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

Reaching the millennium development goal for child mortality : improving equity and efficiency in Ecuador's health budget

health care; infant mortality; health policy;

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

A theorem on the absence of phase transitions in one-dimensional growth models with onsite periodic potentials

We rigorously prove that a wide class of one-dimensional growth models with onsite periodic potential, such as the discrete sine-Gordon model, have no phase transition at any temperature $T>0$. The proof relies on the spectral analysis of the transfer operator associated to the models. We show that this operator is Hilbert-Schmidt and that its maximum eigenvalue is an analytic function of temperature.Comment: 6 pages, no figures, submitted to J Phys A: Math Ge

Catastrophic regime shifts in model ecological communities are true phase transitions

Ecosystems often undergo abrupt regime shifts in response to gradual external changes. These shifts are theoretically understood as a regime switch between alternative stable states of the ecosystem dynamical response to smooth changes in external conditions. Usual models introduce nonlinearities in the macroscopic dynamics of the ecosystem that lead to different stable attractors among which the shift takes place. Here we propose an alternative explanation of catastrophic regime shifts based on a recent model that pictures ecological communities as systems in continuous fluctuation, according to certain transition probabilities, between different micro-states in the phase space of viable communities. We introduce a spontaneous extinction rate that accounts for gradual changes in external conditions, and upon variations on this control parameter the system undergoes a regime shift with similar features to those previously reported. Under our microscopic viewpoint we recover the main results obtained in previous theoretical and empirical work (anomalous variance, hysteresis cycles, trophic cascades). The model predicts a gradual loss of species in trophic levels from bottom to top near the transition. But more importantly, the spectral analysis of the transition probability matrix allows us to rigorously establish that we are observing the fingerprints, in a finite size system, of a true phase transition driven by background extinctions.Comment: 19 pages, 11 figures, revised versio

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

Fluid-fluid phase separation in hard spheres with a bimodal size distribution

The effect of polydispersity on the phase behaviour of hard spheres is examined using a moment projection method. It is found that the Boublik-Mansoori-Carnahan-Starling-Leland equation of state shows a spinodal instability for a bimodal distribution if the large spheres are sufficiently polydisperse, and if there is sufficient disparity in mean size between the small and large spheres. The spinodal instability direction points to the appearance of a very dense phase of large spheres.Comment: 7 pages, 3 figures, moderately REVISED following referees' comments (original was 4 pages, 3 postscript figures