\documentclass[10pt]{letter}
\address{
Jan-Hendrik Prinz\\
Computational Molecular Biology\\
Arnimallee 6\\
FU Berlin\\
14195 Berlin, Germany \\
phone: +49 (0)30 838 75775\\
email: \href{mailto:jan-hendrik.prinz@fu-berlin.de}{jan-hendrik.prinz@fu-berlin.de}\\
\name{John D. Chodera}
}

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Jan-Hendrik Prinz, corresponding author
} 

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\begin{document}
\begin{letter}{Marsha I. Lester, Editor\\
\emph{The Journal of Chemical Physics}\\
Department of Chemistry\\
University of Pennsylvania\\
231 S.~34th St.\\
Philadelphia, PA 19104-6323, USA}

\opening{Dear Editor,}

We are submitting the following manuscript for consideration for publication as a {\bf full length article} in the Journal of the Chemical Physics:

{\bf Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics} \\ by Jan-Hendrik Prinz, John D. Chodera, Vijay S. Pande, William C. Swope, Jeremy C. Smith and Frank No\'{e}.

This work extends earlier work by Gerhard Hummer [{\bf Peptide folding kinetics from replica exchange molecular dynamics} PRE 77:002354, 2008], in that we show how to make optimal use of data collected from \emph{all}
temperatures build a temperature-dependent Markov model for \emph{any} temperature of interest.

The manuscript effectively demonstates the usfulness and practicality of the new method and applies it finally to the reconstruction of dynamic properties using data collected from the full parallel tempering simulation at all temperatures with increased accuracy and richness in detail.

The framework we use to optimally incorporate data from all temperatures is laid out in the theory article from John Chodera et al. [{\bf Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures}], which is to be submitted to JCP as well.
We request our manuscript be reviewed together with the Chodera et al. manuscript for publication of both articles in the same issue, if possible. The submitted Chodera et al. manuscript is included in this submission as 'supplementary material for review only'.

We suggest the following list of people to be suitable referees: 
\begin{itemize}

  \item {\bf Ron Levy}, Department of Chemistry \& Chemical Biology Rutgers, The State University of New Jersey \\
%  			610 Taylor Road \\
%			Piscataway, NJ 08854, USA \\
	\href{mailto:ronlevy@lutece.rutgers.edu}{ronlevy@lutece.rutgers.edu}
% 			\emph{phone:} 732.445.3947 \\
% 			\emph{fax:} 732.445.5958

  \item {\bf Gerhard Hummer}, Theoretical Biophysics Section, NIDDK, National Institutes of Health \\
%			5 Memorial Dr., Building 5 , Room 132 \\
%			Bethesda, MD 20892 \\
	\href{mailto:hummer@helix.nih.gov}{hummer@helix.nih.gov}
%			\emph{phone:} 301-402-6290 \\
%			\emph{fax:} 301-496-0825

  \item {\bf Nicolae-Viorel Buchete}, Computational Nano-Bio Physics, University College Dublin\\
	\href{mailto:buchete@ucd.ie}{buchete@ucd.ie}

  \item {\bf Beno\^{i}t Roux}, Departments of Biochemistry and Molecular Biophysics, The University of Chicago\\
%           929 East 57th St, Room W323B\\
%           Chicago, IL 60637, USA\\
           \href{mailto:roux@uchicago.edu}{roux@uchicago.edu}
%           \emph{phone:} 773.834.3557\\
%           \emph{fax:} 773.702.0439 

  \item {\bf Angel Garcia}, Department of Physics, Applied Physics, and Astronomy Rensselaer Polytechnic Institute\\
%			110 Eighth Street \\
%			Troy, New York 12180-3590, USA \\
	\href{mailto:angel@rpi.edu}{angel@rpi.edu}
%			\emph{phone:} 518.276.6310 \\
%			\emph{fax:} 518.276.6680 

  \item {\bf Adrian Roitberg}, Quantum Theory Project, Department of Chemistry, University of Florida\\
%
%
	\href{mailto:adrian@qtp.ufl.edu}{adrian@qtp.ufl.edu}
%			\emph{phone:} 352.392.6972 \\
%			\emph{fax:} 352.392.8722

  \item {\bf Carlos Simmerling}, Department of Chemistry, State University of New York \\
%    		Stony Brook, NY 11794-3400 \\
	\href{mailto:carlos.simmerling@sunysb.edu}{carlos.simmerling@sunysb.edu}
%			\emph{phone:} 631.632.1336 \\
%			\emph{fax:} 631.632.7960

  \item {\bf Alessandro Laio},  International School for Advanced Studies (SISSA), Trieste \\
%
	\href{mailto:laio@sissa.it}{laio@sissa.it}
%			\emph{phone:} +39 040 3787528 \\
%			\emph{fax:} +39 040 3787426

  \item {\bf Arthur Voter}, Theoretical Division, T-12, Los Alamos National Laboratory\\
%			Los Alamos, NM 87545 \\
	\href{mailto:afv@lanl.gov}{afv@lanl.gov}
% 			\emph{phone:} 505.667.6198 \\ 
%			\emph{fax:} 505.665.3909
            
%  \item {\bf Vijay S. Pande}, Departments of Chemistry and Structural Biology, Stanford University \\
%           Clark Center, MC 5447\\
%           Stanford University\\
%           Stanford, CA 94305-5447\\
%           \href{mailto:pande@stanford.edu}{pande@stanford.edu}
%           \emph{phone:} 650.723.3660\\
%           \emph{fax:} 650.725.0259 

%  \item {\bf Nina Singhal Hinrichs}, Departments of Statistics and Computer Science, The University of Chicago \\
%	\href{mailto:nshinrichs@uchicago.edu}{nshinrichs@uchicago.edu}

%   \item {\bf Attila Szabo}, Laboratory of Chemical Physics, NIDDK, NIH\\
%           \href{mailto:attilas@niddk.nih.gov}{attilas@niddk.nih.gov}


\end{itemize}

All authors have seen and approved of the submitted version of this manuscript.
The corresponding author is Jan-Hendrik Prinz.

This manuscript has been submitted exclusively to JCP.

\closing{Kind regards,}
\end{letter}
\end{document}
