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J. M. Romero

Publications and source records attributed to J. M. Romero.

2 recordsLinked to original sources

Classical and quantum nonlinear localized excitations in discrete systems

Discrete breathers, or intrinsic localized modes, are spatially localized, time--periodic, nonlinear excitations that can exist and propagate in systems of coupled dynamical units. Recently, some experiments show the sighting of a form of discrete breather that exist at the atomic scale in a magnetic solid. Other observations of breathers refer to systems such as Josephson--junction arrays, photonic crystals and optical-switching waveguide arrays. All these observations underscore their importance in physical phenomena at all scales. The authors review some of their latest theoretical contributions in the field of classical and quantum breathers, with possible applications to these widely different physical systems and to many other such as DNA, proteins, quantum dots, quantum computing, etc.

nlin.PS↗

Modeling the thermal evolution of enzyme-created bubbles in DNA

The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the frame of a nonlinear dynamics approach we model the structure of the DNA duplex by a nonlinear network of coupled oscillators. We show that in fact from certain local structural distortions there originate oscillating localized patterns, that is radial and torsional breathers, which are associated with localized H-bond deformations, being reminiscent of the replication bubble. We further study the temperature dependence of these oscillating bubbles. To this aim the underlying nonlinear oscillator network of the DNA duplex is brought in contact with a heat bath using the Nos$\rm{\acute{e}}$-Hoover-method. Special attention is paid to the stability of the oscillating bubbles under the imposed thermal perturbations. It is demonstrated that the radial and torsional breathers, sustain the impact of thermal perturbations even at temperatures as high as room temperature. Generally, for nonzero temperature the H-bond breathers move coherently along the double chain whereas at T=0 standing radial and torsional breathers result.

q-bio.BM↗