Related papers: A Simple Model for the DNA Denaturation Transition
In this comment we argue that while the conclusions in the original paper (Y. Kafri, D. Mukamel and L. Peliti, Phys. Rev. Lett. 85, 4988 (2000)) are correct for asymptotically long DNA chains, they do not apply to the chains used in typical…
Symmetry-breaking order at low temperatures is often accompanied by slow relaxation dynamics, due to diverging free-energy barriers arising from interfaces between different ordered states. Here, we extend this correspondence to classical…
In these proceedings, we first summarize some general properties of phase transitions in the presence of quenched disorder, with emphasis on the following points: the need to distinguish typical and averaged correlations, the possible…
Polymer chains with hard-core interaction on a two-dimensional lattice are modeled by directed random walks. Two models, one with intersecting walks (IW) and another with non-intersecting walks (NIW) are presented, solved and compared. The…
We study a heteropolymer model with random contact interactions introduced some time ago as a simplified model for proteins. The model consists of self-avoiding walks on the simple cubic lattice, with contact interactions between nearest…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We combine the microcanonical formulation of lattice gauge theories (LGTs) developed by Callaway and the microcanonical inflection point analysis (MIPA) proposed by Bachmann et al. to achieve a systematic characterization of phase…
Near the melting transition the bending elastic constant, $\kappa$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $\kappa$ with temperature is…
The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has…
We study numerically the effect of sequence heterogeneity on the thermodynamic properties of a Poland-Scheraga model for DNA denaturation taking into account self-avoidance, i.e. with exponent c_p=2.15 for the loop length probability…
In this short note, a correction is made to the recently proposed solution [1] to a 1D biased diffusion model for linear DNA translocation and a new analysis will be given to the data in [1]. It was pointed out [2] by us recently that this…
An 1d model with time-dependent random hopping is proposed to describe charge transport in DNA. It admits to investigate both diffusion of electrons and their tunneling between different sites in DNA. The tunneling appears to be strongly…
We investigate in this paper the ground state and the nature of the transition from an orientational ordered phase at low temperature to the disordered state at high temperature in a molecular crystal. Our model is a Potts model which takes…
A system of neutral atoms trapped in an optical lattice and dispersively coupled to the field of an optical cavity can realize a variation of the Bose-Hubbard model with infinite-range interactions. This model exhibits a first order quantum…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
A dynamical study of the decay of a metastable state by quantum tunneling through an anisotropic, non separable, two-dimensional potential barrier is performed by the numerical solution of the time-dependent Schrodinger equation. Initial…
The present paper considers some classical ferromagnetic lattice--gas models, consisting of particles that carry $n$--component spins ($n=2,3$) and associated with a $D$--dimensional lattice ($D=2,3$); each site can host one particle at…
Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…