Related papers: An Asymmetric Elastic Rod Model for DNA
This paper is devoted to describe the deformations and the elastic energy for structures made of straight rods of thickness $2\delta$ when $\delta$ tends to 0. This analysis relies on the decomposition of the large deformation of a single…
Nonlinear molecular excitations in DNA have traditionally been modelled using the nonlinear Schr\"odinger equation (NLSE). An alternative approach is based on the plane-base rotator model and the SU(2)/U(1) generalized spin coherent states,…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
It is well known that transcription can induce torsional stress in DNA, affecting the activity of nearby genes or even inducing structural transitions in the DNA duplex. It has long been assumed that the generation of significant torsional…
We study the elasticity of a two-dimensional random network of rigid rods (``Mikado model''). The essential features incorporated into the model are the anisotropic elasticity of the rods and the random geometry of the network. We show that…
Isomorphs are curves in the thermodynamic phase diagram of invariant excess entropy, structure, and dynamics, while pseudoisomorphs are curves of invariant structure and dynamics, but not of the excess entropy. The latter curves have been…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
We propose a model for DNA dynamics by introducing the helical structure through twist deformation in analogy with the structure of helimagnet and cholesteric liquid crystal system. The dynamics in this case is found to be governed by the…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…
While isotropic in-plane swelling problems for thin elastic sheets have been studied extensively in recent years, many shape-programmable materials, including nematic solids and 3D-printed structures, are anisotropic, as are most industrial…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
We measure the rheology of transient hydrogels comprised of a single type of DNA nanostar that makes both strong and weak bonds. These gels exhibit power-law frequency-dependence of their storage and loss moduli, with scaling exponents that…
Nonlinear bending phenomena of thin elastic structures arise in various modern and classical applications. Characterizing low energy states of elastic rods has been investigated by Bernoulli in 1738 and related models are used to determine…
We present a model to study Young's modulus and Poisson's ratio of the composite material of amorphous nanowires. It is an extension of the model derived by two of us [Da Fonseca and Galvao, Phys. Rev. Lett. 92, 175502 (2004)] to study the…
The nonlinear mechanics of a flexible elastic rod constrained at its edges by a pair of sliding sleeves is analyzed. The planar equilibrium configurations of this variable-length elastica are found to have shape defined only by the…
We present a procedure to map the constitutive laws of elasticity (both in the linear and nonlinear regime) onto a discrete atomic lattice and we apply the resulting elastic lattice model to investigate the strain field within an embedded…
We show that gels formed by arrested spinodal decomposition of protein solutions exhibit elastic properties in two distinct frequency domains, both elastic moduli exhibiting a remarkably strong dependence on volume fraction. Considering the…
We introduce a family of models incorporating random segmental substitutions and point mutations and demonstrate that such models reproduce algebraic length distributions of exact matches with the slope $-4$ observed earlier in pairwise…
We present Molecular Dynamics simulations of a single stranded unprotonated DNA i-motif in explicit solvent. Our results indicate that the native structure in non-acidic solution at 300 K is unstable and completely vanishes on a time scale…