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2014

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Polyaniline And Cellulose Acetate Chemomechanical Actuator And Its Selectivity For Acetone, Jing Zhang Dec 2014

Polyaniline And Cellulose Acetate Chemomechanical Actuator And Its Selectivity For Acetone, Jing Zhang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Polyaniline (PANI) belongs to the conducting polymers and has been studied for so many years. PANI has three different states depending on the redox process. In this thesis, we used the completely reduced form leucoemeraldine base (LEB) to synthesize the Chemomechanical actuator. Cellulose Acetate (CA) was used to be the matrix because CA can provide a strong mechanical property for the film synthesizing. PANI and CA molecules interconnected and form the Chemomechanical actuator, which has the selectivity for acetone vapor. We tested and recorded the Chemomechanical actuator's bending angle and time, and its unique character for acetone selectivity. Scanning electron …

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Space Of Kã¤Hler Potentials On Singular And Non-Compact Manifolds | Space Of Kähler Potentials On Singular And Non-Compact Manifolds, Seyed Ali Aleyasin Dec 2014

Space Of Kã¤Hler Potentials On Singular And Non-Compact Manifolds | Space Of Kähler Potentials On Singular And Non-Compact Manifolds, Seyed Ali Aleyasin

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Let H be the space of Kähler metrics in a fixed cohomology class. This space may be endowed with a Weil-Petersson-type metric, referred to as the Mabuchi metric, which allows one to study the geometry of H. It is now well-known that the geometry of the space of Kähler potentials, in particular, the geodesics in H, may be used for studying `canonical metrics' on the base manifold. In order to be interpreted as the potential of a Kähler metric, however, one needs to prove certain regularity for such solutions. In the first part, I shall discuss deriving of weighted estimates …

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Applications Of The Seiberg-Witten Equations To The Differential Geometry Of Non-Compact Kahler Manifolds, Ilya Elson Dec 2014

Applications Of The Seiberg-Witten Equations To The Differential Geometry Of Non-Compact Kahler Manifolds, Ilya Elson

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Soon after the introduction of the Seiberg-Witten equations, and their magnificent application to the differential topology of 4-manifolds, LeBrun [LeB95] used these equations to study differential geometry and prove a rigidity theorem for compact complex hyperbolic manifolds. Biquard [Biq97] extended these results to non-compact, finite volume complex hyperbolic manifolds, and Rollin [Rol04] extended these techniques to CH2. Finally, Di Cerbo[DC12b, DC11] applied Biquard's techniques to the product of two negatively curved Riemann surfaces. The main tool that allows one to use the Seiberg-Witten equations to study differential geometry is an integral scalar curvature estimate The principle difficulty in …

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Braiding Non-Ribbon Surfaces And Constructing Broken Fibrations On Smooth 4-Manifolds, Mark Clifford Hughes Dec 2014

Braiding Non-Ribbon Surfaces And Constructing Broken Fibrations On Smooth 4-Manifolds, Mark Clifford Hughes

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this thesis we study various notions of surface braidings in 4-space, and their applications to the construction of singular fibrations on smooth oriented 4-manifolds. We define the notion of braided link cobordisms in S3 × [0,1], which generalize Viro's closed 2-braids in S4. We prove that via isotopy any properly embedded oriented surface W in S3 × [0,1] can be brought to this special position, and that the isotopy can be taken rel boundary when the boundary already consists of closed braids. These surfaces are closely related to another notion of surface braiding in D2 × D2, called braided …

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On The Uniqueness Of Singular Kaehler-Einstein Metrics, Long Li Dec 2014

On The Uniqueness Of Singular Kaehler-Einstein Metrics, Long Li

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Bando and Mabuchi proved the uniqueness of Kaehler-Einstein metrics on Fano manifolds up to a holomorphic automorphism in 1987. Then recently Berndtsson generalized the uniqueness result of Kaehler-Einstein metrics to bounded potentials. We give a new proof of the Bando-Mabuch-Berndtsson uniqueness theorem in a different aspect, based on a new technique developed from Chen's C^{1,1} geodesic and Futaki's spectral formula. Finally, the uniqueness of the conical Kaehler-Einstein metrics will be discussed under the assumption of properness of twisted Ding-functional. | 61 pages

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Uniqueness Of Ricci Flow Solution On Non-Compact Manifolds And Integral Scalar Curvature Bound, Xiaojie Wang Dec 2014

Uniqueness Of Ricci Flow Solution On Non-Compact Manifolds And Integral Scalar Curvature Bound, Xiaojie Wang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this dissertation, we prove two results. The first is about the uniqueness of Ricci flow solution. B.-L. Chen and X.-P. Zhu first proved the uniqueness of Ricci flow solution to the initial value problem by assuming bilaterally bounded curvature over the space-time. Here we show that, when the initial data has bounded curvature and is non-collapsing, the complex sectional curvature bounded from below over the space-time guarantees the short-time uniqueness of solution. The second is about the integral scalar curvature bound. A. Petrunin proved that for any complete boundary free Riemannian manifold, if the sectional curvature is bounded from …

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Shintani Zeta Functions And Weyl Group Multiple Dirichlet Series, Jun Wen Dec 2014

Shintani Zeta Functions And Weyl Group Multiple Dirichlet Series, Jun Wen

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In recent years, substantial progresses have been made towards the development of a general theory of multiple Dirichlet series with functional equations. In this dissertation, we investigate the Shintani zeta function associated to a prehomogeneous vector space and identify it with a Weyl group multiple Dirichlet series. The example under consideration is the set of 2 by 2 by 2 integer cubes, that is the integral lattice in a certain pre-homogeneous vector space acted on by three copies of GL(2). One of M. Bhargava's achievements is the determination of the corresponding integral orbits and the discovery of an extension of …

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Numerical Modeling And Combustion Studies Of Scramjet Problem, Ying Xu Dec 2014

Numerical Modeling And Combustion Studies Of Scramjet Problem, Ying Xu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Physical and numerical modeling of turbulent mixing and turbulent combustion in a Scramjet combustion chamber is studied. A high-order finite volume scheme is applied to the flow, accompanied with dynamic subgrid-scale model and local averaging procedure to account for the effect of unresolved small length scales turbulent fluid behavior. The Arrhenius law kinetic mechanism is applied to describe the nonlinearity of chemical reactions. To model combustion, the finite rate chemistry is developed to characterize the combustion process inside the combustion chamber. Results are compared among the finite rate model, the flamelet model/progress variable approach adopted by Stanford PSAAP center and …

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On Geometric And Motivic Realizations Of Variations Of Hodge Structure Over Hermitian Symmetric Domains, Zheng Zhang Dec 2014

On Geometric And Motivic Realizations Of Variations Of Hodge Structure Over Hermitian Symmetric Domains, Zheng Zhang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Based on the work of Gross and Sheng and Zuo, Friedman and Laza show that over every irreducible Hermitian symmetric domain there exists a canonical variation of real Hodge structure of Calabi-Yau type. The first part of the thesis concerns motivic realizations of the canonical Calabi-Yau variations over irreducible Hermitian symmetric domains of tube type. In particular, we show that certain rational descents of the canonical variations of Calabi-Yau type over irreducible tube domains of type $A$ can be realized as sub-variations of Hodge structure of certain variations which are naturally associated to families of abelian varieties of Weil type. …

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Hybrid Technique Of Analysis And Development Of Heat Exchangers For Vuilleumier Heat Pumps, Yogesh Bhalchandra Bedekar Dec 2014

Hybrid Technique Of Analysis And Development Of Heat Exchangers For Vuilleumier Heat Pumps, Yogesh Bhalchandra Bedekar

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Vuilleumier heat pumps (VHPs) are heat driven heat pumps working on the Vuilleumier cycle. The Vuilleumier heat pump is a closed system that captures heat at lower temperatures and deposits the captured heat energy to some intermediate temperature at the expense of high temperature heat energy. The heat energy is the input to the system by burning fuel externally. Due to the interfacing between the heat pump and the outside heat sources and heat sinks, heat exchangers represent critical components in the VHP and have a major impact on overall coefficient of performance. High operating pressures, minimal dead volume and …

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Effects Of Marine Environments And Cyclic Loading On Carbon Fiber-Vinyl Ester Composites, Arash Afshar Dec 2014

Effects Of Marine Environments And Cyclic Loading On Carbon Fiber-Vinyl Ester Composites, Arash Afshar

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Fiber-reinforced composites are increasingly being employed in advanced composite based military marine crafts as they can assist in achieving cost savings, weight reductions and increased stealth capabilities. In these crafts, composites are considered for a wide range of applications, such as for superstructures, decks, bulkheads, masts and propellers, among others. However, in marine applications, composites are often exposed to aggressive environments, which include: ultraviolet radiation, salt water and cyclic loadings, to name a few. With time, such harsh elements can individually and cooperatively degrade the mechanical properties of fiber-reinforced polymer composites, diminishing their structural integrity and durability. Accordingly, ensuring the …

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On The Dynamics Of Non-Linear Systems And Actuation Devices, Dake Feng Dec 2014

On The Dynamics Of Non-Linear Systems And Actuation Devices, Dake Feng

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The research results being presented in this thesis is divided into two areas. The first area is related to the development of a systematic method for model parameter identification of a large class of fully and not fully controlled nonlinear dynamics systems such as robot manipulators. The developed method is based on Trajectory Pattern Method (TPM). The developed method uses trajectory patterns with feed-forward controls to identify the system model parameters. The developed method ensures full system stability; does not require close initial estimated values for the system parameters to be identified; and provides a systematic method of emphasizing on …

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Analysis And Design Of Thermal Management System For Thermoelectric Generators For Nuclear Power Plant Safety, Chih-Chieh Lin Dec 2014

Analysis And Design Of Thermal Management System For Thermoelectric Generators For Nuclear Power Plant Safety, Chih-Chieh Lin

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This project aims to develop thermoelectric generators (TEG)-based devices for sensing during normal and off-normal conditions in Small Modular Reactors (SMRs). Locations such as reactor core vessels, steam generators, housings of pumps, heat exchangers, and steam pipe housings in primary loop and secondary loop are potential installation sites. The heat is conducted through an adaptor to the TEGs and removed by a heat sink by means of natural convection. The electrical power generated by the TEGs is then used to drive sensors and wireless communications. Additional power can be stored in batteries or in super capacitors for emergency operations. The …

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A Cultural Trade? Canadian Magazine Illustrators At Home And In The United States, 1880-1960, Shannon Jaleen Grove Dec 2014

A Cultural Trade? Canadian Magazine Illustrators At Home And In The United States, 1880-1960, Shannon Jaleen Grove

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This dissertation analyzes nationalisms in the work of Canadian magazine illustrators in Toronto and New York, 1880 to 1960. Using a continentalist approach--rather than the nationalist lens often employed by historians of Canadian art--I show the existence of an integrated, joint North American visual culture. Drawing from primary sources and biography, I document the social, political, corporate, and communication networks that illustrators traded in. I focus on two common visual tropes of the day--that of the pretty girl and that of wilderness imagery. Through visual and verbal rhetoric, and through institutional controls to exclude particular kinds of illustration from counting …

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Finding Place: The Art Of Wangechi Mutu, Maria Magdalena Campos-Pons And Ingridmwangiroberthutter, Eva Susanne Hericks-Bares Dec 2014

Finding Place: The Art Of Wangechi Mutu, Maria Magdalena Campos-Pons And Ingridmwangiroberthutter, Eva Susanne Hericks-Bares

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This dissertation examines the issue of " place" in the lives and works of three contemporary women artists of the African Diaspora: Maria Magdalena Campos-Pons, IngridMwangiRobertHutter, and Wangechi Mutu. Place as a location is a core challenge of globalism: though fundamental to our existence, it has ceased to be permanent or definite. However, place is more than location--it is cultural, gendered, historical, interactive, personal and social, among other things--and can only be fully understood in considering several of these different facets. Each of the artists in this dissertation has had to navigate through instances of bias (such as racism and …

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Characterization Of Trifunctional Glycinamide Ribonucleotide Synthetase And Its Role In Purinosome Complex, Iva Chitrakar Dec 2014

Characterization Of Trifunctional Glycinamide Ribonucleotide Synthetase And Its Role In Purinosome Complex, Iva Chitrakar

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The human de novo purine biosynthetic pathway consists of six proteins, which come together to form a protein complex called the purinosome. The tri-functional enzyme, TGART, which contains three domains, is one of the purinosome proteins. Protein-protein interaction studies have shown that TGART, along with two other de novo purine pathway proteins FGAMS and PPAT, is at the core of purinosome complex. Little is known, however about the interacting surface, stoichiometry or interaction mechanism. In order to understand this, we hope to solve the X-ray crystal structure of full-length human TGART, run quantitative protein interaction measurements on TGART, FGAMS and …

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Cpi-613, A Non-Redox Active Lipoic Acid Analog, Causes Hyper-Phosphorylation Of Bckdc E1Α In H460 Lung Cancer Cells In Vitro, Michael Simon Dahan Dec 2014

Cpi-613, A Non-Redox Active Lipoic Acid Analog, Causes Hyper-Phosphorylation Of Bckdc E1Α In H460 Lung Cancer Cells In Vitro, Michael Simon Dahan

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The production of lipids and proteins for growth, as well as nucleotides for the replication of the genome, are key requirements that loom as importantly as the need for the production of energy in the transformed metabolic state of cancer cells. The remodeling of the TCA cycle (extensive anaplerosis and cataplerosis) reflects this need for biosynthetic macromolecules. CPI-613, a non-redox active lipoic acid analog that has been shown to selectively increase phosphorylation of the pyruvate dehydrogenase (PDH) E1 α subunit, thereby inactivating the entire complex, was investigated for its role in causing phosphorylation of the branched-chain amino acid dehydrogenase complex …

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Identification Of Binding Partners With The Negatively Charged Zip1 C-Terminus Using A Two-Hybrid Screen, Matthew Murray Dec 2014

Identification Of Binding Partners With The Negatively Charged Zip1 C-Terminus Using A Two-Hybrid Screen, Matthew Murray

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Recombination is an essential meiotic process to ensure proper chromosome distribution. Recombination is promoted by the synaptonemal complex, a structure which bridges two pairs of homologous sister chromatids, bringing them into close proximity. The synaptonemal complex is formed by condensation of the sister chromatids on protein cores called axial elements. Homologous axial elements are then held together in budding yeast by a protein called Zip1. Zip1 is part of the ZMM group of proteins that work together during meiosis to promote the formation of crossovers which are distributed throughout the genome by interference. Four phosphorylation sites have been identified in …

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Expression, Purification, And Characterization Of The Short Isoform Of Adenylosuccinate Lyase, Benjamin Rajan Dec 2014

Expression, Purification, And Characterization Of The Short Isoform Of Adenylosuccinate Lyase, Benjamin Rajan

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Cells require purines for critical biological processes that can be created by the de novo biosynthetic pathway or maintained by the salvage pathways. The de novo pathway in humans requires 6 enzymes, some of which are multifunctional. Adenylosuccinate lyase (ASL) catalyzes step 8 of the de novo pathway converting susuccinylaminoimidazolecarboxamide ribonucleotide (SAICAR) to aminoimidazolecarboxamide ribotide (AICAR). It also catalyzes the second step of the purine nucleotide cycle by converting SAMP to AMP. A short isoform of ASL (sASL) is ubiquitously expressed in all cell types at a lower concentration. This shortened splice variant does not perform catalysis on either of …

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Analysis Of The Oncogenic Cooperation Between Mutp53 And Her2 To Propose Mutp53 As A Biomarker For Her2-Positive Breast Cancer, Amanda Deanna Russo Dec 2014

Analysis Of The Oncogenic Cooperation Between Mutp53 And Her2 To Propose Mutp53 As A Biomarker For Her2-Positive Breast Cancer, Amanda Deanna Russo

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Breast cancer is the second deadliest cancer in the United States and is classified into four main subtypes including HER2-positive breast cancer. There have been a number of HER2-targeted therapeutic treatments that were discovered, but they are expensive and patients frequently exhibit a resistance for these treatments. To alleviate patients undergoing expensive therapy with the possibility of not benefitting from the treatment, it is important to understand the cooperation between HER2 and mutp53, a tumor suppressor gene that is mutated in the majority of breast cancers. Analysis of scientific articles illustrate that HER2 and mutp53 cooperate to promote tumorigenesis via …

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Orbitofrontal Cortex And The Decision-Making Process, Youran Wu Dec 2014

Orbitofrontal Cortex And The Decision-Making Process, Youran Wu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Orbitofrontal cortex (OFC) is situated at the ventral floor of the prefrontal cortex region. OFC and some of its related structure (ventral striatum, ventral tegmental area, basolateral amygdala) are considered to be part of the valuation system that is essential to the decision-making process. In order to understand the exact role OFC plays in the decision-making process, we sought to find out how decision variables are represented in different OFC projections, and what will happen if OFC projections were disrupted. The first specific aim of this project is to find out whether projections to OFC related structures are originated from …

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The Versatile Applications Of 6-Alkynyl Fucose And Other Fucose Analogs In Studying Protein Fucosylation, Esam Al-Shareffi Dec 2014

The Versatile Applications Of 6-Alkynyl Fucose And Other Fucose Analogs In Studying Protein Fucosylation, Esam Al-Shareffi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Glycosylation is the modification of a target molecule with carbohydrate. It is a common and complex co- or post-translational protein modification that is responsible for diverse and essential biological roles including cellular communication, modulation of function, and the provision of specific ligands for carbohydrate-binding proteins. Fucosylation is a specific type of glycosylation that results from the transfer of fucose, a unique monosaccharide with the L-configuration, to its target proteins or glycans through the action of fucosyltransferases. Thirteen fucosyltransferases have been identified, including protein O-fucosyltransferases 1 and 2 (POFUT1 and POFUT2), responsible for addition of fucose to the hydroxyl group of …

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Redox Regulation Of Protein Tyrosine Phosphatases In Oncogene-Induced Senescence, Ming Yang Dec 2014

Redox Regulation Of Protein Tyrosine Phosphatases In Oncogene-Induced Senescence, Ming Yang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Oncogene expression in normal cells can cause an irreversible growth arrest called oncogene-induced senescence (OIS), which serves as a barrier to cancer initiation. Elevated reactive oxygen species (ROS) have been detected in most senescent cells and are thought to play a causal role in OIS. ROS are believed to have a second messenger function in transducing signals, however their molecular role in senescence remains elusive. We hypothesize that PTPs, which are prone to redox regulation, act as specific target of ROS and the redox regulation of PTPs mediates the signaling transduction in oncogene-induced senescence. In our study, we utilized a …

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Development Of A Line-Scanned Dual-Axis Confocal Microscope For Video-Rate Diagnostic Imaging, Danni Wang Dec 2014

Development Of A Line-Scanned Dual-Axis Confocal Microscope For Video-Rate Diagnostic Imaging, Danni Wang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The prevalence of oral cancer has been increasing at an alarming rate in recent years. Due to a limited understanding of the cause and progression of this disease, patient prognosis remain poor, and the mortality and morbidity of the disease remain significant. The need to diagnose cancerous regions early is key to patient survival. However, the high cost and invasive nature of standard pathological analysis motivates the search for an alternative real-time imaging technology that provides accurate non-invasive early diagnosis of the disease. The goal of this thesis is to develop a line-scanned dual-axis confocal (LS-DAC) microscope for high-resolution, high-contrast, …

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Transition Metal Borates As Cathode Materials For Rechargeable Batteries, Shou-Hang Bo Dec 2014

Transition Metal Borates As Cathode Materials For Rechargeable Batteries, Shou-Hang Bo

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

High-capacity rechargeable batteries play a central role in a variety of emerging technologies, including mobile electronics, plug-in and hybrid electric vehicles, and grid-scale storage. All of these technologies will greatly benefit from the design and discovery of next-generation cathode materials that can deliver substantially higher energy densities at reduced cost. Transition metal borates are promising cathode candidates for battery applications, since the mass/charge ratio (m/z) of borate group (BO33-) is the lowest among all common polyanion groups. A variety of borate based compounds were therefore explored as potential Li-ion and Mg-ion battery cathodes in this dissertation Comprehensive studies were carried …

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Macrocyclic Hosts For Polymerization Of Diiodobutadiyne, Ce Chen Dec 2014

Macrocyclic Hosts For Polymerization Of Diiodobutadiyne, Ce Chen

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

All-carbon materials have been widely investigated because of their potential thermal, electrical and physical properties. Carbyne, which would have all sp hybridized carbons, has received considerable attention. Polydiiododiacetylene (PIDA), which has a carbon backbone and iodine atom substituents, serves as a potential precursor to carbyne. We propose that carbyne could result from complete deiodination of PIDA in the presence of Lewis bases such as triethyl amine, pyridine and pyrrolidine. To avoid aggregation of PIDA or carbyne strands during this process, we aim to prepare PIDA as a polyrotaxane through topochemical polymerization, using a macrocyclic cocrystallizing agent, or " host" , …

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Metal Complexes For Structural Modeling Of Active Sites Of Metalloenzymes Relevant To Gas Catalysis, Soumya Bhattacharya Dec 2014

Metal Complexes For Structural Modeling Of Active Sites Of Metalloenzymes Relevant To Gas Catalysis, Soumya Bhattacharya

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Sulfur rich metal coordinated active sites is a prominent feature of many metalloenzymes (hydrogenase, nitrogenase, carbon monoxide dehydrogenase) involved in catalytically producing and/or absorbing helpful and/or toxic gases. As the mechanism of gas production and/or absorption heavily depends on the structural intricacies, biomimetic modelling of the active sites is of paramount importance to understand the structure-function relationship. It has been established that the small molecule models with steric bulk of the thiols at the ortho- position of derivatized benzenethiols can provide the stability. Millar and Koch were pioneers in introducing a series of ortho-steric benzene thiols and achieving stabilization of …

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Enhanced Backbone Dihedral Parameters For Protein Simulations, Carmenza Martinez Dec 2014

Enhanced Backbone Dihedral Parameters For Protein Simulations, Carmenza Martinez

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Molecular Dynamics (MD) and Monte Carlo (MC) simulations of biomolecules have become a supportive tool to experimental methods for structure refinement, protein folding, drug discovery and many more applications. This is due to the increase in computational power and necessity of finding a method capable of describing the forces at work in chemical systems without the need to do extensive quantum calculations. All of these are possible because of the classical definition of the potential force field function. The force field function is essential to perform MD simulations, since this equation carries the physical description of the molecules being studied. …

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Mechanism And Inhibition Of The Enoyl-Acp Reductases From Biodefense And Emerging Opportunistic Pathogens, Carla Maya Neckles Dec 2014

Mechanism And Inhibition Of The Enoyl-Acp Reductases From Biodefense And Emerging Opportunistic Pathogens, Carla Maya Neckles

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The enoyl-acyl-carrier-protein reductase (ENR) catalyzes the last reaction in the elongation cycle in the fatty acid biosynthesis type II (FAS-II) pathway. To date, there are four known ENR isoenzymes: FabI, FabK, FabL, and FabV. We have rigorously characterized the FabV ENR from Burkholderia mallei (BmFabV) and have shown that this enzyme catalyzes substrate reduction via an ordered bi-bi mechanism, in which NADH binds first to the enzyme followed by the enoyl substrate [Lu, H. (2010) Biochemistry 49, 1281-1289]. However, this pathogen contains both FabI and FabV ENRs, and mechanistic insights into ENR substrate recognition are lacking in pathogens that solely …

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Improved Generalized Born Solvent Model Parameters For Protein And Nucleic Acid Simulations, Hai Minh Nguyen Dec 2014

Improved Generalized Born Solvent Model Parameters For Protein And Nucleic Acid Simulations, Hai Minh Nguyen

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Generalized Born solvent model offers inexpensive approach for solvation energy calculation as compared to explicit solvent and Poisson-Boltzmann (PB) method. Thanks to its speed, GB models have been widely used in molecular dynamics (MD) simulations. However the speed comes with tradeoffs. Literatures have pointed out the weaknesses of GB models in inaccurately calculating solvation energy that leads to helical bias in protein simulation or unstable DNA/RNA duplex in nucleic acid simulation. Here we introduced the reparameterization of the recently developed GB-Neck model to improve its accuracy. Compared to other pairwise GB models (e.g. GB-OBC and GB-Neck) the new GB models …

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