Dr. Lloyd M. Davis
Professor of Physics

Center for Laser Applications
The University of Tennessee Space Institute
Tullahoma, TN 37388-9700
Phone: (931) 393-7335
Fax: (931) 454-2271
E-mail: ldavis@utsi.edu
Demonstration of Monte Carlo Simulation of Single-Molecule Detection, Fluorescence Correlation Spectroscopy, and Fluorescence Cross-Correlation Spectroscopy (11/10/2003)

In order to study the effects of realistic experimental conditions, such as triplet crossing, photobleaching, excitation saturation, detector dead time, and optical misalignment, to evaluate the effects of systematic and random errors in the ACF with short duration acquisition times, and to facilitate comparison of different data analysis strategies, a sophisticated Monte Carlo simulation of single-molecule detection (SMD), FCS and fluorescence cross correlation spectroscopy (FCCS) has recently been developed. A key difference compared to our prior simulations is that the new code generates the exact time of arrival (TOA) of each detected photon. Our previous FCS simulation, which determined the photon TOAs to within 50 ns by use of a 50 ns time step, would take approximately 10 hours to simulate a 10 second experiment, and hence was executed on a 100-CPU Condor cluster. The new simulation uses a completely rewritten algorithm in which molecule locations are confined to a discrete grid and time increases continuously for all processes except molecule transport. Molecules may enter or leave the simulation volume by diffusion or flow. The simulation can model one or two independently aligned laser excitation beams, one or two single photon detectors, several different chromophore types, and several particle types with different mobilities, labeled by specified numbers of the defined chromophore types. The code uses multiple threads, with key parts written in C and compiled using the Intel compiler.

To download a demonstration version of the FCS Simulation click here:

Simulation Demo.zip (14225 kB)

This will download a zip file which includes files to install the
LabView Run-Time Engine and the simulation:

  • On opening the zip file, click Install in the menu bar and then OK.
  • The installation will automatically begin and prompt the user for a directory
    (the default being C:\Program Files\Simulation_Demo )
  • Once the installation is finished, the program can be run by
    Start > All Programs > Simulation_ Demo
  • The program operates best  on Pentium 4 machines but will work on
    Pentium 2 and 3 machines
  • Email ldavis@utsi.edu for questions

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