Molecular flexibility controls a number of key processes ranging from protein folding to the design of advanced materials. However, the detailed understanding of its impact on a given process is poorly understood. Direct investigation of this phenomenon by experimental means, is a challenging endeavor, as the microscopic details are frequently hidden from macroscopic observations. Computational simulations, on the other hand, provide detailed information regarding molecular dynamics and flexibility. The theoretical approach is thus crucial in both understanding the experimental results and in expanding the underlying conceptual framework.