Development of RYUGA for three-dimensional dynamic visualization of molecular dynamics results

Miura, Ryuji; Yamano, Hideo; Yamauchi, Ryo; Katagiri, Masahiko; Kubo, Momoji; Vetrivel, R.; Miyamoto, Akira

doi:10.1016/0920-5861(94)00157-w

Cited by 58 publications

(14 citation statements)

References 6 publications

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“…In the present simulations, 5000 steps with a time interval of 0.2 fs were performed. The structures during the simulations were visualized using our RYUGA software of MIYAMOTO lab [36].…”

Section: Computational Detailsmentioning

confidence: 99%

Quantum chemical molecular dynamical investigation of alkyl nitrite photo-dissociated on copper surfaces

Wang

Han

et al. 2008

Applied Surface Science

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“…In the present simulations, 5000 steps with a time interval of 0.2 fs were performed. The structures during the simulations were visualized using our RYUGA software of MIYAMOTO lab [36].…”

Section: Computational Detailsmentioning

confidence: 99%

Quantum chemical molecular dynamical investigation of alkyl nitrite photo-dissociated on copper surfaces

Wang

Han

et al. 2008

Applied Surface Science

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“…The simulation results of TB-QCMD were visualized by the New-RYUGA program developed in our laboratory [28].…”

Section: First-principles Parameterizationmentioning

confidence: 99%

Chemical reaction dynamics of PeCB and TCDD decomposition: A tight‐binding quantum chemical molecular dynamics study with first‐principles parameterization

Suzuki

Selvam

Kusagaya

et al. 2004

Int J of Quantum Chemistry

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ABSTRACT:The decomposition reaction dynamics of 2,3,4,4Ј,5-penta-chlorinated biphenyl (2,3,4,4Ј,3,3Ј,4,4Ј,3Ј,4,4Ј,and 2,3,7,3,7, was clarified for the first time at atomic and electronic levels, using our novel tight-binding quantum chemical molecular dynamics method with first-principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional firstprinciples molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first-principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4Ј,5-PeCB, 3,3Ј,4,4Ј,5-PeCB, and 2,3,7,8-TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight-binding quantum chemical molecular dynamics method with firstprinciples parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures.

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“…The dynamic features of the system are observed by using the real-time solid modeling visualization program RYUGA (Miura et al, 1995). Feuston and Garofalini (1989).…”

Section: De D2rmentioning

confidence: 99%

Permeation dynamics of small molecules through silica membranes: Molecular dynamics study

et al. 1998

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Development of RYUGA for three-dimensional dynamic visualization of molecular dynamics results

Cited by 58 publications

References 6 publications

Quantum chemical molecular dynamical investigation of alkyl nitrite photo-dissociated on copper surfaces

Quantum chemical molecular dynamical investigation of alkyl nitrite photo-dissociated on copper surfaces

Chemical reaction dynamics of PeCB and TCDD decomposition: A tight‐binding quantum chemical molecular dynamics study with first‐principles parameterization

Permeation dynamics of small molecules through silica membranes: Molecular dynamics study

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