Related papers: A Simple Model for the DNA Denaturation Transition
Motivated by Yang-Mills dark energy model, we propose a new model by introducing a logarithmic correction. we find that this model can avoid the coincidence problem naturally and gives an equation of state $w$ smoothly crossing -1 if an…
Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the…
We consider a model of a polymer in $\mathbb{Z}^{d+1}$, constrained to join 0 and a hyperplane at distance $N$. The polymer is subject to a quenched nonnegative random environment. Alternatively, the model describes crossing random walks in…
In this conference proceeding, I discuss in detail the deconfinement to quark matter that takes place at large densities and/or temperatures. The first-order phase transition that is assumed to appear beyond a critical point gives rise to…
Various interacting lattice path models of polymer collapse in two dimensions demonstrate different critical behaviours. This difference has been without a clear explanation. The collapse transition has been variously seen to be in the…
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…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
The exact grand-canonical solution of a generalized interacting self-avoid walk (ISAW) model, placed on a Husimi lattice built with squares, is presented. In this model, beyond the traditional interaction $\omega_1=e^{\epsilon_1/k_B T}$…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
We describe linear and nonlinear transport across a single impurity Anderson model quantum dot with intermediate coupling to the leads, i.e., with tunnel coupling of the order of the thermal energy k_B T. The coupling is large enough that…
Self-organization of charged particles on a 2D lattice, subject to an anisotropic Jahn-Teller-type interaction and 3D Coulomb repulsion is investigated. In the mean-field approximation without Coulomb interaction, the system displays a…
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…
Self-avoiding walks are studied on the 3-simplex fractal lattice as a model of linear polymer conformations in a dilute, non-homogeneous solution. A model is supplemented with bending energies and attractive-interaction energies between…
We consider a model consisting of a self-avoiding polygon occupying a variable density of the sites of a square lattice. A fixed energy is associated with each $90^\circ$-bend of the polygon. We use a grand canonical ensemble, introducing…
We consider a self-avoiding walk model of polymer adsorption where the adsorbed polymer can be desorbed by the application of a force, concentrating on the case of the square lattice. Using series analysis methods we investigate the…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
Four on-lattice and six off-lattice models for active matter are studied numerically, showing that in contact with a wall, they display universal wetting transitions between three distinctive phases. The particles, which interact via…
Using the renormalization group approach, we consider the $O(N)\otimes O(M)$ model in four and more dimensions. We find that independently on $N$ and $M$, for $N\geq M\geq 2$, a transition can be of both the first and second order. In…
The Poland-Scheraga model describes the denaturation transition of two complementary - in particular, equally long - strands of DNA, and it has enjoyed a remarkable success both for quantitative modeling purposes and at a more theoretical…