Spell check for chapter 1-6

chap1.tex

@@ -4,7 +4,7 @@ \chapter{Introduction}
 %% Restart the numbering to make sure that this is definitely page #1!
 \pagenumbering{arabic}
 
-The field of neutrino physics is currently evolving very rapidly.  With its tenuous postulation~\cite{PauliOpenLetter} acting as a future omen, the neutrino's mark on history would not become apparent from its discovery~\cite{Cowan20071956, PhysRevLett.9.36, Kodama2001218}, but rather from a spate of surprising discoveries at the end of the 20th century~\cite{PhysRevLett.81.1562, PhysRevLett.87.071301, PhysRevLett.90.021802} which conclusively proved that the Standard Model, while very successful, was incomplete.  This revelation was experimental proof of Maki, Nagakawa and Sakata's extension~\cite{Maki01111962} to Pontecorvo's theory of neutrino oscillation\Yoshi{}{ADDRESSED - there was a space here}~\cite{Pontecorvo} \Yoshi{with the inclusion of the Mikheyev-Smirnov-Wolfenstein (MSW) effect which is the alteration of the oscillation effect due to differences in the coherent forward scattering of the three neutrino flavours with electrons in matter}{ADDRESSED - this is not very clear. Add a few words to remind readers of what the MSW effect is.}~\cite{PhysRevD.17.2369,Mikheev:1986gs}.  The findings were groundbreaking as the underlying theory requires \Yoshi{neutrinos to be massive}{ADDRESSED - massive neutrinos}, which is in direct contradiction to the Standard Model.  The, now, standard theory of neutrino oscillation defines three neutrino flavours and three neutrino masses.  However, the map between flavour and mass is not one-to-one, but rather a rotation of mass space onto flavour space.  The main consequence of this rotation is that the flavour eigenstates are a superposition of mass eigenstates, namely
+The field of neutrino physics is currently evolving very rapidly.  With its tenuous postulation~\cite{PauliOpenLetter} acting as a future omen, the neutrino's mark on history would not become apparent from its discovery~\cite{Cowan20071956, PhysRevLett.9.36, Kodama2001218}, but rather from a spate of surprising discoveries at the end of the 20th century~\cite{PhysRevLett.81.1562, PhysRevLett.87.071301, PhysRevLett.90.021802} which conclusively proved that the Standard Model, while very successful, was incomplete.  This revelation was experimental proof of Maki, Nagakawa and Sakata's extension~\cite{Maki01111962} to Pontecorvo's theory of neutrino oscillation\Yoshi{}{ADDRESSED - there was a space here}~\cite{Pontecorvo} \Yoshi{with the inclusion of the Mikheyev-Smirnov-Wolfenstein (MSW) effect which is the alteration of the oscillation effect due to differences in the coherent forward scattering of the three neutrino flavours with electrons in matter}{ADDRESSED - this is not very clear. Add a few words to remind readers of what the MSW effect is.}~\cite{PhysRevD.17.2369,Mikheev:1986gs}.  The findings were ground breaking as the underlying theory requires \Yoshi{neutrinos to be massive}{ADDRESSED - massive neutrinos}, which is in direct contradiction to the Standard Model.  The, now, standard theory of neutrino oscillation defines three neutrino flavours and three neutrino masses.  However, the map between flavour and mass is not one-to-one, but rather a rotation of mass space onto flavour space.  The main consequence of this rotation is that the flavour eigenstates are a superposition of mass eigenstates, namely
 \begin{equation}
 \ket{\nu_\alpha} = \sum^{3}_{i=k}U^{\ast}_{\alpha k}\ket{\nu_k},
 \label{eq:NeutrinoEigenstates}
@@ -30,7 +30,7 @@ \chapter{Introduction}
 ,
 \label{eq:PMNSMatrix}
 \end{equation}
-where $c_{ij} \equiv \cos\theta_{ij}$ and $s_{ij} \equiv \sin\theta_{ij}$. $\theta_{ij}$ are known as the mixing angles \Yoshi{and}{ADDRESSED - was which} parameterise how strong mixings between the flavour and mass eigenstates are\Yoshi{,}{ADDRESSED - comma} and $\delta$ is a CP violating phase.  The most surprising observable feature of this mechanism is the non-zero probability to detect a neutrino of specific flavour which was created at source in a different flavour state.  By propagating the mass eigenstates through time, one can arrive at this probability which has the following form\Yoshi{:}{ADDRESSED - ``has the following form'' needs a colon; ``has the form'' does not}
+where $c_{ij} \equiv \cos\theta_{ij}$ and $s_{ij} \equiv \sin\theta_{ij}$. $\theta_{ij}$ are known as the mixing angles \Yoshi{and}{ADDRESSED - was which} parametrise how strong mixings between the flavour and mass eigenstates are\Yoshi{,}{ADDRESSED - comma} and $\delta$ is a CP violating phase.  The most surprising observable feature of this mechanism is the non-zero probability to detect a neutrino of specific flavour which was created at source in a different flavour state.  By propagating the mass eigenstates through time, one can arrive at this probability which has the following form\Yoshi{:}{ADDRESSED - ``has the following form'' needs a colon; ``has the form'' does not}
 \begin{equation}
 P(\nu_\alpha \rightarrow \nu_\beta) = |\braket{\nu_\beta|\nu\left(t\right)}|^2 = |U_{\beta k} e^{-iE_{k}t}  U^{\ast}_{\alpha k}|^2,
 \label{eq:NeutrinoOscillationProbability}
@@ -81,13 +81,13 @@ \section{The state of the field}
 
 \section{The future}
 \label{sec:NeutrinoFieldFuture}
-It should be clear that an immense amount of progress has been made in the field, with remarkable contributions to the picture coming \Yoshi{in only}{ADDRESSED - was ``only in'', which excludes any remarkable contributions before 20 years ago. But the discovery of neutrinos and the solar neutrino problem etc were pretty remarkable too....} the last 20 years.  However, there are several key questions which remain unanswered.  
+It should be clear that an immense amount of progress has been made in the field, with remarkable contributions to the picture coming \Yoshi{in only}{ADDRESSED - was ``only in'', which excludes any remarkable contributions before 20 years ago. But the discovery of neutrinos and the solar neutrino problem etc. were pretty remarkable too....} the last 20 years.  However, there are several key questions which remain unanswered.  
 \newline
 \newline
 By far the most sought\Yoshi{-}{ADDRESSED - hyphen}after answer is whether CP violation occurs in the lepton sector.  The magnitude of CP violation is encapsulated in the CP violating phase $\delta$ and so it is this parameter which current and future long-baseline experiments are aiming towards.  \Yoshi{Currently, only T2K and NO$\nu$A can provide hints for values of $\delta$, with the possibility of future constraints.}{ADDRESSED - reword this sentence -- it sounds almost as if you are saying they do provide the strongest constraints, because of the word `Currently'. Right now they just provide the only hints we have and if we are lucky they will be able to provide constraints, perhaps} The future long-baseline experiments, Hyper-Kamiokande~\cite{Abe:2014oxa} and DUNE (formerly LBNE)~\cite{Adams:2013qkq} are being designed with a possible measurement of $\delta$ as a primary goal.
 \newline
 \newline
-The second question still to be answered is the ordering of the mass eigenstates.  \Yoshi{It is not known whether $\nu_1$, which is dominated by the electron neutrino, or $\nu_3$ is the lighest mass eigenstate.}{ADDRESSED - you need something here}  Written more succinctly, is $m_3 \gg m_2 > m_1$ (the normal mass hierarchy) or $m_2 > m_1 \gg m_3$ (the inverted mass hierarchy)?  This is known as the mass hierarchy problem and its two possible solutions are shown in Fig.~\ref{fig:MassHierarchy}.  The matter effects introduced by the MSW effect are mass hierarchy\Yoshi{-}{ADDRESSED - hyphen}dependent.  So, for very long-baseline experiments, there is mass hierarchy sensitivity.  Currently NO$\nu$A has \Yoshi{the potential to resolve}{ADDRESSED - set to resolve is too strong} the mass hierarchy problem.  However, both Hyper-Kamiokande (via atmospheric measurements) and DUNE have measurement of the mass hierarchy as a primary goal.
+The second question still to be answered is the ordering of the mass eigenstates.  \Yoshi{It is not known whether $\nu_1$, which is dominated by the electron neutrino, or $\nu_3$ is the lightest mass eigenstate.}{ADDRESSED - you need something here}  Written more succinctly, is $m_3 \gg m_2 > m_1$ (the normal mass hierarchy) or $m_2 > m_1 \gg m_3$ (the inverted mass hierarchy)?  This is known as the mass hierarchy problem and its two possible solutions are shown in Fig.~\ref{fig:MassHierarchy}.  The matter effects introduced by the MSW effect are mass hierarchy\Yoshi{-}{ADDRESSED - hyphen}dependent.  So, for very long-baseline experiments, there is mass hierarchy sensitivity.  Currently NO$\nu$A has \Yoshi{the potential to resolve}{ADDRESSED - set to resolve is too strong} the mass hierarchy problem.  However, both Hyper-Kamiokande (via atmospheric measurements) and DUNE have measurement of the mass hierarchy as a primary goal.
 \begin{figure}%
   \centering
   \includegraphics[width=10cm]{images/introduction/mass_hierarchy.pdf}

chap2.tex

@@ -1,14 +1,3 @@
-%\begin{sidewaysfigure}
-%  \begin{center}
-%  \includegraphics[width=0.8\textheight]{lhcb-detector-cross-section}
-%  \caption[Cross-section view of \LHCb, cut in the non-bending $y$--$z$ plane]%
-%    {Cross-section view of \LHCb, cut in the non-bending $y$--$z$ plane.}
-%  \label{fig:LHCbCrossSection}
-%  \end{center}
-%\end{sidewaysfigure}
-
-
-
 \chapter{Neutrino interactions with atomic nuclei}
 \label{chap:NeutrinoInteractionsAtomicNuclei}
 The neutrino is a strictly weakly\Yoshi{-}{ADDRESSED - hyphen}interacting particle.  This has difficult implications for any experiment aiming to study neutrinos as particle detectors generally rely on the electromagnetic force.  In fact, the only proven method of neutrino detection is to utilise a high mass target in which the neutrinos can interact\Yoshi{}{ADDRESSED - was ` with'}.  Generally speaking, charged particles are produced by this interaction which can be detected by the usual means.  The collected information from these charged final states can then be used to infer information about the incident neutrino.  \Yoshi{Many modern neutrino experiments}{ADDRESSED - no they don't! Tritium decay mass measurements and the helicity measurement, the Homestake experiment -- all these are neutrino experiments that use other methods!} rely on this method and so, generally speaking, attempted measurements (e.g. \Yoshi{a measurement of $\delta$)}{ADDRESSED - this is not a ``measurement''} rely on our understanding \Yoshi{of}{ADDRESSED -  was `on'} neutrino interactions with atomic nuclei.  Our understanding of such processes is encompassed in the models we use to simulate the interactions.
@@ -70,7 +59,7 @@ \section{Neutrino interactions at the GeV-scale}
 \end{figure}
 \newline
 \newline
-While the value of a particular interaction cross-section should depend on the nuclear environment, it is possible to make comparisons of the measured cross-section per nucleon.  Fig.~\ref{fig:CrossSectionMeasurements}\Yoshi{}{Make this figure bigger. Say something about the data points as well as the curves, and how up-to-date it is etc} shows a comparison of $\nu_\mu$ CC cross-section measurements per nucleon from different experiments, all of which sample a different neutrino energy range.  There are large uncertainties for many of the cross-section measurements, particularly for the ones sampling the lower energy ranges.  The T2K beam energy is $\sim$700~MeV, which sits in the region of higher uncertainty.
+While the value of a particular interaction cross-section should depend on the nuclear environment, it is possible to make comparisons of the measured cross-section per nucleon.  Fig.~\ref{fig:CrossSectionMeasurements}\Yoshi{}{Make this figure bigger. Say something about the data points as well as the curves, and how up-to-date it is etc.} shows a comparison of $\nu_\mu$ CC cross-section measurements per nucleon from different experiments, all of which sample a different neutrino energy range.  There are large uncertainties for many of the cross-section measurements, particularly for the ones sampling the lower energy ranges.  The T2K beam energy is $\sim$700~MeV, which sits in the region of higher uncertainty.
 \begin{figure}[b]%
   \centering
   \includegraphics[width=12cm]{images/neutrino_interactions/CrossSectionMeasurements.pdf}

chap4.tex

@@ -38,7 +38,7 @@ \subsection{ND280 detector simulation}
 nd280mc constructs a ROOT geometry of ND280 based on the design specifications of its subdetectors and then propagates the particles given to it by the neutrino generator through the geometry, simulating energy deposition, scattering and particle decay during propagation.
 \newline
 \newline
-The sand MC is largely treated the same at this point; the surrounding pit geometry (and ND280) is constructed in nd280mc and the corresponding sand MC vectors provide the final state particles which are propagated by geant4 through the geometry.  After this point, the sand MC is treated identically to the beam MC described above.
+The sand MC is largely treated the same at this point; the surrounding pit geometry (and ND280) is constructed in nd280mc and the corresponding sand MC vectors provide the final state particles which are propagated by Geant4 through the geometry.  After this point, the sand MC is treated identically to the beam MC described above.
 
 \subsection{Detector response simulation}
 \label{subsec:DetectorResponseSimulation}

chap5.tex

@@ -242,7 +242,7 @@ \subsection{3D track reconstruction}
 \end{figure}
 \newline
 \newline
-The second input to the likelihood, called $\Delta_{\textrm{layer, first}}$, is the difference in the starting layer of each 2D track which forms the matching candidate pair, where starting layer refers to the layer closest to the ND280 Tracker.  For 2D tracks which should be matched together, $\Delta_{\textrm{layer, first}}$ should be 1.  The separation ability of this variable for the two track, barrel is shown in Fig.~\ref{fig:3DMatchingBarrel2TrackDFLSeparation}.  The discreet probability density function was created using eqn.~\ref{eq:BinProbabilityPDF}.  It was not necessary to interpolate using splines as $\Delta_{\textrm{layer, first}}$ is itself discreet.  The probability density function for $\Delta_{\textrm{layer, first}}$ is shown in Fig.~\ref{fig:3DMatchingBarrel2TrackDFLPDF} for the two track, barrel case.  For each matching candidate pair, the value of $\Delta_{\textrm{layer, first}}$ is calculated and the corresponding $\mathcal{L}_{\Delta_{\textrm{layer, first}}}$ is retrieved from the probability density function.
+The second input to the likelihood, called $\Delta_{\textrm{layer, first}}$, is the difference in the starting layer of each 2D track which forms the matching candidate pair, where starting layer refers to the layer closest to the ND280 Tracker.  For 2D tracks which should be matched together, $\Delta_{\textrm{layer, first}}$ should be 1.  The separation ability of this variable for the two track, barrel is shown in Fig.~\ref{fig:3DMatchingBarrel2TrackDFLSeparation}.  The discreet probability density function was created using equation~\ref{eq:BinProbabilityPDF}.  It was not necessary to interpolate using splines as $\Delta_{\textrm{layer, first}}$ is itself discreet.  The probability density function for $\Delta_{\textrm{layer, first}}$ is shown in Fig.~\ref{fig:3DMatchingBarrel2TrackDFLPDF} for the two track, barrel case.  For each matching candidate pair, the value of $\Delta_{\textrm{layer, first}}$ is calculated and the corresponding $\mathcal{L}_{\Delta_{\textrm{layer, first}}}$ is retrieved from the probability density function.
 \begin{figure}%
 \Yoshi{}{Say what the reader should take away from these plots. The reader should not have to go to the body text to figure this out.}
   \centering
@@ -267,7 +267,7 @@ \subsection{3D track reconstruction}
 \begin{equation}
   \mathcal{L} = \mathcal{L}_{Q_{\textrm{ratio}}} \times \mathcal{L}_{\Delta_{\textrm{layer, first}}} \times \mathcal{L}_{\Delta_{\textrm{layer, last}}}.
 \end{equation}
-As described bove, $\mathcal{L}$ is calculated for every matching candidate pair and the pair which maximise $\mathcal{L}$ is selected as a match and removed from the pool.  The process is then repeated until no more matches can be made.
+As described above, $\mathcal{L}$ is calculated for every matching candidate pair and the pair which maximise $\mathcal{L}$ is selected as a match and removed from the pool.  The process is then repeated until no more matches can be made.
 \newline
 \newline
 3D tracks have now been formed, but the associated directions and positions of those tracks still need to be calculated.  The track fitting process for the newly formed 3D tracks is very similar to that described in section~\ref{subsec:ECal3DHitReconstruction}.  The tracks are briefly separated into their constituent 2D views and a charge-weighted average position of each layer is calculated using the track's constituent hits.  Then, the hits in the opposing view are used to estimate the third coordinate of a given layer using a least-squares fit.  After all of the coordinates have been estimated, a full 3D least-squares fit of the positions in each layer is performed to estimate the 3D track's direction and position in that ECal layer.

chap6.tex

@@ -102,7 +102,7 @@ \section{Effect of magnetic field on the ECal}
   \caption{Comparisons of data and Monte Carlo in the bottom-left barrel ECal with the magnetic field model described in section~\ref{sec:MagneticFieldModel} implemented.  The red and pink histograms are Monte Carlo simulation of T2K beam neutrinos incident on ND280 and the surrounding pit respectively.  The blue data points are collected data from run 3C.  Both of the plots are POT normalized.  Comparing the shown distributions with those in Fig.~\ref{fig:BLBNoField}, the effect of the simple magnetic field model is clearly visible.}
   \label{fig:BLBWithField}
 \end{figure}
-To test this hypothesis, the simple magnetic field model in the flux return yoke described in section~\ref{sec:MagneticFieldModel} was implemented in nd280mc and a batch of beam and \Yoshi{sand Monte Carlo}{ADDRESSED (sand MC described in software chapter (chapter4)) - ``sand Monte Carlo'' is very much jargon. Introduce it properly} was produced to test its effect.  To get an idea of the magnetic field's effect on the rates measured by the ECals, the same variables as shown in Fig.~\ref{fig:BLBNoField} are shown in Fig.~\ref{fig:BLBWithField}, but with the magnetic field activated.  The difference is very clear; Fig.~\ref{fig:NHitsBLBWithField} shows that the excess in the 10 to 30 hits region is now gone.  It is also clear that the effect of the magnetic field has propagated through to the high level discriminators, as shown in Fig.~\ref{fig:TMRBLBWithField}.
+To test this hypothesis, the simple magnetic field model in the flux return yoke described in section~\ref{sec:MagneticFieldModel} was implemented in nd280mc and a batch of beam and \Yoshi{sand Monte Carlo}{ADDRESSED (sand MC described in software chapter (chapter 4)) - ``sand Monte Carlo'' is very much jargon. Introduce it properly} was produced to test its effect.  To get an idea of the magnetic field's effect on the rates measured by the ECals, the same variables as shown in Fig.~\ref{fig:BLBNoField} are shown in Fig.~\ref{fig:BLBWithField}, but with the magnetic field activated.  The difference is very clear; Fig.~\ref{fig:NHitsBLBWithField} shows that the excess in the 10 to 30 hits region is now gone.  It is also clear that the effect of the magnetic field has propagated through to the high level discriminators, as shown in Fig.~\ref{fig:TMRBLBWithField}.
 \newline
 \newline
 Despite this study only briefly investigating the presence of a magnetic field in the UA1 flux return yoke, the improvement provided is undeniable.  It was decided that the model would be a permanent feature of the ND280 simulation and is now used in all software productions including the inputs to this analysis.