Related papers: An Asymmetric Elastic Rod Model for DNA
Locally periodic rods, which show approximate invariance with respect to translations, are constructed by joining $N$ unit cells. The spectrum then shows a band spectrum. We then break the local periodicity by including one or more defects…
The continuum-rod model has emerged as an efficient tool to describe the long-length-scale structural-deformations of DNA which are critical to understanding the nature of many biological processes such as gene expression. However, a…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
The choice of elastic energies for thin plates and shells is an unsettled issue with consequences for much recent modeling of soft matter. Through consideration of simple deformations of a thin body in the plane, we demonstrate that four…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
Understanding nanomechanical response of materials represents a scientific challenge. Here, we have used in-situ electron microscopy to reveal drastic for the first time changes of structural behavior during deformation of 1-nm-wide metal…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
We study the evolution of diffuse elastodynamic spectral energy density under the influence of weak nonlinearity. It is shown that the rate of change of this quantity is given by a convolution of the linear energy at two frequencies.…
We study the anomalous elasticity of nematic elastomers by employing the powers of renormalized field theory. Using general arguments of symmetry and relevance, we introduce a minimal Landau-Ginzburg-Wilson elastic energy for nematic…
The theoretical study of deformability of special sequence of DNA double helix TATA-box is presentated. The paper elaborates on the mechanisms of abnormal deformation of DNA TATA-box double helix that cannot be explained using the standard…
The elasticity of DNA catenanes, i.e. multiply linked DNA rings, is investigated using the Gauss invariant as a minimal model for topology conservation. An effective elastic free energy as a function of the distance $R$ between segments…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics.…
The macroscopic curvature induced in double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount and…
Nonlinear elastic theory studies the elastic constants of a material (such as Young's modulus or bulk modulus) as a power series in the applied load. The inverse bulk modulus K, for example depends on the compression P: $ {1/ K(P)} = c_0 +…