Algorithmic approaches to high speed atomic force microscopy

Thesis (Ph.D.)--Boston UniversityThe atomic force microscope (AFM) has a unique set of capabilities for investigating biological systems, including sub-nanometer spatial resolution and the ability to image in liquid and to measure mechanical properties. Acquiring a high quality image, however, can take from minutes to hours. Despite this limited frame rate, researchers use the instrument to investigate dynamics via time-lapse imaging, driven by the need to understand biomolecular activities at the molecular level. Studies of processes such as DNA digestion with DNase, DNA-RNA polymerase binding and RNA transcription from DNA by RNA polymerase redefined the potential of AFM in biology. As a result of the need for better temporal resolution, advanced AFMs have been developed. The current state of the art in high-speed AFM (HS-AFM) for biological studies is an instrument developed by Toshio Ando at Kanazawa University in Japan. This instrument can achieve 12 frames/sec and has successfully visualized the motion of protein motors at the molecular level. This impressive instrument as well as other advanced AFMs, however, comes with tradeoffs that include a small scan size, limited imaging modes and very high cost. As a result, most AFM users still rely on standard commercial AFMs. The work in this thesis develops algorithmic approaches that can be implemented on existing instruments, from standard commercial systems to cutting edge HS-AFM units, to enhance their capabilities. There are four primary contributions in this thesis. The first is an analysis of the signals available in an AFM with respect to the information they carry and their suitability for imaging at different scan speeds. The next two are algorithmic approaches to HS-AFM that take advantage of these signals in different ways. The first algorithm involves a new sample profile estimator that yields accurate topology at speeds beyond the bandwidth of the limiting actuator. The second involves more efficient sampling, using the data in real time to steer the tip. Both algorithms yield at least an order of magnitude improvement in imaging rate but with different tradeoffs. The first operates beyond the bandwidth of the controller managing the tip-sample interaction and therefore the applied force is not well-regulated. The second keeps this control intact but is effective only on a limited set of samples, namely biopolymers or other string-like samples. Experiments on calibration samples and λ-DNA show that both of the algorithms improve the imaging rate by an order of magnitude. In the fourth contribution, extended applications of AFMs equipped with the algorithmic approaches are the tracking of a macromolecule moving along a string-like sample and a time optimal path for repetitive non-raster scans along string-like samples

An adaptive non-raster scanning method in atomic force microscopy for simple sample shapes

It is a significant challenge to reduce the scanning time in atomic force microscopy while retaining imaging quality. In this paper, a novel non-raster scanning method for high-speed imaging is presented. The method proposed here is developed for a specimen with the simple shape of a cell. The image is obtained by scanning the boundary of the specimen at successively increasing heights, creating a set of contours. The scanning speed is increased by employing a combined prediction algorithm, using a weighted prediction from the contours scanned earlier, and from the currently scanned contour. In addition, an adaptive change in the height step after each contour scan is suggested. A rigorous simulation test bed recreates the x-y specimen stage dynamics and the cantilever height control dynamics, so that a detailed parametric comparison of the scanning algorithms is possible. The data from different scanning algorithms are compared after the application of an image interpolation algorithm (the Delaunay interpolation algorithm), which can also run on-line.We would like to acknowledge the support of the Engineering and Physical Sciences Research Council (EPSRC) (grant nos. EP/I034882/1 & EP/I034831/1)

Force-induced acoustic phonon transport across single-digit nanometre vacuum gaps

Heat transfer between bodies separated by nanoscale vacuum gap distances has been extensively studied for potential applications in thermal management, energy conversion and data storage. For vacuum gap distances down to 20 nm, state-of-the-art experiments demonstrated that heat transport is mediated by near-field thermal radiation, which can exceed Planck's blackbody limit due to the tunneling of evanescent electromagnetic waves. However, at sub-10-nm vacuum gap distances, current measurements are in disagreement on the mechanisms driving thermal transport. While it has been hypothesized that acoustic phonon transport across single-digit nanometre vacuum gaps (or acoustic phonon tunneling) can dominate heat transfer, the underlying physics of this phenomenon and its experimental demonstration are still unexplored. Here, we use a custom-built high-vacuum shear force microscope (HV-SFM) to measure heat transfer between a silicon (Si) tip and a feedback-controlled platinum (Pt) nanoheater in the near-contact, asperity-contact, and bulk-contact regimes. We demonstrate that in the near-contact regime (i.e., single-digit nanometre or smaller vacuum gaps before making asperity contact), heat transfer between Si and Pt surfaces is dominated by force-induced acoustic phonon transport that exceeds near-field thermal radiation predictions by up to three orders of magnitude. The measured thermal conductance shows a gap dependence of $d^{-5.7\pm1.1}$ in the near-contact regime, which is consistent with acoustic phonon transport modelling based on the atomistic Green's function (AGF) framework. Our work suggests the possibility of engineering heat transfer across single-digit nanometre vacuum gaps with external force stimuli, which can make transformative impacts to the development of emerging thermal management technologies.Comment: 9 pages with 4 figures (Main text), 13 pages with 7 figures (Methods), and 13 pages with 6 figures and 1 table (Supplementary Information

Design and Implementation of a Near-field Scanning Optical Module for Inverted Microscopes

This dissertation describes the design and implementation of a home-built near-field scanning optical microscope (NSOM) module for inverted microscopes. In this design, the NSOM module is built atop an inverted fluorescence microscope. This is particularly well suited for applications in which the normal imaging modes of the inverted microscope are still required to locate and study the sample before performing NSOM experiments. This module is used as a near-field instrument for nanostructure investigation of various samples including plane-ruled reflection gratings, AFM calibration standards, nanospheres and gold nanoparticles. In addition, we will demonstrate the ability to achieve nanometer-scale surface modification of specific polymer films using this technique

Master of Science

thesisThe focus of this thesis has been developing and validating new methods of streamlining expensive function calls. These new methods of streamlining are applied to the problem of modeling electrodynamic response in in nite two-dimensional nanoparticle (NP) arrays. Using these methods, an exact analytical solution for electromagnetic interaction with two-dimensional spherical periodic in nite arrays has been developed. The new solution o ers fundamental insight into the singularities responsible for dramatic sensitivity in- creases seen in sensory applications. The new analytical solution also provides increased computational time with 60x improvement demonstrated in this work. In addition, a new electroless deposition method followed by thermal annealing was developed by Ahn et al. for spherical Au array fabrication. To complement the model and fabrication technique, additional improvements in NP array sample analysis have been adapted and developed. Algorithms for NP particle density, size, and shape analysis are described using Atomic Force Microscope (AFM) and Scanning Electron Microscope (SEM) with a comparison between the two microscopy methods. Using fabrication and analysis, the methods of streamlining expensive function calls can be tested and improved

On Demand Nanoscale Phase Manipulation of Vanadium Dioxide by Scanning Probe Lithography

This dissertation focuses on nanoscale phase manipulations of Vanadium Dioxide. Nanoscale control of material properties is a current obstacle for the next generation of optoelectronic and photonic devices. Vanadium Dioxide is a strongly correlated material with an insulator-metal phase transition at approximately 345 K that generates dramatic electronic and optical property changes. However, the development of industry device application based on this phenomenon has been limited thus far due to the macroscopic scale and the volatile nature of the phase transition. In this work these limitations are assessed and circumvented. A home-built, variable temperature, scanning near-field optical microscope was engineered for Vanadium Dioxide manipulations and detections. Using this instrument, various scanning probe lithography based methods are implemented to induce new nanoscale phases. Three new phase transitions are discovered; a monoclinic metallic at the nanoscale, a rutile metallic metastable phase, and a van der Waals layered insulator. These new phases are studied and characterized to further understand phase manipulations in strongly correlated materials. One of the new phase transitions, monoclinic metallic, showcases plasmonic excitations. This phenomenon is used to demonstrate various nanoplasmonic devices such as rewritable waveguides, spatially modulated resonators, and reconfigurable planar optics. Finally, Oxygen Vacancy diffusion of the monoclinic structure is monitored to determine the temporal limitation for device applications. The discovery, demonstration, and study of these phases clearly shows the ability to manipulate Vanadium Dioxide on the nanoscale for the first time. Phase control is accomplished under ambient conditions and is stable over long periods of time. This technology opens the door for multifunctional device application using strongly correlated materials