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We present NanoImprint Lithography(NIL)technique to align block copolymers(BCP)lamellar phases perpendicularly to the substrate without in-plane defects over distances much larger than the natural lamellar periodicity.The NanoImprint technique is found to be an efficient tool to organize the direction of BCP lamellar.Our modeling relies on self-consistent field(SCFT)calculations done in two-and three-dimensions [1-3].We also addressed the combined effects of nano-patterned substrates and the polymer/air free interface on the self-assembly of BCP thin films.We have treated air as a bad solvent and modified the SCFT accordingly in order to study the phase behavior of finite volume films.We obtained an undulating polymer/air interfaces when the films are casted on chemically patterned substrates.We also studied the self-assembly of BCP thin films on topographic substrates and found that it is more efficient to confine a BCP film between a solid mold and a counter planner surface in order to obtain a perfect perpendicular lamellar structure [4].