaging (iSPR) are emerging for label-free microarray-based assay applications, where multiple biomolecular interactions can be measured simultaneously. However, conventional iSPR microarray systems rely on protein printing techniques for ligand immobilization to the gold imaging surface and external pumps for analyte transport. In this article, we present an integrated microfluidics and iSPR platform that uses only electrokinetic transport and guiding of ligands and analytes and, therefore, requires only electrical inputs for sample transport. An important advantage of this new approach, compared to conventional systems, is the ability to direct a single analyte to a specific ligand location in the microarray, which can facilitate analysis parallelization. Additionally, this simple approach does not require complicated microfluidic channel arrangements, external pumps, or valves. As a demonstration, kinetics and affinity have been extracted from measured binding responses of human IgG and goat antihuman IgG using a simple 1:1 model and compared to responses measured with conventional pressure driven analyte transport. The measured results indicate similar binding kinetics and affinity between the electrokinetic and pressure-driven sample manipulation methods and no cross contamination to adjacent measurement locations has been observed.

Electrokinetic label-free screening chip: a marriage of multiplexing and high throughput analysis using surface plasmon resonance imaging

We present an electrokinetic label-free biomolecular screening chip (Glass/PDMS) to screen up to 10 samples simultaneously using surface plasmon resonance imaging (iSPR). This approach reduces the duration of an experiment when compared to conventional experimental methods. This new device offers a high degree of parallelization not only for analyte samples, but also for multiplex analyte interactions where up to 90 ligands are immobilized on the sensing surface. The proof of concept has been demonstrated with well-known biomolecular interactant pairs. The new chip can be used for high throughput screening applications and kinetics parameter extraction, simultaneously, of interactant-protein complex formation.

A packaged optical slot-waveguide ring resonator sensor array for multiplex label-free assays in labs-on-chips

We present the design, fabrication, and characterisation of an array of optical slot-waveguide ring resonator sensors, integrated with microfluidic sample handling in a compact cartridge, for multiplexed real-time label-free biosensing. Multiplexing not only enables high throughput, but also provides reference channels for drift compensation and control experiments. Our use of alignment tolerant surface gratings to couple light into the optical chip enables quick replacement of cartridges in the read-out instrument. Furthermore, our novel use of a dual surface-energy adhesive film to bond a hard plastic shell directly to the PDMS microfluidic network allows for fast and leak-tight assembly of compact cartridges with tightly spaced fluidic interconnects. The high sensitivity of the slot-waveguide resonators, combined with on-chip referencing and physical modelling, yields a volume refractive index detection limit of 5 x 10(-6) refractive index units (RIUs) and a surface mass density detection limit of 0.9 pg mm(-2), to our knowledge the best reported values for integrated planar ring resonators.

Dynamics of virus spread in the presence of fluid flow

The dynamics of viral infection spread, whether in laboratory cultures or in naturally infected hosts, reflects a coupling of biological and physical processes that remain to be fully elucidated. Biological processes include the kinetics of virus growth in infected cells while physical processes include transport of virus progeny from infected cells, where they are produced, to susceptible cells, where they initiate new infections. Mechanistic models of infection spread have been widely developed for systems where virus growth is coupled with transport of virus particles by diffusion, but they have yet to be developed for systems where viruses move under the influence of fluid flows. Recent experimental observations of flow-enhanced infection spread in laboratory cultures motivate here the development of initial continuum and discrete virus-particle models of infection spread. The magnitude of a dimensionless group, the Damköhler number, shows how parameters that characterize particle adsorption to cells, strain rates that reflect flow profiles, and diffusivities of virus particles combine to influence the spatial pattern of infection spread.

Modeling of a competitive microfluidic heterogeneous immunoassay: sensitivity of the assay response to varying system parameters

We present a fractional sensitivity analysis of a competitive microfluidic heterogeneous immunoassay for a small molecule analyte. A simple two-dimensional finite element model is used to determine the fractional sensitivity of the assay signal with respect to analyte concentration, flow rate, initial surface density of binding sites, and antibody concentration. The fractional sensitivity analysis can be used to identify (1) the system parameters for which it is most crucial to control or quantify the variability between assays and (2) operating ranges for these parameters that improve assay sensitivity (within the constraints of the experimental system). Experimental assay results for the drug phenytoin, obtained using surface plasmon resonance imaging, are shown to be consistent with the predictions of the model.

A microfluidic detection system based upon a surface immobilized biobarcode assay

The biobarcode assay (BCA) is capable of achieving low detection limits and high specificity for both protein and DNA targets. The realization of a BCA in a microfluidic format presents unique opportunities and challenges. In this work, we describe a modified form of the BCA called the surface immobilized biobarcode assay (SI-BCA). The SI-BCA employs microchannel walls functionalized with antibodies that bind with the intended targets. Compared with the conventional BCA, it reduces the system complexity and results in shortened process time, which is attributed to significantly reduced diffusion times in the micro-scale channels. Raw serum samples, without any pretreatment, were evaluated with this technique. Prostate specific antigen in the samples was detected at concentrations ranging from 40 pM to 40 fM. The detection limit of the assay using buffer samples is 10 fM. The entire assay, from sample injection to final data analysis was completed in 80 min.

Effect of volume- and time-based constraints on capture of analytes in microfluidic heterogeneous immunoassays

Despite the prevalence of microfluidic-based heterogeneous immunoassays (where analytes in solution are captured on a solid surface functionalized with a capture molecule), there is incomplete understanding of how assay parameters influence the amount of captured analytes. This study presents computational results and corresponding experimental binding assays in which the capture of analytes is studied under variations in both mass transfer and surface binding, constrained by real-world assay conditions of finite sample volume, assay time, and capture area. Our results identify: 1) a "reagent-limited" regime which exists only under the constraints of finite sample volume and assay time; 2) a critical flow rate (e.g. 0.5 microL min(-1) under our assay conditions) to gain the maximum signal with the fastest assay time; 3) an increase in signal by using a short concentrated plug (e.g. 5 microL, 100 nM) rather than a long dilute plug (e.g. 50 microL, 10 nM) of sample; 4) the possibility of spending a considerable fraction of the assay time out of the reaction-limited regime. Overall, an improved understanding of fundamental physical processes may be particularly beneficial for the design of point-of-care assays, where volumes of reagents and available samples are limited, and the desired time-to-result short.