153 citations · 301 across the 9 of their papers we have counts for
9 papers
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…
Relaxation Mode Analysis and Markov State Relaxation Mode Analysis for Chignolin in Aqueous Solution near a Transition Temperature
Ayori Mitsutake, Hiroshi Takano
It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between the…
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…