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Open Access Publications from the University of California

Scholarly Works (18 results)

  • Thesis
  • Peer Reviewed
UC San Francisco Electronic Theses and Dissertations (1994)

    Cover page: Mutational analysis of antibody-antigen interactions
    • Thesis
    • Peer Reviewed
    UC Berkeley Electronic Theses and Dissertations (2021)

    The advance in nanofabrication and characterization methods enables researchers to study nanomaterials at small scales. Rich physics can emerge in nanomaterials due to their low-dimensional nature, such as boundary effect, quantum confinement effect etc. Also, nanomaterials usually have the most single-crystalline pristine qualities. This opens opportunities to study the intrinsic properties of many materials, which is hard to probe in bulk counterparts as the gain boundaries and defects in bulk samples can degrade their qualities. Combining the nanofabricated suspended microdevice and nanomaterials such as nanowires or nanoribbon, we can probe the intrinsic properties of materials which have interesting physics. Nanomaterials also have their unique structure and thermal physics properties which are very different from those of their bulk counterparts. In this dissertation, the author presents his work, in his pursuits of PhD degree at UC Berkeley, focused on exploring the thermal and transport physics of nanowire via transport measurement realized by using nanofabricated suspended microdevices.

    Chapter 2 and 3 are focused on vanadium dioxide (VO2), a strongly correlated materials with metal-to-insulator transition (MIT) occurring at temperature of 341 K. Although the first observation of the MIT of VO2 was more than 60 years ago, the transition mechanism and the correlation physics of VO2 is still under debate among theorists. Thanks to the advances in nanofabrication, measuring and modulating the MIT of single-crystalline VO2 nanowires are made possible and accessible to experimentalist. This provides us an efficient tool to study the intrinsic properties of VO2 and could help unveil its correlated nature. In chapter 2, a discovery of the recovery of Wiedemann-Franz (W-F) law in metallic VO2 is reported. This recovery is realized by introducing point defects using energetic ion irradiation. The experimental measurements and theoretical explanations are demonstrated to explain this full restoration of otherwise violated W-F law in strongly correlated system. In chapter 3, a deeply supercooled intrinsic VO2 metal is first realized by technique called irradiation shielding supported on suspended microdevices. Nucleation seeds created by ion surface milling are then introduced on nanowires’ surface and the critical nucleation sizes of supercooled metallic VO2 are measured for the first time. A model derived from classical nucleation theory is also presented.

    In chapter 4, experimental observations of abnormal thermal transport behaviors of twisted layered GeS nanowires with a screw dislocation core in the center is reported. The thermal conductivity of twisted GeS nanowires is measured by using suspended microdevices, which increases by decreasing diameters of nanowires. This trend is against to the prediction from boundary scattering, which is commonly observed in nanowires such as silicon, silver etc. In contrast, the thermal conductivities of non-twisted layered GeS nanowires and GeS nanoribbon are also measured. Their thermal transport behaves the same as common nanowires, that is thinner wires have lower thermal conductivity. The abnormal increasement of thermal conductivity at smaller diameters of twisted nanowires must origin from either their dislocation cores or the twisting topology between layers. New thermal physics may arise in this type of materials as classical explanation of the measured results fails to give full explanations.

      Cover page: Exploring the Thermal Transport and Phase Nucleation Physics of Nanowires via Suspended Microdevices
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2013)
      The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was determined previously by X-ray crystallography. In an attempt to obtain atomic structural information of HBV core in a near native, non-crystalline environment, we reconstructed a 3.5Å-resolution structure of a recombinant core assembled from full-length HBc by cryo electron microscopy (cryoEM) and derived an atomic model. The structure shows that the 240 molecules of full-length HBc form a core with two layers. The outer layer, composed of the N-terminal assembly domain, is similar to the crystal structure of the truncated HBc, but has three differences. First, unlike the crystal structure, our cryoEM structure shows no disulfide bond between the Cys61 residues of the two subunits within the dimer building block, indicating such bond is not required for core formation. Second, our cryoEM structure reveals up to four more residues in the linker region (amino acids 140-149). Third, the loops in the cryoEM structures containing this linker region in subunits B and C are oriented differently (~30° and ~90°) from their counterparts in the crystal structure. The inner layer, composed of the C-terminal arginine-rich domain (ARD) and the ARD-bound RNAs, is partially-ordered and connected with the outer layer through linkers positioned around the two-fold axes. Weak densities emanate from the rims of positively charged channels through the icosahedral three-fold and local three-fold axes. We attribute these densities to the exposed portions of some ARDs, thus explaining ARD's accessibility by proteases and antibodies. Our data supports a role of ARD in mediating communication between inside and outside of the core during HBV maturation and envelopment.
        Cover page: 3.5Å cryoEM Structure of Hepatitis B Virus Core Assembled from Full-Length Core Protein
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2022)
        In a first-order phase transition, critical nucleus size governs nucleation kinetics, but the direct experimental test of the theory and determination of the critical nucleation size have been achieved only recently in the case of ice formation in supercooled water. The widely known metal-insulator phase transition (MIT) in strongly correlated VO_{2} is a first-order electronic phase transition coupled with a solid-solid structural transformation. It is unclear whether classical nucleation theory applies in such a complex case. In this Letter, we directly measure the critical nucleus size of the MIT by introducing size-controlled nanoscale nucleation seeds with focused ion irradiation at the surface of a deeply supercooled metal phase of VO_{2}. The results compare favorably with classical nucleation theory and are further explained by phase-field modeling. This Letter validates the application of classical nucleation theory as a parametrizable model to describe phase transitions of strongly correlated electron materials.
          Cover page: Probing the Critical Nucleus Size in the Metal-Insulator Phase Transition of VO2Creative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2020)
          At temperatures higher than 341 K, vanadium dioxide (VO2) is a strongly correlated metal with resistivity exceeding the Mott-Ioffe-Regel limit. Its electronic thermal conductivity is lower than that predicted by the Wiedemann-Franz (WF) law, and can be explained by nonquasiparticle transport where heat and charge currents follow separate diffusive modes. In contradiction, the Wiedemann-Franz law is a direct consequence of quasiparticle transport where charge carriers are elastically scattered. In this work, we enhance elastic electron scattering in VO2 by introducing atomic disorder with ion irradiation. A gradual and eventually full recovery of the WF law is observed at high defect densities. This observation provides an example that connects hydrodynamic quasiparticle transport to nonquasiparticle transport in metallic systems.
            Cover page: Disorder recovers the Wiedemann-Franz law in the metallic phase of VO2
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2020)
            Charge and thermal transport in a crystal is carried by free electrons and phonons (quantized lattice vibration), the two most fundamental quasiparticles. Above the Debye temperature of the crystal, phonon-mediated thermal conductivity (κ L) is typically limited by mutual scattering of phonons, which results in κ L decreasing with inverse temperature, whereas free electrons play a negligible role in κ L. Here, an unusual case in charge-density-wave tantalum disulfide (1T-TaS2) is reported, in which κ L is limited instead by phonon scattering with free electrons, resulting in a temperature-independent κ L. In this system, the conventional phonon-phonon scattering is alleviated by its uniquely structured phonon dispersions, while unusually strong electron-phonon (e-ph) coupling arises from its Fermi surface strongly nested at wavevectors in which phonons exhibit Kohn anomalies. The unusual temperature dependence of thermal conduction is found as a consequence of these effects. The finding reveals new physics of thermal conduction, offers a unique platform to probe e-ph interactions, and provides potential ways to control heat flow in materials with free charge carriers. The temperature-independent thermal conductivity may also find thermal management application as a special thermal interface material between two systems when the heat conduction between them needs to be maintained at a constant level.
              Cover page: Anomalously Suppressed Thermal Conduction by Electron‐Phonon Coupling in Charge‐Density‐Wave Tantalum Disulfide
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2022)
              Isotopically purified semiconductors potentially dissipate heat better than their natural, isotopically mixed counterparts as they have higher thermal conductivity (κ). But the benefit is low for Si at room temperature, amounting to only ∼10% higher κ for bulk ^{28}Si than for bulk natural Si (^{nat}Si). We show that in stark contrast to this bulk behavior, ^{28}Si (99.92% enriched) nanowires have up to 150% higher κ than ^{nat}Si nanowires with similar diameters and surface morphology. Using a first-principles phonon dispersion model, this giant isotope effect is attributed to a mutual enhancement of isotope scattering and surface scattering of phonons in ^{nat}Si nanowires, correlated via transmission of phonons to the native amorphous SiO_{2} shell. The Letter discovers the strongest isotope effect of κ at room temperature among all materials reported to date and inspires potential applications of isotopically enriched semiconductors in microelectronics.
                Cover page: Giant Isotope Effect of Thermal Conductivity in Silicon NanowiresCreative Commons 'BY-NC' version 4.0 license
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2013)
                Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like ('Johnson') for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering. DOI: http://dx.doi.org/10.7554/eLife.01299.001.
                  Cover page: A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 Å resolution
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2020)
                  Characterizing and controlling the out-of-equilibrium state of nanostructured Mott insulators hold great promises for emerging quantum technologies while providing an exciting playground for investigating fundamental physics of strongly-correlated systems. Here, we use two-color near-field ultrafast electron microscopy to photo-induce the insulator-to-metal transition in a single VO2 nanowire and probe the ensuing electronic dynamics with combined nanometer-femtosecond resolution (10-21 m ∙ s). We take advantage of a femtosecond temporal gating of the electron pulse mediated by an infrared laser pulse, and exploit the sensitivity of inelastic electron-light scattering to changes in the material dielectric function. By spatially mapping the near-field dynamics of an individual nanowire of VO2, we observe that ultrafast photo-doping drives the system into a metallic state on a timescale of ~150 fs without yet perturbing the crystalline lattice. Due to the high versatility and sensitivity of the electron probe, our method would allow capturing the electronic dynamics of a wide range of nanoscale materials with ultimate spatiotemporal resolution.
                    Cover page: Nanoscale-femtosecond dielectric response of Mott insulators captured by two-color near-field ultrafast electron microscopy
                    • Article
                    • Peer Reviewed
                    UC Berkeley Previously Published Works (2019)
                    Considerable advances in manipulating heat flow in solids have been made through the innovation of artificial thermal structures such as thermal diodes, camouflages, and cloaks. Such thermal devices can be readily constructed only at the macroscale by mechanically assembling different materials with distinct values of thermal conductivity. Here, we extend these concepts to the microscale by demonstrating a monolithic material structure on which nearly arbitrary microscale thermal metamaterial patterns can be written and programmed. It is based on a single, suspended silicon membrane whose thermal conductivity is locally, continuously, and reversibly engineered over a wide range (between 2 and 65 W/m·K) and with fine spatial resolution (10-100 nm) by focused ion irradiation. Our thermal cloak demonstration shows how ion-write microthermotics can be used as a lithography-free platform to create thermal metamaterials that control heat flow at the microscale.
                      Cover page: Ion Write Microthermotics: Programing Thermal Metamaterials at the Microscale
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