Related papers: Bethe approximation for a DNA-like self-avoiding w…
Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
We study the effect of phase separating diffusive dynamics on the mean time to extinction in several reaction-diffusion models with slow reactions. We consider a continuum theory similar to model AB, and a simple model where individual…
A discrete Boltzmann model (DBM) is developed to investigate the hydrodynamic and thermodynamic non-equilibrium (TNE) effects in phase separation processes. The interparticle force drives changes and the gradient force, induced by gradients…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
The nested algebraic Bethe ansatz is presented for the anisotropic supersymmetric $U$ model maintaining quantum supersymmetry. The Bethe ansatz equations of the model are obtained on a one-dimensional closed lattice and an expression for…
We study the features on the unzipping process of a modified version of the Peyrard-Bishop- Dauxois model. We show that the inclusion of a barrier in the on-site potential allows for the existence of stable domain wall solutions between…
Exactly solvable models of ultracold Fermi gases are reviewed via their thermodynamic Bethe Ansatz solution. Analytical and numerical results are obtained for the thermodynamics and ground state properties of two- and three-component…
We analyze the Bethe ansatz equations describing the complete spectrum of the transition matrix of the partially asymmetric exclusion process on a finite lattice and with the most general open boundary conditions. We extend results obtained…
We study the localisation of lattice polymer models near a permeable interface in two dimensions. Localisation can arise due to an interaction between the polymer and the interface, and can be altered by a preference for the bulk solvent on…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
We study the dynamical low temperature behaviour of the Ising spin glass on the Bethe lattice. Starting from Glauber dynamics we propose a cavity like Ansatz that allows for the treatment of the slow (low temperature) part of dynamics.…
We studied how the inhomogeneity of a sequence affects the phase transition that takes place at DNA melting. Unlike previous works, which considered thermodynamic quantities averaged over many different inhomogeneous sequences, we focused…
For every physical model defined on a generic graph or factor graph, the Bethe $M$-layer construction allows building a different model for which the Bethe approximation is exact in the large $M$ limit and it coincides with the original…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
We present a new and efficient method for deriving finite-size effects in statistical physics models solvable by Bethe Ansatz. It is based on the study of the functional that maps a function to the sum of its evaluations over the Bethe…
We give a pedagogical introduction to the thermodynamic Bethe ansatz, a method that allows us to describe the thermodynamics of integrable models whose spectrum is found via the (asymptotic) Bethe ansatz. We set the stage by deriving the…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…