Dynamics of individual flexible polymers in a shear flow

LeDuc, Philip R.; Haber, Charbel; Bao, Gang; Wirtz, Denis

doi:10.1038/21148

Cited by 208 publications

(234 citation statements)

References 22 publications

(14 reference statements)

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“…[1][2][3][4][5]. However, this single-molecule imaging approach is restricted to the study of polymers which are larger in size than the diffraction limit of the imaging optics.…”

mentioning

confidence: 99%

Polymer Dynamics, Fluorescence Correlation Spectroscopy, and the Limits of Optical Resolution

Enderlein

2012

Phys. Rev. Lett.

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In recent years, fluorescence correlation spectroscopy has been increasingly applied for the study of polymer dynamics on the nanometer scale. The core idea is to extract, from a measured autocorrelation curve, an effective mean-square displacement function that contains information about the underlying conformational dynamics. The paper presents a fundamental study of the applicability of fluorescence correlation spectroscopy for the investigation of nanoscale conformational and diffusional dynamics. We find that fluorescence correlation spectroscopy cannot reliably elucidate processes on length scales much smaller than the resolution limit of the optics used and that its improper use can yield spurious results for the observed dynamics.

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“…[1][2][3][4][5]. However, this single-molecule imaging approach is restricted to the study of polymers which are larger in size than the diffraction limit of the imaging optics.…”

mentioning

confidence: 99%

Polymer Dynamics, Fluorescence Correlation Spectroscopy, and the Limits of Optical Resolution

Enderlein

2012

Phys. Rev. Lett.

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“…1.30, oil-immersion lens was used to monitor the conformation of individual, fluorescently labeled DNA molecules at equilibrium. We used monodisperse Coliphage T2-phage DNA (T2-DNA) molecules (19) suspended at a concentration Ϸ20 ng͞ml (much smaller than the overlap concentration Ϸ0.13 mg͞ml) in Tris⅐EDTA buffer and an oxygen-scavenging system to reduce photobleaching (20)(21)(22). DNA molecules were stained with an intercalating dye (YOYO-1, Molecular Probes), which we verified did not affect the overall shape distribution of DNA.…”

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confidence: 99%

Shape anisotropy of a single random-walk polymer

Haber

Ruiz

Wirtz

2000

Proc. Natl. Acad. Sci. U.S.A.

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Random walks have been used to describe a wide variety of systems ranging from cell colonies to polymers. Sixty-five years ago, Kuhn [Kuhn, W. (1934) Kolloid-Z. 68, 2-11] made the prediction, backed later by computer simulations, that the overall shape of a random-walk polymer is aspherical, yet no experimental work has directly tested Kuhn's general idea and subsequent computer simulations. By using fluorescence microscopy, we monitored the conformation of individual, long, random-walk polymers (fluorescently labeled DNA molecules) at equilibrium. We found that a polymer most frequently adopts highly extended, nonfractal structures with a strongly anisotropic shape. The ensemble-average ratio of the lengths of the long and short axes of the best-fit ellipse of the polymer was much larger than unity. R andom walks have been extensively used to describe a multitude of phenomena, ranging from cell migration within connective tissues, to Markov processes in DNA sequences, to time series in the stock market, to diffusion in gas, liquids, and solids (1-5). Sixty-five years ago, Kuhn (6) predicted that the shape of a random-walk polymer is not spherically symmetric, i.e., a regular random walk has an overall shape which is anisotropic. The intuitive idea of a spherical shape is based on a flexible polymer (or a random walk) having an isotropic end-to-end vector distribution and on the implicit rotational averaging typically done in polymer theories and experiments (7-10), yet the shape of individual polymers has not been probed directly (5, 9).The lack of direct conformational information has so far prevented a direct test of Kuhn's prediction (6), which is supported by computer simulations (11-16) and analytical calculations (5). Bulk measurements such as light scattering and rheology (17, 18) are inappropriate to probe the behavior of individual polymers in solution. These bulk experimental methods average the orientation, shape, and dynamics of a large ensemble of molecules simultaneously. Here, by monitoring the conformation, orientation, and dynamics of individual flexible polymers in dilute solutions, we directly measure the distributions of conformational parameters. We therefore test Kuhn's central prediction directly. Materials and MethodsLight microscopy (Nikon) equipped with a ϫ100, n.a. 1.30, oil-immersion lens was used to monitor the conformation of individual, fluorescently labeled DNA molecules at equilibrium. We used monodisperse Coliphage T2-phage DNA (T2-DNA) molecules (19) suspended at a concentration Ϸ20 ng͞ml (much smaller than the overlap concentration Ϸ0.13 mg͞ml) in Tris⅐EDTA buffer and an oxygen-scavenging system to reduce photobleaching (20)(21)(22). DNA molecules were stained with an intercalating dye (YOYO-1, Molecular Probes), which we verified did not affect the overall shape distribution of DNA. T2-DNA is a highly flexible polymer with a contour length of L Ϸ 56 m and a persistence length of l p Ϸ 52 nm. Hence, this polymer is a linear sequence of Ϸ1,075 (ϭ L͞l P Ͼ Ͼ 1) statistical segme...

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“…The simplest example, discussed in details, is the two peaks model for Gaussian manifold instability in polymer dynamics. This type of models opens a way to create the computational models for the "molecular individualism" [48][49][50].…”

Section: Resultsmentioning

confidence: 99%

“…A benefit of using Eq. (51) is also in that m α m α = M α+α , and we have to perform less calculations in (50). This set of the deformed energies can be used for both the initial potential U and the set of additional potentials.…”

Section: Macroscopic Variables and Quasiequilibrium Distribution Funcmentioning

confidence: 99%

Legendre integrators, post-processing and quasiequilibrium

Gorban

Karlin

2004

Journal of Non-Newtonian Fluid Mechanics

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A toolbox for the development and reduction of the dynamical models of nonequilibrium systems is presented. The main components of this toolbox are: Legendre integrators, dynamical post-processing, and the thermodynamic projector. The thermodynamic projector is the tool to transform almost any anzatz to a thermodynamically consistent model. The post-processing is the cheapest way to improve the solution obtained by the Legendre integrators. Legendre integrators give the opportunity to solve linear equations instead of nonlinear ones for quasiequilibrium ("maximum entropy", MaxEnt) approximations. The essentially new element of this toolbox, the method of thermodynamic projector, is demonstrated on application to the FENE-P model of polymer kinetic theory. The multi-peak model of polymer dynamics is developed.

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Dynamics of individual flexible polymers in a shear flow

Cited by 208 publications

References 22 publications

Polymer Dynamics, Fluorescence Correlation Spectroscopy, and the Limits of Optical Resolution

Polymer Dynamics, Fluorescence Correlation Spectroscopy, and the Limits of Optical Resolution

Shape anisotropy of a single random-walk polymer

Legendre integrators, post-processing and quasiequilibrium

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