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We address the problem of persistent monitoring, where a finite set of mobile agents has to persistently visit a finite set of targets. Each of these targets has an internal state that evolves with linear stochastic dynamics. The agents can observe these states, and the observation quality is a function of the distance between the agent and a given target. The goal is then to minimize the mean squared estimation error of these target states. We approach the problem from an infinite horizon perspective, where we prove that, under some natural assumptions, the covariance matrix of each target converges to a limit cycle. The goal, therefore, becomes to minimize the steady state uncertainty. Assuming that the trajectory is parameterized, we provide tools for computing the steady state cost gradient. We show that, in one-dimensional (1D) environments with bounded control and non-overlapping targets, when an optimal control exists it can be represented using a finite number of parameters. We also propose an efficient parameterization of the agent trajectories for multidimensional settings using Fourier curves. Simulation results show the efficacy of the proposed technique in 1D, 2D and 3D scenarios.