Physical Sciences and Mathematics Commons^™

Interactions Of Eukaryotic Translation Initiation Factors And 3' Untranslated Region Of Barley Yellow Dwarf Virus Mrna During Protein Synthesis: A Study Of Equilibrium Binding, Kinetics And Thermodynamics, Bidisha Banerjee

Dissertations, Theses, and Capstone Projects

Eukaryotic initiation factor (eIF) 4F binding to mRNA is the first committed step in cap-dependent protein synthesis. Barley Yellow Dwarf Virus (BYDV) employs a cap-independent mechanism of translation initiation which is mediated by a structural element BTE (BYDV translation element) located in the 3’ UTR of its mRNA. eIF4F bound the BTE and a translational inactive mutant with high affinity; thus questioning the role of eIF4F in translation of BYDV. To examine the effects of eIF4F in BYDV translation initiation, BTE mutants with widely different in vitro translation efficiencies ranging from 5-164% compared to WT were studied. Using fluorescence anisotropy …

Automated Classification Of Argument Stance In Student Essays: A Linguistically Motivated Approach With An Application For Supporting Argument Summarization, Adam Robert Faulkner

Dissertations, Theses, and Capstone Projects

This study describes a set of document- and sentence-level classification models designed to automate the task of determining the argument stance (for or against) of a student argumentative essay and the task of identifying any arguments in the essay that provide reasons in support of that stance. A suggested application utilizing these models is presented which involves the automated extraction of a single-sentence summary of an argumentative essay. This summary sentence indicates the overall argument stance of the essay from which the sentence was extracted and provides a representative argument in support of that stance.

A novel set …

The Evolution Of And Starburst-Agn Connection In Luminous And Ultraluminous Infrared Galaxies And Their Link To Globular Cluster Formation, Stephanie L. Fiorenza

Dissertations, Theses, and Capstone Projects

The evolutionary connection between nuclear starbursts and active galactic nuclei (AGN) in luminous infrared galaxies (LIRGs; 1011o

Using new spectrophotometric data, I classify the primary source of IR radiation as being a nuclear starburst or a type of AGN by using the Baldwin-Phillips-Terlevich (BPT) diagrams. I show that for the U/LIRGs in my sample the properties that describe their nuclear starbursts and AGN (e.g. star formation rate (SFR), L[O III], optical D parameter, D4000, and EW(Hδ)) are independent of one another, ensuring that no biases affect correlations between these properties and objects' locations on the BPT diagrams. I then derive …

Data-Based Perfect-Deficit Approach To Understanding Climate Extremes And Forest Carbon Assimilation Capacity, Suhua Wei, Chuixiang Yi, George Hendrey, Timothy Eaton, Gerald Rustic, Shaoqiang Wang, Heping Liu, Nir Y. Krakauer, Weiguo Wang, Ankur R. Desai, Leonardo Montagnani, Kyaw Tha Paw U, Matthias Falk, Andrew Black, Christian Bernhofer, Thomas Grünwald, Tuomas Laurila, Alessandro Cescatti, Eddy Moors, Rosvel Bracho, Riccardo Valentini

Publications and Research

Several lines of evidence suggest that the warming climate plays a vital role in driving certain types of extreme weather. The impact of warming and of extreme weather on forest carbon assimilation capacity is poorly known. Filling this knowledge gap is critical towards understanding the amount of carbon that forests can hold. Here, we used a perfect-deficit approach to identify forest canopy photosynthetic capacity (CPC) deficits and analyze how they correlate to climate extremes, based on observational data measured by the eddy covariance method at 27 forest sites over 146 site-years. We found that droughts severely affect the carbon assimilation …

In Harm's Way: How Philadelphia's Urban Renewal Practices Steered Marginal People To Marginal Land, Katera Ya'shea Moore

Dissertations, Theses, and Capstone Projects

The dumping of locally unwanted land uses (LULUs) on marginal communities has been well documented, however environmental justice scholars have rarely written about how marginal groups have come to occupy their landscapes, particularly when natural hazards lie beneath.

This dissertation research focuses on a broad definition of the environment that includes the built, social, and physical. I am interested in extending Logan and Molotch's Growth Machine theory to consider how the political and economic elite guided the urban renewal process to place particular communities on particular landscapes, despite the presence of a flooding hazard. To understand this issue, I examined …

China’S Water Sustainability In The 21st Century: A Climate-Informed Water Risk Assessment Covering Multi-Sector Water Demands, X. Chen, Naresh Devineni, L. Upmanu, Z. Hao, L. Dong, Q. Ju, J. Wang, S. Wang

Publications and Research

China is facing a water resources crisis with growing concerns as to the reliable supply of water for agricultural, industrial and domestic needs. High inter-annual rainfall variability and increasing consumptive use across the country exacerbates the situation further and is a constraint on future development. For water sustainability, it is necessary to examine the differences in water demand and supply and their spatio-temporal distribution in order to quantify the dimensions of the water risk. Here, a detailed quantitative assessment of water risk as measured by the spatial distribution of cumulated deficits for China is presented. Considering daily precipitation and temperature …

Intelligent Sampling For Big Data Using Bootstrap Sampling And Chebyshev Inequality, Ashwin Satyanarayana

Publications and Research

The amount of data being generated and stored is growing exponentially, owed in part to the continuing advances in computer technology. These data present tremendous opportunities in data mining, a burgeoning field in computer science that focuses on the development of methods that can extract knowledge from data. In many real world problems, these data mining algorithms have access to massive amounts of data. Mining all the available data is prohibitive due to computational (time and memory) constraints. Much of the current research is concerned with scaling up data mining algorithms (i.e. improving on existing data mining algorithms for larger …

1207-3900_Opt_Mage, Jonathan Gagné

Publications and Research

No abstract provided.

1207-3900_Nir_Spex, Jonathan Gagné

Publications and Research

No abstract provided.

Decoding Quantitative Language, Steven Cosares, Evelyn Burg

Open Educational Resources

We all need some “quantitative literacy” in order to communicate effectively. This means being able to read, write or speak intelligently in a medium where some quantitative information is a part the discussion, proof, or argument. The readers of these materials are expected to have sufficient wherewithal to understand this language so as to draw appropriate conclusions. Developing this type of literacy requires practice. It means using everyday language to describe the ways in which quantities relate to one another.

Multi-Leg One-Loop Massive Amplitudes From Integrand Reduction Via Laurent Expansion, Hans Van Deurzen, Gionata Luisoni, Pierpaolo Mastrolia, Edoardo Mirabella, Giovanni Ossola, Tiziano Peraro

Publications and Research

We present the application of a novel reduction technique for one-loop scattering amplitudes based on the combination of the integrand reduction and Laurent expansion. We describe the general features of its implementation in the computer code Ninja, and its interface to GoSam. We apply the new reduction to a series of selected processes involving massive particles, from six to eight legs.

Uranium And Radon In Private Bedrock Well Water In Maine: Geospatial Analysis At Two Scales, Qiang Yang, Paul Smitherman, C. T. Hess, Charles W. Culbertson, Robert G. Marvinney, Andrew E. Smith, Yan Zheng

Publications and Research

In greater Augusta of central Maine, 53 out of 1093 (4.8%) private bedrock well water samples from 1534 km2 contained [U] >30 μg/L, the U.S. Environmental Protection Agency’s (EPA) Maximum Contaminant Level (MCL) for drinking water; and 226 out of 786 (29%) samples from 1135 km2 showed [Rn] >4,000 pCi/L (148 Bq/L), the U.S. EPA’s Alternative MCL. Groundwater pH, calcite dissolution and redox condition are factors controlling the distribution of groundwater U but not Rn due to their divergent chemical and hydrological properties. Groundwater U is associated with incompatible elements (S, As, Mo, F, and Cs) in water samples within …

Economic Growth Assumptions In Climate And Energy Policy, Nir Y. Krakauer

Publications and Research

The assumption that the economic growth seen in recent decades will continue has dominated the discussion of future greenhouse gas emissions and the mitigation of and adaptation to climate change. Given that long-term economic growth is uncertain, the impacts of a wide range of growth trajectories should be considered. In particular, slower economic growth would imply that future generations will be relatively less able to invest in emissions controls or adapt to the detrimental impacts of climate change. Taking into consideration the possibility of economic slowdown therefore heightens the urgency of reducing greenhouse gas emissions now by moving to renewable …

Nnll Momentum-Space Resummation For Stop-Pair Production At The Lhc, Alessandro Broggio, Andrea Ferroglia, Matthias Neubert, Leonardo Vernazza, Li Lin Yang

Publications and Research

If supersymmetry near the TeV scale is realized in Nature, the pair production of scalar top squarks is expected to be observable at the Large Hadron Collider. Recently, effective field-theory methods were employed to obtain approximate predictions for the cross section for this process, which include soft-gluon emission effects up to nextto- next-to-leading order (NNLO) in perturbation theory. In this work we employ the same techniques to resum soft-gluon emission effects to all orders in perturbation theory and with next-to-next-to-logarithmic (NNLL) accuracy. We analyze the effects of NNLL resummation on the stop-pair production cross section by obtaining NLO+NNLL predictions in …

Synergism Between Airborne Singlet Oxygen And A Trisubstituted Olefin Sulfonate For The Inactivation Of Bacteria, Rajib Choudhury, Alexander Greer

Publications and Research

The reactivity of a trisubstituted alkene surfactant (8-methylnon-7-ene-1 sulfonate, 1) to airborne singlet oxygen in a solution containing E. coli was examined. Surfactant 1 was prepared by a Strecker-type reaction of 9-bromo-2-methylnon-2-ene with sodium sulfite. Submicellar concentrations of 1 were used that reacted with singlet oxygen by an “ene” reaction to yield two hydroperoxides (7-hydroperoxy-8-methylnon-8-ene-1 sulfonate and (E)-8-hydroperoxy-8-methylnon-6-ene-1 sulfonate) in a 4:1 ratio. Exchanging the H₂O solution for D₂O where the lifetime of solution-phase singlet oxygen increases by 20-fold led to an ∼2-fold increase in the yield of hydroperoxides pointing to surface activity …

Cretaceous-Paleogene Dinoflagellate Biostratigraphy And The Age Of The Clayton Formation, Southeastern Missouri, Usa, Natalie R. Dastas, John A. Chamberlain Jr., Matthew P. Garb

Publications and Research

Sedimentary deposits in Stoddard County, southeastern Missouri, reveal a K-Pg transition sequence represented by the uppermost Maastrichtian Owl Creek Formation and the Paleocene Clayton Formation. The Clayton Formation is characterized by a basal fossiliferous coquinite that contains reworked late Maastrichtian macrofossils. Dinoflagellate biostratigraphy is used to determine the age of the coquinite layer and specifically whether or not it is an end-K tsunamite deposit resulting from the Chicxulub impact event. Results indicate a mixed assemblage of late Maastrichtian and early Danian dinocysts within the basal coquinite of the Clayton Formation. Maastrichtian dinocyst taxa identified are Riculacysta amplexa, Pierceites pentagonus, Phelodinium …

Capping Amyloid Β‑Sheets Of The Tau-Amyloid Structure Vqivyk With Hexapeptides Designed To Arrest Growth. An Oniom And Density Functional Theory Study, Joshua A. Plumley, Jorge Ali-Torres, Gabor Pohl, J. J. Dannenberg

Publications and Research

We present ONIOM calculations using density functional theory (DFT) as the high and AM1 as the medium level that explore the abilities of different hexapeptide sequences to terminate the growth of a model for the tau-amyloid implicated in Alzheimer’s disease. We delineate and explore several design principles (H-bonding in the side chains, using antiparallel interactions on the growing edge of a parallel sheet, using all-D residues to form rippled interactions at the edge of the sheet, and replacing the H-bond donor N−H’s that inhibit further growth) that can be used individually and in combination to design such peptides that will …

Groundwater Flow Across Spatial Scales: Importance For Climate Modeling, Nir Krakauer, Haibin Li, Ying Fan

Publications and Research

Current regional and global climate models generally do not represent groundwater flow between grid cells as a component of the water budget. We estimate the magnitude of between cell groundwater flow as a function of grid cell size by aggregating results from a numerical model of equilibrium groundwater flow run and validated globally. We find that over a broad range of cell sizes spanning that of state of the art regional and global climate models, mean between cell groundwater flow magnitudes scale with the reciprocal of grid cell length. We also derive this scaling a priori from a simple statistical …

Intramolecular Nitrogen Delivery For The Synthesis Of C-Glycosphingolipids. Application To The C-Glycoside Of The Immunostimulant Krn7000, Ahmad Sabri Altiti, David R. Mootoo

Publications and Research

The key reaction in this approach to C-glycosphingolipids is the stereoselective iodocyclization of a sugar-linked homoallylic carbonimidothioate. E and Z reaction substrates were assembled in a convergent fashion via an alkene metathesis strategy and exhibited the same alkene facial selectivity in the iodocyclization irrespective of alkene geometry, although the E alkene was found to be less reactive.

Are Climate Model Simulations Useful For Forecasting Precipitation Trends? Hindcast And Synthetic-Data Experiments, Nir Y. Krakauer, Balázs M. Fekete

Publications and Research

Water scientists and managers currently face the question of whether trends in climate variables that affect water supplies and hazards can be anticipated. We investigate to what extent climate model simulations may provide accurate forecasts of future hydrologic nonstationarity in the form of changes in precipitation amount. We compare gridded station observations (GPCC Full Data Product, 1901–2010) and climate model outputs (CMIP5 Historical and RCP8.5 simulations, 1901–2100) in real and syntheticdata hindcast experiments. The hindcast experiments show that imputing precipitation trends based on the climate model mean reduced the root mean square error of precipitation trend estimates for 1961–2010 by …

A Review Of Air–Ice Chemical And Physical Interactions (Aici): Liquids, Quasi-Liquids, And Solids In Snow, T. Bartels-Rausch, H-W Jacobi, T. F. Kahan, J. L. Thomas, E. S. Thomson, J. P. D. Abbatt, M. Ammann, J. R. Blackford, H. Bluhm, Chris Boxe, F. Domine, M. M. Frey, I. Gladich, M. I. Guzmán, D. Heger, Th. Huthwelker, P. Klán, W. F. Kuhs, M. H. Kuo, S. Maus, S. G. Moussa, V. F. Mcneill, J. T. Newberg, J. B. C. Pettersson, M. Roeselová, J. R. Sodeau

Publications and Research

Snow in the environment acts as a host to rich chemistry and provides a matrix for physical exchange of contaminants within the ecosystem. The goal of this review is to summarise the current state of knowledge of physical processes and chemical reactivity in surface snow with relevance to polar regions. It focuses on a description of impurities in distinct compartments present in surface snow, such as snow crystals, grain boundaries, crystal surfaces, and liquid parts. It emphasises the microscopic description of the ice surface and its link with the environment. Distinct differences between the disordered air–ice interface, often termed quasi-liquid …

Deconstructing A Plant Macromolecular Assembly: Chemical Architecture, Molecular Flexibility, And Mechanical Performance Of Natural And Engineered Potato Suberins, Olga Serra, Subhasish Chatterjee, Merce Figueras, Marisa Molinas, Ruth E. Stark

Publications and Research

Periderms present in plant barks are essential protective barriers to water diffusion, mechanical breakdown, and pathogenic invasion. They consist of densely packed layers of dead cells with cell walls that are embedded with suberin. Understanding the interplay of molecular structure, dynamics, and biomechanics in these cell wall-associated insoluble amorphous polymeric assemblies presents substantial investigative challenges. We report solid-state NMR coordinated with FT-IR and tensile strength measurements for periderms from native and wound-healing potatoes and from potatoes with genetically modified suberins. The analyses include the intact suberin aromatic; aliphatic polymer and cell-wall polysaccharides, previously reported soluble depolymerized transmethylation products, and undegraded …

Data-Driven Synthesis Of Animations Of Spatially Inflected American Sign Language Verbs Using Human Data, Pengfei Lu

Dissertations, Theses, and Capstone Projects

Techniques for producing realistic and understandable animations of American Sign Language (ASL) have accessibility benefits for signers with lower levels of written language literacy. Previous research in sign language animation didn’t address the specific linguistic issue of space use and verb inflection, due to a lack of sufficiently detailed and linguistically annotated ASL corpora, which is necessary for modern data-driven approaches. In this dissertation, a high-quality ASL motion capture corpus with ASL-specific linguistic structures is collected, annotated, and evaluated using carefully designed protocols and well-calibrated motion capture equipment. In addition, ASL animations are modeled, synthesized, and evaluated based on samples …

Property Enhancements Of Dielectric Nanoparticles Via Surface Functionalization, Andrew Byro

Dissertations, Theses, and Capstone Projects

This thesis describes the surface modification of barium strontium titanate nanoparticles for use in polymer/ceramic composite thin film capacitors with resultant improved dielectric and film-making properties. Phosphonic acid-type ligands proved to be most effective for surface conjugation to the surface of the barium strontium titanate nanoparticles. Amine-terminated ligands proved to be effective at removing surface adsorbed water before being almost entirely removed during the sample washing stage. Carboxylic acid terminated ligands proved to adhere less well to the nanoparticle than the phosphonic acid, but resulted in thin films with a higher dielectric constant, which was more stable in the measured …

Suburban Heat Islands: The Influence Of Residential Minimum Lot Size Zoning On Surface Heat Islands In Somerset County, New Jersey, Jennifer Renee Cox

Dissertations, Theses, and Capstone Projects

The process of suburbanization blurs regional bounds, forms mega-regions and fosters the expansion of multifaceted environmental problems, such as the urban heat island (UHI) effect. Defined by differences in air- and surface- temperature between rural and urban areas, UHI is the result of the characteristics of urbanization which modify the land surface condition, urban geometry, thermal properties of construction materials, anthropogenic heat and air pollution, which increase storage and re-radiation of heat to the atmosphere. Climate change is predicted to worsen the UHI effect. Hence, the objective of this research to characterize the UHI effect as it pertains to suburban …

Phylogenetic Trees And Their Analysis, Eric Ford

Dissertations, Theses, and Capstone Projects

Determining the best possible evolutionary history, the lowest-cost phylogenetic tree, to fit a given set of taxa and character sequences using maximum parsimony is an active area of research due to its underlying importance in understanding biological processes. As several steps in this process are NP-Hard when using popular, biologically-motivated optimality criteria, significant amounts of resources are dedicated to both both heuristics and to making exact methods more computationally tractable. We examine both phylogenetic data and the structure of the search space in order to suggest methods to reduce the number of possible trees that must be examined to find …

Fabrication And Assembly Of Patchy Particles With Uniform Patches, Zhenping He

Dissertations, Theses, and Capstone Projects

Patchy colloidal particles have been widely studied as the self-assembly building blocks to illustrate their potential for forming complex structures. The parameters affecting the final assembly structures include (i) patch size, shape, and number per particle, (ii) their relative positions, and (iii) the surface properties of the patch material. Recent computational studies have highlighted the impact of patch shape on assembly structure; however, there are only a limited number of methods that can provide control over patch shape and size. In this thesis, a template is introduced to the Glancing Angle Vapor Deposition method (GLAD) to create surface anisotropy on …

Development Of Mesoporous Silicas, Responsive Polymer Microgels, And Related Nanocomposites, Yingyu Li

Dissertations, Theses, and Capstone Projects

This dissertation covers research on polymer-templated nanoporous materials and functional soft materials, and it consists of four major parts. The first part is on introduction. The next part (Chapters 2-3) describes the research work on the synthesis of silicas with spherical mesopores. Chapter 2 is focused on the synthesis of large-pore FDU-12 silicas at room temperature by using surfactants with large hydrophilic blocks and relatively small hydrophobic blocks (such as Pluronic F108 (EO132PO50EO132)) as the template. Chapter 3 discusses an interesting mesopore structure, which is the hollow silica nanosphere (HSN). The single-micelle-templating strategy provides a general approach for the synthesis …

Gauge/ Gravity Correspondence, Bulk Locality And Quantum Black Holes, Debajyoti Sarkar

Dissertations, Theses, and Capstone Projects

The aim of this dissertation is threefold. We begin by the study of two parallel ideal cosmic strings in the presence of non-minimal scalar fields and spin- 1 gauge fields. We show that the contributions of the non-minimal term on the interaction energy between the strings are similar to that of the gauge field for a particular value of non-minimal coupling parameter. In this context we clarify some of the issues that arise when comparing the renormalization of black hole entropy and entanglement entropy using the replica trick.

In the second part of the dissertation we study the process of …

Intelligent Nano/Microgels For Cell Scaffold And Drug Delivery System, Jing Shen

Dissertations, Theses, and Capstone Projects

Stimulus-responsive polymer microgels swell and shrink reversibly upon exposure to various environmental stimuli such as change in pH, temperature, ionic strength or magnetic fields. Therefore, they become ideal candidates for biomaterial applications. For this work, we focus on the several intelligent microgels and their application on two areas: the cell scaffold and the drug delivery system.

As for the cell scaffold, it can be realized by colloidal supra-structure microgels, which constructed by the thermo-driven gelation of the colloidal dispersion of poly(N-isopropylacrylamide-co-acrylamide) poly(NIPAM-co-AAm) microgels (Chapter 3). Such microgels exhibit a reversible and continuous volume transition in water with volume phase transition …