The study of interactions between different types of molecules on, or near, surfaces and their self-assembly into patterns is an exciting and challenging area of research in chemical engineering. In particular, a self-assembled monolayer (SAM), formed by the adsorption of molecules on a surface, is an attractive system to model, modify and study surface properties. Research in this field has gained momentum due to an increased interest in nanostructured surfaces like nanoparticles, nanotubes, nanotetrapods, etc. Phase-separated domains in SAMs coating these particles can act as attractive, repulsive or reactive patches that influence interparticle interactions and can act as catalytic sites. The ability to control the placement of such patches can also help arrange the particles into higher order structures. The use of SAMs to arrange sticky patches on a nanoparticle is therefore a powerful method for assembling hierarchical structures from the bottom-up.

Using computer simulations we try to understand the factors that drive molecular self-assembly and phase separation on nanostructured surfaces. In this thesis, we describe results from dissipative particle dynamics simulations used to simulate phase separation and pattern formation in SAMs comprising of two incompatible species. We describe an entropic driving force, resulting from length or bulkiness difference between the co-adsorbed molecules, which leads to the formation of striped patterns and two-dimensional micelles in SAMs on nanospheres, nanocylinders and flat surfaces. We describe why Janus particles will form if the substrate has a sharp curvature. We explain how surface stress, arising from curvature, is important for formation of ordered stripes. We predict that phase separation in SAMs can be used as a useful tool to obtain alternating rings around nanorods and nanowires. Our understanding of patterned substrates allows us to explain an unexpected, non-monotonic dependence of work of adhesion of striped nanoparticles on the compositions of surfactants on their surface.

In general, we study pattern formation in SAMs on surfaces as a function of substrate curvature, surface coverage, composition, immiscibility and length/bulkiness of adsorbed molecules. Results from these simulations have important applications in fields ranging from catalysis to biosensing.