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Wataru Shinoda

Wataru Shinoda

D-Index & Metrics

Chemistry

D-Index
53
Citations
9978
World Ranking
13093
National Ranking
988

Overview

Wataru Shinoda is a researcher affiliated with Nagoya University in Japan, focusing on interdisciplinary studies primarily in the fields of Biochemistry, Genetics and Molecular Biology, Engineering, and Materials Science. Their work spans a broad range of topics, often intersecting molecular biological processes with advanced materials and engineering applications.

Their primary areas of research include:

  • Lipid Membrane Structure and Behavior
  • Advanced Battery Materials and Technologies
  • Advancements in Battery Materials
  • Nanopore and Nanochannel Transport Studies
  • Spectroscopy and Quantum Chemical Studies
  • Protein Structure and Dynamics
  • Force Microscopy Techniques and Applications

Frequent co-authors collaborating with Wataru Shinoda are:

  • Yusuke Miyazaki (19 publications)
  • Kazuhide Ueno (13 publications)
  • Masayoshi Watanabe (12 publications)
  • Seiji Tsuzuki (11 publications)
  • Keisuke Shigenobu (11 publications)

The researcher has contributed to multiple scholarly journals, with notable recurrent publication venues including:

  • Journal of Chemical Theory and Computation (6 publications)
  • The Journal of Physical Chemistry B (5 publications)
  • bioRxiv (Cold Spring Harbor Laboratory) (5 publications)
  • The Journal of Physical Chemistry C (3 publications)
  • Physical Chemistry Chemical Physics (3 publications)

Among recent scientific papers authored or co-authored by Wataru Shinoda are:

  • "Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure," published in 2021 in Proceedings of the National Academy of Sciences
  • "Pragmatic Coarse-Graining of Proteins: Models and Applications," published in 2023 in Journal of Chemical Theory and Computation
  • "Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study," published in 2022 in Science Advances
  • "SPICA Force Field for Proteins and Peptides," published in 2022 in Journal of Chemical Theory and Computation
  • "Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement," published in 2020 in Journal of Chemical Theory and Computation

Wataru Shinoda's research portfolio includes significant contributions to molecular biology and materials chemistry, with cross-disciplinary work that integrates aspects of electrical and electronic engineering and biomedical engineering. Their scientific work reflects engagement with both theoretical and experimental approaches, including molecular simulations, spectroscopy, and structural analysis methodologies.

Best Publications

  • Rapid estimation of elastic constants by molecular dynamics simulation under constant stress

    Wataru Shinoda;Motoyuki Shiga;Masuhiro Mikami

  • Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants

    W. Shinoda;R. DeVane;M. L. Klein

  • Large-scale molecular dynamics simulations of self-assembling systems.

    Michael L. Klein;Wataru Shinoda

  • Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field

    Wataru Shinoda;Russell DeVane;Michael L Klein

  • Permeability across lipid membranes

    Wataru Shinoda

  • Molecular Dynamics Simulations of Ionic Liquids: Cation and Anion Dependence of Self-Diffusion Coefficients of Ions

    Seiji Tsuzuki;Wataru Shinoda;Hiroaki Saito;Masuhiro Mikami

  • Direct Evidence for Li Ion Hopping Conduction in Highly Concentrated Sulfolane-Based Liquid Electrolytes.

    Kaoru Dokko;Daiki Watanabe;Yosuke Ugata;Morgan L. Thomas

  • Coarse-grained molecular modeling of non-ionic surfactant self-assembly

    Wataru Shinoda;Wataru Shinoda;Russell DeVane;Michael L. Klein

  • Molecular dynamics simulation of swollen membrane of perfluorinated ionomer.

    Shingo Urata;Jun Irisawa;Akira Takada;Wataru Shinoda

  • Molecular Dynamics Study on the Effects of Chain Branching on the Physical Properties of Lipid Bilayers: 2. Permeability

    Wataru Shinoda;Masuhiro Mikami;Teruhiko Baba;Masakatsu Hato

  • Janus dendrimersomes coassembled from fluorinated, hydrogenated, and hybrid Janus dendrimers as models for cell fusion and fission.

    Qi Xiao;Samuel E. Sherman;Samantha E. Wilner;Xuhao Zhou

  • A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids.

    Russell DeVane;Wataru Shinoda;Preston B. Moore;Michael L. Klein

  • Cholesterol effect on water permeability through DPPC and PSM lipid bilayers: a molecular dynamics study.

    Hiroaki Saito;Wataru Shinoda

  • Computer simulation studies of self-assembling macromolecules.

    Wataru Shinoda;Russell DeVane;Michael L Klein

  • Rigid-Body Dynamics in the Isothermal-Isobaric Ensemble: A Test on the Accuracy and Computational Efficiency

    Wataru Shinoda;Masuhiro Mikami

  • A Voronoi analysis of lipid area fluctuation in a bilayer

    Wataru Shinoda;Susumu Okazaki

  • Structures of [Li(glyme)](+) complexes and their interactions with anions in equimolar mixtures of glymes and Li[TFSA]: analysis by molecular dynamics simulations.

    Seiji Tsuzuki;Wataru Shinoda;Masaru Matsugami;Yasuhiro Umebayashi

  • Intermolecular Interactions in Li+‐glyme and Li+‐glyme–TFSA− Complexes: Relationship with Physicochemical Properties of [Li(glyme)][TFSA] Ionic Liquids

    Seiji Tsuzuki;Wataru Shinoda;Shiro Seki;Yasuhiro Umebayashi

  • Molecular Dynamics Study of Bipolar Tetraether Lipid Membranes

    Wataru Shinoda;Keiko Shinoda;Keiko Shinoda;Teruhiko Baba;Masuhiro Mikami

  • SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol

    Sangjae Seo;Wataru Shinoda

  • Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation.

    Nobuyuki Matubayasi;Wataru Shinoda;Masaru Nakahara

  • United-atom acyl chains for CHARMM phospholipids.

    Jérôme Hénin;Wataru Shinoda;Michael L. Klein

Frequent Co-Authors

Masuhiro Mikami
Masuhiro Mikami National Institute of Advanced Industrial Science and Technology
Michael L. Klein
Michael L. Klein Temple University
Seiji Tsuzuki
Seiji Tsuzuki University of Tokyo
Masayoshi Watanabe
Masayoshi Watanabe Yokohama National University
Kaoru Dokko
Kaoru Dokko Yokohama National University
Kazuhide Ueno
Kazuhide Ueno Yokohama National University
Michio Murata
Michio Murata Osaka University
Yasuhiro Umebayashi
Yasuhiro Umebayashi Niigata University
Atsushi Ikeda
Atsushi Ikeda Hiroshima University
Yasuhito Tanaka
Yasuhito Tanaka Kumamoto University

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