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2013

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Molecular Movie Magic: Real-Time Picosecond To Microsecond Structural Dynamics Of Photoactive Flavoproteins, Richard James Brust Dec 2013

Molecular Movie Magic: Real-Time Picosecond To Microsecond Structural Dynamics Of Photoactive Flavoproteins, Richard James Brust

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

Femtosecond (fs) excitation of photoreceptors results in protein structural changes that occur on the microsecond to millisecond timescale or longer. It is thus of fundamental interest to understand how these fast timescale events dictate large scale protein dynamics that occur on much longer (106 orders of magnitude) timescales. AppA is a blue light using FAD (BLUF) protein which acts as a transcriptional antirepressor in Rhodobacter sphaeroides. The ultrafast photocycle and IR spectra are well characterized and involve a near instantaneous (<100 fs) response of the protein matrix that surrounds the chromophore. While there has been extensive study on the ultrafast time scales there has never been an observation of the kinetics of the light induced structural changes in the protein. Here we investigated the ultrafast (ps) to ms structural dynamics through transient IR. The data show that significant structural changes occur on the sub microsecond timescale following photoactivation. In addition our work has expanded to other BLUF proteins. BlsA is a BLUF protein found in the pathogenic bacterium Acinetobacter baumannii. Vibrational data together with homology modeling identify significant differences in β 5 strand caused by photoactivation, a region of BLUF photoreceptors proposed to be essential for signal modulation, that are unique for BlsA. In addition, the BLUF protein PixD, from Synechocystis, was characterized by transient IR, where photoexcitation results in radical pair formation, an event not observed in AppA. Transient IR also revealed that light state formation is complete within nanoseconds for PixD, suggesting a unique mechanism for single and multidomain BLUF systems. | 254 pages

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(I) Synthesis And Application Of Chiral Biphenol-Based Phosphorus Ligands To Catalytic Asymmetric Synthesis; (Ii) Rhodium-Catalyzed Cycloaddition Reactions For Rapid Construction Of Polycyclic Skeletons Of Biological Interest, Chih-Wei Chien Dec 2013

(I) Synthesis And Application Of Chiral Biphenol-Based Phosphorus Ligands To Catalytic Asymmetric Synthesis; (Ii) Rhodium-Catalyzed Cycloaddition Reactions For Rapid Construction Of Polycyclic Skeletons Of Biological Interest, Chih-Wei Chien

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

Chiral ligand design is crucial for the asymmetric transformations. In our laboratory, libraries of fine-tunable phosphorus ligands based on axially chiral biphenol have been well developed. These ligands exhibit excellent enantioselectivity in various transition-metal catalyzed asymmetric reactions. We present here the application of the monodentate phosphoramidite (MPN) ligand library to the Pd-catalyzed intramolecular asymmetric allylic amination (AAA) for the formation of chiral 1-vinyltetrahydroiso-quinoline skeleton, a versatile key intermediate in the synthesis of natural products such as isopyruthaline and (− )-O-methylthaicanine. We also studied the Pd-catalyzed inter-molecular AAA reaction using our bidentate diphosphonite (BOP) ligands. The BOP ligands exhibit excellent efficacy …

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Untangling The Interactions: Structural Basis Of Nitric Oxide Regulated Cyclic-Di-Gmp Metabolism In Bacteria, Tanaya Lahiri Dec 2013

Untangling The Interactions: Structural Basis Of Nitric Oxide Regulated Cyclic-Di-Gmp Metabolism In Bacteria, Tanaya Lahiri

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

Bacteria use numerous small molecules for cellular signaling. These primary and secondary messengers act within the cell to relay signal transduction and regulate distinct pathways. Among these the diatomic gas molecule nitric oxide (NO) and the nucleotide cyclic-di-GMP play central role in virulence, quorum sensing, and biofilm formation. In this dissertation, we have focused on H-NOX, a heme-nitric oxide/oxygen binding protein in the biofilm-dwelling bacterium Shewanella woodyi (Sw), which mediates NO-induced biofilm dispersal by modulating the activity of a dual-functioning diguanylate cyclase/phosphodiesterase enzyme that we have named HaCE, (H-NOX-associated cyclic-di-GMP enzyme). These enzymes tightly regulate the intracellular spatio-temporal concentrations of …

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Prey Plasticity Responses To A Native And Nonnative Predator, Alexandra Hooks Dec 2013

Prey Plasticity Responses To A Native And Nonnative Predator, Alexandra Hooks

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

Phenotypic plasticity in response to environmental stimuli is exceedingly common across systems and taxa. For instance, predation risk in many gastropods can induce a variety of defenses including growing thicker shells, growing shells of different shapes, and developing apertural teeth. However, the role of coevolution between species that produce these defense responses and their consumers is not well known. This thesis examines the responses of an ovoviviparous gastropod (Littorina saxatilis) with low dispersal from three different habitats (marsh habitat, rocky habitat, and cobble stone habitat) to the presence of chemical cues from a native (Dyspanopeus sayi) and nonnative (Hemigrapsus sanguineus) …

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A Distributed Mac Protocol For Efficient Channelization In Wireless Networks, Seyed Kaveh Fayazbakhsh Dec 2013

A Distributed Mac Protocol For Efficient Channelization In Wireless Networks, Seyed Kaveh Fayazbakhsh

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

There is a significant interest in designing new wireless multiple access protocols that split a wide frequency channel into multiple sub-channels and assign these sub-channels to competing transmissions. Doing this adaptively depending on the number of competing transmissions has a tremendous potential both in high-speed and white-space networks. While such protocols have been developed, they suffer from limitations such as considerable protocol overheads, dependence on a centralized controller, and assumptions about the network being static, etc. In this work, we develop a new multiple access protocol, Ez-Channel, that adaptively and efficiently channelizes the spectrum for improving throughput, without encountering the …

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System Evaluation And Design Of Delay-Sensitive Wireless Networks, Xi Deng Dec 2013

System Evaluation And Design Of Delay-Sensitive Wireless Networks, Xi Deng

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

Wireless networks have now been widely used and enjoyed in many aspects of human life and the society. Delay-sensitive wireless network, in a strict sense, is not a particular type of wireless networks. It represents a large number of wireless networks whose performance is greatly affected by the packet end-to-end delay, defined as the duration between a packet's generation at the source node and its delivery to the destination. Such network has been growing rapidly in recently years due to the tremendous demands from network applications. Emerging multimedia applications including Video-on-demand (VOD) and Voice-over-IP (VoIP) have become one of the …

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Integration Of Regenerative Shock Absorber Into Vehicle Electric System, Chongxiao Zhang Dec 2013

Integration Of Regenerative Shock Absorber Into Vehicle Electric System, Chongxiao Zhang

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

For cars with combustion engine, fuel is wasted on powering electric devices and conquering resistant forces from the road while driving forward. Regenerative shock absorber can help to harvest kinetic energy from vehicle suspension and power on-car electric system. One innovative design of energy harvesting shock absorber with mechanical motion rectifier is used in this thesis to harvest power and to be integrated with existing vehicle electric system. Interfacing circuits are developed and tested to regulate unstable power and achieve input current control for damping adjustment purpose. The overall integration of car alternator, electric load and regenerative shock absorber is …

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Biomimetic Calcium Phosphate Coatings Synthesized By Electrochemical Deposition And Air Plasma Spray: Morphology, Composition And Bioactive Performance, Ling Li Dec 2013

Biomimetic Calcium Phosphate Coatings Synthesized By Electrochemical Deposition And Air Plasma Spray: Morphology, Composition And Bioactive Performance, Ling Li

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

In this project, with the aim to develop bioactive biomimetic coatings for dental and orthopedic applications, calcium phosphate based coatings deposited by electrochemical deposition and plasma spray were investigated. Different combinations of process parameters were used to achieve coatings with various chemical compositions and morphologies. The obtained coating composition was investigated by energy dispersive X-ray spectroscopy and X-ray diffraction. The microstructure of the coatings were studied through scanning electron microscopy while the cytocompatibility and bioactivity of the strontium-doped calcium phosphate coatings were evaluated using bone cell culture using MC3T3-E1 osteoblast-like cells. A set of designed experiments were performed to study …

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Characterization Of Defects In Single Crystal Epitaxial Silicon For Solar Cells, Hao Wang Dec 2013

Characterization Of Defects In Single Crystal Epitaxial Silicon For Solar Cells, Hao Wang

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

In semiconductor technology for solar applications, the demand for high level of structural perfection in single crystal silicon has increased. The defects in the crystals can affect the efficiency of solar cells, so the study of imperfections is important for providing feedback to develop high quality crystal. X-ray topography is a nondestructive method and a powerful tool to evaluate crystals for technological applications, growth and processing. In this study, defects in homoepitaxial silicon epilayers grown by chemical vapor deposition (CVD) for solar cell application with the dislocation density of 9.4×〖 10〗 ^3cm-2 have been mapped and characterized by synchrotron white …

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Plasmonic Nanoclusters Based On Conjugated Polymer For Controlled Optical Output, Xuyi Wang Dec 2013

Plasmonic Nanoclusters Based On Conjugated Polymer For Controlled Optical Output, Xuyi Wang

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

Rational design and assembly of colloidal metal nanoparticles with fluorescent materials like organic dyes, conjugated polymers or colloidal quantum dots has stimulated intense research interest in the past decade in view of obtaining nanomaterials with controllable optical properties and with applicability in optoelectronics and biosensing. The interaction between a fluorescent molecule and a metal nanoparticle, also known as plasmon-exciton interaction, is determined by several factors such as type, shape and size of the metal nanoparticle, electronic properties of the fluorescent molecule, metal nanoparticle-fluorescence molecule separation distance and local nanoenvironment. By tuning one or more of such factors one can achieve …

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Influence Of Hydrogel Substrate On Cell Growth And Virus Infection, Fan Yang Dec 2013

Influence Of Hydrogel Substrate On Cell Growth And Virus Infection, Fan Yang

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

The interaction of cells with their extracellular matrix is of great importance when cells adapt to their environment. The purpose of this thesis is to design substrates with controllable properties and to study cellular interaction on these substrates. Firstly, enzymatically cross-linked gelatin hydrogels with different elastic modulus were prepared. Then, we studied the condition of cell growth and virus infection on these hydrogels as a followed-up. In the first part of the study, we made enzymatically cross-linked gelatin hydrogels with five different elastic modulus. As a parameter of stiffness, elastic modulus varies from 2.4 KPa to 7.5 KPa based on …

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Novel Catalytic Nanoparticles And Nanostructures For Environmental And Energy Applications, Shen Zhao Dec 2013

Novel Catalytic Nanoparticles And Nanostructures For Environmental And Energy Applications, Shen Zhao

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

Semiconductor photocatalysis is a dynamic field at the forefront of environmental and energy research. This dissertation has focused on the development of novel nanomaterials to exceed performance for environmental and energy related applications in both liquid and gas phases as compared to traditional materials. This project investigated the impact of size of noble metal clusters on photocatalytic activity induced by UV and visible light. Compared to larger particles, sub-nanometer particles have shown much better activity for catalytic reactions in both liquid and gas phases. These nanoclusters supported on various semiconductors, such as TiO2 and CdS showed outstanding catalytic properties for …

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Characterization Of Magnesium Silicide Processed With Thermal Spray For Thermoelectric Energy Harvesting, Chao Nie Dec 2013

Characterization Of Magnesium Silicide Processed With Thermal Spray For Thermoelectric Energy Harvesting, Chao Nie

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

Mg2Si has long been recognized as one of the promising thermoelectric materials; the fabrication methods are hot press, spark plasma sintering, high temperature sintering, etc. however, application of thermoelectric materials requires large scale manufacturing but traditional manufacturing process cannot reach this goal by its nature; thus we employed thermal spray technology to fabricate such thermoelectric material. In collaboration with Thermal Spray Center in Stony Brook University, we manufactured Mg¬2¬Si coatings on titanium substrate by plasma thermal spray technology. Samples were further characterized in various methods: scanning electron microscopy (SEM) exhibits the micro structures of sprayed Mg2Si coatings; X-ray spectroscopy (XRD) …

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The Design, Synthesis And Biological Evaluation Of Novel Taxoid Anticancer Agents And Their Tumor-Targeted Drug Conjugates, Joshua Seitz Dec 2013

The Design, Synthesis And Biological Evaluation Of Novel Taxoid Anticancer Agents And Their Tumor-Targeted Drug Conjugates, Joshua Seitz

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

Cancer is the second leading cause of death in the United States and is responsible for one in eight deaths worldwide. Traditional chemotherapeutics target the processes involved in cell division and consequently produce dangerous and dose-limiting side effects. In an effort to identify the therapeutic windown of these drugs, tumor targeted drug conjugates (TTDCs) are currently under development. The Ojima lab has developed and extensive panel of next-generation taxoids that possess the requisite sub-nanomolar potency for incorporation into effective conjugates. A small library of 17 taxoids was synthesized and their cytotoxicity investigated. Selected taxoids were synthesized on the half-gram to …

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Analysis Of The Interaction Of H-Nox With Dgc Using In Vivo Methods And Analytical Ultracentrifugation, Patryk Zielinski Dec 2013

Analysis Of The Interaction Of H-Nox With Dgc Using In Vivo Methods And Analytical Ultracentrifugation, Patryk Zielinski

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

Biofilms are a naturally occurring phenomenon and are known to be a significant problem in various fields including both the industrial and health environments. Bacterial biofilms are defined as the attachment and aggregation of a community of bacteria to solid surfaces. This behavior can lead to infections via medical transplants and compromise the functionality and durability of industrial equipment. Two proteins, Heme-Nitric oxide/Oxygen (H-NOX) and di-guanylate cyclase (DGC), are known to play an important role in the regulation of biofilm formation in bacteria. These two proteins down regulate the concentration of c-di-GMP, a second messenger molecule, in a cell. Since …

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Reconstructing Latina Images: Modern Family, Ugly Betty, And The Confirmation Hearings Of Supreme Court Justice Sonia Sotomayor, Betty E. Muller Dec 2013

Reconstructing Latina Images: Modern Family, Ugly Betty, And The Confirmation Hearings Of Supreme Court Justice Sonia Sotomayor, Betty E. Muller

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

Latina. 122 pages

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When The Personal Became Political: First-Person Fictions And Second-Wave Feminism, Megan Elizabeth Behrent Dec 2013

When The Personal Became Political: First-Person Fictions And Second-Wave Feminism, Megan Elizabeth Behrent

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

Second-wave feminism made famous the slogan, " The personal is political." This dissertation explores the relationship between the personal and political in fictional narratives associated with the development of second-wave feminism in the United States in the 1960s and 70s. Deeply engaged with the political movements that arose amidst this turbulent period in American history, these narratives reflect--in both form and content--the political discourses that dominated both the women's liberation movement and the New Left. The first-person fictions of feminist writers that emerge in this period traverse, and subvert, the boundaries between truth and fiction as well the personal and …

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Scalable Particle And Mesh Algorithms For Elliptic Components Of Multiphase Problems, Tongfei Guo Dec 2013

Scalable Particle And Mesh Algorithms For Elliptic Components Of Multiphase Problems, Tongfei Guo

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

New mesh and meshless algorithms for elliptic boundary and elliptic interface problems have been developed. By utilizing the embedded boundary method, a mesh based algorithm to solve elliptic interface problem is implemented as an extension of hybrid Eulerian-Lagrangian hydrodynamic library FronTier which employs the method of front tracking for interface propagation and this implementation is parallelized for distributed memory clusters. The use of embedded boundary method supports arbitrary discontinuities of density and other physics properties across the interfaces and significantly improves methods that smear interface discontinuities across several grid cells. This code has been applied to process simulation for heat …

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Development Of Microreactor System For In Situ Investigation Of Rock-Brine-Co2 Interactions, Ashley Elizabeth Thompson Dec 2013

Development Of Microreactor System For In Situ Investigation Of Rock-Brine-Co2 Interactions, Ashley Elizabeth Thompson

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

A microreactor has been developed for in situ, high-energy x-ray diffraction investigations of reaction process between carbon dioxide, brines and rocks. Our design is an evolution of a previous existing reaction cell developed by Diefenbacher et al [1]. | Several changes and improvements have been made to the new cell design: (i) the reactor chamber will be accessible through two points, whereby any combination of gases, liquids or fluids can be injected and investigated,(ii) the CO2 flow and pressure will be controlled through a supercritical fluid pump which allows the cell to operate under a well-controlled pressure and flow …

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What You Like In Design Use To Correct Bad-Smells, Marouane Kessentini, Rim Mahaouachi, Khaled Ghedira Dec 2013

What You Like In Design Use To Correct Bad-Smells, Marouane Kessentini, Rim Mahaouachi, Khaled Ghedira

Computer Science Faculty Research & Creative Works

Over the past decades, many techniques and tools have been developed to support maintenance activities in order to improve software quality. One of the most efficient ones is software refactoring to eliminate bad smells. A majority of existing work propose "standard" refactoring solutions that can be applied by hand for each kind of defect. However, it is difficult to prove or ensure the generality of these solutions to any kind of bad-smells or software codes. In this paper, we propose an approach to correct bad smells using well-designed code. We use genetic algorithms to generate correction solutions defined as a …

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December 2013 Committee Reports/Updates Dec 2013

December 2013 Committee Reports/Updates

NASIG Newsletter

No abstract provided.

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December 2013 Full Issue Dec 2013

December 2013 Full Issue

NASIG Newsletter

No abstract provided.

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Good Hair, Bad Hair, Dominican Hair, Haitian Hair, Katie E. Saunders Dec 2013

Good Hair, Bad Hair, Dominican Hair, Haitian Hair, Katie E. Saunders

Master's Theses - Sociology and Anthropology

The goal of this research is to build on the literature concerning presentation practices of racial and national identity. The research examines presentation practices of race and national identity among Haitian heritage residents of the Dominican Republic (DR). Haitian immigrants have been an important part of the Dominican economy and the Dominican way of life since the beginning of the 20th century. Their descendants have to manage between Haitian and Dominican identities, while under the incredible pressure of anti-Haitian prejudices. The current literature concerning Dominican presentation practices asserts that normative presentation practices hide racial blackness. However, more recent literature questions …

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Openline Newsletter, December 2013, Civil Service Council Dec 2013

Openline Newsletter, December 2013, Civil Service Council

OpenLine Newsletter

A monthly newsletter for Civil Service employees, Volume XXXVIII, Number 6, December 2013.

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Social Networks Sites: Usage And Effects, Ahmed Y. Abdelraheem Dec 2013

Social Networks Sites: Usage And Effects, Ahmed Y. Abdelraheem

Journal of Educational and Psychological Studies

The aim of this paper is to explore the students’ use of social networks sites (SNSs) and its effects on students’ achievement. A questionnaire using a Liker type scale was distributed to a sample of 120 undergraduate students who participated in the study. The results show that students use SNSs for social matters more than for academic purposes. In this regard, there is no significant difference in the use of social network sites between female and male students. Students with smart mobile phones use SNSs more than those with normal mobiles. Facebook was the most used site. There is no …

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Students’ Perceptions Of Religious Beliefs As Gained From Jordanian Universities Religious Educational Courses, Mahir S. Al-Hawamleh Dec 2013

Students’ Perceptions Of Religious Beliefs As Gained From Jordanian Universities Religious Educational Courses, Mahir S. Al-Hawamleh

Journal of Educational and Psychological Studies

The present study looked at the educational religious beliefs as gained from university courses using a self-reported questionnaire as well as semi-structured interviews. 591 students chosen through stratified random design responded to the questionnaire. 64 students from the study's sample were interviewed. The current study presented evidence to support the identification and comparison of the educational religious perceptions held by the two sets of students from Mu'tah University and Al al-Bayt University. The analysis concluded that religious education courses influenced deeply and with varying degrees students’ perceptions of religious affiliation to a large extent at Al-al Bayt University; nevertheless, it …

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Determining The Feasibility Of Implementing An Effective Fungiculture Program With The Peace Garden At Illinois Wesleyan University, Mackenzie Rivkin '14 Dec 2013

Determining The Feasibility Of Implementing An Effective Fungiculture Program With The Peace Garden At Illinois Wesleyan University, Mackenzie Rivkin '14

Outstanding Senior Seminar Papers

The Peace Garden at Illinois Wesleyan University (IWU), the organic garden at the small liberal-arts university in Bloomington, Illinois, is devoted to growing nutritious, pesticide-free food to be sold locally in an attempt to counterbalance the various food-related issues which stem from conventional food systems. Mushrooms, fungi with many nutritional benefits, are not currently produced by the Peace Garden. However, the unique nature of mushrooms may be attractive to certain consumers and could further contribute to the Peace Garden's mission if produced. This study, conducted September to December 2013 is guided by the following question: What is the feasibility of …

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Establishing Key Performance Indicators To Measure The Benefit Of Introducing The Facilities Manager At An Early Stage In The Building Information Modelling Process, Barry Mcauley Dec 2013

Establishing Key Performance Indicators To Measure The Benefit Of Introducing The Facilities Manager At An Early Stage In The Building Information Modelling Process, Barry Mcauley

Conference papers

The Facilities Manager occupies a unique position within the lifecycle of a building asset, as he/she is one of the only AEC / FM professionals who is in a position to view the product of the entire design and build process and, is responsible for the operational phase which incurs approximately five times the initial capital cost. Despite the potential benefits that the Facilities Manager offers, this profession still does not command the recognition it deserves within the AEC/FM sector. This is beginning to change through the introduction of Building Information Modelling (BIM). In order for the BIM process to …

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Understanding The Attitude-Behavior Gap For Renewable Energy Systems Using Behavioral Reasoning Theory, Marius Claudy, Mark Peterson, Aidan O'Driscoll Dec 2013

Understanding The Attitude-Behavior Gap For Renewable Energy Systems Using Behavioral Reasoning Theory, Marius Claudy, Mark Peterson, Aidan O'Driscoll

Articles

Consumer adoption of renewable energies is an important step towards less carbon-intensive and more sustainable energy systems. But despite growing ecological awareness and articulated preferences for green products, renewable energies face slow rates of diffusion in consumer markets. This has been hard to explain given consumers’ favorability to the concept of products that lower one’s impact on the natural environment. This study uses data from 254 homeowners in Ireland to investigate the psychological process of adopting a renewable energy system – solar energy panels. Applying Behavioral Reasoning Theory (BRT), this research examines a proposed model in which reasons both for …

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Waveguiding Of Surface Phonon Polariton, Franklin Manene, Brian A. Lail, Edward C. Kinzel Dec 2013

Waveguiding Of Surface Phonon Polariton, Franklin Manene, Brian A. Lail, Edward C. Kinzel

Mechanical and Aerospace Engineering Faculty Research & Creative Works

Metal losses lead to unacceptably low propagation lengths in THz and LWIR waveguides. While SPP based waveguides provide relatively good confinement and attenuation in the near-IR and visible these are insufficiently bound to the surface in the THz and LWIR. We study using surface phonon polaritons for waveguiding at these frequencies. An eigenmode approach was applied to model a hybrid waveguide structure at λ=10.6 μm. The results show that phonon-coupled hybrid waveguide of silicon carbide BCB and gold exhibit enhanced propagation length and confinement at LWIR. © 2013 IEEE.

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