Nanotechnology and fluid mechanics are two scientific areas where recent progress has disclosed a variety of new posibilities. The advances in both fields stablished the grounds for interdisciplinary approaches and recent findings promise novel applications that are leading to a technological revolution. Novel nanofabrication techniques have opened up possibilities for the development of small-scale integrated devices, such as lab-on-a-chip for biochemical synthesis and analysis, the integration is achieved by miniaturization of the functional elements e.g., of the channels transporting the fluid and of the sensors performing the analysis, and as the size of these devices reaches the sub-micron range we enter the field of nanofluidics. Nanofluidics is defined as the study of flows in and around nanosized objects. Modeling of transport in nanofluidic systems differs from microfluidic systems because changes in transport caused by the walls become more dominant and the fluid consists of fewer molecules. Carbon nanotubes are tubular graphite molecules which can be imagined to function as nanoscale pipes or conduits. Another important material for nanofluidics applications is silica. Nowadays, silica nanochannels are produced in nanometer scale using different nanofabrication techniques. Silica nanochannels are being implemented in several nanotechnology applications such as nanosensor devices, nano separators, nanofilters and a plethora of devices for nanobiological and biochemical applications. Experiments at the nanoscale are expensive and time consuming moreover the time scale associated to several nanoscale phenomena requires a very high time resolution of the devices performing nanoscale measurements. Computational nanofluidics is the enabling technology for fundamental studies, development, and design of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics methodology. In the second part of this thesis, we present the results of three different research projects. Fristly, we present a computational study of thermophoresis as a suitable mechanism to drive water droplets confined in different types of carbon nanotubes. We observe a motion of the water droplet in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate that the motion of the capsule (inner carbon nanotube) can be controlled by thermophoretic forces induced by thermal gradients. The simulations find large terminal velocities of 100 to 400 nmns−1 for imposed thermal gradients in the range of 1 to 3 Knm−1. Moreover, the results indicate that the thermophoretic force is velocity dependent and its magnitude decreases for increasing velocity. Finally, we present an extensive computational study of nanoscale systems including silica substrates and channels, water and air. This study includes the calibration of a force field to describe the silica-water-air interactions. Moreover, In this study we perform very long simulations of nanoscale systems containing silica, water and air. We investigate the solubility of air at different pressures in silica-water systems. From our simulations we infer a layer with high air density close to silica surface. Furthermore, we conduct simulations to analyze the earlier stage of the capillary filling process of silica nanochannels, we focus this study on the roll of air in this system. We find that air at high pressures can affect the capillarity in silica channels below 10 nm height.