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.

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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.

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

Pseudomonas aeruginosa is extremely harmful to immunocompromised individuals. An atomic force microscope was used to measure the surface forces of this bacteria’s exopolymers. These forces were characterized with the AdG force model, which is a function of brush length, probe radius, temperature, separation distance and an indefinite density variable, s. This last parameter could represent the root spacing or mesh spacing of the exopolymers. This study aims to clarify s by obtaining force values as a function of temperature. The data suggest that s represents the mesh spacing. If s is the root spacing it should remain constant regardless of the changing polymer lengths, on the other hand if it is the mesh spacing it will vary with changing temperature, as shown by the data presented in this research. This knowledge will aid in understanding and characterizing how bacteria cause infections.

"American cranberry (Vacciniumm macrocarpon) has been long known for its benefits in maintaining urinary tract health. Clinical trials have shown that drinking cranberry juice can prevent urinary tract infections (UTIs) in various subpopulations that are prone to UTIs, especially women, but the mechanisms by which cranberry acts against uropathogenic bacteria are still unclear. Studies showed that when exposed to cranberry juice or A- PACs, a group of tannins that are unique to cranberry, the adhesion activity and biofilm formation of uropathogenic bacteria were reduced. However, the metabolism of cranberry juice has not be elucidated, therefore further study is needed to find out whether the anti-bacterial components in cranberry could survive the digestive system and reach the urinary tract, and how the components or metabolites remaining in urine act against uropathogenic bacteria. We used atomic force microscopy (AFM) to study the surface adhesion force of uropathogenic E. coli incubated with urine samples that were collected from volunteers after drinking 16 oz. of cranberry juice cocktail (CJC) or water. The urine samples were collected at 0, 2, 4, 6, and 8 hours after CJC or water consumption. When incubated with post-water urine, the adhesion forces of pathogenic bacteria that have fimbriae (E. coli B37, B73, B78, BF1023, CFT 073, and J96) did not change; whereas the adhesion forces of these strains decreased over the 8 hour period after CJC consumption. The control strain that does not have frimbriae, E. coli HB101, showed low adhesion force when incubated with post-water and post-CJC urine. In a human red blood cell agglutination (HRBC) assay, the attachment of pathogenic E. coli to red blood cells was significantly lower after exposed to post-CJC urine, compared to those exposed to post-water urine. These results indicate the anti-bacteria components or metabolites of CJC stay active in urine, and these compounds prevent adhesion of E. coli by reducing fimbriae-mediated adhesion. We also examined the effects of drinking CJC on biofilm formation of uropathogenic bacteria. Female volunteers were given 16 oz. of CJC or placebo, and their urine was collected at 0, 2, 8, 24, and 48 hours after consumption. Bacteria (E. coli B37, CFT073, BF1023, HB101, and S. aureus ATCC43866) were cultured in a mixture of urine and growth media in 96 well microtiters. The biofilm formed was quantified by staining the biofilm dissolved in a solvent with crystal violet and measuring the absorbance at 600 nm. The results showed that biofilm formation was reduced within 24 hours after CJC consumption, and it started to increase after 48 hours, possibly due to the washout of CJC in the system. These studies suggest that CJC can be an effective preventive measure for UTIs as it inhibits adhesion and biofilm formation of uropathogenic bacteria."

"Steric forces related to the lipopolysaccharide (LPS) brush on bacterial surfaces is of great importance in biofilm research. However, the atomic force microscopy (AFM) data, or force curves, produced require extensive analysis to obtain any useful information about the sample. Normally, after several force curves have been measured, the individual curves would be fit to a model for analysis. This process is not only time-consuming, but it is also extremely subjective as it lends itself to user bias throughout the analysis. A Matlab program to analyze force curves from an AFM efficiently, accurately, and with minimal user bias has been developed and is presented here. The analysis is based on a modified version of the Alexander and de Gennes (AdG) polymer model, which is a function of equilibrium polymer brush length, probe radius, temperature, separation distance, and a density variable. The program runs efficiently by cropping curves to the region specified by the model and then fitting the data. Automating the procedure reduces the amount of time required to process 100 force curves from several days to less than two minutes. Accuracy is ensured by making the program highly adjustable. The user can specify experimental constants such as the temperature and cantilever tip geometry, as well as adjust many cropping and fitting parameters to better analyze the data. Additionally, as part of this program, researchers can compare data from related experiments by choosing to plot the calculated fit parameters using either error bars or box plots to quickly identify relationships or trends. The use of this program to crop and fit force curves to the AdG model will allow researchers to ensure proper processing of large amounts of experimental data and reduce the time required for analysis and comparison of data, thereby enabling higher quality results in a shorter period of time. "