Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Landscape Diversity Influences Dispersal and Establishment of Pest with Complex Nutritional Ecology

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Planejamento de reativos em sistemas elétricos de potência multi-área através de modelos estocásticos

Pós-graduação em Engenharia Elétrica - FEIS

Spatial dynamics of a population with stage-dependent diffusion

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Yang-Lee zeros of the two- and three-state Potts model defined on π3 Feynman diagrams

We present both analytical and numerical results on the position of partition function zeros on the complex magnetic field plane of the q=2 state (Ising) and the q=3 state Potts model defined on phi(3) Feynman diagrams (thin random graphs). Our analytic results are based on the ideas of destructive interference of coexisting phases and low temperature expansions. For the case of the Ising model, an argument based on a symmetry of the saddle point equations leads us to a nonperturbative proof that the Yang-Lee zeros are located on the unit circle, although no circle theorem is known in this case of random graphs. For the q=3 state Potts model, our perturbative results indicate that the Yang-Lee zeros lie outside the unit circle. Both analytic results are confirmed by finite lattice numerical calculations.

Temporal variability of soil CO2 emission after conventional and reduced tillage described by an exponential decay in time model

A quantificação do impacto das práticas de preparo sobre as perdas de carbono do solo é dependente da habilidade de se descrever a variabilidade temporal da emissão de CO2 do solo após preparo. Tem sido sugerido que as grandes quantidades de CO2 emitido após o preparo do solo podem servir como um indicador das modificações nos estoques de carbono do solo em longo termo. Neste trabalho é apresentado um modelo de duas partes baseado na temperatura e na umidade do solo e que inclui um termo exponencial decrescente do tempo que é eficiente no ajuste das emissões intermediárias após preparo: arado de disco seguido de uma passagem com a grade niveladora (convencional) e escarificador de arrasto seguido da passagem com rolo destorroador (reduzido). As emissões após o preparo do solo são descritas utilizando-se estimativa não linear com um coeficiente de determinação (R²) tão alto quanto 0.98 após preparo reduzido. Os resultados indicam que nas previsões da emissão de CO2 após o preparo do solo é importante considerar um termo exponencial decrescente no tempo após preparo.

Dynamics of extinction in coupled populations of the flour beetle Tribolium castaneum

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Radiative Omega(-)->Xi(-)gamma decay and physics beyond the standard model

We investigate the impact of new physics beyond the Standard Model to the s --> d gamma process, which is responsible for the short-distance contribution to the radiative decay Omega-( )--> Xi(-) gamma. We study three representative extensions of the Standard Model, namely a one-family technicolor model, a two Higgs doublet model and a model containing scalar leptoquarks. When constraints arising from the observed b --> s gamma transition and the upper limit on D-0-(D) over bar(0) mixing are taken into account, we find no significant contributions of new physics to the s --> d gamma process.

Dynamic critical behavior of percolation observables in the 2d Ising model

We present preliminary results of our numerical study of the critical dynamics of percolation observables for the two-dimensional Ising model. We consider the (Monte-Carlo) short-time evolution of the system obtained with a local heat-bath method and with the global Swendsen-Wang algorithm. In both cases, we find qualitatively different dynamic behaviors for the magnetization and Omega, the order parameter of the percolation transition. This may have implications for the recent attempts to describe the dynamics of the QCD phase transition using cluster observables.

Microscopic origin of non-Gaussian distributions of financial returns

In this paper we study the possible microscopic origin of heavy-tailed probability density distributions for the price variation of financial instruments. We extend the standard log-normal process to include another random component in the so-called stochastic volatility models. We study these models under an assumption, akin to the Born-Oppenheimer approximation, in which the volatility has already relaxed to its equilibrium distribution and acts as a background to the evolution of the price process. In this approximation, we show that all models of stochastic volatility should exhibit a scaling relation in the time lag of zero-drift modified log-returns. We verify that the Dow-Jones Industrial Average index indeed follows this scaling. We then focus on two popular stochastic volatility models, the Heston and Hull-White models. In particular, we show that in the Hull-White model the resulting probability distribution of log-returns in this approximation corresponds to the Tsallis (t-Student) distribution. The Tsallis parameters are given in terms of the microscopic stochastic volatility model. Finally, we show that the log-returns for 30 years Dow Jones index data is well fitted by a Tsallis distribution, obtaining the relevant parameters. (c) 2007 Elsevier B.V. All rights reserved.

Path integral approach to the full Dicke model

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Robust tori in a double-waved Hamiltonian model

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Performance of UASB reactors in two stages under different HRT and OLR treating residual waters of swine farming

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

REDUCTION OF TODA LATTICE HIERARCHY TO GENERALIZED KDV HIERARCHIES AND THE 2-MATRIX MODEL

Toda lattice hierarchy and the associated matrix formulation of the 2M-boson KP hierarchies provide a framework for the Drinfeld-Sokolov reduction scheme realized through Hamiltonian action within the second KP Poisson bracket. By working with free currents, which Abelianize the second KP Hamiltonian structure, we are able to obtain a unified formalism for the reduced SL(M + 1, M - k) KdV hierarchies interpolating between the ordinary KP and KdV hierarchies. The corresponding Lax operators are given as superdeterminants of graded SL(M + 1, M - k) matrices in the diagonal gauge and we describe their bracket structure and field content. In particular, we provide explicit free field representations of the associated W(M, M - k) Poisson bracket algebras generalising the familiar nonlinear W-M+1 algebra. Discrete Backlund transformations for SL(M + 1, M - k) KdV are generated naturally from lattice translations in the underlying Toda-like hierarchy. As an application we demonstrate the equivalence of the two-matrix string model to the SL(M + 1, 1) KdV hierarchy.

Use of progeny testing in beef cattle: Prediction of genetic gain in a Nelore Cattle Breeding Program

Genetic gains predicted for selection, based on both individual performance and progeny testing, were compared to provide information to be used in implementation of progeny testing for a Nelore cattle breeding program. The prediction of genetic gain based on progeny testing was obtained from a formula, derived from methodology of Young and Weiler (J. Genetics 57: 329-338, 1960) for two-stage selection, which allows prediction of genetic gain per generation when the individuals under test have been pre-selected on the basis of their own performance. The application of this formula also allowed determination of the number of progeny per tested bull needed to maximize genetic gain, when the total number of tested progeny is limited.