Enzymatic Reaction Mechanisms of RNA Enzyme (Ribozyme) Revealed by First Principles Molecular Dynamics Simulations

Masaru TATENO; Mauro BOERO

doi:10.2142/biophys.48.216

Enzymatic Reaction Mechanisms of RNA Enzyme (Ribozyme) Revealed by First Principles Molecular Dynamics Simulations

Seibutsu Butsuri ◽

10.2142/biophys.48.216 ◽

2008 ◽

Vol 48 (4) ◽

pp. 216-220

Author(s):

Masaru TATENO ◽

Mauro BOERO

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Reaction Mechanisms ◽

Enzymatic Reaction ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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A Study on Electrochemical Machining Method in Ultrapure Water-First-Principles Molecular-Dynamics Simulations of Etching Process on Al(001) Cathode Surface-

Journal of the Japan Society for Precision Engineering ◽

10.2493/jjspe.69.1332 ◽

2003 ◽

Vol 69 (9) ◽

pp. 1332-1336

Author(s):

Hidekazu GOTO ◽

Kikuji HIROSE ◽

Yasushi TOMA ◽

Itsuki KOBATA ◽

Takashi INADA ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Cathode Surface ◽

Electrochemical Machining ◽

Etching Process ◽

Ultrapure Water ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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Alumina(0001)/Water Interface: Structural Properties and Infrared Spectra from First-Principles Molecular Dynamics Simulations

The Journal of Physical Chemistry C ◽

10.1021/jp4123002 ◽

2014 ◽

Vol 118 (17) ◽

pp. 8944-8951 ◽

Cited By ~ 33

Author(s):

Patrick Huang ◽

Tuan Anh Pham ◽

Giulia Galli ◽

Eric Schwegler

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Structural Properties ◽

Infrared Spectra ◽

First Principles ◽

Water Interface ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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Anharmonic lattice dynamics ofAg2Ostudied by inelastic neutron scattering and first-principles molecular dynamics simulations

Physical Review B ◽

10.1103/physrevb.89.054306 ◽

2014 ◽

Vol 89 (5) ◽

Cited By ~ 23

Author(s):

Tian Lan ◽

Chen W. Li ◽

J. L. Niedziela ◽

Hillary Smith ◽

Douglas L. Abernathy ◽

...

Keyword(s):

Molecular Dynamics ◽

Neutron Scattering ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Lattice Dynamics ◽

Inelastic Neutron Scattering ◽

Inelastic Neutron ◽

Anharmonic Lattice ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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Structure of Liquid BaTiO3 by First-principles Molecular Dynamics Simulations

Journal of the Physical Society of Japan ◽

10.7566/jpsj.90.044604 ◽

2021 ◽

Vol 90 (4) ◽

pp. 044604

Author(s):

Tamotsu Hashimoto ◽

Hiroki Moriwake

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Dynamics Simulations ◽

Structure Of Liquid ◽

First Principles Molecular Dynamics

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Surface acidity of 2:1-type dioctahedral clay minerals from first principles molecular dynamics simulations

Geochimica et Cosmochimica Acta ◽

10.1016/j.gca.2014.05.044 ◽

2014 ◽

Vol 140 ◽

pp. 410-417 ◽

Cited By ~ 47

Author(s):

Xiandong Liu ◽

Jun Cheng ◽

Michiel Sprik ◽

Xiancai Lu ◽

Rucheng Wang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Clay Minerals ◽

First Principles ◽

Surface Acidity ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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Nature of Water Transport and Electro-Osmosis in Nafion: Insights from First-Principles Molecular Dynamics Simulations under an Electric Field

The Journal of Physical Chemistry B ◽

10.1021/jp8041878 ◽

2008 ◽

Vol 112 (37) ◽

pp. 11586-11594 ◽

Cited By ~ 41

Author(s):

Yoong-Kee Choe ◽

Eiji Tsuchida ◽

Tamio Ikeshoji ◽

Shunsuke Yamakawa ◽

Shi-aki Hyodo

Keyword(s):

Molecular Dynamics ◽

Electric Field ◽

Molecular Dynamics Simulations ◽

Water Transport ◽

First Principles ◽

Electro Osmosis ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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First-Principles Molecular Dynamics Simulations for Se8and Se8+Clusters

Molecular Simulation ◽

10.1080/08927029708024140 ◽

1997 ◽

Vol 19 (2) ◽

pp. 75-84 ◽

Cited By ~ 3

Author(s):

K. Uehara ◽

M. Ishitobi ◽

T. Oda ◽

Y. Hiwatari

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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FIRST PRINCIPLES MOLECULAR DYNAMICS SIMULATIONS USING DENSITY-FUNCTIONAL THEORY

Reviews of Modern Quantum Chemistry ◽

10.1142/9789812775702_0056 ◽

2002 ◽

pp. 1684-1734 ◽

Cited By ~ 4

Author(s):

Marat Valiev ◽

Eric J. Bylaska ◽

A. Gramada ◽

John H. Weare

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Density Functional ◽

Functional Theory ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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Mechanistic Insight into the Framework Methylation of H-ZSM-5 for Varying Methanol Loadings and Si/Al Ratios Using First-Principles Molecular Dynamics Simulations

ACS Catalysis ◽

10.1021/acscatal.0c01454 ◽

2020 ◽

Vol 10 (15) ◽

pp. 8904-8915 ◽

Cited By ~ 1

Author(s):

Stefan A. F. Nastase ◽

Pieter Cnudde ◽

Louis Vanduyfhuys ◽

Kristof De Wispelaere ◽

Veronique Van Speybroeck ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Mechanistic Insight ◽

Dynamics Simulations ◽

Insight Into ◽

First Principles Molecular Dynamics

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Structure and Dynamics of Water at the Water–Air Interface Using First-Principles Molecular Dynamics Simulations. II. NonLocal vs Empirical van der Waals Corrections

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.9b00253 ◽

2019 ◽

Vol 15 (6) ◽

pp. 3836-3843 ◽

Cited By ~ 3

Author(s):

Mayank Dodia ◽

Tatsuhiko Ohto ◽

Sho Imoto ◽

Yuki Nagata

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Van Der Waals ◽

Structure And Dynamics ◽

Air Interface ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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