Related papers: An Asymmetric Elastic Rod Model for DNA
DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic…
In this paper we study the asymptotic behavior of a structure made of curved rods of thickness 2\delta when \delta rightarrow 0. This study is carried on within the frame of linear elasticity by using the unfolding method. It is based on…
This review presents the elastic theory of low-dimensional (one- and two-dimensional) continua and its applications in bio- and nano-structures. First, the curve and surface theory, as the geometric representation of the low-dimensional…
We phenomenologically analyze short DNA rings' stability by discussing the second variation of its elastic free energy. Through expanding the perturbation functions as Fourier series, we obtain DNA rings' stability condition in a general…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
We propose a method for deriving equivalent one-dimensional models for slender non-linear structures. The approach is designed to be broadly applicable, and can handle in principle finite strains, finite rotations, arbitrary cross-sections…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
This paper is devoted to describe the asymptotic behavior of a structure made by a thin plate and a thin rod in the framework of nonlinear elasticity. We scale the applied forces in such a way that the level of the total elastic energy…
Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in…
We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the…
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
A revised Marko-Siggia elastic model for DNA double helix [Macromolecules 27, 981 (1994)] is proposed, which includes the WLC bending energy and a new chiral twisting energy term. It is predicted that the mean helical repeat length (HRL)…
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…
Motivated by an application involving additively manufactured bioresorbable polymer scaffolds supporting bone tissue regeneration, we investigate the impact of uncertain geometry perturbations on the effective mechanical properties of…
Physical experiments can characterize the elastic response of granular materials in terms of macroscopic state-variables, namely volume (packing) fraction and stress, while the microstructure is not accessible and thus neglected. Here, by…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
Minuscule molecular forces can transform DNA into a structure that is elongated by more than half its original length. We demonstrate that this pronounced conformational transition is of relevance to ongoing experimental and theoretical…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…