List of works - Nobuyuki Matubayasi

Anion-cation contrast of small molecule solvation in salt solutions

scientific article published on 02 February 2022

Binding free energy analysis of protein-protein docking model structures by evERdock

scientific article published in March 2018

Boson peak, elasticity, and glass transition temperature in polymer glasses: Effects of the rigidity of chain bending

scientific article published on 20 December 2019

Communication: Exploring the reorientation of benzene in an ionic liquid via molecular dynamics: Effect of temperature and solvent effective charge on the slow dynamics ⬇️

scientific article published on May 21, 2011

Communication: Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c ⬇️

scientific article published on January 28, 2011

Computation of the free energy change associated with one-electron reduction of coenzyme immersed in water: a novel approach within the framework of the quantum mechanical/molecular mechanical method combined with the theory of energy representation

scientific article

Diffusion dynamics of supercooled water modeled with the cage-jump motion and hydrogen-bond rearrangement

scientific article published on 01 May 2019

Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions.

scientific article published on 21 February 2017

Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory.

scientific article published on 18 July 2017

Energetic Analysis of Adsorption and Absorption of Small Molecule to Nanodroplet of Water.

scientific article published on 9 June 2017

Fluctuation adsorption theory: quantifying adsorbate-adsorbate interaction and interfacial phase transition from an isotherm

scientific article published on 09 December 2020

Free-Energy Analysis of Peptide Binding in Lipid Membrane Using All-Atom Molecular Dynamics Simulation Combined with Theory of Solutions.

scientific article published on 10 January 2018

Free-energy analysis of physisorption on solid-liquid interface with the solution theory in the energy representation

scientific article published on 01 July 2018

Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation ⬇️

scientific article published on January 28, 2012

Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation

scientific article published on 01 April 2019

Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation ⬇️

scientific article published on December 21, 2012

How do hydrogen bonds break in supercooled water?: Detecting pathways not going through saddle point of two-dimensional potential of mean force

scientific article published on 01 June 2018

In Situ Kinetic Study on Hydrothermal Transformation ofd-Glucose into 5-Hydroxymethylfurfural throughd-Fructose with13C NMR ⬇️

scientific article published on November 9, 2011

Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme.

scientific article published in June 2017

Investigation of the dominant hydration structures among the ionic species in aqueous solution: novel quantum mechanics/molecular mechanics simulations combined with the theory of energy representation

scientific article published in February 2008

Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide

scientific article published on 01 August 2020

Local viscoelasticity at resin-metal interface analyzed with spatial-decomposition formula for relaxation modulus

scientific article published on 01 September 2019

Noncatalytic Hydrothermal Elimination of the Terminal d-Glucose Unit from Malto- and Cello-Oligosaccharides through Transformation to d-Fructose ⬇️

scientific article published on October 5, 2012

Nuclear magnetic resonance study on rotational dynamics of water and benzene in a series of ionic liquids: Anion and cation effects ⬇️

scientific article published on November 21, 2012

Probabilistic analysis for identifying the driving force of protein folding

scientific article published on 01 March 2018

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations

scientific article published on 01 November 2018

Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T1 measurements ⬇️

scientific article published on February 21, 2012

Self-Consistent Scheme Combining MD and Order-N DFT Methods: An Improved Set of Nonpolarizable Force Fields for Ionic Liquids

scientific article published on 24 December 2019

Simple and exact approach to the electronic polarization effect on the solvation free energy: Formulation for quantum-mechanical/ molecular-mechanical system and its applications to aqueous solutions ⬇️

scientific article published on 01 June 2012

Solubilization power of surfactant-free microemulsions

scientific article published on 19 August 2020

Solvation Thermodynamics from the Perspective of Endpoints DFT

scientific article published on 11 December 2020

Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method

scientific article published on 16 April 2019

Structure and Dynamics of the Hydration Shell: Spatially Decomposed Time Correlation Approach

scientific article published on 31 December 2018

Structure and permeability of ionomers studied by atomistic molecular simulation combined with the theory of solutions in the energy representation