A molecular dynamics coarse-grained block copolymer (BCP) model was developed and used to studied directed self-assembly (DSA), especially in regards to applications for semiconductor manufacturing. Most of the thesis is spent investigating the effect that guiding layer properties and block copolymer properties have on line roughness and defect density in a BCP-DSA process. These two effects are perhaps the most critical in making BCP-DSA a cost efficient industrial process. It is found that guiding patterns have little effect on line roughness and in fact that the BCP heals the majority of roughness in the underlying pattern. BCP properties have a larger effect on line roughness. Segregation strength (as measured by χN, where χ is the Flory- Huggins interaction parameter and N is the degree of polymerization) resulted in a larger than expected increase in line roughness when χN was low. Polydispersity resulted in a moderate increase in line roughness. In regards to equilibrium defect density, free energy calculations showed that χ was the primary determining factor, not χN as many expected. Equilibrium defect density was found to decrease exponentially with increasing χ. Defect density is also found to scale exponentially with polydispersity. Concerning defect heal rate, which can increase the real defect rate of a process if said rate is too low, it is found that increasing χN linearly increased the barrier to defect healing, which means that the defect heal rate decreases exponentially. However, for thin films this is only true for χN > ~ 50. Below χN ~ 50, the barrier is approximately constant. These results give excellent guidance to the type of materials and processes necessary to optimize a BCP-DSA process. A simulation technique designed to more efficiently sample over energy barriers called protracted noise dynamics for polymer systems was developed and studied. It was found that a decrease in simulation time of up to 4 orders of magnitude was achieved. The effect of box size on allowable pitches for a lamellar forming BCP was derived and demonstrated. It was found that more elongated boxes yielded more possible pitches and more accurate results. A short study on the effect of multiblock copolymers on the location of the order-disorder transition was also carried out and it was found that multiblock copolymers had small effect on the ODT. The distribution of chain conformations was also calculated.