Related papers: Why is the DNA Denaturation Transition First Order…
Poland-Scheraga models were introduced to describe the DNA denaturation transition. We give a rigorous and refined discussion of a family of these models. We derive possible scaling functions in the neighborhood of the phase transition…
We examine the statistical mechanics of a 1-dimensional gas of both adjoint and fundamental representation quarks which interact with each other through 1+1-dimensional U(N) gauge fields. Using large-N expansion we show that, when the…
The pattern of isentropes in the vicinity of a first-order phase transition is proposed as a key for a sub-classification. While the confinement--deconfinement transition, conjectured to set in beyond a critical end point in the QCD phase…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
Possibility of structured mixed phases at first order phase transitions is examined with taking into account of charge screening and surface effects. Hadron-quark phase transition in dense neutron star interior is considered, as concrete…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
We review the differences in first order phase transition of single and multi-component systems, and then discuss the crystalline structure expected to exist in the mixed confined deconfined phase of hadronic matter. The particular context…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…
The hypothesis that phase transitions originate from some topological change of the critical level hypersurface of the potential energy receives direct evident support by our study of the Bishop--Peyrard model of DNA thermal denaturation.
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…
For the DNA denaturation transition in the presence of random contact energies, or equivalently the disordered wetting transition, we introduce a Strong Disorder Renewal Approach to construct the optimal contacts in each disordered sample…
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…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
Using a field theory equivalent to a lattice version of the Poland-Scheraga (PS) model, the phase diagram for a long DNA molecule is derived in closed form. A one-loop renormalization group calculation for the generalized PS model with…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…