Sharif Digital Repository

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... 

Molecular Dynamics as a powerful method in the field of Nano-simulation has been widely used in recent years. Different contact processes such as Nano-manipulation, AFM Imaging, and Nano-indentation can be simulated using this method. There have been numerous researches done on calculating techniques of simulation of different phenomena in Nano-technology. Specifically, friction and Nano-indentation which are parts of Nano-contact processes have been simulated by different investigators. However, on some other parts, e.g. Nano-manipulation and AFM Imaging, there are few studies done up to now. Thus, a simulation and computational software seems necessary in this field. The main goal of... 

Nowadays, the atomic force microscopy (AFM) has become a useful laboratory tool with variety of applications. In the traditional imaging technique, usually the amplitude or frequency of AFM tip oscillations is set at a desired value using a feedback control system which is a relatively slow process. In the current research, we propose an estimation approach which uses an adaptive fading extended Kalman filter (augmented with forgetting factor) as a system observer and couples with the system dynamics to determine the sample topography. As a result, in addition to state variables of system dynamic, the sample height as an unknown parameter is estimated with high accuracy in a relatively short...