Is DNA a Good Model Polymer?

Tree, Douglas R.; Muralidhar, Abhiram; Doyle, Patrick S.; Dorfman, Kevin D.

doi:10.1021/ma401507f

Cited by 117 publications

(221 citation statements)

References 111 publications

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“…Chain growth simulations in a tube of diameter D were performed with the PrunedEnriched Rosenbluth Method (PERM) [61,62], using the modification of our standard code [59,63] for soft potentials [64]. Briefly, a given tour starts with a bead located at a random radial position within the tube.…”

Section: Simulation Model and Methodsmentioning

confidence: 99%

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Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

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Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths. * dorfman@umn.edu

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Section: Simulation Model and Methodsmentioning

confidence: 99%

“…Since the trial moves in our implementation [59,63] are drawn from the distribution for a wormlike chain, the reference state for the free energy in Eq. (9) is an unconfined, ideal wormlike chain.…”

Section: Simulation Model and Methodsmentioning

confidence: 99%

Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

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“…28 This conclusion extends to lower ionic strengths 28 because the effective width and persistence length have different dependencies on ionic strength. 27 A detailed justification for this argument is given in the supplementary material. 32 …”

Section: A Device Fabricationmentioning

confidence: 99%

“…27,41 The model consists of a discretized chain of contour length L with N b + 1 beads connected by rigid rods of length l b . The bond angles between the rods are constrained using the bending potential…”

Section: A Discrete Wormlike Chain Modelmentioning

confidence: 99%

“…To this end, we use Pruned-Enriched Rosenbluth Method (PERM) simulations 25,26 of an off-lattice, discrete wormlike chain model of confined DNA, following our recent work in this area. 14,27,28 We first simulated the mean extension and its variance for the rectangular channels used in our experiments, using the ionic strength of the buffer to compute the effective width 29 and persistence length 30,31 of the DNA. The increase of the backbone length due to the intercalating dye is thus the only free parameter.…”

Section: Introductionmentioning

confidence: 99%

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Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

Gupta

Sheats²,

Muralidhar

et al. 2014

The Journal of Chemical Physics

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We have used a combination of fluorescence microscopy experiments and Pruned Enriched Rosenbluth Method simulations of a discrete wormlike chain model to measure the mean extension and the variance in the mean extension of λ-DNA in 100 nm deep nanochannels with widths ranging from 100 nm to 1000 nm in discrete 100 nm steps. The mean extension is only weakly affected by the channel aspect ratio. In contrast, the fluctuations of the chain extension qualitatively differ between rectangular channels and square channels with the same cross-sectional area, owing to the "mixing" of different confinement regimes in the rectangular channels. The agreement between experiment and simulation is very good, using the extension due to intercalation as the only adjustable parameter.

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Rheology of Unentangled Polymer Solutions Depends on Three Macromolecular Properties: Flexibility, Extensibility, and Segmental Dissymmetry

Dinic

Narváez

Sharma

2022

Macromolecular Engineering

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We elucidate the influence of chemical structure on macromolecular hydrodynamics and rheological response using poly(ethylene oxide) or PEO and 2‐hydroxyethyl cellulose (HEC). We contrast the shear rheology response measured using torsional rheometry and find the wellknown universalities like comparable shear viscosity for dilute solutions at comparable degree of chain overlap. We show that dripping‐onto‐substrate (DoS) rheometry protocols that we developed facilitate characterization of pinching dynamics and extensional rheology response even for weakly elastic, low viscosity fluids. Even for unentangled solutions with comparable shear viscosity and molecular weights, the PEO solutions exhibit distinctively higher values of extensional relaxation time, extent of strain hardening, transient extensional viscosity, and an overall delay in pinch‐off. We find that the extensional relaxation times exhibit concentration dependence distinct from shear rheology response, or anticipated by blob models, developed for relaxation of weakly perturbed chains. Most significantly, we show that the influence of polymer choice can be evaluated a priori , using three macromolecular parameters: flexibility, extensibility, and segmental dissymmetry, defined as the ratio of Kuhn length to packing length. We identify the minimum concentration above which elastocapillary response appears and define a stretched overlap concentration below which the extensional relaxation time is concentration independent.

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Is DNA a Good Model Polymer?

Cited by 117 publications

References 111 publications

Wall depletion length of a channel-confined polymer

Wall depletion length of a channel-confined polymer

Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

Rheology of Unentangled Polymer Solutions Depends on Three Macromolecular Properties: Flexibility, Extensibility, and Segmental Dissymmetry

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