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\name{John D. Chodera}
\telephone{415.867.7384}
\email{jchodera@berkeley.edu}
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%260J Stanley Hall #3220\\
%University of California\\
%Berkeley, CA 94720-3220}
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\date{\today}

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%John D. Chodera\\
%QB3 Institute\\
%260J Stanley Hall \#3220\\
%University of California\\
%Berkeley, CA 94720-3220, USA \\
%phone: 415.867.7384\\
%email: \href{mailto:jchodera@berkeley.edu}{jchodera@berkeley.edu}\\
%\name{John D. Chodera}
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John D.~Chodera, corresponding author
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%\begin{letter}{To:\\MFPL Faculty Search Committee}
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%\opening{Dear Search Committee,}


\begin{document}
\begin{letter}{Randy Schekman, Editor\\
\emph{Proceedings of the National Academy of Sciences\\
of the United States of America}\\
700 11th Street, NW\\
Suite 450\\
Washington, DC 20001}

\opening{Dear Editor,}

We are submitting the following manuscript for consideration for publication as an {\bf PNAS Plus article} in \emph{Proceedings of the National Academy of Sciences}:

{\bf Nonequilibrium candidate Monte Carlo: A new tool for efficient equilibrium simulation} by Jerome P.~Nilmeier, Gavin E.~Crooks, David D.~L.~Minh, and John D.~Chodera.

We describe a new technique for constructing efficient Monte Carlo moves in simulations of physical systems for chemistry and biology.
These new moves have high acceptance rates and allow rapid transit through configuration space, greatly enhancing convergence rates in simulations of solvated systems, and allowing practitioners to tackle some systems that have been difficult or intractable by existing means.
We generalize the Metropolis Monte Carlo sampling procedure by using \emph{nonequilibrium} processes to generate candidates for \emph{equilibrium} simulations, with the nonequilibrium work replacing the instantaneous energy difference in the acceptance criteria.
Using our method, moves that are efficient for an isolated part of a system but lead to near-universal rejection in standard Monte Carlo simulations can be converted to nonequilibrium processes that generate candidates with greatly improved acceptance probabilities.
While generating these finite-time switching trajectories incurs an additional cost, we demonstrate how driving some degrees of freedom while allowing others to evolve naturally can lead to large enhancements in acceptance probabilities, greatly reducing structural correlation times in simulations of dense solvated systems.
We believe our approach substantially extends and expands the utility of Monte Carlo simulation for a broad class of physical systems in chemistry and biology, and will therefore be of sufficiently broad interest to warrant publication in PNAS.
%Though we do not focus on this issue here, the techniques we present are also applicable to Markov chain Monte Carlo simulations for statistical inference.

We believe the primary audience for our manuscript will be similar to that of several recent PNAS papers:
\begin{itemize}
  \item Ballard AJ and Jarzynski C. {\it Replica exchange with nonequilibrium switches.} PNAS 106:12224, 2009.
  \item Ytreberg FM and Zuckerman DM. {\it A black-box re-weighting analysis can correct flawed simulation data.} PNAS 105:7982, 2008.  
  \item Frenkel D. {\it Speed-up of Monte Carlo simulations by sampling rejected states.} PNAS 101:17571, 2004.  
\end{itemize}


Appropriate PNAS Editorial Board members to evaluate this work and select an editor include:
\begin{itemize}
  \item {\bf David Chandler}
  \item {\bf Michael L. Klein}
  \item {\bf David Baker}
  \item {\bf Michael Levitt}
\end{itemize}

Appropriate NAS Member Editors include:
\begin{itemize}
  \item {\bf David Chandler}
  \item {\bf Attila Szabo}
  \item {\bf Ken A. Dill}
  \item {\bf Bruce J. Berne}
  \item {\bf Robert Zwanzig}
  \item {\bf Ben Widom}
  \item {\bf Martin Karplus}
  \item {\bf Rudolph A. Marcus}
\end{itemize}

Appropriate reviewers of this work include the following scientists:
\begin{itemize}
  \item Gerhard Hummer (NIH)
  \item Michael Shirts (Virginia)
  \item Aaron Dinner (U Chicago)
  \item Thomas F.~Miller, III (Caltech)
  \item Harry Stern (Rochester)
  \item Adrian Roitberg (Florida)
  \item Zhiqiang Tan (Rutgers)
  \item William Swope (IBM Almaden)
  \item Jes\'{u}s Izaguirre (Notre Dame)
  \item Beno\^{i}t Roux (U Chicago)
  \item M. Scott Shell (UCSB)
  \item Scott Schmidler (Duke)
  \item Tom Woolf (John Hopkins)
  \item Dan Zuckerman (Pitt)
  \item F.~Marty Ytreberg (Idaho)
  \item Andrew McCammon (UCSD)
  \item Jun S.~Liu (Harvard)
  \item J.~Ilja Siepmann (UMN)
  \item Juan J.~de Pablo (Madison)
\end{itemize}

All authors have seen and approved of the submitted version of this manuscript.
The corresponding author is John D.~Chodera.
This manuscript has been submitted exclusively to PNAS.

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