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University of Richmond

Series

2014

Articles 1 - 17 of 17

Full-Text Articles in Physical Sciences and Mathematics

Molecular Dynamics Study Of The Opening Mechanism For Dna Polymerase I, Carol A. Parish, Bill R. Miller Iii, Eugene Y. Wu Dec 2014

Molecular Dynamics Study Of The Opening Mechanism For Dna Polymerase I, Carol A. Parish, Bill R. Miller Iii, Eugene Y. Wu

Chemistry Faculty Publications

During DNA replication, DNA polymerases follow an induced fit mechanism in order to rapidly distinguish between correct and incorrect dNTP substrates. The dynamics of this process are crucial to the overall effectiveness of catalysis. Although Xray crystal structures of DNA polymerase I with substrate dNTPs have revealed key structural states along the catalytic pathway, solution fluorescence studies indicate that those key states are populated in the absence of substrate. Herein, we report the first atomistic simulations showing the conformational changes between the closed, open, and ajar conformations of DNA polymerase I in the binary (enzyme:DNA) state to better understand its …

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Silyl Trifluoromethanesulfonate-Activated Para-Methoxybenzyl Methyl Ether As An Alkylating Agent For Thiols And Aryl Ketones, C. Wade Downey, Sarah E. Covington, Derek C. Obenschain, Evan Halliday, James T. Rague, Danielle N. Confair Sep 2014

Silyl Trifluoromethanesulfonate-Activated Para-Methoxybenzyl Methyl Ether As An Alkylating Agent For Thiols And Aryl Ketones, C. Wade Downey, Sarah E. Covington, Derek C. Obenschain, Evan Halliday, James T. Rague, Danielle N. Confair

Chemistry Faculty Publications

para-Methoxybenzyl methyl ether acts as an alkylating agent for thiols in the presence of trimethylsilyl trifluoromethanesulfonate and trialkylamine base in good yields (58-96%). Aryl ketones are alkylated under similar conditions, probably through an enol silane intermediate, also in high yields (67-95%). The active alkylating species is likely a p-methoxybenzyl cation.

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On Quasilinear Parabolic Evolution Equations In Weighted Lp-Spaces Ii, Jeremy Lecrone, Mathias Wilke, Jan Prüss Sep 2014

On Quasilinear Parabolic Evolution Equations In Weighted Lp-Spaces Ii, Jeremy Lecrone, Mathias Wilke, Jan Prüss

Department of Math & Statistics Faculty Publications

Our study of abstract quasi-linear parabolic problems in time-weighted L_p-spaces, begun in 2010, is extended in this paper to include singular lower order terms, while keeping low initial regularity. The results are applied to reaction-diffusion problems, including Maxwell-Stefan diffusion, and to geometric evolution equations like the surface-diffusion flow or the Willmore flow. The method presented here will be applicable to other parabolic systems, including free boundary problems.

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Silyl Triflate-Accelerated Additions Of Catalytically Generated Zinc Acetylides To N-Phenyl Nitrones, C. Wade Downey, Erin N. Maxwell, Danielle N. Confair Aug 2014

Silyl Triflate-Accelerated Additions Of Catalytically Generated Zinc Acetylides To N-Phenyl Nitrones, C. Wade Downey, Erin N. Maxwell, Danielle N. Confair

Chemistry Faculty Publications

Terminal alkynes readily form zinc acetylides in the presence of iPr2NEt and 20 mol% ZnBr2, then attack N-phenyl nitrones activated by trimethylsilyl trifluoromethanesulfonate. Deprotection with aqueous acid yields the N-hydroxyl propargylamine. Yields are generally high for nitrones derived from aromatic aldehydes. Control experiments suggest that the silyl triflate has a significant accelerating effect upon the reaction.

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Climate Justice Advocacy, Mary Finley-Brook Jul 2014

Climate Justice Advocacy, Mary Finley-Brook

Geography and the Environment Faculty Publications

Creating international policy to combat climate change is one of the biggest public diplomacy challenges of our time. With slow progress in “state-led” forums such as the annual Conference of the Parties (COP) to the United Nations Framework Convention on Climate Change (UNFCCC), advocacy coalitions of non-governmental organizations (NGOs) are pressuring decision-makers and working to build global awareness. The power of NGOs is soft since state actors set emissions targets; nonetheless, climate justice organizations persistently broadcast several important messages, including: 1) industrialized nations along with private sector polluters have an obligation to remedy ecological debt; 2) low-income and marginalized populations …

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Recent Cropping Frequency, Expansion, And Abandonment In Mato Grosso, Brazil Had Selective Land Characteristics, Stephanie A. Spera, Avery S. Cohn, Leah K. Vanwey, Jack F. Mustard, Bernardo F.T. Rudorff, Marcos Adami Jun 2014

Recent Cropping Frequency, Expansion, And Abandonment In Mato Grosso, Brazil Had Selective Land Characteristics, Stephanie A. Spera, Avery S. Cohn, Leah K. Vanwey, Jack F. Mustard, Bernardo F.T. Rudorff, Marcos Adami

Geography and the Environment Faculty Publications

This letter uses satellite remote sensing to examine patterns of cropland expansion, cropland abandonment, and changing cropping frequency in Mato Grosso, Brazil from 2001 to 2011. During this period, Mato Grosso emerged as a globally important center of agricultural production. In 2001, 3.3 million hectares of mechanized agriculture were cultivated in Mato Grosso, of which 500 000 hectares had two commercial crops per growing season (double cropping). By 2011, Mato Grosso had 5.8 million hectares of mechanized agriculture, of which 2.9 million hectares were double cropped. We found these agricultural changes to be selective with respect to land attributes —significant …

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Multi-Technique Quantitative Analysis And Socioeconomic Considerations Of Lead, Cadmium, And Arsenic In Children's Toys And Toy Jewelry, Margot M. Hillyer, Lauren E. Finch, Alisha S. Cerel, Jonathan D. Dattelbaum, Michael C. Leopold Feb 2014

Multi-Technique Quantitative Analysis And Socioeconomic Considerations Of Lead, Cadmium, And Arsenic In Children's Toys And Toy Jewelry, Margot M. Hillyer, Lauren E. Finch, Alisha S. Cerel, Jonathan D. Dattelbaum, Michael C. Leopold

Chemistry Faculty Publications

A wide spectrum and large number of children’s toys and toy jewelry items were purchased from both bargain and retail vendors and analyzed for arsenic, cadmium, and lead metal content using multiple analytical techniques, including flame and furnace atomic absorption spectroscopy as well as X-ray fluorescence spectroscopy. Particularly dangerous for young children, metal concentrations in toys/toy jewelry were assessed for compliance with current Consumer Safety Product Commission (CPSC) regulations (F963-11). A conservative metric involving multiple analytical techniques was used to categorize compliance: one technique confirmation of metal in excess of CPSC limits indicated a “suspect” item while confirmation on two …

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Bad Boundary Behavior In Star Invariant Subspaces I, William T. Ross, Andreas Hartmann Jan 2014

Bad Boundary Behavior In Star Invariant Subspaces I, William T. Ross, Andreas Hartmann

Department of Math & Statistics Faculty Publications

We discuss the boundary behavior of functions in star invariant subspaces (BH2)1, where B is a Blaschke product. Extending some results of Ahern and Clark, we are particularly interested in the growth rates of functions at points of the spectrum of B where B does not admit a derivative in the sense of Carathéodory.

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C*-Algebras Generated By Truncated Toeplitz Operators, William T. Ross, Stephan Ramon Garcia, Warren R. Wogen Jan 2014

C*-Algebras Generated By Truncated Toeplitz Operators, William T. Ross, Stephan Ramon Garcia, Warren R. Wogen

Department of Math & Statistics Faculty Publications

We obtain an analogue of Coburn’s description of the Toeplitz algebra in the setting of truncated Toeplitz operators. As a byproduct, we provide several examples of complex symmetric operators which are not unitarily equivalent to truncated Toeplitz operators having continuous symbols.

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A Twisted Dimer Model For Knots, Heather M. Russell, Moshe Cohen, Oliver Dasbach Jan 2014

A Twisted Dimer Model For Knots, Heather M. Russell, Moshe Cohen, Oliver Dasbach

Department of Math & Statistics Faculty Publications

We develop a dimer model for the Alexander polynomial of a knot. This recovers Kauffman's state sum model for the Alexander polynomial using the language of dimers. By providing some additional structure we are able to extend this model to give a state sum formula for the twisted Alexander polynomial of a knot depending on a representation of the knot group.

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A Reduced Set Of Moves On One-Vertex Ribbon Graphs Coming From Links, Heather M. Russell, Susan Abernathy, Cody Armond, Moshe Cohen, Oliver T. Dasbach, Hannah Manuel, Chris Penn, Neal W. Stoltzfus Jan 2014

A Reduced Set Of Moves On One-Vertex Ribbon Graphs Coming From Links, Heather M. Russell, Susan Abernathy, Cody Armond, Moshe Cohen, Oliver T. Dasbach, Hannah Manuel, Chris Penn, Neal W. Stoltzfus

Department of Math & Statistics Faculty Publications

Every link in R3 can be represented by a one-vertex ribbon graph. We prove a Markov type theorem on this subset of link diagrams.

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Promoting Reu Participation From Students In Underrepresented Groups, Heather M. Russell, Heather A. Dye Jan 2014

Promoting Reu Participation From Students In Underrepresented Groups, Heather M. Russell, Heather A. Dye

Department of Math & Statistics Faculty Publications

Research experiences for undergraduates (REUs) are an important component of undergraduate education. However, at the 2012 Trends in Undergraduate Research in the Mathematical Sciences conference, questions were raised about why many REU programs see few applications from students that are members of underrepresented groups. We examine the benefits of REUs and factors preventing or promoting participation in REUs.

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Stability And Bifurcation Of Equilibria For The Axisymmetric Averaged Mean Curvature Flow, Jeremy Lecrone Jan 2014

Stability And Bifurcation Of Equilibria For The Axisymmetric Averaged Mean Curvature Flow, Jeremy Lecrone

Department of Math & Statistics Faculty Publications

We study the averaged mean curvature ow, also called the volume preserving mean curvature ow, in the particular setting of axisymmetric surfaces embedded in R3 satisfying periodic boundary conditions. We establish analytic well-posedness of the ow within the space of little-Holder continuous surfaces, given rough initial data. We also establish dynamic properties of equilibria, including stability, instability, and bifurcation behavior of cylinders, where the radius acts as a bifurcation parameter.

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A Loose Domain Swapping Organization Confers A Remarkable Stability To The Dimeric Structure Of The Arginine Binding Protein From Thermotoga Maritima, Alessia Ruggiero, Jonathan D. Dattelbaum, Maria Staiano, Rita Berisio, Sabato D'Auria, Luigi Vitagliano Jan 2014

A Loose Domain Swapping Organization Confers A Remarkable Stability To The Dimeric Structure Of The Arginine Binding Protein From Thermotoga Maritima, Alessia Ruggiero, Jonathan D. Dattelbaum, Maria Staiano, Rita Berisio, Sabato D'Auria, Luigi Vitagliano

Chemistry Faculty Publications

The arginine binding protein from Thermatoga maritima (TmArgBP), a substrate binding protein (SBP) involved in the ABC system of solute transport, presents a number of remarkable properties. These include an extraordinary stability to temperature and chemical denaturants and the tendency to form multimeric structures, an uncommon feature among SBPs involved in solute transport. Here we report a biophysical and structural characterization of the TmArgBP dimer. Our data indicate that the dimer of the protein is endowed with a remarkable stability since its full dissociation requires high temperature as well as SDS and urea at high concentrations. In order to elucidate …

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Stop Rotating! One Substitution Halts The B19- Motor, Francisco Cervantes-Navarro, Gerarso Martínez-Guajardo, Edison Osorio, Diego Moreno, William Tiznado, Rafael Islas, Kelling J. Donald, Gabriel Merino Jan 2014

Stop Rotating! One Substitution Halts The B19- Motor, Francisco Cervantes-Navarro, Gerarso Martínez-Guajardo, Edison Osorio, Diego Moreno, William Tiznado, Rafael Islas, Kelling J. Donald, Gabriel Merino

Chemistry Faculty Publications

The B19- anion and other boron species have been dubbed ‘Wankel motors’ for the almost barrierless rotation of inner and outer concentric rings relative to each other in these compounds. A single substitution in B19- is shown to shut down the well-established fluxionality in the anion. A carbon atom substituted in the structure to give a neutral CB18 species is shown computationally to enforce bond localization.

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Renewable Energy, Mary Finley-Brook Jan 2014

Renewable Energy, Mary Finley-Brook

Geography and the Environment Faculty Publications

Renewable energy installations are expanding around the globe. Although there is excellent potential for achieving sustainability with multiple types of renewable energy, no energy source is a panacea. There are place-specific costs and benefits from every energy type, and the scale of production influences impacts. Industrial-scale renewable energy sources usually merge into existing energy grids and may often be connected to broader economic and political initiatives. Such as regional integration, development of new growth poles to stimulate economic expansion in areas without infrastructure, job creation, or trade expansion. With the exception of desert solar projects or initiatives in remote areas, …

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Hydropower, Mary Finley-Brook Jan 2014

Hydropower, Mary Finley-Brook

Geography and the Environment Faculty Publications

Hydropower dates back to the use of waterwheels to grind grain in Greece over two thousand years ago. Modern hydropower is a mature industry that has been used to generate electricity since the 1880s by capturing flowing water with a dam or other diversion structure and channeling it through a waterwheel or turbine. According to a 2012 report by the International Energy Agency, internationally dams are responsible for the largest amount of power generation from a renewable source; yet they have come under scrutiny as a result of environmental and social impacts perceived to be unsustainable (McCully 2001). Specific impacts, …

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