"Rapid Prototyping" of Biosensing Surface Plasmon Resonance Devices using COMSOL & Matlab Software Dominic Carrier and Jan J. Dubowski Department of Electrical and Computer Engineering, Université de Sherbrooke Sherbrooke, Québec, J1K 2R1, Canada, E-mail: dominic.carrier@usherbrooke.ca Abstract: We present a Finite Element Method simulation procedure that allows rapid development of prototype devices comprising novel self-referenced interference SPR (surface plasmon resonance) biosensing microstructures. The procedure takes advantage of commercial Comsol Multiphysics and Matlab software and their bi-directional link. Keywords: Biosensor, surface plasmon resonance, FEM, Comsol, phase measurement. 1. Introduction Numerous papers presenting results of research on surface plasmon resonance (SPR) effect for biosensing use commercial apparatus [1, 2]. The focus of our research is to provide a new scheme of biosensing with increased sensitivity and specificity, or to offer other advantages, such as a possibility of integration. To allow this latitude of research, exploration of flexible biosensing geometry must be possible. Computer simulation offers this kind of latitude, albeit also presenting some difficulties of its own [3]. Many approaches have already been applied to model physical effects and carry out computer simulations in plasmonics and photonics. Green's tensor approach [4-6], scattering-matrix formalism [7-9] and FEM simulations [10-12] are common methods employed. Green's tensor and scattering matrix methods are restricted to specific modeling scheme (regular "analytic" background and layered architecture respectively [8, 13-15]) whereas Finite Element Method (FEM) does not present such restrictions. The FEM approach is arguably the most user-friendly computing interface. With commercially available FEM software, designing new models, simulation and visualization of the results has become an increasingly common path of advanced research. Generally, the FEM approach is less convenient in terms of computational power required and the raw form of results or, sometimes, accuracy, but it presents flexibility attractive for undertaking new research. 1.1 SPR biosensing Diverse fundamental methods were and are currently under investigation to create biosensing devices. Surface acoustic waves, micro- cantilevers, surface plasmon resonance and optical mode probing are only common example avenues of development [16-21]. Commercial SPR systems have been available for more than 15 years [22] and methods have been developed to make measurement of the same fundamental phenomenon more sensitive over the years [23- 25]. Combining SPR with phase interference measurement yet still preserving integrability and ease-of-measurement is our goal in the development of a biosensing device. 2. "Rapid-prototyping" methodology for simulation The availability of commercial software to produce FEM simulations has tremendously accelerated the problem-solving process; the solving engine is already built and verified, the user interface (UI) provides CAD tools to design with, and the software generally comes with examples, tutorials and documentation to help users transfer their problem to the simulation environment. Our research makes use of Comsol Multiphysics software and its close integration with Matlab. The close integration of a high- level programming environment with the strengths and ease-of-use of a mature UI was invaluable to our research, as flexibility of design (use of templates) and advanced parameterization were significant to efficiently achieve these results. 2.1 Modularity Rapid development of simulation models has been achieved with a programming paradigm, i.e., modularity [26]. When designing complex Excerpt from the Proceedings of the COMSOL Conference 2009 Boston