Related papers: Generalized Poland-Scheraga denaturation model and…
We show that when an isolated doublet of unbound states of a physical system becomes degenerate for some values of the control parameters of the system, the energy hypersurfaces representing the complex resonance energy eigenvalues as…
The broken symmetric phase of scalar models exhibits an infrared fixed point which is induced by the degenerate effective potential. The definition of the correlation length in the infrared regime enables us to determine the type of the…
We discuss an innovative method for the description of inhomogeneous phases designed to improve the standard Ginzburg-Landau expansion. The method is characterized by two key ingredients. The first one is a moving average of the order…
A complete characterization of the structure of nuclei can be obtained by combining information arising from inelastic scattering, Coulomb excitation and $\gamma-$decay, together with one- and two-particle transfer reactions. In this way it…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications,…
The generalized copolymer model is a disordered system built on a discrete renewal process with inter-arrival distribution that decays in a regularly varying fashion with exponent $1+ \alpha\geq 1$. It exhibits a localization transition…
We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our…
Heterogeneity and uncertainty in a composite microstructure lead to either computational bottlenecks if modeled rigorously or to solution inaccuracies in the stress field and failure predictions if approximated. Although methods suitable…
One-dimensional thermodynamic instabilities are phase transitions not prohibited by Landau's argument, because the energy of the domain wall (DW) which separates the two phases is infinite. Whether they actually occur in a given system of…
We consider a model for strand separation in negatively supercoiled dna, and study the effect of supercoiling on the localization of denaturation, using notions from statistical mechanics. The model is based on on mean field Ising system,…
The denaturation of double-stranded DNA as function of force and temperature is discussed. At room temperature, sequence heterogeneity dominates the physics of single molecule force-extension curves starting about 7 piconewtons of below a…
The quantum dynamics of a two-dimensional charged spin $1/2$ particle is studied for general, symmetry--free curved surfaces and general, nonuniform magnetic fields that are, when different from zero, orthogonal to the defining two surface.…
We consider the hierarchical disordered pinning model studied in [9], which exhibits a localization/delocalization phase transition. In the case where the disorder is i.i.d. (independent and identically distributed), the question of…
Simulations of the generation of the atomic polarization is necessary for interpreting the second solar spectrum. For this purpose, it is important to rigorously determine the effects of the isotropic collisions with neutral hydrogen on the…
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent…
Recent biological evidence suggests the presence of a two-phase ageing process in several species. We introduce a system of two age-structured partial differential equations (PDE) representing two phases of ageing of a wild population. The…
We study DNA adsorption and renaturation in a water-phenol two-phase system, with or without shaking. In very dilute solutions, single-stranded DNA is adsorbed at the interface in a salt-dependent manner. At high salt concentrations the…
We study the steady-state behavior of the open Dicke model, which describes the collective interaction of $N$ spin-$1/2$ particles with a lossy, quantized cavity mode and exhibits a superradiant phase transition above a critical…