Dependence on temperature and GC content of bubble length distributions in DNA

We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bubble sizes up to the order of a hundred base pairs. The dependence of the parameters of bubble length distribution on temperature and the GC content is investigated. We provide simple expressions which approximately describe these relations. The variation of the average bubble length is also presented. We find a temperature dependence of the exponent c that appears in the distribution of bubble lengths. If an analogous dependence exists in the loop entropy exponent of real DNA, it may be relevant to understand overstretching in force-extension experiments.Comment: 8 pages, 6 figures. Published on The Journal of Chemical Physic

Comment on "Can one predict DNA Transcription Start Sites by Studying Bubbles?"

Comment on T.S. van Erp, S. Cuesta-Lopez, J.-G. Hagmann, and M. Peyrard, Phys. Rev. Lett. 95, 218104 (2005) [arXiv: physics/0508094]

Atomistic potential for graphene and other sp2^2 carbon systems

We introduce a torsional force field for sp$^2$ carbon to augment an in-plane atomistic potential of a previous work (Kalosakas et al, J. Appl. Phys. {\bf 113}, 134307 (2013)) so that it is applicable to out-of-plane deformations of graphene and related carbon materials. The introduced force field is fit to reproduce DFT calculation data of appropriately chosen structures. The aim is to create a force field that is as simple as possible so it can be efficient for large scale atomistic simulations of various sp$^2$ carbon structures without significant loss of accuracy. We show that the complete proposed potential reproduces characteristic properties of fullerenes and carbon nanotubes. In addition, it reproduces very accurately the out-of-plane ZA and ZO modes of graphene's phonon dispersion as well as all phonons with frequencies up to 1000~cm$^{-1}$.Comment: 9 pages, 6 figure

Quantum Bose Josephson Junction with binary mixtures of BECs

We study the quantum behaviour of a binary mixture of Bose-Einstein condensates (BEC) in a double-well potential starting from a two-mode Bose-Hubbard Hamiltonian. We focus on the small tunneling amplitude regime and apply perturbation theory up to second order. Analytical expressions for the energy eigenvalues and eigenstates are obtained. Then the quantum evolution of the number difference of bosons between the two potential wells is fully investigated for two different initial conditions: completely localized states and coherent spin states. In the first case both the short and the long time dynamics is studied and a rich behaviour is found, ranging from small amplitude oscillations and collapses and revivals to coherent tunneling. In the second case the short-time scale evolution of number difference is determined and a more irregular dynamics is evidenced. Finally, the formation of Schroedinger cat states is considered and shown to affect the momentum distribution.Comment: 14 pages, 4 figure

Multi-peaked localized states of DNLS in one and two dimensions

Multi-peaked localized stationary solutions of the discrete nonlinear Schrodinger (DNLS) equation are presented in one (1D) and two (2D) dimensions. These are excited states of the discrete spectrum and correspond to multi-breather solutions. A simple, very fast, and efficient numerical method, suggested by Aubry, has been used for their calculation. The method involves no diagonalization, but just iterations of a map, starting from trivial solutions of the anti-continuous limit. Approximate analytical expressions are presented and compared with the numerical results. The linear stability of the calculated stationary states is discussed and the structure of the linear stability spectrum is analytically obtained for relatively large values of nonlinearity.Comment: 34 pages, 12 figure

Nonlocal interactions in doped cuprates: correlated motion of Zhang-Rice polarons

In-plane, inter-carrier correlations in hole doped cuprates are investigated by ab initio multiconfiguration calculations. The dressed carriers display features that are reminiscent of both Zhang-Rice (ZR) CuO4 singlet states and Jahn-Teller polarons. The interaction between these quasiparticles is repulsive. At doping levels that are high enough, the interplay between long-range unscreened Coulomb interactions and long-range phase coherence among the O-ion half-breathing vibrations on the ZR plaquettes may lead to a strong reduction of the effective adiabatic energy barrier associated to each polaronic state. Tunneling effects cannot be neglected for a relatively flat, multi-well energy landscape. We suggest that the coherent, superconducting quantum state is the result of such coherent quantum lattice fluctuations involving the in-plane O ions. Our findings appear to support models where the superconductivity is related to a lowering of the in-plane kinetic energy