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You searched for +publisher:"Vanderbilt University" +contributor:("Prasad Polavarapu"). Showing records 1 – 3 of 3 total matches.

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Vanderbilt University

1. Covington, Cody Lance. Chiroptical Spectroscopic Studies on Surfactants, Other Aggregating Systems, and Natural Products.

Degree: PhD, Chemistry, 2016, Vanderbilt University

Recent experimental studies have shown unexpected chiroptical response from some chiral surfactant molecules. In these cases, the magnitude of the specific optical rotation was seen to change as a function of surfactant concentration, which is considered to be due to molecular aggregation and contrary to that known for typical organic molecules. To explain these experimental results on the +10,000 atom surfactant systems, non-traditional methods are necessary. To that end, a large number of molecular dynamics simulations, quantum mechanical calculations, and extensive analysis have been performed on a model system, the lauryl ester of phenylalanine. Monomer-dimer equilibrium, representing the simplest form of aggregation, and its influence on the Horeau effect, have also been investigated using pantolactone and 2-hydroxy-3-pinanone as test cases. Also a novel chiroptical spectral analysis method utilizing the Dissymmetry Factor (DF) spectrum has been developed. Studies ranging from rigid to flexible molecules have demonstrated the advantages of the DF method, especially when several diastereomers are involved. Using the DF spectrum as an additional means of analysis, the previously undetermined absolute configurations of four natural products have been determined. Advisors/Committee Members: Timothy Hanusa (committee member), Terry Lybrand (committee member), Janet Macdonald (committee member), Kalman Varga (committee member), Prasad Polavarapu (Committee Chair).

Subjects/Keywords: chiroptical spectroscopy

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Covington, C. L. (2016). Chiroptical Spectroscopic Studies on Surfactants, Other Aggregating Systems, and Natural Products. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/11624

Chicago Manual of Style (16th Edition):

Covington, Cody Lance. “Chiroptical Spectroscopic Studies on Surfactants, Other Aggregating Systems, and Natural Products.” 2016. Doctoral Dissertation, Vanderbilt University. Accessed April 20, 2021. http://hdl.handle.net/1803/11624.

MLA Handbook (7th Edition):

Covington, Cody Lance. “Chiroptical Spectroscopic Studies on Surfactants, Other Aggregating Systems, and Natural Products.” 2016. Web. 20 Apr 2021.

Vancouver:

Covington CL. Chiroptical Spectroscopic Studies on Surfactants, Other Aggregating Systems, and Natural Products. [Internet] [Doctoral dissertation]. Vanderbilt University; 2016. [cited 2021 Apr 20]. Available from: http://hdl.handle.net/1803/11624.

Council of Science Editors:

Covington CL. Chiroptical Spectroscopic Studies on Surfactants, Other Aggregating Systems, and Natural Products. [Doctoral Dissertation]. Vanderbilt University; 2016. Available from: http://hdl.handle.net/1803/11624


Vanderbilt University

2. Heinze, Sten. Improvements to BCL::Fold de novo Protein Structure Prediction.

Degree: PhD, Chemistry, 2015, Vanderbilt University

Proteins play a pivotal role in the functions of a cell. Structural information about proteins facilitates the understanding of their function. Limitations of experimental methods make it difficult to determine the structure experimentally for certain proteins. Structure prediction methods and other approaches to derive information from existing experimental data can aid in elucidating protein structure and guide further experiments. BCL::Align is a multiple sequence alignment tool using a dynamic programming algorithm. Its customizable scoring function is a weighted sum of different scoring terms that can be tailored for different applications. Optimal weights for sequence alignment and fold recognition were determined by a Monte Carlo optimization. In a comparison with other methods, BCL::Align ranked best in alignment accuracy with a Cline score of 22.90 for the SABmark Twilight Zone reference set. The de novo protein structure prediction method BCL::Fold was tested in the Critical Assessment of Structure Prediction (CASP) experiment. Of 18 proteins, BCL::Fold sampled the topology correctly for 11 respectively 12 proteins, measured by topology score > 0.8 respectively GDT_TS > 33%. Analysis of models at the different steps resulted in the identification of non-native conformations for loops and beta sheets. Filtering of models by the new loop angle scoring term enriched for native-like models. Small Angle X-ray scattering (SAXS) experiments provide low-resolution information about a protein’s shape. While insufficient to obtain an atomic resolution protein structure, it can be used in BCL::Fold to focus the sampling on models that agree with the SAXS data. Receiver operator characteristic (ROC) curve analysis resulted in an Area under the curve (AUC) of 0.9264 showing that topologies can be discriminated even for BCL models with a reduced representation. In a folding benchmark, using SAXS data improved models. Filtering models by agreement with SAXS data enriches for correct models; and building models with SAXS data yields models that are more native like. Advisors/Committee Members: Andes Hess (committee member), Prasad Polavarapu (committee member), Terry Lybrand (committee member), Jarrod Smith (committee member), Jens Meiler (Committee Chair).

Subjects/Keywords: SABmark; Cline; BCL::Fold; CASP; Topology score; loop predictions; sheet alignment; SAXS; Debye; sequence analysis; BCL::Align; sequence alignment

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Heinze, S. (2015). Improvements to BCL::Fold de novo Protein Structure Prediction. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/12144

Chicago Manual of Style (16th Edition):

Heinze, Sten. “Improvements to BCL::Fold de novo Protein Structure Prediction.” 2015. Doctoral Dissertation, Vanderbilt University. Accessed April 20, 2021. http://hdl.handle.net/1803/12144.

MLA Handbook (7th Edition):

Heinze, Sten. “Improvements to BCL::Fold de novo Protein Structure Prediction.” 2015. Web. 20 Apr 2021.

Vancouver:

Heinze S. Improvements to BCL::Fold de novo Protein Structure Prediction. [Internet] [Doctoral dissertation]. Vanderbilt University; 2015. [cited 2021 Apr 20]. Available from: http://hdl.handle.net/1803/12144.

Council of Science Editors:

Heinze S. Improvements to BCL::Fold de novo Protein Structure Prediction. [Doctoral Dissertation]. Vanderbilt University; 2015. Available from: http://hdl.handle.net/1803/12144


Vanderbilt University

3. Blodgett, Jordan Danielle. Novel methods in chromatographic separations: new chiral stationary phases and molecular tagging.

Degree: PhD, Chemistry, 2004, Vanderbilt University

CHEMISTRY NOVEL METHODS IN CHROMATOGRAPHIC SEPARATIONS: NEW CHIRAL STATIONARY PHASES AND MOLECULAR TAGGING JORDAN DANIELLE HANEY BLODGETT Dissertation under the direction of Professor David M. Hercules A major obstacle for many chemists is the retrieval of desired compounds from a mixture resulting from a chemical reaction or from a complex analytical sample. Even more challenging is the need to separate enantiomers of the same compound from each other. In the past the determination of chiral selectors for chiral HPLC has largely been an empirical process requiring large amounts of time in order to develop new selectors for difficult separations. It is therefore of great importance to pursue methods for faster screening of selectors for a given analyte. We report a powerful method for the screening of peptide-based chiral selectors in a high-throughput manner using parallel combinatorial library technology. In addition, since the practical synthesis of organic compounds is limited not only by yield of specific reactions but also by the ability to isolate products efficiently, strategies to facilitate product isolation are an important development. A new tagging system based on the interaction of beta-cyclodextrin and the 4-tert-butylphenyl group will be described to address this need. Advisors/Committee Members: Ned A. Porter (committee member), Prasad Polavarapu (committee member), David W. Wright (committee member), David M. Hercules (Committee Chair).

Subjects/Keywords: chiral chromatography; separation tagging; solid phase synthesis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Blodgett, J. D. (2004). Novel methods in chromatographic separations: new chiral stationary phases and molecular tagging. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14462

Chicago Manual of Style (16th Edition):

Blodgett, Jordan Danielle. “Novel methods in chromatographic separations: new chiral stationary phases and molecular tagging.” 2004. Doctoral Dissertation, Vanderbilt University. Accessed April 20, 2021. http://hdl.handle.net/1803/14462.

MLA Handbook (7th Edition):

Blodgett, Jordan Danielle. “Novel methods in chromatographic separations: new chiral stationary phases and molecular tagging.” 2004. Web. 20 Apr 2021.

Vancouver:

Blodgett JD. Novel methods in chromatographic separations: new chiral stationary phases and molecular tagging. [Internet] [Doctoral dissertation]. Vanderbilt University; 2004. [cited 2021 Apr 20]. Available from: http://hdl.handle.net/1803/14462.

Council of Science Editors:

Blodgett JD. Novel methods in chromatographic separations: new chiral stationary phases and molecular tagging. [Doctoral Dissertation]. Vanderbilt University; 2004. Available from: http://hdl.handle.net/1803/14462

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