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Open Access Publications from the University of California

Scholarly Works (17 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2021)

State machine replication is at the heart of almost every strongly consistent distributed system. In this thesis, we introduce a novel technique called compartmentalization that involves decoupling a protocol into its simplest components and then scaling each component independently. Compartmentalization is simple yet effective. It can be used to increase the throughput of a protocol, to simplify an exiting protocol, or to design new functionality for a protocol. In this thesis specifically, we apply compartmentalization to state machine replication protocols in a number of different ways. We compartmentalize MultiPaxos and increase its throughput by over an order of magnitude. We then compartmentalize a family of complex state machine protocols called generalized multi-leader protocols. The compartmentalization simplifies the protocols and brings clarity to a family of protocols that were previously extremely difficult to understand. Finally, we use compartmentalization to design a new reconfiguration protocol based on Vertical Paxos that state machine replication protocols can use to replace failed machines with new machines without any downtime.

    Cover page: Compartmentalizing State Machine Replication
    • Article
    • Peer Reviewed
    LBL Publications (2019)
    Phase transformations of carbonates are relevant to a wide range of biological, environmental, and industrial processes. Over the past decade, it emerged that crystallization pathways in these systems can be quite complex. Metastable intermediates such as amorphous calcium carbonate (ACC) were found to greatly impact composition, structure, and properties of more stable phases. However, it has been challenging to create predictive models. Rapid transformation of ACC in bulk has been one obstacle in the determination of nucleation rates. Herein, it is reported that confinement in microfluidic droplets allows separating in time the precipitation of ACC and subsequent nucleation and growth of crystalline CaCO3. An upper limit of 1.2 cm-3 s-1 was determined for the steady-state crystal nucleation rate in the presence of ACC at ambient conditions. This rate has implications for the formation of calcium carbonate in biomineralization, bio-inspired syntheses, and carbon sequestration.
      Cover page: Crystallization kinetics of amorphous calcium carbonate in confinement
      • Article
      • Peer Reviewed
      Journal of Systems Research, Volume 1, Issue 1 (2021)

      MultiPaxos and Raft are the two most popular and widely deployed state machine replication protocols. There is a more sophisticated family of generalized multi-leader state machine replication protocols like EPaxos, Caesar, and Atlas that have better performance, but they are extremely complicated and hard to understand. Due to their complexity, they have seen little to no industry adoption, and academically there has been a lack of clarity in analyzing, comparing, and extending the protocols. This paper is a tutorial on generalized multi-leader protocols. We explain why the protocols work the way they do, what they have in common, where they differ, which parts of the protocols are straightforward, which are more subtle than they appear, and so on. In doing so, we present four new generalized multi-leader protocols, identify key insights into existing protocols, and taxonomize the space.

        Cover page: SoK: A Generalized Multi-Leader State Machine Replication TutorialCreative Commons 'BY-NC' version 4.0 license
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2023)
        Clean energy technologies provide global benefits through climate mitigation and many local environmental benefits for consumers. However, the supply chains that produce them inevitably impose some environmental burden on the communities where they operate. To align with the principles of environmental justice, the burdens and benefits of clean energy supply chains should be distributed equitably, with decision-making processes that empower local communities to participate. Academic research can play a key role as a source of transparent information that addresses the concerns of frontline communities; however, this requires deliberate effort during the initial stages of research to understand what those concerns are and seek data that will respond to them. As a case study, this article analyzes public meetings about a developing lithium industry in Imperial, California, and reviews relevant literature to build a research agenda that is guided by the priorities of local stakeholders. We find that water consumption, public health impacts, local employment, and opportunities to participate are high-priority topics for community members. We also compare the content of discussions across groups, finding that participants in community-focused meetings mainly asked about the local impacts of the process, whereas state-led discussions focused on the sustainability of direct lithium extraction compared to conventional production methods. To address the priorities of frontline communities, we recommend evaluating water consumption in the context of regional availability, including local air emissions and waste streams in sustainability analyses, and monitoring the impact on local employment over time to ensure the promises made during development accrue to communities.
          Cover page: What do frontline communities want to know about lithium extraction? Identifying research areas to support environmental justice in Lithium Valley, CaliforniaCreative Commons 'BY-NC' version 4.0 license
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2020)
          Montmorillonite (MMT) clay - a layered porous nanomaterial used as seals in engineered waste containment barriers for spent nuclear fuel - adopts discrete hydration/swelling states depending upon surrounding water and ion activities and confining pressure. The structure of nanoconfined water and charge-balancing counterions in the clay mineral interlayers dictate the swelling and mechanical behavior of MMT, so a molecular model for this clay with high structural fidelity is required to accurately predict the reliability of long-term nuclear waste storage. Here, we present a molecular model for MMT that is based on high resolution transmission electron microscopy of Wyoming-MMT single crystals. Imaging data unambiguously show a cis-vacant arrangement of structural hydroxyl groups in the octahedral sheet, whereas existing molecular models assume a centrosymmetric trans-vacant configuration for MMT. Using atomistic simulations, we find that the cis-vacant arrangement of structural hydroxyl groups significantly affects the structure of adsorbed water yielding a larger population of hydrogen bonds with bridging oxygens on the tetrahedral sheet and weak hydrogen bonding between the hydroxyl groups in the octahedral sheet and water in the clay mineral interlayers. As a result, water adsorbed in the interlayer is more "ice-like", with stronger ordering and lower density, although the diffusivity of the interlayer species is not significantly diminished. Our improved structural model for MMT provides insight into the energetics of water adsorption, which ultimately dictates its pore- to macro-scale swelling, transport, and fracture properties.
            Cover page: Structural Implications of Interfacial Hydrogen Bonding in Hydrated Wyoming-Montmorillonite Clay
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2019)
            Ion exchange in nanoporous clay-rich media plays an integral role in water, nutrient, and contaminant storage and transport. In montmorillonite (MMT), a common clay mineral in soils, sediments, and muds, the swelling and collapse of clay particles through the addition or removal of discrete molecular layers of water alters cation exchange selectivities in a poorly understood way. Here, we show that ion exchange is coupled to the dynamic delamination and restacking of clay layers, which creates a feedback between the hydration state of the exchanging cation and the composition of the clay interlayer. Particles with different hydration states are distinct phases with unique binding selectivities. Surprisingly, equilibrium achieved through thermal fluctuations in cation concentration and hydration state leads to the exchange of both ions and individual MMT layers between particles, a process we image directly with high-resolution transmission electron microscopy at cryogenic conditions (cryo-TEM). We introduce an exchange model that accounts for the binding selectivities of different phases, which is likely applicable to many charged colloidal or macromolecular systems in which the structural conformation is correlated with the activities of water and counterions within spatially confined compartments.
            • 1 supplemental PDF
            Cover page: Ion exchange selectivity in clay is controlled by nanoscale chemical–mechanical coupling
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2020)
            Clays control carbon, water and nutrient transport in the lithosphere, promote cloud formation5 and lubricate fault slip through interactions among hydrated mineral interfaces. Clay mineral properties are difficult to model because their structures are disordered, curved and dynamic. Consequently, interactions at the clay mineral-aqueous interface have been approximated using electric double layer models based on single crystals of mica and atomistic simulations. We discover that waves of complexation dipoles at dynamically curving interfaces create an emergent long-range force that drives exfoliation and restacking over time- and length-scales that are not captured in existing models. Curvature delocalizes electrostatic interactions in ways that fundamentally differ from planar surfaces, altering the ratio of ions bound to the convex and concave sides of a layer. Multiple-scattering reconstruction of low-dose energy-filtered cryo electron tomography enabled direct imaging of ion complexes and electrolyte distributions at hydrated and curved mineral interfaces with {\aa}ngstrom resolution over micron length scales. Layers exfoliate and restack abruptly and repeatedly over timescales that depend strongly on the counterion identity, demonstrating that the strong coupling between elastic, electrostatic and hydration forces in clays promote collective reorganization previously thought to be a feature only of active matter.
              Cover page: Dynamic clay microstructures emerge via ion complexation waves
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2021)
              Metastable carbonates play important roles in geochemistry, biomineralization and serve as model systems for nonclassical theories of nucleation and growth. Balcite (Ca0.5Ba0.5CO3) is a remarkable carbonate phase that is isostructural with a high-temperature modification of calcite (CaCO3), yet can be synthesized at ambient conditions. Here, we investigate crystallization pathways in the Ba-Ca-CO3-H2O system, with a focus on the transformation of amorphous calcium barium carbonate (ACBC) to balcite and subsequent decomposition into the equilibrium calcite (CaCO3) and witherite (BaCO3) phases. Density functional theory calculations show that balcite is an unstable solid solution (Ca1-xBaxCO3, R3¯ m) in the range 0.17 < x < 0.5, but is accessible through the amorphous ACBC precursor for x ≲ 0.5, and predict its decomposition into calcite and witherite. We confirm this pathway experimentally but found demixing to proceed slowly and remain incomplete even after 9 months. Nucleation kinetics of balcite from ACBC was assessed using a microfluidic assay, where increasing barium content led to a surprising increase in the balcite nucleation rate, despite decreasing thermodynamic driving force. We attribute crystallization rates that dramatically accelerate with time to changes in interfacial structure and composition during coarsening of the amorphous precipitate. By carefully quantifying the thermodynamic and kinetic contributions in the multistep crystallization of a metastable carbonate, we produce insights that allow us to better interpret the formation and persistence of metastable minerals in natural and synthetic environments.
                Cover page: Dynamic Barriers to Crystallization of Calcium Barium Carbonates
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2020)
                The aluminosilicate layers of the swelling clay mineral montmorillonite, and the saturated pores they delineate, control the mechanical properties and the transport of solutes in many natural and engineered environments. However, the structural basis of montmorillonite porosity remains poorly characterized due to the difficulty in visualizing hydrated samples in their native state. Here, we used cryogenic transmission electron microscopy (cryo-TEM) and cryo electron tomography (cryo-ET) to show that stacking defects within minimally altered, fully hydrated montmorillonite particles define multiscale porosity networks. Variations in layer lateral dimensions over tens to thousands of nanometers cause a range of topological and dynamic defects that generate pervasive curvature and introduce previously uncharacterized solute transport pathways. Observations of long-range rotational order between neighboring layers indicate that the layer-layer interactions that govern clay swelling involve three dimensional orienting forces that operate across nanoscale pores. These direct observations of the hierarchical structure of hydrated montmorillonite pore networks with nanoscale resolution reveal potentially general aspects of colloidal interactions in fluid-saturated clay minerals.
                  Cover page: Layer size polydispersity in hydrated montmorillonite creates multiscale porosity networks
                  • Article
                  • Peer Reviewed
                  Energy Geosciences (2017)
                  The direct observation of amorphous barium carbonate (ABC), which transforms into a previously unknown barium carbonate hydrate (herewith named gortatowskite) within a few hundred milliseconds of formation, is described. In situ X-ray scattering, cryo-, and low-dose electron microscopy were used to capture the transformation of nanoparticulate ABC into gortatowskite crystals, highly anisotropic sheets that are up to 1 μm in width, yet only about 10 nm in thickness. Recrystallization of gortatowskite to witherite starts within 30 seconds. We describe a bulk synthesis and report a first assessment of the composition, vibrational spectra, and structure of gortatowskite. Our findings indicate that transient amorphous and crystalline precursors can play a role in aqueous precipitation pathways that may often be overlooked owing to their extremely short lifetimes and small dimensions. However, such transient precursors may be integral to the formation of more stable phases.
                    Cover page: Multi‐Step Crystallization of Barium Carbonate: Rapid Interconversion of Amorphous and Crystalline Precursors
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