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In this article, the targeting of dye molecules as an important goal is probed and simulated by quantum dots and through the particle swarm optimization algorithm and fluorescence resonance energy transfer mechanism. At first, we design a nano-bio sensor, based on the fluorescence resonance energy transfer mechanism, which operates in a wide range of wavelength and is very sensitive to fluorescence resonance energy transfer parameters such as overlapping between donor and acceptor, Föster radius, and energy transfer rate from donor to acceptor. In fact, the alteration of nano-bio sensor parameters acts as the heart of our sensor. The target is detected if the attained parameters of the sensors fulfilled the critical conditions and therefore, by the use of the particle swarm optimization algorithm which simulates the signaling and communication among quantum dots, other agents are called toward the target site. In this simulation, the positions of quantum dots as sensor agents and of the target are randomly considered. Moreover, to attain high targeting efficiency, the two different structures are introduced to maximum coverage of operational wavelength.