Understanding the transport of hydrogen within metallic nanomaterials is crucial for the advancement of energy storage and the mitigation of hydrogen embrittlement. Using nanosized palladium particles as a model, recent experimental studies have revealed several interesting phenomena that occur over long time periods. The time scale of these phenomena is beyond the capability of established atomistic models such as molecular dynamics. In this work, we present the application of a new approach, referred to as diffusive molecular dynamics (DMD), to the simulation of long-term diffusive mass transport at the atomic scale. Specifically, we simulate the absorption of hydrogen by palladium nanocubes with edge lengths in the range of 4 nm and 16 nm. We find that the absorption process is dominated by the initiation and propagation of an atomistically sharp alpha/beta Pd-H phase boundary, with thickness in the range of 0.2 to 1.0 nm, which separates an alpha phase core from a beta phase shell. The evolution of phase boundary and the resulting local lattice deformation are described in this paper in detail. The effects of size on both equilibrium and kinetic properties are also assessed. (C) 2018 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.