Related papers: A Simple Model for the DNA Denaturation Transition
Experimental nuclear level densities at excitation energies below the neutron threshold follow closely a constant-temperature shape. This dependence is unexpected and poorly understood. In this work, a fundamental explanation of the…
We introduce a three-dimensional lattice gas model to study the glass transition. In this model the interactions come from the excluded volume and particles have five arms with an asymmetrical shape, which results in geometric frustration…
We consider the extended Hubbard model on a two-dimensional square lattice at half-filling. The model is investigated using the strong coupling diagram technique. We sum infinite series of ladder diagrams allowing for full-scale charge and…
We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative…
The theory of first order density-driven phase transitions with frustration due to the long range Coulomb (LRC) interaction develop on paper I of this series is applied to the following physical systems: i) the low density electron gas ii)…
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…
The ground state of the antiferromagnetic XY model with a kagome lattice is characterized by a well developed accidental degeneracy. As a consequence the phase transition in this system consists in unbinding of pairs of fractional vortices.…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
The global phase behavior of the lattice restricted primitive model with nearest neighbor exclusion has been studied by grand canonical Monte Carlo simulations. The phase diagram is dominated by a fluid (or charge-disordered solid) to…
We investigate the phase diagram and critical behavior of a three-dimensional lattice CP(N-1) model in the large-N limit. Numerical evidence of first-order transitions is always observed for sufficiently large values of N, i.e. N>2 up to…
We study the large deviations of additive quantities, such as energy or current, in stochastic processes with intermittent reset. Via a mapping from a discrete-time reset process to the Poland-Scheraga model for DNA denaturation, we derive…
We predict a novel temperature-driven phase transition of DNA below the melting transition. The additional, intermediate phase exists for repetitive sequences, when the two strands have different lengths. In this phase, the excess bases of…
The study of the Ornstein--Zernike decay of subcritical two-point functions in equilibrium statistical mechanics has a history going back over a century. Despite this, the crossover from Ornstein--Zernike decay to critical power-law decay…
This paper looks at the early theory of phase transitions. It considers a group of related concepts derived from condensed matter and statistical physics. The key technical ideas here go under the names of "singularity", "order parameter",…
An exactly solvable reaction-diffusion model consisting of first-class particles in the presence of a single second-class particle is introduced on a one-dimensional lattice with periodic boundary condition. The number of first-class…
Lipid monolayers and bilayers have been used as experimental models for the investigation of membrane thermal transitions. The main transition takes place near ambient temperatures for several lipids and reflects the order-disorder…
As the density of matter increases, atomic nuclei disintegrate into nucleons and, eventually, the nucleons themselves disintegrate into quarks. The phase transitions (PT's) between these phases can vary from steep first order to smooth…
Experiments and theory have shown that cell monolayers and epithelial tissues exhibit solid-liquid and glass-liquid transitions. These transitions are biologically relevant to our understanding of embryonic development, wound healing, and…
We study the disruption process of hierarchical 3-body systems with bodies of comparable mass. Such systems have long survival times that vary by orders of magnitude depending on the initial conditions. By comparing with 3-body numerical…