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Author:

Carado, Anthony James

Title:

New Instrumental Developments in Cluster ToF-SIMS

Graduate Program:

Chemistry

Keywords:

c60
cluster tof-sims
orthogonal tof-sims

File:

Download complete_thesis5.pdf

Committee Members:

Nicholas Winograd, Dissertation Advisor/Co-Advisor
Nicholas Winograd, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
David Lawrence Allara, Committee Member
Robert Allen Schlegel, Committee Member

Author:

Szakal, Andrea

Title:

THE HEPATITIS DELTA VIRUS (HDV) RIBOZYME AS A MODEL FOR RNA CATALYSIS AND FOLDING

Graduate Program:

Chemistry

Keywords:

RNA folding
RNA catalysis

File:

Download Szakal_Doctoral_ThesisMaster_041508.pdf

Committee Members:

Sharon Hammes Schiffer, Committee Member
Christine Dolan Keating, Committee Member
Craig Eugene Cameron, Committee Member
Philip C. Bevilacqua, Committee Chair/Co-Chair

Author:

McGraw, Adam Philip

Title:

Protein-RNA interactions involved in regulation of the tryptophan biosynthesis operon (trpEDCFBA) in Bacillus subtilis

Graduate Program:

Chemistry

Keywords:

protein-RNA interactions
mRNA stability
TRAP
RNA structure

File:

Download AM_thesis_FINAL-2-101008.pdf

Committee Members:

Paul Lee Babitzke, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Chair/Co-Chair
Kenneth Charles Keiler, Committee Member
Christine Dolan Keating, Committee Member

Author:

Vu, Bao-Han Christie

Title:

Structural Characterization of the Truncated Hemoglobin from Synechocystis sp. PCC 6803

Graduate Program:

Chemistry

Keywords:

paramagnetic
nmr
truncated hemoglobin
hexacoordinate hemoglobin

File:

Download BCVU_Dissertation.pdf

Committee Members:

Juliette T J Lecomte, Committee Chair/Co-Chair
Alan James Benesi, Committee Member
Philip C. Bevilacqua, Committee Member
Joseph M Bollinger Jr., Committee Member

Author:

Borup, Birthe

Title:

Cysteine Biosynthesis and Sulfur Fixation in the Archaea

Graduate Program:

Chemistry

Keywords:

NifS
cysteine desulfuration
IscS

File:

Download Thesis.pdf

Committee Members:

James Gregory Ferry, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Juliette T J Lecomte, Committee Chair/Co-Chair
Joseph M Bollinger Jr., Committee Member

Author:

Lubner, Carolyn E

Title:

Direct Solar Hydrogen Production From Photosynthetic Nanoconstructs

Graduate Program:

Chemistry

Keywords:

molecular wire
hydrogenase
Photosystem I
solar energy
hydrogen

File:

Download Lubner_Dissertation_final.pdf

Committee Members:

John H Golbeck, Dissertation Advisor/Co-Advisor
John H Golbeck, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Christine Dolan Keating, Committee Member
Bruce Ernest Logan, Committee Member

Author:

Vuletich, David Andrew

Title:

A Phylogenetic and Structural Study of Truncated Hemoglobins

Graduate Program:

Chemistry

Keywords:

truncated hemoglobins
NMR
H/D exchange
Phylogeny
heme-protein crosslinking

File:

Download vuletichthesis.pdf

Committee Members:

Juliette Lecomte, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Michael Thomas Green, Committee Member
Donald Bryant, Committee Member
Lee Kump, Committee Member

Author:

Proctor, David James

Title:

Studies of the Molecular Origins of Thermodynamic Stability in RNA Secondary Structure

Graduate Program:

Chemistry

Keywords:

RNA
biophysics
structure
thermodynamics

File:

Download thesis.pdf

Committee Members:

Philip C. Bevilacqua, Committee Chair/Co-Chair
Juliette T J Lecomte, Committee Member
George I Makhatadze, Committee Member
Paul Lee Babitzke, Committee Member

Author:

Chakravorty, Dhruva Kumar

Title:

HYBRID QUANTUM/CLASSICAL MOLECULAR DYNAMICS SIMULATIONS OF HYDROGEN TRANSFER REACTIONS IN ENZYMES

Graduate Program:

Chemistry

Keywords:

DLPROTEIN
EVB
DHFR
ketosteroid isomerase
KSI
WHAM
Umbrella Integration
hydrogen transfer

File:

Download thesis15-1.pdf

Committee Members:

Prof Sharon Hammes Schiffer, Dissertation Advisor/Co-Advisor
Prof Sharon Hammes Schiffer, Committee Chair/Co-Chair
James Bernhard Anderson, Committee Member
Philip C. Bevilacqua, Committee Member
James David Kubicki, Committee Member

Author:

Moody, Ellen Marie

Title:

Stability in Nucleic Acid Hairpins: 1. Molecular Determinants of Cooperativity and 2. Linkage between Proton Binding and Folding

Graduate Program:

Chemistry

Keywords:

RNA
DNA
pKa shifting
cooperativity
expandability
thermodynamics

File:

Download EMM_thesis.pdf

Committee Members:

Philip C. Bevilacqua, Committee Chair/Co-Chair
Christopher Falzone, Committee Member
Juliette T J Lecomte, Committee Member
James Gregory Ferry, Committee Member

Author:

Whitman, Elisabeth E

Title:

Identification and Biophysical Characterization of Factors Influencing the Thermostability of Biological RNAs

Graduate Program:

Chemistry

Keywords:

RNA folding
macromolecular crowding

File:

Download Masters_Thesis.pdf

Committee Members:

Philip C. Bevilacqua, Thesis Advisor/Co-Advisor
Philip C. Bevilacqua, Thesis Advisor/Co-Advisor

Author:

Knappenberger, Jane A

Title:

MODULATION OF THERMODYNAMIC AND KINETIC PROPERTIES IN b HEMOPROTEINS: CHARACTERIZATION OF A FAMILY OF PsaE-CYTOCHROME b5 CHIMERAS AND SYNECHOCYSTIS sp. PCC 6803 HEMOGLOBIN

Graduate Program:

Chemistry

Keywords:

b hemoproteins
thermodynamic stability
urea-gradient gel electrophoresis
folding kinetics
loop anchor modification

File:

Download thesis.pdf

Committee Members:

Juliette T J Lecomte, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Alan James Benesi, Committee Member
B Tracy Nixon, Committee Member

Author:

Keighron, Jacqueline D

Title:

NANOPARTICLE BIOCONJUGATES AS “BOTTOM-UP” ASSEMBLIES OF ARTIFICAL MULTIENZYME COMPLEXES

Graduate Program:

Chemistry

Keywords:

multienzyme complex
specific activity
bioconjugate

File:

Download keighronfinal.pdf

Committee Members:

Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Christine Dolan Keating, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Scott A Showalter, Committee Member
Peter J Butler, Committee Member

Author:

Sokoloski, Joshua Edward

Title:

Calorimetric Studies of Site-Specific Ligand Binding By RNA

Graduate Program:

Chemistry

Keywords:

Isothermal Titration Calorimetry
RNA

File:

Download JES_Sokoloski_Dissertation_F11_Corrected.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Scott A Showalter, Committee Member
David Lawrence Allara, Committee Member
Song Tan, Committee Member

Author:

Younker, Jarod Michael

Title:

Development and Application of Optimizations in Computational Chemistry

Graduate Program:

Chemistry

Keywords:

Chloroperoxidase
P450
Rate Equations
Principal Components Analysis
Numerical Optimizations
Adomian Decomposition
Density Functional Theory
Ribonucleotide Reductase

File:

Download JarodYounker-Dissertation.pdf

Committee Members:

Michael Thomas Green, Dissertation Advisor/Co-Advisor
Michael Thomas Green, Committee Chair/Co-Chair
Joseph M Bollinger Jr., Committee Member
Carsten Krebs, Committee Member
Philip C. Bevilacqua, Committee Member
James David Kubicki, Committee Member

Author:

Blose, Joshua Matthew

Title:

ELUCIDATING THERMODYNAMIC RELATIONSHIPS IN THE RNA STRUCTURAL HIERARCHY: MOLECULAR ORIGINS OF STABILITY

Graduate Program:

Chemistry

Keywords:

Cooperative Folding
Thermophilic Adaptation
Tetraloop
RNA
Nonlinear Poisson-Boltzmann
NLPB
Electrostatics

File:

Download JMB_Dissertation_082009.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Sharon Hammes Schiffer, Committee Member
Tae Hee Lee, Committee Member
Kenneth Charles Keiler, Committee Member

Author:

Cederquist, Kristin Baine

Title:

Hairpin Nucleic Acid Probes for Metal Nanowire-Based Surface Studies and Biosensing.

Graduate Program:

Chemistry

Keywords:

surface characterization
spectroscopy
nanotechnology
fluorescence
bioconjugate synthesis
biochemical interactions
bioassays
multiplexed sensing

File:

Download kbcederquist_dissertation.pdf

Committee Members:

Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Christine Dolan Keating, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Thomas E Mallouk, Committee Member
James Hansell Adair, Committee Member

Author:

Krise, Keith Michael

Title:

THE EFFECTS OF MICROVISCOSITY, BOUND WATER AND PROTEIN MOBILITY ON THE RADIOLYSIS AND SONOLYSIS OF HEN EGG WHITE

Graduate Program:

Chemistry

Keywords:

egg white protein
sonolysis
radiolysis
pulse radiolysis
diffusion-controlled reaction
microviscosity
bound water

File:

Download Krise_Dissertation_final.pdf

Committee Members:

Bratoljub Milosavljevic, Dissertation Advisor/Co-Advisor
Bratoljub Milosavljevic, Committee Chair/Co-Chair
Alan James Benesi, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Mark Maroncelli, Committee Member
Gary Lee Catchen, Committee Member

Author:

Heinicke, Laurie Ann

Title:

Regulation of the protein kinase PKR by higher-order RNA secondary and tertiary structures

Graduate Program:

Chemistry

Keywords:

innate immune response
kinase
RNA
PKR

File:

Download Heinicke_04_26_10_Thesis.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Christine Dolan Keating, Committee Member
Scott A Showalter, Committee Member
Andrey S Krasilnikov, Committee Member

Author:

Levine, Lauren Aimee

Title:

Demonstrating the versatility of the iDNA scaffold: New synthetic strategies and applications

Graduate Program:

Chemistry

Keywords:

artifical peptides
metal-binding

File:

Download LaurenFinalThesis.pdf

Committee Members:

Mary Elizabeth Williams, Dissertation Advisor/Co-Advisor
Mary Elizabeth Williams, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Scott A Showalter, Committee Member
John H Golbeck, Committee Member

Author:

Dillenback, Lisa

Title:

SELF-ASSEMBLY AND CONTROLLED ASSEMBLY OF NANOPARTICLES

Graduate Program:

Chemistry

Keywords:

metal nanowire
nanowire assembly
nanoparticle assembly
DNA-directed assembly
self-assembly

File:

Download DillenbackThesisFinal.pdf

Committee Members:

Christine Dolan Keating, Committee Chair/Co-Chair
Thomas E Mallouk, Committee Member
Philip C. Bevilacqua, Committee Member
Theresa Stellwag Mayer, Committee Member

Author:

Dominak, Lisa M

Title:

ENCAPSULATION EFFICIENCY AND DYNAMIC MICROCOMPARTMENTATION WITHIN GIANT LIPID VESICLES

Graduate Program:

Chemistry

Keywords:

protein microcompartmentation
synthetic cells
macromolecular crowding
encapsulation efficiency
lipid vesicles
biomimetic chemistry

File:

Download LDominak_PhD_2009_final.pdf

Committee Members:

Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Christine Dolan Keating, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Anne M Andrews, Committee Member
Peter J Butler, Committee Member

Author:

Mullen, Melissa Ann

Title:

Arabidopsis thaliana under stress: Functional implications of G-quadruplex and non-coding RNA structure

Graduate Program:

Chemistry

Keywords:

RNA
Arabidopsis
G-quadruplex
drought stress

File:

Download Mullen_Thesis_071511.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Sarah Mary Assmann, Committee Chair/Co-Chair
Christine Dolan Keating, Committee Member
David D Boehr, Committee Member
Paul Lee Babitzke, Committee Member

Author:

Kumarasiri, Malika Dhananjaya

Title:

Anharmonic Effects of Small Clusters of Molecules and Ranking Activity of Protein Mutants

Graduate Program:

Chemistry

Keywords:

Molecular Dynamics
Mutant Studies

File:

Download Thesis_mdk.pdf

Committee Members:

Prof Sharon Hammes Schiffer, Dissertation Advisor/Co-Advisor
Sharon Hammes Schiffer, Committee Chair/Co-Chair
Will Castleman, Committee Member
Philip C. Bevilacqua, Committee Member
James David Kubicki, Committee Member

Author:

Santillo, Michael

Title:

Microfluidic systems for high-throughput single-cell assays

Graduate Program:

Chemistry

Keywords:

Microfluidics
lab-on-a-chip
confocal
fluorescence
cell assay
bioanalytical chemistry
computational fluid dynamics
CFD
PDMS

File:

Download mf_santillo_dissertation.pdf

Committee Members:

Andrew Ewing, Dissertation Advisor/Co-Advisor
Andrew Ewing, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Thomas E Mallouk, Committee Member
Andrew Zydney, Committee Member

Author:

Matthews, Megan Leigh

Title:

Protein Control of Dioxygen Activation, Substrate-Hydrogen Abstraction, and Ligand-Radical-Transfer Outcome in the Aliphatic Halogenase, SyrB2

Graduate Program:

Chemistry

Keywords:

oxygen activation
carbon-hydrogen bond activation
alpha-ketoglutarate
halogenation

File:

Download thesis_final.pdf

Committee Members:

J Martin Bollinger Jr And Carsten Krebs, Dissertation Advisor/Co-Advisor
Carsten Krebs, Committee Chair/Co-Chair
J Martin Bollinger Jr, Committee Chair/Co-Chair
Squire J Booker, Committee Member
Philip C. Bevilacqua, Committee Member
Christopher Albert Mullin, Committee Member

Author:

Siegfried, Nathan A.

Title:

Folding Cooperativity and Its Influence on pKa Shifting in Nucleic Acids

Graduate Program:

Chemistry

Keywords:

pKa shift
RNA
DNA
nucleic acids
cooperativity
acid base catalysis

File:

Download Siegfried_Thesis.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Squire J Booker, Committee Member
Scott A Showalter, Committee Member
Katsuhiko Murakami, Committee Member

Author:

Davis, Ronald B

Title:

Structural Characterization of Peptides Derived from the Sequence of Cytochrome b5

Graduate Program:

Chemistry

Keywords:

trifluoroethanol
N-cap
cytochrome
helical propensity

File:

Download Dissertation_of_Ron_Davis.pdf

Committee Members:

Dr Juliette Lecomte, Committee Chair/Co-Chair
Alan James Benesi, Committee Member
John H Golbeck, Committee Member
Philip C. Bevilacqua, Committee Member

Author:

Toroney, Rebecca

Title:

Investigating Roles of Unconventional RNA Primary, Secondary, and Tertiary Motifs in Regulation of the Protein Kinase PKR

Graduate Program:

Chemistry

Keywords:

Hepatitis C Virus
RNA-protein interactions
IRES
PKR
innate immunity
triphosphate

File:

Download Toroney_R_Thesis.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Nicholas Winograd, Committee Member
Scott A Showalter, Committee Member
Craig Eugene Cameron, Committee Member

Author:

Wu, Runzhi

Title:

SYNTHESIS OF NOVEL ANTIVIRAL AGENTS AND FLUORESCENT MOLECULAR PROBES

Graduate Program:

Chemistry

Keywords:

antiviral agent
nucleoside
fluorescent molecule

File:

Download Runzhi_Wu_Dissertation_071210.pdf

Committee Members:

Dr Blake R Peterson, Dissertation Advisor/Co-Advisor
Raymond Lee Funk, Committee Chair/Co-Chair
Blake R Peterson, Committee Member
Philip C. Bevilacqua, Committee Member
Gong Chen, Committee Member
Avery August, Committee Member

Author:

Rummel, Sheryl Ann

Title:

DESIGN, SYNTHESIS, AND EVALUATION OF SYNTHETIC MIMICS OF CELL SURFACE RECEPTORS

Graduate Program:

Chemistry

Keywords:

synthetic receptors
VEGF
calixarene
vancomycin

File:

Download SAR_ThesisMaster.pdf

Committee Members:

Blake R Peterson, Committee Chair/Co-Chair
Scott T Phillips, Committee Member
Philip C. Bevilacqua, Committee Member
Avery August, Committee Member

Author:

Reigh, Stephanie Ann

Title:

Syn Bases: Their Prevalence, Relevance, and Functional Utility in Functional RNA

Graduate Program:

Chemistry

Keywords:

RNA

File:

Download Reigh_Final_Thesis.pdf

Committee Members:

Philip C. Bevilacqua, Thesis Advisor/Co-Advisor
Philip C. Bevilacqua, Thesis Advisor/Co-Advisor

Author:

Brunker, Sarah Elizabeth

Title:

SURFACE IMMOBILIZED DNA FOR USE IN BIOSENSING

Graduate Program:

Chemistry

Keywords:

surfaces
encoded nanoparticles
polymerase chain reaction
ligase chain reaction
nucleic acids
biosensing
amplification
soft lithography
microcontact printing
general chemistry lab

File:

Download brunkerfinal.pdf

Committee Members:

Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Christine Dolan Keating, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Raymond Edward Schaak, Committee Member
James Hansell Adair, Committee Member

Author:

Morrow, Thomas J

Title:

Programmed Assembly of Biofunctionalized Nanowires for Biosensing Applications

Graduate Program:

Chemistry

Keywords:

Assembly
Nanowires
Dielectrophoresis
Photolithography
DNA

File:

Download Tom_Morrow_Final_Submitted_Thesis_etd.pdf

Committee Members:

Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Christine Dolan Keating, Committee Chair/Co-Chair
Mary Elizabeth Williams, Committee Member
Philip C. Bevilacqua, Committee Member
Theresa Stellwag Mayer, Committee Member

Author:

Wostenberg, Christopher William

Title:

The role of dsRBDs in the miRNA maturation pathway

Graduate Program:

Chemistry

Keywords:

dsRBD
miRNA
NMR
MD
DGCR8
Dicer
Drosha
IDP
FCP1
RAP74

File:

Download Thesis_final.pdf

Committee Members:

Scott A Showalter, Dissertation Advisor/Co-Advisor
Scott A Showalter, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
David D Boehr, Committee Member
Andrey S Krasilnikov, Committee Member

Author:

Zaccardi, Margot Joan

Title:

mechanistic analysis of the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase

Graduate Program:

Chemistry

Keywords:

indole-3-glycerol phosphate synthase
enzyme kinetics
mechanism of IGPS
thermophilic enzymes
enzyme engineering

File:

Download Zaccardi_Final.pdf

Committee Members:

David D Boehr, Dissertation Advisor/Co-Advisor
Scott A Showalter, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Craig Eugene Cameron, Special Member

Author:

Wilcox, Jennifer Lynn

Title:

Development and utilization of spectroscopic and chemical methodologies for investigating pKa shifting in nucleic acids

Graduate Program:

Chemistry

Keywords:

RNA
nucleic acids
2-aminopurine fluorescence
pKa shifting

File:

Download Wilcox_Thesis.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Squire J Booker, Committee Member
Scott A Showalter, Committee Member
Andrey S Krasilnikov, Committee Member

Author:

Cacace, David Neal

Title:

Biomimetic Mineralization of Calcium Carbonate in Aqueous Biphasic Systems

Graduate Program:

Chemistry

Keywords:

Aqueous two-phase systems
calcium carbonate
intermediate chelation
mineralization vesicles

File:

Download DNC_THESIS_FINAL.pdf

Committee Members:

Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Member
Scott A Showalter, Committee Member
James Hansell Adair, Committee Member

Author:

Kwok, Chun Kit

Title:

Structural and Functional Roles of RNA Structure in Regulatory Processes in Plants

Graduate Program:

Chemistry

Keywords:

RNA
RNA structure
RNA folding
Plants
Arabidopsis thaliana
G-quadruplex
regulation
DMS
SHAPE
LMPCR
Structure-Seq

File:

Download Thesis_CKK_2014.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Sarah Mary Assmann, Dissertation Advisor/Co-Advisor
Scott A Showalter, Committee Member
Tae Hee Lee, Committee Member
Song Tan, Committee Member

Author:

Strulson, Christopher A

Title:

toward understanding RNA structure, folding, and function in cells

Graduate Program:

Chemistry

Keywords:

RNA
ribozyme
molecular crowding
macromolecular crowding
catalysis
compartmentalization
folding cooperativity

File:

Download Christoper_Strulson_Thesis_Toward_Understanding_RNA__Structure_Folding_and_Function_in_Cells.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Squire J Booker, Committee Member
Tae Hee Lee, Committee Member
Kenneth Charles Keiler, Committee Member

Author:

Davis, Bradley William

Title:

Characterization of Intracellular Organization within Aqueous Biphasic Systems Serving as Cellular Mimics

Graduate Program:

Chemistry

Keywords:

aqueous phase separation
partitioning
sequential enzymes
coacervate
macromolecular crowding

File:

Download Davis_Bradley_PhD_dissertation.pdf

Committee Members:

Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Member
Scott A Showalter, Committee Member
Peter J Butler, Committee Member

Author:

Okur, Halil Ibrahim

Title:

Hofmeister Chemistry: weak Cation Binding To Protein Backbones & biomolecular Size Influence On Specific Ion Effects

Graduate Program:

Chemistry

Keywords:

Hofmeister
Ions
Aqueous Solution
Macromolecules

File:

Download Hofmeister_Chemistry-Halil_Okur.pdf

Committee Members:

Paul S Cremer, Dissertation Advisor/Co-Advisor
Paul S Cremer, Committee Chair/Co-Chair
John B Asbury, Committee Member
Philip C. Bevilacqua, Committee Member
Sheereen Majdzarringhalamaraghy, Committee Member

Author:

Nichol, Jessica Lee

Title:

Polyphosphazene Design, Synthesis, and Characterization for Potential Ligament and Tendon Scaffolds

Graduate Program:

Chemistry

Keywords:

polyphosphazene
biomedical
polymer
elastomer

File:

Download JLNichol_Dissertation.pdf

Committee Members:

Harry R Allcock, Dissertation Advisor/Co-Advisor
Benjamin James Lear, Committee Member
Philip C. Bevilacqua, Committee Member
Michael Anthony Hickner, Committee Member

Author:

Thaplyal, Pallavi

Title:

Investigations of the Mechanistic Pathways of the Hepatitis Delta Virus Ribozyme

Graduate Program:

Chemistry

Keywords:

Ribozyme
Kinetics
HDV
pKa
QM/MM
Thio Effects
Metal Ion Rescue

File:

Download Thesis_PTFinal.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Squire J Booker, Committee Member
Lasse Jensen, Committee Member
Katsuhiko Murakami, Special Member

Author:

Wei, Sijie

Title:

Nucleosome structure and dynamics studied with single-molecule methods

Graduate Program:

Chemistry

Keywords:

nucleosome breathing
CENP-A
dinucleosome
single molecule FRET
MLE
FCS
SUMO
Sumolyation

File:

Download Sijie_Wei_Thesis_V0414_final.pdf

Committee Members:

Tae Hee Lee, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Member
Christine Dolan Keating, Committee Member
Song Tan, Committee Member

Author:

Quarles, Kaycee Andrea

Title:

The Impact of Primary MicroRNA Structure on Recognition by the Microprocessor Complex in MicroRNA Maturation

Graduate Program:

Chemistry

Keywords:

RNA structure
Microprocessor
microRNA
protein binding
DGCR8
EMSA

File:

Download Thesis_KayceeAQuarles.pdf

Committee Members:

Scott A Showalter, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Member
Christine Dolan Keating, Committee Member
Katsuhiko Murakami, Committee Member

Author:

Dewey, Daniel Carroll

Title:

Kinetic Stabilization of Interfaces in Biologically Inspired Phase Systems

Graduate Program:

Chemistry

Keywords:

ATPS
aqueous biphasic systems
biomimetic
bioreactor
vesicle
emuslion

File:

Download Dewey_Daniel_PhD_disseration2.pdf

Committee Members:

Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Member
Scott A Showalter, Committee Member
Prof Peter Butler, Committee Member

Author:

Lewis, Gregory Gerald

Title:

Plastics and diagnostic assays with selective and sensitive macroscopic responses

Graduate Program:

Chemistry

Keywords:

diagnostics
assay
point-of-care
analytical
polymers
depolymerization
additive manufacturing

File:

Download GGL_Thesis_Final.pdf

Committee Members:

Scott T Phillips, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Member
Christine Dolan Keating, Committee Member
Enrique Daniel Gomez, Committee Member

Author:

Bastidas, Monique

Title:

Structural and functional characterization of the transcription factor Pdx1 and its interactions with DNA and proteins

Graduate Program:

Chemistry

Keywords:

protein binding
NMR
biophysical
homeodomain

File:

Download Bastidas_dissertation_2015.pdf

Committee Members:

Scott A Showalter, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Member
Christine Dolan Keating, Committee Member
David Scott Gilmour, Committee Member

Author:

Hull, Chelsea Michelle

Title:

Mechanistic Investigation Of Activation Of The Innate Immune Sensor Pkr By Various Levels And Types Of Rna Structure

Graduate Program:

Chemistry

Keywords:

PKR
RNA
bacterial RNA
riboswitch
ribozyme
innate immunity

File:

Download Hull_CM_2016.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Scott A Showalter, Committee Member
Christine Dolan Keating, Committee Member
Craig Eugene Cameron, Committee Member

Author:

Acevedo, Roderico

Title:

Investigation of protein-RNA interactions of the TAR-RNA-binding protein (TRBP)

Graduate Program:

Chemistry

Keywords:

Biophysics
Binding
TRBP
miRNA
RNAi

File:

Download Dissertation_RA.pdf

Committee Members:

Scott A Showalter, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Member
Craig Eugene Cameron, Committee Member
Amie Kathleen Boal, Committee Member
Ken S Feldman, Special Member

Author:

Boehm, Sarah Jane

Title:

Electric Field Directed Nanowire Assembly: Towards Reconfigurable Materials with Switchable Properties

Graduate Program:

Chemistry

Keywords:

gold
silica
dielectrophoresis
metamaterial
electrohydrodynamics
polarizer
lattice

File:

Download S_J_Boehm_Chemistry_Dissertation_2017.pdf

Committee Members:

Christine D. Keating, Dissertation Advisor/Co-Advisor
Christine D. Keating, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Paul S. Cremer, Committee Member
Douglas H. Wener, Outside Member

Author:

Gibbs, Eric Bryant

Title:

THE EFFECTS OF MULTI-SITE PHOSPHORYLATION ON THE STRUCTURE AND FUNCTION OF THE CARBOXYL-TERMINAL DOMAIN OF THE RNA POLYMERASE II LARGE SUBUNIT

Graduate Program:

Chemistry

Keywords:

IDP
RNAPII
CTD
Intrinsically Disordered Protein
NMR
SAXS
P-TEFb
Ssu72

File:

Download Eric_Bryant_Gibbs_Final_Dissertation.pdf

Committee Members:

Scott A. Showalter, Dissertation Advisor/Co-Advisor
Scott A. Showalter, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
William G. Noid, Committee Member
David Gilmour, Outside Member

Author:

Popczun, Nicholas James

Title:

FUNDAMENTAL STUDIES OF MOLECULAR SECONDARY ION MASS SPECTROMETRY IONIZATION PROBABILITY MEASURED WITH FEMTOSECOND, INFRARED LASER POST-IONIZATION

Graduate Program:

Chemistry

Keywords:

secondary ion mass spectrometry
secondary neutral mass spectrometry
mass spectrometry
time-of-flight
ionization
laser post-ionization
femtosecond
organic
surface science
ionization probability

File:

Download Final_Dissertation_NJPopczun_.pdf

Committee Members:

Nicholas Winograd, Dissertation Advisor/Co-Advisor
Nicholas Winograd, Committee Chair/Co-Chair
Barbara Jane Garrison, Committee Member
Philip C. Bevilacqua, Committee Member
Themis Matsoukas, Outside Member

Author:

Frankel, Erica Ann

Title:

Towards Investigation of RNA Catalysis and Compartmentalization

Graduate Program:

Chemistry

Keywords:

RNA
Catalysis
Compartmentalization
Cooperativity
Origins of Life

File:

Download Frankel_Dissertation_Final.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Scott A Showalter, Committee Member
Amie Kathleen Boal, Committee Member
James Kasting, Outside Member
Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Christine Dolan Keating, Committee Chair/Co-Chair

Author:

O'Rourke, Kathleen Faye

Title:

CONFORMATIONAL DYNAMICS AND LONG-RANGE INTERACTIONS IN TRYPTOPHAN BIOSYNTHETIC ENZYMES

Graduate Program:

Chemistry

Keywords:

tryptophan synthase
indole-3-glycerol phosphate synthase
enzyme
conformational dynamics
long-range interactions

File:

Download KFO_dissertation_final.pdf

Committee Members:

David D Boehr, Dissertation Advisor/Co-Advisor
David D Boehr, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Joseph M Bollinger Jr., Committee Member
John H Golbeck, Outside Member

Author:

Bingaman, Jamie Lee

Title:

Identification of novel catalytic strategies of small ribozymes

Graduate Program:

Chemistry

Keywords:

ribozyme
glmS
RNA
catalysis

File:

Download Bingaman_dissertation_2017.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Squire J Booker, Committee Member
David D Boehr, Committee Member
Song Tan, Outside Member

Author:

Leininger, Sarah Elizabeth

Title:

Co-translationally folding proteins generate tensile forces that are determined by the stability and topology of the domain

Graduate Program:

Chemistry

Keywords:

tensile force
cotranslational folding

File:

Download SLeininger_Thesis_v4.pdf

Committee Members:

Edward Patrick O'Brien Jr., Thesis Advisor/Co-Advisor
William George Noid, Committee Member
Philip C. Bevilacqua, Committee Member
William O Hancock, Committee Member