In this work, our recent efforts in the simulation of protein-surface interactions will be reviewed, particularly those related to the molecular-level nonfouling mechanism. Three approaches have been used in our molecular dynamics/Monte Carlo simulations to examine the origin of protein adsorption, including (a) surface hydration around varying surface functional groups, (b) repulsive forces applied to a protein when it approaches a surface, and (c) free energy changes upon protein adsorption. The surfaces studied include oligo(ethylene glycol) (OEG), phosphorylcholine (PC) and carbohydrate self-assembled monolayers. Simulations are performed using a locally developed simulation program, BIO_SURF, which is capable of simulating biomolecular-material interfaces in the presence of explicit water molecules and ions. Furthermore, quantum chemical calculations have been performed to examine the structures and charge distributions of a variety of zwitterionic groups in a vacuum or solvent. Accurate force fields for zwitterionic materials are developed based on ab initio results. With accurate force fields, molecular dynamics simulations are then performed to study how the packing structures of zwitterionic-based materials affect their ability to resist protein adsorption.