In the Standard Model of Cosmology the nature of the Dark Energy has become one of the most significant and conceptual challenges to be resolved. One of the possible approaches to solving it is to introduce modifications to General Relativity, that include Chameleon effects, which allow for a change in the strength of gravity based on the environment. This can provide for a consistent explanation of both large-scale observations and Solar system experiments. In the task to distinguish them from the LCDM model of gravity, or any other competing explanation, we need to study the consequences of these modifications for the growth of perturbations. In this thesis a recently developed Chameleon f(R) modification to gravity is explored. We study its consequences for the distribution of matter on large scale using the Bispectrum. Using 1D simulations we examine the formation of galaxy and cluster halos and its observational effects. Finally we present an investigation of a method for studying gravitational lensing.