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Open Access Publications from the University of California

Scholarly Works (20 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2019)

The advent of attosecond pulse duration light sources has enabled the study of fundamental light-matter interactions. Condensed matter systems are of particular interest, as they are often significantly impacted by many body interactions, and thus provide a natural environment for the observation and study of such interactions in the time domain. In this dissertation, an apparatus for extreme ultraviolet (XUV) transient reflectivity is described, and several studies on ultrafast dynamics in solids are performed. In the first chapter, background on ultrafast spectroscopy, light matter interaction, and reflection from surfaces is provided, giving the necessary underpinnings for the subsequent discussion. In the second chapter, the development and capabilities of the constructed XUV transient reflection apparatus are reviewed. Additionally, the static refractive index of germanium (a commonly employed semiconductor), is recovered from multi angle reflection measurements. In the third chapter, femtosecond dynamics in germanium are studied by XUV transient reflection. The results are analyzed and interpreted in the context of the existing optical literature. In the fourth chapter, preliminary attosecond resolved measurements in germanium are presented, and the results are tentatively interpreted in the context of light dressed states. In the fifth chapter, attosecond dynamics of core excitons in magnesium oxide (MgO) are studied. The results are analyzed and interpreted as a light induced modification of excitonic coherence. This body of work is intended to establish XUV transient reflectivity as a technique for study of solid-state systems and to provide example studies in two representative systems, a semiconductor and an insulator.

    Cover page: Ultrafast Dynamics in Condensed Matter Studied with Attosecond Extreme Ultraviolet Transient Reflectivity
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2016)
    The extreme ultraviolet absorption of vanadium dioxide is probed with attosecond transient absorption during a photoinduced phase transition. Measurements reveal an ultrafast rearrangement in the density of states suggestive of electron correlation and Mott physics.
      Cover page: Ultrafast Dynamics in the Insulator-to-Metal Phase Transition of VO2 via Attosecond Transient Absorption
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2014)
      The detection of bacterial pathogens plays an important role in many biomedical applications, including clinical diagnostics, food and water safety, and biosecurity. Most current bacterial detection technologies, however, are unsuitable for use in resource-limited settings where the highest disease burdens often exist. Thus, there is an urgent need to develop portable, user-friendly biosensors capable of rapid detection of multiple pathogens in situ. We report a microfluidic chip for multiplexed detection of bacterial cells that uses antimicrobial peptides (AMPs) with species-specific targeting and binding capabilities. The AMPs are immobilized onto an electrical impedance microsensor array and serve as biorecognition elements for bacterial cell detection. Characterization of peptide immobilization on the sensors revealed robust surface binding via cysteine-gold interactions and vertical alignment relative to the sensor surface. Samples containing Streptococcus mutans and Pseudomonas aeruginosa were loaded in the chip, and both microorganisms were detected at minimum concentrations of 10⁵ cfu/mL within 25 min. Measurements performed in a variety of solutions revealed that high-conductivity solutions produced the largest impedance values. By integrating a highly specific bacterial cell capture scheme with rapid electrical detection, this device demonstrates great potential as a next-generation, point-of-care diagnostic platform for the detection of disease-causing pathogenic agents.
        Creative Commons 'BY-NC-SA' version 4.0 license
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2014)
        The oral opportunistic pathogen Fusobacterium nucleatum is known to interact with a large number of different bacterial species residing in the oral cavity. It adheres to a variety of Gram-positive bacteria, including oral streptococci via the arginine-inhibitable adhesin RadD. In this study, we describe a novel protein encoded by the predicted open reading frame FN1253 that appears to play a role in interspecies interactions of F. nucleatum, particularly with oral streptococci and related Gram-positive species. We designated FN1253 as aid1 (Adherence Inducing Determinant 1). Expression analyses demonstrated that this gene was induced in F. nucleatum single species biofilms, while the presence of representative members of the oral microbiota known to adhere to F. nucleatum triggered its suppression. Inactivation as well as overexpression of aid1 affected the ability of F. nucleatum to coaggregate with oral streptococci and the closely related Enterococcus faecalis, but not other Gram-positive oral species tested. Furthermore, overexpression of aid1 led to a drastic change in the structure of dual species biofilms of F. nucleatum with oral streptococci. Aid1 function was abolished in the presence of arginine and found to be dependent on RadD. Interestingly, differential expression of aid1 did not affect messenger RNA and protein levels of RadD. These findings indicate that RadD-mediated adhesion to oral streptococci involves more complex cellular processes than the simple interaction of adhesins on the surface of partner strains. Aid1 could potentially play an important role in facilitating RadD-mediated interaction with oral streptococci by increasing binding specificity of F. nucleatum to other microbial species.
          Cover page: Characterization of aid1, a Novel Gene Involved in Fusobacterium nucleatum Interspecies Interactions
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2021)
          In Peierls-distorted materials, photoexcitation leads to a strongly coupled transient response between structural and electronic degrees of freedom, always measured independently of each other. Here we use transient reflectivity in the extreme ultraviolet to quantify both responses in photoexcited bismuth in a single measurement. With the help of first-principles calculations based on density-functional theory (DFT) and time-dependent DFT, the real-space atomic motion and the temperature of both electrons and holes as a function of time are captured simultaneously, retrieving an anticorrelation between the A1g phonon dynamics and carrier temperature. The results reveal a coherent, bidirectional energy exchange between carriers and phonons, which is a dynamical counterpart of the static Peierls-Jones distortion, providing validation of previous theoretical predictions.
            Cover page: Coherent energy exchange between carriers and phonons in Peierls-distorted bismuth unveiled by broadband XUV pulsesCreative Commons 'BY-NC' version 4.0 license
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2016)
            The photoinduced insulator-to-metal phase transition in vanadium dioxide is experimentally investigated by attosecond transient absorption spectroscopy. Ultrafast changes cover a broad ~20-eV-wide spectral range, emphasizing core spectroscopic access and the importance of electron correlation effects.
              Cover page: Ultrafast Dynamics in the Insulator-to-Metal Phase Transition of Vanadium Dioxide Measured by Attosecond Transient Absorption Spectrosopy
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2017)
              Attosecond transient reflectivity is developed to observe the photoexcitation dynamics in germanium. Attosecond time-resolved measurements of the dielectric function reveal a fewfemtosecond collective electronic response time, which renormalizes the Coulomb interaction between the excited carriers.
                Cover page: Attosecond quantum kinetics of photoexcited Germanium
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2018)
                We present an extreme ultraviolet (XUV) transient absorption apparatus tailored to attosecond and femtosecond measurements on bulk solid-state thin-film samples, specifically when the sample dynamics are sensitive to heating effects. The setup combines methodology for stabilizing sub-femtosecond time-resolution measurements over 48 h and techniques for mitigating heat buildup in temperature-dependent samples. Single-point beam stabilization in pump and probe arms and periodic time-zero reference measurements are described for accurate timing and stabilization. A hollow-shaft motor configuration for rapid sample rotation, raster scanning capability, and additional diagnostics are described for heat mitigation. Heat transfer simulations performed using a finite element analysis allow comparison of sample rotation and traditional raster scanning techniques for 100 Hz pulsed laser measurements on vanadium dioxide, a material that undergoes an insulator-to-metal transition at a modest temperature of 340 K. Experimental results are presented confirming that the vanadium dioxide (VO2) sample cannot cool below its phase transition temperature between laser pulses without rapid rotation, in agreement with the simulations. The findings indicate the stringent conditions required to perform rigorous broadband XUV time-resolved absorption measurements on bulk solid-state samples, particularly those with temperature sensitivity, and elucidate a clear methodology to perform them.
                  Cover page: Attosecond transient absorption instrumentation for thin film materials: Phase transitions, heat dissipation, signal stabilization, timing correction, and rapid sample rotation
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2015)
                  One major challenge to studying human microbiome and its associated diseases is the lack of effective tools to achieve targeted modulation of individual species and study its ecological function within multispecies communities. Here, we show that C16G2, a specifically targeted antimicrobial peptide, was able to selectively kill cariogenic pathogen Streptococcus mutans with high efficacy within a human saliva-derived in vitro oral multispecies community. Importantly, a significant shift in the overall microbial structure of the C16G2-treated community was revealed after a 24-h recovery period: several bacterial species with metabolic dependency or physical interactions with S. mutans suffered drastic reduction in their abundance, whereas S. mutans' natural competitors, including health-associated Streptococci, became dominant. This study demonstrates the use of targeted antimicrobials to modulate the microbiome structure allowing insights into the key community role of specific bacterial species and also indicates the therapeutic potential of C16G2 to achieve a healthy oral microbiome.
                    Cover page: Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology
                    • Article
                    • Peer Reviewed
                    UC Berkeley Previously Published Works (2018)
                    The thermalization of hot carriers and phonons gives direct insight into the scattering processes that mediate electrical and thermal transport. Obtaining the scattering rates for both hot carriers and phonons currently requires multiple measurements with incommensurate timescales. Here, transient extreme-ultraviolet (XUV) spectroscopy on the silicon 2p core level at 100 eV is used to measure hot carrier and phonon thermalization in Si(100) from tens of femtoseconds to 200 ps, following photoexcitation of the indirect transition to the Δ valley at 800 nm. The ground state XUV spectrum is first theoretically predicted using a combination of a single plasmon pole model and the Bethe-Salpeter equation with density functional theory. The excited state spectrum is predicted by incorporating the electronic effects of photo-induced state-filling, broadening, and band-gap renormalization into the ground state XUV spectrum. A time-dependent lattice deformation and expansion is also required to describe the excited state spectrum. The kinetics of these structural components match the kinetics of phonons excited from the electron-phonon and phonon-phonon scattering processes following photoexcitation. Separating the contributions of electronic and structural effects on the transient XUV spectra allows the carrier population, the population of phonons involved in inter- and intra-valley electron-phonon scattering, and the population of phonons involved in phonon-phonon scattering to be quantified as a function of delay time.
                      Cover page: Hot phonon and carrier relaxation in Si(100) determined by transient extreme ultraviolet spectroscopy
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