I. Fukuda

发表

Molecular Dynamics Simulations of Double-Stranded DNA in an Explicit Solvent Model with the Zero-Dipole Summation Method

Haruki Nakamura, Narutoshi Kamiya, Ikuo Fukuda, 2013, PloS one.

Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water.

Haruki Nakamura, Narutoshi Kamiya, Yasushige Yonezawa, 2012, The Journal of chemical physics.

Application of zero-dipole summation method to molecular dynamics simulations of a membrane protein system

Haruki Nakamura, N. Kamiya, I. Fukuda, 2013 .

Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions.

Haruki Nakamura, Yoshifumi Fukunishi, Narutoshi Kamiya, 2013, Journal of chemical theory and computation.

Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling

T. Kawabata, Y. Fukunishi, Haruki Nakamura, 2020, bioRxiv.

Symmetric, explicit numerical integrator for molecular dynamics equations of motion with a generalized friction

I. Fukuda, 2019, Journal of Mathematical Physics.

Symmetric, explicit numerical integrator for molecular dynamics equations of motion with a generalized friction

I. Fukuda, 2017, bioRxiv.

Temperature–energy-space sampling molecular dynamics: deterministic and single-replica method utilizing continuous temperature system

K. Moritsugu, I. Fukuda, 2020, Journal of Physics A: Mathematical and Theoretical.

A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex

Haruki Nakamura, Ikuo Fukuda, Kota Kasahara, 2014, PloS one.

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation.

I. Fukuda, S. Sakuraba, K. Kasahara, 2018, The journal of physical chemistry. B.

Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer

Haruki Nakamura, I. Fukuda, M. Shiina, 2017, PloS one.

Consistent Molecular Dynamics Scheme Applying the Wolf Summation for Calculating Electrostatic Interaction of Particles(Atomic and molecular physics)

Haruki Nakamura, Yasushige Yonezawa, Ikuo Fukuda, 2008 .

Temperature–Energy-space Sampling Molecular Dynamics: Deterministic, Iteration-free, and Single-replica Method utilizing Continuous Temperature System

K. Moritsugu, I. Fukuda, 2019, bioRxiv.

Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations

J. Higo, N. Kamiya, I. Fukuda, 2020, Scientific Reports.

A practical guide for perioperative smoking cessation

I. Fukuda, H. Yonekura, H. Iida, 2022, Journal of Anesthesia.

On Ergodicity for Multidimensional Harmonic Oscillator Systems with Nosé – Hoover-type Thermostat

Y. Fukunishi, K. Moritsugu, I. Fukuda, 2021, Regular and Chaotic Dynamics.

Molecular Dynamics Simulation of Structural Phase Transition of AlPO4 Induced by Pressure

I. Fukuda, M. Mikami, 1996 .

Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference

I. Fukuda, Haruki Nakamura, 2022, Biophysical Reviews.

Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation

Y. Fukunishi, K. Moritsugu, J. Higo, 2021, J. Chem. Inf. Model..

Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor.

Haruki Nakamura, Yasushi Okuno, Mitsugu Araki, 2017, Journal of chemical theory and computation.

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme

Haruki Nakamura, Kota Kasahara, Yutaka Akiyama, 2016, Biophysics and physicobiology.

Tsallis dynamics using the Nosé-Hoover approach.

Haruki Nakamura, Ikuo Fukuda, Haruki Nakamura, 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

Non-Ewald methods: theory and applications to molecular systems

Haruki Nakamura, Ikuo Fukuda, I. Fukuda, 2012, Biophysical Reviews.

Deterministic generation of the Boltzmann–Gibbs distribution and the free energy calculation from the Tsallis distribution

Haruki Nakamura, I. Fukuda, 2003 .

Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

Y. Fukunishi, H. Kono, J. Higo, 2022, Scientific Reports.

Molecular dynamics equation designed for realizing arbitrary density: application to sampling method utilizing the Tsallis generalized distribution

Haruki Nakamura, I. Fukuda, 2010 .

Numerical examination of the extended phase‐space volume‐preserving integrator by the Nosé‐Hoover molecular dynamics equations

Haruki Nakamura, Ikuo Fukuda, Séverine Queyroy, 2009, J. Comput. Chem..

Coupled Nosé–Hoover lattice: A set of the Nosé–Hoover equations with different temperatures

I. Fukuda, 2016 .

Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations

J. Higo, N. Kamiya, I. Fukuda, 2020, Scientific Reports.

Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism

Haruki Nakamura, Mitsuhito Wada, Yoshifumi Fukunishi, 2019, Protein engineering, design & selection : PEDS.

Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

Y. Fukunishi, J. Higo, N. Kamiya, 2021, Scientific Reports.

Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling.

Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya, 2020, Journal of chemical information and modeling.

Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle.

Haruki Nakamura, Yasushige Yonezawa, Ikuo Fukuda, 2011, The Journal of chemical physics.

Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system.

Ikuo Fukuda, I. Fukuda, 2013, The Journal of chemical physics.

A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system.

Haruki Nakamura, I. Fukuda, Han Wang, 2016, The Journal of chemical physics.

The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems.

Haruki Nakamura, Narutoshi Kamiya, Ikuo Fukuda, 2014, The Journal of chemical physics.

Numerical Integration Techniques Based on a Geometric View and Application to Molecular Dynamics Simulations

Ikuo Fukuda, Séverine Queyroy, I. Fukuda, 2012 .

Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method.

Haruki Nakamura, Narutoshi Kamiya, Yasushige Yonezawa, 2011, Journal of chemical theory and computation.

Deterministic design for Tsallis distribution sampling

Haruki Nakamura, I. Fukuda, M. Horie, 2005 .

On Ergodicity for Multidimensional Harmonic Oscillator Systems with Nosé – Hoover-type Thermostat

Y. Fukunishi, K. Moritsugu, I. Fukuda, 2020, 2008.07917.

Coupled Nosé–Hoover equations of motions without time scaling

K. Moritsugu, I. Fukuda, 2016, bioRxiv.

mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories

Haruki Nakamura, Kota Kasahara, Neetha Mohan, 2016, Bioinform..

Subglottic neurofibroma in a child.

I. Fukuda, I. Fukuda, K. Sugihara, 1987, International journal of pediatric otorhinolaryngology.

Traumatic disruption of bilateral vertebral arteries and internal carotid arteries: case report.

I. Fukuda, K. Meguro, O. Shigeta, 1989, The Journal of trauma.

Analysis of multiple data sequences with different distributions: defining common principal component axes by ergodic sequence generation and multiple reweighting composition

K. Moritsugu, I. Fukuda, 2021, IOP SciNotes.

Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor.

Haruki Nakamura, Y. Okuno, N. Kamiya, 2017, Journal of chemical theory and computation.

Efficiency in the Generation of the Boltzmann−Gibbs Distribution by the Tsallis Dynamics Reweighting Method

Haruki Nakamura, I. Fukuda, 2004 .