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Open Access Publications from the University of California

Scholarly Works (8 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2016)

Graphene nanoribbons (GNRs) have recently attracted great interest because of their novel electronic and magnetic properties, as well as their significant potential for device applications. Although several top-down techniques exist for fabricating GNRs, only bottom-up synthesis of GNRs from molecular precursors yields nanoribbons with atomic-scale structural control. Furthermore, precise incorporation of dopant species into GNRs, which is possible with bottom-up synthesis, is a potentially powerful way to control the electronic structure of GNRs. However, it is not well understood how these dopants affect the electronic structure of GNRs. Are these effects dependent on the dopant site? Can the band gap be tuned by doping? This dissertation helps to answer these questions through studying the electronic structure of bottom-up grown GNRs with controlled atomic dopants. The effects of edge and interior doping with different atomic species such as sulfur, boron and ketone were investigated and showed significant site dependence. Topographic and local electronic structure characterization was performed via scanning tunneling microscopy & spectroscopy (STM & STS) and compared to first-principle calculations. The chemical structure of GNRs and GNR heterojunctions was characterized by CO-tip-functionalized non-contact atomic force microscopy (nc-AFM) as well as by a newly developed technique of bond-resolved STM (BRSTM).

In an effort to develop a new method for directly synthesizing GNRs on an insulating substrate, we also studied light-induced photo-isomerization of azobenzene molecules adsorbed on an insulating surface of CVD-grown monolayer boron nitride (BN) on Cu(111). This study provides important insights into molecular behavior on an insulating surface, how to couple light to an STM system, and how to utilize local field enhancement effects due to surface plasmon resonance.

    Cover page: Engineering the electronic structure of atomically-precise graphene nanoribbons
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2019)
    Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes that are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. The corresponding endosymbionts, Frankia and the rhizobia, however, are distantly related groups of bacteria, leading to questions about their symbiotic mechanisms and evolutionary history. To date, a stable system of electrotransformation has been lacking in Frankia despite numerous attempts by research groups worldwide. We have identified type IV methyl-directed restriction systems, highly-expressed in a range of actinobacteria, as a likely barrier to Frankia transformation. Here we report the successful electrotransformation of the model strain F. alni ACN14a with an unmethylated, broad host-range replicating plasmid, expressing chloramphenicol-resistance for selection and GFP as a marker of gene expression. This system circumvented the type IV restriction barrier and allowed the stable maintenance of the plasmid. During nitrogen limitation, Frankia differentiates into two cell types: the vegetative hyphae and nitrogen-fixing vesicles. When the expression of egfp under the control of the nif gene cluster promoter was localized using fluorescence imaging, the expression of nitrogen fixation in nitrogen-limited culture was localized in Frankia vesicles but not in hyphae. The ability to separate gene expression patterns between Frankia hyphae and vesicles will enable deeper comparisons of molecular signaling and metabolic exchange between Frankia-actinorhizal and rhizobia-legume symbioses to be made, and may broaden potential applications in agriculture. Further downstream applications are possible, including gene knock-outs and complementation, to open up a range of experiments in Frankia and its symbioses. Additionally, in the transcriptome of F. alni ACN14a, type IV restriction enzymes were highly expressed in nitrogen-replete culture but their expression strongly decreased during symbiosis. The down-regulation of type IV restriction enzymes in symbiosis suggests that horizontal gene transfer may occur more frequently inside the nodule, with possible new implications for the evolution of Frankia.
      Cover page: A Stable Genetic Transformation System and Implications of the Type IV Restriction System in the Nitrogen-Fixing Plant Endosymbiont Frankia alni ACN14a
      • Article
      • Peer Reviewed
      Dermatology Online Journal, Volume 23, Issue 11 (2017)

      Background: Lymphomatoid drug reactions can mimic endogenous T and B cell lymphoproliferative diseases.

      Objectives: We present a novel form of cutaneous drug reaction with features of pityriasis lichenoides (PL), a recognized form of T cell dyscrasia. Methods: Ten cases were studied where a cutaneous eruption exhibiting semblance to PL within a few weeks to months after starting a particular drug. Results: The patient cohort comprised 7 females and 3 males with the mean age of 60 years. Widely distributederythematous cutaneous lesions were present in 6 cases whereas a more localized distribution was seen in three cases. The most frequently implicated drugsassociated with the eruption were antidepressants and statins. Histologic examination showed a morphologic picture identical to PL including marked epitheliotropism of mildly atypical lymphocytes, psoriasiform epidermal hyperplasia, dyskeratosis, hemorrhage, and a thick parakeratotic scale. Therewas a significant reduction in the expression of CD7 and CD62L amid the T cells. Regression of the eruption occurred in all cases excluding one. Conclusion: Thefindings conform the categorization of this process as a form of T-cell dyscrasia albeit one that is reversible, dependent on the drug withdrawal. The limitationof our study includes the retrospective design of the study.

        Cover page: Pityriasis lichenoides-like drug reaction: A clinical histopathologic study of 10 casesCreative Commons 'BY-NC-ND' version 4.0 license
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2015)
        A fundamental requirement for the development of advanced electronic device architectures based on graphene nanoribbon (GNR) technology is the ability to modulate the band structure and charge carrier concentration by substituting specific carbon atoms in the hexagonal graphene lattice with p- or n-type dopant heteroatoms. Here we report the atomically precise introduction of group III dopant atoms into bottom-up fabricated semiconducting armchair GNRs (AGNRs). Trigonal-planar B atoms along the backbone of the GNR share an empty p-orbital with the extended π-band for dopant functionality. Scanning tunneling microscopy (STM) topography reveals a characteristic modulation of the local density of states along the backbone of the GNR that is superimposable with the expected position and concentration of dopant B atoms. First-principles calculations support the experimental findings and provide additional insight into the band structure of B-doped 7-AGNRs.
          Cover page: Site-Specific Substitutional Boron Doping of Semiconducting Armchair Graphene Nanoribbons
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2018)
          Bottom-up fabrication techniques enable atomically precise integration of dopant atoms into the structure of graphene nanoribbons (GNRs). Such dopants exhibit perfect alignment within GNRs and behave differently from bulk semiconductor dopants. The effect of dopant concentration on the electronic structure of GNRs, however, remains unclear despite its importance in future electronics applications. Here we use scanning tunneling microscopy and first-principles calculations to investigate the electronic structure of bottom-up synthesized N = 7 armchair GNRs featuring varying concentrations of boron dopants. First-principles calculations of freestanding GNRs predict that the inclusion of boron atoms into a GNR backbone should induce two sharp dopant states whose energy splitting varies with dopant concentration. Scanning tunneling spectroscopy experiments, however, reveal two broad dopant states with an energy splitting greater than expected. This anomalous behavior results from an unusual hybridization between the dopant states and the Au(111) surface, with the dopant-surface interaction strength dictated by the dopant orbital symmetry.
            Cover page: Concentration Dependence of Dopant Electronic Structure in Bottom-up Graphene Nanoribbons
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2016)
            Substitutional doping of graphene nanoribbons (GNRs) with heteroatoms is a principal strategy to fine-tune the electronic structure of GNRs for future device applications. Here, we report the fabrication and nanoscale characterization of atomically precise N = 13 armchair GNRs featuring regioregular edge-doping with sulfur atoms (S-13-AGNRs) on a Au(111) surface. Scanning tunneling spectroscopy and first-principle calculations reveal modification of the electronic structure of S-13-AGNRs when compared to undoped N = 13 AGNRs.
              Cover page: Bottom-Up Synthesis of N = 13 Sulfur-Doped Graphene Nanoribbons
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2015)
              We report a scanning tunneling microscopy and noncontact atomic force microscopy study of close-packed 2D islands of tetrafluorotetracyanoquinodimethane (F4TCNQ) molecules at the surface of a graphene layer supported by boron nitride. While F4TCNQ molecules are known to form cohesive 3D solids, the intermolecular interactions that are attractive for F4TCNQ in 3D are repulsive in 2D. Our experimental observation of cohesive molecular behavior for F4TCNQ on graphene is thus unexpected. This self-assembly behavior can be explained by a novel solid formation mechanism that occurs when charged molecules are placed in a poorly screened environment. As negatively charged molecules coalesce, the local work function increases, causing electrons to flow into the coalescing molecular island and increase its cohesive binding energy.
                Cover page: Molecular Self-Assembly in a Poorly Screened Environment: F4TCNQ on Graphene/BN
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2017)
                The rational bottom-up synthesis of atomically defined graphene nanoribbon (GNR) heterojunctions represents an enabling technology for the design of nanoscale electronic devices. Synthetic strategies used thus far have relied on the random copolymerization of two electronically distinct molecular precursors to yield GNR heterojunctions. Here we report the fabrication and electronic characterization of atomically precise GNR heterojunctions prepared through late-stage functionalization of chevron GNRs obtained from a single precursor. Post-growth excitation of fully cyclized GNRs induces cleavage of sacrificial carbonyl groups, resulting in atomically well-defined heterojunctions within a single GNR. The GNR heterojunction structure was characterized using bond-resolved scanning tunnelling microscopy, which enables chemical bond imaging at T = 4.5 K. Scanning tunnelling spectroscopy reveals that band alignment across the heterojunction interface yields a type II heterojunction, in agreement with first-principles calculations. GNR heterojunction band realignment proceeds over a distance less than 1 nm, leading to extremely large effective fields.
                  Cover page: Atomically precise graphene nanoribbon heterojunctions from a single molecular precursor
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