Related papers: Renormalisation group determination of the order o…
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…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
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…
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other…
As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite and homogeneous Peyrard-Bishop DNA model. We find and classify…
We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness…
We study numerically a disordered version of the model for DNA denaturation transition (DSAW-DNA) consisting of two interacting SAWs in 3d, which undergoes a first order transition in the homogeneous case. The two possible values eAT and…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
This paper argues that the ideas underlying the renormalization group technique used to characterize phase transitions in condensed matter systems could be useful for distinguishing computational complexity classes. The paper presents a…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
We present a precise equivalence of the Lifson-Poland-Scheraga model with wetting models. Making use of a representation of the former model in terms of random matrices, we obtain, in the limit of weak disorder, a mean--field approximation,…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
We theoretically study the electromagnetic interaction in Dirac systems with $N$ nodes by using the renormalization group, which is relevant to the quantum critical phenomena of topological phase transition ($N=1$) and Weyl semimetals…
Studies of first-order phase transitions through the use of the exact renormalization group are reviewed. In the first part the emphasis is on universal aspects: We discuss the universal critical behaviour near weakly first-order phase…
We study the universal critical behaviour near weakly first-order phase transitions for a three-dimensional model of two coupled scalar fields -- the cubic anisotropy model. Renormalization-group techniques are employed within the formalism…
Based on the direct method of molecular dynamics, the temperature dependence of energy, partition function, entropy and free energy, describing the first-order phase transition, is calculated for the classical Peyrard-Bishop-Dauxois model…
A general theory for the melting of two dimensional solids explaining the universal and non-universal properties is an open problem up to date. Although the celebrated KTHNY theory have been able to predict the critical properties of the…
We present a systematic study to test a recently introduced phenomenological renormalization group, proposed to coarse-grain data of neural activity from their correlation matrix. The approach allows, at least in principle, to establish…