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Open Access Publications from the University of California

Scholarly Works (7 results)

  • Article
  • Peer Reviewed
The Undergraduate Historical Journal at UC Merced, Volume 2, Issue 2 (2015)
    Cover page: The Best Laid Plans of Mice and Men: The Downfall of the Black Panther PartyCreative Commons 'BY-NC-ND' version 4.0 license
    • Thesis
    • Peer Reviewed
    UC Berkeley Electronic Theses and Dissertations (2017)

    Modeling of semiconductor devices plays an important role in determining which future technologies are most promising for the semiconductor industry as well as optimizing the performance and better understanding the underlying physics of existing devices. This thesis focuses on the design, development, and use of software to study transport in low-dimensional materials and explores the physics of negative capacitance in ferroelectrics.

    Quantum transport simulation is used to examine the properties of graphene nanoribbons in geometries that can be fabricated through bottom-up chemical synthesis. The chevron graphene nanoribbon is shown to have an electronic structure analogous to traditional semiconductor superlattices. It is shown how this property could be utilized to create a new type of device, which exhibits both negative differential resistance and steep-slope (< 60 mV/decade) switching for low-power electronics applications. We discuss BerkeleyNano3D, a new quantum transport simulator based on the non-equilibrium Green’s function (NEGF) formalism, which is capable of efficient three-dimensional device simulation on large computing clusters.

    Finally, the phenomenon of ferroelectric negative capacitance is examined through the lens of phase-field simulations based on the time-dependent Ginzburg-Landau equation. This phenomenon has been previously predicted as a means to enable energy-efficient steep-slope device with minimal modification to existing transistor processes. Simulation results from three-dimensional phase-field modeling provide new insight into the underlying mechanisms for negative capacitance and give far better agreement with experiment than previously studied single domain models.

      Cover page: Quantum Transport and Phase-Field Modeling for Next-Generation Logic Devices
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2018)
      We show that recently fabricated Chevron-type graphene nanoribbons act as a monolithic superlattice structure. This is enabled by the large periodic unit cells with regions of different effective bandgaps in these nanoribbons, resulting in minibands and gaps in the density of states above the conduction band edge. Quantum transport calculations based on non-equilibrium Green's function formalism reveal that a negative differential resistance (NDR) is expected to manifest in these nanoribbons. Due to the relatively low density of states, such NDR behavior can also be modulated with a gate electric field. We show that a sub-thermal subthreshold swing (< kT/q) can potentially be obtained in a three-terminal configuration, even in the presence of optical phonon scattering.
        Cover page: Negative Differential Resistance and Steep Switching in Chevron Graphene Nanoribbon Field-Effect Transistors
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2017)
        We demonstrate that a ferroelectric can cause a differential amplification without needing such an external energy source. As the ferroelectric switches from one polarization state to the other, a transfer of energy takes place from the ferroelectric to the dielectric, determined by the ratio of their capacitances, which, in turn, leads to the differential amplification. This amplification is very different in nature from conventional inductor-capacitor based circuits where an oscillatory amplification can be observed. The demonstration of differential voltage amplification from completely passive capacitor elements only has fundamental ramifications for next generation electronics.
          Cover page: Differential voltage amplification from ferroelectric negative capacitance
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2018)
            Cover page: Publisher's Note: “Differential voltage amplification from ferroelectric negative capacitance” [Appl. Phys. Lett. 111, 253501 (2017)]Creative Commons 'BY-SA' version 4.0 license
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2023)
            Rare CD4 T cells that contain HIV under antiretroviral therapy represent an important barrier to HIV cure1-3, but the infeasibility of isolating and characterizing these cells in their natural state has led to uncertainty about whether they possess distinctive attributes that HIV cure-directed therapies might exploit. Here we address this challenge using a microfluidic technology that isolates the transcriptomes of HIV-infected cells based solely on the detection of HIV DNA. HIV-DNA+ memory CD4 T cells in the blood from people receiving antiretroviral therapy showed inhibition of six transcriptomic pathways, including death receptor signalling, necroptosis signalling and antiproliferative Gα12/13 signalling. Moreover, two groups of genes identified by network co-expression analysis were significantly associated with HIV-DNA+ cells. These genes (n = 145) accounted for just 0.81% of the measured transcriptome and included negative regulators of HIV transcription that were higher in HIV-DNA+ cells, positive regulators of HIV transcription that were lower in HIV-DNA+ cells, and other genes involved in RNA processing, negative regulation of mRNA translation, and regulation of cell state and fate. These findings reveal that HIV-infected memory CD4 T cells under antiretroviral therapy are a distinctive population with host gene expression patterns that favour HIV silencing, cell survival and cell proliferation, with important implications for the development of HIV cure strategies.
              Cover page: HIV silencing and cell survival signatures in infected T cell reservoirsCreative Commons 'BY' version 4.0 license
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2015)
              The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
                Cover page: Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
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