Pulse-density modulation control of chemical oscillation far from equilibrium in a droplet open-reactor system

Emerging open-channel droplet arrays for biosensing

Open-channel droplet arrays have attracted much attention in the fields of biochemical analysis, biofluid monitoring, biomarker recognition and cell interactions, as they have advantages with regard to miniaturization, parallelization, high-throughput, simplicity and accessibility. Such droplet arrays not only improve the sensitivity and accuracy of a biosensor, but also do not require sophisticated equipment or tedious processes, showing great potential in next-generation miniaturized sensing platforms. This review summarizes typical examples of open-channel microdroplet arrays and focuses on diversified biosensing integrated with multiple signal-output approaches (fluorescence, colorimetric, surface-enhanced Raman scattering (SERS), electrochemical, etc.). The limitations and development prospects of open-channel droplet arrays in biosensing are also discussed with regard to the increasing demand for biosensors.

Fabrication of Microparticles with Front-Back Asymmetric Shapes Using Anisotropic Gelation

Droplet-based microfluidics is a powerful tool for producing monodispersed micrometer-sized droplets with controlled sizes and shapes; thus, it has been widely applied in diverse fields from fundamental science to industries. Toward a simpler method for fabricating microparticles with front–back asymmetry in their shapes, we studied anisotropic gelation of alginate droplets, which occurs inside a flow-focusing microfluidic device. In the proposed method, sodium alginate (NaAlg) aqueous phase fused with a calcium chloride (CaCl2) emulsion dispersed in the organic phase just before the aqueous phase breaks up into the droplets. The fused droplet with a front–back asymmetric shape was generated, and the asymmetric shape was kept after geometrical confinement by a narrow microchannel was removed. The shape of the fused droplet depended on the size of prefused NaAlg aqueous phase and a CaCl2 emulsion, and the front–back asymmetry appeared in the case of the smaller emulsion size. The analysis of the velocity field inside and around the droplet revealed that the stagnation point at the tip of the aqueous phase also played an important role. The proposed mechanism will be potentially applicable as a novel fabrication technique of microparticles with asymmetric shapes.

Electrochemical Oscillation during Galvanostatic Charging of LiCrTiO4 in Li-Ion Batteries

In the late 1960s, the establishment of Prigogine’s dissipative structure theory laid the foundation for the (electro)chemical oscillation phenomenon, which has been widely investigated in some electrochemical reactions, such as electro-catalysis and electro-deposition, while the electrochemical oscillation of Li-ion batteries has just been discovered in spinel Li₄Ti₅O₁₂ a few years before. In this work, spinel LiCrTiO₄ samples were synthesized by using a high-temperature solid-state method, characterized with SEM (Scanning electron microscope), XRD (X-ray diffraction), Raman and XPS (X-ray photoelectron spectroscopy) measurements, and electrochemically tested in Li-ion batteries to study the electrochemical oscillation. When sintering in a powder form at a temperature between 800 and 900 °C, we achieved the electrochemical oscillation of spinel LiCrTiO₄ during charging, and it is suppressed in the non-stoichiometric LiCrTiO₄ samples, especially for reducing the Li content or increasing the Cr content. Therefore, this work developed another two-phase material as the powder-sintered LiCrTiO₄ exhibiting the electrochemical oscillation in Li-ion batteries, which would inspire us to explore more two-phase electrode materials in Li-ion batteries, Na-ion batteries, etc.

DNA nanotechnology provides an avenue for the construction of programmable dynamic molecular systems

Self-assembled supramolecular structures in living cells and their dynamics underlie various cellular events, such as endocytosis, cell migration, intracellular transport, cell metabolism, and gene expression. Spatiotemporally regulated association/dissociation and generation/degradation of assembly components is one of the remarkable features of biological systems. The significant advancement in DNA nanotechnology over the last few decades has enabled the construction of various-shaped nanostructures via programmed self-assembly of sequence-designed oligonucleotides. These nanostructures can further be assembled into micrometer-sized structures, including ordered lattices, tubular structures, macromolecular droplets, and hydrogels. In addition to being a structural material, DNA is adopted to construct artificial molecular circuits capable of activating/inactivating or producing/decomposing target DNA molecules based on strand displacement or enzymatic reactions. In this review, we provide an overview of recent studies on artificially designed DNA-based self-assembled systems that exhibit dynamic features, such as association/dis-sociation of components, phase separation, stimulus responsivity, and DNA circuit-regulated structural formation. These biomacromolecule-based, bottom-up approaches for the construction of artificial molecular systems will not only throw light on bio-inspired nano/micro engineering, but also enable us to gain insights into how autonomy and adaptability of living systems can be realized.

Dynamic Environments as a Tool to Preserve Desired Output in a Chemical Reaction Network

Current efforts to design functional molecular systems have overlooked the importance of coupling out-of-equilibrium behaviour with changes in the environment. Here, the authors use an oscillating reaction network and demonstrate that the application of environmental forcing, in the form of periodic changes in temperature and in the inflow of the concentration of one of the network components, removes the dependency of the periodicity of this network on temperature or flow rates and enforces a stable periodicity across a wide range of conditions. Coupling a system to a dynamic environment can thus be used as a simple tool to regulate the output of a network. In addition, the authors show that coupling can also induce an increase in behavioural complexity to include quasi-periodic oscillations.

DNA Origami Nanoplate-Based Emulsion with Nanopore Function

Bio-inspired functional microcapsules have attracted increasing attention in many fields from physical/chemical science to artificial-cell engineering. Although particle-stabilised microcapsules are advantageous for their stability and functionalisation potential, versatile methods for their functionalisation are desired to expand their possibilities. This study reports a water-in-oil microdroplet stabilised with amphiphilic DNA origami nanoplates. By utilising DNA nanotechnology, DNA nanoplates were designed as a nanopore device for ion transportation and to stabilise the oil-water interface. Microscopic examination revealed the microcapsule formed by the accumulation of amphiphilic DNA nanoplates at the oil-water interface. Ion current measurements revealed the nanoplate pores functioned as channel to transport ions. These findings provide a general strategy for the programmable design of microcapsules to engineer artificial cells and molecular robots.

Creation of Artificial Cell-Like Structures Promoted by Microfluidics Technologies

The creation of artificial cells is an immensely challenging task in science. Artificial cells contribute to revealing the mechanisms of biological systems and deepening our understanding of them. The progress of versatile biological research fields has clarified many biological phenomena, and various artificial cell models have been proposed in these fields. Microfluidics provides useful technologies for the study of artificial cells because it allows the fabrication of cell-like compartments, including water-in-oil emulsions and giant unilamellar vesicles. Furthermore, microfluidics also allows the mimicry of cellular functions with chip devices based on sophisticated chamber design. In this review, we describe contributions of microfluidics to the study of artificial cells. Although typical microfluidic methods are useful for the creation of artificial-cell compartments, recent methods provide further benefits, including low-cost fabrication and a reduction of the sample volume. Microfluidics also allows us to create multi-compartments, compartments with artificial organelles, and on-chip artificial cells. We discuss these topics and the future perspective of microfluidics for the study of artificial cells and molecular robotics.

Large-Scale Preparation of Giant Vesicles by Squeezing a Lipid-Coated Marshmallow-like Silicone Gel in a Buffer

Giant vesicles were efficiently produced by squeezing a lipid (l-α-phosphatidylcholine from egg yolk)-coated marshmallow-like flexible macroporous silicone monolith in a buffer. The mean diameter of the obtained vesicles was 2 μm, showing a wide distribution, up to tens of micrometers, which was similar to that of vesicles formed by a natural swelling method. It was possible to prepare vesicle dispersions on a scale from several microliters to several hundred milliliters. A protein synthesis system (PURE system) contained in vesicles prepared using this method functioned effectively. Our absorbing-squeezing method is expected to help in studies that use giant vesicles such as artificial cells and drug delivery systems.

Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions

Emulsion drops are often employed as picoliter-sized containers to perform screening assays. These assays usually entail the formation of drops encompassing discrete objects such as cells or microparticles and reagents to study interactions between the different encapsulants. Drops are also used to screen influences of reagent concentrations on the final product. However, these latter assays are less frequently performed because it is difficult to change the reagent concentration over a wide range and with high precision within a single experiment. In this paper, we present a microfluidic double emulsion drop maker containing pneumatic valves that enable real-time formulation of different reagents using pulse width modulation and consequent encapsulation of the mixed solutions. This device can produce drops from reagent volumes as low as 10 µL with minimal sample loss, thereby enabling experiments that would be prohibitively expensive using drop generators that do not contain valves. We employ this device to monitor the kinetics of the cell-free synthesis of green fluorescent proteins inside double emulsions. To demonstrate the potential of this device for real-time formulation, we perform DNA titration experiments to test the influence of DNA concentration on the amount of green fluorescence protein produced in double emulsions by a coupled cell-free transcription / translation system.

Dynamic wettability of polyethylene glycol-modified poly(dimethylsiloxane) surfaces in an aqueous/organic two-phase system

We herein report the preparation of a surface that behaves in a hydrophobic manner but does not undergo protein adsorption in an aqueous/organic two-phase system. We found that polyethylene-glycol (PEG)-modified poly(dimethylsiloxane) (PDMS) exhibits hydrophobic properties when the surface is immersed in an organic solution, while the PEG moiety prevents protein adsorption on the PDMS surface in an aqueous solution at high protein concentrations due to the dynamic behaviour of the PEG moiety. As such, we demonstrated the in-well droplet formation of an aqueous solution containing a high protein concentration. In addition, to demonstrate the feasibility of this method in single cell analyses, a droplet array of a liquid medium containing 10% fetal bovine serum and HeLa cells was formed. The preparation of a droplet array using our PDMS-PEG surface to promote in-well droplet formation avoided the use of flow control equipment and complicated microstructures. We therefore expect that the dynamic wettability of our reported surface will be applicable in single cell and biochemical analyses, such as protein characterisation using crystallography or immunoassays.

Molecular Rotors for Universal Quantitation of Nanoscale Hydrophobic Interfaces in Microplate Format

Hydrophobic self-assembly pairs diverse chemical precursors and simple formulation processes to access a vast array of functional colloids. Exploration of this design space, however, is stymied by lack of broadly general, high-throughput colloid characterization tools. Here, we show that a narrow structural subset of fluorescent, zwitterionic molecular rotors, dialkylaminostilbazolium sulfonates [DASS] with intermediate-length alkyl tails, fills this major analytical void by quantitatively sensing hydrophobic interfaces in microplate format. DASS dyes supersede existing interfacial probes by avoiding off-target fluorogenic interactions and dye aggregation while preserving hydrophobic partitioning strength. To illustrate the generality of this approach, we demonstrate (i) a microplate-based technique for measuring mass concentration of small (20-200 nm), dilute (submicrogram sensitivity) drug delivery nanoparticles; (ii) elimination of particle size, surfactant chemistry, and throughput constraints on quantifying the complex surfactant/metal oxide adsorption isotherms critical for environmental remediation and enhanced oil recovery; and (iii) more reliable self-assembly onset quantitation for chemically and structurally distinct amphiphiles. These methods could streamline the development of nanotechnologies for a broad range of applications.

Droplet microfluidics for synthetic biology

Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility. Liquid handling robotics may reduce labor and improve reproducibility, but are themselves expensive and thus inaccessible to most researchers. Microfluidic platforms offer a lower entry price point alternative to robotics, and maintain high throughput and reproducibility while further reducing operating costs through diminished reagent volume requirements. Droplet microfluidics have shown exceptional promise for synthetic biology experiments, including DNA assembly, transformation/transfection, culturing, cell sorting, phenotypic assays, artificial cells and genetic circuits.

Cell-free extract based optimization of biomolecular circuits with droplet microfluidics

Engineering an efficient biomolecular circuit often requires time-consuming iterations of optimization. Cell-free protein expression systems allow rapid testing of biocircuits in vitro, speeding the design-build-test cycle of synthetic biology. In this paper, we combine this with droplet microfluidics to densely scan a transcription-translation biocircuit space. Our system assays millions of parameter combinations per hour, providing a detailed map of function. The ability to comprehensively map biocircuit parameter spaces allows accurate modeling to predict circuit function and identify optimal circuits and conditions.

Massively parallel and multiparameter titration of biochemical assays with droplet microfluidics

Biochemical systems in which multiple components take part in a given reaction are of increasing interest. Because the interactions between these different components are complex and difficult to predict from basic reaction kinetics, it is important to test for the effect of variations in the concentration for each reagent in a combinatorial manner. For example, in PCR, an increase in the concentration of primers initially increases template amplification, but large amounts of primers result in primer-dimer by-products that inhibit the amplification of the template. Manual titration of biochemical mixtures rapidly becomes costly and laborious, forcing scientists to settle for suboptimal concentrations. Here we present a droplet-based microfluidics platform for mapping of the concentration space of up to three reaction components followed by detection with a fluorescent readout. The concentration of each reaction component is read through its internal standard (barcode), which is fluorescent but chemically orthogonal. We describe in detail the workflow, which comprises the following: (i) production of the microfluidics chips, (ii) preparation of the biochemical mixes, (iii) their mixing and compartmentalization into water-in-oil emulsion droplets via microfluidics, (iv) incubation and imaging of the fluorescent barcode and reporter signals by fluorescence microscopy and (v) image processing and data analysis. We also provide recommendations for choosing the appropriate fluorescent markers, programming the pressure profiles and analyzing the generated data. Overall, this platform allows a researcher with a few weeks of training to acquire ∼10,000 data points (in a 1D, 2D or 3D concentration space) over the course of a day from as little as 100-1,000 μl of reaction mix.

Effects of spatial and temporal noise on a cubic-autocatalytic reaction-diffusion model

We characterize the influence that external noise, with both spatial and temporal correlations, has on the scale dependence of the reaction parameters of a cubic autocatalytic reaction diffusion (CARD) system. Interpreting the CARD model as a primitive reaction scheme for a living system, the results indicate that power-law correlations in environmental fluctuations can either decrease or increase the rates of nutrient decay and the rate of autocatalysis (replication) on small spatial and temporal scales.

Dynamic Rotating Liquid Marble for Directional and Enhanced Mass Transportation in Three-Dimensional Microliter Droplets

The ability of an artificial microdroplet to mimic the rotational behaviors of living systems is crucial for dynamic mass transportation but remains challenging to date. Herein, we report dynamic microdroplet rotation using a liquid marble (RLM) and achieve precise control over mass transportation and distribution in a three-dimensional (3D) microdroplet. RLM rotates synchronously with an external magnetic field, creating circular hydrodynamic flow and an outward centrifugal force. Such spin-induced phenomena direct a spiral movement of entrapped molecules and accelerate their diffusion and homogenization in the entire liquid. Moreover, we demonstrate the rotation rate-controlled (between 0 and 1300 rpm) modulation of shell-catalyzed reaction kinetics from 0.13 to 0.62 min^-1. The directed acceleration of reactants toward a catalytically active shell surface is 3-fold faster than conventional stir bar-based convective flow. RLM as an efficient magnetohydrodynamics transducer will be valuable for dynamical control over mass transportation in microdroplet-based chemical, biological, and biomedical studies.

High-resolution mapping of bifurcations in nonlinear biochemical circuits

Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.