Related papers: Periodically driven DNA: Theory and simulation
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
We study the transport and equilibration properties of a classical Heisenberg chain, whose couplings are random variables drawn from a one-parameter family of power-law distributions. The absence of a scale in the couplings makes the system…
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 consider three mechanisms of hysteresis phenomena in alternating magnetic field: the domain wall motion in a random medium, the nucleation and the retardation of magnetization due to slow (critical) fluctuations. We construct…
The time-dependent relaxation of a dynamical system may exhibit a power-law behavior that is superimposed by log-periodic oscillations. Sornette [Phys. Rep. 297, 239 (1998)] showed that this behavior can be explained by a discrete scale…
A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
We study both theoretically and experimentally switching dynamics in surface stabilized ferroelectric liquid crystal cells with asymmetric boundary conditions. In these cells the bounding surfaces are treated differently to produce…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
We demonstrate quantum signatures of deterministic nonlinear dynamics in the transition to superradiance of a generalized open Dicke model with different coupling strengths for the co- and counter-rotating light-matter interaction terms. A…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
The phonon dynamics in a one dimensional Heisenberg spin chain coupled to finite-frequency bond phonons is studied. We present the first detailed phonon spectra for these systems using Quantum Monte Carlo. The quantum phase transition is…
This work identifies the general approach for linearising any power system component in the harmonic domain, that is with respect to its Fourier series coefficients. This ability enables detailed harmonic analysis, and is key as more power…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
Frequency evolutions of hysteresis loop area and hysteresis tools such as remanence and coercivity of a kinetic Ising model in the presence of quenched bond dilution are investigated in detail. The kinetic equation describing the time…
Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of…
We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a…