Saraswat, Govind2014-04-222014-04-222014-02https://hdl.handle.net/11299/163023University of Minnesota Ph.D. dissertation. February 2014. Major: Electrical Engineering. Advisor: Prof. Murti V. Salapaka. 1 computer file (PDF); ix, 95 pages.This thesis aims to provide a methodology and paradigm to aid emerging research studying and manipulating different mechanical properties (like topography, etc) of material. This material research is immensely enhanced by different probe based microscopy enabling design and discovery at the atomic scale. The Atomic Force Microscope (AFM) is one of the foremost technique for such interrogation of material. AFM is a micro-cantilever based device capable of achieving sub Angstrom resolution. Recently, probe researchers have shifted the focus to interrogate physical properties other than topography, namely stiffness and dissipation. Current AFM methods to determine these properties are not suitable for soft samples. Thus there is a scarcity of real-time techniques to quantify the mechanical properties of soft-matter, that include polymers and bio-matter. A method is reported (REEP algorithm) which is able to provide estimates of sample stiffness and dissipation during intermittent contact mode operation of AFM. A systems approach is first applied to relate the material properties to the parameters of a time-varying linear system. Then a RLS algorithm is used to estimate these paramters. The method is verified using the averaging theory and shown to accurately provide the dissipation estimates when applied on different polymer samples. A FPGA based hardware implementing the REEP algorithm is developed to make use of the real-time capability of the algorithm. The REEP module is then used to study stiffness and dissipation properties of PBMA-PLMA polymer blend. A magnetic excitation hardware is also built to accurately resonate the cantilever in liquid. A clean ac response of the cantilever is thus achieved. REEP module is then used to delineate material properties of microtubules in buffer solution. It is shown that REEP module is able to accurately estimate the stiffness and dissipation properties of the bio-sample during under liquid operation of AFM. Higher eigenmodes of cantilever dynamics often come into play when AFM is operated in liquid (low Q operation). To obtain better estimation of the contribution of these modes, a receding horizon Kalman Filter is reported. Estimates are shown to have an order of magnitude improvement compared to current methods. A high bandwidth detection algorithm is also reported which is useful if just the presence of the higher modes is to be detected. Finally, a a new mode of imaging using the equivalent parameters of the time-varying system as a feedback is proposed. Simulation and experimental results show higher resolution for low Q operation. This thesis separately explores a new hypothesis to understand directed transport in cells. Motor proteins which are the work-horse of intracellular transport, walk on microtubules (tubulin polymers) to transfer cellular cargo from one place to another inside a cell. Almost absolute directed transport is achieved while transport takes place over a random arrangement of microtubules. It is shown via simulation and analytical results that if the motors have an ability to switch between different microtubules, a little bias in the microtubule network can lead to directed transport. This renders useless any kind of recognition factor to be needed for motors to know which microtubule is target ended.en-USAFMMaterial CharacterizationMultifrequencyMultimodeSoft matterSPMThesis or Dissertation