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Open Access Publications from the University of California

Scholarly Works (21 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2013)

Ultrafast femtosecond (10-15 s) dynamics of atomic xenon, vinyl bromide and carbon disulfide molecules are studied using a newly developed method of extreme ultraviolet (XUV) transient absorption spectroscopy. This research work is devoted to a deeper understanding of the fundamental electronic and nuclear dynamics using XUV light pulses from a high-order harmonic generation source. The produced XUV light pulses are utilized to selectively probe the chemical reaction coordinate with femtosecond temporal resolution. The experimental apparatus for transient absorption pump-probe spectroscopy is described in detail. The research described in this thesis contains four different gaseous atomic and molecular systems. The first system in the study is motivated by a goal to gain a better understanding of the core-excited state couplings of atomic xenon near zero delay between an intense NIR pump pulse (780 nm) and an XUV probe pulse. Secondly, the ionization and dissociation dynamics of molecular vinyl bromide (C2H3Br) under the influence of strong-field ionization are investigated. Finally, an ongoing research project of CS2 and thiophene molecules is presented for future studies of spin-orbit wavepacket and ring-opening dynamics, respectively.

The NIR induced core-excited state coupling of atomic xenon is studied using femtosecond XUV transient absorption spectroscopy with photon energies between 50 eV to 70 eV. Coupling of the core-excited states 4d-1(2D5/2)6p(2P3/2) (65.1 eV) and 4d-1(2D3/2)6p(2P1/2) (67.0 eV) to neighboring states by the NIR field results in a threefold enhancement of XUV transmission. The induced transmission at 65.1 eV (67.0 eV) changes from 3.2 ± 0.4% (5.9 ± 0.5%) without the coupling laser to 9 ± 2% (22 ± 5%) at the maximum of the NIR field. A NIR field induced broad XUV absorption feature ranging from 60 eV to 65 eV is explained by the splitting of the field free absorption lines into multiplets when the Rabi frequencies of the coupling transitions higher than the NIR frequency. This assignment is supported by a numerical integration of the von Neumann equation for a few level quantum system.

The dissociative ionization dynamics of vinyl bromide, C2H3Br, initiated by a strong laser field ionization are investigated. XUV light pulses with photon energy between 50 eV and 72 eV are utilized to detect the subsequent dynamics. Several dynamic features are observed including the neutral C2H3Br depletion, the formation of C2H3Br+ ions (X and A states), the production of C2H3Br++ dications, and the emergence of neutral Br (2P3/2) atoms from dissociative ionization. Free Br (2P3/2) atoms appear on a timescale of 330±150 fs. The singly charged ionic A state displays a time-dependent XUV absorption energy shift of ~0.4 eV during the first 300 fs after strong-filed ionization. The signal intensity from Br atoms correlates with the signal intensity from singly charged parent ions in the A state as a function of NIR laser peak intensity. The experimental observations suggest that vibrationally excited C2H3Br+ (A) ions possibly undergo ultrafast intramolecular vibrational energy redistribution concurrent with the C-Br bond dissociation within a time scale of 330±150 fs. The C2H3Br+ (X) and C2H3Br++ ions are relatively stable as a consequence of deeper potential wells and a high dissociation barrier, respectively.

Two ongoing experiments of sulfur-containing molecules are presented that are aimed at future studies of a molecular spin-orbit wavepacket in CS2+ ions and ultrafast ring-opening dynamics of thiophene. Strong-field ionization can coherently populate two spin-orbit states in CS2+ ions. The spin-orbit splitting originates from the atomic sulfur (~60 meV). The small splitting offers the possibility to probe a coherent beating on a time scale of 69 fs, well beyond our temporal resolution of 25 fs. For thiophene, an ultrafast ring-opening process initiated by one-photon excitation at 193 nm is studied through multiphoton ionization at 780 nm. The parent ion population exhibits a fast decay on a time scale of 200±30 fs. This offers a reference for the future XUV transient absorption experiments using one-photon excitation at 193 nm and sulfur (2p) L-edge detection at 165 eV.

    Cover page: Ultrafast chemical dynamics of atoms and molecules studied by femtosecond time-resolved extreme ultraviolet transient absorption spectroscopy
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2014)
    Strong-field induced ionization and dissociation dynamics of vinyl bromide, CH2=CHBr, are probed using femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy. Strong-field ionization is initiated with an intense femtosecond, near infrared (NIR, 775 nm) laser field. Femtosecond XUV pulses covering the photon energy range of 50-72 eV probe the subsequent dynamics by measuring the time-dependent spectroscopic features associated with transitions of the Br (3d) inner-shell electrons to vacancies in molecular and atomic valence orbitals. Spectral signatures are observed for the depletion of neutral C2H3Br, the formation of C2H3Br(+) ions in their ground (X̃) and first excited (Ã) states, the production of C2H3Br(++) ions, and the appearance of neutral Br ((2)P3/2) atoms by dissociative ionization. The formation of free Br ((2)P3/2) atoms occurs on a timescale of 330 ± 150 fs. The ionic à state exhibits a time-dependent XUV absorption energy shift of ∼0.4 eV within the time window of the atomic Br formation. The yield of Br atoms correlates with the yield of parent ions in the à state as a function of NIR peak intensity. The observations suggest that a fraction of vibrationally excited C2H3Br(+) (Ã) ions undergoes intramolecular vibrational energy redistribution followed by the C-Br bond dissociation. The C2H3Br(+) (X̃) products and the majority of the C2H3Br(++) ions are relatively stable due to a deeper potential well and a high dissociation barrier, respectively. The results offer powerful new insights about orbital-specific electronic processes in high field ionization, coupled vibrational relaxation and dissociation dynamics, and the correlation of valence hole-state location and dissociation in polyatomic molecules, all probed simultaneously by ultrafast table-top XUV spectroscopy.
      Cover page: Ionization and dissociation dynamics of vinyl bromide probed by femtosecond extreme ultraviolet transient absorption spectroscopy.
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2016)
      Oligodendroglioma represents a distinctive neoplasm in adults but similar neoplasms occur rarely in children. We studied 20 cases of pediatric oligodendroglioma by SNP array (median age 9 years, range 1-19; 15 grade II and 5 grade III). Cytogenetic abnormalities were present in 8 (53%) grade II and all five anaplastic oligodendrogliomas. Most changes were in the form of deletion and copy neutral loss of heterozygosity (LOH). The most common abnormality was 1p deletion (n = 5). Whole arm 1p19q co-deletion was present in three cases from adolescent patients and 9p loss in 3, including one low-grade oligodendroglioma with CDKN2A homozygous deletion. Common losses were largely limited to the anaplastic subset (n = 5) and included 3q29 (n = 3), 11p (n = 3), 17q (n = 3), 4q (n = 2), 6p (n = 2), 13q (n = 2), 14q (n = 2), 17p (n = 2) and whole Ch 18 loss (n = 2). Gains were non-recurrent except for whole Ch 7 (n = 2) and gain on 12q (n = 2) including the MDM2 locus. Possible germ line LOH (or uniparental disomy) was present in seven cases (35%), with one focal abnormality (22q13.1-13.2) in two. BRAF-KIAA1549 fusions and BRAF p.V600E mutations were absent (n = 13 and 8). In summary, cytogenetic alterations in pediatric oligodendrogliomas are characterized mostly by genomic losses, particularly in anaplastic tumors.
        Cover page: Molecular analysis of pediatric oligodendrogliomas
        • Article
        • Peer Reviewed
        LBL Publications (2022)
        Magnetic skyrmions are topologically wound nanoscale textures of spins whose ambient stability and electrical manipulation in multilayer films have led to an explosion of research activities. While past efforts focused predominantly on isolated skyrmions, recently ensembles of chiral spin textures, consisting of skyrmions and magnetic stripes, are shown to possess rich interactions with potential for device applications. However, several fundamental aspects of chiral spin texture phenomenology remain to be elucidated, including their domain wall (DW) structure, thermodynamic stability, and morphological transitions. Here the evolution of these textural characteristics are unveiled on a tunable multilayer platform-wherein chiral interactions governing spin texture energetics can be widely varied-using a combination of full-field electron and soft X-ray microscopies with numerical simulations. With increasing chiral interactions, the emergence of Néel helicity, followed by a marked reduction in domain compressibility, and finally a transformation in the skyrmion formation mechanism are demonstrated. Together with an analytical model, these experiments establish a comprehensive microscopic framework for investigating and tailoring chiral spin texture character in multilayer films.
          Cover page: Unveiling the Emergent Traits of Chiral Spin Textures in Magnetic Multilayers
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          • Peer Reviewed
          UC San Francisco Previously Published Works (2015)

          Background

          Preoperative tumor aggressiveness biomarkers may help surgeons decide the extent of an operation. However, whether serum angiogenetic factors can be used to predict the prognosis of patients with differentiated thyroid cancer is still unclear.

          Methods

          Seventy-six DTC patients were prospectively recruited. Preoperative serum samples were collected and measured for Tie-2, Ang-1, Ang-2, VEGF-A, and VEGF-D levels. The potential correlations between their serum levels and clinicopathologic features as well as their prognoses were analyzed.

          Results

          Older age (>45 years old) and higher VEGF-A serum levels were independent predictors of extrathyroidal extension. The VEGF-D serum level was an independent factor for lymph node metastases and VEGF-A was an independent factor for distant metastases. None of these serum angiogenetic factors were significantly different between patients who were disease free and those with recurrences. The presence of lymph node metastases was the only independent factor for recurrence over the 2-year follow-up.

          Conclusion

          Preoperative serum VEGF-A and VEGF-D levels were significantly elevated in DTC patients with distant and lymph node metastases. These findings, when combined with other clinicopathological factors, may help in surgical decisions.
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2018)
            The SORBS1 gene plays an important role in insulin signaling. We aimed to examine whether common single-nucleotide polymorphisms (SNPs) of SORBS1 are associated with prevalence and incidence of diabetes, age at onset of diabetes, and the related traits of glucose homeostasis. A total of 1135 siblings from 492 ethnic Chinese families were recruited at baseline, and 630 were followed up for 5.19 ± 0.96 years. Nine SNPs including rs7081076, rs2281939, rs3818540, rs2274490, rs61739184, rs726176, rs2296966, rs17849148, and rs3193970 were genotyped and examined. To deal with correlated data of subjects within the same families, the generalized estimating equations approach was applied throughout all association analyses. The GG genotype of rs2281939 was associated with a higher risk of diabetes at baseline, an earlier onset of diabetes, and higher steady-state plasma glucose levels in the modified insulin suppression test. The minor allele T of rs2296966 was associated with higher prevalence and incidence of diabetes, an earlier onset of diabetes, and higher 2-h glucose during oral glucose tolerance test. These two SNPs revealed independent associations with age of diabetes onset as well as risk of diabetes at baseline. These findings supported that SORBS1 gene participates in the pathogenesis of diabetes.
              Cover page: Genetic variation of SORBS1 gene is associated with glucose homeostasis and age at onset of diabetes: A SAPPHIRe Cohort Study
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              • Peer Reviewed
              UC Irvine Previously Published Works (2014)
              C-arm cone-beam computed tomography (CBCT) is a new imaging technology integrated in modern angiographic systems. Due to its ability to obtain cross-sectional imaging and the possibility to use dedicated planning and navigation software, it provides an informed platform for interventional oncology procedures. In this paper, we highlight the technical aspects and clinical applications of CBCT imaging and navigation in the most common loco-regional oncological treatments.
                Cover page: C-arm cone-beam computed tomography in interventional oncology: technical aspects and clinical applications
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2020)
                We employ few-femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy to reveal simultaneously the intra- and interband carrier relaxation and the light-induced structural dynamics in nanoscale thin films of layered 2H-MoTe2 semiconductor. By interrogating the valence electronic structure via localized Te 4d (39-46 eV) and Mo 4p (35-38 eV) core levels, the relaxation of the photoexcited hole distribution is directly observed in real time. We obtain hole thermalization and cooling times of 15 ± 5 fs and 380 ± 90 fs, respectively, and an electron-hole recombination time of 1.5 ± 0.1 ps. Furthermore, excitations of coherent out-of-plane A1g (5.1 THz) and in-plane E1g (3.7 THz) lattice vibrations are visualized through oscillations in the XUV absorption spectra. By comparison to Bethe-Salpeter equation simulations, the spectral changes are mapped to real-space excited-state displacements of the lattice along the dominant A1g coordinate. By directly and simultaneously probing the excited carrier distribution dynamics and accompanying femtosecond lattice displacement in 2H-MoTe2 within a single experiment, our work provides a benchmark for understanding the interplay between electronic and structural dynamics in photoexcited nanomaterials.
                  Cover page: Simultaneous Observation of Carrier-Specific Redistribution and Coherent Lattice Dynamics in 2H-MoTe2 with Femtosecond Core-Level Spectroscopy
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2021)
                  Commercialization of the lithium-sulfur battery is hampered by bottlenecks like low sulfur loading, high cathode porosity, uncontrollable Li2 Sx deposition and sluggish kinetics of Li2 S activation. Herein, we developed a densely stacked redox-active hexaazatrinaphthylene (HATN) polymer with a surface area of 302 m2  g-1 and a very high bulk density of ca. 1.60 g cm-3 . Uniquely, HATN polymer has a similar redox potential window to S, which facilitates the binding of Li2 Sx and its transformation chemistry within the bulky polymer host, leading to fast Li2 S/S kinetics. The compact polymer/S electrode presents a high sulfur loading of ca. 15 mgs  cm-2 (200-μm thickness) with a low cathode porosity of 41 %. It delivers a high areal capacity of ca. 14 mAh cm-2 and good cycling stability (200 cycles) at electrolyte-sulfur (E/S) ratio of 5 μL mgs -1 . The assembled pouch cell delivers a cell-level high energy density of 303 Wh kg-1 and 392 Wh L-1 .
                    Cover page: Dense‐Stacking Porous Conjugated Polymer as Reactive‐Type Host for High‐Performance Lithium Sulfur Batteries
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2021)

                    Background

                    Clonal immunoglobulin and T-cell receptor rearrangements serve as tumor-specific markers that have become mainstays of the diagnosis and monitoring of lymphoid malignancy. Next-generation sequencing (NGS) techniques targeting these loci have been successfully applied to lymphoblastic leukemia and multiple myeloma for minimal residual disease detection. However, adoption of NGS for primary diagnosis remains limited.

                    Methods

                    We addressed the bioinformatics challenges associated with immune cell sequencing and clone detection by designing a novel web tool, CloneRetriever (CR), which uses machine-learning principles to generate clone classification schemes that are customizable, and can be applied to large datasets. CR has 2 applications-a "validation" mode to derive a clonality classifier, and a "live" mode to screen for clones by applying a validated and/or customized classifier. In this study, CR-generated multiple classifiers using 2 datasets comprising 106 annotated patient samples. A custom classifier was then applied to 36 unannotated samples.

                    Results

                    The optimal classifier for clonality required clonal dominance ≥4.5× above background, read representation ≥8% of all reads, and technical replicate agreement. Depending on the dataset and analysis step, the optimal algorithm yielded sensitivities of 81%-90%, specificities of 97%-100%, areas under the curve of 91%-94%, positive predictive values of 92-100%, and negative predictive values of 88%-98%. Customization of the algorithms yielded 95%-100% concordance with gold-standard clonality determination, including rescue of indeterminate samples. Application to a set of unknowns showed concordance rates of 83%-96%.

                    Conclusions

                    CR is an out-of-the-box ready and user-friendly software designed to identify clonal rearrangements in large NGS datasets for the diagnosis of lymphoid malignancies.
                      Cover page: CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies
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