ETD at Indian Institute of Science
Repository of Theses and Dissertations of Indian Institute of Science, Bangalore, India. The repository has been developed to capture, disseminate and preserve research theses of Indian Institute of Science.
Supercomputer Education and Research Centre (serc)
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Long-Running Multi-Component Climate Applications On Grids - Sundari, Sivagama M
Climate science or climatology is the scientific study of the earth’s climate, where climate is the term representing weather conditions averaged over a period of time. Climate models are mathematical models used to quantitatively describe, simulate and study the interactions among the components of the climate system -atmosphere, ocean, land and sea-ice. CCSM (Community Climate System Model) is a state-of-the-art climate model, and a long-running coupled multicomponent parallel application involving component models for simulating the components of the climate system. Each of the component models is a large-scale parallel application, and the parallel components exchange climate data through a specialized...
Efficient Fault Tolerance In Chip Multiprocessors Using Critical Value Forwarding - Subramanyan, Pramod
Relentless CMOS scaling coupled with lower design tolerances is making ICs increasingly susceptible to transient faults, wear-out related permanent faults and process variations. Decreasing CMOS reliability implies that high-availability systems which were previously restricted to the domain of mainframe computers or specially designed fault-tolerant systems may be come important for the commodity market as well. In this thesis we tackle the problem of enabling efficient, low cost and configurable fault-tolerance using Chip Multiprocessors (CMPs).
Our work studies architectural fault detection methods based on redundant execution, specifically focusing on “leader-follower” architectures. In such architectures redundant execution is performed on two cores/threads of...
An Extension Of Multi Layer IPSec For Supporting Dynamic QoS And Security Requirements - Kundu, Arnab
Governments, military, corporations, financial institutions and others exchange a great deal of confidential information using Internet these days. Protecting such confidential information and ensuring their integrity and origin authenticity are of paramount importance. There exist protocols and solutions at different layers of the TCP/IP protocol stack to address these security requirements. Application level encryption viz. PGP for secure mail transfer, TLS based secure TCP communication, IPSec for providing IP layer security are among these security solutions. Due to scalability, wide acceptance of the IP protocol, and its application independent character, the IPSec protocol has become a standard for providing Internet...
Search-Optimized Disk Layouts For Suffix-Tree Genomic Indexes - Bhavsar, Rajul D
Over the last decade, biological sequence repositories have been growing at an exponential rate. Sophisticated indexing techniques are required to facilitate efficient searching through these humongous genetic repositories. A particularly attractive index structure for such sequence processing is the classical suffix-tree, a vertically compressed trie structure built over the set of all suffixes of a sequence. Its attractiveness stems from its linearity properties -- suffix-tree construction times are linear in the size of the indexed sequences, while search times are linear in the size of the query strings.
In practice, however, the promise of suffix-trees is not realized for extremely long...
Hardware Consolidation Of Systolic Algorithms On A Coarse Grained Runtime Reconfigurable Architecture - Biswas, Prasenjit
Application domains such as Bio-informatics, DSP, Structural Biology, Fluid Dynamics, high resolution direction finding, state estimation, adaptive noise cancellation etc. demand high performance computing solutions for their simulation environments. The core computations of these applications are in Numerical Linear Algebra (NLA) kernels. Direct solvers are predominantly required in the domains like DSP, estimation algorithms like Kalman Filter etc, where the matrices on which operations need to be performed are either small or medium sized, but dense. Faddeev's Algorithm is often used for solving
dense linear system of equations. Modified Faddeev's algorithm (MFA) is a general algorithm on which LU decomposition, QR...
Computational Studies Of Uncertainty In Intra-Cellular Biochemical Reaction Systems - Dana, Saswati
With an increased popularity for systems-based approaches in biology, a wide spectrum of techniques has been applied to the simulation and analysis of biochemical systems which involves uncertainty and stochasticity. It is particularly concerned with modelling and analysis of metabolic pathways, regulatory and signal transduction networks for understanding intra-cellular pathway behaviour. Typically, parameter estimation in ordinary differential equations(ODEs) models is used for this purpose when there is large number of molecules involved in the reaction system. However this approach is correct when the system is large enough to be deterministic in nature. But there are uncertainty involved in the system...
A Computational Study Of Ion Crystals In Paul Traps - Kotana, Appala Naidu
In this thesis we present a computational study of “ion crystals”, the interesting patterns in which ions arrange themselves in ion traps such as Paul and Penning traps. In ion crystals the ions are in equilibrium due to the balance of the repulsive forces between the ions and the overall tendency of the ion trap to pull ions towards the trap centre. We have carried out a detailed investigation of ion crystals in Paul traps by solving their equations of motion numerically.
We also propose a model called the spring–mass model to explain the formation of ion crystals. This model...
Structural Studies On Bovine Pancreatic Phospholipase A2 And Proteins Involved In Molybdenum Cofactor Biosynthesis - Kanaujia, Shankar Prasad
We have carried out structural studies on bovine pancreatic phospholipase A2 (BPLA2) and two proteins involved in molybdenum cofactor (Moco) biosynthesis pathway. In addition, molecular-dynamics simulations and other analyses have been performed to corroborate the findings obtained from the crystal structures.
Crystal structures of the three active-site mutants (H48N, D49N and D49K) of BPLA2 were determined to understand the mechanism by which the mutant H48N is able to catalyze the reaction of phospholipid hydrolysis and to see the effect of the loss of Ca 2+ ion in the active site of D49N and D49K mutants. We found that Asp49 could...