Deferred-update database replication:theory and algorithms

This thesis is about the design of high-performance fault-tolerant computer systems. More specifically, it focuses on how to develop database systems that behave correctly and with good performance even in the event of failures. Both performance and dependability can be improved by means of the same technique, namely replication. If several database replicas are available, performance can be improved by distributing the load among them. Moreover, if one of the replicas cannot be accessed due to failures, users can still rely on the other ones. However, providing the interface of a single database system out of several replicas is not an easy task since one has to ensure they are always consistent with each other. Allowing replicas to diverge would easily break the illusion of having a single high-performance fault-tolerant database system. Although we would like to have replicas as independent of each other as possible for performance and dependability reasons, we must keep them synchronized if we want to provide a consistent interface to users. In this work, we study how we can balance this trade-off to provide good performance and fault-tolerance without compromising consistency. Our basis is a widely used technique for database replication known as the deferred update technique. In this technique, transactions are initially executed in a single replica. Passive transactions, which do not change the state of the database, can commit locally to the replica they execute. Active transactions, which change the database state, must be synchronized with the transactions running on other replicas. This thesis makes four major contributions. First, we introduce an abstract specification that generalizes the deferred update technique. This specification provides a strong model to prove lower bounds on replication algorithms, design new correct-by-construction protocols tailor-made for specific settings, and prove existing protocols correct more easily, in a standard way. Using this model, we show that the problem of termination of active transactions in deferred-update protocols is highly related to the problem of sequence agreement among a set of processes. In this context, we study the problem of implementing latency-optimal fault-tolerant solutions to sequence agreement and present a novel, highly-dynamic, algorithm that can quickly adapt to system changes in order to preserve its optimal latency. Our algorithm is based on a new agreement problem we introduce that seems to be more suitable to solve problems like sequence agreement than previously used abstractions. Our last two contributions are in the context of specific deferred-update algorithms, where we present two new fault-tolerant protocols derived from our general abstraction. The first algorithm uses no extra assumptions about database replicas. Yet, it has very little overhead associated with the termination of active transactions, propagating only strictly necessary information to replicas. Our second protocol uses strong assumptions about the concurrency control mechanism used by database replicas to reduce even more the latency and the burden associated with transaction termination. These algorithms are good examples of how our general abstraction can be extended to create new protocols and prove them correct

Advances in coinage metal nanoclusters: From synthesis strategies to electrocatalytic performance

Due to the powerful quantum confined space effects and multiple modes of small atomic sizes, metal nanoclusters (NCs) like thiolate-protected noble metals, such as silver (Ag) and gold (Au), which have a core sizes less than 3 nm, have developed a class of "metallic molecules" with multiple optical, magnetic, and electronic properties. To find a well-defined nanocatalysts, especially ligand-passivated metal NCs, great strides have been achieved in the efficient synthesis of atomically precise nanoparticles. Methods of synthesis such as bottom-up growth, top-down approach, ligand engineering, and interconversion system, are mentioned in this overview. Such clearly defined metal NCs have demonstrated considerable promise in catalysis research and have evolved into a distinct class of model catalysts. Focusing on the oxygen reduction reaction (ORR), hydrogen evolution reaction (HER), and oxygen evolution reaction (OER), this article attempts to outline current developments in NCs of molecular metals employed in electrocatalytic reactions. The paper highlights the relationship between the structure and performance of the catalytic mechanism and examines the potential effects of metal cluster sizes, metal core structures, charges, ligands, and metal–ligand binding patterns on their electrocatalytic activity. Future research opportunities and challenges are also proposed

A software architecture for consensus based replication

Orientador: Luiz Eduardo BuzatoTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Esta tese explora uma das ferramentas fundamentais para construção de sistemas distribuídos: a replicação de componentes de software. Especificamente, procuramos resolver o problema de como simplificar a construção de aplicações replicadas que combinem alto grau de disponibilidade e desempenho. Como ferramenta principal para alcançar o objetivo deste trabalho de pesquisa desenvolvemos Treplica, uma biblioteca de replicação voltada para construção de aplicações distribuídas, porém com semântica de aplicações centralizadas. Treplica apresenta ao programador uma interface simples baseada em uma especificação orientada a objetos de replicação ativa. A conclusão que defendemos nesta tese é que é possível desenvolver um suporte modular e de uso simples para replicação que exibe alto desempenho, baixa latência e que permite recuperação eficiente em caso de falhas. Acreditamos que a arquitetura de software proposta tem aplicabilidade em qualquer sistema distribuído, mas é de especial interesse para sistemas que não são distribuídos pela ausência de uma forma simples, eficiente e confiável de replicá-losAbstract: This thesis explores one of the fundamental tools for the construction of distributed systems: the replication of software components. Specifically, we attempted to solve the problem of simplifying the construction of high-performance and high-availability replicated applications. We have developed Treplica, a replication library, as the main tool to reach this research objective. Treplica allows the construction of distributed applications that behave as centralized applications, presenting the programmer a simple interface based on an object-oriented specification for active replication. The conclusion we reach in this thesis is that it is possible to create a modular and simple to use support for replication, providing high performance, low latency and fast recovery in the presence of failures. We believe our proposed software architecture is applicable to any distributed system, but it is particularly interesting to systems that remain centralized due to the lack of a simple, efficient and reliable replication mechanismDoutoradoSistemas de ComputaçãoDoutor em Ciência da Computaçã

The 2.3A crystal structure of the antibody Fab HPC-4 in complex with calcium and the epitope peptide.

The murine monoclonal antibody HPC-4, directed against the activation region of the human anticoagulant zymogen protein C (PC), is one of the few immunoglobulins known to display calcium-dependent antigen binding. Unlike the more common class of antibodies that merely recognize a calcium-bound conformation of their antigen, HPC-4 interacts directly with calcium in the high affinity PC-HPC-4 complex.Metal ions can have considerable affinities for proteins, and give rise to geometric constraints that are often taken advantage of in protein-protein interactions. The coordination shell of metal ions can be filled by atoms provided by two different proteins, resulting in a high affinity protein complex. Surprisingly, this highly efficient binding strategy is rarely observed in immunoglobulins, despite the great number of known antibody structures determined in complex with their protein antigens.The structure reveals a mode of calcium binding which underlies a novel mechanism of metal aided antigen recognition. The ion is located at the antibodyantigen interface, where it functions both as an electrostatic bridge and as a conformational effector of the antibody. The antigen is further stabilized by an extensive and diverse array of interactions spanning a large surface area of contact. Our results provide a structural explanation for many of the observed characteristics of HPC-4, the first member of a unique class of calcium binding antibodies. As such, it represents a significant contribution to the study of interfacial metals and the structural biology of antibodies.To provide a structural understanding of HPC-4 function and of the particular antibody class to which it belongs, we have solved the X-ray crystal structure of the HPC-4 Fab fragment in ternary complex with its epitope peptide in the presence of calcium at a resolution of 2.3A. Within the crystal, the antigen-binding region is undistorted by crystalline lattice contacts. All complementarity-determining regions and the peptide antigen have well-defined electron density

Selective Oxidative Homo- and Cross-Coupling of Phenols

The efforts described in this dissertation initially focus on the asymmetric coupling of phenols. We have developed Schiff base vanadium catalyst for the oxidative coupling of phenols with high reactivity and enantioselectivity. To the best of our knowledge, this example constitutes the first highly selective asymmetric coupling of phenols. Several substrates were coupled with our vanadium catalyst with good enantioselectivity (72-89% ee). The first simple catalystic system that uses atom-economical oxygen as the terminal oxidant to accomplish selective ortho−ortho, ortho−para, or para−para homo-couplings of phenols was developed. Chromium salen catalysts have been discovered and verified as uniquely effective in the cross-coupling of different phenols with high chemo- and regio-selectivity. A broad scope of phenol substrates was found for these reaction conditions giving cross-coupling products with good yield (up to 88%). In order to understand the mechanism of cross-coupling reaction, spectroscopic methods, additive experiments, SAR studies, and kinetic experiments were performed and a mechanism was postulated. Finally, we established an efficient route for the total synthesis of honokiol by utilizing a novel disconnection that transits new structures. This five step (six chemical reactions) synthesis was initiated by oxidative cross-coupling of inexpensive commercial phenols with high yield (91%). Following retro Friedel-Crafts alkylation, a protection reaction proceeded smoothly with excellent yield (89% for three steps). The remaining steps of radical bromination, Kumada coupling and demethylation were each optimized. The total yield over five steps was 34% and gram-scale reactions were conducted for each step

Synthesis and characterisation of mesoporous transition metal ion modified silica-zirconia and silica-sulfated zirconia materials towards NOx catalysis

Cataloged from PDF version of article.The purpose of this work is to design and investigate mesostructured material as a potential support for the reaction of the methane with surface NOx species. Several objectives have been pursued in achievement of the goals. The first objective is to develop a facile procedure for the synthesis of mesoporous silica-zirconia mixed oxide supports that are modified with the sulphate (SO4 2-), cobalt (Co2+) and palladium (Pd2+) ions. The support with requisite catalytic properties was obtained through the adjustment of the synthetic steps and optimisation of the composition. The second objective is to explore the effect of cobalt and zirconia loading in the reaction of the NOx species with methane over the Co-, Pd-, and Co-Pd-silica-sulfated zirconia (Si-SZr). A one-pot synthesis procedure has been developed to prepare the mesoporous silica-zirconia (Si-Zr), Si-SZr supports and the supermicroporous Co(II) incorporated Si-SZr catalysts with a wide range of zirconia loadings. Introduction of the Co(II) active sites by various post-synthesis methods leads to the modification of the surface, whereas the direct (co-precipitation) techniques have provided the modification of both surface and bulk of the supports. The palladium ions were introduced by the conventional impregnation methods onto the calcined solid materials. The detailed analysis of the materials has revealed that the silica and zirconia are well mixed in the framework, whereas the cobalt and sulfate ions are uniformly dispersed on the internal surface of the silica-zirconia supports. The materials prepared in this thesis possess sufficient stability, requisite catalytic properties, as well as good Bronsted and Lewis acidity. However, the high cobalt loading renders the catalytic performance of the Pd-Si-SZr catalysts. Among the investigated catalysts, the interaction of the NOx species with the CH4 takes place at the lowest temperature over the Co-, Pd-, Co-Pd-supported zirconia rich (Zr/Si = 28) Si-SZr catalysts.Samarskaya, OlgaPh.D

Towards a worldwide storage infrastructure

Peer-to-peer systems have recently gained a lot of attention in the academic community especially through the design of KBR (Key-Based Routing) algorithms and DHT (Distributed Hash Table)s. On top of these constructs were built promising applications such as video streaming applications but also storage infrastructures benefiting from the availability and resilience of such scalable network protocols. Unfortunately, rare are the storage systems designed to be scalable and fault-tolerant to Byzantine behaviour, conditions required for such systems to be deployed in an environment such as the Internet. Furthermore, although some means of access control are often provided, such file systems fail to offer the end-users the flexibility required in order to easily manage the permissions granted to potentially hundreds or thousands of end-users. In addition, as for centralised file systems which rely on a special user, referred to as root on Unices, distributed file systems equally require some tasks to operate at the system level. The decentralised nature of these systems renders impossible the use of a single authoritative entity for performing such tasks since implicitly granting her superprivileges, unacceptable configuration for such decentralised systems. This thesis addresses both issues by providing the file system objects a completely decentralised access control and administration scheme enabling users to express access control rules in a flexible way but also to request administrative tasks without the need for a superuser. A prototype has been developed and evaluated, proving feasible the deployment of such a decentralised file system in large-scale and untrustworthy environments