Simulations of mechanical properties of crystalline units of Bombyx mori silkworm silk

Bombyx Mori silkworm silk (Mulberry silk) is the subject of this thesis which is the one of the many types of natural harvastable silkworm silk (Bombyx mori, Tasar, Eri, Mugan, …). Due to its exceptional physicochemical properties, such as high Young's modulus, stiffness, strength, biocompatibility and biodegradability. Silk has a wide range of application areas from textile to biomedical. Complicated squence of simple amino acid components, mostly Glysine and Alanine, gives the silk these remarkable properties. Bombyx mori silk fiber is considered as a semicrystalline polymer consting of highly oriented polar-antiparallel and antipolar-antiparallel β- sheet crystalline regions connected with amorphous regions. Therefore it is of great importance to study mechanical properties of the crystalline region in order to shed light on some unknow properties, increase our understanding on structure and mechanics relation, and antribute to the production of composite materials. Simulation methods are cheep and practical to study such materials at atomic level and extreme conditions. We have used Steered Molecular Dynamics simulation method to investigate mechanical properties (local pulling test) of model crystalline region in vacume and water. Applying the mechanical pulling test to different chains and sheets will let us understant the relation between local structure effect of water, hydrogen bonding, strength and toughtness of silk. Moreover, the effect of the size along the chain direction, that depends on the type of the silkworm, has been also examined. This thesis was suportted by TUBITAK under the project 115F524 High Performance Applications for Molecular Dynamics Simulation of Thermo-Mechanical Properties of Bombyx Mori Silk Fibroin Crystallite Unit. Keywords: Bombyx mori silk, β- sheet crystallite, mechanical pulling test, Steered MD