
% BB Nov 4 2006

\begin{thebibliography}{12}

% \markboth{Markov Chain Monte Carlo Simulations and Their Statistical 
% Analysis}{ Bibliography }  %CHANGE HERE

% \addcontentsline{toc}{chapter}{Bibliography}%

% AAA

% \bibitem[Alves {\it et~al}. (1990)]{AlBe90} Alves, N.A., Berg, B.A. and 
\bibitem{AlBe90} Alves, N.A., Berg, B.A. and 
Villanova, R. (1990). {\it Ising-Model Monte Carlo Simulations: Density 
of States and Mass Gap}, Phys. Rev. B {\bf 41}: 383--394.

% BBB

\bibitem{BeNe91} Berg, B.A. and Neuhaus, T. (1991). {\it Multicanonical 
Algorithms for First Order Phase Transitions}, Phys. Lett. B {\bf 267}:
249--253.

% \bibitem[Berg and Neuhaus (1992)]{BeNe92} Berg, B.A. and Neuhaus, T.
\bibitem{BeNe92} Berg, B.A. and Neuhaus, T.
(1992). {\it Multicanonical Ensemble: A New Approach to Simulate 
First-Order Phase Transitions}, Phys. Rev. Lett. {\bf 68}: 9--12.

% \bibitem[Berg and Celik (1992)]{BeCe92} Berg, B.A. and Celik, T.
\bibitem{BeCe92} Berg, B.A. and Celik, T.
(1992). {\it A New Approach to Spin Glass Simulations}, 
Phys. Rev. Lett. {\bf 69}: 2292--2295.

% \bibitem[Berg {\it et~al}. (1993)]{BeHaNe93} Berg, B.A., Hansmann, U.H. 
\bibitem{BeHaNe93} Berg, B.A., Hansmann, U.H. 
and Neuhaus, T. (1993). {\it Properties of Interfaces in the Two and 
Three Dimensional Ising Model}, Z. Phys. B {\bf 90}: 229--239.

\bibitem{BeCeHa04} Berg, B.A., Celik T. and Hansmann, U.H. (1994). 
{\it Groundstate Properties of the 3D Ising spin glass}, Phys. Rev. 
B {\bf 50}: 16444--16452.

\bibitem{Be96} Berg, B.A. (1996). {\it Multicanonical Recursions}, 
J. Stat.  Phys. {\bf 82}: 323--342.

\bibitem{Bi82} Binder, K. (1982). {\it The Monte Carlo 
Calculation of the Surface Tensions for Two- and Three-Dimensional 
Lattice-Gas Models}, Phys. Rev. A {\bf 25}: 1699--1709.

% CCC

\bibitem{Ch82} Chandler, D. (1987). {\it Introduction to Modern
Statistical Mechanics}, Oxford University Press (chapter 6.3).

% DDD

\bibitem{DiKa99} Dinner, A.R., Lazaridis, T. and Karplus, M. (1999). 
{\it Understanding $\beta$-hairpin formation}, Proc. Nat. Acad. Sci. 
USA {\bf 96}: 9068--9073.

% FFF

\bibitem{FaMa82} Falcioni, M., Marinari, E., Paciello, L, Parisi, G. 
and Taglienti, B. (1982). {\it Complex Zeros in the Partition Function 
of Four-Dimensional $SU(2)$ Lattice Gauge Model.} Phys. Lett. B 
{\bf 108}: 331--332.

% \bibitem[Ferrenberg and Swendsen (1988)]{FeSw88} Ferrenberg, A.M. and 
\bibitem{FeSw88} Ferrenberg, A.M. and 
Swendsen, R.H. (1988). {\it New Monte Carlo Technique for Studying Phase 
Transitions}, Phys. Rev.  Lett. {\bf 61}: 2635--2638; {\bf 63}: 1658.

% \bibitem[Ferrenberg and Swendsen (1989)]{FeSw89} Ferrenberg, A.M. and 
\bibitem{FeSw89} Ferrenberg, A.M. and 
Swendsen, R.H. (1989). {\it Optimized Monte Carlo Data Analysis}, 
Phys. Rev. Lett. {\bf 63}: 1195--1198.

% \bibitem[Frantz {\it et~al.} (1990)]{Fr90} Frantz, D.D., Freemann,
\bibitem{Fr90} Frantz, D.D., Freemann,
D.L. and Doll, J.D. (1990). {\it Reducing quasi-ergodic behavior in
Monte Carlo simulations by J-walking: Applications to atomic clusters}, 
J. Chem. Phys. {\bf 93}: 2769--2784.

\bibitem{Fu00} Fukunishi, H., Watanabe, O., and Takada, S. (2000). {\it
On the Hamiltonian replica exchange method for efficient sampling of
biomolecular systems: Application to protein structure prediction},
J. Chem. Phys. {\bf 116}: 9058--9067.

% GGG

% \bibitem[Geyer (1991)]{Ge91} Geyer, G.J. (1991). {\it Markov Chain Monte 
\bibitem{Ge91} Geyer, G.J. (1991). {\it Markov Chain Monte 
Carlo Maximum Likelihood}, in {\it Computing Science and Statistics}, 
Proceedings of the 23rd Symposium on the Interface, Keramidas, E.M. 
(editor), Interface Foundation, Fairfax, Virginia, pp.~156--163.

% HHH

% \bibitem[Hansmann and Okamoto (1993)]{HaOk93} Hansmann, U.H. and 
\bibitem{HaOk93} Hansmann, U.H. and 
Okamoto, Y. (1993). {\it Prediction of Peptide Conformation by 
Multicanonical Algorithm: New Approach to the Multiple-Minima Problem}, 
J. Comp. Chem. {\bf 14}: 1333--1338.

% \bibitem[Hansmann (1997)]{Ha97} Hansmann, U.H. (1997). {\it Parallel 
\bibitem{Ha97} Hansmann, U.H. (1997). {\it Parallel tempering algorithm 
for conformational studies of biological molecules}, Chem. Phys. Lett. 
{\bf 281}: 140--150.

\bibitem{HaOk99} Hansmann, U.H. and Okamoto, Y. (1999). {\it 
Finite-size scaling of helix-coil transitions in poly-alanine 
studied by by multicanonical simulations}, J. Chem. Phys. {\bf 110}:
1267--1276; erratum {\bf 111}: 1339.

% JJJ

% LLL

\bibitem{LiYa06} Li, H. Fajer, M. and Yang, W. (2006). {\it Simulated 
Scaling Method for Localized Enhanced Sampling and Simultaneous 
``Alchemical'' Free Energy Simulations: A General Method for MM, QM, 
and QM/MM Simulations}, J. Chem. Phys, in press.

\bibitem{LiSc88} Li, Z. and Scheraga, H.A. (1988). {\it Structure 
and Free Energy of Complex Thermodynamic Systems}, J. Mol.  Struct.  
(Theochem) {\bf 179}: 333--352.

\bibitem{Liu05} Liu, P., Kim, B., Friesner, A., and Berne, B.J. (2005). 
{\it Replica exchange with solute tempering: A method for sampling
biological systems in explicit water}, Proc. Nat. Acad. Sci. USA 
{\bf 102}: 13749--13754. 

% \bibitem[Lyubartsev {\it et~al}. (1992)]{LyMa92} Lyubartsev, A.P.,
\bibitem{LyMa92} Lyubartsev, A.P.,
Martsinovski, A.A., Shevkanov, S.V. and Vorontsov-Velyaminov, P.N. 
(1992).  {\it New Approach to Monte Carlo Calculation of the Free Energy: 
Method of Expanded Ensembles}, J.  Chem. Phys. {\bf 96}: 1776--1783.

% MMM

%\bibitem[Marinari and Parisi (1992)]{MaPa92} Marinari, E. and Parisi, 
\bibitem{MaPa92} Marinari, E. and Parisi, 
G.  (1992). {\it Simulated Tempering: A New Monte Carlo Scheme}, 
Europhys. Lett. {\bf 19}: 451--458.

\bibitem{MiYa06} Min, D., Li, H., Li, G., Bitteti-Putzer, and Yang, W.
(2006). {\it A Synergistic Approach to  Improve ``Alchemical'' Free
Energy Calculations in Rough Energy Landscapes}, J. Chem. Phys, 
in press.

% \bibitem{MiYa07} Min, D., Liu, Y., and Yang, W. (2007). {\it 
% Wang-Landau Flooding Algorithm to Improve the Conformational Free 
% Energy Sampling}, submitted to J. Phys. Chem.

% \bibitem[McDonald and Singer (1967)]{McSi67} McDonald, I.R. and Singer, 
\bibitem{McSi67} McDonald, I.R. and Singer, 
K. (1967). {\it Calculation of Thermodynamic Properties of Liquid Argon
from Lennard-Jones Parameters by a Monte Carlo Method}, Discussions
Faraday Soc. {\bf 43}: 40--49.

% NNN

% \bibitem[Hukusima and Nemoto (1996)]{HuNe96} Hukusima, K. and Nemoto, K.
\bibitem{HuNe96} Hukusima, K. and Nemoto, K.
(1996). {\it Exchange Monte Carlo Method and Applications to Spin Glass 
Simulations}, J. Phys. Soc. Japan {\bf 65}: 1604--1608.

% \bibitem[Neuhaus and Hager (2003)]{NeHa02} Neuhaus, T. and Hager, J.S.
\bibitem{NeHa02} Neuhaus, T. and Hager, J.S.
(2003). {\it $2D$ Crystal Shapes, Droplet Condensation and Supercritical 
Slowing Down in Simulations of First Order Phase Transitions}, 
J. Stat. Phys. {\bf 113}: 47--83. %  [cond-mat/0201324].

% PPP

% \bibitem[Pelissetto and Vicari (2002)]{PeVi02} Pelissetto, A. and 
\bibitem{PeVi02} Pelissetto, A. and 
Vicari, E. (2002). {\it Critical Phenomena and Renormali\-zation 
Group Theory}, Phys. Rep. {\bf 368}: 549--727.

% QQQ

\bibitem{Qi02} Qiu, L.L, Pabic, S.A., Roitberg, A.E. and Hagen. S.J. 
(2002). {\it Smaller and Faster: The 20-Residue Trp-Cage Folds within 
4$\mu$s}, J. Am.  Chem. Soc. {\bf 124}:` 12952--12953.

% SSS

% [Salsburg {\it et~al}. (1959)]
\bibitem{Sa59} Salsburg, Z.W.,
Jacobson, J.D., Fickett, W.S. and Wood, W.W. (1959). {\it Applications
of the Monte Carlo Method to the Lattice-Gas Model. I. Two-Dimensional
Triangular Lattice}, J. Chem. Phys. {\bf 30}: 65--72.

% \bibitem[Swendsen and Wang (1986)]{SwWa86} Swendsen, R.H. and Wang, 
\bibitem{SwWa86} Swendsen, R.H. and Wang, 
J.-S. (1986). {\it Replica Monte Carlo Simulations of Spin Glasses}, 
Phys. Rev. Lett. {\bf 57}: 2607--2609.

% \bibitem[Swendsen and Wang (1987)]{SwWa87} Swendsen, R.H. and Wang, 
\bibitem{SwWa87} Swendsen, R.H. and Wang, 
J.-S. (1987). {\it Nonuniversal Critical Dynamics in Monte Carlo 
Simulations}, Phys. Rev. Lett. {\bf 58}: 86--88.

% \bibitem[Wang and Swendsen (2002)]{WaSw02} Wang, J.-S. and 
\bibitem{WaSw02} Wang, J.-S. and Swendsen, R.H. (2002). {\it Transition 
Matrix Monte Carlo Method}, J. Stat. Phys. {\bf 106}: 245--285.

% TTT

% \bibitem[Torrie and Valleau (1977)]{ToVa77} Torrie, G.M. and Valleau, 
\bibitem{ToVa77} Torrie, G.M. and Valleau, 
J.P. (1977). {\it Nonphysical Sampling Distributions in Monte Carlo 
Free-energy Estimation: Umbrella Sampling},
J. Comp. Phys. {\bf 23}: 187-199.

\bibitem{Tr04} Trebst, S., Huse, D.A. and Troyer, M. (2004). {\it 
Optimizing the ensemble for equlibration in broad-histogram Monte
Carlo simulations}, Phys. Rev. E {\bf 70}: 046701.

% VVV

% \bibitem[Valleau and Card (1972)]{VaCa72} Valleau, J.P. and Card, D.N. 
\bibitem{VaCa72} Valleau, J.P. and Card, D.N. 
(1972). {\it Monte Carlo Estimation of the Free Energy by Multistage
Sampling}, J. Chem. Phys. {\bf 37}: 5457--5462.

% WWW

% \bibitem[Wang and Landau (2001)]{WaLa01} Wang, F. and Landau, D.P.
\bibitem{WaLa01} Wang, F. and Landau, D.P.
(2001). {\it Efficient, Multiple-Range Random Walk Algorithm to 
Calculate the Density of States}, Phys. Rev. Lett. {\bf 86}: 
2050--2053.

% \bibitem[Wolff (1989)]{Wo89} Wolff, U. (1989). {\it Collective Monte 
\bibitem{Wo89} Wolff, U. (1989). {\it Collective Monte Carlo Updating 
for Spin Systems}, Phys. Rev. Lett. {\bf 62}: 361--363.

% YYY

\bibitem{Ya00} Yan, Q. and de Pablo, J.J. (1999). {\it Hyper-parallel 
tempering Monte Carlo: Application to the Lennard-Jones fluid and the
restrictive primitive model}, J. Chem. Phys. {\bf 111}: 9509--9516;
{\it Hyper-parallel tempering simulation of polymeric systems}, 
J. Chem. Phys. {\bf 113}: 1276--1282.

\end{thebibliography}
\end{document}
