Molecular simulation studies of peptide aggregation in small finite sized systems and near surfaces [Elektronische Ressource] / vorgeelgt von Gurpreet Singh

Molecular Simulation Studies ofPeptide Aggregation in Small FiniteSized Systems and Near SurfacesDissertationzur Erlangung des Grades einesDoktor der Naturwissenschaften(Dr. rer. nat.)eingereicht beimFachbereich Chemie der Technische Universit¨at Dortmundvorgelegt vonMS (Med. Chem.) Gurpreet SinghNew Delhi, IndiaDortmund, 2008First Referee: Prof. Dr. R. WinterSecond Referee: Prof. Dr. A. GeigerDate of Examination: 05–02–2009AcknowledgementThe work described in this thesis was carried out in the lab of Prof. Dr. Roland Winter,under his direct supervision. I am thankful to him for providing me with an opportunityand resources to work on this project. This thesis wouldn’t have taken its present formwithout the inputs of Dr. Ivan Brovchenko and Dr. Alla Oleinikova, I am greatful toboth of them for their guidance. Dr. Dietmar Paschek helped me with the purchaseand setup of the Linux cluster, and performing simulations with RPMD and Gromacspackages. Replica exchange simulations were carried out on LiDO cluster maintainedby the University. I am greatful to Maximilian Andrews and Dr. Roland Krivanek forhelping me withthe maintenance ofcomputers, andDr. Karsten Vogtt,Michael Sulc, Dr.Claus Czeslik and Diana Radovan for enlightening discussions. I thank Dr. NagarajanPeriasamy, Dr. Nadeem Javid and Dr. Mahesh Kulharia for their help and support.