| Many polymer and organic molecule assemblies have been investigated recently because of their applications in molecular electronics, surface chemistry and bio-sensors. These assemblies are often used in surface studies because they are simple structurally, stable thermodynamically and have well-defined order. Great effort has been made to understand the properties of these systems both experimentally and theoretically. Computer simulations in collaboration with experiments help us understand these systems in greater detail.;In the first project, heterogeneous systems containing of a host alkanethiol molecule (dodecanethiol) monolayer with a thiol-terminated azobenzene molecules were considered. Classical molecular dynamics simulations showed a phase transition that was characterized by the change in the tilt angle, heat capacity and diffusion constant of the host molecules. The results for the pure monolayer were compared to the heterogeneous systems and the results were used to describe recent experiments. The phase transition was found to occur at about 350K for all three systems which is in good agreement with the experimental results.;In the second project, motions of Au atoms on alkanethiol monolayers were described using classical molecular dynamics in conjunction with first principle calculations. Based on quantum-mechanical calculations, the interaction between Au atoms and the monolayer was calibrated and then the motions of the atoms were investigated as a function of coverage and temperature. We found good agreement with experimental results. Gold atoms were observed to penetrate inside the monolayer at room temperature but not below room temperature.;In the third project, inspired by recent experiments, we used classical molecular dynamics to study the motions of Agn clusters with various sizes on alkanethiol self-assembled monolayers. Detailed results on the dynamics, diffusion and sintering processes of these nano-clusters were reported. |
