--- trunk/langevinHull/langevinHull.tex	2010/11/08 20:11:36	3678
+++ trunk/langevinHull/langevinHull.tex	2010/11/09 21:13:27	3684
@@ -40,18 +40,18 @@ Notre Dame, Indiana 46556}
   We have developed a new isobaric-isothermal (NPT) algorithm which
   applies an external pressure to the facets comprising the convex
   hull surrounding the system.  A Langevin thermostat is also applied
-  to facets of the hull to mimic contact with an external heat
-  bath. This new method, the ``Langevin Hull'', performs better than
-  traditional affine transform methods for systems containing
-  heterogeneous mixtures of materials with different
-  compressibilities. It does not suffer from the edge effects of
-  boundary potential methods, and allows realistic treatment of both
-  external pressure and thermal conductivity to an implicit solvent.
-  We apply this method to several different systems including bare
-  metal nanoparticles, nanoparticles in an explicit solvent, as well
-  as clusters of liquid water. The predicted mechanical properties of
-  these systems are in good agreement with experimental data and
-  previous simulation work.
+  to the facets to mimic contact with an external heat bath. This new
+  method, the ``Langevin Hull'', can handle heterogeneous mixtures of
+  materials with different compressibilities.  These are systems that
+  are problematic for traditional affine transform methods.  The
+  Langevin Hull does not suffer from the edge effects of boundary
+  potential methods, and allows realistic treatment of both external
+  pressure and thermal conductivity due to the presence of an implicit
+  solvent.  We apply this method to several different systems
+  including bare metal nanoparticles, nanoparticles in an explicit
+  solvent, as well as clusters of liquid water. The predicted
+  mechanical properties of these systems are in good agreement with
+  experimental data and previous simulation work.
 \end{abstract}
 
 \newpage
@@ -115,11 +115,18 @@ effect.  For example, calculations using typical hydra
 pressure conditions. The use of periodic boxes to enforce a system
 volume requires either effective solute concentrations that are much
 higher than desirable, or unreasonable system sizes to avoid this
-effect.  For example, calculations using typical hydration shells
+effect.  For example, calculations using typical hydration boxes
 solvating a protein under periodic boundary conditions are quite
-expensive. [CALCULATE EFFECTIVE PROTEIN CONCENTRATIONS IN TYPICAL
-SIMULATIONS]
+expensive.  A 62 $\AA^3$ box of water solvating a moderately small
+protein like hen egg white lysozyme (PDB code: 1LYZ) yields an
+effective protein concentration of 100 mg/mL.\cite{Asthagiri20053300}
+
+Typically protein concentrations in the cell are on the order of
+160-310 mg/ml,\cite{Brown1991195} and the factor of 20 difference
+between simulations and the cellular environment may have significant
+effects on the structure and dynamics of simulated protein structures.
 
+
 \subsection*{Boundary Methods}
 There have been a number of approaches to handle simulations of
 explicitly non-periodic systems that focus on constant or
@@ -702,7 +709,7 @@ works as follows:
 \begin{enumerate}
 \item Each processor computes the convex hull for its own atomic sites
   (left panel in Fig. \ref{fig:parallel}).
-\item The Hull vertices from each processor are passed out to all of
+\item The Hull vertices from each processor are communicated to all of
   the processors, and each processor assembles a complete list of hull
   sites (this is much smaller than the original number of points in
   the point cloud).
@@ -718,7 +725,9 @@ works as follows:
   computation, the processors first compute the convex hulls for their
   own sites (dashed lines in left panel). The positions of the sites
   that make up the subset hulls are then communicated to all
-  processors (middle panel).  The convex hull of the system (solid line in right panel) is the convex hull of the points on the union of the subset hulls.}
+  processors (middle panel).  The convex hull of the system (solid line in 
+  right panel) is the convex hull of the points on the union of the subset 
+  hulls.}
 \label{fig:parallel}
 \end{figure}