Handle URI:
http://hdl.handle.net/10754/598875
Title:
Molecular dynamics simulation of ribosome jam
Authors:
Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu
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.
Citation:
Matsumoto S, Takagi F, Shimada T, Ito N (2011) Molecular dynamics simulation of ribosome jam. Computer Physics Communications 182: 1958–1960. Available: http://dx.doi.org/10.1016/j.cpc.2010.12.007.
Publisher:
Elsevier BV
Journal:
Computer Physics Communications
KAUST Grant Number:
KUK-I1-005-04
Issue Date:
Sep-2011
DOI:
10.1016/j.cpc.2010.12.007
Type:
Article
ISSN:
0010-4655
Sponsors:
This work was partly supported by Award No. KUK-I1-005-04 made by King Abdullah University of Science and Technology (KAUST).
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorMatsumoto, Shigenorien
dc.contributor.authorTakagi, Fumikoen
dc.contributor.authorShimada, Takashien
dc.contributor.authorIto, Nobuyasuen
dc.date.accessioned2016-02-25T13:42:53Zen
dc.date.available2016-02-25T13:42:53Zen
dc.date.issued2011-09en
dc.identifier.citationMatsumoto S, Takagi F, Shimada T, Ito N (2011) Molecular dynamics simulation of ribosome jam. Computer Physics Communications 182: 1958–1960. Available: http://dx.doi.org/10.1016/j.cpc.2010.12.007.en
dc.identifier.issn0010-4655en
dc.identifier.doi10.1016/j.cpc.2010.12.007en
dc.identifier.urihttp://hdl.handle.net/10754/598875en
dc.description.abstractWe 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.en
dc.description.sponsorshipThis work was partly supported by Award No. KUK-I1-005-04 made by King Abdullah University of Science and Technology (KAUST).en
dc.publisherElsevier BVen
dc.subjectMolecular dynamics simulationen
dc.subjectRibosomeen
dc.subjectTraffic jamen
dc.titleMolecular dynamics simulation of ribosome jamen
dc.typeArticleen
dc.identifier.journalComputer Physics Communicationsen
dc.contributor.institutionUniversity of Tokyo, Tokyo, Japanen
kaust.grant.numberKUK-I1-005-04en
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