Related papers: Base pair opening and bubble transport in a DNA do…
A physical model of a three-dimensional flow of a viscous bubbly fluid in an intermediate regime between bubble formation and breakage is presented. The model is based on mechanics and thermodynamics of a single bubble coupled to the…
We propose a model for DNA dynamics by introducing the helical structure through twist deformation in analogy with the structure of helimagnet and cholesteric liquid crystal system. The dynamics in this case is found to be governed by the…
The formation of bubble defects of the double stranded DNA is treated according to the Lifshits theory of disordered chains. A molecule of the DNA is modelled on a harmonic lattice with nearest neighbour interaction, elastic constants being…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solvent…
We investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent…
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…
An abstract DNA-type system is defined by a set of nonlinear kinetic equations with polynomial nonlinearities that admit soliton solutions associated with helical geometry. The set of equations allows for two different Lax representations:…
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…
The dynamics of Bose-Einstein condensates trapped in a deep optical lattice is governed by a discrete nonlinear equation (DNL). Its degree of nonlinearity and the intersite hopping rates are retrieved from a nonlinear tight-binding…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
An analysis of discrete systems is important for understanding of various physical processes, such as excitations in crystal lattices and molecular chains, the light propagation in waveguide arrays, and the dynamics of Bose-condensate…
We developed a low-energy model that can be used at any time to describe the dynamics of DNA bubbles at temperatures below the melting point. The Schr\"odinger equation associated with this problem is solved in imaginary time with a quantum…
We propose a model for a chain of particles coupled by nonlinear springs in which each mass has an internal mass and all interactions are assumed to be nonlinear. We show how to construct an asymptotic solution of this system using multiple…
The duality between deformations of elastic bodies and non-inertial flows in viscous liquids has been a guiding principle in decades of research. However, this duality is broken when a spheroidal or other doubly-curved liquid film is…
In the present work we study the nucleation of Dispersive shock waves (DSW) in the {defocusing}, discrete nonlinear Schr{\"o}dinger equation (DNLS), a model of wide relevance to nonlinear optics and atomic condensates. Here, we study the…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…