The process parameters, pattern transfer mechanism, and pattern characterizations of alkanethiol self-assembled monolayers (SAMs) on a dip-pen nanolithography array are studied using molecular dynamics simulations. The effects of the type of probe tip, distance between probe tips, deposition temperature, probe tip velocity, probe tip radius, and humidity are evaluated in terms of molecular transference, alkanethiol meniscus characteristics, surface adsorption energy, number of transferred chains, and pattern characteristics. The simulation results clearly show that the molecular transfer ability of a conical tip array is better than that of a pyramidal tip array. For a conical tip array, the number of transferred chains increases with decreasing distance between tips, whereas for a pyramidal tip array, the number of transferred chains decreases. When the deposition temperature increases, the number of transferred molecules, the size of the pattern deposited on the substrate, and the density of molecular packing significantly increase due to an increase in molecular kinetic energy. The number of transferred chains significantly decreases with increasing tip velocity. The number of transferred molecules and meniscus size increase with increasing humidity. (C) 2011 Elsevier Ltd. All rights reserved.