Simulation of Single Molecule Trapping in a Nanochannel

Trapping of single fluorescent molecules in solution is numerically simulated. Optical trapping provides insufficient force for trapping molecules much smaller than the optical wavelength. Instead, a means for trapping by sensing the molecule position and applying real-time feedback of flow to compensate diffusional displacement is used. The solution is contained in a nanochannel, reducing the problem to one spatial dimension. The position of the molecule is estimated from the fluorescence signals generated by two focused laser beams, which originate from a single laser source that is split and temporally alternated between the two focal spots. Photon collection is time gated, and photons collected in the two detection channels are used to find the maximum-likelihood estimate of the molecule position and adjust the electrokinetic motion to reposition the particle. Adjustment of the simulation parameters leads to a multi-variable analysis of the trapping effectiveness. For the range of parameters considered in this thesis, trapping is found to be robust and stable. However, the maximum speed of electrokinetic motion that would be possible in an experimental implementation limits the capabilities of the trap. Accordingly, the maximum likelihood position estimate provides little or no advantage for trapping over simpler algorithms. A simpler feedback algorithm is proposed and demonstrated to provide effective trapping. Also, in consideration of when molecular photobleaching becomes significant, an algorithm for quickly reloading the trap with a new molecule is developed and tested in a second simulation