We present some attempts to simulate nanoscale phenomena, which involve different length-scales and time-scales, using multiscale molecular-dynamics approaches. To simulate realistically an impurity-segregated nanostructure, we have developed the hybrid quantum/classical approach. The method can describe seamlessly both dynamical changes of local chemical bonding and nanoscale atomic relaxations. We apply the method to hydrogen diffusion in Si grain boundary. We find that the hydrogen is strongly trapped in (001)Σ5 twist boundary below 1000K, whereas it starts diffusing along the grain boundary above 1000K. For long-time processes in nanostructure formation, we apply the stochastic-difference-equation method to accelerate the simulations for microstructure evolution. The method bridges the states separated by high-energy barriers in a configuration space by optimizing an action, defined as an error accumulation along a reaction pathway. As an example, a SDE simulation is performed for Cu thin-film formation via nanocluster deposition. We show that the method can be applied effectively to search for the long-time process which involves a rare event due to a large potential barrier between two atomic configurations.