Related papers: Models of DNA denaturation dynamics: universal pro…
The z-transform of a sequence is a classical tool used within signal processing, control theory, computer science, and electrical engineering. It allows for studying sequences from their generating functions, with many operations that can…
We study critical dynamics through time evolution of quantum field theories driven to a Lifshitz-like fixed point, with $z>1$, under relevant deformations. The deformations we consider are fast smooth quantum quenches, namely when the…
Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
We study numerically a disordered version of the model for DNA denaturation transition (DSAW-DNA) consisting of two interacting SAWs in 3d, which undergoes a first order transition in the homogeneous case. The two possible values eAT and…
We study entanglement degradation when noise on one share of an entangled pair is described by the dissipative Landau-Zener model. We show that spin-coupling direction to the environment significantly affects entanglement dynamics. In…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
A revised Marko-Siggia elastic model for DNA double helix [Macromolecules 27, 981 (1994)] is proposed, which includes the WLC bending energy and a new chiral twisting energy term. It is predicted that the mean helical repeat length (HRL)…
Linear rate equations are used to describe the cascading decay of an initial heavy cluster into fragments. We consider moments of arbitrary orders of the mass multiplicity spectrum and derive scaling properties pertaining to their time…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Dielectric spectroscopy is used to investigate fundamental length scales of 146 bp short-fragment (nucleosomal) dilute Na-DNA solutions. Two relaxation modes are detected: the high- and the low-frequency mode. Dependence of the…
The oxidative damage of DNA is a compelling issue in molecular biophysics as it plays a vital role in the epigenetic control of gene expression and is believed to be associated with mutagenesis, carcinogenesis, and ageing. To understand the…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
Recently Garel, Monthus and Orland (Europhys. Lett. v 55, 132 (2001)) considered a model of DNA denaturation in which excluded volume effects within each strand are neglected, while mutual avoidance is included. Using an approximate scheme…
We study several one dimensional step flow models. Numerical simulations show that the slope of the profile exhibits scaling in all cases. We apply a scaling ansatz to the various step flow models and investigate their long time evolution.…
A mathematical model of genome degradation is proposed that takes into account a variable rate of mutation and increasing number of cells in a developing human organism. The model explains known properties of cancer development, in…
The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
We investigate two distinct universality classes for probe particles that move stochastically in a one-dimensional driven system. If the random force that drives the probe particles is fully generated by the current fluctuations of the…