Simulation of a single molecule detection experiment

A Monte Carlo simulation has been developed to quantitatively understand and explore different physical aspects of a single molecule detection experiment in which individual dye molecules in an aqueous solution pass through a laser beam and emit fluorescence photon bursts. Detected photons are processed by a simple or weighted sliding sum digital Alter, and bursts are distinguished from background by a threshold-ing procedure. The detailed timing of each photon within a burst contains information which is used to produce a spectrum of arrival times in order to estimate the fluores-cence lifetime of a molecule. The simulation was applied in this work under three sets of experimental conditions (1) to compare results with those from a past experiment, (2) to determine the feasibility of an experiment for rapid single molecule detection, and (3) to identify each detected molecule according to its fluorescence lifetime. In the last case, the identification is accomplished by three independent algorithms-a weighted averaging technique, a maximum likelihood estimator of the lifetime, and a direct comparison of the fluorescence decay profile data. The simulation of (1) pro-duced comparable results with the experiment, the simulation of (2) determined rapid detection should be possible, and the simulation of (3) correctly identified molecules with > 85% accuracy when two different types of molecules were to be detected.