Eugenia Kumacheva

Publications of Eugenia Kumacheva

• Digital microfluidic hydrogel microreactors for proteomics.

  Authors: Vivienne N Luk, Lindsey K Fiddes, Victoria M Luk, Eugenia Kumacheva, Aaron R Wheeler

  Proteomics. 05/2012; 12(9):1310-8.

  Proteolytic digestion is an essential step in proteomic sample processing. While this step has traditionally been implemented in homogeneous (solution) format, there is a growing trend to useProteolytic digestion is an essential step in proteomic sample processing. While this step has traditionally been implemented in homogeneous (solution) format, there is a growing trend to use heterogeneous systems in which the enzyme is immobilized on hydrogels or other solid supports. Here, we introduce the use of immobilized enzymes in hydrogels for proteomic sample processing in digital microfluidic (DMF) systems. In this technique, preformed cylindrical agarose discs bearing immobilized trypsin or pepsin were integrated into DMF devices. A fluorogenic assay was used to optimize the covalent modification procedure for enzymatic digestion efficiency, with maximum efficiency observed at 31 μg trypsin in 2-mm diameter agarose gel discs. Gel discs prepared in this manner were used in an integrated method in which proteomic samples were sequentially reduced, alkylated, and digested, with all sample and reagent handling controlled by DMF droplet operation. Mass spectrometry analysis of the products revealed that digestion using the trypsin gel discs resulted in higher sequence coverage in model analytes relative to conventional homogenous processing. Proof-of-principle was demonstrated for a parallel digestion system in which a single sample was simultaneously digested on multiple gel discs bearing different enzymes. We propose that these methods represent a useful new tool for the growing trend toward miniaturization and automation in proteomic sample processing.

• Microfluidic Encapsulation of Cells in Polymer Microgels.

  Authors: Diego Velasco, Ethan Tumarkin, Eugenia Kumacheva

  Small (Weinheim an der Bergstrasse, Germany). 03/2012;

  In this Concept article, recent advances in microfluidic platforms for the generation of cell-laden hydrogel particles (microgels) are reported. Advances in the continuous microfluidic encapsulationIn this Concept article, recent advances in microfluidic platforms for the generation of cell-laden hydrogel particles (microgels) are reported. Advances in the continuous microfluidic encapsulation of cells in droplets and microgels are critically reviewed, and currently used methods for the encapsulation of cells in polymer microgels are discussed. An outlook on current applications and future directions in this field of research are also presented. This article will be of interest to chemists, materials scientists, cell biologists, bioengineers, and pharmacologists.

• Automated microfluidic platform for studies of carbon dioxide dissolution and solubility in physical solvents.

  Authors: Milad Abolhasani, Mayank Singh, Eugenia Kumacheva, Axel Günther

  Lab on a chip. 03/2012; 12(9):1611-8.

  We present an automated microfluidic (MF) approach for the systematic and rapid investigation of carbon dioxide (CO(2)) mass transfer and solubility in physical solvents. Uniformly sized bubbles ofWe present an automated microfluidic (MF) approach for the systematic and rapid investigation of carbon dioxide (CO(2)) mass transfer and solubility in physical solvents. Uniformly sized bubbles of CO(2) with lengths exceeding the width of the microchannel (plugs) were isothermally generated in a co-flowing physical solvent within a gas-impermeable, silicon-based MF platform that is compatible with a wide range of solvents, temperatures and pressures. We dynamically determined the volume reduction of the plugs from images that were accommodated within a single field of view, six different downstream locations of the microchannel at any given flow condition. Evaluating plug sizes in real time allowed our automated strategy to suitably select inlet pressures and solvent flow rates such that otherwise dynamically self-selecting parameters (e.g., the plug size, the solvent segment size, and the plug velocity) could be either kept constant or systematically altered. Specifically, if a constant slug length was imposed, the volumetric dissolution rate of CO(2) could be deduced from the measured rate of plug shrinkage. The solubility of CO(2) in the physical solvent was obtained from a comparison between the terminal and the initial plug sizes. Solubility data were acquired every 5 min and were within 2-5% accuracy as compared to literature data. A parameter space consisting of the plug length, solvent slug length and plug velocity at the microchannel inlet was established for different CO(2)-solvent pairs with high and low gas solubilities. In a case study, we selected the gas-liquid pair CO(2)-dimethyl carbonate (DMC) and volumetric mass transfer coefficients 4-30 s(-1) (translating into mass transfer times between 0.25 s and 0.03 s), and Henry's constants, within the range of 6-12 MPa.

• Standing arrays of gold nanorods end-tethered with polymer ligands.

  Authors: Alla Petukhova, Jesse Greener, Kun Liu, Dmytro Nykypanchuk, Renaud Nicolaÿ, Krzysztof Matyjaszewski, Eugenia Kumacheva

  Small (Weinheim an der Bergstrasse, Germany). 03/2012; 8(5):731-7.

  Nanomaterials with vectoral electromagnetic properties have potential applications in solar cells, plasmonic cavity resonators, light polarizers, and biosensing. Here a new, simple, solution-basedNanomaterials with vectoral electromagnetic properties have potential applications in solar cells, plasmonic cavity resonators, light polarizers, and biosensing. Here a new, simple, solution-based method for producing nanomaterials comprising vertically aligned standing arrays of gold nanorods (NRs) end-functionalized with polymer ligands is reported. The method utilizes the side-by-side assembly of the NRs into large 2D superlattices, followed by the precipitation of the lattices on a solid substrate. The critical design rules for the self-assembly of superlattices are demonstrated, and they show the generality of the method by forming standing arrays from the NRs end-tethered with poly(N-vinylcarbazole) or with polystyrene molecules.

• Education: a microfluidic platform for university-level analytical chemistry laboratories.

  Authors: Jesse Greener, Ethan Tumarkin, Michael Debono, Andrew P Dicks, Eugenia Kumacheva

  Lab on a chip. 02/2012; 12(4):696-701.

  We demonstrate continuous flow acid-base titration reactions as an educational microfluidic platform for undergraduate and graduate analytical chemistry courses. A series of equations were developedWe demonstrate continuous flow acid-base titration reactions as an educational microfluidic platform for undergraduate and graduate analytical chemistry courses. A series of equations were developed for controlling and predicting the results of acid-base neutralisation reactions conducted in a microfluidic format, including the combinations of (i) a strong base and a strong acid, (ii) a strong base and a weak acid, and (iii) a strong base and a multiprotic acid. Microfluidic titrations yielded excellent repeatability. The small experimental footprint is advantageous in crowded teaching laboratories, and it offers limited waste and exposure to potentially hazardous acids and bases. This platform will help promote the utilisation of microfluidics at an earlier stage of students' careers.

• Examining metal nanoparticle surface chemistry using hollow-core, photonic-crystal, fiber-assisted SERS.

  Authors: Fatemeh Eftekhari, Anna Lee, Eugenia Kumacheva, Amr S Helmy

  Optics letters. 02/2012; 37(4):680-2.

  In this Letter, we demonstrate the efficacy of hollow core photonic crystal fibers (HCPCFs) as a surface-enhanced Raman spectroscopy (SERS) platform for investigating the ligand exchange process onIn this Letter, we demonstrate the efficacy of hollow core photonic crystal fibers (HCPCFs) as a surface-enhanced Raman spectroscopy (SERS) platform for investigating the ligand exchange process on the surface of gold nanoparticles. Raman measurements carried out using this platform show the capability to monitor minute amounts of surface ligands on gold nanoparticles used as an SERS substrate. The SERS signal from an HCPCF exhibits a tenfold enhancement compared to that in a direct sampling scheme using a cuvette. Using exchange of cytotoxic cetyltrimethylammonium bromide with α-methoxy-ω-mercaptopoly(ethylene glycol) on the surface of gold nanorods as an exemplary system, we show the feasibility of using HCPCF SERS to monitor the change in surface chemistry of nanoparticles.

• Temperature mediated generation of armoured bubbles.

  Authors: Ethan Tumarkin, Jai Il Park, Zhihong Nie, Eugenia Kumacheva

  Chemical communications (Cambridge, England). 12/2011; 47(47):12712-4.

  This communication describes a novel strategy for the continuous microfluidic generation of highly monodispersed particle-coated microbubbles using temperature-dependent dissolution of carbon dioxide.

• Microfluidic study of fast gas-liquid reactions.

  Authors: Wei Li, Kun Liu, Ryan Simms, Jesse Greener, Dinesh Jagadeesan, Sascha Pinto, Axel Günther, Eugenia Kumacheva

  Journal of the American Chemical Society. 12/2011; 134(6):3127-32.

  We present a new concept for studies of the kinetics of fast gas-liquid reactions. The strategy relies on the microfluidic generation of highly monodisperse gas bubbles in the liquid reaction mediumWe present a new concept for studies of the kinetics of fast gas-liquid reactions. The strategy relies on the microfluidic generation of highly monodisperse gas bubbles in the liquid reaction medium and subsequent analysis of time-dependent changes in bubble dimensions. Using reactions of CO(2) with secondary amines as an exemplary system, we demonstrate that the method enables rapid determination of reaction rate constant and conversion, and comparison of various binding agents. The proposed approach addresses two challenges in studies of gas-liquid reactions: a mass-transfer limitation and a poorly defined gas-liquid interface. The proposed strategy offers new possibilities in studies of the fundamental aspects of rapid multiphase reactions, and can be combined with throughput optimization of reaction conditions.

• Development and applications of a microfluidic reactor with multiple analytical probes.

  Authors: Jesse Greener, Ethan Tumarkin, Michael Debono, Chi-Hang Kwan, Milad Abolhasani, Axel Guenther, Eugenia Kumacheva

  The Analyst. 11/2011; 137(2):444-50.

  We report the development of a versatile microfluidic (MF) reactor with multiple analytical probes, which can be used for (i) quantitative characterisation of molecular vibrational signatures ofWe report the development of a versatile microfluidic (MF) reactor with multiple analytical probes, which can be used for (i) quantitative characterisation of molecular vibrational signatures of reactants or products, (ii) the localised real-time monitoring of temperature and (iii) site-specific measurements of pH of the reaction system. The analytical probes utilised for in situ reaction analysis include an ATR-FTIR probe, a temperature probe, and a pH probe. We demonstrate the applications of the MF reactor with integrated probes for the parallel monitoring of multiple variables in acid/base neutralisation reaction, of changes in buffer pH, temperature, and vibrational absorption bands, and for monitoring the kinetics of the reaction between CO(2) and a buffer system with therapeutic applications.

• Temperature-controlled 'breathing' of carbon dioxide bubbles.

  Authors: Ethan Tumarkin, Zhihong Nie, Jai Il Park, Milad Abolhasani, Jesse Greener, Barbara Sherwood-Lollar, Axel Günther, Eugenia Kumacheva

  Lab on a chip. 08/2011; 11(20):3545-50.

  We report a microfluidic (MF) approach to studies of temperature mediated carbon dioxide (CO(2)) transfer between the gas and the liquid phases. Micrometre-diameter CO(2) bubbles with a narrow sizeWe report a microfluidic (MF) approach to studies of temperature mediated carbon dioxide (CO(2)) transfer between the gas and the liquid phases. Micrometre-diameter CO(2) bubbles with a narrow size distribution were generated in an aqueous or organic liquid and subsequently were subjected to temperature changes in the downstream channel. In response to the cooling-heating-cooling cycle the bubbles underwent corresponding contraction-expansion-contraction transitions, which we term 'bubble breathing'. We examined temperature-controlled dissolution of CO(2) in four exemplary liquid systems: deionized water, a 0.7 M aqueous solution of NaCl, ocean water extracted from Bermuda coastal waters, and dimethyl ether of poly(ethylene glycol), a solvent used in industry for absorption of CO(2). The MF approach can be extended to studies of other gases with a distinct, temperature-dependent solubility in liquids.

• High-throughput combinatorial cell co-culture using microfluidics.

  Authors: Ethan Tumarkin, Lsan Tzadu, Elizabeth Csaszar, Minseok Seo, Hong Zhang, Anna Lee, Raheem Peerani, Kelly Purpura, Peter W Zandstra, Eugenia Kumacheva

  Integrative biology : quantitative biosciences from nano to macro. 06/2011; 3(6):653-62.

  Co-culture strategies are foundational in cell biology. These systems, which serve as mimics of in vivo tissue niches, are typically poorly defined in terms of cell ratios, local cues and supportiveCo-culture strategies are foundational in cell biology. These systems, which serve as mimics of in vivo tissue niches, are typically poorly defined in terms of cell ratios, local cues and supportive cell-cell interactions. In the stem cell niche, the ability to screen cell-cell interactions and identify local supportive microenvironments has a broad range of applications in transplantation, tissue engineering and wound healing. We present a microfluidic platform for the high-throughput generation of hydrogel microbeads for cell co-culture. Encapsulation of different cell populations in microgels was achieved by introducing in a microfluidic device two streams of distinct cell suspensions, emulsifying the mixed suspension, and gelling the precursor droplets. The cellular composition in the microgels was controlled by varying the volumetric flow rates of the corresponding streams. We demonstrate one of the applications of the microfluidic method by co-encapsulating factor-dependent and responsive blood progenitor cell lines (MBA2 and M07e cells, respectively) at varying ratios, and show that in-bead paracrine secretion can modulate the viability of the factor dependent cells. Furthermore, we show the application of the method as a tool to screen the impact of specific growth factors on a primary human heterogeneous cell population. Co-encapsulation of IL-3 secreting MBA2 cells with umbilical cord blood cells revealed differential sub-population responsiveness to paracrine signals (CD14+ cells were particularly responsive to locally delivered IL-3). This microfluidic co-culture platform should enable high throughput screening of cell co-culture conditions, leading to new strategies to manipulate cell fate.

• Probing dynamic generation of hot-spots in self-assembled chains of gold nanorods by surface-enhanced Raman scattering.

  Authors: Anna Lee, Gustavo F S Andrade, Aftab Ahmed, Michele L Souza, Neil Coombs, Ethan Tumarkin, Kun Liu, Reuven Gordon, Alexandre G Brolo, Eugenia Kumacheva

  Journal of the American Chemical Society. 05/2011; 133(19):7563-70.

  Further progress in the applications of self-assembled nanostructures critically depends on developing a fundamental understanding of the relation between the properties of nanoparticle ensembles andFurther progress in the applications of self-assembled nanostructures critically depends on developing a fundamental understanding of the relation between the properties of nanoparticle ensembles and their time-dependent structural characteristics. Following dynamic generation of hot-spots in the self-assembled chains of gold nanorods, we established a direct correlation between ensemble-averaged surface-enhanced Raman scattering and extinction properties of the chains. Experimental results were supported with comprehensive finite-difference time-domain simulations. The established relationship between the structure of nanorod ensembles and their optical properties provides the basis for creating dynamic, solution-based, plasmonic platforms that can be utilized in applications ranging from sensing to nanoelectronics.

• Self-assembly of single-tip metal-semiconductor nanorods in selective solvents.

  Authors: Nana Zhao, Jemma Vickery, Gerald Guerin, Jai Il Park, Mitchell A Winnik, Eugenia Kumacheva

  Angewandte Chemie (International ed. in English). 05/2011; 50(20):4606-10.

• Microgels for the encapsulation and stimulus-responsive release of molecules with distinct polarities.

  Authors: Dinesh Jagadeesan, Irina Nasimova, Ilya Gourevich, Sergey Starodubtsev, Eugenia Kumacheva

  Macromolecular bioscience. 04/2011; 11(7):889-96.

  A microfluidic strategy for the encapsulation and stimulus-responsive release of molecules with distinct polarities from the interior of microgels is reported. The approach relies on (i) theA microfluidic strategy for the encapsulation and stimulus-responsive release of molecules with distinct polarities from the interior of microgels is reported. The approach relies on (i) the generation of a primary O/W emulsion by the ultrasonication method, (ii) MF emulsification of the primary emulsion, and (iii) photopolymerization of the monomer present in the aqueous phase of the droplets, thereby transforming them into microgels. Non-polar molecules are dissolved in oil droplets embedded in the microgels. Polar molecules are physically associated with the hydrogel network. Upon heating, the microgels contract and release polar and non-polar cargo molecules. The approach paves the way for stimuli-responsive vehicles for multiple drug delivery.

• Self-assembly of inorganic nanorods.

  Authors: Kun Liu, Nana Zhao, Eugenia Kumacheva

  Chemical Society reviews. 02/2011; 40(2):656-71.

  Generation of nanostructures containing from several to thousands of inorganic nanorods (NRs) organized in a highly ordered manner paves the way for applications that exploit directional propertiesGeneration of nanostructures containing from several to thousands of inorganic nanorods (NRs) organized in a highly ordered manner paves the way for applications that exploit directional properties of NR arrays. Self-assembly of NRs provides a simple and cost-efficient strategy for producing NR ensembles. This tutorial review highlights recent advances in the field of NR synthesis, summarizes the types of ligands used for NR synthesis and stabilization, reviews experimental and theoretical work on NR self-assembly that is driven by interactions between the ligands and describes current properties and applications of self-assembled NR structures.

• High-throughput generation of hydrogel microbeads with varying elasticity for cell encapsulation.

  Authors: Alexander Kumachev, Jesse Greener, Ethan Tumarkin, Erika Eiser, Peter W Zandstra, Eugenia Kumacheva

  Biomaterials. 02/2011; 32(6):1477-83.

  Elasticity of cellular microenvironments strongly influences cell motility, phagocytosis, growth and differentiation. Currently, the relationship between the cell behaviour and matrix stiffness isElasticity of cellular microenvironments strongly influences cell motility, phagocytosis, growth and differentiation. Currently, the relationship between the cell behaviour and matrix stiffness is being studied for cells seeded on planar substrates, however in three-dimensional (3D) microenvironments cells may experience mechanical signalling that is distinct from that on a two-dimensional matrix. We report a microfluidic approach for high-throughput generation of 3D microenvironments with different elasticity for studies of cell fate. The generation of agarose microgels with different elastic moduli was achieved by (i) introducing into a microfluidic droplet generator two streams of agarose solutions, one with a high concentration of agarose and the other one with a low concentration of agarose, at varying relative volumetric flow rate ratios of the two streams, and (ii) on-chip gelation of the precursor droplets. At 37 degreesC, the method enabled a approximately 35-fold variation of the shear elastic modulus of the agarose gels. The application of the method was demonstrated by encapsulating two mouse embryonic stem cell lines within the agarose microgels. This work establishes a foundation for the high-throughput generation of combinatorial microenvironments with different mechanical properties for cell studies.

• Microbubbles loaded with nanoparticles: a route to multiple imaging modalities.

  Authors: Jai Il Park, Dinesh Jagadeesan, Ross Williams, Wendy Oakden, Siyon Chung, Greg J Stanisz, Eugenia Kumacheva

  ACS nano. 10/2010; 4(11):6579-86.

  We report a single-step approach to producing small and stable bubbles functionalized with nanoparticles. The strategy includes the following events occurring in sequence: (i) a microfluidicWe report a single-step approach to producing small and stable bubbles functionalized with nanoparticles. The strategy includes the following events occurring in sequence: (i) a microfluidic generation of bubbles from a mixture of CO(2) and a minute amount of gases with low solubility in water, in an aqueous solution of a protein, a polysaccharide, and anionic nanoparticles; (ii) rapid dissolution of CO(2) leading to the shrinkage of bubbles and an increase in acidity of the medium in the vicinity of the bubbles; and (iii) co-deposition of the biopolymers and nanoparticles at the bubble-liquid interface. The proposed approach yielded microbubbles with a narrow size distribution, long-term stability, and multiple functions originating from the attachment of metal oxide, metal, or semiconductor nanoparticles onto the bubble surface. We show the potential applications of these bubbles in ultrasound and magnetic resonance imaging.

• A study of polymerization-induced phase separation as a route to produce porous polymer-metal materials.

  Authors: Stanislav Dubinsky, Alla Petukhova, Ilya Gourevich, Eugenia Kumacheva

  Macromolecular rapid communications. 09/2010; 31(18):1635-40.

  We report the results of the experimental study of the preparation of hybrid porous polymer material carrying gold nanorods (NRs) on the surface of pores. The material was prepared by utilizing twoWe report the results of the experimental study of the preparation of hybrid porous polymer material carrying gold nanorods (NRs) on the surface of pores. The material was prepared by utilizing two effects occurring concurrently: the photoinitiated polymerization-induced phase separation in the polymer-solvent mixture and the migration of the NRs to the interface between the polymer and the porogen solvent. We show that the enrichment of the interface with the NRs is enhanced at high polymerization rate leading to the rapid phase separation. By contrast, more rapid increase in viscosity achieved at high polymerization rate does not have a significant effect on the segregation of NRs to the surface of pores.

• Step-growth polymerization of inorganic nanoparticles.

  Authors: Kun Liu, Zhihong Nie, Nana Zhao, Wei Li, Michael Rubinstein, Eugenia Kumacheva

  Science (New York, N.Y.). 07/2010; 329(5988):197-200.

  Self-organization of nanoparticles is an efficient strategy for producing nanostructures with complex, hierarchical architectures. The past decade has witnessed great progress in nanoparticleSelf-organization of nanoparticles is an efficient strategy for producing nanostructures with complex, hierarchical architectures. The past decade has witnessed great progress in nanoparticle self-assembly, yet the quantitative prediction of the architecture of nanoparticle ensembles and of the kinetics of their formation remains a challenge. We report on the marked similarity between the self-assembly of metal nanoparticles and reaction-controlled step-growth polymerization. The nanoparticles act as multifunctional monomer units, which form reversible, noncovalent bonds at specific bond angles and organize themselves into a colloidal polymer. We show that the kinetics and statistics of step-growth polymerization enable a quantitative prediction of the architecture of linear, branched, and cyclic self-assembled nanostructures; their aggregation numbers and size distribution; and the formation of structural isomers.

• Hybrid porous material produced by polymerization-induced phase separation.

  Authors: Stanislav Dubinsky, Alla Petukhova, Ilya Gourevich, Eugenia Kumacheva

  Chemical communications (Cambridge, England). 04/2010; 46(15):2578-80.

  Herein we demonstrate a new, straightforward method for the synthesis of macroporous hybrid polymers coated with gold nanorods, which are strongly and uniformly attached to the surface of pores.