Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1995. / Includes bibliographical references (leaves 190-193). / by Hong Chul. / Ph.D.

Thesis (Civ. E.)--Massachusetts Institute of Technology, Dept. of Civil Engineering, 1991. / Includes 3-1/2 inch computer disc in pocket. / Includes bibliographical references. / by John Laighton Durant. / Civ.E.

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1996. / Includes bibliographical references (p. 148-151). / by Dan S. Alden. / M.Eng.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 195-212). / Metagenomic research has paved the way for a comprehensive understanding of the microbial gene parts list in nature, but a full understanding of microbial gene expression, regulation, and ecology remains a challenge. In this thesis, I present the methodological foundations and applications of deep sequencing-based metatranscriptomics, for profiling community transcriptomes on spatial and temporal scales. Several findings and relevant hypotheses have emerged from this work. I show that transcripts of house-keeping genes necessary for the maintenance of basic cellular machinery are abundant and readily detectable. Habitat-specific transcripts are also discernible when comparing community transcriptomes along distinct geochemical conditions. Normalization of detected transcripts to their corresponding gene abundance suggests that numerically less abundant microorganisms may nevertheless contribute actively to ecologically relevant processes. Along the same lines, it is a recurrent observation that many transcripts are of unknown function or phylogenetic origin, and have not been detected in genomic/metagenomic data sets. These novel sequences may be derived from less abundant species or variable genomic regions that are not represented in sequenced genomes. Furthermore, I applied metatranscriptomics in a microcosm experiment, where a deep water mixing event was simulated and community transcriptomes were monitored over the course of 27 hours. Relative to the control, the treatment sample showed signals of stimulated photosynthesis and carbon fixation by phytoplankton cells, enhanced chemotactic, motility, and growth responses of heterotrophic bacteria, as well as possibly altered phage-host interactions. Such experimental metatranscriptomic studies are well suited to reveal how microorganisms respond during the early stages of environmental perturbations. Finally, I show that metatranscriptomic data sets contain a wealth of highly expressed small RNAs (sRNAs), transcripts that are not translated to proteins but instead function as regulators. I propose a bioinformatics pipeline for identifying these sRNA elements, characterizing their structures and genomic contexts, and predicting possible regulatory targets. The extraordinary abundance of some of the identified sRNAs raises questions about their ecological function, which warrants further biochemical and genetic studies. Overall, this work has extended our knowledge of functional potentials and in situ gene expression of natural microbial communities. / by Yanmei Shi. / Ph.D.

Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2000. / Includes bibliographical references (leaves 80-81). / by Irene W. Yu. / M.Eng.

Thesis: S.M. in Transportation, Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 85-95). / In this thesis, we consider the problem of designing real-time traffic routing systems in urban areas. Optimal dynamic routing for multiple passengers is known to be computationally hard due to its combinatorial nature. To overcome this difficulty, we propose a novel mechanism called User-Centric Dynamic Pricing (UCDP) based on recent advances in algorithmic mechanism design. The mechanism allows for congestion-free traffic in general road networks with heterogeneous users, while satisfying each user's travel preference. The mechanism first informs whether a passenger should use public transportation or the road network. In the latter case, a passenger reports his maximum accepted travel time with a lower bound announced publicly by the road authority. The mechanism then assigns the passenger a path that matches with his preference given the current traffic condition in the network. The proposed mechanism introduces a fairness constrained shortest path (FCSP) problem with a special structure, thus enabling polynomial time computation of path allocation that maximizes the sequential social surplus and guarantees fairness among passengers. The tolls of paths are then computed according to marginal cost payments. We show that reporting true preference is a weakly dominant strategy. The performance of the proposed mechanism is demonstrated on several simulated routing experiments in comparison to user equilibrium and system optimum. / by Kim Thien Bui. / S.M. in Transportation

Massachusetts Institute of Technology. Dept. of Civil Engineering. Thesis. 1970. Ph.D. / MICROFICHE COPY ALSO AVAILABLE IN BARKER ENGINEERING LIBRARY. / Vita. / Bibliography: leaves 289-290. / Ph.D.

Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2001. / Includes bibliographical references (leaf 63). / by Corey M. Smith. / M.Eng.

Thesis (S.M. in Transportation)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 161-163). / In recent years, the proliferation of automatically collected data has allowed many transit agencies to complete more frequent and thorough analyses of service quality. However, while the types and quality of automatically collected data are sure to improve in the future, many transit agencies will be limited to using their current automatically collected data until they have the time and resources to implement new data collection systems. This thesis focuses on improving the analyses undertaken with the currently available data. The primary objective of this thesis is to improve the accuracy of the estimation of platform wait time (PWT) at the London Underground (LU) by determining the methodology that provides the most accurate and robust estimates of PWT. Three methodologies are tested: (1) LU's current PWT methodology using train tracking data that has been made more complete and robust through the use of automated processes; (2) a variant of LU's current PWT methodology; and (3) an improved PWT methodology that avoids the deficiencies of LU's train tracking data. Specifically, this improved PWT methodology relies on the count of trains recorded at stations in order to eliminate the need to use train identification data to verify that a specific train reached a specific destination station and to minimize the effect of data recording errors on the estimation of PWT. The PWT methodologies presented in this thesis are applied to a four-week period on the Bakerloo and Piccadilly lines. For a specific time period and day, it is found that the differences between the PWT estimates from a new PWT methodology and LU's PWT methodology are usually less than 5%. It is concluded that higher quality NetMIS data and improved PWT estimation methods are a worthwhile investment, even if they lead to small changes in estimated PWT, because they ensure that variations in PWT reflect actual operations and are not due to poor NetMIS data or PWT estimation errors. Further, a hybrid approach that combines the best of LU's current PWT methodology and the train-count-based PWT methodology is recommended as one way to improve PWT estimates. / by Samuel Warren Hickey. / S.M.in Transportation

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1995. / Includes bibliographical references (p. 95-96). / by Pierre E. Brunet. / M.S.