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Simulation of the Biomolecule Imaging and Manipulation Via AFM by Molecular Dynamics Method

Kheiroddin, Mohsen | 2015

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 47270 (08)
  4. University: Sharif University of Technology
  5. Department: Mechanical Engineering
  6. Advisor(s): Meghdari, Ali; Moosavi, Ali
  7. Abstract:
  8. In this thesis we try to find optimized parameters for imaging and manipulation of a biosample with AFM. For this we have prepared a numerous Molecular Dynamics simulation and find some reliable result. So, first we have focused on imaging process in Non contact mode (the less harmful mode). Then we headed into the manipulation process. The main problem about manipulating a biosample is the environment. In imaging section, the process of imaging a biomolecule by AFM is modeled using molecular dynamics simulations. Since the large normal force exerted by the tip on the biosample in contact and tapping modes may damage the sample structure and produce irreversible deformation, the non-contact mode of AFM (NC-AFM) is employed as the operating mode. The biosample is scanned using a carbon nanotube (CNT) as the AFM probe. CNTs because of their small diameter, high aspect ratio and high mechanical resistance attract many attentions for imaging purposes. The tip-sample interaction is simulated by the molecular dynamics (MD) method. The protein, which has been considered as the biomolecule, is ubiquitin and a graphene sheet is used as the substrate. The effects of CNT's geometric parameters such as the CNT height, the diameter, the tilt angle, the flexibility and the number of layers on the image quality have been evaluated. And then in the manipulation section, we evaluated the positioning process. Nano-manipulation is one the greatest field of nano-robotics and nano-assembling. Positioning process is almost the most important part of nano-assembling sections and it is poorly investigated, especially for biologic samples. The important point about bio-sample manipulation is that they exist in aqueous media. Thus, this paper is devoted to modeling the process of positioning a bio-sample with AFM via Molecular Dynamics method (MD) in both UHV media and water. The AFM tip is selected to be Carbon Nanotube (CNT) and the substrate is a graphite sheet. Here, we examine several parameters which may affect the quality of manipulating process such as the CNT initial position compared to the sample and substrate, its Diameter, positioning mode (pushing or pulling), thermal fluctuation and solvent media. Results indicate that pulling method with a CNT which has higher diameter and lower gap to the substrate is the most stable condition, especially in UHV media
  9. Keywords:
  10. Molecular Dynamic Simulation ; Atomic Force Microscopy (AFM)Imaging ; Biomolcule Recognition ; Imaging ; Manipulator

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