<p>Fibre suspensions in the fluid medium are common in industry, biology, and the environment. Industrial examples of concentrated suspensions include fresh concrete, uncured solid rocket fuel, and biomass slurries; natural examples include silt transfer in rivers and red blood cells in the blood.  These suspensions often include a Newtonian fluid as their suspending medium; still, these suspensions exhibit a plethora of non-Newtonian properties, such as yield stresses, rate-dependent rheology, and normal stresses, to name a few. Other than volume fraction, the type of fiber material, the presence of fluid-fiber or fiber-fiber interactions such as hydrodynamic, Brownian, colloidal, frictional, chemical, and/or electrostatic determine the rheological behavior of suspension. The average inter-fiber gaps between the neighboring fibers decrease significantly as the suspension volume fraction move towards a concentrated regime. As a result, in this regime, inter-fiber interactions become dominant.  Moreover, the surface asperities are present on the fiber surface even in the case of so-called smooth fibers, as fibers in real suspensions are not perfectly smooth. Hence, contact forces arising from the direct touching of the fibers become one of the essential factors in determining the rheology of suspensions.</p> <p>We first describe the causes of yield stress, shear thinning, and normal stress differences in fibre suspensions. We model the fibers as inextensible continuous flexible slender bodies with the Euler-Bernoulli beam equation governing their dynamics suspended in an incompressible Newtonian fluid. The fiber dynamics and fluid flow coupling is achieved using the immersed boundary method (IBM). In addition, the fiber surface roughness lead to inter-fiber contacts resulting in normal and tangential forces between the fibers, which follow Coulomb’s law of<br> friction. The surface roughness is modeled as hemispherical protrusions on the fiber surfaces. In addition to the comparison of the computational model to the experimental results, we demonstrate that attractive interactions lead to yield stress and shear thinning rheology.</p> <p>Furthermore, we investigate the effects of fiber aspect ratio, roughness, flexibility, and volume fraction on the rheology of concentrated suspensions. We find that the suspension viscosity increases with increasing the volume fraction, roughness, fiber rigidity, and aspect ratio. The increase in relative viscosity is the macroscopic manifestation of a similar increase  in the microscopic contact contribution with these parameters. In addition, we observe positive and negative first and second normal stress differences, respectively, in agreement with previous experiments. Lastly, we propose a modified Maron-Pierce law to quantify the the jamming volume fraction with varying fiber aspect ratio and roughness. Additionally, we provide a constitutive model to calculate the viscosity at various volume fractions, aspect ratios, and shear rates.</p>

Optics are a powerful probe of chemical structure that can often be linked to theoretical predictions, providing robustness as a measurement tool. Not only do optical interactions like second harmonic generation (SHG), single and two-photon excited fluorescence (TPEF), and infrared absorption provide chemical specificity at the molecular and macromolecular scale, but the ability to image enables mapping heterogeneous behavior across complex systems such as biological tissue. This thesis will discuss nonlinear and linear optics, leveraging theoretical predictions to provide frameworks for interpreting analytical measurement. In turn, the causal mechanistic understanding provided by these frameworks will enable structurally specific quantitative tools with a special emphasis on application in biological imaging. The thesis will begin with an introduction to 2nd order nonlinear optics and the polarization analysis thereof, covering both the Jones framework for polarization analysis and the design of experiment. Novel experimental architectures aimed at reducing 1/f noise in polarization analysis will be discussed, leveraging both rapid modulation in time through electro-optic modulators (Chapter 2), as well as fixed-optic spatial modulation approaches (Chapter 3). In addition, challenges in polarization-dependent imaging within turbid systems will be addressed with the discussion of a theoretical framework to model SHG occurring from unpolarized light (Chapter 4). The application of this framework to thick tissue imaging for analysis of collagen local structure can provide a method for characterizing changes in tissue morphology associated with some common cancers (Chapter 5). In addition to discussion of nonlinear optical phenomena, a novel mechanism for electric dipole allowed fluorescence-detected circular dichroism will be introduced (Chapter 6). Tackling challenges associated with label-free chemically specific imaging, the construction of a novel infrared hyperspectral microscope for chemical classification in complex mixtures will be presented (Chapter 7). The thesis will conclude with a discussion of the inherent disadvantages in taking the traditional paradigm of modeling and measuring chemistry separately and provide the multi-agent consensus equilibrium (MACE) framework as an alternative to the classic meet-in-the-middle approach (Chapter 8). Spanning topics from pure theoretical descriptions of light-matter interaction to full experimental work, this thesis aims to unify these two fronts. <br>