DNA denaturation and wetting in the presence of disorder

We present a precise equivalence of the Lifson-Poland-Scheraga model with wetting models. Making use of a representation of the former model in terms of random matrices, we obtain, in the limit of weak disorder, a mean--field approximation, that shows a change of the critical behavior due to disorder.Comment: 4 page

Resonances in one-dimensional Disordered Chain

We study the average density of resonances, $$, in a semi-infinite disordered chain coupled to a perfect lead. The function$$ is defined in the complex energy plane and the distance $y$ from the real axes determines the resonance width. We concentrate on strong disorder and derive the asymptotic behavior of $$ in the limit of small $y$.Comment: latex, 1 eps figure, 9 pages; v2 - final version, published in the JPhysA Special Issue Dedicated to the Physics of Non-Hermitian Operator

Transition from Poisson to gaussian unitary statistics: The two-point correlation function

We consider the Rosenzweig-Porter model of random matrix which interpolates between Poisson and gaussian unitary statistics and compute exactly the two-point correlation function. Asymptotic formulas for this function are given near the Poisson and gaussian limit.Comment: 19 pages, no figure

Structure factor and dynamics of the helix-coil transition

Thermodynamical properties of the helix-coil transition were successfully described in the past by the model of Lifson, Poland and Sheraga. Here we compute the corresponding structure factor and show that it possesses a universal scaling behavior near the transition point, even when the transition is of first order. Moreover, we introduce a dynamical version of this model, that we solve numerically. A Langevin equation is also proposed to describe the dynamics of the density of hydrogen bonds. Analytical solution of this equation shows dynamical scaling near the critical temperature and predicts a gelation phenomenon above the critical temperature. In the case when comparison of the two dynamical approaches is possible, the predictions of our phenomenological theory agree with the results of the Monte Carlo simulations.Comment: 11 pages, 7 figure

Atoms and Quantum Dots With a Large Number of Electrons: the Ground State Energy

We compute the ground state energy of atoms and quantum dots with a large number N of electrons. Both systems are described by a non-relativistic Hamiltonian of electrons in a d-dimensional space. The electrons interact via the Coulomb potential. In the case of atoms (d=3), the electrons are attracted by the nucleus, via the Coulomb potential. In the case of quantum dots (d=2), the electrons are confined by an external potential, whose shape can be varied. We show that the dominant terms of the ground state energy are those given by a semiclassical Hartree-exchange energy, whose N to infinity limit corresponds to Thomas-Fermi theory. This semiclassical Hartree-exchange theory creates oscillations in the ground state energy as a function of N. These oscillations reflect the dynamics of a classical particle moving in the presence of the Thomas-Fermi potential. The dynamics is regular for atoms and some dots, but in general in the case of dots, the motion contains a chaotic component. We compute the correlation effects. They appear at the order N ln N for atoms, in agreement with available data. For dots, they appear at the order N.Comment: 30 pages, 1 figur

Down-Regulation of DNA Mismatch Repair Enhances Initiation and Growth of Neuroblastoma and Brain Tumour Multicellular Spheroids

Multicellular tumour spheroid (MCTS) cultures are excellent model systems for simulating the development and microenvironmental conditions of in vivo tumour growth. Many documented cell lines can generate differentiated MCTS when cultured in suspension or in a non-adhesive environment. While physiological and biochemical properties of MCTS have been extensively characterized, insight into the events and conditions responsible for initiation of these structures is lacking. MCTS are formed by only a small subpopulation of cells during surface-associated growth but the processes responsible for this differentiation are poorly understood and have not been previously studied experimentally. Analysis of gene expression within spheroids has provided clues but to date it is not known if the observed differences are a cause or consequence of MCTS growth. One mechanism linked to tumourigenesis in a number of cancers is genetic instability arising from impaired DNA mismatch repair (MMR). This study aimed to determine the role of MMR in MCTS initiation and development. Using surface-associated N2a and CHLA-02-ATRT culture systems we have investigated the impact of impaired MMR on MCTS growth. Analysis of the DNA MMR genes MLH1 and PMS2 revealed both to be significantly down-regulated at the mRNA level compared with non-spheroid-forming cells. By using small interfering RNA (siRNA) against these genes we show that silencing of MLH1 and PMS2 enhances both MCTS initiation and subsequent expansion. This effect was prolonged over several passages following siRNA transfection. Down-regulation of DNA MMR can contribute to tumour initiation and progression in N2a and CHLA-02-ATRT MCTS models. Studies of surface-associated MCTS differentiation may have broader applications in studying events in the initiation of cancer foci

Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology

Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations

Modèles ecologiques pour l'extrapolation des effets écotoxicologiques enregistrés lors de biotests in situ cheZ Gammarus

[Departement_IRSTEA]Eaux [TR1_IRSTEA]BELCAInternational audienceEvaluating the effects of chemical contamination on populations and ecological communities still constitutes a challenging necessity in environmental management. However the toxic effects of contaminants are commonly measured by means of organism-level responses. Linking such effects measures with ecological models is a promising way to apprehend population-level impacts. In this way, population models are currently increasingly used in predictive risk assessment procedures, but their use in environmental diagnostic framework remains limited due to their lack of ecological realism. The present study with the crustacean amphipod Gammarus fossarum, a sentinel species in freshwater monitoring, combines a dual field and laboratory experimental approach with a population modelling framework. In this way, we developed an ecologically-relevant periodic matrix population model for Gammarus. This model allowed us to capture the population dynamics in the field, and to understand the particular pattern of demographic sensitivities induced by Gammarus life-history phenology. The model we developed provided a robust population-level assessment of in situ-based effects measures recorded during a biomonitoring program on a French watershed impacted by past mining activities. Thus, our study illustrates the potential of population modelling when seeking to decipher the role of environmental toxic contamination in ecological perturbations