The main objective of this work is to demonstrate some new computational methods for estimation, optimization and modeling of dynamical systems that use automatic differentiation. Particular focus will be upon dynamical systems arising in Aerospace Engineering. Automatic differentiation is a recursive computational algorithm, which enables computation of analytically rigorous partial derivatives of any user-specified function. All associated computations occur, in the background without user intervention, as the name implies. The computational methods of this dissertation are enabled by a new automatic differentiation tool, OCEA (Object oriented Coordinate Embedding Method). OCEA has been recently developed and makes possible efficient computation and evaluation of partial derivatives with minimal user coding. The key results in this dissertation details the use of OCEA through a number of computational studies in estimation and dynamical modeling. Several prototype problems are studied in order to evaluate judicious ways to use OCEA. Additionally, new solution methods are introduced in order to ascertain the extended capability of this new computational tool. Computational tradeoffs are studied in detail by looking at a number of different applications in the areas of estimation, dynamical system modeling, and validation of solution accuracy for complex dynamical systems. The results of these computational studies provide new insights and indicate the future potential of OCEA in its further development.