Related papers: Why is the DNA Denaturation Transition First Order…
It has been proposed (Phys. Rev. E {\bf 71}, 026121 (2005)) that unlike the short range contact process, a long-range counterpart may lead to the existence a discontinuous phase transition in one dimension. Aiming at exploring such link,…
We consider random walks evolving on two models of connected and undirected graphs and study the exact large deviations of a local dynamical observable. We prove, in the thermodynamic limit, that this observable undergoes a first-order…
An ever growing number of observational and theoretical evidence suggests that the deuterated fraction (column density ratio between a species containing D and its hydrogenated counterpart, Dfrac) is an evolutionary indicator both in the…
The hadron-quark phase transition in the interior of compact stars is investigated, when the transition proceeds through a mixed phase. The hadronic phase is described in the framework of relativistic mean-field theory, when also the…
We used the Transfer-Integral method to compute, with an uncertainty smaller than 5%, the six fundamental characteristic exponents of two dynamical models for DNA thermal denaturation and investigate the validity of the scaling laws. Doubts…
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…
Using a recently proposed classification scheme for phase transitions in finite systems [Phys.Rev.Lett.{\bf 84},3511 (2000)] we show that within the statistical standard model of nuclear multifragmentation the predicted phase transition is…
Possibility of structured mixed phases at first order phase transitions in neutron stars is re-examined by taking into account charge screening and surface effects. Transition from the hadron $npe$ phase to the quark phase is studied. Two…
The authors measure the persistence and contour lengths of DNA-psoralen complexes, as a function of psoralen concentration, for intercalated and crosslinked complexes. In both cases, the persistence length monotonically increases until a…
In recent years, quantum phase transitions have attracted the interest of both theorists and experimentalists in condensed matter physics. These transitions, which are accessed at zero temperature by variation of a non-thermal control…
The quasispecies model describes processes related to the origin of life and viral evolutionary dynamics. We discuss how the error catastrophe that reflects the transition from localized to delocalized quasispecies population is affected by…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
This paper investigates the dynamics of a deep neural network (DNN) learning interactions. Previous studies have discovered and mathematically proven that given each input sample, a well-trained DNN usually only encodes a small number of…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
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…
A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on…
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…
We investigate the low-energy properties of the orthogonal-dimer spin chain characterized by a frustrated dimer-plaquette structure. When the competing antiferromagnetic couplings are varied, the first-order quantum phase transition occurs…