Finite-difference time-domain modeling and experimental characterization of planar waveguide fluorescence sensors

The finite-difference time-domain method (FDTD) is a powerful numerical technique for solving Maxwell's equations in a discretized space and time grid. Its applications have up to now been in the analysis of electrically large structures in the microwave domain, and the scope of investigations has been extended to the optical region only recently. Because of computer memory limitations, the method is generally restricted to configurations which extend to the order of tens of wavelengths in three dimensions, or hundreds of wavelengths in two dimensions. Optical sensor structures are therefore of suitable size to be modeled with FDTD, and e. g. fluorescence sensor design can benefit from the use of FDTD in optimization of the waveguide structures. In general, the integration of chemical and optical design is difficult, but FDTD can bring the two design approaches closer together. One of the main advantages of FDTD is its ability to include near-field effects, such as distribution of protein molecules on the active surface of optical sensors in the model, which has been shown to be important in estimating the fluorescent excitation and collection efficiencies of molecules on surfaces. In addition, for planar structures, two-dimensional models are adequate for studying many aspects of sensor design. We applied FDTD to design of planar fluorescence sensors. Excitation and emission models were analyzed for planar waveguide structures with side collection of emitted light in mind. Planar waveguides were fabricated on fused silica substrates, and the characteristics of the waveguides were compared to the model. Good agreement was found with the FDTD modeling to the physical model, and based on this knowledge, an FDTD sensor model was prepared predicting good fluorescence excitation and emission side collection efficiencies.