Dynamics of Semiflexible Polymers in Solution

Schaefer, Dale W.; Joanny, J.-F.; Pincus, P.

doi:10.1021/ma60077a048

Cited by 247 publications

(214 citation statements)

References 16 publications

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“…31,41 The chain extent at which this conversion happens is termed the thermal blob size, b, and can be related to the monomer excluded volume factor. Note that in the limit of strong intra-chain repulsions, swelling will commence immediately, with b ≈ ℓ; this is termed the athermal solvent regime, which can be differentiated from the good solvent regime for which b > ℓ.…”

Section: F Summary Of the Theoretical Picture: Force And Length Scalmentioning

confidence: 99%

Perspective: Single polymer mechanics across the force regimes

Saleh

2015

The Journal of Chemical Physics

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I review theoretical and experimental results on the force-extension response of single polymers, with a focus on scaling pictures of low-force elastic regimes, and recent measurements of synthetic and biological chains that explore those regimes. The mechanical response of single polymers is an old theoretical problem whose exploration was instigated by the curious thermomechanical behavior of rubber. Up until the 1990s, the main utility of those calculations was to explain bulk material mechanics. However, in that decade, it became possible to directly test the calculations through high-precision single-chain stretching experiments (i.e., force spectroscopy). I present five major single-chain elasticity models, including scaling results based on blob-chain models, along with analytic results based on linear response theory, and those based on freely jointed chain or worm-like chain structure. Each model is discussed in terms of the regime of force for which it holds, along with the status of its rigorous assessment with experiment. Finally, I show how the experiments can provide new insight into polymer structure itself, with particular emphasis on polyelectrolytes. C 2015 AIP Publishing LLC. [http://dx

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Section: F Summary Of the Theoretical Picture: Force And Length Scalmentioning

confidence: 99%

Perspective: Single polymer mechanics across the force regimes

Saleh

2015

The Journal of Chemical Physics

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“…Diagram of regimes for polymer solutions. Adapted from Figure 3 in the paper by Shaefer et al 35 for Research and Technology's research program in BioSystems and Micromechanics and the National Science Foundation (CBET-1335938). The authors thank the Center for Computational Science and Engineering at National University of Singapore for providing the computational resource.…”

Section: ■ Acknowledgmentsmentioning

confidence: 99%

Extended de Gennes Regime of DNA Confined in a Nanochannel

2014

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Scaling regimes for polymers confined to tubular channels are well established when the channel cross-sectional dimension is either very small (Odjik regime) or large (classic de Gennes regime) relative to the polymer Kuhn length. However, experiments of confined polymers using DNA as a model system are usually located in the intermediate region between these two regimes. In the literature, controversy exists regarding the existence of the extended de Gennes regime in this intermediate region. Here we use simulations and theory to reconcile conflicting theories and confirm the existence of extended de Gennes regime. We show that prior work did not support the notion of this regime because of the use of a wrong confinement free energy. In a broad sense, the extended de Gennes regime corresponds to the situation when excluded volume interaction is weaker than thermal energy. Such a situation also occurs in many other cases, such as semidilute polymer solutions and polymers under tension. This work should benefit the practical applications of nanochannels to stretch DNA, such as deepening the understanding of the relationship between the chain extension and channel size and providing the scaling behaviors of recoiling force for DNA at the entrance of nanochannels.

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“…1). de Gennes developed a scaling argument for the average extension of a confined self-avoiding polymer [8,12] which was later generalized by Schaefer and Pincus to the case of a persistent self-avoiding polymer [14]. The de Gennes theory predicts an extension r that scales with D in the following way:…”

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Statics and Dynamics of Single DNA Molecules Confined in Nanochannels

et al. 2005

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The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics. DOI: 10.1103/PhysRevLett.94.196101 PACS numbers: 81.16.Nd, 82.35.Lr, 82.39.Pj Top-down approaches to nanotechnology have the potential to revolutionize biology by making possible the construction of chip-based devices that can not only detect and separate single DNA molecules by size [1-4] but also-it is hoped in the future-actually sequence at the single molecule level [5]. While a number of top-down approaches have been proposed, all these approaches have in common the confinement of DNA to nanometer scales, typically 5-200 nm. Confinement alters the statistical mechanical properties of DNA. A DNA molecule in a nanochannel will extend along the channel axis to a substantial fraction of its full contour length [1,6]. Moreover, confinement is expected to alter the Brownian dynamics of the confined molecule [1]. While the study of confined DNA is interesting from a physics perspective, it is also critical for device design, potentially leading to new applications of nanoconfinement (for example, the use of nanochannels to prestretch and stabilize DNA before threading through a nanopore [5]). Moreover, available models [7][8][9][10][11] and simulations [12,13] are unable to account for the effect of varying confinement over the entire range of scales used in nanodevices. The theory gives asymptotic results valid only in limits that are not necessarily compatible with device requirements [1].Consider a DNA molecule of contour length L, width w, and persistence length P confined to a nanochannel of width D with D less than the radius of gyration of the molecule. When D P, the molecule is free to coil in the nanochannel and the elongation is due entirely to excluded volume interactions between segments of the polymer greatly separated in position along the backbone (see Fig. 1). de Gennes developed a scaling argument for the average extension of a confined self-avoiding polymer [8,12] which was later generalized by Schaefer and Pincus to the case of a persistent self-avoiding polymer [14]. The de Gennes theory predicts an extension r that scales with D in the following way:If the aspect ratio of the channel is not unity, i.e., the width D D 1 does not equal the depth D 2 , then Eq. (1) is still valid provided that D is replaced by the geometric average of the dimensions. As the channel width drops below the persistence length, the physics is dominated not by excluded volume but by the interplay of confinement and intrinsic DNA elasticity. In the strong confinement limit D P, backfolding is energetically unfavorable and contour length is stored exclusively in deflections made by the polymer with the walls. These deflections occur on average over th...

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Dynamics of Semiflexible Polymers in Solution

Cited by 247 publications

References 16 publications

Perspective: Single polymer mechanics across the force regimes

Perspective: Single polymer mechanics across the force regimes

Extended de Gennes Regime of DNA Confined in a Nanochannel

Statics and Dynamics of Single DNA Molecules Confined in Nanochannels

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