We consider damped stochastic systems in a controlled (time varying) potential and study their transition between specified Gibbs-equilibria states in finite time. By the second law of thermodynamics, the minimum amount of work needed for the transition from one equilibrium state to another is the difference between the Helmholtz free energy of the two states and can only be achieved by a reversible (infinitely slow) process. The minimal gap between the work needed in a finite-time transition and the work during a reversible one, turns out to equal the square of the optimal mass transport (Wasserstein-2) distance between the two end-point distributions times the inverse of the duration needed for the transition. This result, in fact, relates nonequilibrium optimal control strategies (protocols) to gradient flows of entropy functionals via the Jordan-Kinderlehrer-Otto scheme. The purpose of this paper is to introduce ideas and results from the emerging field of stochastic thermodynamics in the setting of the classical regulator theory, and to draw connections and derive such fundamental relations from a control perspective in a multivariable setting.