Prof. Sindy KY Tang is the Kenneth and Barbara Oshman Faculty Scholar and Associate Professor of Mechanical Engineering and by courtesy of Radiology (Precision Health and Integrated Diagnostics) at Stanford University. She received her Ph.D. from Harvard University in Engineering Sciences under the supervision of Prof. George Whitesides. Her lab at Stanford works on the fundamental understanding of fluid mechanics and mass transport in micro-nano systems, and the application of this knowledge towards problems in biology, rapid diagnostics for health and environmental sustainability. The current areas of focus include the flow physics of confined micro-droplets using experimental and machine learning methods, interfacial mass transport and self-assembly, and ultrahigh throughput opto-microfluidic systems for disease diagnostics, water and energy sustainability, and single-cell wound healing studies. She was a Stanford Biodesign Faculty Fellow in 2018. Dr. Tang’s work has been recognized by multiple awards including the NSF CAREER Award, 3M Nontenured Faculty Award, the ACS Petroleum Fund New Investigator Award, and invited lecture at the Nobel Symposium on Microfluidics in Sweden. Website: http://web.stanford.edu/group/tanglab/
Associate Professor, Mechanical Engineering, Stanford University (2018 - Present)
Assistant Professor, Mechanical Engineering, Stanford University (2011 - 2018)
Honors & Awards
Faculty Fellow Award, The Reid and Polly Anderson Foundation (2011-2013)
Junior Faculty Fellow Award, Gabilan (2011-2013)
Petroleum Fund New Investigator Award, ACS (2013-2015)
3M Nontenured Faculty Award, 3M (2013-2015)
NSF CAREER Award, NSF (2015-2020)
Boards, Advisory Committees, Professional Organizations
Editorial Advisory Board, Biomicrofluidics, American Institute of Physics (AIP) Publishing (2019 - Present)
Site Director, NSF Science & Technology Center for Cellular Construction (2017 - Present)
Co-lead of Bio Interfaces Focus Area, Stanford SystemX Alliance (2018 - Present)
Education Advisory Board, San Francisco Girls' School (2018 - Present)
Executive Technical Program Committee uTAS, The Chemical and Biological Microsystems Society (2018 - Present)
Stanford SystemX Alliance
PhD, Harvard University, Engineering Sciences
MS, Stanford University, Electrical Engineering
BS, Caltech, Electrical Engineering
Sindy KY Tang, Craig Criddle, Jaewook Myung, Minkyu Kim. "United States Patent App. 15,418,337 Emulsion-based fermentation for accelerated gas substrate mass transfer", Leland Stanford Junior University
Sindy K.Y. Tang, Ming Pan, Fengjiao Lyu, Ratmir Derda. "United States Patent App. No. 14,922,018 Fluorinated pickering emulsion", Leland Stanford Junior University
Ratmir Derda, Sindy K.Y. Tang, George M. Whitesides. "United States Patent 9,499,813 Systems and methods for amplification and phage display", Harvard University, Dec 11, 0189
Current Research and Scholarly Interests
Our lab is dedicated to solving problems at the interface of engineering, soft matter, and biology. Current focus includes microfluidics fundamentals and applications in disease diagnostics (e.g., tuberculosis, sepsis, allergy), and single-cell wound repair and learning. For details see https://web.stanford.edu/group/tanglab/
- Introduction to Micro and Nano Electromechanical Systems
ENGR 240 (Aut)
- Introductory Fluids Engineering
ME 70 (Win)
- Optofluidics: Interplay of Light and Fluids at the Micro and Nanoscale
ME 321 (Win)
Independent Studies (11)
- Directed Reading in Biophysics
BIOPHYS 399 (Aut, Win, Spr)
- Engineering Problems
ME 391 (Aut, Win, Spr, Sum)
- Engineering Problems and Experimental Investigation
ME 191 (Aut, Win, Spr, Sum)
- Experimental Investigation of Engineering Problems
ME 392 (Aut, Win, Spr, Sum)
- Graduate Research
BIOPHYS 300 (Aut, Win, Spr)
- Honors Research
ME 191H (Aut, Win, Spr)
- Ph.D. Research
MATSCI 300 (Aut, Win, Spr, Sum)
- Ph.D. Research Rotation
ME 398 (Aut, Win)
- Ph.D. Teaching Experience
ME 491 (Aut, Win, Spr, Sum)
- Practical Training
ME 299A (Aut, Win, Spr, Sum)
- Practical Training
ME 299B (Aut, Win, Spr, Sum)
- Directed Reading in Biophysics
Prior Year Courses
- Introduction to Micro and Nano Electromechanical Systems
ENGR 240 (Spr)
- Introductory Fluids Engineering
ME 70 (Win)
- Introduction to Micro and Nano Electromechanical Systems
ENGR 240 (Aut)
- Optofluidics: Interplay of Light and Fluids at the Micro and Nanoscale
ME 321 (Win)
- Introduction to Micro and Nano Electromechanical Systems
Using machine learning to discover shape descriptors for predicting emulsion stability in a microfluidic channel.
In soft matter consisting of many deformable objects, object shapes often carry important information about local forces and their interactions with the local environment, and can be tightly coupled to the bulk properties and functions. In a concentrated emulsion, for example, the shapes of individual droplets are directly related to the local stress arising from interactions with neighboring drops, which in turn determine their stability and the resulting rheological properties. Shape descriptors used in prior work on single drops and dilute emulsions, where droplet-droplet interactions are largely negligible and the drop shapes are simple, are insufficient to fully capture the broad range of droplet shapes in a concentrated system. This paper describes the application of a machine learning method, specifically a convolutional autoencoder model, that learns to: (1) discover a low-dimensional code (8-dimensional) to describe droplet shapes within a concentrated emulsion, and (2) predict whether the drop will become unstable and undergo break-up. The input consists of images (N = 500002) of two-dimensional droplet boundaries extracted from movies of a concentrated emulsion flowing through a confined microfluidic channel as a monolayer. The model is able to faithfully reconstruct droplet shapes, as well as to achieve a classification accuracy of 91.7% in the prediction of droplet break-up, compared with 60% using conventional scalar descriptors based on droplet elongation. It is observed that 4 out of the 8 dimensions of the code are interpretable, corresponding to drop skewness, elongation, throat size, and surface curvature, respectively. Furthermore, the results show that drop elongation, throat size, and surface curvature are dominant factors in predicting droplet break-up for the flow conditions tested. The method presented is expected to facilitate follow-on work to identify the relationship between drop shapes and the interactions with other drops, and to identify potentially new modes of break-up mechanisms in a concentrated system. Finally, the method developed here should also apply to other soft materials such as foams, gels, and cells and tissues.
View details for PubMedID 30570628
Programming self-organizing multicellular structures with synthetic cell-cell signaling
2018; 361 (6398): 156-+
A common theme in the self-organization of multicellular tissues is the use of cell-cell signaling networks to induce morphological changes. We used the modular synNotch juxtacrine signaling platform to engineer artificial genetic programs in which specific cell-cell contacts induced changes in cadherin cell adhesion. Despite their simplicity, these minimal intercellular programs were sufficient to yield assemblies with hallmarks of natural developmental systems: robust self-organization into multidomain structures, well-choreographed sequential assembly, cell type divergence, symmetry breaking, and the capacity for regeneration upon injury. The ability of these networks to drive complex structure formation illustrates the power of interlinking cell signaling with cell sorting: Signal-induced spatial reorganization alters the local signals received by each cell, resulting in iterative cycles of cell fate branching. These results provide insights into the evolution of multicellularity and demonstrate the potential to engineer customized self-organizing tissues or materials.
View details for PubMedID 29853554
Self-repairing cells: How single cells heal membrane ruptures and restore lost structures
2017; 356 (6342): 1022-1025
Many organisms and tissues display the ability to heal and regenerate as needed for normal physiology and as a result of pathogenesis. However, these repair activities can also be observed at the single-cell level. The physical and molecular mechanisms by which a cell can heal membrane ruptures and rebuild damaged or missing cellular structures remain poorly understood. This Review presents current understanding in wound healing and regeneration as two distinct aspects of cellular self-repair by examining a few model organisms that have displayed robust repair capacity, including Xenopus oocytes, Chlamydomonas, and Stentor coeruleus Although many open questions remain, elucidating how cells repair themselves is important for our mechanistic understanding of cell biology. It also holds the potential for new applications and therapeutic approaches for treating human disease.
View details for DOI 10.1126/science.aam6496
View details for PubMedCentralID PMC5664224
Microfluidic guillotine for single-cell wound repair studies.
Proceedings of the National Academy of Sciences of the United States of America
2017; 114 (28): 7283–88
Wound repair is a key feature distinguishing living from nonliving matter. Single cells are increasingly recognized to be capable of healing wounds. The lack of reproducible, high-throughput wounding methods has hindered single-cell wound repair studies. This work describes a microfluidic guillotine for bisecting single Stentor coeruleus cells in a continuous-flow manner. Stentor is used as a model due to its robust repair capacity and the ability to perform gene knockdown in a high-throughput manner. Local cutting dynamics reveals two regimes under which cells are bisected, one at low viscous stress where cells are cut with small membrane ruptures and high viability and one at high viscous stress where cells are cut with extended membrane ruptures and decreased viability. A cutting throughput up to 64 cells per minute-more than 200 times faster than current methods-is achieved. The method allows the generation of more than 100 cells in a synchronized stage of their repair process. This capacity, combined with high-throughput gene knockdown in Stentor, enables time-course mechanistic studies impossible with current wounding methods.
View details for PubMedID 28652371
View details for PubMedCentralID PMC5514750
Spatiotemporal periodicity of dislocation dynamics in a two-dimensional microfluidic crystal flowing in a tapered channel.
Proceedings of the National Academy of Sciences of the United States of America
2016; 113 (43): 12082-12087
When a many-body system is driven away from equilibrium, order can spontaneously emerge in places where disorder might be expected. Here we report an unexpected order in the flow of a concentrated emulsion in a tapered microfluidic channel. The velocity profiles of individual drops in the emulsion show periodic patterns in both space and time. Such periodic patterns appear surprising from both a fluid and a solid mechanics point of view. In particular, when the emulsion is considered as a soft crystal under extrusion, a disordered scenario might be expected based on the stochastic nature of dislocation dynamics in microscopic crystals. However, an orchestrated sequence of dislocation nucleation and migration is observed to give rise to a highly ordered deformation mode. This discovery suggests that nanocrystals can be made to deform more controllably than previously thought. It can also lead to novel flow control and mixing strategies in droplet microfluidics.
View details for PubMedID 27790994
- Timescale and spatial distribution of local plastic events in a two-dimensional microfluidic crystal PHYSICAL REVIEW FLUIDS 2019; 4 (1)
Current biology : CB
2018; 28 (20): R1180–R1184
Although we often think of cells as small, simple building blocks of life, in fact they are highly complex and can perform a startling variety of functions. In our bodies, cells are programmed by complex differentiation pathways and are capable of responding to a bewildering range of chemical and physical signals. Free-living single-celled organisms, such as bacteria or protists, have to cope with varying environments, locate prey and potential mates, and escape from predators - all of the same tasks that a free-living animal is faced with. When animals face complex behavioral challenges, they rely on their cognitive abilities - the ability to learn from experience, to analyse a situation and choose an appropriate course of action. This ability is essential for survival and should, in principle, be a ubiquitous feature of all living things regardless of the complexity of the organism.
View details for PubMedID 30352182
- Phenotyping antibiotic resistance with single-cell resolution for the detection of heteroresistance SENSORS AND ACTUATORS B-CHEMICAL 2018; 270: 396–404
Quantifying phenotypes in single cells using droplet microfluidics.
Methods in cell biology
2018; 148: 133–59
This book chapter describes the use of droplet microfluidics to phenotype single cells. The basic process flow includes the encapsulation of single cells with a specific probe into aqueous micro-droplets suspended in a biocompatible oil. The probe is chosen to measure the phenotype of interest. After incubation, the encapsulated cell turns the probe fluorescent and renders the entire droplet fluorescent. Enumerating drops that are fluorescent quantifies the concentration of cells possessing the phenotype of interest. Examining the distribution of fluorescence further allows one to quantify the heterogeneity among the cell population.
View details for PubMedID 30473067
Internal flow inside droplets within a concentrated emulsion during droplet rearrangement
Physics of Fluids
View details for DOI 10.1063/1.5020313
Towards a droplet radiometric assay for single-cell analysis.
Radiotracers are widely used to track molecular processes, both in vitro and in vivo, with high sensitivity and specificity. However, most radionuclide detection methods have spatial resolution inadequate for single-cell analysis. A few existing methods can extract single-cell information from radioactive decays, but the stochastic nature of the process precludes high-throughput measurement (and sorting) of single cells. In this work, we introduce a new concept for translating radioactive decays occurring stochastically within radiolabeled single-cells into an integrated, long-lasting fluorescence signal. Single cells are encapsulated in radiofluorogenic droplets containing molecular probes sensitive to byproducts of ionizing radiation (primarily reactive oxygen species, or ROS). Different probes were examined in bulk solutions, and dihydrorhodamine 123 (DHRh 123) was selected as the lead candidate due to its sensitivity and reproducibility. Fluorescence intensity of DHRh 123 in bulk increased at a rate of 54% per Gy of X-ray radiation and 15% per MBq/ml of 2-deoxy-2-[18F]-fluoro-d-glucose ([18F]FDG). Fluorescence imaging of microfluidic droplets showed the same linear response, but droplets were less sensitive overall than the bulk ROS sensor (detection limit of 3 Gy per droplet). Finally, droplets encapsulating radiolabeled cancer cells allowed, for the first time, the detection of [18F]FDG radiotracer uptake in single cells through fluorescence activation. With further improvements, we expect this technology to enable quantitative measurement and selective sorting of single cells based on the uptake of radiolabeled small molecules.
View details for DOI 10.1021/acs.analchem.7b00414
View details for PubMedID 28562033
High-Efficiency and High-Throughput On-Chip Exchange of the Continuous Phase in Droplet Microfluidic Systems.
This article describes an integrated platform for the on-chip exchange of the continuous phase in droplet microfluidic systems. The drops used in this work are stabilized by amphiphilic nanoparticles. For some characterizations and applications of these nanoparticle-stabilized drops, including the measurement of adsorption dynamics of nanoparticles to the droplet surface, it is necessary to change the composition of the continuous phase from that used during the droplet generation process. Thus far, no work has reported the exchange of the continuous phase for a large number (>1 million) of drops in a microfluidic system. This article describes the design and characterization of a high-efficiency and high-throughput on-chip exchanger of the continuous phase in a continuous-flow droplet microfluidic system. The efficiency of exchange was higher than 97%. The throughput was greater than 1 million drops/min, and this can be increased further by increasing the number of parallel exchangers used. Because drops are injected into the exchanger in a continuous-flow manner, the method is directly compatible with automation to further increase its reliability and potential scale-up.
View details for DOI 10.1177/2472630317692558
View details for PubMedID 28402212
- Time-varying droplet configuration determines break-up probability of drops within a concentrated emulsion Applied Physics Letters 2017; 111: 124102
- Methods to coalesce fluorinated Pickering emulsions Analytical Methods 2017; 9: 4622-4629
- Encapsulation of Single Nanoparticle in Fast-Evaporating Micro-droplets Prevents Particle Agglomeration in Nanocomposites ACS Applied Materials & Interfaces 2017; 9 (31): 26602–26609
Amphiphilic nanoparticles suppress droplet break-up in a concentrated emulsion flowing through a narrow constriction.
2017; 11 (3): 034117
This paper describes the break-up behavior of a concentrated emulsion comprising drops stabilized by amphiphilic silica nanoparticles flowing in a tapered microchannel. Such geometry is often used in serial droplet interrogation and sorting processes in droplet microfluidics applications. When exposed to high viscous stresses, drops can undergo break-up and compromise their physical integrity. As these drops are used as micro-reactors, such compromise leads to a loss in the accuracy of droplet-based assays. Here, we show droplet break-up is suppressed by replacing the fluoro-surfactant similar to the one commonly used in current droplet microfluidics applications with amphiphilic nanoparticles as droplet stabilizer. We identify parameters that influence the break-up of these drops and demonstrate that break-up probability increases with increasing capillary number and confinement, decreasing nanoparticle size, and is insensitive to viscosity ratio within the range tested. Practically, our results reveal two key advantages of nanoparticles with direct applications to droplet microfluidics. First, replacing surfactants with nanoparticles suppresses break-up and increases the throughput of the serial interrogation process to 3 times higher than that in surfactant system under similar flow conditions. Second, the insensitivity of break-up to droplet viscosity makes it possible to process samples having different composition and viscosities without having to change the channel and droplet geometry in order to maintain the same degree of break-up and corresponding assay accuracy.
View details for PubMedID 28652887
View details for PubMedCentralID PMC5466449
- Internal flow in droplets within a concentrated emulsion flowing in a microchannel PHYSICS OF FLUIDS 2016; 28 (11)
Confinement and viscosity ratio effect on droplet break-up in a concentrated emulsion flowing through a narrow constriction.
Lab on a chip
2016; 16 (16): 3058-3064
This paper describes the dimensionless groups that determine the break-up probability of droplets in a concentrated emulsion during its flow in a tapered microchannel consisting of a narrow constriction. Such channel geometry is commonly used in droplet microfluidics to investigate the content of droplets from a concentrated emulsion. In contrast to solid wells in multi-well plates, drops are metastable, and are prone to break-up which compromises the accuracy and the throughput of the assay. Unlike single drops, the break-up process in a concentrated emulsion is stochastic. Analysis of the behavior of a large number of drops (N > 5000) shows that the probability of break-up increases with applied flow rate, the size of the drops relative to the size of the constriction, and the viscosity ratio of the emulsion. This paper shows that the break-up probability collapses into a single curve when plotted as a function of the product of capillary number, viscosity ratio, and confinement factor defined as the un-deformed radius of the drop relative to the hydraulic radius of the constriction. Fundamentally, the results represent a critical step towards the understanding of the physics governing instability in concentrated emulsions. Practically, the results provide a direct guide for the rational design of microchannels and the choice of operation parameters to increase the throughput of the droplet interrogation step while preserving droplet integrity and assay accuracy.
View details for DOI 10.1039/c6lc00478d
View details for PubMedID 27194099
Low energy emulsion-based fermentation enabling accelerated methane mass transfer and growth of poly(3-hydroxybutyrate)-accumulating methanotrophs.
2016; 207: 302-307
Methane is a low-cost feedstock for the production of polyhydroxyalkanoate biopolymers, but methanotroph fermentations are limited by the low solubility of methane in water. To enhance mass transfer of methane to water, vigorous mixing or agitation is typically used, which inevitably increases power demand and operational costs. This work presents a method for accelerating methane mass transfer without agitation by growing methanotrophs in water-in-oil emulsions, where the oil has a higher solubility for methane than water does. In systems without agitation, the growth rate of methanotrophs in emulsions is five to six times that of methanotrophs in the medium-alone incubations. Within seven days, cells within the emulsions accumulate up to 67 times more P3HB than cells in the medium-alone incubations. This is achieved due to the increased interfacial area of the aqueous phase, and accelerated methane diffusion through the oil phase.
View details for DOI 10.1016/j.biortech.2016.02.029
View details for PubMedID 26896714
- Surface-functionalizable amphiphilic nanoparticles for pickering emulsions with designer fluid-fluid interfaces RSC ADVANCES 2016; 6 (46): 39926-39932
Fluorinated Pickering Emulsions with Nonadsorbing Interfaces for Droplet-based Enzymatic Assays
2015; 87 (15): 7938-7943
This work describes the use of fluorinated Pickering emulsions with nonadsorbing interfaces in droplet-based enzymatic assays. State-of-the-art droplet assays have relied on one type of surfactants consisting of perfluorinated polyether and polyethylene glycol (PFPE-PEG). These surfactants are known to have limitations including the tedious synthesis and interdrop molecular transport which leads to the cross-contamination of droplet contents. Previously we have shown that replacing surfactants with nanoparticles as droplet stabilizers mitigate interdrop transport of small molecules. The nonspecific adsorption of enzymes on nanoparticle surface, however, could cause structural changes in enzymes and consequently the loss of enzymatic activity. To overcome such challenge, we render nanoparticle surface nonadsorbing to enzymes by in situ adsorption of polyethylene glycol (PEG) on particle surfaces. We show that enzyme activities are preserved in droplets stabilized by PEG-adsorbed nanoparticles, and are comparable with those in drops stabilized by PFPE-PEG surfactants. In addition, our nonadsorbing Pickering emulsions successfully prevent interdrop molecular transport, thereby maintaining the accuracy of droplet assays. The particles are also simple and economical to synthesize. The PEG-adsorbed nanoparticles described in this work are thus a competitive alternative to the current surfactant system, and can potentially enable new droplet-based biochemical assays.
View details for DOI 10.1021/acs.analchem.5b01753
View details for Web of Science ID 000359277900062
View details for PubMedID 26153615
- Actuating Fluid-Fluid Interfaces for the Reconfiguration of Light IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS 2015; 21 (4)
Quantitative detection of cells expressing BlaC using droplet-based microfluidics for use in the diagnosis of tuberculosis.
2015; 9 (4): 044120-?
This paper describes a method for the quantitative detection of cells expressing BlaC, a β-lactamase naturally expressed by Mycobacterium tuberculosis, intended for the diagnosis of tuberculosis. The method is based on the compartmentalization of bacteria in picoliter droplets at limiting dilutions such that each drop contains one or no cells. The co-encapsulation of a fluorogenic substrate probe for BlaC allows the quantification of bacteria by enumerating the number of fluorescent drops. Quantification of 10 colony forming units per milliliter is demonstrated. Furthermore, the encapsulation of single cell in drops maintains the specificity of the detection scheme even when the concentration of bacteria that do not express BlaC exceeds that expressing BlaC by one million-fold.
View details for DOI 10.1063/1.4928879
View details for PubMedID 26339319
View details for PubMedCentralID PMC4545073
- Quantitative detection of cells expressing BlaC using droplet-based microfluidics for use in the diagnosis of tuberculosis BIOMICROFLUIDICS 2015; 9 (4)
Optofluidic ultrahigh-throughput detection of fluorescent drops.
Lab on a chip
2015; 15 (6): 1417-1423
This paper describes an optofluidic droplet interrogation device capable of counting fluorescent drops at a throughput of 254 000 drops per second. To our knowledge, this rate is the highest interrogation rate published thus far. Our device consists of 16 parallel microfluidic channels bonded directly to a filter-coated two-dimensional Complementary Metal-Oxide-Semiconductor (CMOS) sensor array. Fluorescence signals emitted from the drops are collected by the sensor that forms the bottom of the channel. The proximity of the drops to the sensor facilitates efficient collection of fluorescence emission from the drops, and overcomes the trade-off between light collection efficiency and field of view in conventional microscopy. The interrogation rate of our device is currently limited by the acquisition speed of CMOS sensor, and is expected to increase further as high-speed sensors become increasingly available.
View details for DOI 10.1039/c4lc01465k
View details for PubMedID 25588522
Fluorinated Pickering Emulsions Impede Interfacial Transport and Form Rigid Interface for the Growth of Anchorage-Dependent Cells
ACS APPLIED MATERIALS & INTERFACES
2014; 6 (23): 21446-21453
This study describes the design and synthesis of amphiphilic silica nanoparticles for the stabilization of aqueous drops in fluorinated oils for applications in droplet microfluidics. The success of droplet microfluidics has thus far relied on one type of surfactant for the stabilization of drops. However, surfactants are known to have two key limitations: (1) interdrop molecular transport leads to cross-contamination of droplet contents, and (2) the incompatibility with the growth of adherent mammalian cells as the liquid-liquid interface is too soft for cell adhesion. The use of nanoparticles as emulsifiers overcomes these two limitations. Particles are effective in mitigating undesirable interdrop molecular transport as they are irreversibly adsorbed to the liquid-liquid interface. They do not form micelles as surfactants do, and thus, a major pathway for interdrop transport is eliminated. In addition, particles at the droplet interface provide a rigid solid-like interface to which cells could adhere and spread, and are thus compatible with the proliferation of adherent mammalian cells such as fibroblasts and breast cancer cells. The particles described in this work can enable new applications for high-fidelity assays and for the culture of anchorage-dependent cells in droplet microfluidics, and they have the potential to become a competitive alternative to current surfactant systems for the stabilization of drops critical for the success of the technology.
View details for DOI 10.1021/am506443e
View details for Web of Science ID 000346326600103
View details for PubMedID 25347285
Time capsule: an autonomous sensor and recorder based on diffusion-reaction.
Lab on a chip
2014; 14 (22): 4324-4328
We describe the use of chemical diffusion and reaction to record temporally varying chemical information as spatial patterns without the need for external power. Diffusion of chemicals acts as a clock, while reactions forming immobile products possessing defined optical properties perform sensing and recording functions simultaneously. The spatial location of the products reflects the history of exposure to the detected substances of interest. We refer to our device as a time capsule and show an initial proof of principle in the autonomous detection of lead ions in water.
View details for DOI 10.1039/c4lc00640b
View details for PubMedID 25190188
- Review and analysis of performance metrics of droplet microfluidics systems MICROFLUIDICS AND NANOFLUIDICS 2014; 16 (5): 921-939
Prospective identification of parasitic sequences in phage display screens.
Nucleic acids research
2014; 42 (3): 1784-1798
Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 10(9) random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the 'parasites'), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 'parasites'. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ∼10(6) diverse clones prevents the biased selection of parasitic clones.
View details for DOI 10.1093/nar/gkt1104
View details for PubMedID 24217917
View details for PubMedCentralID PMC3919620
- Break-up of droplets in a concentrated emulsion flowing through a narrow constriction SOFT MATTER 2014; 10 (3): 421-430
Filter-based assay for Escherichia coli in aqueous samples using bacteriophage-based amplification.
2013; 85 (15): 7213-7220
This paper describes a method to detect the presence of bacteria in aqueous samples, based on the capture of bacteria on a syringe filter, and the infection of targeted bacterial species with a bacteriophage (phage). The use of phage as a reagent provides two opportunities for signal amplification: (i) the replication of phage inside a live bacterial host and (ii) the delivery and expression of the complementing gene that turns on enzymatic activity and produces a colored or fluorescent product. Here we demonstrate a phage-based amplification scheme with an M13KE phage that delivers a small peptide motif to an F(+), α-complementing strain of Escherichia coli K12, which expresses the ω-domain of β-galactosidase (β-gal). The result of this complementation-an active form of β-gal-was detected colorimetrically, and the high level of expression of the ω-domain of β-gal in the model K12 strains allowed us to detect, on average, five colony-forming units (CFUs) of this strain in 1 L of water with an overnight culture-based assay. We also detected 50 CFUs of the model K12 strain in 1 L of water (or 10 mL of orange juice, or 10 mL of skim milk) in less than 4 h with a solution-based assay with visual readout. The solution-based assay does not require specialized equipment or access to a laboratory, and is more rapid than existing tests that are suitable for use at the point of access. This method could potentially be extended to detect many different bacteria with bacteriophages that deliver genes encoding a full-length enzyme that is not natively expressed in the target bacteria.
View details for DOI 10.1021/ac400961b
View details for PubMedID 23848541
Prospective identification of parasitic sequences in phage-display screens
Nucleic Acids Research
View details for DOI 10.1093/nar/gkt1104, 2013.
- Single particle detection in CMOS compatible photonic crystal nanobeam cavities Optics Express 2013; 21: 32225-32233
Uniform amplification of phage display libraries in monodisperse emulsions
2012; 58 (1): 18-27
In this paper, we describe a complete experimental setup for the uniform amplification of libraries of phage. Uniform amplification, which multiplies every phage clone by the same amount irrespective of the growth rate of the clone is essential for phage-display screening. Amplification of phage libraries in a common solution is often non-uniform: it favors fast-growing clones and eliminates those that grow slower. This competition leads to elimination of many useful binding clones, and it is a major barrier to identification of ligands for targets with multiple binding sites such as cells, tissues, or mixtures of proteins. Uniform amplification is achieved by encapsulating individual phage clones into isolated compartments (droplets) of identical volume. Each droplet contains culture medium and an excess of host (Escherichia coli). Here, we describe microfluidics devices that generate mono-disperse droplet-based compartments, and optimal conditions for amplification of libraries of different size. We also describe the detailed synthesis of a perfluoro surfactant, which gives droplets exceptional stability. Droplets stabilized by this compound do not coalesce after many hours in shaking culture. We identified a commercially available compound (Krytox), which destabilizes these droplets to recover the amplified libraries. Overall, uniform amplification is a sequence of three simple steps: (1) encapsulation of mixture of phage and bacteria in droplets using microfluidics; (2) incubation of droplets in a shaking culture; (3) destabilization of droplets to harvest the amplified phage. We anticipate that this procedure can be easily adapted in any academic or industrial laboratory that uses phage display.
View details for DOI 10.1016/j.ymeth.2012.07.012
View details for Web of Science ID 000311526000004
View details for PubMedID 22819853
- Characterization of sensitivity and specificity in leaky droplet-based assays LAB ON A CHIP 2012; 12 (23): 5093-5103
High-Q, Low Index-Contrast Polymeric Photonic Crystal Nanobeam Cavities
Conference on Lasers and Electro-Optics (CLEO)
View details for Web of Science ID 000310362402402
High-Q, low index-contrast polymeric photonic crystal nanobeam cavities
2011; 19 (22): 22191-22197
We present the design, fabrication and characterization of high-Q (Q=36,000) polymeric photonic crystal nanobeam cavities made of two polymers that have an ultra-low index contrast (ratio=1.15) and observed thermo-optical bistability at hundred microwatt power level. Due to the extended evanescent field and small mode volumes, polymeric nanobeam cavities are ideal platform for ultra-sensitive biochemical sensing. We demonstrate that these sensors have figures of merit (FOM=9190) two orders of magnitude greater than surface plasmon resonance based sensors, and outperform the commercial Biacore(TM) sensors. The demonstration of high-Q cavity in low-index-contrast polymers can open up versatile applications using a broad range of functional and flexible polymeric materials.
View details for Web of Science ID 000296568100099
View details for PubMedID 22109061
Bioinspired self-repairing slippery surfaces with pressure-stable omniphobicity
2011; 477 (7365): 443-447
Creating a robust synthetic surface that repels various liquids would have broad technological implications for areas ranging from biomedical devices and fuel transport to architecture but has proved extremely challenging. Inspirations from natural nonwetting structures, particularly the leaves of the lotus, have led to the development of liquid-repellent microtextured surfaces that rely on the formation of a stable air-liquid interface. Despite over a decade of intense research, these surfaces are, however, still plagued with problems that restrict their practical applications: limited oleophobicity with high contact angle hysteresis, failure under pressure and upon physical damage, inability to self-heal and high production cost. To address these challenges, here we report a strategy to create self-healing, slippery liquid-infused porous surface(s) (SLIPS) with exceptional liquid- and ice-repellency, pressure stability and enhanced optical transparency. Our approach-inspired by Nepenthes pitcher plants-is conceptually different from the lotus effect, because we use nano/microstructured substrates to lock in place the infused lubricating fluid. We define the requirements for which the lubricant forms a stable, defect-free and inert 'slippery' interface. This surface outperforms its natural counterparts and state-of-the-art synthetic liquid-repellent surfaces in its capability to repel various simple and complex liquids (water, hydrocarbons, crude oil and blood), maintain low contact angle hysteresis (<2.5°), quickly restore liquid-repellency after physical damage (within 0.1-1 s), resist ice adhesion, and function at high pressures (up to about 680 atm). We show that these properties are insensitive to the precise geometry of the underlying substrate, making our approach applicable to various inexpensive, low-surface-energy structured materials (such as porous Teflon membrane). We envision that these slippery surfaces will be useful in fluid handling and transportation, optical sensing, medicine, and as self-cleaning and anti-fouling materials operating in extreme environments.
View details for DOI 10.1038/nature10447
View details for Web of Science ID 000295080500036
View details for PubMedID 21938066
Denaturation of Proteins by SDS and Tetraalkylammonium Dodecyl Sulfates
2011; 27 (18): 11560-11574
This article describes the use of capillary electrophoresis (CE) to examine the influence of different cations (C(+); C(+) = Na(+) and tetra-n-alkylammonium, NR(4)(+), where R = Me, Et, Pr, and Bu) on the rates of denaturation of bovine carbonic anhydrase II (BCA) in the presence of anionic surfactant dodecylsulfate (DS(-)). An analysis of the denaturation of BCA in solutions of Na(+)DS(-) and NR(4)(+)DS(-) (in Tris-Gly buffer) indicated that the rates of formation of complexes of denatured BCA with DS(-) (BCA(D)-DS(-)(n,sat)) are indistinguishable and independent of the cation below the critical micellar concentration (cmc) and independent of the total concentration of DS(-) above the cmc. At concentrations of C(+)DS(-) above the cmc, BCA denatured at rates that depended on the cation; the rates decreased by a factor >10(4) in the order of Na(+) ≈ NMe(4)(+) > NEt(4)(+) > NPr(4)(+) > NBu(4)(+), which is the same order as the values of the cmc (which decrease from 4.0 mM for Na(+)DS(-) to 0.9 mM for NBu(4)(+)DS(-) in Tris-Gly buffer). The relationship between the cmc values and the rates of formation of BCA(D)-DS(-)(n,sat()) suggested that the kinetics of denaturation of BCA involve the association of this protein with monomeric DS(-) rather than with micelles of (C(+)DS(-))(n). A less-detailed survey of seven other proteins (α-lactalbumin, β-lactoglobulin A, β-lactoglobulin B, carboxypeptidase B, creatine phosphokinase, myoglobin, and ubiquitin) showed that the difference between Na(+)DS(-) and NR(4)(+)DS(-) observed with BCA was not general. Instead, the influence of NR(4)(+) on the association of DS(-) with these proteins depended on the protein. The selection of the cation contributed to the properties (including the composition, electrophoretic mobility, and partitioning behavior in aqueous two-phase systems) of aggregates of denatured protein and DS(-). These results suggest that the variation in the behavior of NR(4)(+)DS(-) with changes in R may be exploited in methods used to analyze and separate mixtures of proteins.
View details for DOI 10.1021/la201832d
View details for Web of Science ID 000294790500037
View details for PubMedID 21834533
- Reconfigurable Self-Assembly of Mesoscale Optical Components at a Liquid-Liquid Interface ADVANCED MATERIALS 2011; 23 (21): 2413-?
Multizone Paper Platform for 3D Cell Cultures
2011; 6 (5)
In vitro 3D culture is an important model for tissues in vivo. Cells in different locations of 3D tissues are physiologically different, because they are exposed to different concentrations of oxygen, nutrients, and signaling molecules, and to other environmental factors (temperature, mechanical stress, etc). The majority of high-throughput assays based on 3D cultures, however, can only detect the average behavior of cells in the whole 3D construct. Isolation of cells from specific regions of 3D cultures is possible, but relies on low-throughput techniques such as tissue sectioning and micromanipulation. Based on a procedure reported previously ("cells-in-gels-in-paper" or CiGiP), this paper describes a simple method for culture of arrays of thin planar sections of tissues, either alone or stacked to create more complex 3D tissue structures. This procedure starts with sheets of paper patterned with hydrophobic regions that form 96 hydrophilic zones. Serial spotting of cells suspended in extracellular matrix (ECM) gel onto the patterned paper creates an array of 200 micron-thick slabs of ECM gel (supported mechanically by cellulose fibers) containing cells. Stacking the sheets with zones aligned on top of one another assembles 96 3D multilayer constructs. De-stacking the layers of the 3D culture, by peeling apart the sheets of paper, "sections" all 96 cultures at once. It is, thus, simple to isolate 200-micron-thick cell-containing slabs from each 3D culture in the 96-zone array. Because the 3D cultures are assembled from multiple layers, the number of cells plated initially in each layer determines the spatial distribution of cells in the stacked 3D cultures. This capability made it possible to compare the growth of 3D tumor models of different spatial composition, and to examine the migration of cells in these structures.
View details for DOI 10.1371/journal.pone.0018940
View details for Web of Science ID 000290305600010
View details for PubMedID 21573103
Externally Applied Electric Fields up to 1.6 x 10(5) V/m Do Not Affect the Homogeneous Nucleation of Ice in Supercooled Water
JOURNAL OF PHYSICAL CHEMISTRY B
2011; 115 (5): 1089-1097
The freezing of water can initiate at electrically conducting electrodes kept at a high electric potential or at charged electrically insulating surfaces. The microscopic mechanisms of these phenomena are unknown, but they must involve interactions between water molecules and electric fields. This paper investigates the effect of uniform electric fields on the homogeneous nucleation of ice in supercooled water. Electric fields were applied across drops of water immersed in a perfluorinated liquid using a parallel-plate capacitor; the drops traveled in a microchannel and were supercooled until they froze due to the homogeneous nucleation of ice. The distribution of freezing temperatures of drops depended on the rate of nucleation of ice, and the sensitivity of measurements allowed detection of changes by a factor of 1.5 in the rate of nucleation. Sinusoidal alternation of the electric field at frequencies from 3 to 100 kHz prevented free ions present in water from screening the electric field in the bulk of drops. Uniform electric fields in water with amplitudes up to (1.6 ± 0.4) × 10(5) V/m neither enhanced nor suppressed the homogeneous nucleation of ice. Estimations based on thermodynamic models suggest that fields in the range of 10(7)-10(8) V/m might cause an observable increase in the rate of nucleation.
View details for DOI 10.1021/jp110437x
View details for Web of Science ID 000286797700038
View details for PubMedID 21174462
Diversity of Phage-Displayed Libraries of Peptides during Panning and Amplification
2011; 16 (2): 1776-1803
The amplification of phage-displayed libraries is an essential step in the selection of ligands from these libraries. The amplification of libraries, however, decreases their diversity and limits the number of binding clones that a screen can identify. While this decrease might not be a problem for screens against targets with a single binding site (e.g., proteins), it can severely hinder the identification of useful ligands for targets with multiple binding sites (e.g., cells). This review aims to characterize the loss in the diversity of libraries during amplification. Analysis of the peptide sequences obtained in several hundred screens of peptide libraries shows explicitly that there is a significant decrease in library diversity that occurs during the amplification of phage in bacteria. This loss during amplification is not unique to specific libraries: it is observed in many of the phage display systems we have surveyed. The loss in library diversity originates from competition among phage clones in a common pool of bacteria. Based on growth data from the literature and models of phage growth, we show that this competition originates from growth rate differences of only a few percent for different phage clones. We summarize the findings using a simple two-dimensional "phage phase diagram", which describes how the collapse of libraries, due to panning and amplification, leads to the identification of only a subset of the available ligands. This review also highlights techniques that allow elimination of amplification-induced losses of diversity, and how these techniques can be used to improve phage-display selection and enable the identification of novel ligands.
View details for DOI 10.3390/molecules16021776
View details for Web of Science ID 000287745400051
View details for PubMedID 21339712
Continuously tunable microdroplet-laser in a microfluidic channel
2011; 19 (3): 2204-2215
This paper describes the generation and optical characterization of a series of dye-doped droplet-based optical microcavities with continuously decreasing radius in a microfluidic channel. A flow-focusing nozzle generated the droplets (~21 μm in radius) using benzyl alcohol as the disperse phase and water as the continuous phase. As these drops moved down the channel, they dissolved, and their size decreased. The emission characteristics from the drops could be matched to the whispering gallery modes from spherical micro-cavities. The wavelength of emission from the drops changed from 700 to 620 nm as the radius of the drops decreased from 21 μm to 7 μm. This range of tunability in wavelengths was larger than that reported in previous work on droplet-based cavities.
View details for Web of Science ID 000286807100058
View details for PubMedID 21369038
Cytoplasmic self-organization of internal membranes, microtubule- and actin-cytoskeleton inside microfluidics generated droplets
Annual Meeting of the American-Society-for-Cell-Biology (ASCB)
AMER SOC CELL BIOLOGY. 2011
View details for Web of Science ID 000305505500248
- Slippery surfaces with omniphobicity, self-repair, high-pressure stability and optical transparency Nature 2011; 447: 443
Monte Carlo simulation of centrosomal self-centering due to pushing by microtubules in large cells.
Annual Meeting of the American-Society-for-Cell-Biology (ASCB)
AMER SOC CELL BIOLOGY. 2011
View details for Web of Science ID 000305505504158
Cofabrication: A Strategy for Building Multicomponent Microsystems
ACCOUNTS OF CHEMICAL RESEARCH
2010; 43 (4): 518-528
This Account describes a strategy for fabricating multicomponent microsystems in which the structures of essentially all of the components are formed in a single step of micromolding. This strategy, which we call "cofabrication", is an alternative to multilayer microfabrication, in which multiple layers of components are sequentially aligned ("registered") and deposited on a substrate by photolithography. Cofabrication has several characteristics that make it an especially useful approach for building multicomponent microsystems. It rapidly and inexpensively generates correctly aligned components (for example, wires, heaters, magnetic field generators, optical waveguides, and microfluidic channels) over very large surface areas. By avoiding registration, the technique does not impose on substrates the size limitations of common registrations tools, such as steppers and contact aligners. We have demonstrated multicomponent microsystems with surface areas exceeding 100 cm(2), but in principle, device size is only limited by the requirements of generating the original master. In addition, cofabrication can serve as a low-cost strategy for building microsystems. The technique is amenable to a variety of laboratory settings and uses fabrication tools that are less expensive than those used for multistep microfabrication. Moreover, the process requires only small amounts of solvent and photoresist, a costly chemical required for photolithography; in cofabrication, photoresist is applied and developed only once to produce a master, which is then used to produce multiple copies of molds containing the microfluidic channels. From a broad perspective, cofabrication represents a new processing paradigm in which the exterior (or shell) of the desired structures are produced before the interior (or core). This approach, generating the insulation or packaging structure first and injecting materials that provide function in channels in liquid phase, makes it possible to design and build microsystems with component materials that cannot be easily manipulated conventionally (such as solid materials with low melting points, liquid metals, liquid crystals, fused salts, foams, emulsions, gases, polymers, biomaterials, and fragile organics). Moreover, materials can be altered, removed, or replaced after the manufacturing stage. For example, cofabrication allows one to build devices in which a liquid flows through the device during use, or is replaced after use. Metal wires can be melted and reset by heating (in principle, repairing a break). This method leads to certain kinds of structures, such as integrated metallic wires with large cross-sectional areas or optical waveguides aligned in the same plane as microfluidic channels, that would be difficult or impossible to make with techniques such as sputter deposition or evaporation. This Account outlines the strategy of cofabrication and describes several applications. Specifically, we highlight cofabricated systems that combine microfluidics with (i) electrical wires for microheaters, electromagnets, and organic electrodes, (ii) fluidic optical components, such as optical waveguides, lenses, and light sources, (iii) gels for biological cell cultures, and (iv) droplets for compartmentalized chemical reactions, such as protein crystallization.
View details for DOI 10.1021/ar900178k
View details for Web of Science ID 000277006400004
View details for PubMedID 20088528
- Uniform Amplification of Phage with Different Growth Characteristics in Individual Compartments Consisting of Monodisperse Droplets ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2010; 49 (31): 5301-5304
Paper-supported 3D cell culture for tissue-based bioassays
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2009; 106 (44): 18457-18462
Fundamental investigations of human biology, and the development of therapeutics, commonly rely on 2D cell-culture systems that do not accurately recapitulate the structure, function, or physiology of living tissues. Systems for 3D cultures exist but do not replicate the spatial distributions of oxygen, metabolites, and signaling molecules found in tissues. Microfabrication can create architecturally complex scaffolds for 3D cell cultures that circumvent some of these limitations; unfortunately, these approaches require instrumentation not commonly available in biology laboratories. Here we report that stacking and destacking layers of paper impregnated with suspensions of cells in extracellular matrix hydrogel makes it possible to control oxygen and nutrient gradients in 3D and to analyze molecular and genetic responses. Stacking assembles the "tissue", whereas destacking disassembles it, and allows its analysis. Breast cancer cells cultured within stacks of layered paper recapitulate behaviors observed both in 3D tumor spheroids in vitro and in tumors in vivo: Proliferating cells in the stacks localize in an outer layer a few hundreds of microns thick, and growth-arrested, apoptotic, and necrotic cells concentrate in the hypoxic core where hypoxia-sensitive genes are overexpressed. Altering gas permeability at the ends of stacks controlled the gradient in the concentration of the O(2) and was sufficient by itself to determine the distribution of viable cells in 3D. Cell cultures in stacked, paper-supported gels offer a uniquely flexible approach to study cell responses to 3D molecular gradients and to mimic tissue- and organ-level functions.
View details for DOI 10.1073/pnas.0910666106
View details for Web of Science ID 000271429800011
View details for PubMedID 19846768
Independent Control of Drop Size and Velocity in Microfluidic Flow-Focusing Generators Using Variable Temperature and Flow Rate
2009; 81 (6): 2399-2402
This paper describes a method to control the volume and the velocity of drops generated in a flow-focusing device dynamically and independently. This method involves simultaneous tuning of the temperature of the nozzle of the device and of the flow rate of the continuous phase; the method requires a continuous phase liquid that has a viscosity that varies steeply with temperature. Increasing the temperature of the flow-focusing nozzle from 0 to 80 degrees C increased the volume of the drops by almost 2 orders of magnitude. Tuning both the temperature and the flow rate controlled the drop volume and the drop velocity independently; this feature is not possible in a basic flow-focusing device. This paper also demonstrates a procedure for identifying the range of possible drop volumes and drop velocities for a given flow-focusing device and shows how to generate drops with a specified volume and velocity within this range. This method is easy to implement in on-chip applications where thermal management is already incorporated in the system, such as DNA amplification using the polymerase chain reaction and nanoparticle synthesis.
View details for DOI 10.1021/ac8026542
View details for Web of Science ID 000264142000049
View details for PubMedID 19209912
A multi-color fast-switching microfluidic droplet dye laser
LAB ON A CHIP
2009; 9 (19): 2767-2771
We describe a multi-color microfluidic dye laser operating in whispering gallery mode based on a train of alternating droplets containing solutions of different dyes; this laser is capable of switching the wavelength of its emission between 580 nm and 680 nm at frequencies up to 3.6 kHz-the fastest among all dye lasers reported; it has potential applications in on-chip spectroscopy and flow cytometry.
View details for DOI 10.1039/b914066b
View details for Web of Science ID 000269799800004
View details for PubMedID 19967111
- Basic Microfluidic and Soft Lithographic Techniques Optofluidics: Fundamentals, Devices, and Applications McGraw-Hill. 2009
- Optical Components Based on Dynamic Liquid-liquid Interfaces Optofluidics: Fundamentals, Devices, and Applications McGraw-Hill. 2009
Dynamically reconfigurable liquid-core liquid-cladding lens in a microfluidic channel
LAB ON A CHIP
2008; 8 (3): 395-401
This paper describes the design and operation of a liquid-core liquid-cladding (L(2)) lens formed by the laminar flow of three streams of liquids in a microchannel whose width expands laterally in the region where the lens forms. Two streams of liquid with a lower refractive index (the cladding) sandwich a stream of liquid with a higher refractive index (the core). As the core stream enters the expansion chamber, it widens and becomes biconvex in shape, for some rates of flow. This biconvex fluidic element focuses light. Manipulating the relative rates of flow of the streams reconfigures the shape, and therefore the focal distance, of the L(2) lens. This paper also describes a technique for beam tracing, and for characterization of a lens in an enclosed micro-scale optical system. The use of a cladding liquid with refractive index matched to that of the material used in the fabrication of the microfluidic system (here, poly(dimethylsiloxane)) improves the quality of the focused beam.
View details for DOI 10.1039/b717037h
View details for Web of Science ID 000254424300005
View details for PubMedID 18305856
- Optical waveguiding using thermal gradients across homogeneous liquids in microfluidic channels APPLIED PHYSICS LETTERS 2006; 88 (6)