Related papers: A Simple Model for the DNA Denaturation Transition
We study the phase transition in a system composed of dimers interacting with each other via a nearest-neighbor (NN) exchange $J$ and competing interactions taken from a truncated dipolar coupling. Each dimer occupies a link between two…
A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular…
We introduce a 3D compact U(1) lattice gauge theory having nonlocal interactions in the temporal direction, and study its phase structure. The model is relevant for the compact QED$_3$ and strongly correlated electron systems like the t-J…
We investigate the generalized Poland-Scheraga model, which is used in the bio-physical literature to model the DNA denaturation transition, in the case where the two strands are allowed to be non-complementary (and to have different…
We study via Monte Carlo simulation a generalisation of the so-called vertex interacting self-avoiding walk (VISAW) model on the square lattice. The configurations are actually not self-avoiding walks but rather restricted self-avoiding…
In the framework of the Poland Scheraga model of DNA denaturation, we derive a recursion relation for the partition function of double stranded DNA, allowing for mismatches between the two strands. This relation is studied numerically using…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
We investigate neighbor-avoiding walks on the simple cubic lattice in the presence of an adsorbing surface. This class of lattice paths has been less studied using Monte Carlo simulations. Our investigation follows on from our previous…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
We numerically study the wetting (adsorption) transition of a polymer chain on a disordered substrate in 1+1 dimension.Following the Poland-Scheraga model of DNA denaturation, we use a Fixman-Freire scheme for the entropy of loops. This…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
The collapse transition of an isolated polymer has been modelled by many different approaches, including lattice models based on self-avoiding walks and self-avoiding trails. In two dimensions, previous simulations of kinetic growth trails,…
In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation…
Studying the properties of the solvent around proteins, we propose a much more sophisticated model of solvation than temperature-independent pairwise interactions between monomers, as is used commonly in lattice representations. We applied…
A two-dimensional square-lattice model for the formation of secondary structures in proteins, the hydrogen-bonding model, is extended to include the effects of solvent quality. This is achieved by allowing configuration-dependent…
We study the thermodynamic phase transition of a spin Hamiltonian comprising two 3D magnetic sublattices. Each sublattice contains XY spins coupled by the usual bilinear exchange, while spins in different sublattices only interact via…
In this paper we review a series of results obtained for 1D and 2D simple N-body dynamical models with infinite-range attractive interactions and without short distance singularities. The free energy of both models can be exactly obtained…