gullydiss.tex

%%  08 April 2002	Version 4				     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%								     %
%%  Innovative Technologies for and Observational Studies of Star and Planet Formation		     %
%%	The University of Texas at Austin			     %
%%								     %
%%  (Modify this ``template'' for your own dissertation.)	     %
%%								     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


\documentclass[12pt]{report}	% The documentclass must be ``report''.

\usepackage{stylefiles/utdiss2}  		% Dissertation package style file.


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Optional packages used for this sample dissertation. If you don't  %
% need a capability in your dissertation, feel free to comment out   %
% the package usage command.					     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%\usepackage{graphicx}
%\usepackage{epstopdf}
\usepackage{amsmath,amsfonts,amsthm,amscd}
\usepackage{amssymb}
%\usepackage{mathabx}
\usepackage{stylefiles/aastex_hack}
				% Some packages to write mathematics.
\usepackage{eucal} 	 	% Euler fonts
\usepackage{verbatim}      	% Allows quoting source with commands.
\usepackage{makeidx}       	% Package to make an index.
\usepackage{stylefiles/psfig}         	% Allows inclusion of eps files.
\usepackage{epsfig}         	% Allows inclusion of eps files.
\usepackage{graphicx}
\usepackage{epstopdf}
\usepackage{stylefiles/citesort}         	% 
\usepackage{subfig}
\usepackage{booktabs}
\usepackage{multirow}
%\usepackage{rotating}
\usepackage{lscape}
\usepackage{pdfpages} 
\usepackage{deluxetable} 
\usepackage{longtable}
\usepackage{url}		% Allows good typesetting of web URLs.
%\usepackage{subfig}

\usepackage[numbers]{natbib}
\usepackage[nottoc]{tocbibind}

\newcommand{\angstrom}{\mbox{\normalfont\AA}}

%\usepackage{setspace}
%\usepackage{subcaption}
%\usepackage{caption}

%\usepackage{hyperref}

%\usepackage{draftcopy}		% Uncomment this line to have the
				% word, "DRAFT," as a background
				% "watermark" on all of the pages of
				% of your draft versions. When ready
				% to generate your final copy, re-comment
				% it out with a percent sign to remove
				% the word draft before you re-run
				% Makediss for the last time.


\author{Michael Anthony Gully-Santiago}  	% Required

\address{igully@gmail.com}  % Required

\title{Innovative Technologies for and Observational Studies of Star and Planet Formation}
                                                    % Required

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% NOTICE: The total number of supervisors and other members %%%%%%%%%%
%%%%%%%%%%%%%%% MUST be seven (7) or less! If you put in more, %%%%%%%
%%%%%%%%%%%%%%% they are put on the page after the Committee %%%%%%%%%
%%%%%%%%%%%%%%% Certification of Approved Version page. %%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Enter names of the supervisor and co-supervisor(s), if any,
% of your dissertation committee. Put one name per line with
% the name in square brackets. The name on the last line, however,
% must be in curly braces.
%
% If you have only one supervisor, the entry below will read:
%
%	\supervisor
%		{Supervisor's Name}
%
% NOTE: Maximum three supervisors. Minimum one supervisor.
% NOTE: The Office of Graduate Studies will accept only two supervisors!
% 
%
\supervisor{Daniel Jaffe}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Enter names of the other (non-supervisor) members(s) of your
% dissertation committee. Put one name per line with the name
% in square brackets. The name on the last line, however, must
% be in curly braces.
%
% NOTE: Maximum six other members. Minimum zero other members.
% NOTE: The Office of Graduate Studies may restrict you to a total
%	of six committee members.
%
%
\committeemembers
	[John Lacy]
	[Neal Evans]
	[Adam Kraus]
	{Alycia Weinberger}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\previousdegrees{B.A. ASTRO. \& PHYS.}
     % The abbreviated form of your previous degree(s).
     % E.g., \previousdegrees{B.S., MBA}.
     %
     % The default value is `B.S., M.S.'

\graduationmonth{May}      
     % Graduation month, either May, August, or December, in the form
     % as `\graduationmonth{May}'. Do not abbreviate.
     %
     % The default value (either May, August, or December) is guessed
     % according to the time of running LaTeX.

\graduationyear{2015}   
     % Graduation year, in the form as `\graduationyear{2001}'.
     % Use a 4 digit (not a 2 digit) number.
     %
     % The default value is guessed according to the time of 
     % running LaTeX.

\typist{`the author'}       
     % The name(s) of typist(s), put `the author' if you do it yourself.
     % E.g., `\typist{Maryann Hersey and the author}'.
     %
     % The default value is `the author'.



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Some optional commands to change the document's defaults.	     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%\singlespacing
%\oneandonehalfspacing

%\singlespacequote
\oneandonehalfspacequote

\topmargin 0.125in	% Adjust this value if the PostScript file output
			% of your dissertation has incorrect top and 
			% bottom margins. Print a copy of at least one
			% full page of your dissertation (not the first
			% page of a chapter) and measure the top and
			% bottom margins with a ruler. You must have
			% a top margin of 1.5" and a bottom margin of
			% at least 1.25". The page numbers must be at
			% least 1.00" from the bottom of the page.
			% If the margins are not correct, adjust this
			% value accordingly and re-compile and print again.
			%
			% The default value is 0.125"

		% If you want to adjust other margins, they are in the
		% utdiss2-nn.sty file near the top. If you are using
		% the shell script Makediss on a Unix/Linux system, make
		% your changes in the utdiss2-nn.sty file instead of
		% utdiss2.sty because Makediss will overwrite any changes
		% made to utdiss2.sty.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Some optional commands to be tested.				     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% If there are 10 or more sections, 10 or more subsections for a section,
% etc., you need to make an adjustment to the Table of Contents with the
% command \longtocentry.
%
\longtocentry 



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%	Some math support.					     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%	Theorem environments (these need the amsthm package)
%
%% \theoremstyle{plain} %% This is the default

%\newtheorem{thm}{Theorem}[section]
%\newtheorem{cor}[thm]{Corollary}
%\newtheorem{lem}[thm]{Lemma}
%\newtheorem{prop}[thm]{Proposition}
%\newtheorem{ax}{Axiom}

%\theoremstyle{definition}
%\newtheorem{defn}{Definition}[section]

%\theoremstyle{remark}
%\newtheorem{rem}{Remark}[section]
%\newtheorem*{notation}{Notation}

%\numberwithin{equation}{section}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%	Macros.							     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%	Here some macros that are needed in this document:


\newcommand{\latexe}{{\LaTeX\kern.125em2%
                      \lower.5ex\hbox{$\varepsilon$}}}

\newcommand{\amslatex}{\AmS-\LaTeX{}}

\chardef\bslash=`\\	% \bslash makes a backslash (in tt fonts)
			%	p. 424, TeXbook

\newcommand{\cn}[1]{\texttt{\bslash #1}}

\makeatletter		% Starts section where @ is considered a letter
			% and thus may be used in commands.
\def\square{\RIfM@\bgroup\else$\bgroup\aftergroup$\fi
  \vcenter{\hrule\hbox{\vrule\@height.6em\kern.6em\vrule}%
                                              \hrule}\egroup}
\makeatother		% Ends sections where @ is considered a letter.
			% Now @ cannot be used in commands.

\makeindex    % Make the index

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%		The document starts here.			     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{document}

\copyrightpage          % Produces the copyright page.


%
% NOTE: In a doctoral dissertation, the Committee Certification page
%		(with signatures) is BEFORE the Title page.
%	In a masters thesis or report, the Signature page
%		(with signatures) is AFTER the Title page.
%
%	If you are writing a masters thesis or report, you MUST REVERSE
%	the order of the \commcertpage and \titlepage commands below.
%
\commcertpage           % Produces the Committee Certification
			%   of Approved Version page (doctoral)
			%   or Signature page (masters).
			%		20 Mar 2002	cwm

\titlepage              % Produces the title page.



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Dedication and/or epigraph are optional, but must occur here.      %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\begin{dedication}
\index{Dedication@\emph{Dedication}}%
Dedicated to all my teachers.
\end{dedication}


\begin{acknowledgments}		% Optional
\index{Acknowledgments@\emph{Acknowledgments}}%

This work would not have been possible without the mentorship of my collaborators Katelyn Allers and Alycia Weinberger, for which I am deeply indebted.  I acknowledge the mentorship and patience of my former student colleagues Dr. Jasmina Marsh and Dr. Casey Deen.  I am grateful for the efforts of my junior colleagues Jared Rand, Amanda Turbyfill, and Carleen Boyer for their contributions to the Silicon Diffractive Optics Group.  Engineers Weisong Wang and Cindy Brooks contributed substantially to the Si diffractive optics fabrication.  I am indebted to my NASA GRSP mentor Daniel Wilson, with whom it was a pleasure to work.  I am thankful for the supervision of Richard Muller and Victor White at the Microdevices Laboratory.  Sungho Lee, Hyeonju Jeong, Taylor Chonis, Mike Pavel, Michelle Grigas, Neal Evans, John Lacy, and Adam Kraus, Rachel Walker, and Gordon Orris made this work possible.

I am delighted to acknowledge support from the NASA Graduate Student Research Program (GSRP) Fellowship, grant NNX10AK82H.  Portions of this research were supported by NASA APRA grant NNX10AC68G, NASA ACT grant NNX12AC31G, NSF ATI grant AST-0705064, and NASA Origins grant number NNX07AI83G.  MGS acknowledges support from the University of Texas in the form of the Graduate Dean's Prestigious Fellowship and from the Department of Astronomy in the form of the David Benfield Memorial Fellowship in Astronomy.  Funding from the McDonald Observatory and the Department of Astronomy's Cox graduate student excellence funds have helped to support travel and other aspects of this research.  Part of the research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration.  Some of the work was carried out at the University of Texas under a contract from the University of Arizona.  The development work for the grisms was supported in part by NASA (grant number NNX07AV15H).  The authors wish to thank Gary Poczulp and the National Optical Astronomy Observatory for assistance in producing some interferograms of early grating prototypes.  Thank you to David Hogg, Dan Foreman-Mackey, Jonathan Sick, Jake Vanderplas, and the participants and organizers of the Astro Data Hack Week (2014).  This dissertation includes data gathered with the 6.5 meter Magellan Telescopes located at Las Campanas Observatory, Chile.

I was lucky to be part of such a talented and creative group of incoming graduate students- Chris, John, Chalence, JJ, Julie, Manuel, Erik, Paul, and Manos.  I look forward to following their promising careers, and crossing paths indefinitely.  Joi Ito and Datri Bean enhanced my creativity.  Thank you to my supportive family members Diana, Tony, Erika, and Vanessa who gave me mettle.  Thank you to Carol for bringing Chelsey into the world, to Alese for introducing us, and to Chelsey for being exceptionally supportive.  Thanks to Mr. Emerson who got me started in astronomy.  Thanks to all my friends.  I acknowledge the kindness of the Wolchover family, who have always been outstanding in their field.

A very special thank you is reserved for my advisor, Daniel Jaffe, for contributing so deeply to my professional growth.  In particular I acknowledge his patient editing of the prose in this document.

\end{acknowledgments}


% The abstract is required. Note the use of ``utabstract'' instead of
% ``abstract''! This was necessary to fix a page numbering problem.
% The abstract heading is generated automatically.
% Do NOT use \begin{abstract} ... \end{abstract}.
%
\utabstract
\index{Abstract}%
\indent

I summarize the optical design, fabrication, and performance of silicon diffractive optics for astronomical spectrographs.  The first set of optical devices includes diffraction-limited, high-throughput silicon grisms for JWST-NIRCam.  These grisms served as pathfinders to Silicon immersion gratings, which offer size and cost savings for high-resolution near-infrared spectrographs.  I demonstrate the production and optical evaluation of the immersion grating that enabled IGRINS at the McDonald Observatory.  This grating provides spectral resolution $R=40,000$ over the $H-$ and $K-$ near-infrared band atmospheric windows (1.5$-$2.5 $\mu$m).  Electron-beam lithography offers much higher precision over contact mask photolithography for the production of Si immersion gratings.  Electron-beam patterned prototypes are stepping-stones to monolithic Si gratings for iSHELL and GMTNIRS.  The monolithic design of Si immersion gratings presents a limitation for scaling up the grating size, since existing fabrication equipment cannot handle monolithic silicon pucks.  The size limitation can be overcome by direct-bonding Si substrates to optical prisms.  I demonstrate a technique to measure interfacial gaps as small as 14 nm between the bonding interfaces, which produce 0.2\% transmission loss.  These technologies will enable the direct measurement of the atmospheric properties of extrasolar planets in the next decade.  IGRINS is now measuring fundamental properties of young \emph{T-Tauri} stars; low mass young brown dwarfs are below the sensitivity limit of existing high spectral resolution near-IR spectrographs.  My approach to the discovery and characterization of young brown dwarfs therefore employs low resolution ($R\sim 2000$) near-IR spectroscopy.  I confirm and characterize 17 candidate young stars and brown dwarfs reported by Allers and collaborators.  All 17 sources have circumstellar disks.

Using deep optical, near-infrared, and mid-infrared photometry, I search an off-core region towards the nearby $\sim1$ Myr \emph{Ophiuchus} star forming cluster for candidate young stars and brown dwarfs.  Multi-object $I-$band spectroscopy of 419 candidates reveals 12 new members.  Ten of these have no evidence for mid-IR excess emission from 3.6 to 8.0 $\mu$m.  The disk fraction for spectral types M4 and later towards this region of \emph{Ophiuchus} is 5/15.  Two of the disk sources have edge-on disks, pointing to a high edge-on disk fraction.  I discuss possible sources of contamination in the survey.

\tableofcontents   % Table of Contents will be automatically
                   % generated and placed here.

\listoftables      % List of Tables and List of Figures will be placed
\listoffigures     % here, if applicable.



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Actual text starts here.					     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Including external files for each chapter makes this document simpler,
% makes each chapter simpler, and allows for generating test documents
% with as few as zero chapters (by commenting out the include statements).
% This allows quicker processing by the Makediss command file in case you
% are not working on a specific, long and slow to compile chapter. You
% can even change the chapter order by merely interchanging the order
% of the include statements (something I found helpful in my own
% dissertation).
%

\include{ch1/chapter-introduction}
\include{chSPIE_2010_JWST/mgs_spie_2010_v1_5}
\include{chSPIE_2012_CA1/chapter-2012-CA1}
\include{chSPIE_2014_ebeam/chapter-2014-ebeam}
\include{chSiGaps/AO_bondedSi}
\include{chCS16/gully-santiago_m}
\include{chIMACS/ms}


%\include{chGratingDesign/chapter-gratingdesign}
%\include{chGratingProcess/chapter-gratingprocess}
%\include{chIshell/chapter-ishellgratings}
%\include{chFabryPerot/chapter-fabryperot}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Appendix/Appendices                                                %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% If you have only one appendix, use the command \appendix instead
% of \appendices.
%
%\appendices
%\index{Appendices@\emph{Appendices}}%

%\include{appendices/chapter-appendix1}

%\include{appendices/chapter-appendix2}

%\include{appendices/chapter-appendix01-S1800}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Generate the bibliography.					     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%								     %
% NOTE: For master's theses and reports, NOTHING is permitted to     %
%	come between the bibliography and the vita. The command      %
%	to generate the index (if used) MUST be moved to before      %
%	this section.						     %
%								     %
\nocite{*}      % This command causes all items in the 		     %
                % bibliographic database to be added to 	     %
                % the bibliography, even if they are not 	     %
                % explicitly cited in the text. 		     %
		%						     %
\bibliographystyle{plainnat}  % Here the bibliography 		     %
\bibliography{gullydiss}        % is inserted.			     %
\index{Bibliography@\emph{Bibliography}}%			     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Generate the index.						     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%								     %
% NOTE: For master's theses and reports, NOTHING is permitted to     %
%	come between the bibliography and the vita. This section     %
%	to generate the index (if used) MUST be moved to before      %
%	the bibliography section.				     %
%								     %
\printindex%    % Include the index here. Comment out this line      %
%		% with a percent sign if you do not want an index.   %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Vita page.							     %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{vita}
Michael Gully-Santiago was born in Boston, and attended high school in Norwell Massachusetts.  He matriculated at Boston University in 2003, where he earned a Bachelor of Arts in Astronomy \& Physics in May 2007.  During his undergraduate years he worked at the McDonald Observatory in Fort Davis, Texas and the Clay Center Observatory in Brookline, Massachusetts, where he remained as a faculty member until 2008.  He enrolled in the University of Texas at Austin Department of Astronomy's Graduate Program in August 2008.  In 2010 he was awarded the NASA Graduate Student Research Program fellowship, which enabled him to work at the NASA JPL Microdevices Laboratory in Pasadena, CA.  
\end{vita}

\end{document}