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Open Access Publications from the University of California

Scholarly Works (56 results)

  • Article
  • Peer Reviewed
Lawrence Berkeley National Laboratory (2010)

An ultrafast x-ray streak camera has been realized using a grazing incidence reflection photocathode. X-rays are incident on a gold photocathode at a grazing angle of 20 degree and photoemitted electrons are focused by a large aperture magnetic solenoid lens. The streak camera has high quantum efficiency, 600fs temporal resolution, and 6mm imaging length in the spectral direction. Its single shot capability eliminates temporal smearing due to sweep jitter, and allows recording of the ultrafast dynamics of samples that undergo non-reversible changes.

    Cover page: A grazing incidence x-ray streak camera for ultrafast, single-shot measurements
    • Thesis
    • Peer Reviewed
    UCLA Electronic Theses and Dissertations (2012)

    Gammaherpesviruses are clinically important human pathogens associated with multiple types of tumors. The life cycle of gammaherpesviruses consists of two distinct phases, latency and lytic replication, both of which are important for the viral-associated pathogenesis. Murine gammaherpesvirus 68 (MHV-68) has been used as a model to study virus-host interactions of human gammaherpesviruses because of its genomic and biological similarities.

    During the course of MHV-68 lytic infection, the virus is highly dependent on cellular machinery to facilitate its replication. Host cells, on the other hand, develop mechanisms to sense and restrict virus replication. Here, we present an integrative systems approach to elucidate the interactions between MHV-68 and its host. Our previous yeast-two-hybrid analysis and genome-wide expression profiling implicated hundreds of cellular factors mediating virus-host interactions. Among the cellular factors identified, those involved in kinase- and transcription factor- regulated signaling are the most highly enriched. Therefore, high-throughput screens of cellular kinome and transcription factors cDNA and siRNA libraries were carried out, which uncovered 125 MHV-68 dependency factors and 213 restriction factors. We found that many cellular factors affect MHV-68 replication by regulating RTA transcription. Characterization of this subset of genes showed they also play roles in KSHV latency maintenance and reactivation. Furthermore, cellular factors regulating later steps of viral replication, such as viral late gene expression and egress, were also identified and validated. Finally we compared the viral restriction factors to the results of a kinome siRNA screen designed to identify cellular regulators of innate immune response to cytosolic DNA. Remarkably, 23 genes were found among the top 10% of the hits of both screens. The MHV-68 restriction factor RIOK3 was confirmed to play a role in IRF3 activation and type I interferon induction mediated by both cytosolic DNA and RNA. RIOK3 is required for cellular antiviral response to both DNA virus (MHV-68) and RNA virus (Influenza A), suggesting a central role in innate immunity. Further analysis revealed that RIOK3 complexes with TBK1 and IRF3, bridging the activity between the two. Collectively, this multilayered approach unfolded a comprehensive map of gammaherpesvirus-host interactions which will provide basis for developing new anti-viral therapies.

      Cover page: Systematic Identification of Cellular Regulators of Gammaherpesvirus Lytic Replication
      • Article
      • Peer Reviewed
      LBL Publications (2016)
      The method of synchrotron X-ray protein footprinting (XF-MS) is used to determine protein conformational changes, folding, protein-protein and protein-ligand interactions, providing information which is often difficult to obtain using X-ray crystallography and other common structural biology methods [1–3]. The technique uses comparative in situ labeling of solvent-accessible side chains by highly reactive hydroxyl radicals (•OH) in buffered aqueous solution under different assay conditions. In regions where a protein is folded or binds a partner, these •OH susceptible sites are inaccessible to solvent, and therefore protected from labeling. The •OH are generated by the ionization of water using high-flux-density X-rays. High-flux density is a key factor for XF-MS labeling because obtaining an adequate steady-state concentration of hydroxyl radical within a short irradiation time is necessary to minimize radiation-induced secondary damage and also to overcome various scavenging reactions that reduce the yield of labeled side chains.
        Cover page: Advancements and Application of Microsecond Synchrotron X-ray Footprinting at the Advanced Light Source
        • Article
        • Peer Reviewed
        Proceedings of the Annual Meeting of the Cognitive Science Society, Volume 41 (2019)
        Neural mechanisms behind noun and verb processing are ubiquitously separate, yet it remains controversial which factor, syntax or semantics, is behind such separation. We conducted an ERP study using Chinese sentences with a specific construction, noun phrase + mei (“not/no”) + noun/verb/noun-verb-ambiguous-word, and excluding other grammatical or syntactic factors that could hint at the target words’ part-of-speech. Results showed significantly distinct P200, N400 and P600 between noun and verb processing in native speakers, indicating that semantic factors are essential for the differentiated neural mechanisms behind noun and verb processing. Similar results were also found between noun-verb-ambiguous-word and noun processing, but not between noun-verb-ambiguous-word and verb processing, suggesting that lacking clues on part-of-speech makes the dynamic properties of the ambiguous words more salient than the static ones, thus causing interpretation of such words more likely as verbs. This further elaborates the crucial role of semantic factors in noun and verb processing.
          Cover page: No Morphological Markers, No Problem: ERP Study Reveals Semantic Factors Differentiating Neural Mechanisms of Noun and Verb Processing
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2017)
          Lithium sulfide (Li2S) is a promising cathode material for lithium-sulfur (Li/S) cells due to its high theoretical specific capacity (1166 mAh g-1) and ability to pair with nonmetallic lithium anodes to avoid potential safety issues. However, when used as the cathode, a high charging voltage (∼4 V versus Li+/Li) is always necessary to activate Li2S in the first charge process, and the voltage profile becomes similar to that of a common sulfur electrode in the following charge processes. In this report, we have prepared an electrode of nanosphere Li2S particles and investigated its charging mechanism of the initial two charge processes by in situ and operando X-ray absorption spectroscopy. The results indicate that Li2S is directly converted to elemental sulfur through a two-phase transformation in the first charge process, while it is oxidized first to polysulfides and then to sulfur in the second charge process. The origin of the different charging mechanisms and corresponding charge-voltage profiles of the first and second charge processes is found to be related to the remaining polysulfides at the end of the first discharge process: they can not only facilitate the charge-transfer process at the Li2S/electrolyte interface but also chemically react with Li2S and act as the polysulfide facilitator for the electrochemical oxidation of Li2S in the following charge processes. Our present study provides a new fundamental understanding of the charging mechanism of the Li2S electrode, which should be of help for the further development of high-performance Li/S cells.
            Cover page: Revealing the Electrochemical Charging Mechanism of Nanosized Li2S by in Situ and Operando X‑ray Absorption Spectroscopy
            • Article
            • Peer Reviewed
            LBL Publications (2019)
            The performance of proton-conducting ionomer membranes used in electrochemical applications such as fuel cells is complicated by an intricate interplay between chemistry and morphology that is challenging to characterize and control. Here, we report on a class of perfluoro ionene chain extended (PFICE) ionomers that contain either one (PFICE-2) or two (PFICE-3) bis(sulfonyl)imide groups on the side-chain in addition to a terminal sulfonic acid group. PFICE ionomers are promising materials, exhibiting greater water uptake and conductivity over a range of relative humidity values compared to prototypical perfluorinated sulfonic acid (PFSA) ionomers. Advanced in situ synchrotron characterization combined with simulations reveals insights into the connections between molecular structure and morphology that dictate performance. Energy-tunable X-rays with sensitivity to sulfur can decipher the unique bonding environment of different protogenic groups on the polymer side-chain. Guided by simulations, X-ray absorption spectroscopy can be sensitive to hydration level and configuration that dictates proton dissociation. In situ resonant X-ray scattering reveals that PFICE ionomers have a phase-separated morphology with enhanced short-range order that persists in both dry and hydrated state, allowing for improved transport pathways across hydration levels. Furthermore, side-chain chemistry and length can be used as a molecular design parameter to predict phase-separated domain spacing. The enhanced conductivity of PFICE ionomers is attributed to a unique side-chain chemistry and structure promoting hydrogen bonding configurations that facilitate proton dissociation at low water content in combination with a well-ordered phase-separated morphology that forms transport pathways. Overall, these results provide guidelines to design new ionomers with improved transport properties and demonstrate the value of in situ characterization methods such as resonant X-ray scattering and spectroscopy for unraveling the structural features in chemically-heterogeneous materials used in electrochemical systems.
              Cover page: Chemical and Morphological Origins of Improved Transport in Perfluoro Ionene Chain Extended Ionomers
              • Article
              • Peer Reviewed
              LBL Publications (2016)
              We describe experiments with a 45-cm long x-ray deformable mirror (XDM) that have been conducted in End Station 2, Beamline 5.3.1 at the Advanced Light Source. A detailed description of the hardware implementation is provided. We explain our one-dimensional Fresnel propagation code that correctly handles grazing incidence and includes a model of the XDM. This code is used to simulate and verify experimental results. Initial long trace profiler metrology of the XDM at 7.5 keV is presented. The ability to measure a large (150-nm amplitude) height change on the XDM is demonstrated. The results agree well with the simulated experiment at an error level of 1 μrad RMS. Direct imaging of the x-ray beam also shows the expected change in intensity profile at the detector.
                Cover page: X-ray metrology and performance of a 45-cm long x-ray deformable mirror
                • Article
                • Peer Reviewed
                LBL Publications (2017)
                Nano-roughness is one of the major factors degrading the emittance of electron beams that can be generated by high efficiency photocathodes, such as the thermally reacted alkali antimonide thin films. In this paper, we demonstrate a co-deposition based method for producing alkali antimonide cathodes that produce near atomic smoothness with high reproducibility. We calculate the effect of the surface roughness on the emittance and show that such smooth cathode surfaces are essential for operation of alkali antimonide cathodes in high field, low emittance radio frequency electron guns and to obtain ultracold electrons for ultrafast electron diffraction applications.
                  Cover page: Near atomically smooth alkali antimonide photocathode thin films
                  • Article
                  • Peer Reviewed
                  UC Santa Cruz Previously Published Works (2017)
                  Polysulfide shuttling has been the primary cause of failure in lithium-sulfur (Li-S) battery cycling. Here, we demonstrate an nucleophilic substitution reaction between polysulfides and binder functional groups can unexpectedly immobilizes the polysulfides. The substitution reaction is verified by UV–visible spectra and X-ray photoelectron spectra. The immobilization of polysulfide is in situ monitored by synchrotron based sulfur K-edge X-ray absorption spectra. The resulting electrodes exhibit initial capacity up to 20.4 mAh/cm2, corresponding to 1199.1 mAh/g based on a micron-sulfur mass loading of 17.0 mg/cm2. The micron size sulfur transformed into nano layer coating on the cathode binder during cycling. Directly usage of nano-size sulfur promotes higher capacity of 33.7 mAh/cm2, which is the highest areal capacity reported in Li-S battery. This enhance performance is due to the reduced shuttle effect by covalently binding of the polysulfide with the polymer binder.
                    Cover page: Nucleophilic substitution between polysulfides and binders unexpectedly stabilizing lithium sulfur battery
                    • Article
                    • Peer Reviewed
                    LBL Publications (2015)
                    Measurements of the intrinsic emittance and transverse momentum distributions obtained from a metal (antimony thin film) photocathode near and below the photoemission threshold are presented. Measurements show that the intrinsic emittance is limited by the lattice temperature of the cathode as the incident photon energy approaches the photoemission threshold. A theoretical model to calculate the transverse momentum distributions near this photoemission threshold is presented. An excellent match between the experimental measurements and the theoretical calculations is demonstrated. These measurements are relevant to low emittance electron sources for Free Electron Lasers and Ultrafast Electron Diffraction experiments.
                      Cover page: Thermal limit to the intrinsic emittance from metal photocathodes
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