1k citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- The Graduate University for Advanced Studies, SOKENDAIJP143 papers
- National Institutes of Natural SciencesJP76 papers
- The University of TokyoJP75 papers
- The University of OsakaJP59 papers
- Kyoto UniversityJP52 papers
- Tohoku UniversityJP46 papers
- Japan Science and Technology AgencyJP32 papers
- Nagoya UniversityJP30 papers
- Hiroshima UniversityJP27 papers
- High Energy Accelerator Research OrganizationJP26 papers
- RIKENJP26 papers
- Tokyo Institute of TechnologyJP26 papers
25 papers · 1 filter
Systematic construction of asymptotic quantum many-body scar states and their relation to supersymmetric quantum mechanics
Masaya Kunimi, Yusuke Kato, Hosho Katsura
We develop a systematic method for constructing asymptotic quantum many-body scar (AQMBS) states. While AQMBS states are closely related to quantum many-body scar (QMBS) states, th…
Anisotropy-induced spin parity effects
Shuntaro Sumita, Akihiro Tanaka, Yusuke Kato
Spin parity effects refer to those special situations where a dichotomy in the physical behavior of a system arises, solely depending on whether the relevant spin quantum number is…
Structural transition induced by a local chemical/mechanical perturbation in biomolecules
Fumio Hirata
Structural transition induced by a local conformational change in biomolecules is formulated based on the generalized Langevin theory for the structural fluctuation of a molecule i…
Does the second critical-point of water really exist in nature?
Fumio Hirata
In the past decade, a literary phrase "No man's land" has been flooded in the scientific papers. The expression is used to describe a meta-stable region in the phase-diagram that c…
Operational derivation of Maxwell-Boltzmann distribution with Maxwell's demon model
Akio Hosoya, Koji Maruyama, Yutaka Shikano
The resolution of the Maxwell's demon paradox linked thermodynamics with information theory through information erasure principle. By considering a demon endowed with a Turing-mach…
Probing a non-biaxial behavior of infinitely thin hard platelets
Hitomi Nomura, Tomonori Koda, Akihiro Nishioka +1
We give a criterion to test a non-biaxial behavior of infinitely thin hard platelets of symmetry based upon the components of three order parameter tensors. We investigate…
Amino-acid-dependent main-chain torsion-energy terms for protein systems
Yoshitake Sakae, Yuko Okamoto
Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of main-chain torsion-energy…
Representation of the nonequilibrium steady-state distribution function for sheared granular systems
Song-Ho Chong, Michio Otsuki, Hisao Hayakawa
We derive the representation of the nonequilibrium steady-state distribution function which is expressed in terms of the excess free energy production. This representation resemble…
Nonequilibrium liquid theory for sheared granular liquids
Hisao Hayakawa, Song-Ho Chong, Michio Otsuki
A noneqilibrium liquid theory for uniformly sheared granular liquids is developed starting from the SLLOD Liouville equation. We derive a generalized Green-Kubo formula and also de…
Statistical-mechanical theory of ultrasonic absorption in molecular liquids
A. E. Kobryn, F. Hirata
We present results of theoretical description of ultrasonic phenomena in molecular liquids. In particular, we are interested in the development of microscopical, i.e., statistical-…
Prediction of transmembrane helix configurations by replica-exchange simulations
Hironori Kokubo, Yuko Okamoto
We propose a method for predicting helical membrane protein structures by computer simulations. Our method consists of two parts. In the first part, amino-acid sequences of the tra…
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…
Optimization of protein force-field parameters with the Protein Data Bank
Yoshitake Sakae, Yuko Okamoto
We propose a novel method to optimize existing force-field parameters for protein systems. The method consists of minimizing the summation of the square of the force acting on each…
Generalized-Ensemble Algorithms: Enhanced Sampling Techniques for Monte Carlo and Molecular Dynamics Simulations
Y. Okamoto
In complex systems with many degrees of freedom such as spin glass and biomolecular systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity problem…
Metropolis Algorithms in Generalized Ensemble
Yuko Okamoto
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…
Monte Carlo Simulations in Multibaric-Multithermal Ensemble
H. Okumura, Y. Okamoto
We propose a new generalized-ensemble algorithm, which we refer to as the multibaric-multithermal Monte Carlo method. The multibaric-multithermal Monte Carlo simulations perform ra…
Multi-Overlap Simulations for Transitions between Reference Configurations
B. A. Berg, H. Noguchi, Y. Okamoto
We introduce a new procedure to construct weight factors, which flatten the probability density of the overlap with respect to some pre-defined reference configuration. This allows…
Interplay between the repulsive and attractive interaction and the spacial dimensionality of an excess electron in a simple fluid
Ashok Sethia, Eric R. Bittner, Fumio Hirata
The behavior of an excess electron in a one, two and three dimensional classical liquid has been studied with the aid of Chandler, Singh and Richardson (CSR) theory [J. Chem. Phys.…
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…
Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms
Y. Sugita, Y. Okamoto
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchan…
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…
Multidimensional replica-exchange method for free-energy calculations
Yuji Sugita, Akio Kitao, Yuko Okamoto
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with d…
Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
Yuji Sugita, Yuko Okamoto
We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical w…