Exploration of Erasure-Coded Storage Systems for High Performance, Reliability, and Inter-operability

With the unprecedented growth of data and the use of low commodity drives in local disk-based storage systems and remote cloud-based servers has increased the risk of data loss and an overall increase in the user perceived system latency. To guarantee high reliability, replication has been the most popular choice for decades, because of simplicity in data management. With the high volume of data being generated every day, the storage cost of replication is very high and is no longer a viable approach. Erasure coding is another approach of adding redundancy in storage systems, which provides high reliability at a fraction of the cost of replication. However, the choice of erasure codes being used affects the storage efficiency, reliability, and overall system performance. At the same time, the performance and interoperability are adversely affected by the slower device components and complex central management systems and operations. To address the problems encountered in various layers of the erasure coded storage system, in this dissertation, we explore the different aspects of storage and design several techniques to improve the reliability, performance, and interoperability. These techniques range from the comprehensive evaluation of erasure codes, application of erasure codes for highly reliable and high-performance SSD system, to the design of new erasure coding and caching schemes for Hadoop Distributed File System, which is one of the central management systems for distributed storage. Detailed evaluation and results are also provided in this dissertation

Collective effects in Single Molecule Magnets

Single molecule magnets (SMMs), such as Mn12-acetate, are composed of transition metal ions and consists of identical molecules with large ground-state spin (S = 10) and a strong uniaxial anisotropy (65 K). Below about 3 K, Mn12-acetate exhibits magnetic hysteresis with steps at specific values of longitudinal magnetic field due to resonant quantum tunneling between spin up and down projections along the easy axis. The intermolecular exchange interactions between spins on molecules are quite small and spins are considered to be independent and non-interacting. However, the molecules do interact with each other both through magnetic dipolar interactions and through the lattice (e.g. phonons). I have investigated collective effects in SMMs due to these intermolecular interactions. In the thesis I will present experiments that explored magnetic ordering due to magnetic dipole interactions in Mn12-acetate and Mn12-acetate-MeOH. I will also present exper- iments on the onset of magnetic de agration in Mn12-acetate due to a thermal instability. The magnetic ordering studies involved investigating the effect of transverse fields on the susceptibility of single crystals of Mn12-acetate and Mn12-acetate- MeOH. Transverse fields increase quantum spin uctuations that suppress long- range order. However, the suppression of the Curie temperature by transverse fields in Mn12-acetate is far more rapid than predicted by the Transverse-Field Ising Ferromagnetic Model (TFIFM) and instead agrees with the predictions of the Random-Field Ising Ferromagnet Model. It appears that solvent disorder in Mn12-acetate gives rise to a distribution of random-fields that further suppress long-range order. Subsequent studies on Mn12-acetate-MeOH, with the same spin and similar lattice constants but without solvent disorder as Mn12-acetate, agrees with the TFIFM. The magnetic de agration studies involved studying the instability that leads to the ignition of magnetic deflagration in a thermally driven Mn 12-acetate crystal. When spins prepared in a metastable state reverse, Zeeman energy is released that diffuses away. In some circumstances, the heat released cannot be compensated by thermal diffusion, resulting in an instability that gives rise to a front of rapidly reversing spins traveling through the crystal. We observed a sharp crossover from relaxation driven by heat diffusion to a self-sustained reversal front that propagates at a constant subsonic speed

Thermodynamic evaluation of a gas turbine in python programming language and comparison of the procedure and the results with the existing MATLAB model

Diese Arbeit bezieht sich auf die systematische und strukturierte Simulation einer Gasturbine in der Python Programmiersprache. Nach kurzer Einführung in der Python Programmiersprache werden an jeder Komponente der Gasturbine thermodynami-schen Eigenschaften der Fluide berechnet sowie die Energie bilanziert. Abschließend werden die Vorgehensweise und die Ergebnisse mit der vorhandenen MATLAB-Be-rechung verglichen.The thesis relates to the systematic and structural simulation of a gas turbine in python programming language. After a small introduction in the python programming lan-gaue, thermodynamic properties of the gases will be calculated, and energy will be balanced. Finally, the python procedure and results of the calculation will be com-pared with the MATLAB one demonstrating the difference between the each method

Novel Electrochemical Measurements on Nanoparticle Ensembles and Actual Single Nanoparticle

The research work in this dissertation is focused on the study of the semiconductor nanoparticles (NPs) for photo conversion of light into electricity. Semiconductor nanoparticles are used not only for photo conversion but also in medicine, environmental pollution removal, material preparations, cosmetics, etc. The main goal of this work is to establish a protocol to capture and study the reaction kinetics of the single semiconductor NP. We have studied cadmium selenide (CdSe) quantum dots and TiO2 NPs suspended in a neat methanol solution as a model system where the methanol gets photooxidized into formaldehyde. The methanol oxidation to formaldehyde is a two-electron process. The particles of quantum dots get agglomerated under illumination which is evident by the current size of the photocurrent obtained in the scale > 1 pA. This observation is also consistent with the stability of the particles in methanol suspension under constant illumination and the collision frequency. We have detected formaldehyde, the product of photooxidation of methanol by FTIR, and quantified the formaldehyde by ESI-MS. We also studied the change in temperature in the vicinity of the ultramicroelectrode (UME) under constant laser illumination. It is very important to study the change in temperature because it can have a significant effect on electron transfer rate. In the last chapter, we studied TiO2 NPs suspended in methanol solution by nano-impact study under laser illumination. The particles were spiked into the solution after turning on the laser and were captured on the UME which was evident by the current steps in i-t traces. We further carried out the surface modification of the electrode and captured an actual single particle of TiO2

Engineering of Microbial Substrate Promiscuous CYP105A5 for Improving the Flavonoid Hydroxylation

Bacterial cytochrome P450 (CYP) enzymes are versatile biocatalysts that are responsible for the biotransformation of diverse endogenous substances. CYP105A5 from Streptomyces sp. showed substrate flexibility with different flavonoids and was able to catalyze O-demethylation of biochanin A, regioselective C3′-hydroxylation of daidzein, genistein, and naringenin, and additional C8-hydroxylation for daidzein using heterologous redox partners putidaredoxin and putidaredoxin reductase. By rational design of substrate-binding pocket based on experimental data, homology modeling, and molecular docking analysis, we enhanced the product formation rate of flavonoids. The double mutant L100A/I302A and L100A/I408N exhibited greatly enhanced in vivo conversion rates for flavonoid hydroxylation. Particularly, the L100A/I302A mutant’s kcat/Km values and in vivo conversion rate increased by 1.68-fold and 2.57-fold, respectively, for naringenin. Overall, our result might facilitate the potential use of CYP105A5 for future modification and application in whole-cell biocatalysts for the production of valuable polyphenols

Engineering of Microbial Substrate Promiscuous CYP105A5 for Improving the Flavonoid Hydroxylation

Bacterial cytochrome P450 (CYP) enzymes are versatile biocatalysts that are responsible for the biotransformation of diverse endogenous substances. CYP105A5 from Streptomyces sp. showed substrate flexibility with different flavonoids and was able to catalyze O-demethylation of biochanin A, regioselective C3′-hydroxylation of daidzein, genistein, and naringenin, and additional C8-hydroxylation for daidzein using heterologous redox partners putidaredoxin and putidaredoxin reductase. By rational design of substrate-binding pocket based on experimental data, homology modeling, and molecular docking analysis, we enhanced the product formation rate of flavonoids. The double mutant L100A/I302A and L100A/I408N exhibited greatly enhanced in vivo conversion rates for flavonoid hydroxylation. Particularly, the L100A/I302A mutant’s kcat/Km values and in vivo conversion rate increased by 1.68-fold and 2.57-fold, respectively, for naringenin. Overall, our result might facilitate the potential use of CYP105A5 for future modification and application in whole-cell biocatalysts for the production of valuable polyphenols

Exploring power budget scheduling opportunities and tradeoffs for amr-based applications

Computational demand has brought major changes to Advanced Cyber-Infrastructure (ACI) architectures. It is now possible to run scientific simulations faster and obtain more accurate results. However, power and energy have become critical concerns. Also, the current roadmap toward the new generation of ACI includes power budget as one of the main constraints. Current research efforts have studied power and performance tradeoffs and how to balance these (e.g., using Dynamic Voltage and Frequency Scaling (DVFS) and power capping for meeting power constraints, which can impact performance). However, applications may not tolerate degradation in performance, and other tradeoffs need to be explored to meet power budgets (e.g., involving the application in making energy-performance-quality tradeoff decisions). This paper proposes using the properties of AMR-based algorithms (e.g., dynamically adjusting the resolution of a simulation in combination with power capping techniques) to schedule or re-distribute the power budget. It specifically explores the opportunities to realize such an approach using checkpointing as a proof-of-concept use case and provides a characterization of a representative set of applications that use Adaptive Mesh Refinement (AMR) methods, including a Low-Mach-Number Combustion (LMC) application. It also explores the potential of utilizing power capping to understand power-quality tradeoffs via simulation30th international symposium on computer architecture and high performance computing (SBAC-PAD)This work is supported in part by National Science Foundation via grants numbers ACI-1464317 and CNS-1305375, and was conducted as part of the Rutgers Discovery Informatics Institute (RDI2). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. We acknowledge Weiqun Zhang and Marcus S. Day, from Lawrence Berkeley National Laboratory, for helping with LMC simulation applicatio

Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from <i>Sphingomonas echinoides</i>

Cytochrome P450 enzymes (CYPs) are heme-containing enzymes that catalyze hydroxylation with a variety of biological molecules. Despite their diverse activity and substrates, the structures of CYPs are limited to a tertiary structure that is similar across all the enzymes. It has been presumed that CYPs overcome substrate selectivity with highly flexible loops and divergent sequences around the substrate entrance region. Here, we report the newly identified CYP101D5 from Sphingomonas echinoides. CYP101D5 catalyzes the hydroxylation of β-ionone and flavonoids, including naringenin and apigenin, and causes the dehydrogenation of α-ionone. A structural investigation and comparison with other CYP101 families indicated that spatial constraints at the substrate-recognition site originate from the B/C loop. Furthermore, charge distribution at the substrate binding site may be important for substrate selectivity and the preference for CYP101D5