Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

Imperfect Imitation Can Enhance Cooperation

The promotion of cooperation on spatial lattices is an important issue in evolutionary game theory. This effect clearly depends on the update rule: it diminishes with stochastic imitative rules whereas it increases with unconditional imitation. To study the transition between both regimes, we propose a new evolutionary rule, which stochastically combines unconditional imitation with another imitative rule. We find that, surprinsingly, in many social dilemmas this rule yields higher cooperative levels than any of the two original ones. This nontrivial effect occurs because the basic rules induce a separation of timescales in the microscopic processes at cluster interfaces. The result is robust in the space of 2x2 symmetric games, on regular lattices and on scale-free networks.Comment: 4 pages, 4 figure

Continuous phase transition in polydisperse hard-sphere mixture

In a previous paper (J. Zhang {\it et al.}, J. Chem. Phys. {\bf 110}, 5318 (1999)) we introduced a model for polydisperse hard sphere mixtures that is able to adjust its particle-size distribution. Here we give the explanation of the questions that arose in the previous description and present a consistent theory of the phase transition in this system, based on the Percus-Yevick equation of state. The transition is continuous, and like Bose-Einstein condensation a macroscopic aggregate is formed due to the microscopic interactions. A BMCSL-like treatment leads to the same conclusion with slightly more accurate predictions.Comment: 7 pages including 5 figures in revte

Fundamental-measure density functional for the fluid of aligned hard hexagons: New insights in fundamental measure theory

In this article we obtain a fundamental measure functional for the model of aligned hard hexagons in the plane. Our aim is not just to provide a functional for a new, admittedly academic, model, but to investigate the structure of fundamental measure theory. A model of aligned hard hexagons has similarities with the hard disk model. Both share "lost cases", i.e. admit configurations of three particles in which there is pairwise overlap but not triple overlap. These configurations are known to be problematic for fundamental measure functionals, which are not able to capture their contribution correctly. This failure lies in the inability of these functionals to yield a correct low density limit of the third order direct correlation function. Here we derive the functional by projecting aligned hard cubes on the plane x+y+z=0. The correct dimensional crossover behavior of these functionals permits us to follow this strategy. The functional of aligned hard cubes, however, does not have lost cases, so neither had the resulting functional for aligned hard hexagons. The latter exhibits, in fact, a peculiar structure as compared to the one for hard disks. It depends on a uniparametric family of weighted densities through a new term not appearing in the functional for hard disks. Apart from studying the freezing of this system, we discuss the implications of the functional structure for new developments of fundamental measure theory.Comment: 10 pages, 9 figures, uses RevTeX

The underpotential deposition that should not be : Cu(1x1) on Au(111)

Peer reviewedPostprin

A white dwarf-neutron star relativistic binary model for soft gamma-ray repeaters

A scenario for SGRs is introduced in which gravitational radiation reaction effects drive the dynamics of an ultrashort orbital period X-ray binary embracing a high-mass donor white dwarf (WD) to a rapidly rotating low magnetised massive neutron star (NS) surrounded by a thick, dense and massive accretion torus. Driven by GR reaction, sparsely, the binary separation reduces, the WD overflows its Roche lobe and the mass transfer drives unstable the accretion disk around the NS. As the binary circular orbital period is a multiple integer number ($m$) of the period of the WD fundamental mode (Pons et al. 2002), the WD is since long pulsating at its fundamental mode; and most of its harmonics, due to the tidal interaction with its NS orbital companion. Hence, when the powerful irradiation glows onto the WD; from the fireball ejected as part of the disk matter slumps onto the NS, it is partially absorbed. This huge energy excites other WD radial ($p$-mode) pulsations (Podsiadlowski 1991,1995). After each mass-transfer episode the binary separation (and orbital period) is augmented significantly (Deloye & Bildsten 2003; Al\'ecyan & Morsink 2004) due to the binary's angular momentum redistribution. Thus a new adiabatic inspiral phase driven by GR reaction starts which brings the binary close again, and the process repeats. This model allows to explain most of SGRs observational features: their recurrent activity, energetics of giant superoutbursts and quiescent stages, and particularly the intriguing subpulses discovered by BeppoSAX (Feroci et al. 1999), which are suggested here to be {\it overtones} of the WD radial fundamental mode (see the accompanying paper: Mosquera Cuesta 2004b).Comment: This paper was submitted as a "Letter to the Editor" of MNRAS in July 17/2004. Since that time no answer or referee report was provided to the Author [MNRAS publication policy limits reviewal process no longer than one month (+/- half more) for the reviewal of this kind of submission). I hope this contribution is not receiving a similar "peer-reviewing" as given to the A. Dar and A. De Rujula's "Cannonball model for gamma-ray bursts", or to the R.K. Williams' "Penrose process for energy extraction from rotating black holes". The author welcomes criticisms and suggestions on this pape

A Cellular Automaton Model for Bi-Directionnal Traffic

We investigate a cellular automaton (CA) model of traffic on a bi-directional two-lane road. Our model is an extension of the one-lane CA model of {Nagel and Schreckenberg 1992}, modified to account for interactions mediated by passing, and for a distribution of vehicle speeds. We chose values for the various parameters to approximate the behavior of real traffic. The density-flow diagram for the bi-directional model is compared to that of a one-lane model, showing the interaction of the two lanes. Results were also compared to experimental data, showing close agreement. This model helps bridge the gap between simplified cellular automata models and the complexity of real-world traffic.Comment: 4 pages 6 figures. Accepted Phys Rev

What do emulsification failure and Bose-Einstein condensation have in common?

Ideal bosons and classical ring polymers formed via self-assembly, are known to have the same partition function, and so analogous phase transitions. In ring polymers, the analogue of Bose-Einstein condensation occurs when a ring polymer of macroscopic size appears. We show that a transition of the same general form occurs within a whole class of systems with self-assembly, and illustrate it with the emulsification failure of a microemulsion phase of water, oil and surfactant. As with Bose-Einstein condensation, the transition occurs even in the absence of interactions.Comment: 7 pages, 1 figure, typeset with EUROTeX, uses epsfi