Iso-Flux Tension Propagation Theory of Driven Polymer Translocation: The Role of Initial Configurations

dc.contributorAalto-yliopistofi
dc.contributorAalto Universityen
dc.contributor.authorSarabadani, J.
dc.contributor.authorIkonen, T.
dc.contributor.authorAla-Nissilä, Tapio
dc.contributor.departmentTeknillisen fysiikan laitosfi
dc.contributor.departmentDepartment of Applied Physicsen
dc.contributor.schoolPerustieteiden korkeakoulufi
dc.contributor.schoolSchool of Scienceen
dc.date.accessioned2015-04-17T09:00:24Z
dc.date.available2015-04-17T09:00:24Z
dc.date.issued2014
dc.description.abstractWe investigate the dynamics of pore-driven polymer translocation by theoretical analysis and molecular dynamics (MD) simulations. Using the tension propagation theory within the constant flux approximation we derive an explicit equation of motion for the tension front. From this we derive a scaling relation for the average translocation time τ, which captures the asymptotic result τ∝N1+ν0 , where N 0 is the chain length and ν is the Flory exponent. In addition, we derive the leading correction-to-scaling term to τ and show that all terms of order N2ν0 exactly cancel out, leaving only a finite-chain length correction term due to the effective pore friction, which is linearly proportional to N 0. We use the model to numerically include fluctuations in the initial configuration of the polymer chain in addition to thermal noise. We show that when the cis side fluctuations are properly accounted for, the model not only reproduces previously known results but also considerably improves the estimates of the monomer waiting time distribution and the time evolution of the translocation coordinate s(t), showing excellent agreement with MD simulations.en
dc.description.versionPeer revieweden
dc.format.extent214907-1-9
dc.format.mimetypeapplication/pdfen
dc.identifier.citationSarabadani, J. & Ikonen, T. & Ala-Nissilä, Tapio. 2014. Iso-Flux Tension Propagation Theory of Driven Polymer Translocation: The Role of Initial Configurations. The Journal of Chemical Physics. Volume 141, Number 214907. P. 214907-1-9. ISSN 0021-9606 (printed). DOI: 10.1063/1.4903176.en
dc.identifier.doi10.1063/1.4903176
dc.identifier.issn0021-9606 (printed)
dc.identifier.urihttps://aaltodoc.aalto.fi/handle/123456789/15676
dc.identifier.urnURN:NBN:fi:aalto-201504162332
dc.language.isoenen
dc.publisherAIP Publishingen
dc.relation.ispartofseriesThe Journal of Chemical Physicsen
dc.relation.ispartofseriesVolume 141, Number 21
dc.rights© 2014 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. http://scitation.aip.org/content/aip/journal/jcpen
dc.rights.holderAmerican Institute of Physics
dc.subject.keywordPolymer translocationen
dc.subject.keywordPolymer dynamicsen
dc.subject.keywordDNA sequencingen
dc.subject.otherPhysicsen
dc.titleIso-Flux Tension Propagation Theory of Driven Polymer Translocation: The Role of Initial Configurationsen
dc.typeA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessäfi
dc.type.dcmitypetexten
dc.type.versionFinal published versionen
Files
Original bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
A1_sarabadani_j._2014.pdf
Size:
1.4 MB
Format:
Adobe Portable Document Format