--- trunk/iceiPaper/iceiPaper.tex	2004/09/15 20:22:21	1461
+++ trunk/iceiPaper/iceiPaper.tex	2004/09/15 20:47:13	1462
@@ -62,7 +62,7 @@ molecules\cite{smallStuff} to complex biological
 
 Molecular dynamics has developed into a valuable tool for studying the
 phase behavior of systems ranging from small or simple
-molecules\cite{smallStuff} to complex biological
+molecules\cite{Matsumoto02andOthers} to complex biological
 species.\cite{bigStuff} Many techniques have been developed in order
 to investigate the thermodynamic properites of model substances,
 providing both qualitative and quantitative comparisons between
@@ -74,22 +74,22 @@ conditions.\cite{lotsOfWaterPapers} Many of these mode
 Water has proven to be a challenging substance to depict in
 simulations, and has resulted in a variety of models that attempt to
 describe its behavior under a varying simulation
-conditions.\cite{lotsOfWaterPapers} Many of these models have been
-used to investigate important physical phenomena like phase
-transitions and the hydrophobic effect.\cite{evenMorePapers} With the
-advent of numerous differing models, it is only natural that attention
-is placed on the properties of the models themselves in an attempt to
-clarify their benefits and limitations when applied to a system of
-interest.\cite{modelProps} One important but challenging property to
-quantify is the free energy, particularly of the solid forms of
-water. Difficulty in these types of studies typically arises from the
-assortment of possible crystalline polymorphs that water that water
-adopts over a wide range of pressures and temperatures. There are
-currently 13 recognized forms of ice, and it is a challenging task to
-investigate the entire free energy landscape.\cite{Sanz04} Ideally,
-research is focused on the phases having the lowest free energy,
-because these phases will dictate the true transition temperatures and
-pressures for their respective model. 
+conditions.\cite{Berendsen81,Jorgensen83,Bratko85,Berendsen87,Liu96,Mahoney00,Fennell04}
+Many of these models have been used to investigate important physical
+phenomena like phase transitions and the hydrophobic
+effect.\cite{evenMorePapers} With the advent of numerous differing
+models, it is only natural that attention is placed on the properties
+of the models themselves in an attempt to clarify their benefits and
+limitations when applied to a system of interest.\cite{modelProps} One
+important but challenging property to quantify is the free energy,
+particularly of the solid forms of water. Difficulty in these types of
+studies typically arises from the assortment of possible crystalline
+polymorphs that water that water adopts over a wide range of pressures
+and temperatures. There are currently 13 recognized forms of ice, and
+it is a challenging task to investigate the entire free energy
+landscape.\cite{Sanz04} Ideally, research is focused on the phases
+having the lowest free energy, because these phases will dictate the
+true transition temperatures and pressures for their respective model.
 
 In this paper, standard reference state methods were applied to the
 study of crystalline water polymorphs in the low pressure regime. This
@@ -97,7 +97,7 @@ themselves\cite{nucleationStudies}; however, the cryst
 arrived at through crystallization of a computationally efficient
 water model under constant pressure and temperature
 conditions. Crystallization events are interesting in and of
-themselves\cite{nucleationStudies}; however, the crystal structure
+themselves\cite{Matsumoto02,Yamada02}; however, the crystal structure
 obtained in this case was different from any previously observed ice
 polymorphs, in experiment or simulation.\cite{Fennell04} This crystal
 was termed Ice-{\it i} in homage to its origin in computational
@@ -222,23 +222,25 @@ cubic switching between 100\% and 85\% of the cutoff v
 \end{figure}
 
 Charge, dipole, and Lennard-Jones interactions were modified by a
-cubic switching between 100\% and 85\% of the cutoff value (9 \AA ). By
-applying this function, these interactions are smoothly truncated,
-thereby avoiding poor energy conserving dynamics resulting from
-harsher truncation schemes. The effect of a long-range correction was
-also investigated on select model systems in a variety of manners. For
-the SSD/RF model, a reaction field with a fixed dielectric constant of
-80 was applied in all simulations.\cite{Onsager36} For a series of the
-least computationally expensive models (SSD/E, SSD/RF, and TIP3P),
-simulations were performed with longer cutoffs of 12 and 15 \AA\ to
-compare with the 9 \AA\ cutoff results. Finally, results from the use
-of an Ewald summation were estimated for TIP3P and SPC/E by performing
+cubic switching between 100\% and 85\% of the cutoff value (9 \AA
+). By applying this function, these interactions are smoothly
+truncated, thereby avoiding poor energy conserving dynamics resulting
+from harsher truncation schemes. The effect of a long-range correction
+was also investigated on select model systems in a variety of
+manners. For the SSD/RF model, a reaction field with a fixed
+dielectric constant of 80 was applied in all
+simulations.\cite{Onsager36} For a series of the least computationally
+expensive models (SSD/E, SSD/RF, and TIP3P), simulations were
+performed with longer cutoffs of 12 and 15 \AA\ to compare with the 9
+\AA\ cutoff results. Finally, results from the use of an Ewald
+summation were estimated for TIP3P and SPC/E by performing
 calculations with Particle-Mesh Ewald (PME) in the TINKER molecular
-mechanics software package. TINKER was chosen because it can also
-propagate the motion of rigid-bodies, and provides the most direct
-comparison to the results from OOPSE. The calculated energy difference
-in the presence and absence of PME was applied to the previous results
-in order to predict changes in the free energy landscape.
+mechanics software package.\cite{Tinker} TINKER was chosen because it
+can also propagate the motion of rigid-bodies, and provides the most
+direct comparison to the results from OOPSE. The calculated energy
+difference in the presence and absence of PME was applied to the
+previous results in order to predict changes in the free energy
+landscape.
 
 \section{Results and discussion}
 
