153 citations · 301 across the 9 of their papers we have counts for
8 papers · 1 filter
Universal relation between instantaneous diffusivity and radius of gyration of proteins in aqueous solution
Eiji Yamamoto, Takuma Akimoto, Ayori Mitsutake +1
Protein conformational fluctuations are highly complex and exhibit long-term correlations. Here, molecular dynamics simulations of small proteins demonstrate that these conformatio…
Enhanced Sampling Algorithms
Ayori Mitsutake, Yoshiharu Mori, Yuko Okamoto
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-en…
Multicanonical Algorithm, Simulated Tempering, Replica-Exchange Method, and All That
Ayori Mitsutake, Yuko Okamoto
We discuss multi-dimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function $E_…
Generalized-Ensemble Algorithms for Protein Folding Simulations
Yuji Sugita, Ayori Mitsutake, Yuko Okamoto
Conventional simulations of complex systems in the canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble overcomes this difficulty by pe…
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 algorithm and diffusion theory have been combined in order to compute the dynamical properties monitored by nuclear magnetic resonance experiments from efficie…
Generalized-ensemble simulations of spin systems and protein systems
T. Nagasima, Y. Sugita, A. Mitsutake +1
In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the gen…
Generalized-Ensemble Algorithms for Molecular Simulations of Biopolymers
Ayori Mitsutake, Yuji Sugita, Yuko Okamoto
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical en…
Replica-Exchange Simulated Tempering Method for Simulations of Frustrated Systems
A. Mitsutake, Y. Okamoto
We propose a new method for the determination of the weight factor for the simulated tempering method. In this method a short replica-exchange simulation is performed and the simul…