Related papers: Tops and Writhing DNA
We present a method for solving the Worm Like Chain (WLC) model for twisting semiflexible polymers to any desired accuracy. We show that the WLC free energy is a periodic function of the applied twist with period 4 pi. We develop an analogy…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
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,…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
The work in this article is inspired by a classical problem: the statistical physical properties of a closed polymer loop that is wound around a rod. Historically the preserved topology of this system has been addressed through…
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…
Ring polymers exhibit unique flow properties due to their closed chain topology. Despite recent progress, we have not yet achieved a full understanding of the nonequilibrium flow behavior of rings in nondilute solutions where intermolecular…
Atomically thin moir\'e materials behave like elastic membranes where at very small twist angles, the van der Waals adhesion energy much exceeds the strain energy. In this ``marginal twist" regime, regions with low adhesion energy expand,…
We present a theoretical description of the dynamics of a semi-flexible polymer being pulled through a nanopore by an external force acting at the pore. Our theory is based on the tensile blob picture of Pincus in which the front of the…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
A number of strange results have been reported for the twist elasticity of a semiflexible filament, actin. In particular dynamic and static methods for determining the torsional twist modulus give very different results. I show here that…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…