Molecular dynamics simulation of ribosome jam

Shigenori Matsumoto; Fumiko Takagi; Takashi Shimada; Nobuyasu Ito

doi:10.1016/j.cpc.2010.12.007

Molecular dynamics simulation of ribosome jam

Shigenori Matsumoto, Fumiko Takagi, Takashi Shimada, Nobuyasu Ito

Research output: Contribution to journal › Article › peer-review

Abstract

We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

Original language	English (US)
Pages (from-to)	1958-1960
Number of pages	3
Journal	Computer Physics Communications
Volume	182
Issue number	9
DOIs	https://doi.org/10.1016/j.cpc.2010.12.007
State	Published - Sep 2011
Externally published	Yes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUK-I1-005-04
Acknowledgements: This work was partly supported by Award No. KUK-I1-005-04 made by King Abdullah University of Science and Technology (KAUST).
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

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10.1016/j.cpc.2010.12.007

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title = "Molecular dynamics simulation of ribosome jam",

abstract = "We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. {\textcopyright} 2010 Elsevier B.V. All rights reserved.",

author = "Shigenori Matsumoto and Fumiko Takagi and Takashi Shimada and Nobuyasu Ito",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): KUK-I1-005-04 Acknowledgements: This work was partly supported by Award No. KUK-I1-005-04 made by King Abdullah University of Science and Technology (KAUST). This publication acknowledges KAUST support, but has no KAUST affiliated authors.",

year = "2011",

month = sep,

doi = "10.1016/j.cpc.2010.12.007",

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AU - Matsumoto, Shigenori

AU - Takagi, Fumiko

AU - Shimada, Takashi

AU - Ito, Nobuyasu

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): KUK-I1-005-04 Acknowledgements: This work was partly supported by Award No. KUK-I1-005-04 made by King Abdullah University of Science and Technology (KAUST). This publication acknowledges KAUST support, but has no KAUST affiliated authors.

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N2 - We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

AB - We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

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VL - 182

SP - 1958

EP - 1960

JO - Computer Physics Communications

JF - Computer Physics Communications

IS - 9

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Molecular dynamics simulation of ribosome jam

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