A Population Genetic Approach to the Quasispecies Model

A population genetics formulation of Eigen's molecular quasispecies model is proposed and several simple replication landscapes are investigated analytically. Our results show a remarcable similarity to those obtained with the original kinetics formulation of the quasispecies model. However, due to the simplicity of our approach, the space of the parameters that define the model can be explored. In particular, for the simgle-sharp-peak landscape our analysis yelds some interesting predictions such as the existence of a maximum peak height and a mini- mum molecule length for the onset of the error threshold transition.Comment: 16 pages, 4 Postscript figures. Submited to Phy. Rev.

Large deviations for non-uniformly expanding maps

We obtain large deviation results for non-uniformly expanding maps with non-flat singularities or criticalities and for partially hyperbolic non-uniformly expanding attracting sets. That is, given a continuous function we consider its space average with respect to a physical measure and compare this with the time averages along orbits of the map, showing that the Lebesgue measure of the set of points whose time averages stay away from the space average decays to zero exponentially fast with the number of iterates involved. As easy by-products we deduce escape rates from subsets of the basins of physical measures for these types of maps. The rates of decay are naturally related to the metric entropy and pressure function of the system with respect to a family of equilibrium states. The corrections added to the published version of this text appear in bold; see last section for a list of changesComment: 36 pages, 1 figure. After many PhD students and colleagues having pointed several errors in the statements and proofs, this is a correction to published article answering those comments. List of main changes in a new last sectio

Finite-size scaling of the quasiespecies model

We use finite-size scaling to investigate the critical behavior of the quasiespecies model of molecular evolution in the single-sharp-peak replication landscape. This model exhibits a sharp threshold phenomenon at Q=Q_c=1/a, where Q is the probability of exact replication of a molecule of length L and a is the selective advantage of the master string. We investigate the sharpness of the threshold and find that its characteristic persist across a range of Q of order L^(-1) about Q_c. Furthermore, using the data collapsing method we show that the normalized mean Hamming distance between the master string and the entire population, as well as the properly scaled fluctuations around this mean value, follow universal forms in the critical region.Comment: 8 pages,tex. Submitted to Physical Review

Group selection models in prebiotic evolution

The evolution of enzyme production is studied analytically using ideas of the group selection theory for the evolution of altruistic behavior. In particular, we argue that the mathematical formulation of Wilson's structured deme model ({\it The Evolution of Populations and Communities}, Benjamin/Cumings, Menlo Park, 1980) is a mean-field approach in which the actual environment that a particular individual experiences is replaced by an {\it average} environment. That formalism is further developed so as to avoid the mean-field approximation and then applied to the problem of enzyme production in the prebiotic context, where the enzyme producer molecules play the altruists role while the molecules that benefit from the catalyst without paying its production cost play the non-altruists role. The effects of synergism (i.e., division of labor) as well as of mutations are also considered and the results of the equilibrium analysis are summarized in phase diagrams showing the regions of the space of parameters where the altruistic, non-altruistic and the coexistence regimes are stable. In general, those regions are delimitated by discontinuous transition lines which end at critical points.Comment: 22 pages, 10 figure

Designing biomaterials based on biomineralization of bone

In nature, organisms control crystal nucleation and growth using organic interfaces as templates. Scientists, in the last decades, have tried to learn from nature how to design biomimetic biomaterials inspired by the hierarchical complex structure of bone and other natural mineralised tissues or to control the biomineralization process onto biomaterials substrates to promote the osteoconductive properties of implantable devices. The design of synthetic bone analogues, i.e., with a structure and properties similar to bone, would certainly constitute a major breakthrough in bone tissue engineering. Moreover, many strategies have been proposed in the literature to develop bioactive bone-like materials, for instance using bioactive glasses. Fundamental aspects of biomineralization may be also important in order to propose new methodologies to improve calcification onto the surface of biomaterials or to develop bioactive tridimensional templates that could be used in regenerative medicine. In particular, it has been shown that some chemical groups and proteins, as well as the tridimensional matrix in which calcification would occur, play a fundamental role on the nucleation and growth of hydroxyapatite. All these distinct aspects will be reviewed and discussed in this paper.I. B. Leonor thanks the Portuguese Foundation for Science and Technology (FCT) for providing her a post-doctoral scholarship (SFRH/BPD/26648/2006). This work was supported by the European NoE EXPERTISSUES (NMP3-CT-2004-500283) and by the Portuguese Foundation for Science and Technology, FCT, through the projects PTDC/CTM/68804/2006, PTDC/CTM/67560/2006 and PTDC/FIS/68209/2006

The Thermal Structure of Gas in Pre-Stellar Cores: A Case Study of Barnard 68

We present a direct comparison of a chemical/physical model to multitransitional observations of C18O and 13CO towards the Barnard 68 pre-stellar core. These observations provide a sensitive test for models of low UV field photodissociation regions and offer the best constraint on the gas temperature of a pre-stellar core. We find that the gas temperature of this object is surprisingly low (~7-8 K), and significantly below the dust temperature, in the outer layers (Av < 5 mag) that are traced by C18O and 13CO emission. As shown previously, the inner layers (Av > 5 mag) exhibit significant freeze-out of CO onto grain surfaces. Because the dust and gas are not fully coupled, depletion of key coolants in the densest layers raises the core (gas) temperature, but only by ~1 K. The gas temperature in layers not traced by C18O and 13CO emission can be probed by NH3 emission, with a previously estimated temperature of ~10-11 K. To reach these temperatures in the inner core requires an order of magnitude reduction in the gas to dust coupling rate. This potentially argues for a lack of small grains in the densest gas, presumably due to grain coagulation.Comment: 33 pages, 11 figures, accepted by Astrophysical Journa

Análise econômica mensal sobre o setor de mandioca e derivados: maio/2010.

Menor oferta sustenta cotação em maio – O mês de maio foi caracterizado pela menor oferta de mandioca para a indústria de fécula, levando à diminuição na quantidade de mandioca processada pelas fecularias. Ainda que seja período de safra, a disponibilidade de mandioca de segundo ciclo é menor em relação a anos anteriores e, além disso, agricultores mantiveram-se retraídos em relação à colheita. Esses produtores não tiveram necessidade de caixa e aguardam preços ainda maiores nos próximos meses. O excesso de chuvas em alguns períodos de maio prejudicou a colheita, dificultando os trabalhos e diminuindo a quantidade ofertada à indústria. Vale destacara, também, que houve menor número de mão-de-obra disponível para a colheita, visto que parte dos agricultores já começou o preparo de solo para o plantio da safra 2010/11. Apesar da menor oferta em maio, o preço médio mensal da raiz de mandioca, considerando as regiões pesquisadas pelo Cepea, foi de R$217,61/tonelada (R$ 0,3785/grama de amido na balança hidrostática de 5 kg), ligeira baixa de 0,5% frente à de abril. Já entre a última semana de abril e a última de maio, o preço médio subiu 18,8%, passando para R$ 237,81/t.Os preços médios mensais nos estados de São Paulo e Mato Grosso do Sul tiveram respectivas quedas de 4,9% e de 2,7% entre abril e maio.bitstream/item/23998/1/05MaiCEPEA.pd