Publications (38)
Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory
Giovanni La Penna, Ayori Mitsutake, Masato Masuya +1
Generalized-ensemble Monte carlo method for systems with rough energy landscape
Ulrich H. E. Hansmann, Yuko Okamoto
Residual Entropy of Ordinary Ice from Multicanonical Simulations
Bernd A. Berg, Chizuru Muguruma, Yuko Okamoto
Generalized-Ensemble Algorithms for the Isobaric-Isothermal Ensemble
Yoshiharu Mori, Yuko Okamoto
Explicit Symplectic Integrators of Molecular Dynamics Algorithms for Rigid-Body Molecules in the Canonical, Isothermal-Isobaric, and Related Ensembles
Hisashi Okumura, Satoru G. Itoh, Yuko Okamoto
Effective Sampling in the Configurational Space by the Multicanonical-Multioverlap Algorithm
Satoru G. Itoh, Yuko Okamoto
Numerical Comparisons of Three Recently Proposed Algorithms in the Protein Folding Problem
Ulrich H. E. Hansmann, Yuko Okamoto
Multidimensional replica-exchange method for free-energy calculations
Yuji Sugita, Akio Kitao, Yuko Okamoto
Generalized-Ensemble Algorithms for Protein Folding Simulations
Yuji Sugita, Ayori Mitsutake, Yuko Okamoto
Optimization of protein force-field parameters with the Protein Data Bank
Yoshitake Sakae, Yuko Okamoto
Thermodynamics of helix-coil transitions studied by multicanonical algorithms
Yuko Okamoto, Ulrich H. E. Hansmann
Multicanonical Algorithm, Simulated Tempering, Replica-Exchange Method, and All That
Ayori Mitsutake, Yuko Okamoto
A Conformational Search Method for Protein Systems Using Genetic Crossover and Metropolis Criterion
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki +2
Application of Simulated Tempering and Magnetizing to a Two-Dimensional Potts Model
Tetsuro Nagai, Yuko Okamoto, Wolfhard Janke
Prediction of Peptide Conformation by the Multicanonical Algorithm
Ulrich H. E. Hansmann, Yuko Okamoto
Thermodynamics of two lattice ice models in three dimensions
Chizuru Muguruma, Yuko Okamoto, Bernd A. Berg
Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble
Ulrich H. E. Hansmann, Yuko Okamoto, Frank Eisenmenger
Secondary-Structure Design of Proteins by a Backbone Torsion Energy
Yoshitake Sakae, Yuko Okamoto
Characteristic Temperatures of Folding of a Small Peptide
Ulrich H. E. Hansmann, Masato Masuya, Yuko Okamoto
Combination of genetic crossover and replica-exchange method for conformational search of protein systems
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki +2
Amino-acid-dependent main-chain torsion-energy terms for protein systems
Yoshitake Sakae, Yuko Okamoto
Optimizations of protein force fields
Yoshitake Sakae, Yuko Okamoto
Prediction of Peptide Conformation by Multicanonical Algorithm: A New Approach to the Multiple-Minima Problem
Ulrich H. E. Hansmann, Yuko Okamoto
Generalized Einstein Theory on Solar and Galactic Scales
Masakatsu Kenmoku, Yuko Okamoto, Kazuyasu Shigemoto
Metropolis Algorithms in Generalized Ensemble
Yuko Okamoto
Replica-Exchange Method in van der Waals Radius Space: Overcoming Steric Restrictions for Biomolecules
Satoru G. Itoh, Hisashi Okumura, Yuko Okamoto
Optimizations of force-field parameters for protein systems with the secondary-structure stability and instability
Yoshitake Sakae, Yuko Okamoto
Predictions of tertiary stuctures of $α$-helical membrane proteins by replica-exchange method with consideration of helix deformations
Ryo Urano, Hironori Kokubo, Yuko Okamoto
Free energy calculations of a proton transfer reaction by simulated tempering umbrella sampling first principles molecular dynamics simulations
Yoshiharu Mori, Yuko Okamoto
Prediction of transmembrane helix configurations by replica-exchange simulations
Hironori Kokubo, Yuko Okamoto
Comment on "Monte Carlo Simulation of a First-Order Transition"
Bernd A. Berg, Ulrich H. E. Hansmann, Yuko Okamoto
Enhanced Sampling Algorithms
Ayori Mitsutake, Yoshiharu Mori, Yuko Okamoto
Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem
Ulrich H. E. Hansmann, Yuko Okamoto
Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms
Yoshiharu Mori, Yuko Okamoto
Simulated Tempering and Magnetizing: An Application of Two-Dimensional Simulated Tempering to Two-Dimensional Ising Model and Its Crossover
Tetsuro Nagai, Yuko Okamoto
Tertiary structure prediction of C-peptide of ribonuclease A by multicanonical algorithm
Ulrich H. E. Hansmann, Yuko Okamoto
Generalized-Ensemble Algorithms for Molecular Simulations of Biopolymers
Ayori Mitsutake, Yuji Sugita, Yuko Okamoto
Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
Yuji Sugita, Yuko Okamoto