Related papers: Periodically driven DNA: Theory and simulation
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…
Energy transport in 1-dimensional oscillator arrays has been extensively studied to date in the conservative case, as well as under weak viscous damping. When driven at one end by a sinusoidal force, such arrays are known to exhibit the…
In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind…
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physical properties have attracted significant interest both from…
We consider one-dimensional infinite chains of harmonic oscillators with random exchanges of momenta and long-range interaction potentials which have polynomial decay rate $|x|^{-\theta}, x \to \infty, \theta > 1$ where $x \in \mathbb{Z}$…
Dynamic hysteresis, the rate-dependent lagged response of materials to external fields, underpins applications from energy-efficient transformers to gas storage systems. A fundamental yet unresolved question is how the hysteresis loop area…
We propose a new mathematical tool for the study of transport properties of models for lattice vibrations in crystalline solids. By replication of dynamical degrees of freedom, we aim at a new dynamical system where the "local" dynamics can…
The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time…
The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of…
We study the classical dynamics of resonantly modulated large-spin systems in a strong magnetic field. We show that these systems have special symmetry. It leads to characteristic nonlinear effects. They include abrupt switching between…
Large-scale DNA deformation is ubiquitous in transcriptional regulation in prokaryotes and eukaryotes alike. Though much is known about how transcription factors and constellations of binding sites dictate where and how gene regulation will…
The hysteresis of the Ising model in a spatially homogeneous AC field is studied using both mean-field calculations and two-dimensional Monte Carlo simulations. The frequency dispersion and the temperature dependence of the hysteresis loop…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…
We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…
We examine kinematic dynamo action driven by an axisymmetric large scale flow that is superimposed with an azimuthally propagating non-axisymmetric perturbation with a frequency $\omega$. Although we apply a rather simple large scale…
Correlation length exponent $\nu$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length $s$ by means of atomic force microscopy (AFM). Linear DNA, up to…
We present numerical simulations of avalanches and critical phenomena associated with hysteresis loops, modeled using the zero-temperature random-field Ising model. We study the transition between smooth hysteresis loops and loops with a…