You searched for +publisher:"Georgia Tech" +contributor:("David Sherrill").
Showing records 1 – 10 of
10 total matches.
No search limiters apply to these results.
1.
Clark, Craig R.
Sympathetic heating and cooling of trapped atomic and molecular ions.
Degree: PhD, Chemistry and Biochemistry, 2012, Georgia Tech
URL: http://hdl.handle.net/1853/43757 
► Laser-cooled atomic ions have led to an unprecedented amount of control over the quantum states of matter. The Coulombic interaction allows for information to be…
(more)
▼ Laser-cooled atomic ions have led to an unprecedented amount of control over the quantum states of matter. The Coulombic interaction allows for information to be transferred between neighboring ions, and this interaction can be used to entangle qubits for logic operations in quantum information processors. The same procedure for logic operations can be used for high resolution atomic spectroscopy, and is the basis for the most accurate atomic optical clocks to date. This thesis describes how laser-cooled atomic ions can impact physical chemistry through the development of molecular ion spectroscopy techniques and the simulation of magnetic systems by ion trap quantum computers.
A new technique developed for spectroscopy, Sympathetic Heating Spectroscopy (SHS), takes advantage of the Coulombic interaction between two trapped ions: the control ion and a spectroscopy ion. SHS uses the back action of the interrogating laser to map spectroscopy ion information onto the Doppler shift of the control ion for measurement. SHS only requires Doppler cooling of the ions and fluorescence measurement and represents a simplification of quantum logic spectroscopy. This technique is demonstrated on two individual isotopes of calcium: Ca-40(+) for cooling and Ca-44(+) as the spectroscopy ion.
Having demonstrated SHS with atomic ions, the next step was to extend the technique by loading and characterizing molecular ions. The identification of an unknown molecular ion is necessary and can be achieved by monitoring the change in motion of the two ion crystal, which is dependent on the molecular ion mass. The motion of two trapped ions is described by their normal modes, which can be accurately measured by performing resolved sideband spectroscopy of the S(1/2)-D(5/2) transition of calcium. The resolved sidebands can be used to identify unknown ions (atomic and molecular) by calculating the mass based on the observed value in axial normal mode frequencies. Again, the trapped molecular ion is sympathetically cooled via the Coulombic interaction between the Ca-40(+) and the unknown molecular ion. The sensitivity of SHS could be improved by implementing sympathetic sideband cooling and determining the heating by measuring single quanta of motion.
The ultimate limit of control would be the development of an ion trap quantum computer. Many theoretical quantum computing researchers have made bold claims of the exponential improvement a quantum computer would have over a classical computer for the simulation of physical systems such as molecules. These claims are true in principle for ideal systems, but given non-ideal components it is necessary to consider the scaling due to error correction. An estimate of the resource requirements, the total number of physical qubits and computational time, required to compute the ground state energy of a 1-D quantum Transverse Ising Model (TIM) of N spin-1/2 particles, as a function of the system size and the numerical precision, is presented. This estimate is based on analyzing…
Advisors/Committee Members: Kenneth R. Brown (Committee Chair), Alex Kuzmich (Committee Member), David Sherrill (Committee Member), Jean-Luc Bredas (Committee Member), Richart Slusher (Committee Member).
Subjects/Keywords: Ion trap; Spectroscopy; Quantum computing; Atomic and molecular physics; Chemistry; Trapped ions; Ions; Quantum theory; Chemistry, Physical and theoretical
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Clark, C. R. (2012). Sympathetic heating and cooling of trapped atomic and molecular ions. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/43757
Chicago Manual of Style (16th Edition):
Clark, Craig R. “Sympathetic heating and cooling of trapped atomic and molecular ions.” 2012. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/43757.
MLA Handbook (7th Edition):
Clark, Craig R. “Sympathetic heating and cooling of trapped atomic and molecular ions.” 2012. Web. 26 Jan 2021.
Vancouver:
Clark CR. Sympathetic heating and cooling of trapped atomic and molecular ions. [Internet] [Doctoral dissertation]. Georgia Tech; 2012. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/43757.
Council of Science Editors:
Clark CR. Sympathetic heating and cooling of trapped atomic and molecular ions. [Doctoral Dissertation]. Georgia Tech; 2012. Available from: http://hdl.handle.net/1853/43757
2.
Ozer, Gungor.
Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives.
Degree: PhD, Chemistry and Biochemistry, 2011, Georgia Tech
URL: http://hdl.handle.net/1853/39577
► In this thesis, we have advanced a set of distinct bioinformatic and computational tools to address the structure and function of proteins. Using data mining…
(more)
▼ In this thesis, we have advanced a set of distinct bioinformatic and computational tools to address the structure and function of proteins. Using data mining of the protein data bank (PDB), we have collected statistics connecting the propensity between the protein sequence and the secondary structure. This new tool has enabled us to evaluate new structures as well as a family of structures. A comparison of the wild type staphylococcal nuclease to various mutants using the proposed tool has indicated long-range conformational deviations spatially distant from the mutation point. The energetics of protein unfolding has been studied in terms of the forces observed in molecular dynamics simulations. An adaptive integration of the steered molecular dynamics is proposed to reduce ground state dominance by the rare low energy trajectories on the estimated free energy profile. The proposed adaptive algorithm is utilized to reproduce the potential of mean force of the stretching of decaalanine in vacuum at lower computational cost. It is then used to construct the potential of mean force of this transition in solvent for the first time as to observe the hydration effect on the helix-coil transformation. Adaptive steered molecular dynamics is also implemented to obtain the free energy change during the unfolding of neuropeptide Y and to confirm that the monomeric form of neuropeptide Y adopts halical-hairpin like pancreatic-polypeptide fold.
Advisors/Committee Members: Rigoberto Hernandez (Committee Chair), C. David Sherrill (Committee Member), Jean-Luc Brédas (Committee Member), Joseph Perry (Committee Member), Stephen Harvey (Committee Member).
Subjects/Keywords: Adaptive steered molecular dynamics; Neuropeptide; Proteins Analysis; Proteins Structure; Algorithms; Proteins Denaturation; Molecular dynamics
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Ozer, G. (2011). Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/39577
Chicago Manual of Style (16th Edition):
Ozer, Gungor. “Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives.” 2011. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/39577.
MLA Handbook (7th Edition):
Ozer, Gungor. “Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives.” 2011. Web. 26 Jan 2021.
Vancouver:
Ozer G. Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives. [Internet] [Doctoral dissertation]. Georgia Tech; 2011. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/39577.
Council of Science Editors:
Ozer G. Understanding protein structure and dynamics: from comparative modeling point of view to dynamical perspectives. [Doctoral Dissertation]. Georgia Tech; 2011. Available from: http://hdl.handle.net/1853/39577
Georgia Tech
3.
Akin, Myles.
Site specific thermodynamic study of OH radical addition to DNA bases.
Degree: MS, Nuclear Engineering/Medical Physics, 2010, Georgia Tech
URL: http://hdl.handle.net/1853/33919
► In medical and health physics, we are interested in the effects of ionizing radiation on biological systems, in particular, human biology. The main process by…
(more)
▼ In medical and health physics, we are interested in the effects of ionizing radiation on biological systems, in particular, human biology. The main process by which ionizing radiations causes damage to biological systems, is through the creation of radicals close to DNA strands. The radicals are very reactive and those created within close proximity to DNA will react with the DNA causing damage, in particular single strand or double strand breaks. This damage to the DNA can cause mutations that can kill the cell, either mitotically or apoptotically, or possibly lead to a cancerous formation. Therefore it is important to study how these radicals interact with DNA strands for a correlation between the resultant products of radical reactions and DNA strand breaks. For this study, we look at the most important radical, the OH radical and it's addition to DNA bases. We will study, through quantum chemistry, the thermodynamics of OH radical addition to the four bases, Adenine, Guanine, Cytosine and Thymine. The Jaguar program developed by Schrodinger was used for DFT calculations of the Gibbs free energy of the addition. In addition, calculations for the partial charge, HOMO's and Fukui indices were calculated and compared to experiment.
Advisors/Committee Members: Chaitany Deo (Committee Chair), Chris Wang (Committee Member), David Sherrill (Committee Member), Sang Cho (Committee Member).
Subjects/Keywords: Hydroxyl radical; Biological radiation damage; Medical physics; Ionizing radiation; Radicals (Chemistry); DNA; Hydroxyl group
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Akin, M. (2010). Site specific thermodynamic study of OH radical addition to DNA bases. (Masters Thesis). Georgia Tech. Retrieved from http://hdl.handle.net/1853/33919
Chicago Manual of Style (16th Edition):
Akin, Myles. “Site specific thermodynamic study of OH radical addition to DNA bases.” 2010. Masters Thesis, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/33919.
MLA Handbook (7th Edition):
Akin, Myles. “Site specific thermodynamic study of OH radical addition to DNA bases.” 2010. Web. 26 Jan 2021.
Vancouver:
Akin M. Site specific thermodynamic study of OH radical addition to DNA bases. [Internet] [Masters thesis]. Georgia Tech; 2010. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/33919.
Council of Science Editors:
Akin M. Site specific thermodynamic study of OH radical addition to DNA bases. [Masters Thesis]. Georgia Tech; 2010. Available from: http://hdl.handle.net/1853/33919
Georgia Tech
4.
Arredondo, Melissa Gayle.
Zero-Dimensional Magnetite.
Degree: PhD, Chemistry and Biochemistry, 2006, Georgia Tech
URL: http://hdl.handle.net/1853/14151
► Low-dimensional magnetic systems are of interest due to several new effects and modifications that occur at sizes below the average domain grain boundary within the…
(more)
▼ Low-dimensional magnetic systems are of interest due to several new effects and modifications that occur at sizes below the average domain grain boundary within the bulk material. Molecule-like magnetite (Fe3O4) nanoparticles, with sizes ranging from one to two nm were synthesized and characterized in order to investigate new properties arising from quantum size effects. These small systems will provide opportunities to investigate magnetism of zero-dimension systems. A zero-dimensional object is usually called a quantum dot or artificial atom because its electronic states are few and sharply separated in energy, resembling those within an atom. Since the surface to volume ratio is the highest for zero-dimensional systems, most of the changes to magnetic behavior will be observed in ultra-fine magnetic particles. Chemically functional magnetic nanoparticles, comprised of a Fe3O4 magnetite core encased in a thin aliphatic carboxylate, have been prepared by sequential high temperature decomposition of organometallic compounds in a coordinating solvent. In this work, aliphatic carboxylic acid chain length, reaction temperature and duration were varied to produce small core diameters. In order to correlate size effects with changes in particle formation, it is important to have a through understanding of the structural components. This includes studies of the core size, surface effects, decomposition, electronic properties and magnetic behavior. Quantum size effects were observed in the (Fe3O4)X(carboxylate)Y monolayer protected clusters (MPCs) when the average core diameter was ≤ 2.0 nm, evidenced by a blue shifted absorbance band maxima, suggesting the onset of quantum confinement. These (Fe3O4)X(carboxylate)Y MPCs also posses a complex interplay between surface and finite size effects, which govern the magnetic properties of these zero-dimensional systems. These MPCs are all superparamagnetic above their blocking temperatures with total magnetic anisotropy values greater than the bulk value due to an increase in surface and magnetocrystalline anisotropy. A non-linear decrease in saturation magnetization (MS) [Bohr Magneton] per cluster) as a function of the reciprocal of core radius have been attributed to surface effects such as a magnetically inactive layer or an increase in spin disorder as core diameter decreases. The reduced core dimensions of these MPCs make them ideal candidates for further investigation of quantum magnetic systems.
Advisors/Committee Members: Robert Whetten (Committee Chair), Lawrence Bottomley, Walt De Heer, Mostafa El-Sayed, Uzi Landman, and David Sherrill (Committee Members).
Subjects/Keywords: Quantum magnetism; Quantum size effects; Magnetite; Nanoclusters; Nanoparticles; Superparamagnetism; Anisotropy; Magnetite; Nanoparticles; Paramagnetism; Quantum biochemistry; Surface chemistry
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Arredondo, M. G. (2006). Zero-Dimensional Magnetite. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/14151
Chicago Manual of Style (16th Edition):
Arredondo, Melissa Gayle. “Zero-Dimensional Magnetite.” 2006. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/14151.
MLA Handbook (7th Edition):
Arredondo, Melissa Gayle. “Zero-Dimensional Magnetite.” 2006. Web. 26 Jan 2021.
Vancouver:
Arredondo MG. Zero-Dimensional Magnetite. [Internet] [Doctoral dissertation]. Georgia Tech; 2006. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/14151.
Council of Science Editors:
Arredondo MG. Zero-Dimensional Magnetite. [Doctoral Dissertation]. Georgia Tech; 2006. Available from: http://hdl.handle.net/1853/14151
Georgia Tech
5.
Sinnokrot, Mutasem Omar.
Theoretical Investigations of pi-pi Interactions and Their Role in Molecular Recognition.
Degree: PhD, Chemistry and Biochemistry, 2004, Georgia Tech
URL: http://hdl.handle.net/1853/5019
► Noncovalent interactions are of pivotal importance in many areas of chemistry, biology, and materials science, and the intermolecular interactions involving aromatic rings in particular, are…
(more)
▼ Noncovalent interactions are of pivotal importance in many areas of chemistry, biology, and materials science, and the intermolecular interactions involving aromatic rings in particular, are fundamental to molecular organization and recognition processes. The work detailed in this thesis involves the application of state-of-the-art ab initio electronic structure theory methods to elucidate the nature of pi-pi interactions. The binding energies, and geometrical and orientational preferences of the simplest prototype of aromatic pi-pi interactions, the benzene dimer, are explored. We obtain the first converged values of the binding energies using highly accurate methods and large basis sets. Results from this study predict the T-shaped and parallel-displaced configurations of benzene dimer to be nearly isoenergetic.
The role of substituents in tuning pi-pi interaction is investigated. By studying dimers of benzene with various monosubstituted benzenes (in the sandwich and two T-shaped configurations), we surprisingly find that all of the substituted sandwich dimers considered bind more strongly than benzene dimer. We also find that these interactions can be tuned by a modest degree of substitution. Energy decomposition analysis using symmetry-adapted perturbation theory (SAPT) reveals that models based solely on electrostatic effects will have difficulty in reliably predicting substituent effects in pi-pi interactions.
Advisors/Committee Members: C. David Sherrill (Committee Chair), James A. Mulholland (Committee Member), Mostafa El-Sayed (Committee Member), Rigoberto Hernandez (Committee Member), Robert L. Whetten (Committee Member).
Subjects/Keywords: Perturbation theory; Benzene dimer; Pi-stacking; Non-covalent interactions; Ab initio methods; Quantum chemistry; Pi electron theory; Electronic structure; Perturbation (Quantum dynamics)
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Sinnokrot, M. O. (2004). Theoretical Investigations of pi-pi Interactions and Their Role in Molecular Recognition. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/5019
Chicago Manual of Style (16th Edition):
Sinnokrot, Mutasem Omar. “Theoretical Investigations of pi-pi Interactions and Their Role in Molecular Recognition.” 2004. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/5019.
MLA Handbook (7th Edition):
Sinnokrot, Mutasem Omar. “Theoretical Investigations of pi-pi Interactions and Their Role in Molecular Recognition.” 2004. Web. 26 Jan 2021.
Vancouver:
Sinnokrot MO. Theoretical Investigations of pi-pi Interactions and Their Role in Molecular Recognition. [Internet] [Doctoral dissertation]. Georgia Tech; 2004. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/5019.
Council of Science Editors:
Sinnokrot MO. Theoretical Investigations of pi-pi Interactions and Their Role in Molecular Recognition. [Doctoral Dissertation]. Georgia Tech; 2004. Available from: http://hdl.handle.net/1853/5019
Georgia Tech
6.
Sears, John Steven.
Minimalistic Descriptions of Nondynamical Electron Correlation: From Bond-Breaking to Transition-Metal Catalysis.
Degree: PhD, Chemistry and Biochemistry, 2007, Georgia Tech
URL: http://hdl.handle.net/1853/19807
► From a theoretical standpoint, the accurate description of potential energy surfaces for bond breaking and the equilibrium structures of metal-ligand catalysts are distinctly similar problems.…
(more)
▼ From a theoretical standpoint, the accurate description of potential energy surfaces for bond breaking and the equilibrium structures of metal-ligand catalysts are distinctly similar problems. Near degeneracies of the bonding and anti-bonding orbitals for the case of bond breaking and of the partially-filled d-orbitals for the case of metal-ligand catalyst systems lead to strong non-dynamical correlation effects. Standard methods of electronic structure theory, as a consequence of the single-reference approximation, are incapable of accurately describing the electronic structure of these seemingly different theoretical problems. The work within highlights the application of multi-reference methods, methods capable of accurately treating these near-degeneracies, for describing the bond-breaking potentials in several small molecular systems and the equilibrium structures of metal-salen catalysts. The central theme of this work is the ability of small, compact reference functions for accurately describing the strong non-dynamical correlation effects in these systems.
Advisors/Committee Members: C. David Sherrill (Committee Chair), Jean-Luc Bredas (Committee Member), Mostafa El-Sayed (Committee Member), Peter J. Ludovice (Committee Member), Thomas Orlando (Committee Member).
Subjects/Keywords: CASPT3; CASPT2; Multi-reference; DFT; CASSCF; Transition-metal; Bond-breaking; Theory; Electronic structure; Ligands; Transition metal complexes; Mathematical models; Chemistry, Physical and theoretical
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Sears, J. S. (2007). Minimalistic Descriptions of Nondynamical Electron Correlation: From Bond-Breaking to Transition-Metal Catalysis. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/19807
Chicago Manual of Style (16th Edition):
Sears, John Steven. “Minimalistic Descriptions of Nondynamical Electron Correlation: From Bond-Breaking to Transition-Metal Catalysis.” 2007. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/19807.
MLA Handbook (7th Edition):
Sears, John Steven. “Minimalistic Descriptions of Nondynamical Electron Correlation: From Bond-Breaking to Transition-Metal Catalysis.” 2007. Web. 26 Jan 2021.
Vancouver:
Sears JS. Minimalistic Descriptions of Nondynamical Electron Correlation: From Bond-Breaking to Transition-Metal Catalysis. [Internet] [Doctoral dissertation]. Georgia Tech; 2007. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/19807.
Council of Science Editors:
Sears JS. Minimalistic Descriptions of Nondynamical Electron Correlation: From Bond-Breaking to Transition-Metal Catalysis. [Doctoral Dissertation]. Georgia Tech; 2007. Available from: http://hdl.handle.net/1853/19807
Georgia Tech
7.
Rohatgi, Priyanka.
Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules.
Degree: PhD, Chemistry and Biochemistry, 2006, Georgia Tech
URL: http://hdl.handle.net/1853/19852
► Small molecule dependent molecular switches that control gene expression are important tool in understanding biological cellular processes and for regulating gene therapy. Nuclear receptors are…
(more)
▼ Small molecule dependent molecular switches that control gene expression are important tool in understanding biological cellular processes and for regulating gene therapy. Nuclear receptors are ligand activated transcription factors that have been engineered to selectively respond to synthetic ligands and used as regulators of gene expression. In this work the retinoid X receptor (RXR), has been used to develop an inducible molecular switch with a near drug like compound LG335. Three RXR variants (Q275C; I310M; F313I), (I268A; I310A; F313A; L436F), (I268V; A272V; I310M; F313S; L436M) were created via site-directed mutagenesis and a structure based approach, such that they preferentially bind to the synthetic ligand LG335 and not its natural ligand, 9-cis retinoic acid. These variants show reverse ligand specificity as designed and have an EC50 for LG335 of 80 nM, 30 nM, 180 nM, respectively. The ligand binding domains of the RXR variants were fused to a yeast transcription factor Gal4 DNA binding domain. This modified chimeric fusion protein showed reverse response element specificity as designed and recognized the Gal4 response element instead of the RXR response element. The modified RXR protein did not heterodimerize with wild type RXR or with other nuclear receptor such as retinoic acid receptor. These RXR-based molecular switches were tested in retroviral vectors using firefly luciferase and green fluorescence protein and they maintain their inducible behavior with LG335. These experiments demonstrate the orthogonality of RXR variants and their possible use in regulating gene therapy.
Advisors/Committee Members: Donald F. Doyle (Committee Chair), C. David Sherrill (Committee Member), H.Trent Spencer (Committee Member), Joseph M. LeDoux (Committee Member), Nicholas V. Hud (Committee Member).
Subjects/Keywords: Protein engineering; Nuclear receptor; Gene therapy; Inducible system; Molecular switches; Gene therapy; Ligands (Biochemistry); Protein engineering
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Rohatgi, P. (2006). Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/19852
Chicago Manual of Style (16th Edition):
Rohatgi, Priyanka. “Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules.” 2006. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/19852.
MLA Handbook (7th Edition):
Rohatgi, Priyanka. “Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules.” 2006. Web. 26 Jan 2021.
Vancouver:
Rohatgi P. Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules. [Internet] [Doctoral dissertation]. Georgia Tech; 2006. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/19852.
Council of Science Editors:
Rohatgi P. Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules. [Doctoral Dissertation]. Georgia Tech; 2006. Available from: http://hdl.handle.net/1853/19852
Georgia Tech
8.
Horowitz, Eric D.
Intercalator-mediated assembly of nucleic acids.
Degree: PhD, Chemistry and Biochemistry, 2009, Georgia Tech
URL: http://hdl.handle.net/1853/33937
► The RNA World hypothesis suggests that RNA, or a proto-RNA, existed in an early form of life that had not yet developed the ability to…
(more)
▼ The RNA World hypothesis suggests that RNA, or a proto-RNA, existed in an early form of life that had not yet developed the ability to synthesize protein enzymes. This hypothesis, by some interpretations, implies that nucleic acid polymers were the first polymers of life, and must have therefore spontaneously formed from simple molecular building blocks in the "prebiotic soup." Although prebiotic chemists have searched for decades for a process by which RNA can be made from plausible prebiotic reactions, numerous problems persist that stand in the way of a chemically-sound model for the spontaneous generation of an RNA World (e.g., strand-cyclization, heterogeneous backbones, non-selective ligation of activated nucleotides). The Molecular Midwife hypothesis, proposed by Hud and Anet in 2000, provides a possible solution to several problems associated with the assembly of the first nucleic acids. In this hypothesis, nucleic acid base pairs are assembled by small, planar molecules that resemble molecules which are known today to intercalate the base pairs of nucleic acid duplexes. Thus, the validity and merits of the Molecular Midwife hypothesis can be, to some extent, explored by studying the effects of intercalation on the non-covalent assembly of nucleic acids.
In this thesis, I explore the role of the sugar-phosphate backbone in dictating the structure and thermodynamics of nucleic acid intercalation by using 2′,5′-linked RNA intercalation as a model system of non-natural nucleic acid intercalation. The solution structure of an intercalator-bound 2′,5′ RNA duplex reveals structural and thermodynamic aspects of intercalation that provide insight into the origin of the nearest-neighbor exclusion principle, a principle that is uniformly obeyed upon the intercalation of natural (i.e. 3′,5′-linked) RNA and DNA. I also demonstrate the ability of intercalator-mediated assembly to circumvent the strand-cyclization problem, a problem that otherwise greatly limits the polymerization of short oligonucleotides into long polymers. Together, the data presented in this thesis illustrate the important role that the nucleic acid backbone plays in governing the thermodynamics of intercalation, and provide support for the proposed role of intercalator-mediated assembly in the prebiotic formation of nucleic acids.
Advisors/Committee Members: Nicholas V. Hud (Committee Chair), David Sherrill (Committee Member), Loren Williams (Committee Member), Roger Wartell (Committee Member), Steve Harvey (Committee Member).
Subjects/Keywords: RNA; Intercalation; DNA; Nucleic acids; Origin of life; Template-directed synthesis; Life Origin; Oligonucleotides; Proteins Synthesis; Proteins
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Horowitz, E. D. (2009). Intercalator-mediated assembly of nucleic acids. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/33937
Chicago Manual of Style (16th Edition):
Horowitz, Eric D. “Intercalator-mediated assembly of nucleic acids.” 2009. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/33937.
MLA Handbook (7th Edition):
Horowitz, Eric D. “Intercalator-mediated assembly of nucleic acids.” 2009. Web. 26 Jan 2021.
Vancouver:
Horowitz ED. Intercalator-mediated assembly of nucleic acids. [Internet] [Doctoral dissertation]. Georgia Tech; 2009. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/33937.
Council of Science Editors:
Horowitz ED. Intercalator-mediated assembly of nucleic acids. [Doctoral Dissertation]. Georgia Tech; 2009. Available from: http://hdl.handle.net/1853/33937
Georgia Tech
9.
Gonzalez, Jose Ignacio.
Quantum Optoelectronics: Nanoscale Transport in a New Light.
Degree: PhD, Chemistry and Biochemistry, 2006, Georgia Tech
URL: http://hdl.handle.net/1853/10521
► Common to molecular electronics studies, nanoscale break junctions created through electromigration also naturally produce electroluminescent arrays of individual gold nanoclusters spanning the electrodes. Due to…
(more)
▼ Common to molecular electronics studies, nanoscale break junctions created through electromigration also naturally produce electroluminescent arrays of individual gold nanoclusters spanning the electrodes. Due to inelastic electron tunneling into cluster electronic energy levels, these several-atom nanoclusters (Au~18-22) exhibit bright, field-dependent, antibunched emission in the near infrared (650800 nm), acting as room-temperature electrically driven single-photon sources. AC electrical excitation with time-stamping of photon arrival times enables fast and local tracking of electrode-nanocluster coupling dynamics demonstrating that charge injection to the clusters is directly modulated by dynamic coupling to individual electrodes. The electrode-nanocluster coupling rate fluctuates by nearly an order of magnitude and, due to the asymmetry of the electromigration process, exhibits preferential charge injection from the anode. Directly reporting on (and often facilitating) nanoscale charge transport, time-tagged single-molecule electroluminescence reveals a significant mechanism for nanoscale charge transport in nanoscale gold break junctions, and offers direct readout of the electrode-molecule interactions that can be correlated with current flow. Single-molecule electroluminescence techniques for characterization of electrode heterogeneity and dynamics as well as implications for future research are discussed.
Advisors/Committee Members: Dr. Robert M. Dickson (Committee Chair), Dr. C. David Sherrill (Committee Member), Dr. C. P. Wong (Committee Member), Dr. Mostafa A. El-Sayed (Committee Member), Dr. Thomas M. Orlando (Committee Member).
Subjects/Keywords: Inelastic electron tunneling; Single molecule; Electroluminescence; Molecular electronics; Nanoscale charge transport; Dynamics
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Gonzalez, J. I. (2006). Quantum Optoelectronics: Nanoscale Transport in a New Light. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/10521
Chicago Manual of Style (16th Edition):
Gonzalez, Jose Ignacio. “Quantum Optoelectronics: Nanoscale Transport in a New Light.” 2006. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/10521.
MLA Handbook (7th Edition):
Gonzalez, Jose Ignacio. “Quantum Optoelectronics: Nanoscale Transport in a New Light.” 2006. Web. 26 Jan 2021.
Vancouver:
Gonzalez JI. Quantum Optoelectronics: Nanoscale Transport in a New Light. [Internet] [Doctoral dissertation]. Georgia Tech; 2006. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/10521.
Council of Science Editors:
Gonzalez JI. Quantum Optoelectronics: Nanoscale Transport in a New Light. [Doctoral Dissertation]. Georgia Tech; 2006. Available from: http://hdl.handle.net/1853/10521
Georgia Tech
10.
Dennison, Kelly Joy.
Understanding HTLV-I Enzymology and Preparation and Characterization of Lead Inhibitors for the Treatment of HTLV-I Infection.
Degree: PhD, Chemistry and Biochemistry, 2005, Georgia Tech
URL: http://hdl.handle.net/1853/7582
► The primary goals of our research are to understand the virology and enzymology of human T-cell leukemia virus type I (HTLV-I) that will lead to…
(more)
▼ The primary goals of our research are to understand the virology and enzymology of human T-cell leukemia virus type I (HTLV-I) that will lead to the development of treatments for patients infected with HTLV-I. HTLV-I is an oncogenic virus of the Retroviridae family and is the causative agent of adult T-cell leukemia/lymphoma (ATL), tropical spastic paraparesis/HTLV-I associated myelopathy (TSP/HAM). HTLV-I has been classified as a dangerous emerging pathogen by the Centers for Disease Control and Prevention with at least 20 million people infected with the virus. This is a significant problem because there are currently no effective treatments to control HTLV-I infection and prevent or treat HTLV-I induced ATL and TSP/HAM.
The protease is necessary for retroviral maturation and replication and is, therefore, an attractive target for inhibitor design. Investigation of peptide mimetic compounds incorporating the tetrahedral intermediate of aspartyl protease catalyzed cleavage are crucial for the development of lead inhibitors. Compounds containing statine, 4-amino-3-hydroxy-5-phenylpentanoic acid (AHPPA), or hydroxyethylamine (HEA) are presented in this work. The best compound was a statine-based inhibitor, which had a Ki = 29 +/- 4 nM and 88% inhibition against an HTLV-I protease native substrate in a FRET assay.
Advisors/Committee Members: Dr. Suzanne B. Shuker (Committee Chair), Dr. Thomas M. Orlando (Committee Co-Chair), Dr. Andreas S. Bommarius (Committee Member), Dr. C. David Sherrill (Committee Member), Dr. Donald F. Doyle (Committee Member), Dr. S. Michele Owen (Committee Member), Dr. Vicky L. H. Bevilacqua (Committee Member).
Subjects/Keywords: Enzymology; Fluorescence quenching; HTLV-I (Virus); Kinetics; Mutation (Biology); Protease inhibitors
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Dennison, K. J. (2005). Understanding HTLV-I Enzymology and Preparation and Characterization of Lead Inhibitors for the Treatment of HTLV-I Infection. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/7582
Chicago Manual of Style (16th Edition):
Dennison, Kelly Joy. “Understanding HTLV-I Enzymology and Preparation and Characterization of Lead Inhibitors for the Treatment of HTLV-I Infection.” 2005. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021.
http://hdl.handle.net/1853/7582.
MLA Handbook (7th Edition):
Dennison, Kelly Joy. “Understanding HTLV-I Enzymology and Preparation and Characterization of Lead Inhibitors for the Treatment of HTLV-I Infection.” 2005. Web. 26 Jan 2021.
Vancouver:
Dennison KJ. Understanding HTLV-I Enzymology and Preparation and Characterization of Lead Inhibitors for the Treatment of HTLV-I Infection. [Internet] [Doctoral dissertation]. Georgia Tech; 2005. [cited 2021 Jan 26].
Available from: http://hdl.handle.net/1853/7582.
Council of Science Editors:
Dennison KJ. Understanding HTLV-I Enzymology and Preparation and Characterization of Lead Inhibitors for the Treatment of HTLV-I Infection. [Doctoral Dissertation]. Georgia Tech; 2005. Available from: http://hdl.handle.net/1853/7582
. 
Open Access Theses and Dissertations
