Atomic-scale study on particle movement mechanism during silicon substrate cleaning using ReaxFF MD

•Water reduces the deposition rate of the nanoparticles on the substrate.•Water increases the initial adhesion between the chemisorption nanoparticles and the substrate.•Water acts as a lubricating layer, accelerating the desorption of interfacial chemical bonds and mitigating damage to the Si substrate.•H2O2 pretreatment of the substrate resultes in more negative surface charge.•H2O2 pretreatment impedes particle deposition due to the increase of electrostatic repulsion and hydrophilicity of substrate surface.•H2O2 pretreatment increases the probability of Si-O-Si bond formation, thus raising the removal difficulty of chemisorption nanoparticles.