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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 many diverse fields. 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. Our goal is to obtain a molecular level understanding about the mechanisms how molecular machines function in order to improve the engineering of such machines. In particular, we apply optical single molecule imaging to measure the directed motion of nanocars on a micrometer length scale. This project is pursued in collaboration with theoretical modeling carried out in the Kolomeisky Lab.

The figure above shows the chemical structure of a nanocar tagged with the dye TRITC (left) and a time series of magnified fluorescence images showing the movement of a single nanocar (right). By recording fluorescence images as a function of time we obtain single nanocar trajectories, which are used to quantify the nanocar motion on different surfaces. Movies constructed from sequential images for TRITC-tagged nanocars (left) and TRITC only (right) are shown below (30x actual speed). While the nanocars move on a glass substrate at room temperature, the TRITC molecules remain stationary. The tracking program developed to analyze the nanocar movement can be downloaded below.

TRITC-tagged Nanocars


Download Tracking Program

SMS_Tracker_pkg – Installer for the standalone application

MCRInstaller – Matlab Runtime (required for .exe file). Unfortunately we cannot host this file, however you can download it from CellTracker.

Manual & Documentation (PDF)

Sample Data (ZIP)


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. If you would like the source .m files to run or modify, please email us and we will be happy to provide them to you.



  1. B. Shuang, C. P. Byers, L. Kisley, L.-Y. Wang, J. Zhao, H. Morimura, S. Link, C. F. Landes, Improved Analysis for Determining Diffusion Coefficients from Short Single-Molecule Trajectories with Photoblinking. Langmuir 29, 228 (2013) . link
  2. P.-L. E. Chu, L.-Y. Wang, S. Khatua, A. B. Kolomeisky, S. Link, J. M. Tour, Synthesis and Single-Molecule Imaging of Highly Mobile Adamantane-Wheeled Nanocars. ACS Nano 7, 1, 35 (2013) link
  3. S. Khatua, J. Godoy, J. M. Tour, S. Link, Influence of the substrate on the mobility of individual nanocars. J. Phys. Chem. Lett. 1, 3288 (2010). link
  4. G. Vives, J. M. Guerrero, J. Godoy, S. Khatua, Y.-P. Wang, J. L. Kiappes, S. Link, J. M. Tour, Synthesis of Fluorescent Dye-Tagged Nanomachines for Single Molecule Fluorescence Spectroscopy. J. Org. Chem. 75, 6631 (2010). link
  5. 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
  6. 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