Related papers: Bethe approximation for a DNA-like self-avoiding w…
We develop the technique of Thermodynamic Bethe Ansatz to investigate the ground state and the spectrum in the thermodynamic limit of the staggered $XXZ$ models proposed recently as an example of integrable ladder model. This model appeared…
The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of…
We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we…
We provide analytical solutions to the thermodynamic Bethe ansatz equations in the large and small density approximations. We extend results previously obtained for leading order behaviour of the scaling function of affine Toda field…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
Using the Bethe ansatz we obtain in a determinant form the exact solution of the master equation for the conditional probabilities of the totally asymmetric exclusion process with particle-dependent hopping rates on Z. From this we derive a…
The solvability of the three-dimensional O($N$) scalar field theory in the large $N$ limit makes it an ideal toy model exhibiting "walking" behavior, expected in some SU($N$) gauge theories with a large number of fermion flavors. We study…
Three, interrelated biologically-relevant examples of biased random walks are presented: (1) A model for DNA melting, modelled as DNA unzipping, which provides a way to illustrate the role of the Boltzmann factor in a venue well-known to…
Given a locally consistent set of reduced density matrices, we construct approximate density matrices which are globally consistent with the local density matrices we started from when the trial density matrix has a tree structure. We…
We present the Bethe ansatz solution for the discrete time zero range and asymmetric exclusion processes with fully parallel dynamics. The model depends on two parameters: $p$, the probability of single particle hopping, and $q$, the…
Recent experiments and computer simulations show that supercooled liquids around the glass transition temperature are "dynamically heterogeneous" [1]. Such heterogeneity is expected from the random first order transition theory of the glass…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
A new class of bootstrap percolation models in which particle culling occurs only for certain numbers of nearest neighbours is introduced and studied on a Bethe lattice. Upon increasing the density of initial configuration they undergo…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i)…