Dynamics of cell–matrix mechanical interactions in three dimensions

The forces cells apply to their surroundings control biological processes such as growth, adhesion, development, and migration. In the past 20 years, a number of experimental techniques have been developed to measure such cell tractions. These approaches have primarily measured the tractions applied by cells to synthetic two-dimensional substrates, which do not mimic in vivo conditions for most cell types. Many cell types live in a fibrous three-dimensional (3D) matrix environment. While studying cell behavior in such 3D matrices will provide valuable insights for the mechanobiology and tissue engineering communities, no experimental approaches have yet measured cell tractions in a fibrous 3D matrix.

This thesis describes the development and application of an experimental technique for quantifying cellular forces in a natural 3D matrix. Cells and their surrounding matrix are imaged in three dimensions with high speed confocal microscopy. The cell-induced matrix displacements are computed from the 3D image volumes using digital volume correlation. The strain tensor in the 3D matrix is computed by differentiating the displacements, and the stress tensor is computed by applying a constitutive law. Finally, tractions applied by the cells to the matrix are computed directly from the stress tensor.

The 3D traction measurement approach is used to investigate how cells mechanically interact with the matrix in biologically relevant processes such as division and invasion. During division, a single mother cell undergoes a drastic morphological change to split into two daughter cells. In a 3D matrix, dividing cells apply tensile force to the matrix through thin, persistent extensions that in turn direct the orientation and location of the daughter cells. Cell invasion into a 3D matrix is the first step required for cell migration in three dimensions. During invasion, cells initially apply minimal tractions to the matrix as they extend thin protrusions into the matrix fiber network. The invading cells anchor themselves to the matrix using these protrusions, and subsequently pull on the matrix to propel themselves forward.

Lastly, this thesis describes a constitutive model for the 3D fibrous matrix that uses a finite element (FE) approach. The FE model simulates the fibrous microstructure of the matrix and matches the cell-induced matrix displacements observed experimentally using digital volume correlation. The model is applied to predict how cells mechanically sense one another in a 3D matrix. It is found that cell-induced matrix displacements localize along linear paths. These linear paths propagate over a long range through the fibrous matrix, and provide a mechanism for cell-cell signaling and mechanosensing. The FE model developed here has the potential to reveal the effects of matrix density, inhomogeneity, and anisotropy in signaling cell behavior through mechanotransduction.

The logic of receptor-ligand interactions in the Notch signaling pathway

The Notch signaling pathway enables neighboring cells to coordinate developmental fates in diverse processes such as angiogenesis, neuronal differentiation, and immune system development. Although key components and interactions in the Notch pathway are known, it remains unclear how they work together to determine a cell's signaling state, defined as its quantitative ability to send and receive signals using particular Notch receptors and ligands. Recent work suggests that several aspects of the system can lead to complex signaling behaviors: First, receptors and ligands interact in two distinct ways, inhibiting each other in the same cell (in cis) while productively interacting between cells (in trans) to signal. The ability of a cell to send or receive signals depends strongly on both types of interactions. Second, mammals have multiple types of receptors and ligands, which interact with different strengths, and are frequently co-expressed in natural systems. Third, the three mammalian Fringe proteins can modify receptor-ligand interaction strengths in distinct and ligand-specific ways. Consequently, cells can exhibit non-intuitive signaling states even with relatively few components.

In order to understand what signaling states occur in natural processes, and what types of signaling behaviors they enable, this thesis puts forward a quantitative and predictive model of how the Notch signaling state is determined by the expression levels of receptors, ligands, and Fringe proteins. To specify the parameters of the model, we constructed a set of cell lines that allow control of ligand and Fringe expression level, and readout of the resulting Notch activity. We subjected these cell lines to an assay to quantitatively assess the levels of Notch ligands and receptors on the surface of individual cells. We further analyzed the dependence of these interactions on the level and type of Fringe expression. We developed a mathematical modeling framework that uses these data to predict the signaling states of individual cells from component expression levels. These methods allow us to reconstitute and analyze a diverse set of Notch signaling configurations from the bottom up, and provide a comprehensive view of the signaling repertoire of this major signaling pathway.

Wave interactions in periodic structures and periodic dielectric waveguides

This work is concerned with a general analysis of wave interactions in periodic structures and particularly periodic thin film dielectric waveguides.

The electromagnetic wave propagation in an asymmetric dielectric waveguide with a periodically perturbed surface is analyzed in terms of a Floquet mode solution. First order approximate analytical expressions for the space harmonics are obtained. The solution is used to analyze various applications: (1) phase matched second harmonic generation in periodically perturbed optical waveguides; (2) grating couplers and thin film filters; (3) Bragg reflection devices; (4) the calculation of the traveling wave interaction impedance for solid state and vacuum tube optical traveling wave amplifiers which utilize periodic dielectric waveguides. Some of these applications are of interest in the field of integrated optics.

A special emphasis is put on the analysis of traveling wave interaction between electrons and electromagnetic waves in various operation regimes. Interactions with a finite temperature electron beam at the collision-dominated, collisionless, and quantum regimes are analyzed in detail assuming a one-dimensional model and longitudinal coupling.

The analysis is used to examine the possibility of solid state traveling wave devices (amplifiers, modulators), and some monolithic structures of these devices are suggested, designed to operate at the submillimeter-far infrared frequency regime. The estimates of attainable traveling wave interaction gain are quite low (on the order of a few inverse centimeters). However, the possibility of attaining net gain with different materials, structures and operation condition is not ruled out.

The developed model is used to discuss the possibility and the theoretical limitations of high frequency (optical) operation of vacuum electron beam tube; and the relation to other electron-electromagnetic wave interaction effects (Smith-Purcell and Cerenkov radiation and the free electron laser) are pointed out. Finally, the case where the periodic structure is the natural crystal lattice is briefly discussed. The longitudinal component of optical space harmonics in the crystal is calculated and found to be of the order of magnitude of the macroscopic wave, and some comments are made on the possibility of coherent bremsstrahlung and distributed feedback lasers in single crystals.

Strong atom-light interactions along nanostructures: Transition from free-space to nanophotonic interfaces

An exciting frontier in quantum information science is the integration of otherwise "simple'' quantum elements into complex quantum networks. The laboratory realization of even small quantum networks enables the exploration of physical systems that have not heretofore existed in the natural world. Within this context, there is active research to achieve nanoscale quantum optical circuits, for which atoms are trapped near nano-scopic dielectric structures and "wired'' together by photons propagating through the circuit elements. Single atoms and atomic ensembles endow quantum functionality for otherwise linear optical circuits and thereby enable the capability of building quantum networks component by component. Toward these goals, we have experimentally investigated three different systems, from conventional to rather exotic systems : free-space atomic ensembles, optical nano fibers, and photonics crystal waveguides. First, we demonstrate measurement-induced quadripartite entanglement among four quantum memories. Next, following the landmark realization of a nanofiber trap, we demonstrate the implementation of a state-insensitive, compensated nanofiber trap. Finally, we reach more exotic systems based on photonics crystal devices. Beyond conventional topologies of resonators and waveguides, new opportunities emerge from the powerful capabilities of dispersion and modal engineering in photonic crystal waveguides. We have implemented an integrated optical circuit with a photonics crystal waveguide capable of both trapping and interfacing atoms with guided photons, and have observed the collective effect, superradiance, mediated by the guided photons. These advances provide an important capability for engineered light-matter interactions, enabling explorations of novel quantum transport and quantum many-body phenomena.

Non-Linear Scale Interactions in a Forced Turbulent Boundary Layer

This thesis explores the dynamics of scale interactions in a turbulent boundary layer through a forcing-response type experimental study. An emphasis is placed on the analysis of triadic wavenumber interactions since the governing Navier-Stokes equations for the flow necessitate a direct coupling between triadically consist scales. Two sets of experiments were performed in which deterministic disturbances were introduced into the flow using a spatially-impulsive dynamic wall perturbation. Hotwire anemometry was employed to measure the downstream turbulent velocity and study the flow response to the external forcing. In the first set of experiments, which were based on a recent investigation of dynamic forcing effects in a turbulent boundary layer, a 2D (spanwise constant) spatio-temporal normal mode was excited in the flow; the streamwise length and time scales of the synthetic mode roughly correspond to the very-large-scale-motions (VLSM) found naturally in canonical flows. Correlation studies between the large- and small-scale velocity signals reveal an alteration of the natural phase relations between scales by the synthetic mode. In particular, a strong phase-locking or organizing effect is seen on directly coupled small-scales through triadic interactions. Having characterized the bulk influence of a single energetic mode on the flow dynamics, a second set of experiments aimed at isolating specific triadic interactions was performed. Two distinct 2D large-scale normal modes were excited in the flow, and the response at the corresponding sum and difference wavenumbers was isolated from the turbulent signals. Results from this experiment serve as an unique demonstration of direct non-linear interactions in a fully turbulent wall-bounded flow, and allow for examination of phase relationships involving specific interacting scales. A direct connection is also made to the Navier-Stokes resolvent operator framework developed in recent literature. Results and analysis from the present work offer insights into the dynamical structure of wall turbulence, and have interesting implications for design of practical turbulence manipulation or control strategies.