Master of Science / Department of Physics / Robert Szoszkiewicz / For proteins in living cells, forces are present at all levels. These range from macroscopic to single molecule levels. Single molecule atomic force microscopy (AFM) in force extension (FX) and force clamp (FC) modes can investigate the mechanical properties of proteins, for example, forces at which proteins unfold, or the kinetics of these processes. In the FX-AFM experiments, proteins are pulled at constant velocity, while in FC-AFM experiments, proteins are pulled at constant force. This thesis describes i) how a single molecule FX/FC-AFM was constructed using various components, ii) how it was calibrated and tested using (I27)4 polyprotein, and iii) how it was applied to the studies of a Notch construct. Building up the single molecule FX/FC-AFM system opened a path to investigate the mechanical properties of proteins. Such a system was tested on a known protein construct, hence the usage of the (I27)4 polyprotein. The Notch protein is a signaling protein that plays a role in triggering breast cancer. It is believed that understanding the mechanical properties of Notch can help to understand its oncogenic functions. We have successfully constructed and calibrated the FX/FC-AFM setup. It was found that the AFM worked for the standard calibration protein of (I27)4. The results on a Notch construct revealed our ability to see some conformational transition state in this molecule under force. These results opened a path for further investigations of a Notch construct at various physiologically relevant conditions.

Single-walled carbon nanotubes (SWNTs) exhibit extraordinary properties: mechanical, thermal, optical and, possibly the most interesting, electrical. These all-carbon cylindrical structures can be metallic or semi-conducting depending on their precise structure. They have the potential to allow faster transistor switching speeds and smaller, more closely-packed interconnects in microelectronics. However, such applications are hindered by the difficulties of positioning the correct type of SWNT in a spatially precise location and orientation. In addition, greater understanding of the fundamental limits of SWNTs, such as the limit of current density, is needed for optimum operation in applications. The primary aim of this project was to increase the understanding of current density limitation by using in situ plasmonically enhanced Raman spectroscopy during electrical transport. The use of plasmonic metal nanostructures to enhance the Raman scattering should allow the acquisition of informative spectra from SWNTs away from their intrinsic resonance conditions. To achieve this aim, SWNTs must be integrated with plasmonic metal structures as well as electrical connections. This thesis presents two approaches for the integration of SWNTs with other nanometre-scaled features, in particular plasmonic nanoparticles. Fountain pen nanolithography uses a hollow nanopipette in place of the probe tip in an atomic force microscope (AFM), through which material can be delivered to a spatially precise position on a surface. Aqueous SWNT dispersion was delivered to chemically-functionalised silicon in this way, through pulled quartz pipettes with aperture diameters of 50 nm, 100 nm and 150 nm. The heights, widths and continuity of lines drawn on the surface by the nanopipette depended on the size, setpoint and lateral speed of the tip. A small bias voltage applied between the SWNT dispersion inside the pipette and the substrate allowed the deposition to be switched on or off depending on the polarity of the voltage, through the action of electroosmotic effects within the quartz capillary. The quality and density of the SWNT dispersion was found to be important for successful deposition to occur, since too low a concentration results in the lines deposited from the pipette being only surfactant but too high a concentration of bundles would quickly block the small tip of the pipette. Polarised Raman spectroscopy on SWNT deposited by fountain pen nanolithography showed that they had a high level of alignment parallel to the direction in which the pipette moved. Spherical gold nanoparticles with plasmonic properties suitable for enhancing Raman scattering were dropped onto samples containing individual SWNTs supported on a Si/SiO2 surface. Nanomanipulation with an atomic force microscope was used to push the gold nanoparticles onto the SWNTs. Raman spectra measured with and without the gold particles showed that the gold nanoparticles gave local enhancement factors of 24 for a single 150 nm nanoshell and 130 for a small cluster of 150 nm nanoshells. Polarised Raman studies on the cluster showed that the angle dependence deviated significantly from that expected of a bare SWNT. Electrical transport experiments with in situ plasmonically enhanced Raman spectroscopy may be performed on samples prepared from the methods described here. Such experiments would increase understanding of the electrical properties of SWNTs and how they relate to the vibrational and optical properties.

Liquid crystalline materials forming columnar mesophases are of importance for both the fundamental research and technological applications due to their supramolecular architecture allowing for one-dimensional charge transport. The potential applications of these materials include light emitting diodes, solar cells, field effect transistors and photovoltaic cells. However, to design a LC material suitable for a particular application, a fundamental understanding of the structure-property relationships is needed. In the present thesis, a variety of systems forming columnar mesophases have been explored. They include small molecular weight compounds (triphenylene, phthalocyanine derivatives and star-shaped mesogens) and polymer materials. The research was focused on the study of the influence of the molecular architecture and specific interactions such as hydrogen bonding on the supramolecular organization in the mesophase, as well as on the influence of columnar mesophase on crystal growth. The main results of the thesis are summarized below. The influence of hydrogen bonding on the structure and charge carrier mobility was investigated for a triphenylene derivative, hexaazatriphenylene, having lateral alkyl chains linked to the core via amide groups. These linking groups provide the possibility to form inter- and intra-molecular hydrogen bonds. Acting as “clamps”, the inter-molecular hydrogen bonds are found to enforce the attractive interactions between the molecules in the column. Thus, the columnar mesophase formed by this system is characterized by the smallest inter-disk distance ever found in columnar mesophases (3.18 Å). The improved intra-columnar order brings about a higher charge carrier mobility (0.02 cm2/Vs) as compared to other triphenylene derivatives without hydrogen bonds. Phthalocyanine derivatives, which are liquid crystalline at ambient temperature, could be suitable for opto-electronic applications due to their improved processibility and self-healing of structural defects. Our interest in these systems was inspired by the fact that, in spite of numerous studies performed to date, only very a few phthalocyanine derivatives were found to exhibit columnar mesophases at ambient temperature. We observed that by introducing branches in alkyl chains close to the core, we were able to render the material LC at ambient temperature. Analysis of X-ray diffraction patterns measured on oriented samples showed that these systems form hexagonal and rectangular ordered columnar mesophases. This finding is in contradiction with the general view stating that non-hexagonal mesophases can be only disordered. Since the absolute majority of applications require fabrication of films, it was very important to achieve the visualization of the organization of the phthalocyanine derivatives at the nanometer scale. AFM images on thick spin-coated films with columnar resolution are presented for the first time. They allowed the examination of columnar curvatures and breaks at the boundaries between different single crystal-like domains. The possibility of templating columnar crystal growth was studied for a star-shaped mesogen using a combination of direct- and reciprocal-space techniques. AFM images with columnar resolution showed that the crystal growth initiated in the monotropic columnar mesophase occurs almost in register with the mesomorphic template. In the final crystalline structure, the placement of the crystalline columns is controlled by the mesomorphic tracks at the scale of an individual column, i.e. at the scale of approximately 3.5 nm. The mesophase-assisted crystallization was also studied for the case of a polymer material forming columnar mesophase, poly(di-n-propylsiloxane). X-ray diffraction on oriented fibers allowed us to correct the previous indexation and solve the structure of the unit cell. The crystallization process was studied on samples crystallized in different conditions. It was found that, depending on crystallization conditions, both folded-chain and extended-chain crystals can be obtained. Thus, crystallization of the material from the mesophase results in the formation of 100-150nm thick crystals, which corresponds to a nearly extended-chain conformation. By contrast, when crystallized from a dilute solution, folded-chain crystals result. The mechanisms of chain unfolding was studied by variable temperature atomic force microscopy on PDPS single crystals. It was found that crystals rapidly thicken above the initial melting point, up to 80 nm.

No description available.

In this thesis, atomic force microscopy (AFM), transmission electron microscopy (TEM) and optical microscopy techniques were used to investigate systematically the self-assembled nanostructure behaviour of two different types of spin-cast polymer thin films: poly(isoprene-b-ethylene oxide), PI-b-PEO diblock copolymers and [poly(9,9-dioctylfluorene-co-benzothiadiazole)]:poly[9,9- dioctyfluorene-co-N-(4-butylphenyl)-diphenylamine], F8BT:TFB conjugated polymer blends. In the particular case of the polymer blend thin films, the morphology of their composites with cadmium selenide (CdSe) quantum dot (QD) nanoparticles was also investigated. For the diblock copolymer thin films, the behaviour of the nanostructures formed and the wetting behaviour on mica, varying the volume fraction of the PEO block (fPEO) and the average film thickness was explored. For the polymer blend films, the effect of the F8BT/TFB blend ratio (per weight), spin-coating parameters and solution concentration on the phase-separated nanodomains was investigated. The influence of the quantum dots on the phase separation when these were embedded in the F8BT:TFB thin films was also examined. It was found that in the case of PI-b-PEO copolymer thin films, robust nanostructures, which remained unchanged after heating/annealing and/or ageing, were obtained immediately after spin coating on hydrophilic mica substrates from aqueous solutions. The competition and coupling of the PEO crystallisation and the phase separation between the PEO and PI blocks determined the ultimate morphology of the thin films. Due to the great biocompatible properties of the PEO block (protein resistance), robust PEO-based nanostructures find important applications in the development of micro/nano patterns for biological and biomedical applications. It was also found that sub-micrometre length-scale phase-separated domains were formed in F8BT:TFB spin cast thin films. The nanophase-separated domains of F8BT-rich and TFB-rich areas were close to one order of magnitude smaller (in the lateral direction) than those reported in the literature. When the quantum dot nanoparticles were added to the blend thin films, it was found that the QDs prefer to lie in the F8BT areas alone. Furthermore, adding quantum dots to the system, purer F8BT and TFB nano-phase separated domains were obtained. Conjugated polymer blend thin films are excellent candidates for alternatives to the inorganic semiconductor materials for use in applications such as light emitting diodes and photovoltaic cells, mainly due to the ease of processing, low-cost fabrication and mechanical flexibility. The rather limited optoelectronic efficiency of the organic thin films can be significantly improved by adding inorganic semiconducting nanoparticles.

An iterative control algorithm (ICA) which uses an approximate inverse-hysteresis model is implemented to compensate for hysteresis to precisely fabricate features on a soft polymer substrate using an atomic force microscope (AFM). The AFM is an important instrument in micro/nanotechnology because of its ability to interrogate, manipulate, and fabricate objects at the micro/nanoscale. The AFM uses a piezoelectric actuator to position an AFM-probe tip relative to the sample surface in three dimensions. In particular, precision lateral control of the AFM-probe tip relative to the sample surface is needed to ensure high-performance operation of the AFM. However, precision lateral positioning of the AFM-probe tip is challenging due to significant positioning error caused by hysteresis effect. An ICA which incorporates an approximate inverse of the hysteresis behavior is proposed to compensate for the hysteresis-caused positioning error. The approach is applied to fabricate a feature using the AFM on a polycarbonate surface, and it is demonstrated that the maximum tracking error can be reduced to 0.225% of the displacement range, underscoring the benefits of the control method.

We examine the design of a high speed atomic force microscope using an optical pickup from a commercially available compact disc/digital versatile disc drive. An investigation of the commercial optical pickup is done with the goal of determining how it can be used for dimensional measurements on nanometer scale. An evaluation of noise sources, imaging capabilities, and functionality is performed.

This study details the dielectrophoretic assembly and mechanical characterization of boron nitride nanotubes on silicon chips with gold electrodes. The chips were fabricated from 4in round silicon wafers with a 100nm-thick low stress silicon nitride insulating layer on the top and bottom. The electrodes were patterned using photo- and electron-beam lithography and dry etching, and the wafers were cut into 4 x 6mm chips. The boron nitride nanotubes studied were obtained from NIA and were synthesized via a unique pressurized vapor/condensor method, which produced long, small-diameter BNNTs without the use of a catalyst. These nanotubes were studied due to their desirable mechanical and electrical properties, which allow for unique applications in various areas of science, engineering, and technology. Applications span from magnetic manipulation to the formation of biocomposites, from nano-transistors to humidity and pH sensors, and from MRI contrast agents to drug delivery. The nanotubes and nanotube bundles characterized were suspended over gaps of 300 to 500nm. This study was unique in that assembly was performed using dielectrophoresis, allowing for batch fabrication of chips and devices. Also, stiffness measurements were performed using AFM, eliminating the reliance of other methods upon electron microscopes, and allowing for imaging and measurements to occur simultaneously and at high resolution. It was found that DEP parameters of V = 2.0Vpp, f = 1kHz, and t = 2min provided the best results for mechanical testing. The nanotubes tested had suspended lengths of 300nm, the width of the electrode gap, and diameters of 15–65nm. Chips were imaged with both scanning electron microscopy and atomic force microscopy. Force-displacement measurements with atomic force microscopy were used to find stiffness values in the range of 1–16N/m. These stiffness values, when plugged into a simple double-clamped beam model, indicated Young’s moduli of approximately 1–1600GPa. Within this wide range, it was shown that a decrease in diameter strongly correlated exponentially to an increase in Young’s modulus. Work in this study was divided between assembly and characterization. Therefore, a lot of time was spent working to optimize dielectrophoresis parameters, followed by SEM and AFM imaging. Parameters that were adjusted included DEP voltage and time, pre-DEP sonication times, as well as adding a centrifuging procedure to attempt to better separate nanotube bundles in solution. Another method discussed but not pursued was the use of surfactants to agitate the solution, thus separating the nanotubes. The reason this material in particular was so difficult to separate was twofold. First, the small size of the nanotubes—individual BNNTs have diameters on the order of ∼5 nanometers—generates very strong nanoscale van der Waals forces holding the nanotubes together. Larger nanotubes—with diameters on the order of 50 to 100nm or more—suffer less from this problem. Also, the dipoles created by the boron-nitrogen bonds cause attraction between adjacent nanotubes. The results shown in this thesis include DEP parameters, SEM and AFM images, and force- displacement curves leading to nanotube stiffness and Young’s modulus values. The force-displacement tests via AFM are also detailed and explained.

The atomic force microscopy (AFM) has been widely used for the investigation of the surface topography and high precision force measurements at the nano-scale. Researchers have utilized AFM to quantify the viscosity of the cell membrane in the vertical direction, which is a primary indicator of a cell's functionality and health condition. A modified lateral force microscopy (LFM) to quantify viscosity through lateral force measurements applied on the sidewall of cell membranes. The resulting twist of the cantilever in mLFM is induced by the contact between sidewalls of the tip and features on the sample. However, the measurement sensitivity of the mLFM requires improvement. This thesis focused on optimizing probe geometries and materials to improve the measurement sensitivity. <div>Probes (cantilevers and tips) with different geometries and materials properties were proposed and their deformations in the mLFM force measurement were studied. The force measurement process, in which the tip contacted the sidewall of control samples, including a hard sample and a soft sample, was modeled by finite element analysis (FEA). This study calculated torsional spring constants and measurement sensitivities according to the data produced from FEA. The impact of various geometric parameters on the torsional spring constant and measurement sensitivity were presented and discussed. The optimal probe configuration and material for measurement sensitivity was found from the parameters tested in this research. For the hard sample, the cantilever with a "T-shape" cross section and a tetrahedral tip made from graphite had optimum measurement sensitivity. For the soft sample, the cantilever with a "T-shape" cross section and a conical tip with a 600nm-radius sphere tip apex had the optimum measurement sensitivity. The reason for the difference in optimum probe combination for hard and soft sample was that the measurement sensitivity for hard sample was more susceptible to change in lever arm distance and measurement sensitivity for soft sample was more susceptible to the change in tip radius. The measurement sensitivity has been improved significantly on both hard sample and soft sample compared to a DNP V-shaped probe. </div>

Thesis (M.Sc.Eng.) PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / The atomic force microscope (AFM) is a prevalent imaging device recognized for its capacity to measure surface topology at the subatomic level. Its exceptional ability to operate in a range of atmospheres from high vacuum to liquid environments and simultaneously quantify various material properties make it particularly well-suited to biological applications. Standard AFMs generate images by transversing a predefined rectangular region with a mechanical probe that maps the surface pixel by pixel. As a result, typical scan times are on the order of seconds to minutes and do not allow for the direct observation of dynamic processes, such as motor protein behavior. State-of-the-art AFMs attempt to improve temporal resolution by employing advanced controllers, converting to mechanical components designed for rapid response, and utilizing scan trajectories that consider actuator dynamics. Successful application of such techniques has delivered scan rates as high as 10 frames per second, with the unfortunate sacrifices of reduced frame size and costly equipment upgrades. A complementary approach aims to enable the substantial base of commercial AFMs to perform with similar high-speed capabilities by autonomous driving scan trajectories along key features. A previously developed technique, the local raster scan (LRS), follows polymer samples, such as DNA or actin filaments, by detecting structural edges in real time and steering the probe in a sinusoidal path across the strand. While this has been shown to reduce scanning time by one order of magnitude, it is limited by computational complexity and to the imaging of smooth curves. In this work, we present the local circular scan (LCS), a novel feature-tracking procedure that successfully addresses these restrictions. By utilizing a local reference frame with pragmatically chosen state variables, trajectory calculations are simply reduced to vector operations. Additionally, the self-intersecting, circular trajectory permits more sophisticated filtering, both in real-time and during post-processing. The contribution of this thesis is the development, implementation, and analysis of the LCS algorithm. A calibration sample with linear, square, and circular features is used for testing. Experimental results demonstrate an ability to track regions of high curvature and robustness to noise. Corrections for sample tilt and thermal drift as well as interpolation techniques used for image processing are detailed. / 2031-01-01