Analysis of DNA Elasticity

Linna, Riku; Kaski, Kimmo

doi:10.1103/physrevlett.100.168104

Cited by 15 publications

(17 citation statements)

References 13 publications

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“…The dotted magenta curves are the analytical ones for an infinite system length, obtained by using Eqs. (3), (9a), and (21), while all the other curves are for finite system sizes which gradually match the analytical curve as N becomes larger. x shows a finite discontinuity at a critical g sc = 1.18.…”

Section: Elastic Constantsupporting

confidence: 61%

Rigidity of melting DNA

Pal

Bhattacharjee

2016

Phys. Rev. E

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The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation.

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Section: Elastic Constantsupporting

confidence: 61%

Rigidity of melting DNA

Pal

Bhattacharjee

2016

Phys. Rev. E

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“…Correspondence to a specific polymer may be adjusted by using the semi-flexible worm-like chain (WLC) model. It has been shown that in free space neither entropic nor intrinsic parts of elasticity differ appreciably for FC and WLC models [30]. In this article we aim to study the general properties of the process.…”

Section: Relating the Model To Real-world Translocation Processesmentioning

confidence: 99%

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

2017

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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∼N^{β}f_{d}^{α} for translocation time τ, the polymer length N, and the bias force f_{d}, 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.

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“…We apply no bending potential, rendering the polymer as a freely-jointed chain (FJC), instead of a worm-like chain (WLC). We have previously shown that the difference of the two models when simulating polymer elasticity in mechanical stretching or in flow is insignificant [13].…”

Section: A the Polymer Modelmentioning

confidence: 99%

Event distributions of polymer translocation

Linna

Kaski

2012

Phys. Rev. E

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We present event distributions for the polymer translocation obtained by extensive Langevin dynamics simulations. Such distributions have not been reported previously and they provide new understanding of the stochastic characteristics of the process. We extract at a high length scale resolution distributions of polymer segments that continuously traverse through a nanoscale pore. The obtained log-normal distributions together with the characteristics of polymer translocation suggest that it is describable as a multiplicative stochastic process. In spite of its clear out-of-equilibrium nature the forced translocation is surprisingly similar to the unforced case. We find forms for the distributions almost unaltered with a common cut-off length. We show that the individual short-segment and short-time movements inside the pore give the scaling relations τ ∼ N α and τ ∼ f −β for the polymer translocation.

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Analysis of DNA Elasticity

Cited by 15 publications

References 13 publications

Rigidity of melting DNA

Rigidity of melting DNA

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

Event distributions of polymer translocation

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