Helical close packings of ideal ropes

Przybyl, Sylwester; Pierański, P.

doi:10.1007/s101890170099

Cited by 42 publications

(46 citation statements)

References 5 publications

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“…satisfied excluded-volume constraints ( a necessary condition is that ρR ex < 1, i.e. the radius of curvature 1/ρ should be greater that the excludedvolume radius R SH [37], -secondly to check whether enough energy is available, using the value A determined above, notwithstanding the excluded-volume effects. Note that these criterions are independent (geometric and energetic respectively) and they can be checked in any order.…”

Section: A Numerical Results For the Elastic Constantsmentioning

confidence: 99%

Chromatin: A tunable spring at work inside chromosomes

2001

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This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the "extensible worm-like rope", allowing a straightforward prediction of the forceextension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance in the initiation and regulation of transcription.

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Section: A Numerical Results For the Elastic Constantsmentioning

confidence: 99%

Chromatin: A tunable spring at work inside chromosomes

2001

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“…This was used in a numerical simulation of packing with the surprising result that the resulting center line defines a helix with a specific shape. In a succeeding paper, Przybył and Pierański [3] gave an analytical argument, which included the consideration of self-contact points for single helices, and led to the determination of the same helix as in the study of Maritan et al [2]. This helix geometry is the one we describe as being tightly packed in the classification suggested below.…”

Section: Introductionmentioning

confidence: 96%

“…Single helices has been investigated by Maritan et al [2], and Przybył and Pierański [3]. Maritan et al [2] introduced the thickness of a tube in terms of a new quantity called global radius of curvature.…”

Section: Introductionmentioning

confidence: 99%

The generic geometry of helices and their close-packed structures

Olsen

Bohr

2009

Theor Chem Acc

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The formation of helices is an ubiquitous phenomenon for molecular structures whether they are biological, organic, or inorganic, in nature. Helical structures have geometrical constraints analogous to closepacking of three-dimensional crystal structures. For helical packing the geometrical constraints involve parameters such as the radius of the helical cylinder, the helical pitch angle, and the helical tube radius. In this communication, the geometrical constraints for single helix, double helix, and for double helices with minor and major grooves are calculated. The results are compared with values from the literature for helical polypeptide backbone structures, the a-, p-, 3 10 -, and c-helices. The a-helices are close to being optimally packed in the sense of efficient use of space, i.e. close-packed. They are also more densely packed than the other three types of helices. For double helices comparisons are made to the A, B, and Z forms of DNA. The helical geometry of the A form is nearly close-packed. The packing density for the B and Z forms of DNA are found to be approximately equal to each other.

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“…With this assumption equations (14)- (16) would need to altered, but equations (17)- (20), in conjunction with (4) and (6), can still be used to define the curvatures u ij of the individual rods. Additionally equations (31) and (32), (33) and (34) would still apply, so we can completely define the kinematic description of the rods in terms of the contact line R, the angles β i and α i , and the function ∆ s . However, the description could be heavily dependent on the potential deformation of the rod.…”

Section: Relaxing Various Model Assumptionsmentioning

confidence: 99%

“…For the case in which we have two inter-wound tubular this phenomenon has been termed lock-up [29,31]. It was demonstrated in [29,43,47] that this results in the mathematical divergence of the mutual pressure exerted in individual rods as the rope is helically tightened towards this limit.…”

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confidence: 99%

Helical Birods: An Elastic Model of Helically Wound Double-Stranded Rods

Prior

2014

J Elast

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Helical close packings of ideal ropes

Cited by 42 publications

References 5 publications

Chromatin: A tunable spring at work inside chromosomes

Chromatin: A tunable spring at work inside chromosomes

The generic geometry of helices and their close-packed structures

Helical Birods: An Elastic Model of Helically Wound Double-Stranded Rods

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