ARCHILLA , Juan F. R.

Novel mechanisms of defect annealing in solids are discussed, which are based on the large amplitude anharmonic lattice vibrations, a.k.a. intrinsic localized modes or discrete breathers (DBs). A model for amplification of defect annealing rate in Ge by low energy plasma-generated DBs is proposed, in which, based on recent atomistic modelling,...

Muscovite mica is a mineral in which the tracks of charged swift particles, from radioactivity or cosmic rays, can be recorded and made visible by decoration with the mineral magnetite. Also, the tracks of quasi-one-dimensional lattice excitations, called quodons, moving along close-packed directions can be recorded. Most quodon tracks evolve...

The developments in hyperconductivity, the loss-free transmission of electric charge at room temperature and above, due to the ballistic transport of electric charge in crystals with quasi-layered structure, are reported. The electric charge is carried by quodons, a type of mobile nonlinear intrinsic localized mode of lattice excitation...

The history of the experimental study of nonlinear lattice excitations in layered silicate materials, when exposed to swift particles of appreciable momentum is described briefly. For brevity, and because of the difficulty of studying the structure of the lattice excitations, the term quodon was adopted to reflect their ballistic and...

We propose two classes of symplecticity-preserving symmetric splitting methods for semi-classical Hamiltonian dynamics of charge transfer by intrinsic localized modes in nonlinear crystal lattice models. We consider, without loss of generality, one-dimensional crystal lattice models described by classical Hamiltonian dynamics, whereas the...

We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi–site breathers in a DNA–shaped double strand. Within a network model of the double helix we take individual motions of the bases within the base pair plane into account. The resulting H-bridge deformations may be asymmetric with respect to the...

We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorpo- rating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special attention to the opening-closing dynamics of double-stranded DNA molecules which are forced into...

We study nonlinear excitations propagating in a hexagonal layer which is a model for the cation layer of silicates. We consider their properties in the frequency–momentum or ω − k representation, extending the theory on pterobreathers in their moving frame for the first time to two dimensions. It can also be easily extended to three dimensions....

In this work we propose new structure-preserving multiple time stepping methods for numerical simulation of charge transfer by intrinsic localized modes in nonlinear crystal lattice models. We consider, without loss of generality, one-dimensional crystal lattice models described by classical Hamiltonian dynamics, whereas charge (electron or...

Time-periodic localized oscillations occur in a variety of contexts, in particular in weakly coupled anharmonic lattices and in disordered harmonic networks of oscillators, where they are known respectively as discrete breathers and Anderson modes. It is shown numerically in some examples of systems which interpolate between these two limits...

We report on studies of hyperconductivity in which electric charge moves in a solid in the absence of an applied electric field. This is indicative of a non-Ohmic mechanism. Our results are consistent with charge being carried ballistically by mobile nonlinear lattice excitations called quodons moving along close-packed atomic chains in the...

Reaction rate theory in solids is modified taking into account intrinsic localized modes or discrete breathers (DBs) that can appear in crystals with sufficient anharmonicity resulting in violation of Arrhenius law. Large amplitude oscillations of atoms about their equilibrium positions in the lattice cause local potentials of alternating sign,...

We study a model for polaron-like charge transportmechanism along DNA molecules with emphasis on the impact of parametrical and structural disorder. Our model Hamiltonian takes into account the coupling of the charge carrier to two different kind of modes representing fluctuating twist motions of the base pairs and H-bond distortions within the...

We study the transport of charge due to polarons in a model of DNA which takes in account its 3D structure and the coupling of the electron wave function with the H–bond distortions and the twist motions of the base pairs. Perturbations of the ground states lead to moving polarons which travel long distances. The influence of parametric and...

The formation of bubbles in nucleic acids (NAs) is fundamental in many biological processes such as DNA replication, recombination, telomere formation and nucleotide excision repair, as well as RNA transcription and splicing. These processes are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the...

In this article we perform a thorough analysis of breathers in a one-dimensional model for a layered silicate for which there exists fossil and experimental evidence of moving excitations along the close-packed lines of the K+ layers. Some of these excitations are likely breathers with a small energy of about 0.2 eV as the numerically obtained...

We study the interaction of moving localized oscillations with a local inhomogeneity in a discrete nonlinear Hamiltonian system. We conjecture that resonance with a static nonlinear localized oscillation centered at the local inhomogeneity is a necessary condition for observing the trapping phenomenon. Analytic calculations and numerical...

Chains of identical ions, for which the dominant interaction is the electrostatic repulsion, appear in layered silicates. The ions can move almost from site to site. The chains do not explode because the surrounding media has a net negative charge which screens the Coulomb's repulsion and become attractive when the ions separate two much....

Most of the studies on mathematical models of DNA are limited to next neighbor interaction. However, the coupling between base pairs is thought to be caused by dipole interaction, and, when the DNA strand is bent, the distances between base pairs become shorter, therefore the interactions with distant base pairs have to be taken into account....

This paper deals with the problem of a particle that diffuses in a potential with a reflecting barrier and has a point of stable equilibrium and a point of unstable equilibrium. Based on the exact solutions obtained earlier for the Fokker-Planck equation of a class of these models, we analyze the behavior of the probability density, the mean...

Lie theory of transformation groups is applied to the study of lambda-omega reaction-diffusion systems in two-dimensional media. Our study proves that they are invariant with respect to a five-parameter symmetry group. Multiple types of invariant solutions with physical interest are possible, and some of them can be found in the literature...