Detection of conformational and structural shifts in biomolecules is of great importance in bioanalytical chemistry and pharmaceutical sciences. Transverse shear mode acoustic wave devices have been used as real-time, label-free detectors of conformational shifts in biomolecules on surfaces. However, material changes in the biochemical monolayer and coupling between the substrate and the surrounding liquid make it difficult to isolate the desired signal, so an understanding of these phenomena is required. In this thesis, interfacial slip, viscoelasticity, and structural changes are used to model acoustic signals due to surface adsorption of the protein neutravidin, immobilisation of HIV-1 TAR RNA, and subsequent interaction of the RNA with tat peptide fragments. Binding of tat peptides induces conformational changes in the TAR. Similar modelling is performed to describe experiments involving the binding of calcium to surface-attached calmodulin, which is also known to result in a conformational shift. The aim of the modelling is to isolate the sensor response due to conformational shifts. The biomolecules are described as hydrated, viscoelastic monolayers and slip is allowed at all interfaces. All models are numerically fit to experimental values using a two-parameter minimisation algorithm. Slip is found on the electrode surface prior to neutravidin adsorption. Neutravidin and TAR are described as distinct viscoelastic monolayers. Binding of tat peptide fragment to the TAR monolayer is modelled using a complex slip parameter and a change in length, corresponding to a straightening of the molecule. Similarly, numerical modelling of calmodulin results reveals a length change in the molecule upon calcium binding. Molecular dynamics (MD) simulations of the TAR-tat fragment system are performed to corroborate the modelling results. Starting structures are computed by molecular docking, and MD simulations of TAR complexed with various length tat fragments are described. The simulations are in general agreement with the modelling results and literature values from similar molecular dynamics experiment. A new parameter is introduced to describe biomolecule-solvent affinity, and is compared to interfacial coupling values obtained from modelling. This research demonstrates that acoustic wave devices can be used to detect conformational shifts in surface-attached biomolecules, provided molecular details about the shifts are known.

This thesis presents an axisymmetric numerical model to simulate interfacial flows near a sharp corner, where contact line pinning occurs. The method has been used to analyze drop imbibition into a capillary. To evaluate the performance of the numerical method, for a liquid drop initially placed partially within a capillary, a thermodynamic model has also been developed, to predict equilibrium states. The first part of this thesis presents an axisymmetric VoF algorithm to simulate interfacial flows near a sharp corner. (1) A new method to exactly calculate the normals and curvatures of any circle with a radius as small as the grid size is presented. This method is a hybrid least squares height function technique which fits a discretized osculating circle to a curve, from which interface normals and curvature can be evaluated. (2) A novel technique for applying the contact angle boundary condition has been devised, based on the definition of an osculating circle near a solid phase. (3) A new flux volume construction technique is presented, which can be applied to any split advection scheme. Unlike the traditional approach where the flux volumes are assumed rectangular, the new flux volumes can be either trapezoidal or triangular. The new technique improves the accuracy and consistency of the advection scheme. (4) Explicit PLIC reconstruction expressions for axisymmetric coordinates have been derived. (5) Finally, a numerical treatment of VoF for contact line motion near a sharp corner is presented, base on the idea of contact line pinning and an edge contact angle. The second part of the thesis is on the imbibition of a drop into an open capillary. A thermodynamic analysis based on minimization of an interfacial surface energy function is presented to predict equilibrium configurations of drops. Based on the drop size compared to the hole size, the equilibrium contact angle, and the geometry of the capillary, the drop can be totally imbibed by the capillary, or may not wet the capillary at all. The thesis concludes with application of the numerical scheme to the same problem, to examine the dynamics of wetting or dewetting of a capillary. All of the simulations yield results that correspond to the equilibrium states predicted by the thermodynamic analysis, but offer additional insight on contact line motion and interface deformation near the capillary edge.

Crosslinking soft tissue has become more common in tissue engineering applications, and recent studies have demonstrated that soft tissue mechanical behavior can be directly altered through crosslinking, but increased understanding of how crosslinking affects intervertebral disc mechanical behavior is needed. In vitro testing of bovine disc and motion segments was used to characterize several important aspects of disc behavior in response to crosslinking after both soaking and injection treatment. The first study was a comparison of different crosslinkers to determine the effect on tensile properties of disc tissue. Circumferential specimens were taken from bovine annulus and then soak treated with an optimized crosslinking formulation or sham solution. A non-contacting laser micrometer was used to measure cross sectional area, after which tension testing until failure was performed to determine yield strain, yield stress, ultimate stress, peak modulus, and resilience. The crosslinkers were observed to produce different changes in the properties, with the measured properties generally increasing. The second study used bilateral annular injections to simulate a clinically relevant delivery method. The dose response of the motion segment’s neutral zone stability metrics against injection concentration was mapped. Concentrations of 20 mM and less had no significant effects on the stability metrics. 40mM demonstrated a change in neutral zone stiffness, while at least 80mM was required to significantly affect neutral zone length. Thus, meaningful changes in joint neutral zone stability were demonstrated using clinically relevant injection and chemical formulations. The third study used combinations of biochemical and accelerated mechanical cyclic loading to degrade gelatin and annulus fibrosus specimens with and without genipin treatment. Genipin crosslinking attenuated changes during cyclic loading to specimen geometry and compliance relative to control samples. Full recovery of genipin treated samples appeared to be hampered, at least partially from continued crosslinking during the accelerated testing. The fourth study tested the effect of genipin crosslinking to resist interlamellar shearing of the annulus lamella. Using a recently reported test method that shears adjacent lamella, crosslinked specimens were noted to have significantly higher yield force, peak force, and resilience compared to sham treated controls, supporting the hypothesis that crosslinking would increase the load bearing ability of the interface.

This thesis presents an axisymmetric numerical model to simulate interfacial flows near a sharp corner, where contact line pinning occurs. The method has been used to analyze drop imbibition into a capillary. To evaluate the performance of the numerical method, for a liquid drop initially placed partially within a capillary, a thermodynamic model has also been developed, to predict equilibrium states. The first part of this thesis presents an axisymmetric VoF algorithm to simulate interfacial flows near a sharp corner. (1) A new method to exactly calculate the normals and curvatures of any circle with a radius as small as the grid size is presented. This method is a hybrid least squares height function technique which fits a discretized osculating circle to a curve, from which interface normals and curvature can be evaluated. (2) A novel technique for applying the contact angle boundary condition has been devised, based on the definition of an osculating circle near a solid phase. (3) A new flux volume construction technique is presented, which can be applied to any split advection scheme. Unlike the traditional approach where the flux volumes are assumed rectangular, the new flux volumes can be either trapezoidal or triangular. The new technique improves the accuracy and consistency of the advection scheme. (4) Explicit PLIC reconstruction expressions for axisymmetric coordinates have been derived. (5) Finally, a numerical treatment of VoF for contact line motion near a sharp corner is presented, base on the idea of contact line pinning and an edge contact angle. The second part of the thesis is on the imbibition of a drop into an open capillary. A thermodynamic analysis based on minimization of an interfacial surface energy function is presented to predict equilibrium configurations of drops. Based on the drop size compared to the hole size, the equilibrium contact angle, and the geometry of the capillary, the drop can be totally imbibed by the capillary, or may not wet the capillary at all. The thesis concludes with application of the numerical scheme to the same problem, to examine the dynamics of wetting or dewetting of a capillary. All of the simulations yield results that correspond to the equilibrium states predicted by the thermodynamic analysis, but offer additional insight on contact line motion and interface deformation near the capillary edge.

Detection of conformational and structural shifts in biomolecules is of great importance in bioanalytical chemistry and pharmaceutical sciences. Transverse shear mode acoustic wave devices have been used as real-time, label-free detectors of conformational shifts in biomolecules on surfaces. However, material changes in the biochemical monolayer and coupling between the substrate and the surrounding liquid make it difficult to isolate the desired signal, so an understanding of these phenomena is required. In this thesis, interfacial slip, viscoelasticity, and structural changes are used to model acoustic signals due to surface adsorption of the protein neutravidin, immobilisation of HIV-1 TAR RNA, and subsequent interaction of the RNA with tat peptide fragments. Binding of tat peptides induces conformational changes in the TAR. Similar modelling is performed to describe experiments involving the binding of calcium to surface-attached calmodulin, which is also known to result in a conformational shift. The aim of the modelling is to isolate the sensor response due to conformational shifts. The biomolecules are described as hydrated, viscoelastic monolayers and slip is allowed at all interfaces. All models are numerically fit to experimental values using a two-parameter minimisation algorithm. Slip is found on the electrode surface prior to neutravidin adsorption. Neutravidin and TAR are described as distinct viscoelastic monolayers. Binding of tat peptide fragment to the TAR monolayer is modelled using a complex slip parameter and a change in length, corresponding to a straightening of the molecule. Similarly, numerical modelling of calmodulin results reveals a length change in the molecule upon calcium binding. Molecular dynamics (MD) simulations of the TAR-tat fragment system are performed to corroborate the modelling results. Starting structures are computed by molecular docking, and MD simulations of TAR complexed with various length tat fragments are described. The simulations are in general agreement with the modelling results and literature values from similar molecular dynamics experiment. A new parameter is introduced to describe biomolecule-solvent affinity, and is compared to interfacial coupling values obtained from modelling. This research demonstrates that acoustic wave devices can be used to detect conformational shifts in surface-attached biomolecules, provided molecular details about the shifts are known.

The development of organic photovoltaics (OPVs) has attracted a lot of attention due to their potential to create a low cost flexible solar cell platform. In general, an OPV is comprised of a number of layers of thin films that include the electrodes, active layers and barrier films. Thus, with all of the interfaces within OPV devices, the potential for failure exists in numerous locations if adhesion at the interface between layers is inherently low or if a loss of adhesion due to device aging is encountered. To date, few studies have focused on the basic properties of adhesion in organic photovoltaics and its implications on device reliability. In this dissertation, we investigated the adhesion between interfaces for a model multilayer barrier film (SiNx/PMMA) used to encapsulate OPVs. The barrier films were manufactured using plasma enhanced chemical vapor deposition (PECVD) and the interfacial fracture toughness (Gc, J/m2) between the SiNx and PMMA were quantified. The fundamentals of the adhesion at these interfaces and methods to increase the adhesion were investigated. In addition, we investigated the adhesive/cohesive behavior of inverted OPVs with different electrode materials and interface treatments. Inverted OPVs were fabricated incorporating different interface modification techniques to understand their impact on adhesion determined through the interfacial fracture toughness (Gc, J/m2). Overall, the goal of this study is to quantify the adhesion at typical interfaces used in inverted OPVs and barrier films, to understand methods that influence the adhesion, and to determine methods to improve the adhesion for the long term mechanical reliability of OPV devices.

No description available.

The pendant drop technique was used to characterize the adsorption behavior of n-dodecane-1-thiol and n-hexane-1-thiol capped gold nanoparticles at the hexane-water interface. The adsorption process was studied by analyzing the dynamic interfacial tension versus nanoparticle concentration, both at early times and at later stages (i.e., immediately after the interface between the fluids is made and once equilibrium has been established). Following free diffusion of nanoparticles from the bulk hexane phase, adsorption leads to ordering and rearrangement of the nanoparticles at the interface and formation of a dense layer. With increasing interfacial coverage, the diffusion-controlled adsorption for the nanoparticles at the interface was found to change to an interaction-controlled assembly and the presence of an adsorption barrier was experimentally verified. At the same bulk concentration, different sizes of n-dodecane-1-thiol nanoparticles showed different absorption behavior at the interface, in agreement with the findings of Kutuzov et al. [1]. The experiments additionally demonstrated the important role played by the capping agent. At the same concentration, gold nanoparticles stabilized by n-hexane-1-thiol exhibited greater surface activity than gold nanoparticles of the same size stabilized by n-dodecane-1-thiol. 1.6 nm, 2.8 nm, and 4.4 nm nanoparticles capped with n-dodecane-1-thiol, and 2.9 nm, and 4.3 nm particles capped with n-hexane-1-thiol were used in this study. The physical size of the gold nanoparticles was determined by TEM image analysis. The pendant drop technique was also used to study the adsorption properties of mixtures of gold nanoparticles at the hexane-water interface; and also investigate the effects of different factors (i.e., temperature, pH or ionic strength) on interfacial tension (IFT). The interfacial properties of mixtures of these nanoparticles, having different sizes and capping agents, were then studied. No interaction was found between the unmixed studied nanoparticles. Using the theory of non-ideal interactions for binary mixtures, the interaction parameters for mixtures of nanoparticles at the interface were determined. The results indicate that nanoparticle concentration of the mixtures has a profound effect on the interfacial nanoparticle composition. A repulsive interaction between nanoparticles of different size and cap was found in the mixtures at the interface layer. The interfacial tension for mixtures was found to be higher than the interfacial tension for non-mixed nanoparticle suspensions. The nanoparticle composition at the interface was found to differ from the composition of nanoparticles in the bulk liquid phase. The activity of unmixed nanoparticles proved to be a poor predictor of the activity of mixtures. It was observed that the most active nanoparticles concentrated at the interface. The effects of temperature, pH and ionic strength concentration on the equilibrium and dynamic IFT of 4.4 nm gold nanoparticles capped with n-dodecane-1-thiol at the hydrocarbon-water interface was studied. The pendant drop technique was also used to study the adsorption properties of these nanoparticles at the hexane-water and nonane-water interface. The addition of NaCl was found to cause a decrease of the equilibrium and dynamic IFT greater than that, which accompanies the adsorption of nanoparticles at the interface in the absence of NaCl. Although IFT values for acidic and neutral conditions were found to be similar, a noticeable decrease in the IFT was found for more basic conditions. Increasing the temperature of the system was found to cause an increase in both dynamic and equilibrium IFT values. The adsorption of functionalized gold nanoparticles at liquid-liquid interfaces is a promising method for self-assembly and the creation of useful nanostructures. These findings contribute to the design of useful supra-colloidal structures by the self-assembly of alkane-thiol capped gold nanoparticles at liquid-liquid interfaces.

The object of this thesis is to explore the low-frequency noise (LFN) in silicon-germanium (SiGe) heterojunction bipolar transistors (HBTs) and lateral bipolar junction transistors (BJTs). The LFN of SiGe HBTs and lateral BJTs not only determines the lowest detectable signal limit but also induces phase noise in high-frequency applications. Characterizing the LFN behavior and understanding the physical noise mechanism, therefore, are very important to improve the device and circuit performance. The dissertation achieves the object by investigating the LFN of SiGe HBTs and lateral BJTs with different structures for performance optimization and radiation tolerance, as well as by building models that explain the physical mechanism of LFN in these advance bipolar technologies. The scope of this research is separated into two main parts: the LFN of SiGe HBTs; and the LFN of lateral BJTs. The research in the LFN of SiGe HBTs includes investigating the effects of interfacial oxide (IFO), temperature, geometrical dimensions, and proton radiation. It also includes utilizing physical models to probe noise mechanisms. The research in the LFN of lateral BJTs includes exploring the effects of doping and geometrical dimensions. The research work is envisioned to enhance the understanding of LFN in SiGe HBTs and lateral BJTs.

While shoaling from deepwater in a stratified ocean, an interfacial solitary wave (ISW) may experience waveform inversion on a continental margin. Although many oceanographers have believed that the inversion from depression to elevation may commence at the turning point where the upper and bottom layers are equal in depth, this phenomenon has not been fully verified in field observations nor in a laboratory. In this study, a series of laboratory experiments and numerical modeling were conducted on the evolution of an ISW of depression across uniform slope joining a horizontal plateau which resembles pseudo slope-shelf topography, in order to clarify this fascinating phenomenon and the variations of wave properties associated with the process. In the laboratory experiments, a depression ISW was produced by a collapse mechanism in a stratified two-layer fluid system within a steel-framed wave flume (12 m long, 0.7 m high by 0.5 m wide) at the National Sun Yat-sen University in Taiwan. The fluid density in the upper (fresh) and bottom (brine) layers was 996 and 1030 kg/m3, respectively. A series of experiments were conducted upon varying the magnitude of the most important physical factors (i.e., nominal thickness of pycnocline, depth ratio between upper and bottom layer, front gradient and shape of pseudo slope-shelf), from which the results are now discussed in four separate chapters in this thesis. Present laboratory results indicate that the process of waveform inversion took place after an ISW had experienced internal run-down, hydraulic jump, vortex motion and surge-up on the front slope, prior to its propagation onto the plateau. Moreover, the fundamental wave period of leading wave on the plateau was significantly smaller than that in the preceding sections on the front slope and the incident stage earlier, thus representing frequency downshift. Amongst the factors involved, the depth ratio between the upper and bottom layer was the most significant one for waveform inversion. Only when the upper layer was thicker than the bottom layer on the plateau of pseudo slope-shelf, waveform inversion could occur, besides the length of the plateau. On the other hand, the front gradient and shape of pseudo slope-shelf also affected the magnitude of the transmitted wave over the plateau as the wave across this specific topography. In the case of a steeper front gradient, waveform inversion became insignificant due to stronger wave reflection and intense energy dissipation caused by turbulent mixing while a depression ISW propagated over a slope-shelf; particularly against a submerged vertical cliff. As a depression ISW across pseudo slope-shelf with short plateau, intense wave breaking might occur again with vortex motion at its rear end as the newly inversed waveform reentering deep water. In this region, the upper layer was smaller than the bottom layer, hence it could not support the continuous existence of an ISW in elevation. Again, energy dissipation occurred due to turbulent mixing beyond the rear end of a short plateau. Finally, a different mode of ISW appeared within pycnocline, while its nominal thickness was larger than the amplitude of the incident wave. In addition to the laboratory investigations, numerical model was also adopted to study the variations in the flow field as an ISW propagated over a pseudo slope-shelf, in order to complement the experimental results. The results of numerical modeling revealed that the horizontal velocity in the bottom layer increased when the wave encountered the front slope, even if the depth of upper layer was thinner than that of the bottom layer on the plateau. Consequently, the velocity in the upper layer became less than that in the bottom layer when the former was thicker than that of the latter on the plateau. On the other hand, the vertical velocity within the self-generated vortex switched direction as waveform inversion commenced after the wave across the shoulder of pseudo slope-shelf where the local depth of the upper layer was larger than that of bottom part. Overall, the significance of the four pertinent factors (i.e., nominal thickness of pycnocline, water depth ratio, front slope, and plateau length) that affected a depression ISW across pseudo slope-shelf is discussed in detail in this thesis, as well as the variation of flow field calculated by the numerical mode presented.