Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation

Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of broken bonds, or bubble, compared to the double stranded state, the inclusion of the molecular conformational degrees of freedom in a more general mesoscopic model is needed. In this paper we do so by presenting a 1D Ising model, which describes the internal base pair states, coupled to a discrete worm like chain model describing the chain configurations [J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. 99, 088103 (2007)]. This coupled model is exactly solved using a transfer matrix technique that presents an analogy with the path integral treatment of a quantum two-state diatomic molecule. When the chain fluctuations are integrated out, the denaturation transition temperature and width emerge naturally as an explicit function of the model parameters of a well defined Hamiltonian, revealing that the transition is driven by the difference in bending (entropy dominated) free energy between bubble and double-stranded segments. The calculated melting curve (fraction of open base pairs) is in good agreement with the experimental melting profile of polydA-polydT. The predicted variation of the mean-square-radius as a function of temperature leads to a coherent novel explanation for the experimentally observed thermal viscosity transition. Finally, the influence of the DNA strand length is studied in detail, underlining the importance of finite size effects, even for DNA made of several thousand base pairs.Comment: Latex, 28 pages pdf, 9 figure

Ionic Capillary Evaporation in Weakly Charged Nanopores

Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration "liquid" phase to an ionic-exclusion "vapor" phase, controlled by nanopore-modified ionic correlations and dielectric repulsion. For weakly charged nanopores, this pseudotransition survives and may shed light on the mechanism behind the rapid switching of nanopore conductivity observed in experiments.Comment: This version is accepted for publication in PR

AN INTEGRATED APPROACH TO PREVENT THE EROSION OF SALT MARSHES IN THE LAGOON OF VENICE

The loss of coastal habitats is a widespread problem in Europe. To protect the intertidal salt marshes of the lagoon of Venice from the erosion due to natural and human causes which is diffusely and intensely impacting them, the European Commission has funded the demonstrative project LIFE VIMINE. LIFE VIMINE aims to protect the most interior, hard-to-access salt marshes in the northern lagoon of Venice through an integrated approach, whose core is the prevention of erosion through numerous, small but spatially-diffuse soil-bioengineering protections works, mainly placed through semi-manual labour and with low impact on the environment and the landscape. The effectiveness of protection works in the long term is ensured through routine, temporally-continuous and spatially-diffuse actions of monitoring and maintenance. This method contrasts the common approach to managing hydraulic risk and erosion in Italy which is based on large, one-off and irreversible protection actions. The sustainability of the LIFE VIMINE approach is ensured by the participatory involvement of stakeholders and the recognition that protecting salt marshes means defending the benefits they provide to society through their ecological functions, as well as protecting the jobs linked to the existence or conservation of this habitat

Variational approach for electrolyte solutions: from dielectric interfaces to charged nanopores

A variational theory is developed to study electrolyte solutions, composed of interacting point-like ions in a solvent, in the presence of dielectric discontinuities and charges at the boundaries. Three important and non-linear electrostatic effects induced by these interfaces are taken into account: surface charge induced electrostatic field, solvation energies due to the ionic cloud, and image charge repulsion. Our variational equations thus go beyond the mean-field theory. The influence of salt concentration, ion valency, dielectric jumps, and surface charge is studied in two geometries. i) A single neutral air-water interface with an asymmetric electrolyte. A charge separation and thus an electrostatic field gets established due to the different image charge repulsions for coions and counterions. Both charge distributions and surface tension are computed and compared to previous approximate calculations. For symmetric electrolyte solutions close to a charged surface, two zones are characterized. In the first one, with size proportional to the logarithm of the coupling parameter, strong image forces impose a total ion exclusion, while in the second zone the mean-field approach applies. ii) A symmetric electrolyte confined between two dielectric interfaces as a simple model of ion rejection from nanopores. The competition between image charge repulsion and attraction of counterions by the membrane charge is studied. For small surface charge, the counterion partition coefficient decreases with increasing pore size up to a critical pore size, contrary to neutral membranes. For larger pore sizes, the whole system behaves like a neutral pore. The prediction of the variational method is also compared with MC simulations and a good agreement is observed.Comment: This version is accepted for publication in Phys. Rev. E

Inhibitory control in mind and brain 2.0: blocked-input models of saccadic countermanding.

The interactive race model of saccadic countermanding assumes that response inhibition results from an interaction between a go unit, identified with gaze-shifting neurons, and a stop unit, identified with gaze-holding neurons, in which activation of the stop unit inhibits the growth of activation in the go unit to prevent it from reaching threshold. The interactive race model accounts for behavioral data and predicts physiological data in monkeys performing the stop-signal task. We propose an alternative model that assumes that response inhibition results from blocking the input to the go unit. We show that the blocked-input model accounts for behavioral data as accurately as the original interactive race model and predicts aspects of the physiological data more accurately. We extend the models to address the steady-state fixation period before the go stimulus is presented and find that the blocked-input model fits better than the interactive race model. We consider a model in which fixation activity is boosted when a stop signal occurs and find that it fits as well as the blocked input model but predicts very high steady-state fixation activity after the response is inhibited. We discuss the alternative linking propositions that connect computational models to neural mechanisms, the lessons to be learned from model mimicry, and generalization from countermanding saccades to countermanding other kinds of responses

Bubble Growth in Superfluid 3-He: The Dynamics of the Curved A-B Interface

We study the hydrodynamics of the A-B interface with finite curvature. The interface tension is shown to enhance both the transition velocity and the amplitudes of second sound. In addition, the magnetic signals emitted by the growing bubble are calculated, and the interaction between many growing bubbles is considered.Comment: 20 pages, 3 figures, LaTeX, ITP-UH 11/9

Dissipation of the 3^He A-B Transition

A rigorous hydrodynamic theory of the A-B transition is presented. All dissipative processes are considered. At low interface velocities, those occurring on hydrodynamic length scales, not considered hitherto, are most probably the dominant ones.Comment: 13 pages, REVTeX, 2 figures, ITP-UH 13/9

Pathological implications of Th1/Th2 cytokine genetic variants in Beh\ue7et's disease: Data from a pilot study in a Sicilian population

Cytokines act as pleiotropic polypeptides able to regulate inflammatory/immune responses and to provide important signals in physiological and pathological processes. Several cytokines (Th1, Th2, and Th17) seem to be involved in the pathophysiology of Beh\ue7et's disease, a chronic immune-mediated disease characterized by oral and genital lesions and ocular inflammation. Its individual susceptibility seems to be modulated by genetic variants in genes codifying these cytokines. Th1 and Th17 seem to be involved in the disease's active phases, and Th2 seems to affect the development or severity of the disease; however, contrasting data are reported. In this study, some genetic variants of the Th1/Th2 cytokine genes were investigated in Sicilian patients and age- and gender-matched controls. Three very significant associations with Beh\ue7et's disease were detected, and combined genotypes associated with increased disease risk were identified. Results obtained point to the key role of Th1/Th2 cytokine genetic variants in disease susceptibility