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Parallel Progressive Multiple Sequence Alignment On Reconfigurable Meshes, Ken Nguyen, Yi Pan, Ge Nong

Computer Science Faculty Publications

Background: One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing extensive task. In addition, the advancement in DNA/RNA and Protein sequencing techniques has created a vast amount of sequences to be analyzed that exceeding the capability of traditional computing models. Therefore, an effective parallel multiple sequence alignment model capable of resolving these issues is in a great demand.

Results: We design O(1) run-time solutions …

Bead Modeling Of Transport Properties Of Macromolecules In Free Solution And In A Gel, Hongxia Pei

Chemistry Dissertations

On the bead modeling methodology, or BMM, a macromolecule is modeled as a rigid, non-overlapping bead array with arbitrary radii. The BMM approach was pioneered by Kirkwood and coworkers (Kirkwood, J.G., Macromolecules, E.P. Auer (Ed.), Gordon and Breach, New York, 1967; Kirkwood, J.G., Riseman, J., J. Chem. Phys., 1948, 16, 565) and applied to such transport properties as diffusion, sedimentation, and viscosity. With the availability of computers, a number of investigators extended the work to account for the detailed shape of biomolecules in the 1970s. A principle objective of my research has been to apply the BMM approach to more …

Design And Synthesis Of Boronic Acid-Modified Nucleotides For Fluorescent Sensing And Cell Imaging, Xiaochuan Yang

Chemistry Dissertations

With the rapidly increasing interest in the field of glycomics, which is the comprehensive study of the roles carbohydrates play in a living system, urgent need for developing quick and highly selective carbohydrate sensors is growing. The boronic acid group, with its electron-deficient structure (6 valence electrons with an open shell), acts as a Lewis acid with high intrinsic affinity towards Lewis bases such as fluoride, cyanide and hydroxyl groups. Specifically, formation of a 5- or 6- membered ring between the boronic acid moiety and a1,2- or 1,3-diol in aqueous solution has been fully explored as a strategy of carbohydrate …

Synthesis, Structure And Function Studies Of Selenium And Tellurium Derivatized Nucleic Acids, Jia Sheng

Chemistry Dissertations

Nucleic acids play important roles in living systems by storing and transferring genetic information and directing protein synthesis. Recently, it was found that nucleic acids can catalyze chemical and biochemical reactions similar to protein enzymes. In addition, they can also serve as drug targets for the treatment of deadly diseases such as AIDS and cancers. As a result, the 3D structure study of nucleic acids and proteinnucleic acids complexes by X-ray crystallography has become one of the most active research areas. However, the two intrinsic bottlenecks of macromolecule X-ray crystallography, including crystallization and phase determination, have significantly limited its application …

X-Irradiation Of Dna Components In The Solid State: Experimental And Computational Studies Of Stabilized Radicals In Guanine Derivatives, Nayana Kumudini Jayatilaka

Physics and Astronomy Dissertations

Single crystals of sodium salt of guanosine dihydrate and 9 Ethyl Guanine were X-irradiated with the objective of identifying the radical products. Study with K-band EPR, ENDOR, and ENDOR-Induced EPR techniques indicated at least four radical species to appear in both crystals in the temperature range of 6K to room temperature. Three of these radicals (Radicals R1, R2, and R3) were present immediately after irradiation at 6K. Computational chemistry and EPR spectrum simulation methods were also used to assist in radical identifications. Radical R1, the product of net hydrogen addition to N7, and Radical R2, the product of electron loss …