The interaction of an evanescent wave and plasmonic nanostructures are simulated in Finite Element Method. Specifically, the optical absorption cross section (Cabs) of a silver nanoparticle (AgNP) and a gold nanoparticle (AuNP) in the presence of metallic (gold) and dielectric (silicon) atomic force microscope (AFM) probes are numerically calculated in COMSOL. The system was illuminated by a transverse magnetic polarized, total internally reflected (TIR) waves or propagating surface plasmon (SP) wave. Both material nanoscale probes localize and enhance the field between the apex of the tip and the particle. Based on the absorption cross section equation the author was able to demonstrate the increment of absorption cross section when the Si tip was brought closer to the AuNP, or when the Si tip apex was made larger. However, the equation was not enough to predict the absorption modification under metallic tips, especially for a AgNP's Cabs; neither it was possible to estimate the optical absorption based on the localized enhanced field caused by a gold tip. With the help of the driven damped harmonic oscillator equation, the Cabs of nanoparticles was explained. In addition, this model was applicable for both TIR and Surface Plasmon Polaritons illuminations. Fitting the numerical absorption data to a driven damped harmonic oscillator (HO) model revealed that the AFM tip modifies both the driving force (F0), consisting of the free carrier charge and the driving field, and the overall damping of the oscillator beta. An increased F0 or a decreased beta will result in an increased Cabs and vice versa. Moreover, these effects of F0 and beta can be complementary or competing, and they combine to either enhance or suppress absorption. Hence, a significantly higher beta with a small increment in F0 will result in an absorption suppression. Therefore, under a Si tip, Cabs of a AuNP is enhanced while Cabs of a AgNP is suppressed. In contrast, a Au tip suppresses the Cabs for both Au and Ag NPs. As an extension of this absorption model, further investigation of the guided mode and a close by nanostructure is proposed, where the scattered wave off the structure attenuates the guided mode with destructive interference.

The diffusible soluble oligomeric amyloid β-peptide (Aβ) has been identified as a toxic agent in Alzheimer’s disease that can cause synaptic dysfunction and memory loss, indicating its role as potential therapeutic targets for AD treatment. Recently an oligomer-specific sandwich biotin-avidin interaction based assay identified the Aβ oligomer dissociation potency of a series of dihydroxybenzoic acid (DHBA) isomers. Because the sandwich assay is an ensemble method providing limited size information, fluorescence correlation spectroscopy (FCS) was employed to provide single molecule resolution of the disassembly mechanism. Using FCS coupled with atomic force microscopy, we investigated the size distribution of fluorescein labeled synthetic Aβ oligomers at physiological concentrations, and monitored in real time the change of size and mole fraction of oligomers in the presence of dissociating agents or conditions. The higher-order dissociation process caused by DHBA isomers produced no transient oligomeric intermediates, a desirable feature for an anti-oligomer therapeutic. Urea and guanidine hydrochloride, in contrast, produced a linear dissociation with a progressive decrease of size and mole fraction of oligomers. FCS allows the facile distinction of small molecule Aβ oligomer dissociators that do not produce stable potentially toxic oligomeric Aβ intermediates.

Scanning probe microscopes (SPMs) are the highest resolution imaging instruments available today and are among the most important tools in nanoscience. Conventional SPMs suffer from several drawbacks owing to their large and bulky construction and to the use of piezoelectric materials. Large scanners have low resonant frequencies that limit their achievable imaging bandwidth and render them susceptible to disturbance from ambient vibrations. Array approaches have been used to alleviate the bandwidth bottleneck; however as arrays are scaled upwards, the scanning speed must decline to accommodate larger payloads. In addition, the long mechanical path from the tip to the sample contributes thermal drift. Furthermore, intrinsic properties of piezoelectric materials result in creep and hysteresis, which contribute to image distortion. The tip-sample interaction signals are often measured with optical configurations that require large free-space paths, are cumbersome to align, and add to the high cost of state-of-the-art SPM systems. These shortcomings have stifled the widespread adoption of SPMs by the nanometrology community. Tiny, inexpensive, fast, stable and independent SPMs that do not incur bandwidth penalties upon array scaling would therefore be most welcome. The present research demonstrates, for the first time, that all of the mechanical and electrical components that are required for the SPM to capture an image can be scaled and integrated onto a single CMOS chip. Principles of microsystem design are applied to produce single-chip instruments that acquire images of underlying samples on their own, without the need for off-chip scanners or sensors. Furthermore, it is shown that the instruments enjoy a multitude of performance benefits that stem from CMOS-MEMS integration and volumetric scaling of scanners by a factor of 1 million. This dissertation details the design, fabrication and imaging results of the first single-chip contact-mode AFMs, with integrated piezoresistive strain sensing cantilevers and scanning in three degrees-of-freedom (DOFs). Static AFMs and quasi-static AFMs are both reported. This work also includes the development, fabrication and imaging results of the first single-chip dynamic AFMs, with integrated flexural resonant cantilevers and 3 DOF scanning. Single-chip Amplitude Modulation AFMs (AM-AFMs) and Frequency Modulation AFMs (FM-AFMs) are both shown to be capable of imaging samples without the need for any off-chip sensors or actuators. A method to increase the quality factor (Q-factor) of flexural resonators is introduced. The method relies on an internal energy pumping mechanism that is based on the interplay between electrical, mechanical, and thermal effects. To the best of the author???s knowledge, the devices that are designed to harness these effects possess the highest electromechanical Qs reported for flexural resonators operating in air; electrically measured Q is enhanced from ~50 to ~50,000 in one exemplary device. A physical explanation for the underlying mechanism is proposed. The design, fabrication, imaging, and tip-based lithographic patterning with the first single-chip Scanning Thermal Microscopes (SThMs) are also presented. In addition to 3 DOF scanning, these devices possess integrated, thermally isolated temperature sensors to detect heat transfer in the tip-sample region. Imaging is reported with thermocouple-based devices and patterning is reported with resistive heater/sensors. An ???isothermal electrothermal scanner??? is designed and fabricated, and a method to operate it is detailed. The mechanism, based on electrothermal actuation, maintains a constant temperature in a central location while positioning a payload over a range of >35??m, thereby suppressing the deleterious thermal crosstalk effects that have thus far plagued thermally actuated devices with integrated sensors. In the thesis, models are developed to guide the design of single-chip SPMs and to provide an interpretation of experimental results. The modelling efforts include lumped element model development for each component of single-chip SPMs in the electrical, thermal and mechanical domains. In addition, noise models are developed for various components of the instruments, including temperature-based position sensors, piezoresistive cantilevers, and digitally controlled positioning devices.

<p>One promising HIV-1 vaccine target is the membrane-proximal external region (MPER) of viral gp41. MPER is poorly immunogenic, however, the two rare neutralizing antibodies (NAbs), 2F5 and 4E10, bind to MPER with great neutralizing ability. Although their neutralizing mechanism represents a promising framework for the design of new HIV-1 liposomal vaccine candidates, this mechanism remains poorly understood. It is known that 2F5 and 4E10 are required to first associate with HIV-1 lipids before binding to the target MPER antigen, however, little is known about how lipid membranes contribute to NAb-antigen binding. To this end we have developed model membrane systems to study NAb and antigen lipid interactions. </p><p>We first created a surface plasmon resonance (SPR) spectroscopy based assay that monitors antibody binding to thiol monolayers, which mimic the surface chemical properties of lipid membranes. Next, we focused on mimicking the lipid phase organization (i.e., domain formation) of native membranes by using supported lipid bilayers (SLBs). We used simple SLB compositions to model the liquid-disordered (Ld) and gel phases. To model the HIV-1 envelope, we used a complex SLB composition that contains an Ld and liquid-ordered (Lo) phase. To reliably create model HIV-1 SLBs, we developed an SLB formation technique that uses amphipathic, &#945;-helical peptides as a catalyst to generate complex SLBs that have a high cholesterol content and contain multiple lipid types. For all SLB surfaces we used atomic force microscopy (AFM) to visualize membrane domains, antigen presentation, and antibody-membrane interactions.</p><p>Results from experiments using thiol surfaces showed that NAb binding to hydrophobic thiol surfaces was significantly greater than that of control monoclonal antibodies. This supports the hypothesis that these NAbs embed into the hydrophobic membrane core. Our results demonstrate that 2F5/4E10 do not interact with the highly ordered gel and Lo domains in the SLB but exclusively bind to the Ld phase. This suggests that 2F5/4E10 require low membrane order and weak lateral lipid-lipid interactions to insert into the hydrophobic membrane interior. Thus, vaccine liposomes that primarily contain an Ld phase are more likely to elicit the production of lipid reactive, 2F5- and 4E10-like antibodies, compared to liposomes that contain an Lo or gel phase. In the context of liposomal antigen presentation, our results show that the presence of the MPER656 antigen can severely limit the Ld area available for antibody interactions. Subsequently, this reduces the amount of MPER656 that is accessible for 2F5/4E10 binding, since MPER656 preferentially localizes to the Ld area. If Ld forming lipid components are used in vaccine liposomes, it is important to ensure that the presence of antigen does not inhibit large-scale Ld formation.</p> / Dissertation

No description available.

Many biological processes, pathogens, and pharmaceuticals act upon, cellular membranes. Accordingly, cell membrane mimics are attractive targets for biosensing, with research, pathology, and pharmacology applications. Lipid bilayers represent a versatile sensor functionalization platform providing antifouling properties, and many receptor integration options, uniquely including transmembrane proteins. Bilayer-coated sensors enable the kinetic characterization of membrane/analyte interactions. Addressed theoretically and experimentally is the self-assembly of model membranes on plasmonic sensors. Two categories of plasmonic sensors are studied in two parts. Part I aims to deposit raft-forming bilayers on planar nanoaperture arrays suitable for multiplexing and device integration. By vesicle fusion, planar bilayers are self-assembled on thiol-acid modified flame-annealed gold without the need for specific lipid head-group requirements. Identification of coexisting lipid phases is accomplished by AFM imaging and force spectroscopy mapping. These methods are successfully extended to metallic, plasmon-active nanohole arrays, nanoslit arrays and annular aperture arrays, with coexisting phases observed among the holes. Vis-NIR transmission spectra of the arrays are measured before and after deposition, indicating bilayer detection. Finally, the extraction of membrane proteins from cell cultures and incorporation into model supported bilayers is demonstrated. These natural membrane proteins potentially act as lipid-bound surface receptors. Part II aims to encapsulate in model lipid bilayers, metallic nanoparticles, which are used as probes in surface enhanced Raman spectroscopy. Three strategies of encapsulating particles, and incorporating Raman-active dyes are demonstrated, each using a different dye: malachite green, rhodamine-PE, and Tryptophan. Dye incorporation is verified by SERS and the bilayer is visualized and measured by TEM, with support from DLS and UV-Vis spectroscopy. In both parts, lipid-coated sensors are successfully fabricated and characterized. These results represent important and novel solutions to the functionalization of plasmonic surfaces with biologically relevant cell membrane mimics.

Hydrophobic interactions guide important molecular self-assembly processes such as protein folding. On the macroscale, hydrophobic interactions consist of the aggregation of "oil-like" objects in water by minimizing the interfacial energy. However, the hydration mechanism of small hydrophobic molecules on the nanoscale (~1 nm) differs fundamentally from its macroscopic counterpart. Theoretical studies over the last two decades have pointed to an intricate dependence of molecular hydration mechanisms on the length scale. The microscopic-to-macroscopic cross-over length scale is critically important to hydrophobic interactions in polymers, proteins and other macromolecules. Accurate experimental determination of hydration mechanisms and their interaction strengths are needed to understand protein folding. This thesis reports the development of experimental and analytical techniques that allow for direct measurements of hydrophobic interactions in a single molecule. Using single molecule force spectroscopy, the mechanical unfolding of a single hydrophobic homopolymer was identified and modeled. Two experiments examined how hydrophobicity at the molecular scale differ from the macroscopic scale. The first experiment identifies macroscopic interfacial tension as a critical parameter governing the molecular hydrophobic hydration strength. This experiment shows that the solvent conditions affect the microscopic and macroscopic hydrophobic strengths in similar ways, consistent with theoretical predictions. The second experiment probes the hydrophobic size effect by studying how the size of a non-polar side-chain affects the thermal signatures of hydration. Our experimental results reveal a cross-over length scale of approximately 1 nm that bridges the transition from entropically driven microscopic hydration mechanism to enthalpically driven macroscopic hydration mechanism. These results indicate that hydrophobic interactions at the molecular scale differ from macroscopic scale, pointing to potential ways to improve our understanding and predictions of molecular interactions. The system established in this thesis forms the foundation for further investigation of polymer hydrophobicity.

Electrical and structural properties of Bismuth thin films were studied simultaneously. Electrical properties of the Bismuth thin films have been characterized by measuring temperature dependent conductivity and Hall effect. Structural analysis were carried out by X-ray diffraction technique and using a room temperature Atomic Force Microscope (RT-AFM).

In this thesis, a direct method of Atomic Force Microscopy (AFM) technique has been developed to measure the adhesion forces between BSA and two different surfaces: mica (a hydrophilic surface); and polystyrene (a hydrophobic surface); in PBS solution. We have shown possible to measure interactions between proteins and substrate surface directly without any modification to the substrate and the AFM tip; this means protein molecules can keep the natural elastic property within the force measurements. The average measured value of adhesion forces between BSA and mica is 0.036 ± 0.002 nN, and between BSA and polystyrene is 0.066 ± 0.003 nN. The polystyrene surface is more adhesive to BSA than the mica surface. This is consistent with previous research, which assessed that hydrophobic surfaces enhance protein adhesion but hydrophilic surfaces do not.

Interactions between hydrophobic surfaces at short separation distances (at the nanometer scale) are very important in a number of industrial applications. For example, in the froth flotation mineral separation process it is the interaction between the hydrophobic particle and the bubble which is paramount in separating the valuable minerals from the gangue. A number of studies, most notably using the atomic force microscope (AFM) and the surface force apparatus (SFA) have found the existence of a long range hydrophobic attractive force between hydrophobic surfaces that cannot be explained by classical colloidal science theories. In many cases, this force is an artefact due to the accumulation of sub-microscopic bubbles, the so called nanobubbles, at the liquid-hydrophobic solid interface. Thus, what was thought to be a hydrophobic force was actually a capillary force resulting from the gaseous bridge formed from the coalescence of nanobubbles, that is, the nanobubble bridging capillary force (NBCF). It is the purpose of this thesis to provide further insight into the accumulation of soluble gases at the liquid-hydrophobic solid interface and the resulting NBCF. Specifically, this thesis studies these phenomena from a fundamental standpoint and additionally relates the findings to froth flotation mineral separation. A systematic method to measure the NBCF by controlling the size of the gaseous capillary bridge was devised in this thesis. Control of the capillary bridge was achieved by utilising the solvent-exchange method to accumulate nanobubbles at the surface, followed by surface scanning of the colloidal probe over the flat surface to harvest nanobubbles. Thus, the NBCF has been controlled to allow for greater success in modelling the interaction, understanding the geometric parameters of the bridge, observing changes in friction force due to nanobubbles and understanding the influence of ethanol on the force. An outcome of this thesis was the development of a capillary force model which describes the NBCF. The model considers a constant volume and constant contact angle assumption for a gaseous capillary bridge of toroidal geometry. The model was very successful in describing the NBCF at long separation distances (>20nm) for both the approach and retract interactions. The close fitting between the experimental data and the model allowed accurate determinations of the advancing and receding contact angles, bridge geometry and volume. The successful implementation of the capillary force model allowed a link between the bridge volume, and the resulting adhesion to the friction force between hydrophobic solid surfaces in water. Additionally, the model allowed the change from an attractive to a repulsive NBCF to be described by a change from a concave to convex bridge geometry. Thus, this thesis has added considerable knowledge to the fundamental aspects of nanobubbles and the NBCF. The final chapters of this thesis utilised the knowledge gained from the fundamental studies to understand the influence of nanobubbles on flotation. In the first study, the influence of NaCl concentration on the morphology of gaseous domains on a graphite surface is discussed in relation to the increased recovery of coal in saline water. In the second study, methanol treatment of a ZnS ore was found to increase the floatability due to slime removal and the artificial formation of nanobubbles.