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Open Access Publications from the University of California

Scholarly Works (7 results)

  • Thesis
  • Peer Reviewed
UC Irvine Electronic Theses and Dissertations (2024)

Open source development is not only a software development paradigm that is widely adopted nowadays, but also a social movement that has profound impacts in our society. Ideology, as “heart and soul”, drives such social movements, and so does open source software ideology (OSS ideology) to open source movement. Thus, it is essential to understand OSS ideology. However, SE literature only conducted preliminary explorations towards OSS ideology, or only focused on particular elements within OSS ideology. In this dissertation, we report our efforts in developing an empirical understanding towards OSS ideology. First, we defined OSS ideology based on a general and explicit definition to encompass our research. Following grounded theory methodology, we collected data from 21 semi-structured interviews with OSS practitioners, and 41 videos of Open Source Initiative (OSI)’s board members’ public interviews/speeches; then we developed an empirical theory of OSS ideology. Such a theory consisted of 42 themes that emerged from the collected data, under six broad categories, i.e., Norms/Values, Membership, Goals, Activities, Resources, and Positions/Group Relations. Then, based on the empirical theory of OSS ideology, we developed an assessment framework to investigate the OSS ideologies within particular open source projects. The assessment only relied on public data sources, and reflected OSS ideologies at the project level. Furthermore, we conducted three case studies by applying the assessment framework to three selected open source projects, D3, Zephyr, and PyTorch. The assessment results demonstrated how open source projects uphold OSS ideology in practice.

This dissertation contributed to SE literature with a foundational understanding of OSS ideology. First, the empirical theory of OSS ideology, featuring comprehensive, contemporary, and empirically-grounded characteristics, significantly extended the SE literature with new themes identified in the study. It also provides an ideological lens to examine open source development. Second, the practical and extensive assessment framework could facilitate both OSS researchers and practitioners to investigate open source development with an ideological lens. Third, the three case studies provided insights into the practices of open source development from an ideological perspective. Moreover, the studies in this dissertation yielded rich theoretical and practical implications regarding open source movement, they also indicated various future research opportunities to further our understanding of OSS ideology and open source movement.

    Cover page: Towards an Empirical Understanding of Open Source Ideologies
    • Article
    • Peer Reviewed
    LBL Publications (2019)
    Accurate microscopic description of the charge-trapping process from semiconductor to defects in the dielectric-oxide layer is of paramount importance for understanding many microelectronic devices such as complementary metal-oxide-semiconductor (CMOS) transistors, as well as electrochemical reactions. Unfortunately, most current microscopic descriptions of such processes are based on empirical models with parameters fitted to experimental device performance results or simplified approximations like the Wentzel-Kramers-Brillouin (WKB) method. Some critical questions are still unanswered, including: What controls the charge-hopping rate, the coupling strength between the defect level to semiconductor level, or the energy difference? How does the hopping rate decay with defect-semiconductor distance? What is the fluctuation of the defect level, especially in amorphous dielectrics? Many of these questions can be answered by ab initio calculations. However, to date, there are few ab initio studies for this problem mainly due to technical challenges from atomic-structure construction to large-system calculations. Here, using the latest advances in calculation methods and codes, we study the carrier-trapping problem using density-functional theory (DFT) based on the Heyd-Scuseria-Ernzerhof (HSE) exchange correlation functional. The valence bond random-switching method is used to construct the crystalline-Si-amorphous-SiO2 (c-Si/a-SiO2) interfacial atomic structure, and the HSE yields a band offset that agrees well with experiments. The hopping rate is calculated with the Marcus theory, and the hopping-rate dependences on the gate potential and defect distances are revealed, as well as the range of fluctuation results from amorphous structural variation. We also analyze the result with the simple WKB model and find a major difference in the description of the coupling constant decay with the defect-semiconductor distance. Our results provide the ab initio simulation insights for this important carrier-trapping process for device operation.
    • 1 supplemental PDF
    Cover page: Ab Initio Investigation of Charge Trapping Across the Crystalline-Si–Amorphous-SiO2 Interface
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2018)
    Neuronal polarity relies on the selective localization of cargo to axons or dendrites. The molecular motor kinesin-1 moves cargo into axons but is also active in dendrites. This raises the question of how kinesin-1 activity is regulated to maintain the compartment-specific localization of cargo. Our in vivo structure-function analysis of endogenous Drosophila melanogaster kinesin-1 reveals a novel role for autoinhibition in enabling the dendrite-specific localization of Golgi outposts. Mutations that disrupt kinesin-1 autoinhibition result in the axonal mislocalization of Golgi outposts. Autoinhibition also regulates kinesin-1 localization. Uninhibited kinesin-1 accumulates in axons and is depleted from dendrites, correlating with the change in outpost distribution and dendrite growth defects. Genetic interaction tests show that a balance of kinesin-1 inhibition and dynein activity is necessary to localize Golgi outposts to dendrites and keep them from entering axons. Our data indicate that kinesin-1 activity is precisely regulated by autoinhibition to achieve the selective localization of dendritic cargo.
      Cover page: Autoinhibition of kinesin-1 is essential to the dendrite-specific localization of Golgi outposts
      • Article
      • Peer Reviewed
      LBL Publications (2021)
      Carrier induced defect creation at the semiconductor-oxide interface has been known as the origin of electronic device degradation for a long time, but how exactly the interface lattice can be damaged by carriers (especially low-energy ones) remains unclear. Here we carry out real-time time-dependent density functional theory simulations on concrete interfaces to study the interaction between excited electrons and interface bonds. We show that the normal interface Si-H bonds are generally resistant to electrons due to the delocalized nature and high energy level of the Si-H antibonding states, and due to the high-energy barrier to break the Si-H bond. However, if an additional hydrogen atom exists by attaching to a nearby oxygen atom (forming a “Si-H···H-O” complex), the Si-H bond will be greatly weakened, including the reduction of energy barrier for bond breaking, and the lowering of the antibonding state energy level which favors electron injection. Together with the multiple vibrational excitation process, the corresponding Si-H bond can be broken much more easily. Thus we propose that the Si-H···H-O complex will be the center for defect creation and device degradation. We also explain why such a center might be relatively easy to form during the hydrogen annealing process.
        Cover page: Electronically induced defect creation at semiconductor/oxide interface revealed by time-dependent density functional theory
        • Article
        • Peer Reviewed
        LBL Publications (2019)
        The complexity of charge trapping in semiconductor devices, such as high-κ MOSFETs, is increasing as the devices themselves become more complicated. To facilitate research into such charge-trapping issues, here we propose an optimized simulation framework that is composed of density-functional theory (DFT) for electronic structure calculation and Marcus theory for the calculation of charge-trapping rates. The DFT simulations are either carried out or corrected by using the Heyd-Scuseria-Ernzerhof hybrid functional. Using this framework, the hole-trapping characteristics along multiple paths in Si/SiO2/HfO2 stacks are investigated, and the relative importance of each path is revealed by calculating its exact hole-trapping rate. Besides the study on crystalline stacks, we also create an amorphous stack, which is more realistic compared with experiments and real devices, to reveal more active trapping centers and to study the statistical feature of charge trapping induced by structural disorder. In addition, to seek effective measures for relieving these charge-trapping problems, the effects of hydrogen and fluorine passivations are discussed, and physical insights for improving the performance of high-κ MOSFETs are provided.
        • 1 supplemental PDF
        Cover page: Characterizing the Charge Trapping across Crystalline and Amorphous Si/SiO2/HfO2 Stacks from First-Principle Calculations
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2018)
        Kinesin-4 motors play important roles in cell division, microtubule organization, and signaling. Understanding how motors perform their functions requires an understanding of their mechanochemical and motility properties. We demonstrate that KIF27 can influence microtubule dynamics, suggesting a conserved function in microtubule organization across the kinesin-4 family. However, kinesin-4 motors display dramatically different motility characteristics: KIF4 and KIF21 motors are fast and processive, KIF7 and its Drosophila melanogaster homologue Costal2 (Cos2) are immotile, and KIF27 is slow and processive. Neither KIF7 nor KIF27 can cooperate for fast processive transport when working in teams. The mechanistic basis of immotile KIF7 behavior arises from an inability to release adenosine diphosphate in response to microtubule binding, whereas slow processive KIF27 behavior arises from a slow adenosine triphosphatase rate and a high affinity for both adenosine triphosphate and microtubules. We suggest that evolutionarily selected sequence differences enable immotile KIF7 and Cos2 motors to function not as transporters but as microtubule-based tethers of signaling complexes.
          Cover page: Altered chemomechanical coupling causes impaired motility of the kinesin-4 motors KIF27 and KIF7
          • Article
          • Peer Reviewed
          LBL Publications (2022)
          Heparins are widely used anticoagulants for surgical procedures and extracorporeal therapies. However, all of them have bleeding risks. Protamine sulfate, the only clinically approved antidote for unfractionated heparin (UFH), has adverse effects. Moreover, protamine can only partially neutralize low-molecular-weight heparins (LMWHs) and is not effective for fondaparinux. Here, an inclusion-sequestration strategy for efficient neutralization of heparin anticoagulants by cationic porous supramolecular organic frameworks (SOFs) and porous organic polymers (POPs) is reported. Isothermal titration calorimetric and fluorescence experiments show strong binding affinities of these porous polymers toward heparins, whereas dynamic light scattering and zeta potential analysis confirm that the heparin sequences are adsorbed into the interior of the porous hosts. Activated partial thromboplastin time, anti-FXa, and thromboelastography assays indicate that their neutralization efficacies are higher than or as high as that of protamine for UFH and generally superior to protamine for LMWHs and fondaparinux, which is further confirmed by tail-transection model in mice and ex vivo aPTT or anti-FXa analysis in rats. Acute toxicity evaluations reveal that one of the SOFs displays outstanding biocompatibility. This work suggests that porous polymers can supply safe and rapid reversal of clinically used heparins, as protamine surrogates, providing an improved approach for their neutralization.
            Cover page: Porous Polymers as Universal Reversal Agents for Heparin Anticoagulants through an Inclusion–Sequestration MechanismCreative Commons 'BY-NC' version 4.0 license
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