The pattern transfer mechanism of an alkanethiol self-assembled monolayer (SAM) on various rough surfaces during the dip-pen nanolithography (DPN) process and pattern characterizations are studied using molecular dynamics (MD) simulations. The mechanisms of molecular transference, alkanethiol meniscus characteristics, surface adsorbed energy, number of molecular transfer, contact angle and pattern characteristics are evaluated during the DPN process at room temperature. The simulation results clearly show that the molecular transfer ability in DPN is optimum for deposition on a smooth surface, because surface defects create a potential diffusion barrier for the control of the spreading of excess ink molecules. The adsorbed area of SAMs, number of molecular transfer and pattern size are significantly inversely proportional to the degrees of roughness of a substrate. The adsorbed area of SAMs is increased by the pull-off process and the growth rate of adsorbed area is about 11-38%. The effect of surface roughness on the DPN process can be decreased by increasing the indentation depth of a tip.
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