This dissertation presents our research on hydrophilic and hydrophobic interactions performed using molecular dynamics (MD) simulations with nanoscale model plates. Hydrophobic and hydrophilic interactions have been discussed in many places of chemistry and biology to explain water-involved phenomena such as solute aggregation and protein folding. However, until recently, the absence of appropriate methodology and insufficient computing power has prevented quantitatively detailed discussions of these phenomena. In this dissertation, we design model hydrophilic and hydrophobic plates and use MD methodology to study the nature of the hydrophobic and hydrophilic interactions. These plates are simple enough to be computationally accessible but still applicable for understanding the essence of hydrophobic and hydrophilic phenomena in nature. Since the hydrophobic and hydrophilic interactions are considered to be medium effects involving water molecules, we extract this medium contribution from the total interaction between two plates in water and analyze it. This analysis is applied to the case of two interacting model lipid plates across water and it demonstrates that the monotonic repulsive interaction between lipid bilayers, known as the hydration force, originates from the water-induced interaction, and not from the steric repulsions between the headgroups. Further detailed thermodynamic and hydrogen bonding analyses indicate that strong plate-water interaction is responsible for the repulsive water-mediated interaction. Interestingly, when we remove electric charges from the model lipid plate, the repulsive character due to water changes to the attractive character and the overall shape of the total interaction is very similar to typical hydrophobic interaction. We investigate the hydrophobic property of the charge-removed model lipid plate by comparing it with other hydrophobic plates based on the graphene plate model. From this comparison, we find that the roughness of the surface enhances the hydrophobic interaction. The graphene plates are also used to study the fluctuation of water between hydrophobic plates, which is considered to be a signature of the hydrophobic interaction
