Please use this identifier to cite or link to this item: https://hdl.handle.net/20.500.11851/10471
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dc.contributor.authorWang, Yiren-
dc.contributor.authorDemir, Büşra-
dc.contributor.authorMohammad, Hashem-
dc.contributor.authorÖren, Ersin Emre-
dc.contributor.authorAnantram, M. P.-
dc.date.accessioned2023-07-14T20:17:07Z-
dc.date.available2023-07-14T20:17:07Z-
dc.date.issued2023-
dc.identifier.issn2470-0045-
dc.identifier.issn2470-0053-
dc.identifier.urihttps://doi.org/10.1103/PhysRevE.107.044404-
dc.identifier.urihttps://hdl.handle.net/20.500.11851/10471-
dc.description.abstractDNA naturally exists in a solvent environment, comprising water and salt molecules such as sodium, potas-sium, magnesium, etc. Along with the sequence, the solvent conditions become a vital factor determining DNA structure and thus its conductance. Over the last two decades, researchers have measured DNA conductivity both in hydrated and almost dry (dehydrated) conditions. However, due to experimental limitations (the precise control of the environment), it is very difficult to analyze the conductance results in terms of individual contributions of the environment. Therefore, modeling studies can help us to gain a valuable understanding of various factors playing a role in charge transport phenomena. DNA naturally has negative charges located at the phosphate groups in the backbone, which provides both the connections between the base pairs and the structural support for the double helix. Positively charged ions such as the sodium ion (Na+), one of the most commonly used counterions, balance the negative charges at the backbone. This modeling study investigates the role of counterions both with and without the solvent (water) environment in charge transport through double-stranded DNA. Our computational experiments show that in dry DNA, the presence of counterions affects electron transmission at the lowest unoccupied molecular orbital energies. However, in solution, the counterions have a negligible role in transmission. Using the polarizable continuum model calculations, we demonstrate that the transmission is significantly higher at both the highest occupied and lowest unoccupied molecular orbital energies in a water environment as opposed to in a dry one. Moreover, calculations also show that the energy levels of neighboring bases are more closely aligned to ease electron flow in the solution.en_US
dc.description.sponsorshipNational Science Foundation [1807391, 1807555, 2036865]en_US
dc.description.sponsorshipWe acknowledge National Science Foundation Grants No. 1807391 and No. 1807555 (SemiSynBio Program) and Grant No. 2036865 (Future of Manufacturing) for support.en_US
dc.language.isoenen_US
dc.publisherAmer Physical Socen_US
dc.relation.ispartofPhysical Review Een_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectCharge-Transferen_US
dc.subjectTransporten_US
dc.subjectMoleculesen_US
dc.subjectSimulationen_US
dc.subjectCoherenten_US
dc.subjectSeriesen_US
dc.titleComputational Study of the Role of Counterions and Solvent Dielectric in Determining the Conductance of B-Dnaen_US
dc.typeArticleen_US
dc.departmentTOBB ETÜen_US
dc.identifier.volume107en_US
dc.identifier.issue4en_US
dc.authoridOren, Ersin Emre/0000-0001-5902-083X-
dc.authoridAnantram, M/0000-0003-2539-7457-
dc.authoridWang, Yiren/0000-0003-1102-4609-
dc.authoridDemir, Busra/0000-0002-3911-2291-
dc.identifier.wosWOS:000988190300003en_US
dc.identifier.scopus2-s2.0-85158833604en_US
dc.institutionauthor-
dc.identifier.pmid37198817en_US
dc.identifier.doi10.1103/PhysRevE.107.044404-
dc.authorwosidOren, Ersin Emre/AGQ-5958-2022-
dc.authorwosidDemir, Busra/W-1919-2018-
dc.authorscopusid57225920866-
dc.authorscopusid57204554850-
dc.authorscopusid57202959503-
dc.authorscopusid35846321000-
dc.authorscopusid57203174991-
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.identifier.scopusqualityQ1-
item.openairetypeArticle-
item.languageiso639-1en-
item.grantfulltextnone-
item.fulltextNo Fulltext-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.cerifentitytypePublications-
crisitem.author.dept02.2. Department of Biomedical Engineering-
Appears in Collections:PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
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