Gauge invariance in the theoretical description of time-resolved angle-resolved pump/probe photoemission spectroscopy

Nonequilibrium calculations in the presence of an electric field are usually performed in a gauge, and need to be transformed to reveal the gauge-invariant observables. In this work, we discuss the issue of gauge invariance in the context of time-resolved angle-resolved pump/probe photoemission. If the probe is applied while the pump is still on, one must ensure that the calculations of the observed photocurrent are gauge invariant. We also discuss the requirement of the photoemission signal to be positive and the relationship of this constraint to gauge invariance. We end by discussing some technical details related to the perturbative derivation of the photoemission spectra, which involve processes where the pump pulse photoemits electrons due to nonequilibrium effects.

Time-resolved investigation of low-density plasma channels produced by a kilohertz femtosecond laser in air

By employing pump-probe back longitudinal diffractometry, the electron density and decay dynamics of a weak plasma channel created by a 1-KHz fs laser in air has been investigated. With ultrashort laser pulses of 50 fs and low energy of 0.6 mJ, we observe weak plasma channels with a length similar to 2 cm in air. An analytical reconstruction method of electron density has been analyzed, which is sensitive to the phase shift and channel size. The electron density in the weak plasma channel is extracted to be about 4x10(16) cm(-3). The diameters of the plasma channel and the filament are about 50 and 150 mu m, respectively, and the measurable electron density can be extended to less than 10(15) cm(-3). Moreover, a different time-frequency technique called linearly chirped longitudinal diffractometry is proposed to time-resolved investigate ultrafast ionization dynamics of laser-irradiated gas, laser interaction with cluster beam, etc.

Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging

Bio-orthogonal non-canonical amino acid tagging (BONCAT) is an analytical method that allows the selective analysis of the subset of newly synthesized cellular proteins produced in response to a biological stimulus. In BONCAT, cells are treated with the non-canonical amino acid L-azidohomoalanine (Aha), which is utilized in protein synthesis in place of methionine by wild-type translational machinery. Nascent, Aha-labeled proteins are selectively ligated to affinity tags for enrichment and subsequently identified via mass spectrometry. The work presented in this thesis exhibits advancements in and applications of the BONCAT technology that establishes it as an effective tool for analyzing proteome dynamics with time-resolved precision.

Chapter 1 introduces the BONCAT method and serves as an outline for the thesis as a whole. I discuss motivations behind the methodological advancements in Chapter 2 and the biological applications in Chapters 2 and 3.

Chapter 2 presents methodological developments that make BONCAT a proteomic tool capable of, in addition to identifying newly synthesized proteins, accurately quantifying rates of protein synthesis. I demonstrate that this quantitative BONCAT approach can measure proteome-wide patterns of protein synthesis at time scales inaccessible to alternative techniques.

In Chapter 3, I use BONCAT to study the biological function of the small RNA regulator CyaR in Escherichia coli. I correctly identify previously known CyaR targets, and validate several new CyaR targets, expanding the functional roles of the sRNA regulator.

In Chapter 4, I use BONCAT to measure the proteomic profile of the quorum sensing bacterium Vibrio harveyi during the time-dependent transition from individual- to group-behaviors. My analysis reveals new quorum-sensing-regulated proteins with diverse functions, including transcription factors, chemotaxis proteins, transport proteins, and proteins involved in iron homeostasis.

Overall, this work describes how to use BONCAT to perform quantitative, time-resolved proteomic analysis and demonstrates that these measurements can be used to study a broad range of biological processes.

Time-resolved volumetric measurement of fine-scale coherent structures in turbulence.

We present full volumetric (three-dimensional) time-resolved (+one-dimensional) measurements of the velocity field in a large water mixing tank, allowing us to assess spatial and temporal rotational energy (enstrophy) and turbulent energy dissipation intermittency. In agreement with previous studies, highly intermittent behavior is observed, with intense coherent flow structures clustering in the periphery of larger vortices. However, further to previous work the full volumetric measurements allow us to separate out the effects of advection from other effects, elucidating not only their topology but also the evolution of these intense events, through the local balance of stretching and diffusion. These findings contribute toward a better understanding of the intermittency phenomenon, which should pave the way for more accurate models of the small-scale motions based on an understanding of the underlying flow physics.