Elastic rod model incorporating shear and extension, generalized nonlinear Schrödinger equations, and novel closed-form solutions for supercoiled DNA

Shi, Yang; Borovik, A. E.; Hearst, John E.

doi:10.1063/1.470250

Cited by 29 publications

(27 citation statements)

References 36 publications

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“…4 A A/ps using the scalings in Eq. (15) and are based on the rodÕs mechanical properties. For the molecular dynamics simulation, the wave speed was estimated to be 2.2 A A/ps based on graphical observations.…”

Section: Functionmentioning

confidence: 99%

“…Closed form expressions for the equilibrium conformations of a Kirchhoff rod [14] and an elastic rod with shear and extension [15] have been obtained by Shi and Hearst and related to the observed folding of DNA into extended and condensed chromatin [16][17][18]. Goriely and co-workers extended the mathematical analysis by providing a classification of the equilibrium conformations [19] and a theoretical framework for determining their dynamic stability [20].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Investigation of bend and shear waves in a geometrically exact elastic rod model

Bishop¹,

Cortez²,

Zhmudsky³

2004

Journal of Computational Physics

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Section: Functionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Investigation of bend and shear waves in a geometrically exact elastic rod model

Bishop¹,

Cortez²,

Zhmudsky³

2004

Journal of Computational Physics

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“…Benham [2,3] and Le Bret [4,5] firstly used the elastic model to analyze the equilibrium configuration of DNA. In the framework of this model, varied subjects related with the DNA configuration were investigated extensively [6][7][8][9][10]. Some geometrical configurations appearing in the DNA condensation have been explained perfectly.…”

Section: Introductionmentioning

confidence: 99%

An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution

2014

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As a coarse-gained model, a super-thin elastic rod subjected to interfacial interactions is used to investigate the condensation of DNA in a multivalent salt solution. The interfacial traction between the rod and the solution environment is determined in terms of the Young-Laplace equation. Kirchhoff's theory of elastic rod is used to analyze the equilibrium configuration of a DNA chain under the action of the interfacial traction. Two models are established to characterize the change of the interfacial traction and elastic modulus of DNA with the ionic concentration of the salt solution, respectively. The influences of the ionic concentration on the equilibrium configuration of DNA are discussed. The results show that the condensation of DNA is mainly determined by competition between the interfacial energy and elastic strain energy of the DNA itself, and the interfacial traction is one of forces that drive DNA condensation. With the change of concentration, the DNA segments will undergo a series of alteration from the original configuration to the condensed configuration, and the spiral-shape appearing in the condensed configuration of DNA is independent of the original configuration.

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“…Subsequently, the elastic rod model of DNA was extended and refined in a variety of ways. By introducing shear and extension, Shi et al expanded the set of allowable deformations of DNA [8]. They found a closed-form solution to the rod model of DNA.…”

mentioning

confidence: 99%

Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding

Huang

2010

J Biol Phys

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As a continuum model of DNA, a thin elastic rod subjected to interfacial interactions is used to investigate the equilibrium configuration of DNA in intracellular solution. The interfacial traction between the rod and the solution environment is derived in detail. Kirchhoff's theory of elastic rods is used to analyze the equilibrium configuration of a DNA segment under the action of the interfacial traction. The influences of the interfacial energy factor and bending stiffness on the toroidal spool formation of the DNA segment are discussed. The results show that the equilibrium configuration of DNA is mainly determined by competition between the interfacial energy and elastic strain energy of the DNA itself, and the interfacial traction is one of the forces that drives DNA folding and unfolding.

show abstract

Elastic rod model incorporating shear and extension, generalized nonlinear Schrödinger equations, and novel closed-form solutions for supercoiled DNA

Cited by 29 publications

References 36 publications

Investigation of bend and shear waves in a geometrically exact elastic rod model

Investigation of bend and shear waves in a geometrically exact elastic rod model

An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution

Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding

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