Research Activities of Yuko OKAMOTO

1. Generalized-ensemble simulations of biomolecular systems
   
2. Prediction of three-dimensional structures of biomolecules such as proteins by computer simulations
   
3. Protein folding, misfolding, and unfolding studied by generalized-ensemble simulations
   
4. Quantum simulations by generalized-ensemble algorithms
   
5. Development of effective generalized-ensemble algorithms for molecular simulations
   

• Y. Okamoto, "Protein folding problem as studied by new simulation algorithms," Recent Research Developments in Pure & Applied Chemistry 2, 1 - 23 (1998).
  
• U.H.E. Hansmann and Y. Okamoto, "The generalized-ensemble approach for protein folding simulations," in Annual Reviews of Computational Physics VI, D. Stauffer (ed.) (World Scientific, Singapore, 1999), pp. 129-157.
  
• U.H.E. Hansmann and Y. Okamoto, "New Monte Carlo algorithms for protein folding," Current Opinion in Structural Biology 9, 177 - 183 (1999).
  
• Y. Okamoto and U.H.E. Hansmann, "Protein folding simulations by a generalized-ensemble algorithm based on Tsallis statistics," in Lecture Notes in Physics: Nonextensive Statistical Mechanics and Its Applications, S. Abe and Y. Okamoto (eds.) (Springer-Verlag, Berlin, 2001), pp. 259 - 274.
  
• A. Mitsutake, Y. Sugita, and Y. Okamoto, "Generalized-ensemble algorithms for molecular simulations of biopolymers," (PDF: 984 KB) Biopolymers (Peptide Science) 60, 96 - 123 (2001).
  
• Y. Sugita and Y. Okamoto, "Free-energy calculations in protein folding by generalized-ensemble algorithms," (PDF: 492 KB) in Lecture Notes in Computational Science and Engineering, T. Schlick and H.H. Gan (eds.) (Springer-Verlag, Berlin, 2002), pp. 303 - 331.
  
• Y. Okamoto, "Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations," Journal of Molecular Graphics and Modelling 22, 425 - 439 (2004).
  

• H. Kawai, T. Kikuchi, and Y. Okamoto, "A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method," Protein Engineering 3, 85 - 94 (1989).
  
• Y. Okamoto, M. Fukugita, T. Nakazawa, and H. Kawai, "ƒ¿-Helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A," Protein Engineering 4, 639 - 647 (1991).
  
• T. Nakazawa, H. Kawai, Y. Okamoto, and M. Fukugita, "ƒÀ-Sheet folding of bovine pancreatic trypsin inhibitor fragment [16-36] as predicted by Monte Carlo simulated annealing," Protein Engineering 5, 495 - 503 (1992).
  
• U.H.E. Hansmann and Y. Okamoto, "Prediction of peptide conformation by multicanonical algorithm: new approach to the multiple-minima problem," Journal of Computational Chemistry 14, 1333 - 1338 (1993).
  
• Y. Okamoto and U.H.E. Hansmann, "Thermodynamics of helix-coil transitions studied by multicanonical algorithms," Journal of Physical Chemistry 99, 11276 - 11287 (1995).
  
• U.H.E. Hansmann, Y. Okamoto, and F. Eisenmenger, "Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble," Chemical Physics Letters 259, 321 - 330 (1996).
  
• U.H.E. Hansmann and Y. Okamoto, "Numerical comparisons of three recently proposed algorithms in the protein folding problem," Journal of Computational Chemistry 18, 920 - 933 (1997).
  
• U.H.E. Hansmann and Y. Okamoto, "Generalized-ensemble Monte Carlo method for systems with rough energy landscape," Physical Review E 56, 2228 - 2233 (1997).
  
• U.H.E. Hansmann, M. Masuya, and Y. Okamoto, "Characteristic temperatures of folding of a small peptide," Proceedings of National Academy of Sciences USA 94, 10652 - 10656 (1997).
  
• M. Kinoshita, Y. Okamoto, and F. Hirata, "Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: robust and efficient algorithm," Journal of Computational Chemistry 18, 1320 - 1326 (1997).
  
• U.H.E. Hansmann, Y. Okamoto, and J.N. Onuchic, "The folding funnel landscape for the peptide Met-enkephalin," PROTEINS: Structure, Function, and Genetics 34, 472 - 483 (1999).
  
• A. Mitsutake, M. Irisa, Y. Okamoto, and F. Hirata, "Classification of low-energy conformations of Met-enkephalin in the gas phase and in a model solvent based on the extended scaled particle theory," Bulletin of the Chemical Society of Japan 72, 1717 - 1729 (1999).
  
• Y. Sugita and Y. Okamoto, "Replica-exchange molecular dynamics method for protein folding," Chemical Physics Letters 314, 141 - 151 (1999).
  
• A. Mitsutake and Y. Okamoto, "Helix-coil transitions of amino-acid homo-oligomers in aqueous solution studied by multicanonical simulations," Journal of Chemical Physics 112, 10638 - 10647 (2000).
  
• Y. Sugita and Y. Okamoto, "Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape," Chemical Physics Letters 329, 261 - 270 (2000).
  
• A. Mitsutake and Y. Okamoto, "Replica-exchange simulated tempering method for simulations of frustrated systems," Chemical Physics Letters 332, 131 - 138 (2000).
  
• Y. Sugita, A. Kitao, and Y. Okamoto, "Multidimensional replica-exchange method for free-energy calculations," Journal of Chemical Physics 113, 6042 - 6051 (2000).
  
• M. Kinoshita, Y. Okamoto, and F. Hirata, "Peptide conformations in alcohol and water: analyses by the reference interaction site model theory," Journal of the American Chemical Society 122, 2773 - 2779 (2000).
  
• T. Nishikawa, H. Ohtsuka, Y. Sugita, M. Mikami, and Y. Okamoto, "Replica-exchange Monte Carlo method for Ar fluid," Progress of Theoretical Physics Supplement No. 138, 270 - 271 (2000).
  
• Y. Ishikawa, Y. Sugita, T. Nishikawa, and Y. Okamoto, "Ab initio replica-exchange Monte Carlo method for cluster studies," Chemical Physics Letters 333, 199 - 206 (2001).
  
• T. Nagasima, Y. Sugita, A. Mitsutake, and Y. Okamoto, "Generalized-ensemble simulations of spin systems and protein systems," Computer Physics Communications 146, 69 - 76 (2002).
  
• T. Hiroyasu, M. Miki, M. Ogura, and Y. Okamoto, "Examination of parallel simulated annealing using genetic crossover," (in Japanese), IPSJ TOM 43, 70 - 79 (2002).
• A. Mitsutake, Y. Sugita, and Y. Okamoto, "Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides," Journal of Chemical Physics 118, 6664 - 6675 (2003); ibid. 118, 6676 - 6688 (2003).
  
• G. La Penna, A. Mitsutake, M. Masuya, and Y. Okamoto, "Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory," Chemical Physics Letters 380, 609 - 619 (2003).
  
• B.A. Berg, H. Noguchi, and Y. Okamoto, "Multioverlap simulations for transitions between reference configurations," Physical Review E 68, 036126 (11 pages) (2003).
  
• Y. Sakae and Y. Okamoto, "Optimization of protein force-field parameters with the Protein Data Bank," Chemical Physics Letters 382, 626 - 636 (2003).
  
• H. Okumura and Y. Okamoto, "Monte Carlo simulations in multibaric-multithermal ensemble," Chemical Physics Letters 383, 391 - 396 (2004).
  
• H. Kokubo and Y. Okamoto, "Prediction of transmembrane helix configurations by replica-exchange simulations," Chemical Physics Letters 383, 397 - 402 (2004).
  
• K. Murata, Y. Sugita, and Y. Okamoto, "Free energy calculations for DNA base stacking by replica-exchange umbrella sampling," Chemical Physics Letters 385, 1 - 7 (2004).
  
• T. Yoda, Y. Sugita, and Y. Okamoto, "Comparisons of force fields for proteins by generalized-ensemble simulations," Chemical Physics Letters 386, 460 - 467 (2004).
  
• C. Muguruma, Y. Okamoto, and M. Mikami, "New approach to the first-order phase transition of Lennard-Jones fluids," Journal of Chemical Physics 120, 7557 - 7563 (2004).
  
• H. Okumura and Y. Okamoto, "Molecular dynamics simulations in the multibaric-multithermal ensemble," Chemical Physics Letters 391, 248 - 253 (2004).
  
• H. Kokubo and Y. Okamoto, "Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange Monte Carlo simulation," Chemical Physics Letters 392, 168 - 175 (2004).
  
• A. Mitsutake and Y. Okamoto, "Replica-exchange extensions of simulated tempering method," Journal of Chemical Physics 121, 2491 - 2504 (2004).
  
• H. Okumura and Y. Okamoto, "Monte Carlo simulations in generalized isobaric-isothermal ensembles," Physical Review E 70, 026702 (14 pages) (2004).
  
• H. Kokubo and Y. Okamoto, "Classification and prediction of low-energy membrane protein helix configurations by replica-exchange Monte Carlo method," Journal of the Physical Society of Japan 73, 2571 - 2585 (2004).
  
• H. Okumura and Y. Okamoto, "Liquid-gas phase transition studied by multibaric-multithermal Monte Carlo simulations," Journal of the Physical Society of Japan 73, 3304 - 3311 (2004).
  
• A. Mitsutake, M. Kinoshita, Y. Okamoto, and F. Hirata, "Combination of the replica-exchange Monte Carlo method and the reference interaction site model theory for simulating a peptide molecule in aqueous solution," Journal of Physical Chemistry B 108, 19002 - 19012 (2004).
  
• S.G.. Itoh and Y. Okamoto, "Multi-overlap molecular dynamics methods for biomolecular systems," Chemical Physics Letters 400, 308 - 313 (2004).
  
• Y. Sugita and Y. Okamoto, "Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent," Biophysical Journal 88, 3180 - 3190 (2005).
  
• K. Yoshida, T. Yamaguchi, and Y. Okamoto, "Replica-exchange molecular dynamics simulation of small peptide in water and in ethanol," Chemical Physics Letters 412, 280 - 284 (2005).
  
• M. Nishino, Y. Sugita, T. Yoda, and Y. Okamoto, "Structures of a peptide fragment of beta2-microglobulin studied by replica-exchange molecular dynamics simulations - towards the understanding of the mechanism of amyloid formation," FEBS Letters 579, 5425 - 5429 (2005).
  
• K. Kawashima, Y. Sugita, T. Yoda, and Y. Okamoto, "Effects of the fixed end in single-molecule imaging techniques: A replica-exchange molecular dynamics study," Chemical Physics Letters 414, 449 - 455 (2005).
  
• H. Okumura and Y. Okamoto, "Multibaric-multithermal ensemble molecular dynamics simulations," Journal of Computational Chemistry 27, 379 - 395 (2006).
  
• S.G. Itoh and Y. Okamoto, "Theoretical studies of transition states by the multi-overlap molecular dynamics methods," Journal of Chemical Physics 124, 104103 (14 pages) (2006).
  
• Y. Sakae and Y. Okamoto, "Secondary-structure design of proteins by a backbone torsion energy," Journal of the Physical Society of Japan 75, 054802 (9 pages) (2006).