Related papers: Effects of Sequence Disorder on DNA Looping and Cy…
Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a…
We propose that the distribution of DNA words in genomic sequences can be primarily characterized by a double Pareto-lognormal distribution, which explains lognormal and power-law features found across all known genomes. Such a distribution…
We study numerically the effect of sequence heterogeneity on the thermodynamic properties of a Poland-Scheraga model for DNA denaturation taking into account self-avoidance, i.e. with exponent c_p=2.15 for the loop length probability…
It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA…
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 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 nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated…
The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair…
We study the effect of quenched randomness in the arc-length dependent spontaneous curvature of a wormlike chain under tension. In the weakly bending approximation in two dimensions, we obtain analytic results for the force-elongation curve…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
We investigate the localization property of an electron in the disordered two-chain system (ladder model) with long-range correlation as a simple model for electronic property in DNA sequence. The chains are constructed by repetition of the…
In recent years, disorder has been shown to be crucial for the understanding of diluted magnetic semiconductors. Effects of disorder in these materials are reviewed with the emphasis on theoretical works. The types and spatial distribution…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
The model of the deformation of DNA macromolecule is developed with the accounting of two types of components of deformation: external and internal. External components describe the bend, twist and stretch of the double helix. The internal…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
The effects of quenched disorder on a single and many active run-and-tumble particles is studied in one dimension. For a single particle, we consider both the steady-state distribution and the particle's dynamics subject to disorder in…
We derive exact equations for the spectral density of sparse networks with an arbitrary distribution of the number of single edges and triangles per node. These equations enable a systematic investigation of the effect of clustering on the…
We study the effects of disorders on the transport through small interacting systems based on a two-dimensional Hubbard cluster of finite size connected to two noninteracting leads. This system can be regarded as a model for the…
We consider a model for an infectious disease in the onset of an outbreak. We introduce contact tracing incorporating a tracing delay. The effect of randomness in the delay and the effect of the length of this delay in comparison to the…
We study one-dimensional systems with random diagonal disorder but off-diagonal short-range correlations imposed by structural constraints. We find that these correlations generate effective conduction channels for finite systems. At a…