Related papers: Resonant helical deformations in nonhomogeneous Ki…
The tridimensional configuration and the twist density of helical rods with varying cross section radius are studied within the framework of the Kirchhoff rod model. It is shown that the twist density increases when the cross section radius…
The Kirchhoff elastic theory of thin filaments with spontaneous curvature is employed in the understanding of the onset of the kink transitions observed in short DNA rings. Dynamical analysis shows that when its actual curvature is less…
The equilibrium three dimensional shape of relatively short loops of DNA is studied using an elastic model that takes into account anisotropy in bending rigidities. Using a reasonable estimate for the anisotropy, it is found that cyclized…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modelled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of…
We numerically study stochastic resonance in the unzipping of a model double-stranded DNA by a periodic force. We observe multiple peaks in stochastic resonance in the output signal as the driving force frequency is varied for different…
The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities caused by the double-helical structure. It is shown that the anisotropy introduces an effective nonlinear twist-bend…
Real filaments are not perfectly homogeneous. Most of them have various materials composition and shapes making their stiffnesses not constant along the arclength. We investigate the existence of circular and helical equilibrium solutions…
A computational and experimental approach based on a natural vibration of a free prismatic thick beam with square cross-section is suggested. Three variants of the beam sample were used (one with skin and two without skin). From 13 to 16…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
We have theoretically studied how resonant spin wave modes in an elliptical nanomagnet are affected by fabrication defects, such as small local thickness variations. Our results indicate that defects of this nature, which can easily result…
We study nonlinear resonance of coupled modes in nano-mechanical systems. To reveal the qualitative features of the dynamics, we consider the limiting cases, where the results can be obtained analytically. For 1:3 resonance, we find the…
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.…
We present a method for the in-situ determination of Young's modulus of a nanomechanical string resonator subjected to tensile stress. It relies on measuring a large number of harmonic eigenmodes and allows to access Young's modulus even…
We study the effective dynamics of ferromagnetic spin chains in presence of long-range interactions. We consider the Heisenberg Hamiltonian in one dimension for which the spins are coupled through power-law long-range exchange interactions…
We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both…
Stacks of intrinsic Josephson junctions in the resistive state can by efficiently synchronized by the internal cavity mode resonantly excited by the Josephson oscillations. We study the stability of dynamic coherent states near the…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…