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Single Molecule Imaging of Molecular Machines
Molecular machines are a promising class of molecules that are designed to exhibit controlled mechanical motions.
In contrast to breaking macroscopic objects into smaller pieces to form functional materials, nanoscale science is driven
by a bottom-up synthesis approach. Inspiration for this strategy can be found in nature where self-assembly of smaller
molecules into larger networks plays a fundamental role. The possibility of performing mechanical operations with specifically
designed molecules presents the ultimate limit of miniaturization with profound impact on diverse fields such as molecular
electronics and medicine.
Using single molecule fluorescence imaging, we are investigating the translational motion of molecular machines, which resemble
the chassis and wheels of a car. These organic molecules are called nanocars, which have been designed and synthesized in the Tour
lab. The figure above shows a fluorescence image of single nanocars. Each bright spot in the image (left) corresponds to an
individual molecule as is verified by a single step photobleaching event in the fluorescence trajectory (right). The two traces
correspond to orthogonal polarizations of the detected fluorescence, which gives information about the orientation of the molecule.
By recording fluorescence images as a function of time we can record single nanocar trajectories. Movies constructed from sequential
images for TRITC-tagged nanocars (left) and TRITC only (right) are shown below (30x actual speed).
Our goal is to obtain a molecular level understanding about the mechanism how molecular machines function in order to improve the
engineering of such machines. This goal is pursued in collaboration with the synthetic group of Professor Tour ,
the theoretical chemistry group of Professor Kolomeisky , and the STM imaging
group of Professor Kelly . Optical single molecule imaging carried out in our
lab is aimed at measuring directed transport on a micrometer length scale.
Download Tracking Program
SMS_Tracker_pkg - The installer for the standalone application
MCRInstaller - Matlab Runtime (Required for .exe file). Unfortunately we cannot host this file, however you can download it here (from cell tracker), here (from CGcgh), or here (from Soares group).
Manual & Documentation (PDF)
Sample Data (ZIP)
If you would like the source .m files to run or modify, please e-mail any of us and we will be happy to provide them to you.
Installation:
Download and run the MCRInstaller to install the Matlab Runtime only if you have not done this before. Then run SMS_Tracker_pkg.exe. This will create SMS_Tracker.exe which will run the tracking program. Data output will be saved in matlab .mat format.
The main screen. From this screen you can load up the individual Images for analysis. Once Images have been loaded, they are analyzed for intensity, allowing the user to set cut-offs for target molecules against random noise. This screen allows for an overview of the key points of the data. While the data is being processed, it shows the actual image files with an overlay of molecules that will be kept for further analysis.
 
(Left) The search radius plot. This proved to be one of the more useful plots. It plots points assocaiated as a function of search radius. If there were immobile particles, there would be a large peak within a few pixels of zero, however, for more mobile samples the peak would shift out, and the distribution would change. See publication 2 below for more info. (Right) A plot of the log of the diffusion constant calculated for several hundred simulated single molecules. Each distribution corresponds to a different simulation case. "Fixed" means that the samples had high intensities, but were imaged with noise. "No noise" is exactly that, low amplitude molecules without noise. "Noise and Diffusion" was a class where some molecules were stationary (with low intensity molecules, with noise added to the signal, resulting in a higher diffusion constant than the previous distributions), and molecules with the same parameters, but that were actively moving, giving rise to the second peak.
Group members involved:
Publications:
- S. Khatua, J. M. Guerrero, K. Claytor, G. Vives, A. B. Kolomeisky, J. M. Tour, S. Link, Micrometer-Scale Translation and Monitoring of Individual Nanocars on Glass. ACS Nano 3, 351 (2009). link
- K. Claytor, S. Khatua, J. M. Guerrero, J. M. Tour, S. Link, Accurately Determining Single Molecule Trajectories of Molecular Motion on Surfaces. J. Chem. Phys. 130, 164710 (2009). link
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