Chemical and Biological Dynamics Using Droplet-Based Microfluidics

Microfluidic mimicry of the Golgi-linked N-glycosylation machinery

The complexity of the eukaryotic glycosylation machinery hinders the development of cell-free protein glycosylation since in vitro methods struggle to simulate the natural environment of the glycosylation machinery. Microfluidic technologies have the potential to address this limitation due to their ability to control glycosylation parameters, such as enzyme/substrate concentrations and fluxes, in a rapid and precise manner. However, due to the complexity and sensitivity of the numerous components of the glycosylation machinery, very few "glycobiology-on-a-chip" systems have been proposed or reported in the literature. Herein, we describe the design, fabrication and proof-of-concept of a droplet-based microfluidic platform able to mimic N-linked glycan processing along the secretory pathway. Within a single microfluidic device, glycoproteins and glycosylation enzymes are encapsulated and incubated in water-in-oil droplets. Additional glycosylation enzymes are subsequently supplied to these droplets via picoinjection, allowing further glycoprotein processing in a user-defined manner. After system validation, the platform is used to perform two spatiotemporally separated consecutive enzymatic N-glycan modifications, mirroring the transition between the endoplasmic reticulum and early Golgi.

Photo-Induced Bandgap Engineering of Metal Halide Perovskite Quantum Dots In Flow

Over the past decade, lead halide perovskite (LHP) nanocrystals (NCs) have attracted significant attention due to their tunable optoelectronic properties for next-generation printed photonic and electronic devices. High-energy photons in the presence of haloalkanes provide a scalable and sustainable pathway for precise bandgap engineering of LHP NCs via photo-induced anion exchange reaction (PIAER) facilitated by in situ generated halide anions. However, the mechanisms driving photo-induced bandgap engineering in LHP NCs remain not fully understood. This study elucidates the underlying PIAER mechanisms of LHP NCs through an advanced microfluidic platform. Additionally, the first instance of a PIAER, transforming CsPbBr3 NCs into high-performing CsPbI3 NCs, with the assistance of a thiol-based additive is reported. Utilizing an intensified photo-flow microreactor accelerates the anion exchange rate 3.5-fold, reducing material consumption 100-fold compared to conventional batch processes. It is demonstrated that CsPbBr3 NCs act as photocatalysts, driving oxidative bond cleavage in dichloromethane and promoting the photodissociation of 1-iodopropane using high-energy photons. Furthermore, it is demonstrated that a thiol-based additive plays a dual role: surface passivation, which enhances the photoluminescence quantum yield, and facilitates the PIAER. These findings pave the way for the tailored design of perovskite-based optoelectronic materials.

High-Throughput Absorbance-Activated Droplet Sorting for Engineering Aldehyde Dehydrogenases

Recent decades have seen a dramatic increase in the commercial use of biocatalysts, transitioning from energy-intensive traditional chemistries to more sustainable methods. Current enzyme engineering techniques, such as directed evolution, require the generation and testing of large mutant libraries to identify optimized variants. Unfortunately, conventional screening methods are unable to screen such large libraries in a robust and timely manner. Droplet-based microfluidic systems have emerged as a powerful high-throughput tool for library screening at kilohertz rates. Unfortunately, almost all reported systems are based on fluorescence detection, restricting their use to a limited number of enzyme types that naturally convert fluorogenic substrates or require the use of surrogate substrates. To expand the range of enzymes amenable to evolution using droplet-based microfluidic systems, we present an absorbance-activated droplet sorter that allows droplet sorting at kilohertz rates without the need for optical monitoring of the microfluidic system. To demonstrate the utility of the sorter, we rapidly screen a 105-member aldehyde dehydrogenase library towards D-glyceraldehyde using a NADH mediated coupled assay that generates WST-1 formazan as the colorimetric product. We successfully identify a variant with a 51 % improvement in catalytic efficiency and a significant increase in overall activity across a broad substrate spectrum.

Droplet-based microfluidics for drug delivery applications

The microfluidic method primainly utilizes two incompatible liquids as continuous phase and dispersed phase respectively. It controls the formation of droplets by managing the microchannel structure and the flow rate ratio of the two phases. Droplet-based microfluidics is a rapidly expanding interdisciplinary research field encompassing physics, biochemistry, and Microsystems engineering. Droplet microfluidics offer a diverse and practical toolset that enables chemical and biological experiments to be conducted at high speeds and with greater efficiency compared to traditional instruments. The applications of droplet-based microfluidics are vast, including areas such as drug delivery, owing to its compatibility with numerous chemical and biological reagents and its ability to carry out various operations. This technology has been extensively researched due to its promising features. In this review, we delve into the materials used in droplet generation-based microfluidic devices, manufacturing techniques, methods for droplet generation in channels, and, finally, we summarize the applications of droplet generation-based microfluidics in drug delivery vectors, encompassing nanoparticles, microspheres, microcapsules, and hydrogel particles. We also discuss the challenges and future prospects of this technology across a wide array of applications.

A simple guideline for designing droplet microfluidic chips to achieve an improved single (bio)particle encapsulation rate using a stratified flow-assisted particle ordering method

Encapsulation of a single (bio)particle into individual droplets (referred to as single encapsulation) presents tremendous potential for precise biological and chemical reactions at the single (bio)particle level. Previously demonstrated successful strategies often rely on the use of high flow rates, gel, or viscoelastic materials for initial cell ordering prior to encapsulation into droplets, which could potentially challenge the system's operation. We propose to enhance the single encapsulation rate by using a stratified flow structure to focus and pre-order the (bio)particles before encapsulation. The stratified flow structure is formed using two simple aqueous Newtonian fluids with a viscosity contrast, which together serve as the dispersed phase. The single encapsulation rate is influenced by many parameters, including fluid viscosity contrast, geometric conditions, flow conditions and flow rate ratios, and dimensionless numbers such as the capillary number. This study focuses on investigating the influences of these parameters on the focused stream of the stratified flow, which is key for single encapsulation. The results allow the proposal of a simple guideline that can be adopted to design droplet microfluidic chips with an improved single encapsulation rate demanded by a wide range of applications. The guideline was validated by performing the single encapsulation of mouse embryonic stem cells suspended in a gelatin-methacryloyl solution in individual droplets of phosphate buffer saline, achieving a single encapsulation efficiency of up to 70%.

Droplet digital molecular beacon-LAMP assay via pico-injection for ultrasensitive detection of pathogens

A pico-injection-aided digital droplet detection platform is presented that integrates loop-mediated isothermal amplification (LAMP) with molecular beacons (MBs) for the ultrasensitive and quantitative identification of pathogens, leveraging the sequence-specific detection capabilities of MBs. The microfluidic device contained three distinct functional units including droplet generation, pico-injection, and droplet counting. Utilizing a pico-injector, MBs are introduced into each droplet to specifically identify LAMP amplification products, thereby overcoming issues related to temperature incompatibility. Our methodology has been validated through the quantitative detection of Escherichia coli, achieving a detection limit as low as 9 copies/μL in a model plasmid containing the malB gene and 3 CFU/μL in a spiked milk sample. The total analysis time was less than 1.5 h. The sensitivity and robustness of this platform further demonstrated the potential for rapid pathogen detection and diagnosis, particularly when integrated with cutting-edge microfluidic technologies.

Droplet-based microfluidics and enzyme evolution

Enzymes are widely used as catalysts in the chemical and pharmaceutical industries. While successful in many situations, they must usually be adapted to operate efficiently under nonnatural conditions. Enzyme engineering allows the creation of novel enzymes that are stable at elevated temperatures or have higher activities and selectivities. Current enzyme engineering techniques require the production and testing of enzyme variant libraries to identify members with desired attributes. Unfortunately, traditional screening methods cannot screen such large mutagenesis libraries in a robust and timely manner. Droplet-based microfluidic systems can produce, process, and sort picoliter droplets at kilohertz rates and have emerged as powerful tools for library screening and thus enzyme engineering. We describe how droplet-based microfluidics has been used to advance directed evolution.

Simultaneous Separating, Splitting, Collecting, and Dispensing by Droplet Pinch-Off for Droplet Cell Culture

Simultaneous separating, splitting, collecting, and dispensing a cell suspension droplet has been demonstrated by aspiration and subsequent droplet pinch-off for use in microfluidic droplet cell culture systems. This method is applied to cell manipulations including aliquots and concentrations of microalgal and mammalian cell suspensions. Especially, medium exchange of spheroid droplets is successfully demonstrated by collecting more than 99% of all culture medium without damaging the spheroids, demonstrating its potential for a 3D cell culture system. Through dimensional analysis and systematic parametric studies, it is found that initial mother droplet size together with aspiration flow rate determines three droplet pinch-off regimes. By observing contact angle changes during aspiration, the difference in the large and the small droplet pinch-off can be quantitatively explained using force balance. It is found that the capillary number plays a significant role in droplet pinch-off, but the Bond number and the Ohnesorge number have minor effects. Since the dispensed droplet size is mainly determined by the capillary number, the dispensed droplet size can be controlled simply by adjusting the aspiration flow rate. It is hoped that this method can contribute to various fields using droplets, such as droplet cell culture and digital microfluidics, beyond the generation of small droplets.

Marangoni-driven spreading of a droplet on a miscible thin liquid layer

HYPOTHESIS

The coalescence of droplets with liquid-gas interfaces of different surface tensions is common in nature and industrial applications, where the Marangoni-driven film spreading is an essential process. Unlike immiscible fluids governed by triple contact line dynamics, the mixing between two miscible fluids strongly couples with the film spreading process, which are expected to manifest distinct power-law relations for the temporal increase in the film radius.

EXPERIMENTS

We experimentally investigate the Marangoni-driven film spreading phenomenon for a droplet with lower surface tension dropping onto a miscible, thin liquid layer. The temporal growth of the film radius was detected by using a novel deep convolutional neural network, the U2-net method. Scaling analysis was performed to interpret the spreading dynamics of the film.

FINDINGS

We find that the film radius exhibits a three-stage power-law relation over time, with the exponent varying from 1/2 to 1/8, and back to 1/2. The diffusion-affected Marangoni stresses in these three stages were derived, and two estimations of viscous stress were considered. Through estimating and balancing the viscous stress with the Marangoni stress, the three-stage power-law relation was derived and validated.

Genetically Encoded Biosensor Engineering for Application in Directed Evolution

Although rational genetic engineering is nowadays the favored method for microbial strain improvement, building up mutant libraries based on directed evolution for improvement is still in many cases the better option. In this regard, the demand for precise and efficient screening methods for mutants with high performance has stimulated the development of biosensor-based high-throughput screening strategies. Genetically encoded biosensors provide powerful tools to couple the desired phenotype to a detectable signal, such as fluorescence and growth rate. Herein, we review recent advances in engineering several classes of biosensors and their applications in directed evolution. Furthermore, we compare and discuss the screening advantages and limitations of two-component biosensors, transcription-factor-based biosensors, and RNA-based biosensors. Engineering these biosensors has focused mainly on modifying the expression level or structure of the biosensor components to optimize the dynamic range, specificity, and detection range. Finally, the applications of biosensors in the evolution of proteins, metabolic pathways, and genome-scale metabolic networks are described. This review provides potential guidance in the design of biosensors and their applications in improving the bioproduction of microbial cell factories through directed evolution.

A microfluidic double emulsion platform for spatiotemporal control of pH and particle synthesis

The temporal control of pH in microreactors such as emulsion droplets plays a vital role in applications including biomineralisation and microparticle synthesis. Typically, pH changes are achieved either by passive diffusion of species into a droplet or by acid/base producing reactions. Here, we exploit an enzyme reaction combined with the properties of a water-oil-water (W/O/W) double emulsion to control the pH-time profile in the droplets. A microfluidic platform was used for production of ∼100-200 μm urease-encapsulated double emulsions with a tuneable mineral oil shell thickness of 10-40 μm. The reaction was initiated on-demand by addition of urea and a pulse in base (ammonia) up to pH 8 was observed in the droplets after a time lag of the order of minutes. The pH-time profile can be manipulated by the diffusion timescale of urea and ammonia through the oil layer, resulting in a steady state pH not observed in bulk reactive solutions. This approach may be used to regulate the formation of pH sensitive materials under mild conditions and, as a proof of concept, the reaction was coupled to calcium phosphate precipitation in the droplets. The oil shell thickness was varied to select for either brushite microplatelets or hydroxyapatite particles, compared to the mixture of different precipitates obtained in bulk.

Substantial Improvement of an Epimerase for the Synthesis of D-Allulose by Biosensor-Based High-Throughput Microdroplet Screening

Biosynthesis of D-allulose has been achieved using ketose 3-epimerases (KEases), but its application is limited by poor catalytic performance. In this study, we redesigned a genetically encoded biosensor based on a D-allulose-responsive transcriptional regulator for real-time monitoring of D-allulose. An ultrahigh-throughput droplet-based microfluidic screening platform was further constructed by coupling with this D-allulose-detecting biosensor for the directed evolution of the KEases. Structural analysis of Sinorhizobium fredii D-allulose 3-epimerase (SfDAE) revealed that a highly flexible helix/loop region exposes or occludes the catalytic center as an essential lid conformation regulating substrate recognition. We reprogrammed SfDAE using structure-guided rational design and directed evolution, in which a mutant M3-2 was identified with 17-fold enhanced catalytic efficiency. Our research offers a paradigm for the design and optimization of a biosensor-based microdroplet screening platform.

Cell Culture in Microfluidic Droplets

Cell manipulation in droplets has emerged as one of the great successes of microfluidic technologies, with the development of single-cell screening. However, the droplet format has also served to go beyond single-cell studies, namely by considering the interactions between different cells or between cells and their physical or chemical environment. These studies pose specific challenges linked to the need for long-term culture of adherent cells or the diverse types of measurements associated with complex biological phenomena. Here we review the emergence of droplet microfluidic methods for culturing cells and studying their interactions. We begin by characterizing the quantitative aspects that determine the ability to encapsulate cells, transport molecules, and provide sufficient nutrients within the droplets. This is followed by an evaluation of the biological constraints such as the control of the biochemical environment and promoting the anchorage of adherent cells. This first part ends with a description of measurement methods that have been developed. The second part of the manuscript focuses on applications of these technologies for cancer studies, immunology, and stem cells while paying special attention to the biological relevance of the cellular assays and providing guidelines on improving this relevance.

Droplet-based microfluidics in biomedical applications

Droplet-based microfluidic systems have been employed to manipulate discrete fluid volumes with immiscible phases. Creating the fluid droplets at microscale has led to a paradigm shift in mixing, sorting, encapsulation, sensing, and designing high throughput devices for biomedical applications. Droplet microfluidics has opened many opportunities in microparticle synthesis, molecular detection, diagnostics, drug delivery, and cell biology. In the present review, we first introduce standard methods for droplet generation (i.e., passive and active methods) and discuss the latest examples of emulsification and particle synthesis approaches enabled by microfluidic platforms. Then, the applications of droplet-based microfluidics in different biomedical applications are detailed. Finally, a general overview of the latest trends along with the perspectives and future potentials in the field are provided.

Effect of Surfactant Dynamics on Flow Patterns Inside Drops Moving in Rectangular Microfluidic Channels

Drops contained in an immiscible liquid phase are attractive as microreactors, enabling sound statistical analysis of reactions performed on ensembles of samples in a microfluidic device. Many applications have specific requirements for the values of local shear stress inside the drops and, thus, knowledge of the flow field is required. This is complicated in commonly used rectangular channels by the flow of the continuous phase in the corners, which also affects the flow inside the drops. In addition, a number of chemical species are present inside the drops, of which some may be surface-active. This work presents a novel experimental study of the flow fields of drops moving in a rectangular microfluidic channel when a surfactant is added to the dispersed phase. Four surfactants with different surface activities are used. Flow fields are measured using Ghost Particle Velocimetry, carried out at different channel depths to account for the 3-D flow structure. It is shown that the effect of the surfactant depends on the characteristic adsorption time. For fast-equilibrating surfactants with a characteristic time scale of adsorption that is much smaller than the characteristic time of surface deformation, this effect is related only to the decrease in interfacial tension, and can be accounted for by the change in capillary number. For slowly equilibrating surfactants, Marangoni stresses accelerate the corner flow, which changes the flow patterns inside the drop considerably.

Functional liquid droplets for analyte sensing and energy harvesting

Over the past century, rapid miniaturization of technologies has helped in the development of efficient, flexible, portable, robust, and compact applications with minimal wastage of materials. In this direction, of late, the usage of mesoscale liquid droplets has emerged as an alternative platform because of the following advantages: (i) a droplet is incompressible and at the same time deformable, (ii) interfacial area of a spherical droplet is minimum for a given amount of mass; and (iii) a droplet interface allows facile mass, momentum, and energy transfer. Subsequently, such attributes have aided towards the design of diverse droplet-based microfluidic technologies. For example, the microdroplets have been utilized as micro-reactors, colorimetric or electrochemical (EC) sensors, drug-delivery vehicles, and energy harvesters. Further, a number of recently reported lab-on-a-chip technologies exploit the motility, storage, and mixing capacities of the microdroplets. In view of this background, the review initiates discussion by highlighting the different attributes of the microdroplets such as size, shape, surface to volume ratio, wettability, and contact line. Thereafter, the effects of the surface or body forces on the properties of the droplets have been elaborated. Finally, the different aspects of such liquid droplet systems towards technological adaptations in health care, sensing, and energy harvesting have been presented. The review concludes with a tight summary on the potential avenues for further developments.

Active Flow Control and Dynamic Analysis in Droplet Microfluidics

Droplet-based microfluidics has emerged as an important subfield within the microfluidic and general analytical communities. Indeed, several unique applications such as digital assay readout and single-cell sequencing now have commercial systems based on droplet microfluidics. Yet there remains room for this research area to grow. To date, most analytical readouts are optical in nature, relatively few studies have integrated sample preparation, and passive means for droplet formation and manipulation have dominated the field. Analytical scientists continue to expand capabilities by developing droplet-compatible method adaptations, for example, by interfacing to mass spectrometers or automating droplet sampling for temporally resolved analysis. In this review, we highlight recently developed fluidic control techniques and unique integrations of analytical methodology with droplet microfluidics-focusing on automation and the connections to analog/digital domains-and we conclude by offering a perspective on current challenges and future applications.

Intelligent acoustofluidics enabled mini-bioreactors for human brain organoids

Acoustofluidics, by combining acoustics and microfluidics, provides a unique means to manipulate cells and liquids for broad applications in biomedical sciences and translational medicine. However, it is challenging to standardize and maintain excellent performance of current acoustofluidic devices and systems due to a multiplicity of factors including device-to-device variation, manual operation, environmental factors, sample variability, etc. Herein, to address these challenges, we propose "intelligent acoustofluidics" - an automated system that involves acoustofluidic device design, sensor fusion, and intelligent controller integration. As a proof-of-concept, we developed intelligent acoustofluidics based mini-bioreactors for human brain organoid culture. Our mini-bioreactors consist of three components: (1) rotors for contact-free rotation via an acoustic spiral phase vortex approach, (2) a camera for real-time tracking of rotational actions, and (3) a reinforcement learning-based controller for closed-loop regulation of rotational manipulation. After training the reinforcement learning-based controller in simulation and experimental environments, our mini-bioreactors can achieve the automated rotation of rotors in well-plates. Importantly, our mini-bioreactors can enable excellent control over rotational mode, direction, and speed of rotors, regardless of fluctuations of rotor weight, liquid volume, and operating temperature. Moreover, we demonstrated our mini-bioreactors can stably maintain the rotational speed of organoids during long-term culture, and enhance neural differentiation and uniformity of organoids. Comparing with current acoustofluidics, our intelligent system has a superior performance in terms of automation, robustness, and accuracy, highlighting the potential of novel intelligent systems in microfluidic experimentation.

μIVC-Seq: A Method for Ultrahigh-Throughput Development and Functional Characterization of Small RNAs

For a long time, artificial RNAs have been developed by in vitro selection methodologies like Systematic Evolution of Ligands by EXponential enrichment (SELEX). Yet, even though this technology is extremely powerful to isolate specific and high-affinity binders, it is less suited for the isolation of RNAs optimized for more complex functions such as fluorescence emission or multiple-turnover catalysis. Whereas such RNAs should ideally be developed by screening approaches, conventional microtiter plate assays become rapidly cost-prohibitive. However, the advent of droplet-based microfluidics recently enabled us to devise microfluidic-assisted In Vitro Compartmentalization (μIVC), a strongly miniaturized and highly parallelized screening technology allowing to functionally screen millions of mutants in a single day while using a very low amount of reagent. Used in combination with high-throughput sequencing, the resulting μIVC-seq pipeline described in this chapter now allows rapid and semiautomated screening to be performed at low cost and in an ultrahigh-throughput regime.

Utility of low-cost, miniaturized peristaltic and Venturi pumps in droplet microfluidics

Many laboratory applications utilizing droplet microfluidics rely on precision syringe pumps for flow generation. In this study, the use of an open-source peristaltic pump primarily composed of 3D printed parts and a low-cost commercial Venturi pump are explored for their use as an alternative to syringe pumps for droplet microfluidics. Both devices provided stable flow (<2% RSD) over a range of 1-7 μL/min and high reproducibility in signal intensity at a droplet generation rate around 0.25 Hz (<3% RSD), which are comparable in performance to similar measurements on standard syringe pumps. As a novel flow generation source for microfluidic applications, the use of the miniaturized Venturi pump was also applied to droplet signal monitoring studies used to measure changes in concentration over time, with average signal reproducibility <4% RSD for both single-stream fluorometric and reagent addition colorimetric applications. These low-cost flow methods provide stable flow sufficient for common droplet microfluidic approaches and can be implemented in a wide variety of simple, and potentially portable, analytical measurement devices.

High-throughput screening for high-efficiency small-molecule biosynthesis

Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.

Nanotechnology-Assisted Isolation and Analysis of Circulating Tumor Cells on Microfluidic Devices

Circulating tumor cells (CTCs), a type of cancer cell that spreads from primary tumors into human peripheral blood and are considered as a new biomarker of cancer liquid biopsy. It provides the direction for understanding the biology of cancer metastasis and progression. Isolation and analysis of CTCs offer the possibility for early cancer detection and dynamic prognosis monitoring. The extremely low quantity and high heterogeneity of CTCs are the major challenges for the application of CTCs in liquid biopsy. There have been significant research endeavors to develop efficient and reliable approaches to CTC isolation and analysis in the past few decades. With the advancement of microfabrication and nanomaterials, a variety of approaches have now emerged for CTC isolation and analysis on microfluidic platforms combined with nanotechnology. These new approaches show advantages in terms of cell capture efficiency, purity, detection sensitivity and specificity. This review focuses on recent progress in the field of nanotechnology-assisted microfluidics for CTC isolation and detection. Firstly, CTC isolation approaches using nanomaterial-based microfluidic devices are summarized and discussed. The different strategies for CTC release from the devices are specifically outlined. In addition, existing nanotechnology-assisted methods for CTC downstream analysis are summarized. Some perspectives are discussed on the challenges of current methods for CTC studies and promising research directions.

Rapid isolation of rare targets from large fluid volumes

Rapidly isolating rare targets from larger, clinically relevant fluid volumes remains an unresolved problem in biomedicine and diagnosis. Here, we describe how 3D particle sorting can enrich targets at ultralow concentrations over 100-fold within minutes not possible with conventional approaches. Current clinical devices based on biochemical extraction and microfluidic solutions typically require high concentrations and/or can only process sub-milliliter volumes in time. In a proof-of-concept application, we isolated bacteria from whole blood as demanded for rapid sepsis diagnosis where minimal numbers of bacteria need to be found in a 1–10 mL blood sample. After sample encapsulation in droplets and target enrichment with the 3D particle sorter within a few minutes, downstream analyses were able to identify bacteria and test for antibiotic susceptibility, information which is critical for successful treatment of bloodstream infections.

Seeded droplet microfluidic system for small molecule crystallization

A microfluidic approach to seeded crystallization has been demonstrated using abacavir hemisulfate, a nucleoside analog reverse transcriptase inhibitor, in droplet reactors to control polymorphism and produce particles with a low particle size distribution. Two techniques are introduced: (1) the first technique involves an emulsion system consisting of a dispersed phase solvent and a continuous phase, which holds slight solubility of the dispersed phase solvent. The dispersed phase contains both a dissolved active pharmaceutical ingredient (API) and seeds of the desired polymorph. While the continuous phase enables solvent extraction, the negligible solubility of the API allows for growth of seeds inside droplets via extraction and subsequent API saturation. This technique demonstrates the ability to crystallize the API in spherical agglomerates via slow extraction of droplets. (2) The second technique utilizes a combined dispersed phase by joining in-flow a seed suspension stream with a supersaturated active pharmaceutical ingredient (API) stream. The combined dispersed phase is emulsified in a continuous phase for which the dispersed phase solvent and the API are both insoluble - droplets are incubated at temperatures below their saturation limit to induce crystal growth. Decreasing the concentration of seeds in its input stream resulted in a decreased number of crystals per droplet, increase in crystal size, and decrease in PSD. Temperature cycling was utilized as a proof of concept to demonstrate the ability to reduce the number of seeds per droplet where the optimal goal is to obtain a single seed per droplet for all droplets. Utilizing this approach in conjunction with the ability to produce monodispersed droplet reactors allows for enhanced control of particle size distribution (PSD) by precisely controlling the available mass for each individual seed crystal. The development of this technique as a proof-of-concept for crystallization can be expanded to manufacturing scales in a continuous manner using parallelized droplet generators and flow reactors to precisely control the temperature and crystal growth kinetics of individual droplets.

A Counter Propagating Lens-Mirror System for Ultrahigh Throughput Single Droplet Detection

Fluorescence-based detection schemes provide for multiparameter analysis in a broad range of applications in the chemical and biological sciences. Toward the realization of fully portable analysis systems, microfluidic devices integrating diverse functional components have been implemented in a range of out-of-lab environments. That said, there still exits an unmet and recognized need for miniaturized, low-cost, and sensitive optical detection systems, which provide not only for efficient molecular excitation, but also enhanced photon collection capabilities. To this end, an optofluidic platform that is adept at enhancing fluorescence light collection from microfluidic channels is presented. The central component of the detection module is a monolithic parabolic mirror located directly above the microfluidic channel, which acts to enhance the number of emitted photons reflected toward the detector. In addition, two-photon polymerization is used to print a microscale-lens below the microfluidic flow channel and directly opposite the mirror, to enhance the delivery of excitation radiation into the channel. Using such an approach, it is demonstrated that fluorescence signals can be enhanced by over two orders of magnitude, with component parallelization enabling the detection of pL-volume droplets at rates up to 40 000 droplets per second.

Droplet-Based Microfluidics Methods for Detecting Enzyme Inhibitors

Sub-nanoliter droplets produced in microfluidic devices have gained an enormous importance for performing all kinds of biochemical assays. One of the main reasons is that the amounts of reagents employed can be reduced in approximately five orders of magnitude compared to conventional microplate assays. In this chapter, we describe how to carry out the design, fabrication, and operation of a microfluidic device that allows performing enzyme kinetics and enzyme inhibition assays in droplets. This procedure can be used effectively to screen a small size library of compounds. Then, we describe how to use this droplet microfluidic setup to screen for potential inhibitor compounds eluted from a coupled high-performance liquid chromatography (HPLC) system that separates crude natural extracts.

Droplet microfluidics: from proof-of-concept to real-world utility?

Droplet microfluidics constitutes a diverse and practical tool set that enables chemical and biological experiments to be performed at high speed and with enhanced efficiency when compared to conventional instrumentation. Indeed, in recent years, droplet-based microfluidic tools have been used to excellent effect in a range of applications, including materials synthesis, single cell analysis, RNA sequencing, small molecule screening, in vitro diagnostics and tissue engineering. Our 2011 Chemical Communications Highlight Article [Chem. Commun., 2011, 47, 1936-1942] reviewed some of the most important technological developments and applications of droplet microfluidics, and identified key challenges that needed to be addressed in the short term. In the current contribution, we consider the intervening eight years, and assess the contributions that droplet-based microfluidics has made to experimental science in its broadest sense.

Mass Transfer Accompanying Coalescence of Surfactant-Laden and Surfactant-Free Drop in a Microfluidic Channel

The coalescence of two different drops, one surfactant-laden and the other surfactant-free, was studied under the condition of confined flow in a microchannel. The coalescence was accompanied by penetration of the surfactant-free drop into the surfactant-laden drop because of the difference in the capillary pressure and Marangoni flows causing a film of surfactant-laden liquid to spread over the surfactant-free drop. The penetration rate was dependent on the drop order, with considerably better penetration observed for the case when the surfactant-laden drop goes first. The penetration rate was found to increase with an increase of interfacial tension difference between the two drops, an increase of flow rate and drop confinement in the channel (for the case of the surfactant-laden drop going first), an increase of viscosity of the continuous phase, and a decrease of viscosity of the dispersed phase. Analysis of flow patterns inside the coalescing drops has shown that, unlike coalescence of identical drops, only two vortices are formed by asymmetrical coalescence, centered inside the surfactant-free drop. The vortices were accelerated by the flow of the continuous phase if the surfactant-laden drop preceded the surfactant-free one, increasing the rate of penetration; the opposite was observed if the drop order was reversed. The mixing patterns on a longer time scale were also dependent on the drop order, with better mixing being observed for the case when the surfactant-laden drop goes first.

Droplets for Sampling and Transport of Chemical Signals in Biosensing: A Review

The chemical, temporal, and spatial resolution of chemical signals that are sampled and transported with continuous flow is limited because of Taylor dispersion. Droplets have been used to solve this problem by digitizing chemical signals into discrete segments that can be transported for a long distance or a long time without loss of chemical, temporal or spatial precision. In this review, we describe Taylor dispersion, sampling theory, and Laplace pressure, and give examples of sampling probes that have used droplets to sample or/and transport fluid from a continuous medium, such as cell culture or nerve tissue, for external analysis. The examples are categorized, as follows: (1) Aqueous-phase sampling with downstream droplet formation; (2) preformed droplets for sampling; and (3) droplets formed near the analyte source. Finally, strategies for downstream sample recovery for conventional analysis are described.

Microfluidic triple-gradient generator for efficient screening of chemical space

Generation of a combinatorial gradient for multiple chemicals is essential for studies of biochemical stimuli, chemoattraction, protein crystallization and others. While currently available platforms require complex design/settings to obtain a double-gradient chemical matrix, we herein report for the first time a simple triple-gradient matrix (TGM) device for efficient screening of chemical space. The TGM device is composed of two glass slides and works following the concept of SlipChip. The device utilizes XYZ space to distribute three chemicals and establishes a chemical gradient matrix within 5 min. The established matrix contains 24 or 104 screening conditions depending on the device used, which covers a concentration range of [0.117-1, 0.117-1 and 0.686-1] and [0.0830-1, 0.0830-1, 0.686-1] respectively for the three chemicals. With the triple gradients built simultaneously, this TGM device provides order-of-magnitude improvement in screening efficiency over existing single- or double-gradient generators. As a proof of concept, we applied the device to screen the crystallization conditions for two model proteins of lysozyme and trypsin and confirmed the crystal structures using X-ray diffraction. Furthermore, we successfully obtained the crystallization condition of adhesin competence repressor, a protein that senses the alterations in intracellular zinc concentrations. We expect the TGM system to be widely used as an analytical platform for material synthesis and chemical screening beyond for protein crystallization.

Reaction injection molding of hydrophilic-in-hydrophobic femtolitre-well arrays

Patterning of micro- and nanoscale topologies and surface properties of polymer devices is of particular importance for a broad range of life science applications, including cell-adhesion assays and highly sensitive bioassays. The manufacturing of such devices necessitates cumbersome multiple-step fabrication procedures and results in surface properties which degrade over time. This critically hinders their wide-spread dissemination. Here, we simultaneously mold and surface energy pattern microstructures in off-stoichiometric thiol-ene by area-selective monomer self-assembly in a rapid micro-reaction injection molding cycle. We replicated arrays of 1,843,650 hydrophilic-in-hydrophobic femtolitre-wells with long-term stable surface properties and magnetically trapped beads with 75% and 87.2% efficiency in single- and multiple-seeding events, respectively. These results form the basis for ultrasensitive digital biosensors, specifically, and for the fabrication of medical devices and life science research tools, generally.

High-Precision Stereolithography of Biomicrofluidic Devices

Stereolithography (SL) is emerging as an attractive alternative to soft lithography for fabricating microfluidic devices due to its low cost and high design efficiency. Low molecular weight poly(ethylene glycol)diacrylate (MW = 258) (PEG-DA-258) has been used for SL 3D-printing of biocompatible microdevices at submillimeter resolution. However, 3D-printing resins that simultaneously feature high transparency, high biocompatibility, and high resolution are still lacking. It is found that photosensitizer isopropyl thioxanthone can, in a concentration-dependent manner, increase the absorbance of the resin (containing PEG-DA-258 and photoinitator Irgacure-819) by over an order of magnitude. This increase in absorbance allows for SL printing of microdevices at sub pixel resolution with commercially available desktop printers and without compromising transparency or biocompatibility. The assembly-free, rapid (<15 h) 3D-printing of a variety of complex 3D microfluidic devices such as a 3D-fluid router, a passive chaotic micro-mixer, an active micro-mixer with pneumatic microvalves, and high-aspect ratio (37:1) microchannels of single pixel width is demonstrated. These manufacturing capabilities are unavailable in conventional microfluidic rapid prototyping techniques. The low absorption of small hydrophobic molecules and microfluidic labeling of cultured mammalian cells in 3D-printed PEG-DA-258 microdevices is demonstrated, indicating the potential of PEG-DA-based fabrication of cell-based assays, drug discovery, and organ-on-chip platforms.

One Sensor for Multiple Colors: Fluorescence Analysis of Microdroplets in Microbiological Screenings by Frequency-Division Multiplexing

High-speed multiwavelength fluorescence measurements are of paramount importance in microfluidic analytics. However, multicolor detection requires an intricate arrangement of multiple detectors and meticulously aligned filters and dichroic beamsplitters that counteract the simplicity, versatility, and low cost of microfluidic approaches. To break free from the restrictions of optical setup complexity, we introduce a simpler single-sensor setup based on laser-frequency modulation and frequency-division multiplexing (FDM). We modulate lasers to excite the sample with four non-overlapping frequency signals. A single photomultiplier tube detects all the modulated emitted light collected by an optical fiber in the microfluidic chip. Signal demodulation is performed with a lock-in amplifier separating the emitted light into four color channels in real time. This approach not only reduces complexity and provides setup flexibility but also results in improved signal quality and, thus, higher signal-to-noise ratios that translate into increased sensitivity. To validate the setup for high-throughput biological applications, we measured multiple signals from different microorganisms and fluorescently encoded droplet populations for exploring beneficial or antagonistic roles in microbial cocultivation systems, as is the case for antibiotic screening assays.

Fluorescence lifetime-activated droplet sorting in microfluidic chip systems

We present a highly efficient microfluidic fluorescence lifetime-activated droplet sorting (FLADS) approach as a novel technology for droplet manipulation in lab-on-a-chip devices. In a proof-of-concept study, we successfully applied the approach to sort droplets containing two different fluorescent compounds on the basis of their corresponding fluorescence lifetime. Towards this end, a technical set-up was developed enabling on-the-fly fluorescence lifetime determination of passing droplets. The herein developed LabVIEW program enabled fast triggering of a downstream dielectrophoretic force sorting functionality depending on average fluorescence lifetimes of individual droplets. The approach worked reliably at individual substrate concentrations from 1 nM to 1 mM. This not only allowed reliable sorting of droplets containing species with different fluorescence lifetimes but also enabled differentiation of mixtures in individual droplets.

Coding of Experimental Conditions in Microfluidic Droplet Assays Using Colored Beads and Machine Learning Supported Image Analysis

To efficiently exploit the potential of several millions of droplets that can be considered as individual bioreactors in microfluidic experiments, methods to encode different experimental conditions in droplets are needed. The approach presented here is based on coencapsulation of colored polystyrene beads with biological samples. The decoding of the droplets, as well as content quantification, are performed by automated analysis of triggered images of individual droplets in-flow using bright-field microscopy. The decoding strategy combines bead classification using a random forest classifier and Bayesian inference to identify different codes and thus experimental conditions. Antibiotic susceptibility testing of nine different antibiotics and the determination of the minimal inhibitory concentration of a specific antibiotic against a laboratory strain of Escherichia coli are presented as a proof-of-principle. It is demonstrated that this method allows successful encoding and decoding of 20 different experimental conditions within a large droplet population of more than 10⁵ droplets per condition. The decoding strategy correctly assigns 99.6% of droplets to the correct condition and a method for the determination of minimal inhibitory concentration using droplet microfluidics is established. The current encoding and decoding pipeline can readily be extended to more codes by adding more bead colors or color combinations.

Reinforcement Learning for Dynamic Microfluidic Control

Recent years have witnessed an explosion in the application of microfluidic techniques to a wide variety of problems in the chemical and biological sciences. Despite the many considerable advantages that microfluidic systems bring to experimental science, microfluidic platforms often exhibit inconsistent system performance when operated over extended timescales. Such variations in performance are because of a multiplicity of factors, including microchannel fouling, substrate deformation, temperature and pressure fluctuations, and inherent manufacturing irregularities. The introduction and integration of advanced control algorithms in microfluidic platforms can help mitigate such inconsistencies, paving the way for robust and repeatable long-term experiments. Herein, two state-of-the-art reinforcement learning algorithms, based on Deep Q-Networks and model-free episodic controllers, are applied to two experimental "challenges," involving both continuous-flow and segmented-flow microfluidic systems. The algorithms are able to attain superhuman performance in controlling and processing each experiment, highlighting the utility of novel control algorithms for automated high-throughput microfluidic experimentation.

High-Throughput Incubation and Quantification of Agglutination Assays in a Microfluidic System

In this paper, we present a two-phase microfluidic system capable of incubating and quantifying microbead-based agglutination assays. The microfluidic system is based on a simple fabrication solution, which requires only laboratory tubing filled with carrier oil, driven by negative pressure using a syringe pump. We provide a user-friendly interface, in which a pipette is used to insert single droplets of a 1.25-µL volume into a system that is continuously running and therefore works entirely on demand without the need for stopping, resetting or washing the system. These assays are incubated by highly efficient passive mixing with a sample-to-answer time of 2.5 min, a 5⁻10-fold improvement over traditional agglutination assays. We study system parameters such as channel length, incubation time and flow speed to select optimal assay conditions, using the streptavidin-biotin interaction as a model analyte quantified using optical image processing. We then investigate the effect of changing the concentration of both analyte and microbead concentrations, with a minimum detection limit of 100 ng/mL. The system can be both low- and high-throughput, depending on the rate at which assays are inserted. In our experiments, we were able to easily produce throughputs of 360 assays per hour by simple manual pipetting, which could be increased even further by automation and parallelization. Agglutination assays are a versatile tool, capable of detecting an ever-growing catalog of infectious diseases, proteins and metabolites. A system such as this one is a step towards being able to produce high-throughput microfluidic diagnostic solutions with widespread adoption. The development of analytical techniques in the microfluidic format, such as the one presented in this work, is an important step in being able to continuously monitor the performance and microfluidic outputs of organ-on-chip devices.

Label-Free Sensing in Microdroplet-Based Microfluidic Systems

Droplet microfluidic systems have evolved as fluidic platforms that use much less sample volume and provide high throughput for biochemical analysis compared to conventional microfluidic devices. The variety of droplet fluidic applications triggered several detection techniques to be applied for analysis of droplets. In this review, we focus on label-free droplet detection techniques that were adapted to various droplet microfluidic platforms. We provide a classification of most commonly used droplet platform technologies. Then we discuss the examples of various label-free droplet detection schemes implemented for these platforms. While providing the research landscape for label-free droplet detection methods, we aim to highlight the strengths and shortcomings of each droplet platform so that a more targeted approach can be taken by researchers when selecting a droplet platform and a detection scheme for any given application.

Passive Mixing inside Microdroplets

Droplet-based micromixers are essential units in many microfluidic devices for widespread applications, such as diagnostics and synthesis. The mixers can be either passive or active. When compared to active methods, the passive mixer is widely used because it does not require extra energy input apart from the pump drive. In recent years, several passive droplet-based mixers were developed, where mixing was characterized by both experiments and simulation. A unified physical understanding of both experimental processes and simulation models is beneficial for effectively developing new and efficient mixing techniques. This review covers the state-of-the-art passive droplet-based micromixers in microfluidics, which mainly focuses on three aspects: (1) Mixing parameters and analysis method; (2) Typical mixing element designs and the mixing characters in experiments; and, (3) Comprehensive introduction of numerical models used in microfluidic flow and diffusion.

3D-glass molds for facile production of complex droplet microfluidic chips

In order to leverage the immense potential of droplet microfluidics, it is necessary to simplify the process of chip design and fabrication. While polydimethylsiloxane (PDMS) replica molding has greatly revolutionized the chip-production process, its dependence on 2D-limited photolithography has restricted the design possibilities, as well as further dissemination of microfluidics to non-specialized labs. To break free from these restrictions while keeping fabrication straighforward, we introduce an approach to produce complex multi-height (3D) droplet microfluidic glass molds and subsequent chip production by PDMS replica molding. The glass molds are fabricated with sub-micrometric resolution using femtosecond laser machining technology, which allows directly realizing designs with multiple levels or even continuously changing heights. The presented technique significantly expands the experimental capabilities of the droplet microfluidic chip. It allows direct fabrication of multilevel structures such as droplet traps for prolonged observation and optical fiber integration for fluorescence detection. Furthermore, the fabrication of novel structures based on sloped channels (ramps) enables improved droplet reinjection and picoinjection or even a multi-parallelized drop generator based on gradients of confinement. The fabrication of these and other 3D-features is currently only available at such resolution by the presented strategy. Together with the simplicity of PDMS replica molding, this provides an accessible solution for both specialized and non-specialized labs to customize microfluidic experimentation and expand their possibilities.

Speeding up enzyme discovery and engineering with ultrahigh-throughput methods

Exploring the sequence space of enzyme catalysts is ultimately a numbers game. Ultrahigh-throughput screening methods for rapid analysis of millions of variants are therefore increasingly important for investigating sequence-function relationships, searching large metagenomic libraries for interesting activities, and accelerating enzyme evolution in the laboratory. Recent applications of such technologies are reviewed here, with a particular focus on the practical benefits of droplet-based microfluidics for the directed evolution of natural and artificial enzymes. Broader implementation of such rapid, cost-effective screening technologies is likely to redefine the way enzymes are studied and engineered for academic and industrial purposes.