Engineering Commons^™

Semi-Automated Curation Of Metabolic Models Via Flux Balance Analysis: A Case Study With Mycoplasma Gallisepticum, Eddy J. Bautista, Joseph Zinski, Steven M. Szczepanek, Erik L. Johnson, Edan R. Tulman, Steven J. Geary, Ranjan Srivastava

Open Access Author Fund Awardees' Articles

Primarily used for metabolic engineering and synthetic biology, genome-scale metabolic modeling shows tremendous potential as a tool for fundamental research and curation of metabolism. Through a novel integration of flux balance analysis and genetic algorithms, a strategy to curate metabolic networks and facilitate identification of metabolic pathways that may not be directly inferable solely from genome annotation was developed. Specifically, metabolites involved in unknown reactions can be determined, and potentially erroneous pathways can be identified. The procedure developed allows for new fundamental insight into metabolism, as well as acting as a semi-automated curation methodology for genome-scale metabolic modeling. To validate …

Senior Design Report: Workstation For Paige Librandi, Ana C. Groff

Honors Scholar Theses

The workstation senior design project is a wheelchair accessible, left-side desk. It is for the client, Paige Librandi, who has cerebral palsy and is left-hand dominant. The purpose of the desk is to provide multitasking features to create an efficient work space for Paige to work on. It aims to also increase her independence by incorporating tools that prevent items from falling off the floor where she can't retrieve them.

The workstation design has several features, including a rotating surface, sliding bookcase, and gliding platform. These tools provide simultaneous work spaces and storage in a small amount of space to …

Urban Parking Economics And Land Consumption: A Case Study Of New Haven, Connecticut And Cambridge, Massachusetts, Bryan P. Blanc

Honors Scholar Theses

It has become increasingly apparent that providing copious off-street parking has deleterious effects on urban form and function. This study compares parking policy in New Haven, Connecticut and Cambridge, Massachusetts that have pursued very different types of parking policies that have resulted in different outcomes in terms of land use. Since 1951, off-street parking provision has increased by nearly 400% in New Haven, meanwhile both employment and residential population have declined in the city. In contrast, off-street parking provision in Cambridge has risen around 140% since 1952, while employment and residential populations in the city have increased by 50% and …

Hollow Fiber Module For Continuous Ethanol Fermentation, Leia M. Dwyer

Honors Scholar Theses

Continuous processes have several advantages over their batch counterparts and are prevalent across the chemical engineering industry today. The process of brewing beer, however, remains a batch process. Transforming the brewing process into a continuous process could have many advantages including lowered process down-time, increased profits, and higher product homogeneity. This project looked into several aspects of the brewing process to gain insight into the potential for continuous ethanol fermentation. First, a kinetic model was developed for the enzymatic breakdown of starch to simple sugars in the production of wort from malted barley. Next, the growth kinetics of brewer’s yeast, …

Volatility In Mrna Secondary Structure As A Design Principle For Antisense, Erik Johnson, Ranjan Srivastava

Open Access Author Fund Awardees' Articles

Designing effective antisense sequences is a formidable problem. A method for predicting efficacious antisense holds the potential to provide fundamental insight into this biophysical process. More practically, such an understanding increases the chance of successful antisense design as well as saving considerable time, money and labor. The secondary structure of an mRNA molecule is believed to be in a constant state of flux, sampling several different suboptimal states. We hypothesized that particularly volatile regions might provide better accessibility for antisense targeting. A computational framework, GenAVERT was developed to evaluate this hypothesis. GenAVERT used UNAFold and RNAforester to generate and compare …