Nonlinear Optics and Carrier Dynamics in Nanostructured and Two-Dimensional Materials

Understanding and measuring the interaction of light with sub-wavelength structures and atomically thin materials is of critical importance for the development of next generation photonic devices.  One approach to achieve the desired optical properties in a material is to manipulate its mesoscopic structure or its composition in order to affect the properties of the light-matter interaction.  There has been tremendous recent interest in so called two-dimensional materials, consisting of only a single to a few layers of atoms arranged in a planar sheet.  These materials have demonstrated great promise as a platform for studying unique phenomena arising from the low-dimensionality of the material and for developing new types of devices based on these effects.  A thorough investigation of the optical and electronic properties of these new materials is essential to realizing their potential.  In this work we present studies that explore the nonlinear optical properties and carrier dynamics in nanoporous silicon waveguides, two-dimensional graphite (graphene), and atomically thin black phosphorus. We first present an investigation of the nonlinear response of nanoporous silicon optical waveguides using a novel pump-probe method. A two-frequency heterodyne technique is developed in order to measure the pump-induced transient change in phase and intensity in a single measurement. The experimental data reveal a characteristic material response time and temporally resolved intensity and phase behavior matching a physical model dominated by free-carrier effects that are significantly stronger and faster than those observed in traditional silicon-based waveguides.  These results shed light on the large optical nonlinearity observed in nanoporous silicon and demonstrate a new measurement technique for heterodyne pump-probe spectroscopy. Next we explore the optical properties of low-doped graphene in the terahertz spectral regime, where both intraband and interband effects play a significant role. Probing the graphene at intermediate photon energies enables the investigation of the nonlinear optical properties in the graphene as its electron system is heated by the intense pump pulse. By simultaneously measuring the reflected and transmitted terahertz light, a precise determination of the pump-induced change in absorption can be made. We observe that as the intensity of the terahertz radiation is increased, the optical properties of the graphene change from interband, semiconductor-like absorption, to a more metallic behavior with increased intraband processes. This transition reveals itself in our measurements as an increase in the terahertz transmission through the graphene at low fluence, followed by a decrease in transmission and the onset of a large, photo-induced reflection as fluence is increased.  A hybrid optical-thermodynamic model successfully describes our observations and predicts this transition will persist across mid- and far-infrared frequencies.  This study further demonstrates the important role that reflection plays since the absorption saturation intensity (an important figure of merit for graphene-based saturable absorbers) can be underestimated if only the transmitted light is considered. These findings are expected to contribute to the development of new optoelectronic devices designed to operate in the mid- and far-infrared frequency range.  Lastly we discuss recent work with black phosphorus, a two-dimensional material that has recently attracted interest due to its high mobility and direct, configurable band gap (300 meV to 2eV), depending on the number of atomic layers comprising the sample. In this work we examine the pump-induced change in optical transmission of mechanically exfoliated black phosphorus flakes using a two-color optical pump-probe measurement. The time-resolved data reveal a fast pump-induced transparency accompanied by a slower absorption that we attribute to Pauli blocking and free-carrier absorption, respectively. Polarization studies show that these effects are also highly anisotropic - underscoring the importance of crystal orientation in the design of optical devices based on this material. We conclude our discussion of black phosphorus with a study that employs this material as the active element in a photoconductive detector capable of gigahertz class detection at room temperature for mid-infrared frequencies.

Slot Film Cooling: A Comprehensive Experimental Characterization

When components of a propulsion system are exposed to elevated flow temperatures there is a risk for catastrophic failure if the components are not properly protected from the thermal loads. Among several strategies, slot film cooling is one of the most commonly used, yet poorly understood active cooling techniques. Tangential injection of a relatively cool fluid layer protects the surface(s) in question, but the turbulent mixing between the hot mainstream and cooler film along with the presence of the wall presents an inherently complex problem where kinematics, thermal transport and multimodal heat transfer are coupled. Furthermore, new propulsion designs rely heavily on CFD analysis to verify their viability. These CFD models require validation of their results, and the current literature does not provide a comprehensive data set for film cooling that meets all the demands for proper validation, namely a comprehensive (kinematic, thermal and boundary condition data) data set obtained over a wide range of conditions. This body of work aims at solving the fundamental issue of validation by providing high quality comprehensive film cooling data (kinematics, thermal mixing, heat transfer). 3 distinct velocity ratios (VR=uc/u∞) are examined corresponding to wall-wake (VR~0.5), min-shear (VR ~ 1.0), and wall-jet (VR~2.0) type flows at injection, while the temperature ratio TR= T∞/Tc is approximately 1.5 for all cases. Turbulence intensities at injection are 2-4% for the mainstream (urms/u∞, vrms/u∞,), and on the order of 8-10% for the coolant (urms/uc, vrms/uc,). A special emphasis is placed on inlet characterization, since inlet data in the literature is often incomplete or is of relatively low quality for CFD development. The data reveals that min-shear injection provides the best performance, followed by the wall-jet. The wall-wake case is comparably poor in performance. The comprehensive data suggests that this relative performance is due to the mixing strength of each case, as well as the location of regions of strong mixing with respect to the wall. Kinematic and thermal data show that strong mixing occurs in the wall-jet away from the wall (y/s>1), while strong mixing in the wall-wake occurs much closer to the wall (y/s<1). Min-shear cases exhibit noticeably weaker mixing confined to about y/s=1. Additionally to these general observations, the experimental data obtained in this work is analyzed to reveal scaling laws for the inlets, near-wall scaling, detecting and characterizing coherent structures in the flow as well as to provide data reduction strategies for comparison to CFD models (RANS and LES).

Guided Migration and Collective Behavior: Cell Dynamics during Cancer Progression

This dissertation focuses on gaining understanding of cell migration and collective behavior through a combination of experiment, analysis, and modeling techniques. Cell migration is a ubiquitous process that plays an important role during embryonic development and wound healing as well as in diseases like cancer, which is a particular focus of this work. As cancer cells become increasingly malignant, they acquire the ability to migrate away from the primary tumor and spread throughout the body to form metastatic tumors. During this process, changes in gene expression and the surrounding tumor environment can lead to changes in cell migration characteristics. In this thesis, I analyze how cells are guided by the texture of their environment and how cells cooperate with their neighbors to move collectively. The emergent properties of collectively moving groups are a particular focus of this work as collective cell dynamics are known to change in diseases such as cancer. The internal machinery for cell migration involves polymerization of the actin cytoskeleton to create protrusions that---in coordination with retraction of the rear of the cell---lead to cell motion. This actin machinery has been previously shown to respond to the topography of the surrounding surface, leading to guided migration of amoeboid cells. Here we show that epithelial cells on nanoscale ridge structures also show changes in the morphology of their cytoskeletons; actin is found to align with the ridge structures. The migration of the cells is also guided preferentially along the ridge length. These ridge structures are on length scales similar to those found in tumor microenvironments and as such provide a system for studying the response of the cells' internal migration machinery to physiologically relevant topographical cues. In addition to sensing surface topography, individual cells can also be influenced by the pushing and pulling of neighboring cells. The emergent properties of collectively migrating cells show interesting dynamics and are relevant for cancer progression, but have been less studied than the motion of individual cells. We use Particle Image Velocimetry (PIV) to extract the motion of a collectively migrating cell sheet from time lapse images. The resulting flow fields allow us to analyze collective behavior over multiple length and time scales. To analyze the connection between individual cell properties and collective migration behavior, we compare experimental flow fields with the migration of simulated cell groups. Our collective migration metrics allow for a quantitative comparison between experimental and simulated results. This comparison shows that tissue-scale decreases in collective behavior can result from changes in individual cell activity without the need to postulate the existence of subpopulations of leader cells or global gradients. In addition to tissue-scale trends in collective behavior, the migration of cell groups includes localized dynamic features such as cell rearrangements. An individual cell may smoothly follow the motion of its neighbors (affine motion) or move in a more individualistic manner (non-affine motion). By decomposing individual motion into both affine and non-affine components, we measure cell rearrangements within a collective sheet. Finally, finite-time Lyapunov exponent (FTLE) values capture the stretching of the flow field and reflect its chaotic character. Applying collective migration analysis techniques to experimental data on both malignant and non-malignant human breast epithelial cells reveals differences in collective behavior that are not found from analyzing migration speeds alone. Non-malignant cells show increased cooperative motion on long time scales whereas malignant cells remain uncooperative as time progresses. Combining multiple analysis techniques also shows that these two cell types differ in their response to a perturbation of cell-cell adhesion through the molecule E-cadherin. Non-malignant MCF10A cells use E-cadherin for short time coordination of collective motion, yet even with decreased E-cadherin expression, the cells remain coordinated over long time scales. In contrast, the migration behavior of malignant and invasive MCF10CA1a cells, which already shows decreased collective dynamics on both time scales, is insensitive to the change in E-cadherin expression.

PHYTOPLANKTON AND NUTRIENT DYNAMICS WITH A FOCUS ON NITROGEN FORM IN THE ANACOSTIA RIVER, IN WASHINGTON, D.C. AND WEST LAKE, IN HANGZHOU, CHINA

Nutrient loading has been linked with severe water quality impairment, ranging from hypoxia to increased frequency of harmful algal blooms (HABs), loss of fisheries, and changes in biodiversity. Waters around the globe are experiencing deleterious effects of eutrophication; however, the relative amount of nitrogen (N) and phosphorus (P) reaching these waters is not changing proportionately, with high N loads increasingly enriched in chemically-reduced N forms. Research involving two urban freshwater and nutrient enriched systems, the Anacostia River, USA, a tributary of the Potomac River feeding into the Chesapeake Bay, and West Lake, Hangzhou, Zhejiang Province, China, was conducted to assess the response of phytoplankton communities to changing N-form and N/P-ratios. Field observations involving the characterization of ambient phytoplankton communities and N-forms, as well as experimental (nutrient enrichment) manipulations were used to understand shifts in phytoplankton community composition with increasing NH4+ loads. In both locations, a >2-fold increase in ambient NH4+:NO3- ratios was followed by a shift in the phytoplankton community, with diatoms giving way to chlorophytes and cyanobacteria. Enrichment experiments mirrored this, in that samples enriched with NH4+ lead to increased abundance of chlorophytes and cyanobacteria. This work shows that in both of these systems experiencing nutrient enrichment that NH4+ supports communities dominated by more chlorophytes and cyanobacteria than other phytoplankton groups.

Effects of Drive Speed Modulation on Dynamics of Slender Rotating Structures

Slender rotating structures are used in many mechanical systems. These structures can suffer from undesired vibrations that can affect the components and safety of a system. Furthermore, since some these structures can operate in a harsh environment, installation and operation of sensors that are needed for closed-loop and collocated control schemes may not be feasible. Hence, the need for an open-loop non-collocated scheme for control of the dynamics of these structures. In this work, the effects of drive speed modulation on the dynamics of slender rotating structures are studied. Slender rotating structures are a type of mechanical rotating structures, whose length to diameter ratio is large. For these structures, the torsion mode natural frequencies can be low. In particular, for isotropic structures, the first few torsion mode frequencies can be of the same order as the first few bending mode frequencies. These situations can be conducive for energy transfer amongst bending and torsion modes. Scenarios with torsional vibrations experienced by rotating structures with continuous rotor-stator contact occur in many rotating mechanical systems. Drill strings used in the oil and gas industry are an example of rotating structures whose torsional vibrations can be deleterious to the components of the drilling system. As a novel approach to mitigate undesired vibrations, the effects of adding a sinusoidal excitation to the rotation speed of a drill string are studied. A portion of the drill string located within a borewell is considered and this rotating structure has been modeled as an extended Jeffcott rotor and a sinusoidal excitation has been added to the drive speed of the rotor. After constructing a three-degree-of-freedom model to capture lateral and torsional motions, the equations of motions are reduced to a single differential equation governing torsional vibrations during continuous stator contact. An approximate solution has been obtained by making use of the Method of Direct Partition of Motions with the governing torsional equation of motion. The results showed that for a rotor undergoing forward or backward whirling, the addition of sinusoidal excitation to the drive speed can cause an increase in the equivalent torsional stiffness, smooth the discontinuous friction force at contact, and reduce the regions of negative slope in the friction coefficient variation with respect to speed. Experiments with a scaled drill string apparatus have also been conducted and the experimental results show good agreement with the numerical results obtained from the developed models. These findings suggest that the extended Jeffcott rotordynamics model can be useful for studies of rotor dynamics in situations with continuous rotor-stator contact. Furthermore, the results obtained suggest that the drive speed modulation scheme can have value for attenuating drill-string vibrations.

Guided Migration and Collective Behavior: Cell Dynamics during Cancer Progression

This dissertation focuses on gaining understanding of cell migration and collective behavior through a combination of experiment, analysis, and modeling techniques. Cell migration is a ubiquitous process that plays an important role during embryonic development and wound healing as well as in diseases like cancer, which is a particular focus of this work. As cancer cells become increasingly malignant, they acquire the ability to migrate away from the primary tumor and spread throughout the body to form metastatic tumors. During this process, changes in gene expression and the surrounding tumor environment can lead to changes in cell migration characteristics. In this thesis, I analyze how cells are guided by the texture of their environment and how cells cooperate with their neighbors to move collectively. The emergent properties of collectively moving groups are a particular focus of this work as collective cell dynamics are known to change in diseases such as cancer. The internal machinery for cell migration involves polymerization of the actin cytoskeleton to create protrusions that---in coordination with retraction of the rear of the cell---lead to cell motion. This actin machinery has been previously shown to respond to the topography of the surrounding surface, leading to guided migration of amoeboid cells. Here we show that epithelial cells on nanoscale ridge structures also show changes in the morphology of their cytoskeletons; actin is found to align with the ridge structures. The migration of the cells is also guided preferentially along the ridge length. These ridge structures are on length scales similar to those found in tumor microenvironments and as such provide a system for studying the response of the cells' internal migration machinery to physiologically relevant topographical cues. In addition to sensing surface topography, individual cells can also be influenced by the pushing and pulling of neighboring cells. The emergent properties of collectively migrating cells show interesting dynamics and are relevant for cancer progression, but have been less studied than the motion of individual cells. We use Particle Image Velocimetry (PIV) to extract the motion of a collectively migrating cell sheet from time lapse images. The resulting flow fields allow us to analyze collective behavior over multiple length and time scales. To analyze the connection between individual cell properties and collective migration behavior, we compare experimental flow fields with the migration of simulated cell groups. Our collective migration metrics allow for a quantitative comparison between experimental and simulated results. This comparison shows that tissue-scale decreases in collective behavior can result from changes in individual cell activity without the need to postulate the existence of subpopulations of leader cells or global gradients. In addition to tissue-scale trends in collective behavior, the migration of cell groups includes localized dynamic features such as cell rearrangements. An individual cell may smoothly follow the motion of its neighbors (affine motion) or move in a more individualistic manner (non-affine motion). By decomposing individual motion into both affine and non-affine components, we measure cell rearrangements within a collective sheet. Finally, finite-time Lyapunov exponent (FTLE) values capture the stretching of the flow field and reflect its chaotic character. Applying collective migration analysis techniques to experimental data on both malignant and non-malignant human breast epithelial cells reveals differences in collective behavior that are not found from analyzing migration speeds alone. Non-malignant cells show increased cooperative motion on long time scales whereas malignant cells remain uncooperative as time progresses. Combining multiple analysis techniques also shows that these two cell types differ in their response to a perturbation of cell-cell adhesion through the molecule E-cadherin. Non-malignant MCF10A cells use E-cadherin for short time coordination of collective motion, yet even with decreased E-cadherin expression, the cells remain coordinated over long time scales. In contrast, the migration behavior of malignant and invasive MCF10CA1a cells, which already shows decreased collective dynamics on both time scales, is insensitive to the change in E-cadherin expression.