Title: Combination of generalized-ensemble algorithms and one-dimensional reference interaction site model theory
Author(s):

	A.Mitsutake (Department of Physics, Keio University, Yokohama, Kanagawa 223-8522, Japan) ,
	M.Kinoshita (Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan) ,
	F.Hirata (Department of Theoretical Studies, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan; Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan) ,
	Y.Okamoto (Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan)

The article reports an attempt to study the protein folding problem by generalized-ensemble Monte Carlo simulations with reference interaction site model theory. Generalized-ensemble algorithms greatly enhance the configurational space sampling in computer simulations. The reference interaction site model theory treat solvent effects with solvent molecular shape and estimate solvation free energy around proteins. We have developed simulation algorithms which combine generalized-ensemble algorithms and one-dimensional reference interaction site model theory. This treatment can also use a simulation with three-dimensional reference interaction site model theory. In this review, we describe the methods and present the results of these simulations for a peptide.

Key words: generalized-ensemble algorithm, multicanonical algorithm, replica-exchange method, RISM, Monte Carlo, protein folding
PACS: 31.15.Qg, 61.25.Em, 87.15.Aa

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