7146

467 دكتري

دكتري

شيمي فيزيك

اصفهان: دانشگاه صنعتي اصفهان، دانشكده شيمي

1391

پانزده،119ص.: مصور،جدول،نمودار

ص.ع.به فارسي و انگليسي

بيژن نجفي، سيف ا... جليلي، سامان علوي

حسين فرخ پور

3/8/91

حسين اسلامي، سعيد يگانگي، تهمينه كشاورزي، مهران غياثي

شيمي

ID467 دكتري

به فارسي و انگليسي: قابل رويت در نسخه ديجيتالي

Molecular Dynamics Simulations of Biological Molecules on Surfaces and in Membranes Adsorption and Pattern Formation of DNA Bases on the Au 111 Surface and the Amyline Peptide in the Dioleoylphosphatidylcholine Bilayer Membrane Afsaneh Maleki maleki afsaneh@ch iut ac ir April 24 2012 Department of Chemistry Isfahan University of Technology 84156 83111 Isfahan Iran1st Supervisor Bijan Najafi E mail najafi@cc iut ac ir2nd Supervisor Seifollah Jalili E mail sjalili@kntu ac ir3nd Supervisor Saman Alavi E mail saman alavi@nrc cnrc gc caAdvisor hossein Farrokhpour E mail farrokhphossein@gmail comDepartment Graduate Coordinator Bijan Najafi Department of Chemistry Isfahan University of Technology Isfahan 84156 83111 Iran fax 983113912350 Department of Chemistry K N Toosi University of Technology Tehran P O Box 15875 4416 Iran Department of Chemistry University of Ottawa Ottawa Ontario K1N 6N5 Canada Department of Physics Isfahan University of Technology Isfahan 84156 83111 IranAbstractInvestigating of the mechanism of self assembly of bases of deoxyribonucleic acid DNA on the Au 111 surface showes that at 300 and 400 K and at low coverage guanine adenine and thymine form hydrogen bondedchains on the surface while cytosine molecules cluster into islands At larger coverage simulations indicate thatadenine molecules form ordered two dimensional hexagonal structures while guanine cytosine and thyminemolecules aggregate into small random clusters These observations agree with scanning tunneling microscopy STM experiments of the DNA bases on gold surfaces The hydrogen bond interactions and stability ofbase base homopairs which are the smallest components of the self assembled structures on the Au 111 surface are calculated and compared with calculations of the homopairs in the gas phase and with values available in theliterature The binding energies per base on the surface initially decrease in magnitude with increasing surfacecoverage and then reach constant plateau at large coverages The mechanisms of molecular mobility for the baseswith one molecule coverage on the surface are analyzed at two temperatures The study of amylin peptid in dioleoylphosphatidylcholine DOPC is performed using molecular dynamicssimulations Dynamics and transport properties of the peptide and phospholipids bilayer are investigated Thelateral diffusion of DOPC is in the order of 10 8 cm2 s 1 and is in agreement with the experimental results Orderparameter thickness density profile and area per head group of lipids in membranes are calculated The secondstructure shows that the amino acids in two terminals are structureless and two helix segments in the peptideare connected through an unstructured link This structure is similar to experimental structure in the quasimembrane Root mean square deviations and root mean square fluctuations of peptide are calculated Free energycalculations of the mutation of Ile 26 Pro 26 in the amylin peptide are performed in bilayer membrane andaqueous solution using molecular dynamics simulations and cyclic thermodynamics It is shown that the amountof helix of mutated peptide in aqueous solution reduce to 5 helix whereas this configuration preserve in bilayermembrane It is interesting that accessible surface areas increase for hydrophobic amino acids in membraneenvironment and for hydrophilic amino acids in aqueous solution when coupling parameter changes from 0 to 1 At the end radius of gyration of peptide are calculated Keywords DeoxyriboNucleic Acid base gold surface molecular dynamics simulation Amylin peptide Dioleoylphosphatidylcholine lipid Gibbs free energy difference second structure

بيژن نجفي، سيف ا... جليلي، سامان علوي

حسين فرخ پور

حسين اسلامي، سعيد يگانگي، تهمينه كشاورزي، مهران غياثي