Quantification of tension to explain bias dependence of driven polymer translocation dynamics

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dc.contributor Aalto-yliopisto fi
dc.contributor Aalto University en
dc.contributor.author Suhonen, P. M.
dc.contributor.author Piili, J.
dc.contributor.author Linna, R. P.
dc.date.accessioned 2018-08-01T13:29:09Z
dc.date.available 2018-08-01T13:29:09Z
dc.date.issued 2017-12-06
dc.identifier.citation Suhonen , P M , Piili , J & Linna , R P 2017 , ' Quantification of tension to explain bias dependence of driven polymer translocation dynamics ' Physical Review E , vol 96 , no. 6 , 062401 , pp. 1-15 . DOI: 10.1103/PhysRevE.96.062401 en
dc.identifier.issn 2470-0045
dc.identifier.issn 1550-2376
dc.identifier.other PURE UUID: 7026c045-f9f4-4769-89da-cca98272f7b3
dc.identifier.other PURE ITEMURL: https://research.aalto.fi/en/publications/quantification-of-tension-to-explain-bias-dependence-of-driven-polymer-translocation-dynamics(7026c045-f9f4-4769-89da-cca98272f7b3).html
dc.identifier.other PURE LINK: http://www.scopus.com/inward/record.url?scp=85038212982&partnerID=8YFLogxK
dc.identifier.other PURE FILEURL: https://research.aalto.fi/files/26774437/PhysRevE.96.062401.pdf
dc.identifier.uri https://aaltodoc.aalto.fi/handle/123456789/32808
dc.description.abstract Motivated by identifying the origin of the bias dependence of tension propagation, we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here, the motion of flexible polymer chains through a narrow pore is simulated using Langevin dynamics. We measure tension forces, bead velocities, bead distances, and bond angles along the polymer at all stages of translocation with unprecedented precision. Measurements are done at a standard temperature used in simulations and at zero temperature to pin down the effect of fluctuations. The measured quantities were found to give qualitatively similar characteristics, but the bias dependence could be determined only using tension force. We find that in the scaling relation τ∼Nβfdα for translocation time τ, the polymer length N, and the bias force fd, the increase of the exponent β with bias is caused by center-of-mass diffusion of the polymer toward the pore on the cis side. We find that this diffusion also causes the exponent α to deviate from the ideal value -1. The bias dependence of β was found to result from combination of diffusion and pore friction and so be relevant for polymers that are too short to be considered asymptotically long. The effect is relevant in experiments all of which are made using polymers whose lengths are far below the asymptotic limit. Thereby, our results also corroborate the theoretical prediction by Sakaue's theory [Polymers 8, 424 (2016)2073-436010.3390/polym8120424] that there should not be bias dependence of β for asymptotically long polymers. By excluding fluctuations we also show that monomer crowding at the pore exit cannot have a measurable effect on translocation dynamics under realistic conditions. en
dc.format.extent 1-15
dc.format.mimetype application/pdf
dc.language.iso en en
dc.relation.ispartofseries Physical Review E en
dc.relation.ispartofseries Volume 96, issue 6 en
dc.rights openAccess en
dc.subject.other Statistical and Nonlinear Physics en
dc.subject.other Statistics and Probability en
dc.subject.other Condensed Matter Physics en
dc.subject.other 114 Physical sciences en
dc.subject.other 113 Computer and information sciences en
dc.title Quantification of tension to explain bias dependence of driven polymer translocation dynamics en
dc.type A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä fi
dc.description.version Peer reviewed en
dc.contributor.department Professorship Lampinen J.
dc.contributor.department Department of Computer Science
dc.subject.keyword Statistical and Nonlinear Physics
dc.subject.keyword Statistics and Probability
dc.subject.keyword Condensed Matter Physics
dc.subject.keyword 114 Physical sciences
dc.subject.keyword 113 Computer and information sciences
dc.identifier.urn URN:NBN:fi:aalto-201808014209
dc.identifier.doi 10.1103/PhysRevE.96.062401
dc.type.version publishedVersion


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