By applying fluorescent dyes to the cell body and the flagella, the motion of flagellar filaments can be discerned from that of the cell body, which is extermely important for the study of flagellar interactions in densely packed bacterial carpets. We are studying fluid interactions with nanostructures in a variety of microfluidic environments. Video captured by Bill Hesse (July 2008)

A rectangular bacterial transportation system (50 x 100 sq. micron meters) in microfluidic environments reveals rotational velocity of 0.39 rad/s before UV exposure. The system stops withing the first second of a 7 seconds UV exposure. Rotation again resumes within 1 second and rotation of 0.47 rad/s is observed. After a second UV exposure and stop, rotational motion again resumes [PDF].

Transmission electron microscope (TEM) tomography, based on tilt series, can be used to create three-dimensional structure of solid-state nanopore, which is formed by high intensity of electron beam. After collecting the tilted (- 45 degree to 45 degree) 2-D images, we can reconstructure the 3-D nanopore structure using an advanced back-projection algorithm in Automated Reconstruction of Tomographic Tilt Series (ARTS). With single-digit nanometer pores, we are able to investigate ssDNA/dsDNA/RNA kinetics as well as DNA sequencing at single base resolution. The pore shown in this video has a 8 nm diameter [PDF].

Our objective is to understand and model the mechanics of bacterial flagellar bundling. Full-scale flagella are 10 micron meters in length, 20 nm in diameter, and turn at a rate of 100 Hz. To accurately simulate bundling at a more easily observable scale, we built a scale model in which 20 cm long helices are rotated in 100,000 cp silicone oil (poly-di-methyl-siloxane). The highly viscous oil ensures an appropriately low Reynolds number. We developed a macroscale particle image velocimetry (PIV) system to measure the full-field velocity distribution for rotating rigid helices and rotating flexible helices [PDF].