MOLECULAR MOVIES COLLECTION


Links for BE.330J, Fields, Forces and Flows in Biological Systems

• Fields: Textbook 'Electromagnetic Fields and Energy'
  • By Herman Haus and James Melcher
    
• Fields: Video Demonstration for 'Electromagnetic Fields and Energy'
  • This link contains a video of experimental demonstrations of the textbook.
    
• Electrokinetics: Electrophoretic Motion of DNA (Craighead Group, Cornell Unversity)
  • From the Craighead Group website. In these video, one can clearly see an individual lambda DNA (48.5 kbp) forms a spherical 'blob' (with the radius of gyration of 0.7 µm) in the open, deeper part of the microchannel (called as 'deep region'), while they get stretched when they enter the ~ 100 nm thin nanofluidic channel (called as 'shallow region').
    
• Fluids: Various Aspects of Fluid Dynamics (MIT only)
  • This site contains several old, but enlightening videos regarding the basic fluid dynamics. A must for any BE.330 student to browse.
    
• Forces: Dielectrophoresis (Prof. Ronald Pethig, IBMM, UK)
  • On this page, one can see both positive (particles are drawn near to the high field gradient) and negative (particles are pushed away from high field gradient region) dielectrophoretic movement of microbeads. (Video files take time to load. Be patient.) In positive dielectrophoresis, particles align in a 'pearl-chain'-like geometry, while one cannot see such behavior in negative dielectrophoresis. (Why?) (video file to be linked soon)
  • Another example from the lab of Prof. Joel Voldman (MIT)
  • Another example from the lab of Prof. Sangeeta Bhatia (MIT)
    
• Forces: K. Autumn's Research Group page (Lewis and Clark Univ.)
  • Prof. Autumn pioneered the study of biomechanics of Gekko gecko, a lizard from Southeast Asia that excels in the ability of 'walking on the roof'. In his research, he demonstrated that the Van der Waals force is playing the main role in the amazing ability this little lizard to adhere virtually ANY surfaces (hydrophilic/ hydrophobic, rough/ smooth, charged, etc.).

Links for 6.021J, Quantitative Physiology: Cells and Tissues

• Microfluidics Project Laboratory Home Page
  
• Bacterial Chemotaxis in microfluidic channel (Freeman and Han group, EECS, MIT) (chemotaxis)
• A tri-laminar flow is formed in a microfluidic channel, where buffer containing many E-coli cells is merging with two other streams of buffer. Right-hand side stream contains very high concentration (1 M) of L-serine, which is acting as chemo-repellent at that concentration (so that E-coli cells are driven away from it), while the left-hand side stream contains lower concentration (0.01 mM) of L-serine, which is acting as a chemo-attractant (E-coli cells are drawn near it). The bacteria in this experiment produce green fluorescent proteins (GFP), which allows visualization (fluorescence microscopy) of the cells. Video obtained by Eugene Lim (EECS, MIT)

Molecular Videos from the Han lab
This site contains experimental data from the Han lab in video format.

• Ion-enrichment and depletion behavior in a nanofluidic concentrator
  • By Sung Jae Kim. The basic ion-enrichment and ion-depletion behavior in single gate device (two microchannels are connected each other by nanofluidic channels). Depletion voltage condition (same voltage at anodic side and ground at cathodic side) was applied. Ion enrichment was observed at the cathodic side and depletion was observed at the anodic side, with rapid expansion of both regions observed. Fluorescent BODIPY disulfonate dyes were used to visualize this behavior.  Phys. Rev. Letts. 99, 044501.1-4, 2007
• Vortex generation in ion-depletion zone
  (SG.avi) (DG.avi) (SSG.avi)(SDG.avi)
  • By Sung Jae Kim.  The first video (SG.avi) show fast vortex generation in single gate device at steady state. The electroosmotic flow of the second kind inside the ion-depletion zone induced the vortex at the entrance of nanofluidic channel. By extending this result, one can expect the four independent vortex formations in dual gate device (three microchannels are connected each other by nanofluidic channel and the center channel is used for main channel) as shown in the second video (DG.avi). We additionally put BODIPY disulfonate only in dual gate device for better visualization of depletion boundary (Bright parts in both sides of vortices). To enhance the concentration polarization, the vortices were suppressed by fabricating shallow single gate (SSG.avi) and shallow dual gate devices (SDG.avi). The depth of the microchannel in shallow device was 2 um which is 5 times smaller than normal device. The size of the vortex was ~2 um which was similar value of the microchannel depth. Phys. Rev. Letts. 99, 044501.1-4, 2007
• Continuous-flow separation of proteins under denaturing conditions in the ANA, with the Ogston sieving mechanism
• By Jianping Fu. This video shows separation of Alexa Fluor 488-conjugated cholera toxin subunit B (11.4 kDa) and β-galactosidase (116.3 kDa). Video was taken with exposure time of 1000 ms/image and image size of 3270 µm X 4080 µm. The time scale in this movie has been compressed by a factor of 20. At the beginning of the movie, only the vertical field Ey = 50 V/cm was applied. The horizontal field Ex = 75 V/cm was applied at 1 sec in the movie, and the separation was finished at about 6 sec in the movie.
• Continuous-flow separation of long DNA (λ DNA - Hind III digest) in the ANA, with the entropic trapping mechanism
  • By Jianping Fu. This video was taken with exposure time of 600 ms/image and image size of 3270 µm X 4080 µm. The time scale in this movie has been compressed by a factor of 20. At the beginning of the movie, only Ey = 100 V/cm was applied. The orthogonal field Ex = 185 V/cm was applied at 1 sec in the movie, and the separation was finished at about 5 sec in the movie.
• Continuous-flow separation of short DNA (the PCR marker) in the ANA, with the Ogston sieving mechanism
  • By Jianping Fu. This video was taken with exposure time of 1300 ms/image and image size of 1300 µm X 1620 µm. The time scale in this movie has been compressed by a factor of 20. At the beginning of the movie, only Ey = 25 V/cm was applied. The orthogonal field Ex = 35 V/cm was applied at 3 sec in the movie, and the separation was finished at about 12 sec in the movie.

• Suppressing air bubbles trapped in the one-dimensional nanofilter array

  • By Jianping Fu. Real time. Air bubbles were suppressed by running EOF flow. Unpublished results.
• Separation of denatured proteins in a nanofluidic filters (10X speed, Eav = 100 V/cm)
  • By Jianping Fu. In this video, the channel on the left of the loading region contains an array of nanofluidic filters (60 nm gap size), with a density of 1 filter/µm. The thickness of 'deep regions' is 250 nm. The sample stream contains three different proteins (11.4 kD, 120 kD, and 179 kD) coated with SDS. Three peaks are quickly separated within ~ 30 sec as the sample plug is mobilized through the nanofluidic filter array device. Result presented in Appl. Phys. Lett. 87, 263902.1-3, 2005.
• Nonlinear electrokinetic flow profile near nanofluidic channel
  • By Ying-Chih Wang. In this video, 40 nm nanofluidic filter (which was connected to the main channel) was used to create a local ion depletion region within the microchannel. In this region, the flow pattern is chaotic and the speed of the flow is much higher, perhaps due to the creation of induced charges by ion-selective nanofluidic filter. This transition can be seen clearly in this video by following a large DNA molecule in the channel, which enters the region and engages in a fast, circular motion with the flow, then escapes.