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dc.contributor.authorPohjolainen, Emmi
dc.date.accessioned2014-06-27T07:53:08Z
dc.date.available2014-06-27T07:53:08Z
dc.date.issued2014
dc.identifier.otheroai:jykdok.linneanet.fi:1438161
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/43854
dc.description.abstractCovalently attaching thiol-functionalized gold nanoclusters to virus surfaces could provide new visualization method for tracking viruses with TEM [1]. This type of imaging could provide better resolution images and shed light, e.g., on virus infection pathways [1]. The controllable binding of these nanoclusters would be essential, and this requires atomic scale information on potential binding sites. In addition atomic scale structural information on virus-nanocluster complexes and their dynamics are needed. Both types of information are potentially obtainable from an all-atom simulation. The aim of this work was to construct a valid model system and set up simulation for full Echovirus 1 capsid in salt solution. A model system of the full Echovirus 1 in salt solution is proposed and simulated up to 200 ns. Also comparative systems with different ligands are proposed and simulated. Based on the simulation the validity of the model is assessed and established in terms of convergence of energy terms, structure and relations to experiments. More detailed look is given considering behavior of potential binding sites, hydrophobic pocket and different pocket factors and cysteine residues. The recognized points of interest to be studied in further simulations are discussed. The proposed model then lays foundation for more extensive studies of this virus with molecular dynamics simulations.en
dc.format.extent1 verkkoaineisto (81 sivua)
dc.language.isoeng
dc.rightsThis publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.en
dc.rightsJulkaisu on tekijänoikeussäännösten alainen. Teosta voi lukea ja tulostaa henkilökohtaista käyttöä varten. Käyttö kaupallisiin tarkoituksiin on kielletty.fi
dc.titleMolecular dynamics simulations of Echovirus1
dc.identifier.urnURN:NBN:fi:jyu-201406272169
dc.type.dcmitypeTexten
dc.type.ontasotPro gradufi
dc.type.ontasotMaster's thesisen
dc.contributor.tiedekuntaMatemaattis-luonnontieteellinen tiedekuntafi
dc.contributor.tiedekuntaFaculty of Sciencesen
dc.contributor.laitosFysiikan laitosfi
dc.contributor.laitosDepartment of Physicsen
dc.contributor.yliopistoUniversity of Jyväskyläen
dc.contributor.yliopistoJyväskylän yliopistofi
dc.contributor.oppiaineFysiikkafi
dc.contributor.oppiainePhysicsen
dc.date.updated2014-06-27T07:53:09Z
dc.rights.accesslevelopenAccessfi
dc.contributor.oppiainekoodi4021
dc.subject.ysovirukset
dc.subject.ysoECHO-virukset


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