This paper reports the results of an effort directed toward developing a consistent methodology to assess the impacts of traffic disruption due to major transportation reconstruction/rehabilitation projects during the period of implementation. In the approach taken by this research, state-of-the-art traffic simulation models are used to estimate the performance of the transportation system during various construction phases. Alternative construction and traffic redirection strategies designed to minimize both the direct and indirect losses associated with the construction/rehabilitation are then evaluated with the  development of a systematic, computerized procedure designed to: 

1. provide for the creation and comparison of multiple and 'layered' reconstruction/rehabilitation scenarios,

2. minimize the required knowledge of both the detailed interactions with the model as well as the host computer, and 

3. produce meaningful, comparative outputs that assist in the selection of reasonable alternatives. 

The resulting modeling environment is viewed as a convenient tool to assist both the traffic engineer and the transportation planner in selection of reasonable reconstruction/rehabilitation plans and schedules. 

Vertical-cavity surface-emitting lasers (VCSELs) have a long history of development in GaAs-based and InP-based systems, however III-nitride VCSELs research is still in its infancy. Yet, over the past several years we have made dramatic improvements in the lasing characteristics of these highly complex devices. Specifically, we have reduced the threshold current density from ~100 kA/cm2 to ~3 kA/cm2, while simultaneously increasing the output power from ~10 µW to ~550 µW. These developments have primarily come about by focusing on the aperture design and intracavity contact design for flip-chip dual dielectric DBR III-nitride VCSELs. We have carried out a number of studies developing an Al ion implanted aperture (IIA) and photoelectrochemically etched aperture (PECA), while simultaneously improving the quality of tin-doped indium oxide (ITO) intracavity contacts, and demonstrating the first III-nitride VCSEL with an n-GaN tunnel junction intracavity contact. Beyond these most notable research fronts, we have analyzed numerous other parameters, including epitaxial growth, flip-chip bonding, substrate removal, and more, bringing further improvement to III-nitride VCSEL performance and yield. This thesis aims to give a comprehensive discussion of the relevant underlying concepts for nonpolar VCSELs, while detailing our specific experimental advances. In Section 1, we give an overview of the applications of VCSELs generally, before describing some of the potential applications for III-nitride VCSELs. This is followed by a summary of the different material systems used to fabricate VCSELs, before going into detail on the basic design principles for developing III-nitride VCSELs. In Section 2, we outline the basic process and geometry for fabricating flip-chip nonpolar VCSELs with different aperture and intracavity contact designs. Finally, in Section 3 and 4, we delve into the experimental results achieved in the last several years, beginning with a discussion on the epitaxial growth developments. In Section 4, we discuss the most noteworthy accomplishments related to the nonpolar VCSELs structural design, such as different aperture and intracavity contact developments. Overall, this thesis is focused on the nonpolar VCSEL, however our hope is that many of the underlying insights will be of great use for the III-nitride VCSELs community as a whole. Throughout this report, we have taken great effort to highlight the future research fronts that would advance the field of III-nitride VCSELs generally, with the goal of illuminating the path forward for achieving efficient CW operating III-nitride VCSELs.

Chromatin remodelers are molecular motors that reposition and restructure nucleosomes to regulate gene expression and genome organization. The human ATP-dependent chromatin assembly factor (ACF) is a dimeric chromatin remodeler that evenly spaces nucleosomes to promote the formation of silent heterochromatin. Two copies of its ATPase subunit, SNF2h, bind opposite sides of a nucleosome, but how the two protomers work together remains poorly understood.

Central to the nucleosome spacing activity of ACF is the ability of SNF2h to equalize the length of DNA flanking either side of a nucleosome. SNF2h senses flanking DNA length via its conserved HAND-SANT-SLIDE (HSS) domain, yet it is unclear 1) how this interaction contributes to remodeling, and 2) whether or how the HSS communicates with the ATPase domain.

In this work, we address these questions with a combination of biochemical, biophysical and protein engineering methods. Using covalently connected SNF2h dimers we show that dimerization accelerates remodeling and that the HSS contributes to communication between protomers in trans. Moreover, we find that the state of the ATPase domain influences the function of the HSS domain within the same protomer in cis. Using thermodynamic analyses and new FRET-based assays, we further examine how nucleotide state regulates interactions between the HSS domain and the nucleosome. We identify a large, nucleotide-dependent conformational change in SNF2h: in one conformation the HSS binds flanking DNA, and in another conformation the HSS retracts to engage the nucleosome core. Finally, we examine the role of a recently identified regulatory motif, termed NegC, in nucleosome remodeling by SNF2h. We find that mutating NegC impairs flanking DNA length sensing, abolishes mononucleosome centering, and reduces the dependence of SNF2h activity on the histone H4 tail.

Based on these new results and previously published work, we propose a model in which DNA length sensing and translocation are performed by two distinct conformational states of SNF2h. We speculate that the ATP-dependent switch between DNA length-sensing and translocation-competent forms of the enzyme represents a rate-limiting regulatory step that enables nucleosome spacing by ACF. Such separation of function suggests that these two activities could be independently regulated to fine-tune remodeling outcomes.