In this thesis, a series of molecular dynamics simulations have been performed in order to explore some fundamental mechanisms in biological research, such as salting effects and ion-mediated molecular interactions. A general goal of this research is to obtain an atomic level understanding of the structure, dynamics and thermodynamics of co-solutes (including typical ions like Na+, Mg2+ and complex molecules like urea, guanidinium chloride) and their effects on molecular and electrostatic interactions in protein folding/unfolding and DNA packaging. More interest was paid to the mechanisms that cause protein denaturation in urea solution, the electrostatic and conformational effects that induce, stabilize and regulate DNA condensation in the presence of counterions. These aims are realized by using a combination of molecular dynamics simulation and advanced sampling techniques like umbrella sampling and thermodynamic integration method.