Comment on "Can one predict DNA transcription start sites by studying bubbles?".
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DNA↗
Biomedical subjects
G Kalosakas
Publications and source records attributed to G Kalosakas.
ac conductivity in a DNA charge transport model.
We present the ac response of a DNA charge transport model, where the charge in the pi-stack interacts with the base-pair opening dynamics of the double strand. The calculated ac conductivity exhibits prominent peaks at polaron normal modes with electronic character, while weaker response appears at lower frequencies in the vibrational part of the polaron normal mode spectrum. Examples of the former, strong peaks, show redshifts as the amplitude of the ac field increases.
Computer Simulation↗
Breather-induced anomalous charge diffusion.
We present results on the diffusive motion of a charge interacting with the nonlinear dynamics of a thermalized underlying lattice. Signatures of anomalous diffusive properties are found at relatively high temperatures, where highly nonlinear excitations are present. A sublinear diffusion and a plateau appear before the standard long-time diffusion during the evolution of the mean-squared displacement and a significant degree of heterogeneity is exhibited among individual trajectories. Both properties are connected with the existence of vibrational hot spots (breather or multibreather excitations). Transport parameters of the charge are strongly affected in this case, as can be exemplified by the significant suppression of the diffusion coefficient D. The variation of D with temperature follows a stretched exponential law. The results are contrasted with those of the linearized case, in the absence of breathers. Such anomalous diffusion of a charge coupled to a thermalized lattice may be relevant in low-dimensional soft materials with strong anharmonicities, such as biomolecules, conducting polymers, etc.
Biopolymers↗
Multipeaked polarons in soft potentials.
We consider a minimal coupled charge / excitation-lattice model capturing a competition between linear polaronic self-trapping and the self-focusing effects of a soft nonlinear on-site potential. The standard single-humped polaron ceases to exist above a critical value of the coupling strength, closely related to the inflection point in the nonlinear potential. For couplings beyond this critical value, we find that successive multihumped polaronic solutions correspond to the lowest-energy stationary states of the system, which may admit interesting quantum resonance behavior.
Journal Article↗
Localization in physical systems described by discrete nonlinear Schrodinger-type equations.
Following a short introduction on localized modes in a model system, namely the discrete nonlinear Schrodinger equation, we present explicit results pertaining to three different physical systems described by similar equations. The applications range from the Raman scattering spectra of a complex electronic material through intrinsic localized vibrational modes, to the manifestation of an abrupt and irreversible delocalizing transition of Bose-Einstein condensates trapped in two-dimensional optical lattices, and to the instabilities of localized modes in coupled arrays of optical waveguides.
Journal Article↗
Delocalizing transition of Bose-Einstein condensates in optical lattices.
A Bose-Einstein condensate trapped in a two-dimensional optical lattice exhibits an abrupt transition manifested by the macroscopic wave function changing character from spatially localized to extended. Resulting from a bifurcation, this irreversible transition takes place as the interwell potential barrier is adiabatically decreased below a critical value. This is in sharp contrast to the corresponding one-dimensional case where such a bifurcation is absent and the extent of a localized mode is continuously tunable. We demonstrate how these phenomena can be experimentally explored.
Journal Article↗
Effects of intrinsic base-pair fluctuations on charge transport in DNA.
We investigate propagation of a charge carrier along intrinsically dynamically disordered double-stranded DNA. This is realized by the semiclassical coupling of the charge with a nonlinear lattice model that can accurately describe the statistical mechanics of the large amplitude fluctuations of the base pairs leading to the thermal denaturation transition of DNA. We find that the fluctuating intrinsic disorder can trap the charge and inhibit polaronic charge transport. The dependence of the mean distance covered by the charge carrier until its trapping, as a function of the energy of the fluctuations of the base pairs is also presented.
Base Pairing↗
Reactive dynamics on two-dimensional supports: Monte Carlo simulations and mean-field theory.
Monte Carlo simulations and mean-field models are used for the study of nonequilibrium reactions taking place on the surface of a catalyst. The model represents the catalytic reduction of NO with H2 on a Pt surface. Both Monte Carlo simulations and mean-field results predict the existence of a critical surface in the parameter space where the catalyst remains active for long times. Outside this critical region the catalyst remains active for finite times only. A discrete version of the mean-field model is proposed that takes into account the discrete, two-dimensional nature of the catalyst. For homogeneous initial conditions this improved model provides better quantitative agreement with the Monte Carlo results.
Journal Article↗