This dissertation examines two of the most important behaviors of amorphous polymers: the glass transition and plastic deformation. These phenomena are examined using atomic-scale molecular dynamics simulations, in which the atomic interactions are described through empirical bonded and non-bonded interatomic potentials representing amorphous polyethylene. Molecular dynamics simulations were performed to elucidate the effects of temperature and thermodynamic constraints on the glass transition. The simulation results are found to be in excellent agreement with experimentally established trends in glass transition behavior. Analyses of these data show that the glass transition is primarily associated with the freezing of the torsional degree...