Related papers: Expansion-modificaction systems: an explanation fo…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
We introduce a simple model for DNA evolution. Using the method of Peng et al.$^1$, we investigate the fractal properties of the system. For small chains and chains of intermediate size we find a fractal exponent that indicates the…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
This work is devoted to the study of the scaling, and the consequent power-law behavior, of the correlation function in a mutation-replication model known as the expansion-modification system. The latter is a biology inspired random…
We study the stochastic dynamics of sequences evolving by single site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
A new approach to describing correlation properties of complex dynamic systems with long-range memory based on a concept of additive Markov chains (Phys. Rev. E 68, 061107 (2003)) is developed. An equation connecting a memory function of…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in…
We calculate the mutual information function for each of the 24 chromosomes in the human genome. The same correlation pattern is observed regardless the individual functional features of each chromosome. Moreover, correlations of different…
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…
A theory of additive Markov chains with long-range memory, proposed earlier in Phys. Rev. E 68, 06117 (2003), is developed and used to describe statistical properties of long-range correlated systems. The convenient characteristics of such…
The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$…
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…
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 extend the notions of multipole and subsystem symmetries to more general {\it spatially modulated} symmetries. We uncover two instances with exponential and (quasi)-periodic modulations, and provide simple microscopic models in one, two…
Localization property in the disordered few-chain DNA systems with a long-range correlation is numerically investigated. We apply the chain system with the correlated disorder in the interchain and/or intrachain hoppings to the simple model…