Abstract: I will present molecular dynamics computer simulations of several examples of conformational transitions that nucleic acids and their complexes undergo upon the application of external forces and/or torques: (1) DNA supercoil relaxation by topoisomerases, (2) the condensation of DNA by  dendrimers and (3) DNA ejection from viruses. Then I will showcase the use of a formalism in the theory of stochastic processes to deduce the kinetics of these transitions, from simulation trajectories or experimental single molecule recordings of the transition, under other conditions that those that are actually simulated or recorded.