V0.4 (#6)

* adding preamble and refs.bib * adding images * adding pdfs * update chapters
GuillermoFidalgo · Mar 24, 2024 · 5ce1b82 · 5ce1b82
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diff --git a/.gitignore b/.gitignore
@@ -302,4 +302,4 @@ TSWLatexianTemp*
 
 
 # precommit autofixes??
-*.bak0
+*.bak*
diff --git a/Images/DQM GUI.png b/Images/DQM GUI.png
diff --git a/Images/DQM Workflow.png b/Images/DQM Workflow.png
diff --git a/Images/Loss_function1.png b/Images/Loss_function1.png
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diff --git a/Images/pdfs/Ratio histograms.pdf b/Images/pdfs/Ratio histograms.pdf
diff --git a/Images/pdfs/Testing Ratios.pdf b/Images/pdfs/Testing Ratios.pdf
diff --git a/Images/pdfs/fits_16-APV-HIPM.pdf b/Images/pdfs/fits_16-APV-HIPM.pdf
diff --git a/Images/pdfs/fits_16.pdf b/Images/pdfs/fits_16.pdf
diff --git a/Images/pdfs/fits_17.pdf b/Images/pdfs/fits_17.pdf
diff --git a/Images/pdfs/fits_18.pdf b/Images/pdfs/fits_18.pdf
diff --git a/Images/pdfs/fits_closeup_16-APV-HIPM.pdf b/Images/pdfs/fits_closeup_16-APV-HIPM.pdf
diff --git a/Images/pdfs/fits_closeup_16.pdf b/Images/pdfs/fits_closeup_16.pdf
diff --git a/Images/pdfs/fits_closeup_17.pdf b/Images/pdfs/fits_closeup_17.pdf
diff --git a/Images/pdfs/fits_closeup_18.pdf b/Images/pdfs/fits_closeup_18.pdf
diff --git a/Images/pdfs/modelTB.pdf b/Images/pdfs/modelTB.pdf
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diff --git a/chapters/Chapter02.tex b/chapters/Chapter02.tex
@@ -41,9 +41,9 @@ \chapter{The CMS Detector\label{ch:CMS}}
 \autoref{CMSLayers} depicts the particle detection process in CMS. Charged particles leave signatures in the inner tracking system, and the vertices from decaying short-lived particles can be identified. Photons, electrons, neutral pions and kaons are stopped in the crystals of the electromagnetic calorimeter (ECAL) and the scintillation light is used to determine the deposited energy. Hadrons punch through further and are generally stopped by the hadronic calorimeter (HCAL), where jets are confined and only the highest-energy hadrons and muons pass through the superconducting solenoid into the outer regions of the CMS barrel. Finally, muons are detected in the various muon detectors which interleave the return yoke of the magnet. Neutrinos escape from the CMS detector and are inferred from an imbalance of energy in the reconstructed event called missing transverse energy (MET or $\vec{p}_T^{\text{miss}}$).
 More detailed descriptions of the CMS detector, together with a definition of the coordinate system used and the relevant kinematic variables, can be found in Refs.~\cite{CMS:2008xjf,CMS:2023gfb}.
 
-\begin{figure}
+\begin{figure}[h]
 	\centering
-	\includegraphics[width=\linewidth]{CMSLayers.png}
+	\includegraphics[width=.9\linewidth]{CMSLayers.png}
 	\caption[Particle trajectories and footprint in CMS]{The trajectory of a particle traveling through the layers of the detector leaving behind it's signature footprint\label{CMSLayers}}
 \end{figure}
 

diff --git a/chapters/Chapter03.tex b/chapters/Chapter03.tex
diff --git a/chapters/Chapter05.tex b/chapters/Chapter05.tex
diff --git a/chapters/Conclusion.tex b/chapters/Conclusion.tex
@@ -1,11 +1,11 @@
 \chapter{Conclusion}\label{ch:conclusion}
 
-There are three major topics of research that were discussed in this dissertation: The simulation studies involving the counting of L1-stubs for the HL-LHC CMS Inner Tracker upgrade ({stubs}), the overall 2016 search for SUSY in the all-hadronic channel using a customized top-tagger ({AnalysisChap}) and the improvements made for the estimation of the Z$\rightarrow \nu\bar{\nu}$+ jets background using an additional control region from $\gamma$+ jets events ({estimation}). These studies were explained in detail in their respective chapters and their individual results are provided. A summary of the most important results from each study is provided in this chapter.
+% There are three major topics of research that were discussed in this dissertation: The simulation studies involving the counting of L1-stubs for the HL-LHC CMS Inner Tracker upgrade ({stubs}), the overall 2016 search for SUSY in the all-hadronic channel using a customized top-tagger ({AnalysisChap}) and the improvements made for the estimation of the Z$\rightarrow \nu\bar{\nu}$+ jets background using an additional control region from $\gamma$+ jets events ({estimation}). These studies were explained in detail in their respective chapters and their individual results are provided. A summary of the most important results from each study is provided in this chapter.
 
-\section{L1 Stub Counting for the HL-LHC CMS Tracker Upgrade}
+% \section{L1 Stub Counting for the HL-LHC CMS Tracker Upgrade}
 
-Results from this study (detailed in {stubs}) reflect the overall effects that were expected beforehand. The removal of discs from the standard pixel geometry (consisting of 8 small and 4 large discs) results in a noticeable reduction of stub hits in the upgraded CMS Outer Tracker. This effect is specially apparent if the disc that is removed is closer to the interaction point, due to the much larger volume of particles that are present in this region. Therefore, the reduction in stubs is more pronounced when a small disc is removed (as in the case of the $7s4l$ geometry) than if a large disc is removed (as in the $8s3l$ pixel geometry). The reason for this effect stems from the fact that as particles travel through the various layers of the Inner Tracker material, some of them are bound to interact with it, producing particles that did not originate from the initial proton-proton collision. The stubs produced via such processes are considered to be ``fake'' stubs. To confirm these findings, an additional study was conducted using a sample that was virtually indistinguishable from the standard pixel geometry, but with the second disc on the positive side ``turned off'' or ``dead''. The results from this study confirm the initial findings and shows that there is indeed a correlation between the average number of stubs detected in the Outer Tracker and the total amount of material present in the upgraded Inner Tracker. An important factor that needs to be taken into account when interpreting these results is the re-optimization of the disc positions after removing a disc in the different pixel geometries considered. This feature could provide a possible explanation as to why the $6s3l$ geometry, which has two less small discs than the standard geometry (and one less large one), was found to have less of an effect on the average number of stubs than the $7s4l$ geometry.
+% Results from this study (detailed in {stubs}) reflect the overall effects that were expected beforehand. The removal of discs from the standard pixel geometry (consisting of 8 small and 4 large discs) results in a noticeable reduction of stub hits in the upgraded CMS Outer Tracker. This effect is specially apparent if the disc that is removed is closer to the interaction point, due to the much larger volume of particles that are present in this region. Therefore, the reduction in stubs is more pronounced when a small disc is removed (as in the case of the $7s4l$ geometry) than if a large disc is removed (as in the $8s3l$ pixel geometry). The reason for this effect stems from the fact that as particles travel through the various layers of the Inner Tracker material, some of them are bound to interact with it, producing particles that did not originate from the initial proton-proton collision. The stubs produced via such processes are considered to be ``fake'' stubs. To confirm these findings, an additional study was conducted using a sample that was virtually indistinguishable from the standard pixel geometry, but with the second disc on the positive side ``turned off'' or ``dead''. The results from this study confirm the initial findings and shows that there is indeed a correlation between the average number of stubs detected in the Outer Tracker and the total amount of material present in the upgraded Inner Tracker. An important factor that needs to be taken into account when interpreting these results is the re-optimization of the disc positions after removing a disc in the different pixel geometries considered. This feature could provide a possible explanation as to why the $6s3l$ geometry, which has two less small discs than the standard geometry (and one less large one), was found to have less of an effect on the average number of stubs than the $7s4l$ geometry.
 
-\section{Search for SUSY in the All-Hadronic Channel}
+% \section{Search for SUSY in the All-Hadronic Channel}
 
-The analysis presented in {AnalysisChap} shows the results of a search for SUSY in the 0-lepton final state using a customized top-tagger. The data was obtained from proton-proton collisions at the CMS detector during 2016 with a total integrated luminosity of 35.9 fb$^{-1}$ at a center-of-mass energy of 13 TeV. The search was conducted by specifying 84 non-overlapping regions of phase space with varying requirements on the $N_\text{b}$, $N_\text{t}$, $p_{\text{T}}^{miss}$, $H_\text{T}$ and $m_\text{T2}$ variables ({SearchBinDef}). Several dominant and non-dominant backgrounds were identified and estimated to account for all the majority of the processes that were seen in the collected data. The estimation procedures and their respective systematic and statistical uncertainties are discussed in {backgrounds}. The total background prediction vs. data for all 84 search bins ({SearchBinResults}) shows no statistically significant deviation from the predicted SM background. The biggest sources background were shown to be the t$\bar{\text{t}}$ and W+jets processes, followed by Z($\nu\bar{\nu}$)+jets, which were seen to be dominant in regions with a high $p_\text{T}$ threshold. Meanwhile, the contributions from the QCD multijet and rare backgrounds are found to be nearly negligible in all of the 84 search bins. Exclusion limits were calculated from these results for each of the signal models used, by applying a binned likelihood fit on the data. The likelihood function was obtained for each of the 84 search regions as well as for each of the background data control samples from the product of the Poisson probability density function. Exclusion limits were placed on the top squark, gluino and LSP production cross-sections with a 95\% confidence level (CL), calculated using a modified frequentist approach with the CL$_s$ criterion and asymptotic results for the test statistic. The 95\% CL exclusion limits obtained for the T2tt model, which consists of direct top squark production, excludes top squark masses up to 1020 GeV and LSP masses up to 430 GeV. For the T1tttt model, gluino masses of up to 2040 GeV and LSP masses up to 1150 GeV are excluded, with corresponding limits of 2020 and 1150 GeV for the T1ttbb model, 2020 and 1150 GeV for the T5tttt model, and 1810 and 1100 GeV for the T5ttcc model.
+% The analysis presented in {AnalysisChap} shows the results of a search for SUSY in the 0-lepton final state using a customized top-tagger. The data was obtained from proton-proton collisions at the CMS detector during 2016 with a total integrated luminosity of 35.9 fb$^{-1}$ at a center-of-mass energy of 13 TeV. The search was conducted by specifying 84 non-overlapping regions of phase space with varying requirements on the $N_\text{b}$, $N_\text{t}$, $p_{\text{T}}^{miss}$, $H_\text{T}$ and $m_\text{T2}$ variables ({SearchBinDef}). Several dominant and non-dominant backgrounds were identified and estimated to account for all the majority of the processes that were seen in the collected data. The estimation procedures and their respective systematic and statistical uncertainties are discussed in {backgrounds}. The total background prediction vs. data for all 84 search bins ({SearchBinResults}) shows no statistically significant deviation from the predicted SM background. The biggest sources background were shown to be the t$\bar{\text{t}}$ and W+jets processes, followed by Z($\nu\bar{\nu}$)+jets, which were seen to be dominant in regions with a high $p_\text{T}$ threshold. Meanwhile, the contributions from the QCD multijet and rare backgrounds are found to be nearly negligible in all of the 84 search bins. Exclusion limits were calculated from these results for each of the signal models used, by applying a binned likelihood fit on the data. The likelihood function was obtained for each of the 84 search regions as well as for each of the background data control samples from the product of the Poisson probability density function. Exclusion limits were placed on the top squark, gluino and LSP production cross-sections with a 95\% confidence level (CL), calculated using a modified frequentist approach with the CL$_s$ criterion and asymptotic results for the test statistic. The 95\% CL exclusion limits obtained for the T2tt model, which consists of direct top squark production, excludes top squark masses up to 1020 GeV and LSP masses up to 430 GeV. For the T1tttt model, gluino masses of up to 2040 GeV and LSP masses up to 1150 GeV are excluded, with corresponding limits of 2020 and 1150 GeV for the T1ttbb model, 2020 and 1150 GeV for the T5tttt model, and 1810 and 1100 GeV for the T5ttcc model.
diff --git a/chapters/Introduction.tex b/chapters/Introduction.tex
@@ -7,6 +7,11 @@ \chapter{Introduction}
 The process gives physicists clues about how the particles interact and provides insights into the fundamental laws of nature. Nine\footnote{\url{https://home.cern/science/experiments}} experiments at the LHC use detectors to analyze particles produced by proton-proton collisions.
 The biggest of these experiments, ATLAS and CMS, are general-purpose detectors designed to study the
 fundamental nature of matter and fundamental forces and to look for new physics or evidence of particles that are beyond the Standard Model\footnote{\url{https://home.cern/about/physics/standard-model}}. Having two independently designed detectors is vital for cross-confirmation of any new discoveries made with minimal bias. The other two major detectors ALICE and LHCb, respectively, study a state of matter that was present just moments after the Big Bang and a preponderance of matter than antimatter.  Each experiment does important research that is key to understanding the universe that surrounds and makes us.
+
+In particular, this work is focused on studies done for the Emerging Jets analysis and efforts on the development of tools that provide a mechanism to filter, evaluate and certify the quality of data collected in the CMS experiment.
+
+% Add more on the origins of the QCD-like hidden sector. Talk about the need for DQM
+
 \Cref{ch:CMS} presents a basic description of the Large Hadron Collider and the CMS Detector.
 \Cref{ch:emj} presents a description and background on the Emerging Jets theory and analysis.
 % \Cref{ch:HLT} develops the technical aspects and usage of the HLT system in CMS.

diff --git a/preamble.tex b/preamble.tex
@@ -11,6 +11,11 @@
 % bindingoffset=6mm]{geometry} % for book
 \usepackage[letterpaper,margin=1in]{geometry} % for article
 \usepackage{graphicx,wrapfig}
+
+%Set images folder
+\graphicspath{ {Images/} }
+
+
 \usepackage{bm}
 \usepackage{indentfirst}
 \usepackage{verbatim}
@@ -52,10 +57,6 @@
 %\bibliography{references.bib}
 \usepackage[nameinlink]{cleveref}
 
-%\linenumbers
-
-%Set images folder
-\graphicspath{ {Images/} }
 
 %Set Header and Footer for all pages
 \usepackage{fancyhdr}
@@ -93,15 +94,30 @@
 %Main Body
 
 \usepackage{lineno}
-\makeatletter
-\def\makeLineNumberLeft{%
-	\linenumberfont\llap{\hb@xt@\linenumberwidth{\LineNumber\hss}\hskip\linenumbersep}% left line number
-	\hskip\columnwidth% skip over a column of text
-	\rlap{\hskip\linenumbersep\hb@xt@\linenumberwidth{\hss\LineNumber}}\hss}% right line number
-\leftlinenumbers% Re-issue [left] option
-\makeatother
+% \makeatletter
+% \def\makeLineNumberLeft{%
+% 	\linenumberfont\llap{\hb@xt@\linenumberwidth{\LineNumber\hss}\hskip\linenumbersep}% left line number
+% 	\hskip\columnwidth% skip over a column of text
+% 	\rlap{\hskip\linenumbersep\hb@xt@\linenumberwidth{\hss\LineNumber}}\hss}% right line number
+% \leftlinenumbers% Re-issue [left] option
+% \makeatother
 \linenumbers
 
 
 % Adding custom packages
 \usepackage{physics}
+\usepackage{xspace}
+\usepackage{graphbox}
+
+%  Personal definitions
+\newcommand{\Qdark}{\ensuremath{Q_{DK}}\xspace}
+\newcommand{\pidark}{\ensuremath{\pi_{DK}}\xspace}
+\newcommand{\Mdark}{\ensuremath{X_{DK}}\xspace}
+
+\newcommand{\dark}{ {DK} }
+\newcommand{\ctau}{\ensuremath{c\tau}\xspace}
+\newcommand{\dpi}{\ensuremath{\pi_\dark}\xspace}
+\newcommand{\ctaudpi}{\ensuremath{\ctau_{\dpi}}\xspace}
+
+\newcommand{\pgroup}[1]{\ensuremath{\left(#1\right)}}
+\newcommand{\HT}{\ensuremath{H_T}\xspace}
diff --git a/references.bib b/references.bib
@@ -1,3 +1,32 @@
+
+@misc{hl-lhc, title={The HL-LHC project}, url={https://hilumilhc.web.cern.ch/content/hl-lhc-project}, journal={The HL-LHC project | High Luminosity LHC Project}}
+@article{Bai_2014,
+   title="{Scale of dark QCD}",
+   volume={89},
+   ISSN={1550-2368},
+   url={http://dx.doi.org/10.1103/PhysRevD.89.063522},
+   DOI={10.1103/physrevd.89.063522},
+   number={6},
+   journal={Physical Review D},
+   publisher={American Physical Society (APS)},
+   author={Bai, Yang and Schwaller, Pedro},
+   year={2014},
+   month=mar }
+
+@article{Renner_2018,
+   title={A flavoured dark sector},
+   volume={2018},
+   ISSN={1029-8479},
+   url={http://dx.doi.org/10.1007/JHEP08(2018)052},
+   DOI={10.1007/jhep08(2018)052},
+   number={8},
+   journal={Journal of High Energy Physics},
+   publisher={Springer Science and Business Media LLC},
+   author={Renner, Sophie and Schwaller, Pedro},
+   year={2018},
+   month=aug }
+
+
 @article{CMS:2024gxp,
     author = "Hayrapetyan, Aram and others",
     collaboration = "CMS",
@@ -116,16 +145,18 @@ @article{archer2022emerging
   doi       = {10.1007/JHEP02(2022)027}
 }
 
-@article{DQM2019,
-  author  = {{Azzolini, Virginia} and {Broen van, Besien} and {Bugelskis, Dmitrijus} and {Hreus, Tomas} and {Maeshima, Kaori} and {Javier Fernandez, Menendez} and {Norkus, Antanas} and {James Fraser, Patrick} and {Rovere, Marco} and {Andre Schneider, Marcel}},
-  title   = {The {Data Quality Monitoring Software for the CMS experiment at the LHC: past, present and future}},
-  doi     = {10.1051/epjconf/201921402003},
-  url     = {https://doi.org/10.1051/epjconf/201921402003},
-  journal = {EPJ Web Conf.},
-  year    = 2019,
-  volume  = 214,
-  pages   = {02003}
-}
+
+@article{refId0,
+	author = {{Azzolini, Virginia} and {Broen van, Besien} and {Bugelskis, Dmitrijus} and {Hreus, Tomas} and {Maeshima, Kaori} and {Javier Fernandez, Menendez} and {Norkus, Antanas} and {James Fraser, Patrick} and {Rovere, Marco} and {Andre Schneider, Marcel}},
+	doi = {10.1051/epjconf/201921402003},
+	journal = {EPJ Web Conf.},
+	pages = {02003},
+	title = {The Data Quality Monitoring Software for the CMS experiment at the LHC: past, present and future},
+	url = {https://doi.org/10.1051/epjconf/201921402003},
+	volume = 214,
+	year = 2019,
+	bdsk-url-1 = {https://doi.org/10.1051/epjconf/201921402003}}
+
 @article{CMS:2016ngn,
       author         = "Khachatryan, Vardan and others",
       title              = "{The CMS trigger system}",
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