Ce travail de thèse a démontré la possibilité de mesurer la relaxation d’un complexe biomoléculaire ainsi que son hétérogénéité structurale, en associant la microfluidique et la fluorescence résolue en temps (FRT). Je présente de quelle façon la FRT permet d’obtenir une information sur la structure d’une molécule et comment on la mesure, notamment grâce à une caméra à balayage de fente. J’introduis ensuite la microfluidique de gouttes, permettant de mélanger deux réactifs en quelques millisecondes et de suivre la relaxation du complexe au cours de la propagation des micro-réacteurs. Puis, la mesure d’une cinétique avec un couple de molécules modèle démontre la preuve de principe, faisant l’objet d’un article soumis. Enfin la mesure de FRT par comptage de photons uniques dans des gouttes uniques est décrite. Elle ouvre une perspective d’application pour le criblage à haut débit : un brevet a été déposé. / This thesis has proven the feasibility of measuring the relaxation of a biomolecular complex as well as its structural heterogeneity, by associating microfluidics and time resolved fluorescence (TRF). I present in which way TRF allows for probing the structure of a molecule and how it is measured, in particular by using a streak camera. I then introduce droplet microfluidics, which enables to mix two reagents in a few milliseconds and to follow the relaxation of the complex, along propagation of the micro-reactors. Next, the measurement of a kinetics with test molecules validates the proof of concept, reported in a submitted article. Finally, the measurement of TRF by single photon counting in single droplets is described. It opens a perspective for an application in high-throughput screening: a patent has been registered.

Doctor of Philosophy / Department of Physics / Zenghu Chang / The first part of this thesis describes our novel design, test, and application of our X-ray streak camera to the pulse duration measurement of soft X-rays. We demonstrated a significant improvement in the resolution of the x-ray streak camera by reducing the electron beam size in the deflection plates. This was accomplished by adding a slit in front of the focusing lens and the deflection plates. The temporal resolution reached 280 fs when the slit width was 5 μm. The camera was operated in an accumulative mode and tested by using a 25 fs laser with 2 kHz repetition rate and 1-2% RMS pulse energy stability. We conclude that deflection aberrations, which limit the resolution of the camera, can be appreciably reduced by eliminating the wide-angle electrons. We also employed the same streak camera to demonstrate that it is capable of measuring the pulse duration of X-rays. We measured the pulse duration of X-rays emitted from Ni-like Ag and Cd grazing-incidence laser to be ~5ps. The measured value agrees with the prediction made by the model and the measurement made by changing the delay as a function of the pulse duration. The streak camera was also tested with various sources of X-ray such as high harmonics generation of soft x-rays from an argon atom using a high power Ti:sapphire laser source of KLS. The result of the measurement manifests its capability for serving as a detector in the study of ultrafast dynamics in the field of physics, chemistry, biology and medical sciences. The second part of this thesis describes our design of a spectrometer to study the effect of the Carrier envelope (CE) phase on polarization gated extreme-ultraviolet (XUV) super-continuum generation. Because the challenge of making single shot experiment possible is to generate a sufficient number of photons, our setup has been built to allow generation of high order harmonics at the maximum phase matched pressure. This is the first time to our knowledge that phase matching in the polarization gating process has been studied so far. We measured the maximum phase matching pressure to be ~ 55 Torr which is the pressure above which quadratic increase in intensity of the high harmonics spectrum ceases to appear. At this pressure the number of photons per laser shot was 104 which is sufficient for measuring the single shot XUV spectrum in the range 34 to 45 eV. The spectral profile was a super-continuum for some shots and discrete high harmonics for other shots. It is believed that the shot to shot variation of the spectra is due to the changes of the carrier envelope phase of the few-cycle laser pulses used for the polarization gating. An improved CE phase stabilization system in KLS further eliminated the statistical noise in our observation by allowing us to integrate data over several laser cycles for each CE phase value. The effect of CE phase on a polarization gated XUV spectrum was tested by changing the CE phase with two different methods. In the first method, the CE phase was changed by changing the thickness of fused silica plates on the beam path, and the result shows the shift in the spectral peak of the XUV when the gate width approached less than one optical cycle. As gate width was made less than half the optical cycle, the spectrum was observed with continuum harmonics separated by π radians. We believe that the presence of continuum and discrete harmonics spectra in the observation is due to single and double attosecond pulses generated in the polarization gating. In the second method the carrier-envelope phase of pulses from a grating-based chirped pulse amplification laser was varied smoothly to cover a 2π range by controlling the grating separation. The phase is measured simultaneously by an f-to-2f setup and by the variation of XUV spectra from polarization gated high harmonic generation. A very good similarity between the effect of single and double slits in Yong’s experiment and that of CE phase on the XUV spectrum in the polarization gating experiment has been found, giving better agreement with the theory. The effect of optical properties such as the Gouy phase shift on the polarization gated spectrum has also been studied in the course of investigating the best experimental optimizations to generate the most CE phase sensitive XUV spectrum with less statistical noise. This is the first time to our knowledge experimental study of the effect of the Gouy phase shift on a polarization gated XUV spectrum has been made.

In the present thesis, two positive sense single-stranded RNA viruses have been used as models to understand the structure and function of viral-encoded proteins. One of them, Pepper Vein Banding Virus (PVBV; genus Potyvirus; family Potyviridae) is a flexuous, rod-shaped virus that encodes for a polyprotein of size ~340 kDa. The polyprotein undergoes proteolytic processing by viral-encoded proteases, of which Nuclear Inclusion-a Protease (NIa-Pro) is the major protease. It is a serine-like cysteine protease which cleaves between a Q/A or Q/S, present in the context of the heptapeptide recognition sequence. The temporal regulation of intermediates and mature proteins released by NIa-Pro cleavage is crucial for a successful infection. In the present study, histidine-tagged NIa-Pro, Viral Protein genome-linked (VPg), and the cleavage site mutant (E191A) VPg-Pro were over-expressed in E. coli and purified. The protease activity of NIa-Pro was monitored using an HPLC-based protease assay developed using a peptide substrate. NIa-Pro protease activity was found to get modulated upon interaction with VPg and upon undergoing phosphorylation. Both these events have been found to involve the face of NIa-Pro which contains the solvent-exposed Trp143. Mutational studies and molecular dynamics analyses provide evidence that this residue is buried upon interaction of NIa-Pro with VPg, and any perturbation of its orientation influences the active site Cys151 via an extensive interaction network. This interaction was found to enhance the velocity of NIa-Pro protease activity, especially if the two domains were present in trans (VPg+Pro). In addition, the main-chain –NH2 group of Trp143 was found to be hydrogen-bonded to the side chain –OH group of Ser129, the residue which was identified to undergo phosphorylation by host plant kinases. Interestingly, when the two domains were present in cis (E191A VPg-Pro), no phosphorylation was observed. Mutations of Ser129 (to phosphorylation-mimic Asp or phosphorylation-deficient Ala residues) which affected this H-bond were found to disturb Trp143 and Cys151 orientation, which drastically reduced the protease activity of NIa-Pro. Within the polyprotein, VPg is present at the N-terminus of NIa-Pro and the cleavage site between them is suboptimal (E/A). In the present study, VPg-Pro was shown to be covalently linked to the genomic RNA present in the virions. Interestingly, during purification, VPg could only be purified from the soluble when it was expressed at the N-terminus of NIa-Pro. A series of bioinformatics and biophysical analysis of VPg showed that PVBV VPg, like other potyviral VPgs, exists as a molten-globule. Moreover, while VPg was shown to harbour the Walker motifs, it was found to exhibit an ATPase activity only when it was present with the NIa-Pro (especially in cis). Lys47 and Asp88:Glu89 were found crucial for optimal activity. Over all the results demonstrated that there is a reciprocal modulation of structure and function of the VPg and NIa-Pro domains. These results can explain the possible significance of an impeded cleavage rate between the two domains of VPg-Pro during PVBV infection. The precursor, VPg-Pro, could offer the advantage of evading the inhibitory phosphorylation of NIa-Pro by the host, as well as drive certain viral processes by virtue of its ATPase activity. And subsequent cleavage of the domains and their trans interaction could offer a higher turnover rate which might assist sufficient CP production required for viral morphogenesis. Another virus, Tobacco Streak Virus (TSV) that belongs to the Ilarvirus genus of the Bromoviridae family is a spherical virus which forms pleiomorphic icosahedral virus particles. It has a tripartite genome and each RNA is encapsidated individually. In the present thesis, TSV was used as a model to understand the properties of its structural protein-the coat protein (CP), with the aim of deciphering TSV assembly process. Thus, the CP gene from TSV RNA 3 was cloned and over-expressed in E. coli. The coat protein thus expressed formed virus-like particles (VLPs), which could be disassembled into dimers using high CaCl2 concentrations. Reassembly of VLPs was possible from dimers even in the absence of any nucleic acid. Mutational analysis of the N-terminal disordered domain showed that 26 amino acid residues from the amino-terminus could be crucial for capsid heterogeneity while, zinc-binding domain was essential for assembly. Overall, the present study shows that the flexible W-C loop of PVBV NIa-Pro, the disordered N-terminal region of PVBV VPg and the disordered N-terminal region of TSV CP harbour residues crucial for regulation of protein function. Such regulatory elements would ultimately allow viruses to maintain a smaller protein number, and thus a smaller genome size.

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<p>Print quality (PQ) is one of the most significant issues with electrophotographic printers. There are many reasons for PQ issues, such as limitations of the electrophotographic process, faulty printer components, or other failures of the print mechanism. These reasons can produce different PQ issues, like streaks, bands, gray spots, text fading, and color fading defects. It is important to analyze the nature and causes of different print defects to more efficiently repair printers and improve the electrophotographic process. </p> <p><br></p> <p>We design a general framework for print quality detection and analysis of customer content. This print quality analysis framework inputs the original digital image saved on the computer and then the scanned image. This framework includes two main modules: image pre-processing, print defects feature vector extraction, and classification. The first module, image pre-processing, includes image registration, color calibration, and region of interest (ROI) extraction. The ROI extraction part is designed to extract four different kinds of ROI from the digital master image. Because different ROIs include different print defects, for example, the symbol ROI includes the text fading defect, and the raster ROI includes the color fading defect. The second module includes different ROI print defects detection and analysis algorithms. We classify different ROI print defects using their feature vector based on their severity. This module proposed four important defects detection methods: uniform color area streak detection, symbol ROI color text fading detection, raster ROI color fading detection using a novel unsupervised clustering method, and raster ROI streak detection. We will introduce the details of these algorithms in this thesis. </p> <p><br></p> <p>We will also show two other interesting print quality projects: print margin skew detection and print velocity simulation and estimation. Print margin skew detection proposes an algorithm that uses the Hough Lines Detection algorithm to detect printing margin and skew errors based on factual scanned image verification. In the print velocity simulation and estimation project, we propose a print velocity simulation tool, design a specific print velocity test page, and design a print velocity estimation algorithm using the dynamic time warping algorithm. </p>

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No description available.

<p dir="ltr">In recent years, nanosecond repetitively pulsed (NRP) plasma discharges have garnered significant interest due to their rapid generation of reactive excited-state species, reactive radicals, and localized heat release within nanosecond (ns) timescale. To effectively harness these plasmas for altering system-level thermal and chemical behavior, a thorough understanding of their governing physics is crucial. This knowledge enables the development of predictive plasma kinetic models for tailoring NRP plasmas to specific applications. However, achieving this requires high-fidelity experimental data to validate models and deepen our understanding of fundamental plasma physics. Advancing experimental spectroscopy and laser diagnostics methods is essential for probing such temporally highly dynamic and optically complex nonequilibrium environments. This includes developing novel <i>test platforms</i>, conducting <i>fundamental research</i> to address existing knowledge gaps, and constructing custom <i>ultrafast laser architectures</i> for probing plasma properties. </p><p dir="ltr">The pioneering development of Streak-based <i>test platform</i> in the diagnostics field of nanosecond pulsed plasmas and its successful application towards inferring the underlying ultrafast spatio-temporal evolution of nanosecond pulsed plasma discharges with an unprecedented time-resolution as short as ~25 ps is presented for the first time. Spectrally filtered, 1D line-imaging of nanosecond pulsed plasma discharges in a single-shot, jitter-free, continuously sweeping manner is obtained, and differences in discharge dynamics of air and N2 plasma environments are studied. Successive <i>test platform</i> advancement includes spectrally resolved Streak-spectroscopy measurements of thermal regime-transition evolution from early-nonequilibrium to local-thermal-equilibrium (LTE) to attain time-resolved quantitative insights into N2(C) state rotational/vibrational nonequilibrium temperatures, electron temperature/density, and spectral lifetime dynamics. </p><p dir="ltr">Ultrafast laser-based progression includes detailed <i>fundamental</i> investigation of higher-order optical nonlinearity perturbations of fs-EFISH by considering of – self-phase modulation induced spectral characteristic of fs-EFISH signal, calibration mapping during-below-and-beyond optical breakdown regime, optical Kerr effect consequences, impact of femtosecond (fs) laser seeding on the noninvasiveness of fs-EFISH, and spectral emission characteristics of fs laser filaments. To infer N2(X) state nonequilibrium of NRP pulsed plasmas, two hybrid fs/ps ro-vibrational coherent anti-Stokes Raman scattering (CARS) <i>ultrafast laser architectures</i> are developed. First architecture, single-laser-solution, reduces system’s energy budget by ~3 mJ/pulse for generating narrowband (~21 ps), high-energy (~420 μJ/pulse), 532 nm probe pulses through incorporation of custom built visible fs optical parametric amplifier (OPA) coupled with an Nd:YAG power amplifier module. The second architecture, two-laser-solution, improves system’s robustness through the development of a 1 kHz, 532 nm, high-energy (~600 μJ/pulse), low-jitter (<1 ps), narrowband (~27 ps), master-oscillator-power-amplification (MOPA) based picosecond probe pulse laser time-synchronized with fs master-oscillator. Single-shot, hybrid fs/ps narrowband ro-vibrational CARS demonstration in a combusting flame up to temperatures of ~2400 K is demonstrated. Experimental ro-vibrational CARS investigation includes polarization based nonresonant background suppression and demonstration of preferential Raman coherence excitation shift, a temperature sensitivity enhancing strategy for vibrationally hot mediums like nanosecond pulsed plasmas. Lastly, an ultrafast pulse-friendly optically accessible vacuum cell is designed and fabricated for controlled experiments of NRP fs/ps CARS. Special care is taken to prevent self-focusing and spectral-temporal chirp of fs CARS beams while maintaining Gaussian focusing beam caustic.</p>