Related papers: Models of DNA denaturation dynamics: universal pro…
We model long range correlations of nucleotides in the human DNA sequence using the long range one dimensional Ising model. We show that for distances between $10^3$ and $10^6$ bp the correlations show an universal behaviour and may be…
We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. These experiments are performed in the low-force regime from…
We study a random circuit model of constrained fracton dynamics, in which particles on a one-dimensional lattice undergo random local motion subject to both charge and dipole moment conservation. The configuration space of this system…
We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness…
Current-voltage characteristics and the linear resistance of the two-dimensional XY model with and without external uniform current driving are studied by Monte Carlo simulations. We apply the standard finite-size scaling analysis to get…
We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and…
The relaxation dynamics of a polymer wound around a fixed obstacle constitutes a fundamental instance of polymer with twist and torque and it is of relevance also for DNA denaturation dynamics. We investigate it by simulations and Langevin…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
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…
The extinction transition in the presence of a localized quenched defect is studied numerically. When the bulk is at criticality, the correlation length diverges and even an infinite system cannot "decouple" from the defect. The results…
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast.…
DNA deformations play crucial roles in many biological processes and material applications. During DNA deformation, DNA structural parameters often exhibit non-trivial and counterintuitive couplings, such as the twist-stretch and…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
A linear external perturbation is introduced in the action of the partition function of the random matrix model of RNA [G. Vernizzi, H. Orland and A. Zee, Phys. Rev. Lett. 94, 168103 (2005)]. It is seen that (i). the perturbation…
We revisit the kink-like parametrization of the deceleration parameter q(z), which considers a transition, at $z_t$, from cosmic deceleration to acceleration. In this parametrization the initial, at $z \gg z_t$, value of the q-parameter is…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
The dynamical equations describing the evolution of a physical system generally have a freedom in the choice of units, where different choices correspond to different physical systems that are described by the same equations. Since there…
One of the fundamental representation learning tasks is unsupervised sequential disentanglement, where latent codes of inputs are decomposed to a single static factor and a sequence of dynamic factors. To extract this latent information,…
We perform a single molecule force spectroscopy study to characterize the role of the size (molecular weight) and concentration of depleting agents on DNA condensation and on the stabilization of the double-helix structure, showing that…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…