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Fluorescence Lifetime Imaging of Molecular Rotors in Living Cells
09:45

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Published on: February 9, 2012

Sensitivity field for nonautonomous molecular rotors.

A V Akimov1, N A Sinitsyn

  • 1Department of Chemistry, Rice University, Houston, Texas 77005, USA. alexey.akimov85@gmail.com

The Journal of Chemical Physics
|December 16, 2011
PubMed
Summary

We developed a new numerical method using geometric phases to measure how molecular rotors respond to controlled changes. This approach quantifies molecular motion control, aiding in designing molecular machines.

Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Physical chemistry

Background:

  • Controlling nonautonomous molecular rotor motion is crucial for molecular machine design.
  • Traditional methods like explicit time-dependent simulations are computationally intensive.
  • Geometric phase theory offers an alternative framework for analyzing molecular dynamics.

Purpose of the Study:

  • To propose a novel numerical approach for quantifying the control of nonautonomous molecular rotor motion.
  • To establish a method based on geometric phases for characterizing molecular response to perturbations.
  • To demonstrate the practical application of this method for surface-mounted molecular rotors.

Main Methods:

  • Utilizing the theory of geometric phases to define a sensitivity field (SF).

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  • Employing equilibrium free energy sampling techniques to compute the SF.
  • Generating density plots of the SF to visualize molecular response to parameter evolution.

    • Main Results:

    • The sensitivity field (SF) quantifies the average motion of a molecule induced by cyclic perturbations.
    • The SF can be calculated using equilibrium free energy sampling, avoiding complex time-dependent simulations.
    • Numerical SFs were obtained for two surface-mounted molecular rotor models.

    Conclusions:

    • The proposed geometric phase-based method provides an efficient way to quantify molecular rotor control.
    • This approach allows for the characterization of molecular response to adiabatic parameter changes.
    • The findings are relevant for the experimental control of molecular rotors using techniques like STM tips.