Heat conductivity of the DNA double helix

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dc.contributorVirginia Techen
dc.contributor.authorSavin, A. V.en
dc.contributor.authorMazo, M. A.en
dc.contributor.authorKikot, I. P.en
dc.contributor.authorManevitch, L. I.en
dc.contributor.authorOnufriev, Alexey V.en
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentPhysicsen
dc.date.accessed2013-12-18en
dc.date.accessioned2014-02-11T13:45:57Zen
dc.date.available2014-02-11T13:45:57Zen
dc.date.issued2011-06-20en
dc.description.abstractThermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by six particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For homogeneous (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains ("beads on a spring") that predict anomalous (infinite) thermal conductivity. Thus, the full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing thermal properties of DNA at a single molecule level.en
dc.description.sponsorshipRFBR 08-04-91118-aen
dc.description.sponsorshipCRDF RUB2-2920-MO-07en
dc.identifier.citationSavin, Alexander V. ; Mazo, Mikhail A. ; Kikot, Irina P. ; et al., Jun 20, 2011. "Heat conductivity of the DNA double helix," PHYSICAL REVIEW B 83(24): 245406. DOI: 10.1103/PhysRevB.83.245406en
dc.identifier.doihttps://doi.org/10.1103/PhysRevB.83.245406en
dc.identifier.issn1098-0121en
dc.identifier.urihttp://hdl.handle.net/10919/25377en
dc.identifier.urlhttp://link.aps.org/doi/10.1103/PhysRevB.83.245406en
dc.language.isoen_USen
dc.publisherAmerican Physical Societyen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectMolecular-dynamics simulationsen
dc.subjectImplicit solvent simulationsen
dc.subjectEmpiricalen
dc.subjectForce-fielden
dc.subjectNucleic-acidsen
dc.subjectB-DNAen
dc.subjectThermal conductivityen
dc.subjectConsensus viewen
dc.subjectSoft materialsen
dc.subjectBase-stackingen
dc.subjectSolvationen
dc.subjectPhysicsen
dc.titleHeat conductivity of the DNA double helixen
dc.title.serialPhysical Review Ben
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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