Hydrogen bonding of nucleotide base pairs: Application of the PM3 method

The ability of the pm3 semiempirical quantum mechanical method to reproduce hydrogen bonding in nucleotide base pairs was assessed. Results of pm3 calculations on the nucleotides 2′-deoxyadenosine 5′-monophosphate (pdA), 2′-deoxyguanosine 5′-monophosphate (pdG), 2′-deoxycytidine 5′-monophosphate (pdC), and 2′-deoxythymidine 5′-monophosphate (pdT) and the base pairs pdA–pdT, pdG–pdC, and pdG(syn)–pdC are presented and discussed. The pm3 method is the first of the parameterized nddo quantum mechanical models with any ability to reproduce hydrogen bonding between nucleotide base pairs. Intermolecular hydrogen bond lengths between nucleotides displaying Watson–Crick base pairing are 0.1–0.2 Å less than experimental results. Nucleotide bond distances, bond angles, and torsion angles about the glycosyl bond (χ), the C4′C5′ bond (γ), and the C5′O5′ bond (β) agree with experimental results. There are many possible conformations of nucleotides. pm3 calculations reveal that many of the most stable conformations are stabilized by intramolecular CHO hydrogen bonds. These interactions disrupt the usual sugar puckering. The stacking interactions of a dT–pdA duplex are examined at different levels of gradient optimization. The intramolecular hydrogen bonds found in the nucleotide base pairs disappear in the duplex, as a result of the additional constraints on the phosphate group when part of a DNA backbone. Sugar puckering is reproduced by the pm3 method for the four bases in the dT–pdA duplex. pm3 underestimates the attractive stacking interactions of base pairs in a B-DNA helical conformation. The performance of the pm3 method implemented in SPARTAN is contrasted with that implemented in MOPAC. At present, accurate ab initio calculations are too timeconsuming to be of practical use, and molecular mechanics methods cannot be used to determine quantum mechanical properties such as reaction-path calculations, transition-state structures, and activation energies. The pm3 method should be used with extreme caution for examination of small DNA systems. Future parameterizations of semiempirical methods should incorporate base stacking interactions into the parameterization data set to enhance the ability of these methods.

Shading Silhouettes of Smaller Ones

I am truly honored to have been given the amazing opportunity to create this original piece, this powerful journey through memory and emotive exploration of the loss of childhood. How do we feel about the loss of our child-self? Could we ever get them back? How long, how deep would one have to dig in the graveyards, the playgrounds of memory, to uncover what was buried there... to un-erase what waserased? shading silhouettes of smaller ones will ultimately encourage a reconnection with the Inner Child hidden inside all of us, as well as an intimate awareness of the adult version of the self by looking back to the smaller ones. The main inspiration for this piece is then of course, Inner Child Work. Most people may not be familiar with this therapeutic exploration of childhood... It wasimportant to me then, to present this concept in an imaginative, theatrical way, as a gift to you - a comprehensive and intensely moving gift. Speaking from experience, working on my Inner Child - my little Bianca - has been the most painful, frightening, yetrewarding and powerful experience within my personal life. Some people spend their entire lives trying to love themselves, to prove themselves, or be accepted. Some are too afraid to look back to where it all began. The characters within this piece will face thatfear... in a regression from the complexities of adulthood to the confusion of adolescence, all the way back to the wonder and bliss of childhood. They will reveal memories, of both joy and pain, love and abandonment, journeying backwards through time - through memory - through a playground - back to the beginning... We will enter a world where a push of a merry-go-round spins us to games of Truth or Dare after a high school dance at 16 - or the slam of a metal fence reminds us of the door Dad slammed in our face at 9 - where the sound of chain links swings us back to scrapping our knee by the sandbox at 5 This piece will attempt to connect everyone, both cast and audience, through a universal understanding and discussion of what it means to grow up, as well as a discovery of WHY we are the way we are - how experiences or relationships from our childhood have shaped our adult lives. We will attempt to challenge your honesty and nerve by inviting you to ask questions of yourselves, your past - to remember what it's like to have the innocence and hope of a child, to engage with and discover your Inner Child, to realize when or why you left them behind, and if you want to this magical part of yourself. It is my hope that you will join us in a collective journey - gather the courage to dig up the little kid you buried so long ago...* The creation, design, choreography, and direction for shading silhouettes of smaller ones mark the culminating experience of a year-long independent study in Theatre.

Hoisting C Structures Into Clay In Device Drivers

This project addresses the unreliability of operating system code, in particular in device drivers. Device driver software is the interface between the operating system and the device's hardware. Device drivers are written in low level code, making them difficult to understand. Almost all device drivers are written in the programming language C which allows for direct manipulation of memory. Due to the complexity of manual movement of data, most mistakes in operating systems occur in device driver code. The programming language Clay can be used to check device driver code at compile-time. Clay does most of its error checking statically to minimize the overhead of run-time checks in order to stay competitive with C's performance time. The Clay compiler can detect a lot more types of errors than the C compiler like buffer overflows, kernel stack overflows, NULL pointer uses, freed memory uses, and aliasing errors. Clay code that successfully compiles is guaranteed to run without failing on errors that Clay can detect. Even though C is unsafe, currently most device drivers are written in it. Not only are device drivers the part of the operating system most likely to fail, they also are the largest part of the operating system. As rewriting every existing device driver in Clay by hand would be impractical, this thesis is part of a project to automate translation of existing drivers from C to Clay. Although C and Clay both allow low level manipulation of data and fill the same niche for developing low level code, they have different syntax, type systems, and paradigms. This paper explores how C can be translated into Clay. It identifies what part of C device drivers cannot be translated into Clay and what information drivers in Clay will require that C cannot provide. It also explains how these translations will occur by explaining how each C structure is represented in the compiler and how these structures are changed to represent a Clay structure.

Monitoring and Modeling of the Hydraulic and Sediment Processes at In-Stream Restoration Structures in the Vicinity of a Bridge Crossing

The long-term performance of infrastructure depends on reliable and sustainable designs. Many of Pennsylvania’s streams experience sediment transport problems that increase maintenance costs and lower structural integrity of bridge crossings. A stream restoration project is one common mitigation measure used to correct such problems at bridge crossings. Specifically, in an attempt to alleviate aggradation problems with the Old Route 15 Bridge crossing on White Deer Creek, in White Deer, PA, two in-stream structures (rock cross vanes) and several bank stabilization features were installed along with a complete channel redevelopment. The objectives of this research were to characterize the hydraulic and sediment transport processes occurring at the White Deer Creek site, and to investigate, through physical and mathematical modeling, the use of instream restoration structures. The goal is to be able to use the results of this study to prevent aggradation or other sediment related problems in the vicinity of bridges through improved design considerations. Monitoring and modeling indicate that the study site on White Deer Creek is currently unstable, experiencing general channel down-cutting, bank erosion, and several local areas of increased aggradation and degradation of the channel bed. An in-stream structure installed upstream of the Old Route 15 Bridge failed by sediment burial caused by the high sediment load that White Deer Creek is transporting as well as the backwater effects caused by the bridge crossing. The in-stream structure installed downstream of the Old Route 15 Bridge is beginning to fail because of the alignment of the structure with the approach direction of flow from upstream of the restoration structure.

The Intersection of Economics and Politics in a Small OPEC Country: the Case of Ecuador, 1990 - March 2014

Today, crude oil remains a vital resource all around the world. This non-renewable resource powers countries worldwide. Besides serving as an energy source, crude oil is also the most important component for different world economies, especially in developing countries. Ecuador, a small member of the OPEC oil cartel, presents a case where its economy is oil dependent. A great percentage of the country¿s GDP and government¿s budget comes from oil revenues. Ecuador has always been a primary exporter of raw materials. In the last centuries, the country experienced three important economic booms: cacao, bananas, and, ultimately, crude oil. In this sense, the country has not been able to fully industrialize and begin to export manufactured goods, i.e., Ecuador suffers from the Dutch disease. The latter has deterred Ecuador from achieving broad-based economic development. Given crude oil¿s importance for the Ecuadorian economy, the government has always tried to influence the oil industry in search of profits and benefits. Therefore, this thesis, explores the question: how and to what extent have political interventions affected the oil industry in Ecuador from 1990 until March 2014? In general, this thesis establishes an economic history context during the last twenty-four years, attempting to research how political interventions have shaped Ecuador¿s oil industry and economy. In the analysis, it covers a period where political instability prevailed, until Rafael Correa became president. The thesis examines Ecuador¿s participation in OPEC, trying to find explanations as to why the country voluntarily left the organization in 1992, only to rejoin in 2007 when Correa rose to power. During the ¿Revolución Ciudadana¿ period, the thesis researches reforms to the Law of Hydrocarbons, variations in the relations with other nations, the controversy surrounding the Yasuní-ITT oil block, and the ¿Refinería del Pacífico¿ construction. The thesis is an Industrial Organization detailed case study that analyzes, updates, and evaluates the intersection of economics and politics in Ecuador¿s crude oil industry during the last 24 years. In this sense I have consulted past theses, newspaper articles, books, and other published data about the petroleum industry, both from a global and Ecuadorian perspective. In addition to published sources, I was able to interview sociologists, public figures, history and economics academics, and other experts, accessing unique unpublished data about Ecuador¿s oil industry. I made an effort to collect information that shows the private and public side of the industry, i.e., from government-related and independent sources. I attempted to remain as objective as possible to make conclusions about the appropriate Industrial Organization policy for Ecuador¿s oil industry, addressing the issue from an economic, social, political, and environmental point of view. I found how Ecuador¿s political instability caused public policy to fail, molding the conduct and market structure of the crude oil industry. Throughout history, developed nations have benefited from low oil prices, but things shifted since oil prices began to rise, which is more beneficial for the developing nations that actually possess and produce the raw material. Nevertheless, Ecuador, a victim of the Dutch disease due to its heavy reliance on crude oil as a primary product, has not achieved broad-based development.