13986

12706

كارشناسي ارشد

ماده چگال

اصفهان: دانشگاه صنعتي اصفهان، دانشكده فيزيك

1397

يازده، ۶۴ص.: مصور، جدول، نمودار

مجتبي اعلائي، مجيد مسيبي

جواد هاشمي فر

ممتحن مدعو: فرهاد شهبازي; ممتحن داخلي: اسماعيل عبدالحسيني سارسري

1397/07/24

كتابنامه

فيزيك

فيزيك

ID12706

Simulation of DNA strand in fluid Shirin Shafiee shirin shafiee@ph iut ac ir June 24 2018 Department of Physics Isfahan University of Technology Isfahan 84156 83111 Iran University Code IUT 77142 Degree M S c Language Farsi supervisor Dr M Alaei Dr M Mosayebi m alaei@cc iut ac ir majid mosayebi@bristol ac uk Abstract All of the organisms are made of cells In the last recent decads scientists and researchers study significently on biological phenomenon Deoxyribonucleic acid DNA as the most known biomolecule is interested by biologists and genetic engineers DNA molecules is made of two nucleotide strand which is twisted to each other like a helix For the special and unique structural properties of DNA there are many research which is done on it not only in genetics but also in other fields like nanotechnology For these reasons predicting and describing DNA behaviors is crucial So there are many models and simulations on DNA to help this purpose In this work first we will introduce DNA as a biomolecule then review some of particle simulation methods and study some DNA modeling like coarse graining models The purpose of this work is to calculate the forces on each parts of a DNA strand which is modeled by bead spring model in the presence of a oscillating plate in a fluid For this reason we use LAMMPS code and SRD package to simulate fluid and DNA strand So at first we simulate the fluid by use of stochastic rotation dynamics Then we put an oscillating plate in our system to obtain velocity profile for the second stokes problem In the next step we define a polymer strand by use of bead spring model and attach it to the plate and calculate force on each bead Keywords deoxyribonucleic acid fluid stochastic rotation dynamics flow near oscillating plate bead spring model LAMMPS

مجتبي اعلائي، مجيد مسيبي

جواد هاشمي فر

ممتحن مدعو: فرهاد شهبازي; ممتحن داخلي: اسماعيل عبدالحسيني سارسري