Related papers: Nonlinear excitations in DNA: Aperiodic models vs …
It is tempting to believe that we now own the genome. The ability to read and re-write it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles heel exposed by all of the genomic data that has…
A widespread approach to characterise the aggregated flexibility of active distribution networks (ADNs) is to estimate the boundary of the feasible network operating areas using convex polygons in the P-Q space. However, such approximations…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
We have examined the dynamical behavior of the kink solutions of the one-dimensional sine-Gordon equation in the presence of a spatially periodic parametric perturbation. Our study clarifies and extends the currently available knowledge on…
We analyze typical models which intend to describe (parts of) the dynamics of H-Bonds in DNA. We show that these models generically allow for nonlinear localized excitatons (NLEs) (discrete breathers). We especially study the scattering of…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
In this paper, we study the single kink and the kink-antikink collisions of a nonlinear beam equation bearing a fourth-derivative term. We numerically explore some of the key characteristics of the single kink both in its standing wave and…
The response of a semiflexible polyelectrolyte chain to stretching in the regimes of moderate and weak screening is studied theoretically, with a special focus on DNA experiments. By using the nonlinear Poisson--Boltzmann description of…
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…
We consider Klein-Gordon models with a $\delta$-correlated spatial disorder. We show that the properties of immobile kinks exhibit strong dependence on the assumptions as to their statistical distribution over the minima of the effective…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…
We address the problem of a front propagation in chains with a bi-stable nondegenerate on-site potential and a nonlinear gradient coupling. For a generic nonlinear coupling, one encounters a special regime of transitions, characterized by…
The way tension propagates along a chain is a key to govern many of anomalous dynamics in macromolecular systems. After introducing the weak and the strong force regimes of the tension propagation, we focus on the latter, in which the…
A discrete nonlinear Schrodinger (NLS) model with long-range dispersive interactions describing the dynamical structure of DNA is proposed. Dispersive interactions of two types: the power dependence $r^{-s}$ and the exponential dependence…
When a quantum system exhibiting a second order phase transition is quenched across the critical point in large but finite time, the dynamics are not adiabatic in the critical region and the Kibble-Zurek (KZ) mechanism provides a framework…
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…
Based on the result of an unzipping phase transition by a force in a model of DNA, we hypothesize that the DnaA-type proteins act as a pulling agent with a force slightly less than the critical force for unzipping. The dynamic (space-time)…
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…