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8 September 2010Simulations for guiding the delivery and trapping of single biomolecules in a nanofluidic device
A microfluidic device has been developed wherein single molecules in solution are electrokinetically transported along a
nanochannel. The nanochannel is irradiated by two adjacently focused laser beams so that the timing of fluorescence
photons induced by each beam indicates the position of a molecule along the nanochannel. This is then used to actively
control the electrokinetic flow, so that the molecule may be held within the confocal volume for a prolonged time and
then rapidly replaced following photobleaching or completion of the single-molecule measurement. Here we focus on
Monte Carlo computer simulations of the physical processes that occur during the delivery and trapping. The simulations
help in understanding the constraints imposed by experimental limitations, such as the latency of feedback, the
maximum achievable speed of electrokinetic flow, and photophysical processes such as triplet crossing and
photobleaching. They also aid in evaluating the effects of shot noise and photon timing error and in predicting optimum
experimental operating parameters. Studies indicate that the 6 μs latency of feedback in our experiments is well below
that required for stable trapping (~100 μs); for small freely diffusing molecules, a limited flow speed of ~2 μm/ms can
result in ~10-20 % of molecules escaping before they photobleach; there is an optimum laser power of ~30-40 μW that
provides a sufficient rate of fluorescence photons for trapping while reducing loss due to photobleaching; an increase in
the spacing between the beams or increase in relative power of the down-stream beam increases the trapping time.
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Lloyd M. Davis, William N. Robinson, "Simulations for guiding the delivery and trapping of single biomolecules in a nanofluidic device," Proc. SPIE 7750, Photonics North 2010, 775005 (8 September 2010);