Current Search:   Raley, Elizabeth Anne (x)

View All Items

  • CSV Spreadsheet
(1 - 2 of 2)
Gapless alignment revisited
Title
Gapless alignment revisited.
Creator
Raley, Elizabeth Anne, Florida Atlantic University, Yu, Yi-Kuo
Abstract/Description
The purpose of sequence alignment is to detect mutual similarity, characterized by the so-called "alignment score", between sequences compared. To quantitatively assess the confidence level of an alignment result requires the knowledge of alignment score statistics under a certain null model and is the central issue in sequence alignment. In this thesis, the score statistics of Markov null model were revisited and the score statistics of non-Markov null model were investigated for two state...
Show moreThe purpose of sequence alignment is to detect mutual similarity, characterized by the so-called "alignment score", between sequences compared. To quantitatively assess the confidence level of an alignment result requires the knowledge of alignment score statistics under a certain null model and is the central issue in sequence alignment. In this thesis, the score statistics of Markov null model were revisited and the score statistics of non-Markov null model were investigated for two state-of-the-art algorithms, namely, the gapless Smith-Waterman and Hybrid algorithms. These two algorithms were further used to find highly related signals in unrelated sequences and in weakly related sequences corresponding, respectively, to Markov null model and non-Markov null model. The confidence levels of these models were also studied. Since the sequence similarity we are interested in comes from evolutionary history, we also investigated the relationship between sequence alignment, the tool to find similarity, and evolution. The average evolution distance between the daughter sequences was found and compared with their expected values, for individual trees and as an average over many trees.
Show less
Date Issued
2001
PURL
http://purl.flvc.org/fcla/dt/12856
Subject Headings
Bioinformatics, Amino acid sequence--Databases, Markov processes
Format
Document (PDF)
Analysis of fluid instabilities in core collapse supernova progenitors by a semi-analytical methodology and by two dimensional radiation-hydrodynamical simulations
Title
Analysis of fluid instabilities in core collapse supernova progenitors by a semi-analytical methodology and by two dimensional radiation-hydrodynamical simulations.
Creator
Raley, Elizabeth Anne, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Physics
Abstract/Description
We have performed an analysis of fluid instabilities below the neutrinospheres of the collapsed cores of supernova progenitors using a methodology introduced by Bruenn and Dineva [28, 29, 31]. In an extensive survey we found that the rate of lepton diffusion always exceeds the rate of thermal diffusion and as a result we do not anywhere see the neutron finger instability as described by the Livermore group [16, 17]. A new instability, lepto-entropy fingers, extending from a radius of 10--15...
Show moreWe have performed an analysis of fluid instabilities below the neutrinospheres of the collapsed cores of supernova progenitors using a methodology introduced by Bruenn and Dineva [28, 29, 31]. In an extensive survey we found that the rate of lepton diffusion always exceeds the rate of thermal diffusion and as a result we do not anywhere see the neutron finger instability as described by the Livermore group [16, 17]. A new instability, lepto-entropy fingers, extending from a radius of 10--15 km out to the vicinity of the neutrinosphere, driven by the cross-response functions (i.e. the dependence of lepton transport on entropy perturbations and vice versa) was discovered. This instability has a maximum growth rate of the order of 100 s-1 with a scale of approximately 1/20 the distance of a perturbed fluid element from the core center [18]. This instability has probably already been seen in some multi-dimensional core collapse calculations. To test our results predicting the presence of doubly diffusive instabilities below the neutrinosphere of a proto-supernova, we have performed two dimensional hydrodynamic simulations with radial ray neutrino transport. This entailed rewriting RadHyd, which is the merger of EVH-1 hydrodynamics and MGFLD neutrino transport developed by Bruenn and DiNisco [43], for two dimensions. In particular, hydrodynamic evolution along angular arrays was included, as was MPI message passing capabilities, in order to utilize massively parallel computer platform such as FAU's BOCA4 Beowulf cluster. This work was partially funded by a grant from the DOE Office of Science, Scientific Discovery through Advanced Computing Program.
Show less
Date Issued
2004
PURL
http://purl.flvc.org/fcla/dt/12094
Subject Headings
Physics, Astronomy and Astrophysics
Format
Document (PDF)