15067

1441 دكتري

دكتري

مكانيك كاربردي

اصفهان : دانشگاه صنعتي اصفهان

1398

هشت، 205ص. : مصور، جدول، نمودار

سعيد ضيايي راد

عليرضا شهيدي

امير لهراسبي، كورش حسن پور، مجتبي اعلايي، محمود اشرفي زاده، مهدي جوانبخت

1398/06/31

كتابنامه

مكانيك جامدات

مهندسي مكانيك

1398/06/31

2560006

ب 2 مقدمه 951 ب 3 پیادهسازی محاسبات نیرو 161 ب 3 1 میدانهای نیرویی مبتنی بر ذرات 161 ب 3 2 میدانهای نیرویی مبتنی بر اجسام صلب 161 ضمیمه ج روشی برای شبیهسازی میکروساختار مواد چندبلورهای 761 ج 1 چکیده 761 ج 2 مقدمه 861 ج 3 روش و مراحل کار 171 ج 3 1 بستهبندی ذرات 171 ج 3 2 گسسته سازی فضا 871 ج 3 3 شبیهسازی مرز و ناحیه اتصال 971 ج 4 شبیهسازی عددی 181 ج 4 1 مثال اول میکروساختار مخلوط آسفالت 181 ج 4 2 مثال دوم میکروساختار سهبعدی از فوالد دوفازی 481 ج 4 3 مثال سوم کنترل سرعت در برابر 186 ج 5 نتیجهگیری 881 ضمیمه د شیوه حداقل مربعات در رگرسیون کانفرمال چندخطی 981 مراجع 291 یازده

Developing a Molecular Dynamic Method for All Atom and Coarse Grain Simulations of Cell Membrane and Its Application in Membrane Mechanical Sculpting by I BAR Protein Nima Nouri n nouri@me iut ac ir August 3 2019 Department of Mechanical Engineering Isfahan University of Technology Isfahan 84156 83111 IranSaeed Ziaei Rad 1 szrad@cc iut ac irAlireza Shahidi2 shahidi@cc iut ac irAbstractThis thesis aims to investigate the effects of BAR domain proteins on the shape of cellmembranes by the use of molecular dynamics simulations The curvature of the lipidmembranes can be made by different sources The most important source is proteins Proteinscan change the shape of lipids by various phenomena such as binding to the membrane localinsertion and scaffolding Researchers have shown that the BAR domain proteins shift themembrane curvature by scaffolding In this thesis the effects of a single I BAR protein as wellas different patterns of I BAR proteins on the shape of the membrane are studied First acomprehensive literature survey on the BAR proteins and their roles in the cell mechanisms iscarried out Because of the high computational cost of all atom simulations the use of a coarsegrain model is inevitable Next a coarse grain model of the I BAR proteins on the membraneis constructed Finally the effects of one and a group of proteins on the curvature of the cellmembrane are studied Simulations show that the obtained results depend on many parameterssuch as protein density alignment arrangement on the lipid membrane patch Finally theobtained results compared to the available numerical and experimental data in the literature Keywords I BAR Protein Shape Based Coarse Grain Molecular Dynamics Membrane Bending IntroductionThe unique and extraordinary beautiful shapes of cells and organs created by the physicalforces acting on the cell membrane The main aim of molecular cell biology is to understandthe physics and mathematics of the underlying mechanisms used by the cell to form themembrane Each cell shape is formed due to a physiological reason Cells without internal membranes likeProkaryotic cells and erythrocytes cells can produce an array of shapes regarding theiroperational purpose The surface of a cell or cellular organelle is covered by a biomembranewhich is why that the shape of a cell is defined by its membrane shape This information showsthe importance of understanding the underlying mechanism on reshaping a bio membrane 1 1 The physical principals that alter membrane curvatureProteins are among the tools that can change the membrane curvature by applying surfaceforces to them The curvature on bio membranes can be created by proteins which can adhereto them Although there are many mechanisms available on membrane reshaping only three ofthem are introduced here 1 Department of Mechanical Engineering Isfahan University of Technology 84156 83111 Isfahan Iran2 Department of Mechanical Engineering Isfahan University of Technology 84156 83111 Isfahan Iran

سعيد ضيايي راد

عليرضا شهيدي

امير لهراسبي، كورش حسن پور، مجتبي اعلايي، محمود اشرفي زاده، مهدي جوانبخت