A Universal Approximation for Conductance Blockade in Thin Nanopore Membranes

Nanopore-based sensing platforms have transformed single-molecule detection and analysis. The foundation of nanopore translocation experiments lies in conductance measurements, yet existing models, which are largely phenomenological, are inaccurate in critical experimental conditions such as thin and tightly fitting pores. Of the two components of the conductance blockade, channel and access resistance, the access resistance is poorly modeled. We present a comprehensive investigation of the access resistance and associated conductance blockade in thin nanopore membranes. By combining a first-principles approach, multiscale modeling, and experimental validation, we propose a unified theoretical modeling framework. The analytical model derived as a result surpasses current approaches across a broad parameter range. Beyond advancing our theoretical understanding, our framework's versatility enables analyte size inference and predictive insights into conductance blockade behavior. Our results will facilitate the design and optimization of nanopore devices for diverse applications, including nanopore base calling and data storage.

Orthogonal Gelations to Synthesize Core-Shell Hydrogels Loaded with Nanoemulsion-Templated Drug Nanoparticles for Versatile Oral Drug Delivery

Hydrophobic active pharmaceutical ingredients (APIs) are ubiquitous in the drug development pipeline, but their poor bioavailability often prevents their translation into drug products. Industrial processes to formulate hydrophobic APIs are expensive, difficult to optimize, and not flexible enough to incorporate customizable drug release profiles into drug products. Here, a novel, dual-responsive gelation process that exploits orthogonal thermo-responsive and ion-responsive gelations is introduced. This one-step "dual gelation" synthesizes core-shell (methylcellulose-alginate) hydrogel particles and encapsulates drug-laden nanoemulsions in the hydrogel matrices. In situ crystallization templates drug nanocrystals inside the polymeric core, while a kinetically stable amorphous solid dispersion is templated in the shell. Drug release is explored as a function of particle geometry, and programmable release is demonstrated for various therapeutic applications including delayed pulsatile release and sequential release of a model fixed-dose combination drug product of ibuprofen and fenofibrate. Independent control over drug loading between the shell and the core is demonstrated. This formulation approach is shown to be a flexible process to develop drug products with biocompatible materials, facile synthesis, and precise drug release performance. This work suggests and applies a novel method to leverage orthogonal gel chemistries to generate functional core-shell hydrogel particles.

Injectable hydrogel particles for amorphous solid formulation of biologics

The fast pace of breakthroughs in cancer immunotherapy, combined with the new paradigm of moving toward high-concentration dosages and combinatorial treatments, is generating new challenges in the formulation of biologics. To address these challenges, we describe a method of formulation that enables high-concentration injectable and stable formulation of biologics as amorphous solids in aqueous suspension. This technology combines the benefits of liquid formulation with the stability of solid formulation and eliminates the need for drying and reconstitution. This widely applicable formulation integrates the amorphous solid forms of antibodies with the injectability, lubricity, and tunability of soft alginate hydrogel particles using a minimal process. The platform was evaluated for anti-PD-1 antibody pembrolizumab and human immunoglobulin G at concentrations up to 300 mg/mL with confirmed quality after release. The soft nature of the hydrogel matrix allowed packing the particles to high volume fractions.

Templated Reactive Crystallization of Active Pharmaceutical Ingredient in Hydrogel Microparticles Enabling Robust Drug Product Processing

Commercialization of most promising active pharmaceutical ingredients (APIs) is impeded either by poor bioavailability or challenging physical properties leading to costly manufacture. Bioavailability of ionizable hydrophobic APIs can be enhanced by its conversion to salt form. While salt form of the API presents higher solution concentration than the non-ionized form, poor physical properties resulting from particle anisotropy or non-ideal morphology (needles) and particle size distribution not meeting dissolution rate targets can still inhibit its commercial translation. In this regard, API physical properties can be improved through addition of non-active components (excipients or carriers) during API manufacture. In this work, a facile method to perform reactive crystallization of an API salt in presence of the microporous environment of a hydrogel microparticle is presented. Specifically, the reaction between acidic antiretroviral API, raltegravir and base potassium hydroxide is performed in the presence of polyethylene glycol diacrylamide hydrogel microparticles. In this bottom-up approach, the spherical template hydrogel microparticles for the reaction lead to monodisperse composites loaded with inherently micronized raltegravir-potassium crystals, thus improving API physical properties without hampering bioavailability. Overall, this technique provides a novel approach to reactive crystallization while maintaining the API polymorph and crystallinity.

Crystalline Antibody-Laden Alginate Particles: A Platform for Enabling High Concentration Subcutaneous Delivery of Antibodies

Subcutaneous (SC) administration is a desired route for monoclonal antibodies (mAbs). However, formulating mAbs for small injection volumes at high concentrations with suitable stability and injectability is a significant challenge. Here, this work presents a platform technology that combines the stability of crystalline antibodies with injectability and tunability of soft hydrogel particles. Composite alginate hydrogel particles are generated via a gentle centrifugal encapsulation process which avoids use of chemical reactions or an external organic phase. Crystalline suspension of anti-programmed cell death protein 1 (PD-1) antibody (pembrolizumab) is utilized as a model therapeutic antibody. Crystalline forms of the mAb encapsuled in the hydrogel particles lead to stable, high concentration, and injectable formulations. Formulation concentrations as high as 315 mg mL^-1 antibody are achieved with encapsulation efficiencies in the range of 89-97%, with no perceivable increase in the number of antibody aggregates. Bioanalytical studies confirm superior maintained quality of the antibody in comparison with formulation approaches involving organic phases and chemical reactions. This work illustrates tuning the alginate particles' disintegration by using partially oxide alginates. Crystalline mAb-laden particles are evaluated for their biocompatibility using cell-based in vitro assays. Furthermore, the pharmacokinetics (PK) of the subcutaneously delivered human anti-PD-1 mAb in crystalline antibody-laden alginate hydrogel particles in Wistar rats is evaluated.

Microfluidic Particle Engineering of Hydrophobic Drug with Eudragit E100─Bridging the Amorphous and Crystalline Gap

Co-processing active pharmaceutical ingredients (APIs) with excipients is a promising particle engineering technique to improve the API physical properties, which can lead to more robust downstream drug product manufacturing and improved drug product attributes. Excipients provide control over critical API attributes like particle size and solid-state outcomes. Eudragit E100 is a widely used polymeric excipient to modulate drug release. Being cationic, it is primarily employed as a precipitation inhibitor to stabilize amorphous solid dispersions. In this work, we demonstrate how co-processing of E100 with naproxen (NPX) (a model hydrophobic API) into monodisperse emulsions via droplet microfluidics followed by solidification via solvent evaporation allows the facile fabrication of compact, monodisperse, and spherical particles with an expanded range of solid-state outcomes spanning from amorphous to crystalline forms. Low E100 concentrations (≤26% w/w) yield crystalline microparticles with a stable NPX polymorph distributed uniformly across the matrix at a high drug loading (∼89% w/w). Structurally, E100 incorporation reduces the size of primary particles comprising the co-processed microparticles in comparison to neat API microparticles made using the same technique and the as-received API powder. This reduction in primary particle size translates into an increased internal porosity of the co-processed microparticles, with specific surface area and pore volume ∼9 times higher than the neat API microparticles. These E100-enabled structural modifications result in faster drug release in acidic media compared to neat API microparticles. Additionally, E100-NPX microparticles have a significantly improved flowability compared to neat API microparticles and as-received API powder. Overall, this study demonstrates a facile microfluidics-based co-processing method that broadly expands the range of solid-state outcomes obtainable with E100 as an excipient, with multiscale control over the key attributes and performance of hydrophobic API-laden microparticles.

Producing shape-engineered alginate particles using viscoplastic fluids

Non-spherical hydrogel particles are of fundamental interest and can find use in a variety of applications ranging from pharmaceuticals to biomedical to food. Here, we report a new method that leverages the yield stress property of viscoplastic fluids to synthesize shape-engineered alginate particles. By dripping an aqueous viscoplastic solution composed of sodium alginate and a yield-stress material into an ionic gelation bath, droplets are controllably deformed and crosslinked, producing a wide assortment of shapes. We find that by tuning the yield stress of the solution and the nozzle tip orientation, a range of shapes from symmetric and near-spherical, to asymmetric and anisotropic (e.g., egg-, rice grain-, arc-, ring-, snail shell-, tear-, and tadpole-like) can be produced. We explain our observations using scaling analysis of the forces exerted on the droplet at different stages of particle production. We show that the main factors that determine the degree of droplet deformation during bath entry and the final appearance of the alginate particles are the initial shape of the droplets, the timescales of the viscoplastic fluid relaxation versus the crosslinking reaction, and the physico-chemical properties of the yield-stress material.

Coarse-grained molecular dynamics simulations of immobilized micelle systems and their interactions with hydrophobic molecules

Micelles immobilized in polymer materials are of emerging interest in drug delivery, water treatment and other applications. Immobilization removes the need for membrane-based separation to eliminate micelles from the medium, enabling facile extraction and delivery in diverse industries. This work lays out a coarse-grained molecular dynamics simulations framework for the rapid identification of surfactants for use in immobilized micelle systems. Micelles are immobilized by constraining one end of the constituent surfactants in space, mimicking what would occur in a copolymer system. We demonstrate that constraints affect how the micelles interact with small hydrophobic molecules, making it important to account for their effects in various drug-micelle and pollutant-micelle simulations. Our results show that in several systems there is stronger interaction between hydrophobic small molecules and micelles in immobilized systems compared to unconstrained systems. These strengthened interactions can have important implications for the design of new micelle-based extraction and delivery processes.

Quantitative and Multiplex Detection of Extracellular Vesicle-Derived MicroRNA via Rolling Circle Amplification within Encoded Hydrogel Microparticles

Extracellular vesicle-derived microRNA (EV-miRNA) represent a promising cancer biomarker for disease diagnosis and monitoring. However, existing techniques to detect EV-miRNA rely on complex, bias-prone strategies, and preprocessing steps, making absolute quantification highly challenging. This work demonstrates the development and application of a method for quantitative and multiplex detection of EV-miRNA, via rolling circle amplification within encoded hydrogel particles. By a one-pot extracellular vesicle lysis and microRNA capture step, the bias and losses associated with standard RNA extraction techniques is avoided. The system offers a large dynamic range (3 orders of magnitude), ease of multiplexing, and a limit of detection down to 2.3 zmol (46 × 10^-18 m), demonstrating its utility in clinical applications based on liquid biopsy tests. Furthermore, orthogonal measurements of EV concentrations coupled with the direct, absolute quantification of miRNA in biological samples results in quantitative measurements of miRNA copy numbers per volume sample, and per extracellular vesicle.

Hydrogel Microparticle-Templated Anti-Solvent Crystallization of Small-Molecule Drugs

Conventional formulation strategies for hydrophobic small-molecule drug products frequently include mechanical milling to decrease active pharmaceutical ingredient (API) crystal size and subsequent granulation processes to produce an easily handled powder. A hydrogel-templated anti-solvent crystallization method is presented for the facile fabrication of microparticles containing dispersed nanocrystals of poorly soluble API. Direct crystallization within a porous hydrogel particle template yields core-shell structures in which the hydrogel core containing API nanocrystals is encased by a crystalline API shell. The process of controllable loading (up to 64% w/w) is demonstrated, and tailored dissolution profiles are achieved by simply altering the template particle size. API release is well described by a shrinking core model. Overall, the approach is a simple, scalable and potentially generalizable method that enables novel means of independently controlling both API crystallization and excipient characteristics, offering a "designer" drug particle system.

Control of Drug-Excipient Particle Attributes with Droplet Microfluidic-based Extractive Solidification Enables Improved Powder Rheology

PURPOSE

Industrial implementation of continuous oral solid dosage form manufacturing has been impeded by the poor powder flow properties of many active pharmaceutical ingredients (APIs). Microfluidic droplet-based particle synthesis is an emerging particle engineering technique that enables the production of neat or composite microparticles with precise control over key attributes that affect powder flowability, such as particle size distribution, particle morphology, composition, and the API's polymorphic form. However, the powder properties of these microparticles have not been well-studied due to the limited mass throughputs of available platforms. In this work, we produce spherical API and API-composite microparticles at high mass throughputs, enabling characterization and comparison of the bulk powder flow properties of these materials and greater understanding of how particle-scale attributes correlate with powder rheology.

METHODS

A multi-channel emulsification device and an extractive droplet-based method are harnessed to synthesize spherical API and API-excipient particles of artemether. As-received API and API crystallized in the absence of droplet confinement are used as control cases. Particle attributes are characterized for each material and correlated with a comprehensive series of powder rheology tests.

RESULTS

The droplet-based processed artemether particles are observed to be more flowable, less cohesive, and less compressible than conventionally synthesized artemether powder. Co-processing the API with polycaprolactone to produce composite microparticles reduces the friction of the powder on stainless steel, a common equipment material.

CONCLUSIONS

Droplet-based extractive solidification is an attractive particle engineering technique for improving powder processing and may aid in the implementation of continuous solid dosage form manufacturing.

Phase Transition of Catenated DNA Networks in Poly(ethylene glycol) Solutions

Conformational phase transitions of macromolecules are an important class of problems in fundamental polymer physics. While the conformational phase transitions of linear DNA have been extensively studied, this feature of topologically complex DNA remains unexplored. We report herein the polymer-and-salt-induced (Ψ) phase transition of 2D catenated DNA networks, called kinetoplasts, using single-molecule fluorescence microscopy. We observe that kinetoplasts can undergo a reversible transition from the flat phase to the collapsed phase in the presence of NaCl as a function of the crowding agent poly(ethylene glycol). The nature of this phase transition is tunable through varying ionic strengths. For linear DNA, the coexistence of coil and globule phases was attributed to a first order phase transition associated with a double well potential in the transition regime. Kinetoplasts, however, navigate from the flat to the collapsed phase by passing through an intermediate regime, characterized by the coexistence of a multipopulation with varying shapes and sizes. Conformations of individual molecules in the multipopulation are long-lived, which suggests a rugged energy landscape.

Patterning of interconnected human brain spheroids

Brain spheroids are emerging as valuable in vitro models that are accelerating the pace of research in various diseases. For Alzheimer's disease (AD) research, these models are enhanced using genetically engineered human neural progenitor cells and novel cell culture methods. However, despite these advances, it remains challenging to study the progression of AD in vitro as well as the propagation of pathogenic amyloid-β (Aβ) and tau tangles between diseased and healthy neurons using the brain spheroids model. To address this need, we designed a microfluidic system of connected microwells for arranging two types of brain spheroids in complex patterns and enabling the formation of thick bundles of neurites between the brain spheroids and the accumulation of pathogenic Aβ within the spheroids.

Equilibrium Conformation of Catenated DNA Networks in Slitlike Confinement

A kinetoplast is a planar network of catenated DNA rings with topology that resembles that of chain mail armor. In this work, we use single-molecule experiments to probe the conformation of kinetoplasts confined to slits. We find that the in-plane size of kinetoplasts increases with degree of confinement, akin to the slitlike confinement of linear DNA. The change in kinetoplast size with channel height is consistent with the scaling prediction from a Flory-type approach for a 2D polymer. With an increase in extent of confinement, the kinetoplasts appear to unfold and take on more uniform circular shapes, in contrast to the broad range of conformations observed for kinetoplasts in bulk.

Design and Use of a Thermogelling Methylcellulose Nanoemulsion to Formulate Nanocrystalline Oral Dosage Forms

Oral drug products have become indispensable in modern medicine because of their exceptional patient compliance. However, poor bioavailability of ubiquitous low-water-soluble active pharmaceutical ingredients (APIs) and lack of efficient oral drug formulations remain as significant challenges. Nanocrystalline formulations are an attractive route to increase API solubility, but typically require abrasive mechanical milling and several processing steps to create an oral dosage form. Using the dual amphiphilic and thermoresponsive properties of methylcellulose (MC), a new thermogelling nanoemulsion and a facile thermal dripping method are developed for efficient formulation of composite particles with the MC matrix embedded with precisely controlled API nanocrystals. Moreover, a fast and tunable release performance is achieved with the combination of a fast-eroding MC matrix and fast-dissolving API nanocrystals. Using the versatile thermal processing approach, the thermogelling nanoemulsion is easily formulated into a wide variety of dosage forms (nanoparticle suspension, drug tablet, and oral thin film) in a manner that avoids nanomilling. Overall, the proposed thermogelling nanoemulsion platform not only broadens the applications of thermoresponsive nanoemulsions but also shows great promise for more efficient formulation of oral drug products with high quality and tunable fast release.

Evaluation of 3D-printed molds for fabrication of non-planar microchannels

Replica obtained from micromolds patterned by simple photolithography has features with uniform heights, and attainable microchannels are thus quasi-two-dimensional. Recent progress in three-dimensional (3D) printing has enabled facile desktop fabrication of molds to replicate microchannels with varying heights. We investigated the replica obtained from four common techniques of 3D printing-fused deposition modeling, selective laser sintering, photo-polymer inkjet printing (PJ), and stereolithography (SL)-for the suitability to form microchannels in terms of the surface roughness inherent to the mechanism of 3D printing. There have been limited quantitative studies that focused on the surface roughness of a 3D-printed mold with different methods of 3D printing. We discussed that the surface roughness of the molds affected (1) transparency of the replica and (2) delamination pressure of poly(dimethylsiloxane) replica bonded to flat glass substrates. Thereafter, we quantified the accuracy of replication from 3D-printed molds by comparing the dimensions of the replicated parts to the designed dimensions and tested the ability to fabricate closely spaced microchannels. This study suggested that molds printed by PJ and SL printers were suitable for replica molding to fabricate microchannels with varying heights. The insight from this study shall be useful to fabricate 3D microchannels with controlled 3D patterns of flows guided by the geometry of the microchannels.

High-Resolution Patterning of Hydrogel Sensing Motifs within Fibrous Substrates for Sensitive and Multiplexed Detection of Biomarkers

There has been an increasing and urgent demand to develop nucleic acid bioassays which not only offer high analytical performance but which are also amenable with point-of-care testing. Hydrogels present a versatile class of materials with biocompatible antifouling properties and the ability to be engineered for a range of advanced sensing applications. Fibrous substrates like nitrocellulose offer low-cost and durable platforms to run complex bioassays while enabling portability and ease of handling. We demonstrate herein the ability to synergistically combine these two materials into a portable biosensing platform by leveraging projection lithography. We demonstrate the direct polymerization of hydrogel sensing motifs within a range of fibrous substrates with precise control over their shape, size, location, and functionality. Spatial encoding of the hydrogel motifs enables the multiplex detection of multiple biomarkers on the same test. As a proof-of-concept, we apply the platform to the detection of microRNA, an emerging class of circulating biomarkers with promising potential for early diagnosis and monitoring of cancer. The assay offers a large dynamic range (over three orders of magnitude), high sensitivity (limit of detection of 2.5 amol), as well as versatility and ease of handling. Finally, the bioassay is validated using real biological samples, namely, total RNA extracted from the sera of late-stage breast cancer patients, demonstrating its utility and compatibility with clinical biosensing applications.

Nanoemulsion-Loaded Capsules for Controlled Delivery of Lipophilic Active Ingredients

Nanoemulsions have become ideal candidates for loading hydrophobic active ingredients and enhancing their bioavailability in the pharmaceutical, food, and cosmetic industries. However, the lack of versatile carrier platforms for nanoemulsions hinders advanced control over their release behavior. In this work, a method is developed to encapsulate nanoemulsions in alginate capsules for the controlled delivery of lipophilic active ingredients. Functional nanoemulsions loaded with active ingredients and calcium ions are first prepared, followed by encapsulation inside alginate shells. The intrinsically high viscosity of the nanoemulsions ensures the formation of spherical capsules and high encapsulation efficiency during the synthesis. Moreover, a facile approach is developed to measure the nanoemulsion release profile from capsules through UV-vis measurement without an additional extraction step. A quantitative analysis of the release profiles shows that the capsule systems possess a tunable, delayed-burst release. The encapsulation methodology is generalized to other active ingredients, oil phases, nanodroplet sizes, and chemically crosslinked inner hydrogel cores. Overall, the capsule systems provide promising platforms for various functional nanoemulsion formulations.

A platform for multiplexed colorimetric microRNA detection using shape-encoded hydrogel particles

We report a platform utilizing a reporter enzyme, which produces a chromogenic indigo precipitate that preferentially localizes within a hydrogel microparticle. The 3D network of the hydrogel maintains the rapid target binding kinetics found in solution, while multiplexed target detection is achieved through shape-encoding of the particles. Moreover, the precipitate-laden hydrogels can be imaged with a simple phone camera setup. We used this system to detect microRNA (miRNA) down to 0.22 fmol. We then showed the compatibility of this system with real samples by performing multiplexed miRNA measurements from total RNA from matched colon cancer and normal adjacent tissue.

Deformation Response of Catenated DNA Networks in a Planar Elongational Field

A kinetoplast is a complex catenated DNA network that bears resemblance to a two-dimensional polymeric system. In this work, we use single-molecule experiments to study the transient and steady-state deformation of kinetoplasts in a planar elongational field. We demonstrate that kinetoplasts deform in a stagewise manner and undergo transient deformation at large strains, due to conformational rearrangements from an intermediate metastable state. Kinetoplasts in an elongational field achieve a steady-state deformation that depends on strain rate, akin to the deformation of linear polymers. We do not observe an abrupt transition between the nondeformed and deformed states of a kinetoplast, in contrast to the coil-stretch transition for a linear polymer.

Spatially resolved and multiplexed MicroRNA quantification from tissue using nanoliter well arrays

Spatially resolved gene expression patterns are emerging as a key component of medical studies, including companion diagnostics, but technologies for quantification and multiplexing are limited. We present a method to perform spatially resolved and multiplexed microRNA (miRNA) measurements from formalin-fixed, paraffin-embedded (FFPE) tissue. Using nanoliter well arrays to pixelate the tissue section and photopatterned hydrogels to quantify miRNA, we identified differentially expressed miRNAs in tumors from a genetically engineered mouse model for non-small cell lung cancer (K-ras^LSL-G12D/+; p53^fl/fl). This technology could be used to quantify heterogeneities in tissue samples and lead to informed, biomarker-based diagnostics.

Design of a Multiplexed Analyte Biosensor using Digital Barcoded Particles and Impedance Spectroscopy

Multiplexing allows quantifying multiple analytes in a single step, providing advantages over individual testing through shorter processing time, lower sample volume, and reduced cost per test. Currently, flow cytometry is the gold standard for biomedical multiplexing, but requires technical training, extensive data processing, and expensive operational and capital costs. To solve this challenge, we designed digital barcoded particles and a microfluidic architecture for multiplexed analyte quantification. In this work, we simulate and model non-fluorescence-based microfluidic impedance detection with a single excitation and detection scheme using barcoded polymer microparticles. Our barcoded particles can be designed with specific coding regions and generate numerous distinct patterns enabling digital barcoding. We found that signals based on adhered microsphere position and relative orientation were evaluated and separated based on their associated electrical signatures and had a 7 µm microsphere limit of detection. Our proposed microfluidic system can enumerate micron-sized spheres in a single assay using barcoded particles of various configurations. As representation of blood cells, the microsphere concentrations may provide useful information on disease onset and progression. Such sensors may be used for diagnostic and management of common critical care diseases like sepsis, acute kidney injury, urinary tract infections, and HIV/AIDS.

Tuning Material Properties of Nanoemulsion Gels by Sequentially Screening Electrostatic Repulsions and Then Thermally Inducing Droplet Bridging

Nanoemulsions are widely used in applications such as food products, cosmetics, pharmaceuticals, and enhanced oil recovery for which the ability to engineer material properties is desirable. Moreover, nanoemulsions are emergent model colloidal systems because of the ease in synthesizing monodisperse samples, flexibility in formulations, and tunable material properties. In this work, we study a nanoemulsion system previously developed by our group in which gelation occurs through thermally induced polymer bridging of droplets. We show here that the same system can undergo a sol-gel transition at room temperature through the addition of salt, which screens the electrostatic interaction and allows the system to assemble via depletion attraction. We systematically study how the addition of salt followed by a temperature jump can influence the resulting microstructures and rheological properties of the nanoemulsion system. We show that the salt-induced gel at room temperature can dramatically restructure when the temperature is suddenly increased and achieves a different gelled state. Our results offer a route to control the material properties of an attractive colloidal system by carefully tuning the interparticle potentials and sequentially triggering the colloidal self-assembly. The control and understanding of the material properties can be used for designing hierarchically structured hydrogels and complex colloid-based materials for advanced applications.

Hydrogel-Based Colorimetric Assay for Multiplexed MicroRNA Detection in a Microfluidic Device

Although microRNA (miRNA) expression levels provide important information regarding disease states owing to their unique dysregulation patterns in tissues, translation of miRNA diagnostics into point-of-care (POC) settings has been limited by practical challenges. Here, we developed a hydrogel-based microfluidic platform for colorimetric profiling of miRNAs, without the use of complex external equipment for fluidics and imaging. For sensitive and reliable measurement without the risk of sequence bias, we employed a gold deposition-based signal amplification scheme and dark-field imaging, and seamlessly integrated a previously developed miRNA assay scheme into this platform. The assay demonstrated a limit of detection of 260 fM, along with multiplexing of small panels of miRNAs in healthy and cancer samples. We anticipate this versatile platform to facilitate a broad range of POC profiling of miRNAs in cancer-associated dysregulation with high-confidence by exploiting the unique features of hydrogel substrate in an on-chip format and colorimetric analysis.

Embedded droplet printing in yield-stress fluids

Microfluidic tools and techniques for manipulating fluid droplets have become core to many scientific and technological fields. Despite the plethora of existing approaches to fluidic manipulation, non-Newtonian fluid phenomena are rarely taken advantage of. Here we introduce embedded droplet printing-a system and methods for the generation, trapping, and processing of fluid droplets within yield-stress fluids, materials that exhibit extreme shear thinning. This technique allows for the manipulation of droplets under conditions that are simply unattainable with conventional microfluidic methods, namely the elimination of exterior influences including convection and solid boundaries. Because of this, we believe embedded droplet printing approaches an ideal for the experimentation, processing, or observation of many samples in an "absolutely quiescent" state, while also removing some troublesome aspects of microfluidics including the use of surfactants and the complexity of device manufacturing. We characterize a model material system to understand the process of droplet generation inside yield-stress fluids and develop a nascent set of archetypal operations that can be performed with embedded droplet printing. With these principles and tools, we demonstrate the benefits and versatility of our method, applying it toward the diverse applications of pharmaceutical crystallization, microbatch chemical reactions, and biological assays.

Weak acids as an alternative anti-microbial therapy

Weak acids such as acetic acid and N-acetyl cysteine (NAC) at pH less than their pKa can effectively eradicate biofilms due to their ability to penetrate the biofilm matrix and the cell membrane. However, the optimum conditions for their activity against drug resistant strains, and safety, need to be understood for their application to treat infections or to inactivate biofilms on hard surfaces. Here, we investigate the efficacy and optimum conditions at which weak acids can eradicate biofilms. We compared the efficacy of various mono and triprotic weak acids such as N-acetyl cysteine (NAC), acetic acid, formic acid and citric acid, in eradicating biofilms. We found that monoprotic weak acids/acid drugs can kill mucoid P. aeruginosa mucA biofilm bacteria provided the pH is less than their pKa, demonstrating that the extracellular biofilm matrix does not protect the bacteria from the activity of the weak acids. Triprotic acids, such as citric acid, kill biofilm bacteria at pH ​< ​pKa1. However, at a pH between pKa1 and pKa2, citric acid is effective in killing the bacteria at the core of biofilm microcolonies but does not kill the bacteria on the periphery. The efficacy of a monoprotic weak acid (NAC) and triprotic weak acid (citric acid) were tested on biofilms formed by Klebsiella pneumoniae KP1, Pseudomonas putida OUS82, Staphylococcus aureus 15981, P. aeruginosa DK1-NH57388A, a mucoid cystic fibrosis isolate and P. aeruginosa PA_D25, an antibiotic resistant strain. We showed that weak acids have a broad spectrum of activity against a wide range of bacteria, including antibiotic resistant bacteria. Further, we showed that a weak acid drug, NAC, can kill bacteria without being toxic to human cells, if its pH is maintained close to its pKa. Thus weak acids/weak acid drugs target antibiotic resistant bacteria and eradicate the persister cells in biofilms which are tolerant to other conventional methods of biofilm eradication.

Equilibrium structure and deformation response of 2D kinetoplast sheets

The considerable interest in two-dimensional (2D) materials and complex molecular topologies calls for a robust experimental system for single-molecule studies. In this work, we study the equilibrium properties and deformation response of a complex DNA structure called a kinetoplast, a 2D network of thousands of linked rings akin to molecular chainmail. Examined in good solvent conditions, kinetoplasts appear as a wrinkled hemispherical sheet. The conformation of each kinetoplast is dictated by its network topology, giving it a unique shape, which undergoes small-amplitude thermal fluctuations at subsecond timescales, with a wide separation between fluctuation and diffusion timescales. They deform elastically when weakly confined and swell to their equilibrium dimensions when the confinement is released. We hope that, in the same way that linear DNA became a canonical model system on the first investigations of its polymer-like behavior, kinetoplasts can serve that role for 2D and catenated polymer systems.

Complex DNA knots detected with a nanopore sensor

Equilibrium knots are common in biological polymers-their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.

Conformational State Hopping of Knots in Tensioned Polymer Chains

We use Brownian dynamics simulations to study the conformational states of knots on tensioned chains. Focusing specifically on the 8₁ knot, we observe knot conformational state hopping and show that the process can be described by a two-state kinetic model in the presence of an external force. The distribution of knot conformational states depends on the applied chain tension, which leads to a force-dependent distribution of knot untying pathways. We generalize our findings by considering the untying pathways of other knots and find that the way knots untie is generally governed by the force applied to the chain. From a broader perspective, being able to influence how a knot unties via external force can potentially be useful for applications of single-molecule techniques in which knots are unwanted.

Long-Lived Self-Entanglements in Ring Polymers

The entanglement of ring polymers remains mysterious in many aspects. In this Letter, we use electric fields to induce self-entanglements in circular DNA molecules, which serve as a minimal system for studying chain entanglements. We show that self-threadings give rise to entanglements in ring polymers and can slow down polymer dynamics significantly. We find that strongly entangled circular molecules remain kinetically arrested in a compact state for very long times, thereby providing experimental evidence for the severe topological constraints imposed by threadings.

Colloidal Gelation through Thermally Triggered Surfactant Displacement

Colloidal systems that undergo gelation attract much attention in both fundamental studies and practical applications. Rational tuning of interparticle interactions allows researchers to precisely engineer colloidal material properties and microstructures. Here, contrary to the traditional approaches where modulating attractive interactions is the major focus, we present a platform wherein colloidal gelation is controlled by tuning repulsive interactions. By including amphiphilic oligomers in colloidal suspensions, the ionic surfactants on the colloids are replaced by the nonionic oligomer surfactants at elevated temperatures, leading to a decrease in electrostatic repulsion. The mechanism is examined by carefully characterizing the colloids, and subsequently allowing the construction of interparticle potentials to capture the material behaviors. With the thermally triggered surfactant displacement, the dispersion assembles into a macroporous viscoelastic network and the gelling mechanism is robust over a wide range of compositions, colloid sizes, and component chemistries. This stimulus-responsive gelation platform is general and offers new strategies to engineer complex viscoelastic soft materials.

Thermoresponsive nanoemulsion-based gel synthesized through a low-energy process

Thermoresponsive nanoemulsions find utility in applications ranging from food to pharmaceuticals to consumer products. Prior systems have found limited translation to applications due to cytotoxicity of the compositions and/or difficulties in scaling-up the process. Here, we report a route to thermally gel an oil-in-water nanoemulsion using a small amount of FDA-approved amphiphilic triblock Pluronic copolymers which act as gelling agents. At ambient temperature the suspension displays liquid-like behavior, and quickly becomes an elastic gel at elevated temperatures. We propose a gelation mechanism triggered by synergistic action of thermally-induced adsorption of Pluronic copolymers onto the droplet interface and an increased micelle concentration in the aqueous solution. We demonstrate that the system's properties can be tuned via many factors and report their rheological properties. The nanoemulsions are prepared using a low-energy process which offers an efficient route to scale-up. The nanoemulsion formulations are well-suited for use in cosmetics and pharmaceutical applications.

Self-assembly of droplets in three-dimensional microchannels

Self-assembly of droplets guided by microfluidic channels have potential applications ranging from high throughput assays to materials synthesis, but such demonstrations have been limited primarily to two-dimensional (2D) assembly of droplets in planar microfluidic devices. We demonstrated the use of three-dimensional (3D) microchannels to self-assemble droplets into ordered 2D and 3D arrays by designing microchannels with axial gradients in height and controlling the volume fraction of the droplets in the channel. In contrast to previous demonstrations, ordered 2D arrays of droplets were assembled at low volume fractions of the dispersed phase. Interestingly, we found that the self-assembly of droplets in microchannels was highly path dependent. The assembly of droplets was governed by transitions in the cross-sectional shapes of the microchannel, not the final geometry of the chamber for the assembly of droplet, which is a hitherto rarely explored phenomenon. The assembled droplets were used as templates for the fabrication of millimeter scale, anisotropic hydrogel fibers with ordered pore sizes (∼250 μm). These demonstrations suggested that 3D microchannels would be a viable platform for the manipulation of droplets, and applicable for the continuous synthesis of complex materials with 3D morphologies.

Noninvasive monitoring of single-cell mechanics by acoustic scattering

Monitoring mechanics of the same cell throughout the cell cycle has been hampered by the invasiveness of mechanical measurements. Here, we quantify mechanical properties via acoustic scattering of waves from a cell inside a fluid-filled vibrating cantilever with a temporal resolution of <1 min. Through simulations, experiments with hydrogels and chemically perturbed cells, we show that our readout, the size-normalized acoustic scattering (SNACS), measures stiffness. We demonstrate the noninvasiveness of SNACS over successive cell cycles using measurements that result in < 15 nm deformations. Cells maintain constant SNACS throughout interphase but exhibit dynamic changes during mitosis. Our work provides a basis for understanding how growing cells maintain mechanical integrity and demonstrates that acoustic scattering can non-invasively probe subtle and transient dynamics.

Photopolymerized Micelle-Laden Hydrogels Can Simultaneously Form and Encapsulate Nanocrystals to Improve Drug Substance Solubility and Expedite Drug Product Design

Formulation technologies are critical for increasing the efficacy of drug products containing poorly soluble hydrophobic drugs, which compose roughly 70% of small molecules in commercial pipelines. Nanomedicines, such as nanocrystal formulations and amorphous solid suspensions, are effective approaches to increasing solubility. However, existing techniques require additional processing into a final dosage form, which strongly influences drug delivery and clinical performance. To enhance hydrophobic drug product efficacy and clinical throughput, a hydrogel material is developed as a sacrificial template to simultaneously form and encapsulate nanocrystals. These hydrogels contain micelles chemically bound to the hydrogel matrix, where the surfactant structure dictates the crystal size and drug loading. Therefore, nanocrystals can be produced in high yield (up to 90% drug loading, by weight) with precisely controlled sizes as small as 4 nm independently of hydrogel composition. Nanocrystals and surfactant are then released together to increase the solubility up to 70 times above bulk crystalline material. By integrating nanocrystals into a final dosage form, micelle-laden hydrogels simplify hydrophobic drug product design.

Multifunctional Hierarchically-Assembled Hydrogel Particles with Pollen Grains via Pickering Suspension Polymerization

Hierarchical assembly of heterogeneous particles is of great importance to interface and colloid science. In this work, a facile but powerful approach for the large-scale production of multifunctional hydrogel particles armored with biological colloidal species is developed by combining Pickering stabilization and photopolymerization. Biocompatible hollow pollen grains extracted from naturally occurring pollen species with an average diameter of ∼32 μm serve as universal solid emulsifiers dispersed in an oil phase and are self-assembled at the interface between an oil phase and a photo-cross-linkable hydrogel to make water-in-oil (W/O) emulsion droplets. While droplets are solidified into hydrogel particles by UV-induced free-radical polymerization, self-assembled hollow pollen grains are transformed to a robust shell on hydrogel particles with supracolloidal structures. The physically adsorbed hollow pollen grains on the hydrogel core can be released by a hydration-induced swelling of hollow pollen grains, leading to a transient floating behavior of core-shell particles. The size of the resultant core-shell particles is easily controlled by tailoring the process parameters such as a liquid volume or a loading mass of hollow pollen grains. The incorporation of magnetic or upconverting luminescent nanoparticles into a hydrogel core successfully expands the functionality of core-shell particles that can provide new design opportunities for floating drug delivery or ecofriendly proppants.

Designable 3D Microshapes Fabricated at the Intersection of Structured Flow and Optical Fields

3D structures with complex geometric features at the microscale, such as microparticles and microfibers, have promising applications in biomedical engineering, self-assembly, and photonics. Fabrication of complex 3D microshapes at scale poses a unique challenge; high-resolution methods such as two-photon-polymerization have print speeds too low for high-throughput production, while top-down approaches for bulk processing using microfabricated template molds have limited control of microstructure geometries over multiple axes. Here, a method for microshape fabrication is presented that combines a thermally drawn transparent fiber template with a masked UV-photopolymerization approach to enable biaxial control of microshape fabrication. Using this approach, high-resolution production of complex microshapes not producible using alternative methods is demonstrated, such as octahedrons, dreidels, and axially asymmetric fibers, at throughputs as high as 825 structures/minute. Finally, the fiber template is functionalized with conductive electrodes to enable hierarchical subparticle localization using dielectrophoretic forces.

Calcium-mediated Protein Folding and Stabilization of Salmonella Biofilm-associated Protein A

Biofilm-associated proteins (BAPs) are important for early biofilm formation (adhesion) by bacteria and are also found in mature biofilms. BapA from Salmonella is a ~386-kDa surface protein, comprising 27 tandem repeats predicted to be bacterial Ig-like (BIg) domains. Such tandem repeats are conserved for BAPs across different bacterial species, but the function of these domains is not completely understood. In this work, we report the first study of the mechanical stability of the BapA protein. Using magnetic tweezers, we show that the folding of BapA BIg domains requires calcium binding and the folded domains have differential mechanical stabilities. Importantly, we identify that >100 nM concentration of calcium is needed for folding of the BIg domains, and the stability of the folded BIg domains is regulated by calcium over a wide concentration range from sub-micromolar (μM) to millimolar (mM). Only at mM calcium concentrations, as found in the extracellular environment, do the BIg domains have the saturated mechanical stability. BapA has been suggested to be involved in Salmonella invasion, and it is likely a crucial mechanical component of biofilms. Therefore, our results provide new insights into the potential roles of BapA as a structural maintenance component of Salmonella biofilm and also Salmonella invasion.

Rapid prototyping of fluoropolymer microchannels by xurography for improved solvent resistance

Microchannels made of fluoropolymers show potential merits due to their excellent solvent resistance, but such channels have not been widely used because of the complexity to fabricate them. This communication describes a method to prototype microfluidic devices using fluoropolymer films. The fabrication requires only two steps; cutting fluoropolymer films with a desktop cutting plotter and applying heat and pressure to laminate them. The method is rapid, simple, and low-cost. The conditions for heat press were identified for two common fluoropolymers: polytetrafluoroethylene and fluorinated ethylene propylene. The laminated films were confirmed to remain sealed with an internal pressure of at least 300 kPa. The fabricated devices were tested for the resistance to a set of organic solvents that would not be compatible with typical devices fabricated in polydimethylsiloxane. To highlight the potential of the fluoropolymer devices fabricated in this method, generation of droplets in a continuous stream of organic solvent using a T-junction channel was demonstrated. Our method offers a simple avenue to prototype microfluidic devices to conduct experiments involving organic solvents such as organic chemistry and in-channel synthesis of microparticles.

Design of Hydrogel Particle Morphology for Rapid Bioassays

Hydrogel microparticles have been extensively used in the field of medical diagnostics for detecting targets ranging from proteins to nucleic acids. However, little is known about how the shape of hydrogel particles impacts the signal from a bioassay. In this article, we analyze the flux into porous hydrogel particles to develop scaling laws for the signal from a point-of-care bioassay. The signal can be increased by increasing the ratio of the surface area of the hydrogel particle to the two-dimensional projected imaging area used for analysis. We show that adding internal surface area to hydrogel particles increases the assay signal in a biotin-streptavidin bioassay. We also demonstrate the application of this technique to a protein-based assay for thyroid-stimulating hormone, reducing the limit of detection of the assay sixfold by changing particle shape. We anticipate that these strategies can be used broadly to optimize hydrogel-based systems for point-of-care diagnostics.

Oil Recovery from Micropatterned Triangular Troughs during a Surfactant Flood

We study the recovery of oil trapped inside micropatterned triangular troughs after injecting a surfactant solution. In our experiments, we track the trapped oil volume with duration of surfactant flood for different capillary numbers. We observe that the capillary number affects the amount of oil recovered as the well as the rate of oil recovery. We employ multiphase flow simulations to analyze our system and show a qualitative agreement between the simulations and experimental results. We also discover that beyond a capillary number, the volume of oil recovered plateaus, and no additional oil is released with an increase in capillary number. We develop a theoretical model to predict the dependence of maximum oil recovery on geometrical features and find that the theoretical predictions compare favorably with the trends obtained from our simulations. Though approximate, theoretical relation provides insights into the efficiency of oil recovery and can be utilized to understand the effect of sharp bends and dead ends in enhanced oil recovery and soil remediation.

Nonfouling, Encoded Hydrogel Microparticles for Multiplex MicroRNA Profiling Directly from Formalin-Fixed, Paraffin-Embedded Tissue

MicroRNAs (miRNA) are short, noncoding RNAs that have been implicated in many diseases, including cancers. Because miRNAs are dysregulated in disease, miRNAs show promise as highly stable biomarkers. Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable sample type to assay for biomolecules because it is a convenient storage method and is often used by pathologists for histological staining. However, extracting biomolecules from FFPE tissue is challenging because of the presence of cellular and extracellular proteins, formaldehyde cross-links, and paraffin. Moreover, most protocols to measure miRNA in FFPE tissue are time-consuming and laborious. Here, we report a simple protocol to directly measure miRNA from formalin-fixed cells, FFPE tissue sections after paraffin is removed, and FFPE tissue sections using encoded hydrogel microparticles fabricated using stop flow lithography. Measurements by these particles show agreement between formalin-fixed cells and fresh cells, and measurement of FFPE tissue with paraffin is 10% less than FFPE tissue when paraffin is removed before the assay. When normal and tumor FFPE tissue are compared using this microparticle assay, we observe differential miRNA signal for oncogenic miRNAs and tumor suppressing miRNAs. This approach reduces assay times, reduces the use of hazardous chemicals to remove paraffin, and provides a sensitive, quantitative, and multiplexed measurement of miRNA in FFPE tissue.