This work presents three chapters, each of which detail a recent advancement in the field of molecular dynamics simulations research. Chapter One describes the molecular dynamics method to simulate the transport processes in nanofluids and the molecular dynamics simulation of transport processes in confined conditions and in nanochannels in particular. Chapter Two provides a comprehensive review on the investigations into the nanoscopic deformation mechanisms of silicon carbide (SiC) and potassium dihydrogen phosphate (KDP) crystals using molecular dynamics simulations under various mechanical loading conditions. Chapter Three reports the effects of pressures applied during rapid solidification of local structures formed in the glassy NiTi alloy based on molecular dynamics simulation results.