Thermofluids/ Microflows/ Simulation



  • Micro-/Nanofluidics Concentrator Array for Quantitative Predaton Assays of Predatory Microbes


We present a microfabricated concentrator array device that makes it possible to quantify the predation rate of Bdellovibrio bacteriovorus, a predatory microbe, toward its prey, Escherichia coli str. MG1655. The device can accumulate both prey and predator microbes sequentially within a series of concentrator arrays using the motility of the microbes and microfabricated arrowhead-shaped ratchet structures. Since the device can constrain both prey and predator cells within 200 pL chambers at a desired range of cell densities, it was demonstrated that the device cannot only enhance the possibility of studying predation processes/cycles directly at a single cell level but can also quantify the predation rates indirectly by measuring the time-dependent fluorescent intensity signals from the prey. Furthermore, the device can produce a wide range of initial prey to predator density ratios within various concentrator arrays through the use of microfluidic mixer structures on a single array chip, which allows us to study many different conditions with a single set of cultures, and quantitatively characterize the predation behaviour/rate. Lastly, we note that this novel concentrator array device can be a very powerful tool facilitating studies of microbial predations and microbe–microbe interaction and may be broadly used in other microbial biotechnological applications.

--Seongyong Park, Dasol Kim, Robert J. Mitchell, and Taesung Kim*, A Microfluidic Concentrator Array for Quantitative Predaton Assays of Predatory Microbes, Lab-on-a-chip, 2011. PDF

Microfluidic Device for Analyzing Preferential Chemotaxis and Chemoreceptor Sensitivity of Bacterial Cells Toward Carbon Sources

We present a novel microfluidic device that enables high sensitive analyses of the chemotactic response of motile bacterial cells (Escherichia coli) that swim toward a preferred nutrient by sorting and concentrating them. The device consists of the Y-shaped microchannel that has been widely used in chemotaxis studies to attract cells toward a high concentration and a concentrator array integrated with arrowhead-shaped ratchet structures beside the main microchannel to trap and accumulate them. Since the number of accumulated cells in the concentrator array continuously increases with time, the device makes it possible to increase the sensitivity of detecting chemotactic responses of the cells about 10 times greater than Y-shaped channel devices in 60 min. In addition, the device can characterize the relative chemotactic sensitivity of chemoreceptors to chemoeffectors by comparing the number of cells in the concentrator array at different distances from the channel junction. Since the device allows the analysis of both the chemotactic responses and the sensitivity of chemoreceptors with high resolution, we believe that not only can the device be broadly used for various microbial chemotaxis assays but it also can further the advancement of microbiology and even synthetic biology.

-- Minseok Kim, Su Hyun Kim, Sung Kuk Lee* and Taesung Kim*, Microfluidic Device for Analyzing Preferential Chemotaxis and Chemoreceptor Sensitivity of Bacterial Cells Toward Carbon Sources, Analyst, 2011PDF 


Microfluidic Technologies for Synthetic Biology


Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

--Parisutham Vinuselvi, Seongyong Park, Minseok Kim, Jung Min Park, Taesung Kim* and Sung Kuk Lee*, Microfluidic Technologies for Synthetic Biology, Int. J. of Mol. Sci., 2011, 12(6), 3576-3593PDF


Multi-cellular bacterial cell patterns produced by a materials printer (BMB Report, 2011)


 AHL-expressing cells that contain no fluorescence protein genes are printed together with control cells that constitutively express RFP to visualize their printed location. The AHL- expressing cells activate the cells printed in the upper left part of each letter to express GFP, resulting in brighter GFP signals. On the other hand, the cells printed in the lower right part of the diagonal line initially express GFP but their fluorescence intensities decrease with time because AHL molecules produced by and diffused from the AHL expressing cells inhibit the expression of GFP. These cells were sequentially printed and then grown on an agar surface containing nutrients to demonstrate synthetic bacterial  cell-to-cell communication. 'UNIST' stands for Ulsan National Institute of Science and Technology and 'μFNM" for Microfluidics and Nanomechanics Laboratory at UNIST. The images are approximately 5.0 mm by 1.2 mm in size. 
 
-- Robert J. Mitchell†, Sung Kuk Lee†, Taesung Kim†Cheol-Min Ghim*, Microbial Linguistics: Perspectivesand Applications of Microbial Cell-to-Cell Communication, BMB reports, 2011, 44(1) pp. 1~10. PDF



Synthetic multicellular cell-to-cell communication in inkjet printed bacterial cell
systems (Biomaterials 2011)


We utilized a commercially available materials printer to investigate synthetic multicellular cell-to-cell communication because inkjet printing technology makes it easy to print spatiotemporal patterns of soluble biomolecules and live cells. Since cells are genetically programmed to communicate with one another via synthetic biology, cell signaling molecules secreted by one cell microcolony can induce two neighboring cell microcolonies to respond by expressing or stopping the expression of fluorescent protein genes. 
  Printing multicellular bacteria in checkerboard pattern. The SCs and control cells expressing RFP are printed at the center, while the RCs and IRCs are printed at the diagonal corners 1.41 mm away from the center. As clearly shown in the insets, initially only the control cells and IRCs give off distinct fluorescent signals. While the fluorescent intensities of the RCs continue to decrease with time, the RCs gradually fluorescence and the intensities continue to increase significantly with time. 

-- Woon Sun Choi, Dokyeong Ha, Seongyong Park, and Taesung Kim*, Synthetic Multi-cellular Cell-to-Cell Communication in Inkjet Printed Bacterial Cell Systems, Biomaterials, 2011, 32 2500-2507. (IF=7.365) PDF


Diffusion-based and Long-range Concentration Gradients of Multiple Chemicals for Bacterial Chemotaxis Assays (Anal. Chem. 2010)

(A) Schematic view of the long-range concentration gradient generator for use with multiple compounds. Each channel is 8 mm long from the center chamber to the reservoir and a constant flow is used to provided fresh media the center chamber, in which the cells are introduced after generation of the chemical gradients. (B) The H-shaped microfluidic channel structure was designed to integrate the agarose gel into the microchannel near the reservoirs. (C) The microimage shows a hydrogel plug mixed with fluorescent dye which prevents convection flows in the microchannel but allows diffusion of small molecules from the reservoir to the center chamber. (D) After a hydrogel plug was made, the channel was filled with a medium by removing the air trapped within the channel through PDMS. The medium contains 50 µM of FITC for demonstration.

-- M. Kim and T. Kim*, Diffusion-based and long-range concentration gradients of multi-chemicals for bacterial chemotaxis assays, Anal. Chem., 82(22), pp. 9401-9409, 2010. PDF 


Microfabricated ratchet structures for concentrating and patterning motile
bacterial cells (J. Micromech. and Microeng. 2010)

(A) The SEM image of a series of arrowhead-shaped structures (inlet: 40 μm, intermediate: 20 μm and outlet: 10 μm). (B) The concentrator consists of a chamber at the center and four arrowhead-shaped structures. Cells in the circular channel are forced to move into the arrowhead-shaped structures by the protruding wall, which is indicated with the white arrow. (C) Cells are highly concentrated by duplicating and enlarging the basic concentrator unit along the arrows, as indicated by e1 through e4. Three rings were repeated to highly concentrate cells around the concentrator.

-- S. Y. Kim†, E. S. Lee†, H. J. Lee†, S. Y. Lee†, S. K. Lee* and T. Kim*, Microfabricated Ratchet Structures for Concentrating and Patterning Motile Bacterial Cells, J. Micromech. Microeng. 20 (9), 2010, 095006. PDF


Micro-interface systems for studying cellular responses from single and multiple cells (Annals of Biomedical Eng. 2010)


Various microinterface systems can be utilized in studying cellular responses from single and multiple cells. Microfluidics-based interfaces impose extracellular, biochemical, mechanical, and electrical stimuli onto cells; nanoparticle-based interfaces both impose and detect intracellular stimuli into cells; and SECM-based monitoring interfaces read out the responses of cells. Cyclic experiments will help develop biomedical applications.

-- Y.-K. Cho, H. Shin, S. K. Lee and T. Kim*, Current Application of Micro/Nano-interfaces to
Stimulate and Analyze Cellular Responses, Annals of Biomedical Engineering, 2010, 38, (6), pp. 2056–2067.(invited review). PDF


Nanotechnological Applications of Biomolecular Motors and Microtubules Systems (Lab chip, 2009)



    For example, the pictures above show a biosensor 
that was developed for the pre-concentration of protein/biomolecule analytes to help detect biohazard molecules and diagnose disease. The investigation involved a combination of biocompatible microfabrication, experimental studies, theoretical modeling, and numerical analysis. Due to the advantages of miniaturized analytical systems over traditional biochemical analysis instrumentation, micro-/nanofluidic technologies on which our research interests are focused not only enable shorter analysis times and much smaller sample sizes, but also hold the potential for massively parallel analysis for high-throughput.
  • For stand-alone, self-contained and efficient micro Total Analysis Systems (microTAS)
  • Efficiently sort and concentrate (bio-)analyte molecules by using kinesin motors and microtubules as a chemomechanical transduction machine
  • Hundreds of targeted molecules per second from an analyte stream were removed by translocating functionalized microtubules with kinesin across the stream and concentrating them at a horseshoe-shaped collector  
  • Target biomolecule concentrations increase up to three orders of magnitude within one hour of operation  


Multifunctional Microenvironment for Cell Culture (BMMD, 2008)
  
  • Producing Spatial and Temporal Chemical/Reagent Gradients.
  • Cellular BioMEMS for cell sorting, culture and patterning.
  • Cancer cell metastasis.
  • Embryo development.

    As another example, micro-/nano-fluidic technologies have been applied to engineering a microenvironment for cell culture as shown above. Such a microenvironment makes it possible to sense cell to cell signals, ultimately providing the tools allowing scientists to access and control the chemical message underlying developmental programs of cells. For biologists, such a tool would present new ways of investigating the chemical control systems that develop cells (e.g. human embryonic cells) into a whole organism. 



Chemical micro-interface systems for Synthetic Biology
 
  • Hacking the metabolic signaling pathways of bacterial cells using a micro-interface
  • For example, a chemical microsystem capable of modulating bacterial cells to express different sets of genes.
  • Dynamic pattern formations and theoretical modeling (i.e., Turing's Reaction-Diffusion Model). 
  • The pictures below show that bacterial cells are controlled to express different amount of GFP but the same amount of RFP using a microfabricated-interface.



Micro-/Nanofluidics + Electrokinetics = Bio-sensor


Biosensor for (bio-)molecule Detection, Separation and Concentration 
  • Nanofluidic channel networks/structures enabling selective ion/molecule filtering.
  • Biomolecule Carrier using microtubules (one of cytoskeletonl filaments).
  • NanoTweezer Array Transducing Chemcial Signals of Antibody-Antigen Systems into Mechanical Signals (would be one of our future directions)
 
  • This device makes it possible to selectively extract target molecules such as streptavidin and bovine serum albumin and then highly concentrate them up to higher than 5 orders of magnitude from a complex mixture of analytes ranging from 1 nM to 10 fM.


Nanofluidic and Electrokinetic Flow Phenomena  
  • Experimental Investigation of Flow Instability, Circulation and Vortex in the presence of Electric fields.
  • Theoretical and Numerical Approach using CFD to confirm Experimental Results.
  • Applications of the Phenomena to microfluidic Pump and Mixer.
 

Nanofluidic target ‎‎(bio-)‎‎molecule filter

 
 

Electroosmotic flow expels non-target biomolecules

  
 
  


Biophysical studies and mechanistic modeling on t
he responses of cells and proteins to external mechanical and electrical disturbances
  • The movie below shows that microtubules ( one of cytoskeleton filaments) on a kinesin (biomolecular motor)-coated surface are aligned with an electric field due to electrophoretic forces.
  • Also, the traslocation of a single microtubule by kinesin is guided to move along a circle by manipulating the direction and strength of electric fields.   

    Active microtubule alignment using an electric field

     

Guiding a microtubule to move along an arbitary circle ‎(30 um in diameter)‎

 


Fluid Mechanics+Heat Transfer+Simulation


- COMSOL Multiphysics Simulation: Pre-concentration of target biomolecules at the anodic side (left) of the nanoporous, perm-selective memebrane patterned on the microchannel surface. 


- Simulation of Ion Concentration Polarization and Nonlinear EOF flow (ongoing). Click the image.

2nd EOF U.avi



DC-Concentration.avi



- If you are interested in Multiphysics Simulation, please contact me.

Fluid Mechanics+Heat Transfer+Simulation


- COMSOL Multiphysics Simulation: Pre-concentration of target biomolecules at the anodic side (left) of the nanoporous, perm-selective memebrane patterned on the microchannel surface.


- Simulation of Ion Concentration Polarization and Nonlinear EOF flow (ongoing). Click the image.

2nd EOF U.avi



DC-Concentration.avi



- If you are interested in Multiphysics Simulation, please contact me.


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