Three-body model of the final state interaction in heavy meson decay

We develop a relativistic three-body model for the final state interaction in D(+) -> K(-) pi(+) pi(+) decay based on the ladder approximation of the Bethe-Salpeter equation. The decay amplitude has the standard two-meson resonant transition matrix modulated by a spectator amplitude that carries a fully interacting three-body contribution and a smooth background term from the partonic amplitude. Our calculations are compared with D decay data.

Study of the (D)over-barN Interaction in a QCD Coulomb Gauge Quark Model

We study the (D) over barN interaction at low energies with a quark model inspired in the QCD Hamiltonian in Coulomb gauge. The model Hamiltonian incorporates a confining Coulomb potential extracted from a self-consistent quasiparticle method for the gluon degrees of freedom, and transverse-gluon hyperfine interaction consistent with a finite gluon propagator in the infrared. Initially a constituent-quark mass function is obtained by solving a gap equation and baryon and meson bound-states are obtained in Fock space using a variational calculation. Next, having obtained the constituent-quark masses and the hadron waves functions, an effective meson-nucleon interaction is derived from a quark-interchange mechanism. This leads to a short range meson-baryon interaction and to describe long-distance physics vector- and scalar-meson exchanges described by effective Lagrangians are incorporated. The derived effective (D) over barN potential is used in a Lippmann-Schwinger equation to obtain phase shifts. The results are compared with a recent similar calculation using the nonrelativistic quark model.

Interaction of pulses in the nonlinear Schrödinger model

A study was conducted on the interaction of two pulses in the nonlinear Schrodinger (NLS) model. The presence of different scenarios of the behavior depending on the initial parameters of the pulses, such as the pulse areas, the relative phase shift, the spatial and frequency separations were shown. It was observed that a pure real initial condition of the NLS equation can result in additional moving solitons.

Mean-field model of interaction between bright vortex solitons in Bose-Einstein condensates

Using the explicit numerical solution of the axially symmetric Gross-Pitaevskii equation we study the dynamics of interaction among vortex solitons in a rotating matter-wave bright soliton train in a radially trapped and axially free Bose-Einstein condensate to understand certain features of the experiment by Strecker et al (2002 Nature 417 150). In a soliton train, solitons of opposite phase (phase δ = π) repel and stay apart without changing shape; solitons with δ = 0 attract, interact and coalesce, but eventually come out; solitons with a general δ usually repel but interact inelastically by exchanging matter. We study this and suggest future experiments with vortex solitons.

Factors that cause genotype by environment interaction and use of a multiple-trait herd-cluster model for milk yield of Holstein cattle from Brazil and Colombia

Descriptive herd variables (DVHE) were used to explain genotype by environment interactions (G x E) for milk yield (MY) in Brazilian and Colombian production environments and to develop a herd-cluster model to estimate covariance components and genetic parameters for each herd environment group. Data consisted of 180,522 lactation records of 94,558 Holstein cows from 937 Brazilian and 400 Colombian herds. Herds in both countries were jointly grouped in thirds according to 8 DVHE: production level, phenotypic variability, age at first calving, calving interval, percentage of imported semen, lactation length, and herd size. For each DVHE, REML bivariate animal model analyses were used to estimate genetic correlations for MY between upper and lower thirds of the data. Based on estimates of genetic correlations, weights were assigned to each DVHE to group herds in a cluster analysis using the FASTCLUS procedure in SAS. Three clusters were defined, and genetic and residual variance components were heterogeneous among herd clusters. Estimates of heritability in clusters 1 and 3 were 0.28 and 0.29, respectively, but the estimate was larger (0.39) in Cluster 2. The genetic correlations of MY from different clusters ranged from 0.89 to 0.97. The herd-cluster model based on DVHE properly takes into account G x E by grouping similar environments accordingly and seems to be an alternative to simply considering country borders to distinguish between environments.

The inhibition of 5-enolpyruvylshikimate-3-phosphate synthase as a model for development of novel antimicrobials

EPSP synthase (EPSPS) is an essential enzyme in the shikimate pathway, transferring the enolpyruvyl group of phosphoenolpyruvate to shikimate-3-phosphate to form 5-enolpyruvyl-3-shikimate phosphate and inorganic phosphate. This enzyme is composed of two domains, which are formed by three copies of βαβαββ-folding units; in between there are two crossover chain segments hinging the nearly topologically symmetrical domains together and allowing conformational changes necessary for substrate conversion. The reaction is ordered with shikimate-3-phosphate binding first, followed by phosphoenolpyruvate, and then by the subsequent release of phosphate and EPSP. N-[phosphomethyl]glycine (glyphosate) is the commercial inhibitor of this enzyme. Apparently, the binding of shikimate-3-phosphate is necessary for glyphosate binding, since it induces the closure of the two domains to form the active site in the interdomain cleft. However, it is somehow controversial whether binding of shikimate-3-phosphate alone is enough to induce the complete conversion to the closed state. The phosphoenolpyruvate binding site seems to be located mainly on the C-terminal domain, while the binding site of shikimate-3-phosphate is located primarily in the N-terminal domain residues. However, recent results demonstrate that the active site of the enzyme undergoes structural changes upon inhibitor binding on a scale that cannot be predicted by conventional computational methods. Studies of molecular docking based on the interaction of known EPSPS structures with (R)- phosphonate TI analogue reveal that more experimental data on the structure and dynamics of various EPSPS-ligand complexes are needed to more effectively apply structure-based drug design of this enzyme in the future. © 2007 Bentham Science Publishers Ltd.

Relativistic three-body model for final state interaction in D+ → K-π+π+ decay

A challenge in mesonic three-body decays of heavy mesons is to quantify the contribution of re-scattering between the final mesons. D decays have the unique feature that make them a key to light meson spectroscopy, in particular to access the Kn S-wave phase-shifts. We built a relativis-tic three-body model for the final state interaction in D+ → K -π+π+ decay based on the ladder approximation of the Bethe-Salpeter equation projected on the light-front. The decay amplitude is separated in a smooth term, given by the direct partonic decay amplitude, and a three-body fully interacting contribution, that is factorized in the standard two-meson resonant amplitude times a reduced complex amplitude that carries the effect of the three-body rescattering mechanism. The off-shell reduced amplitude is a solution of an inhomogeneous Faddeev type three-dimensional integral equation, that includes only isospin 1/2 K -π+ interaction in the S-wave channel. The elastic K-π+ scattering amplitude is parameterized according to the LASS data[1]. The integral equation is solved numerically and preliminary results are presented and compared to the experimental data from the E791 Collaboration[2, 3] and FOCUS Collaboration[4, 5].

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.

D̄N interaction in a color-confining chiral quark model

We investigate the low-energy elastic D̄N interaction using a quark model that confines color and realizes dynamical chiral symmetry breaking. The model is defined by a microscopic Hamiltonian inspired in the QCD Hamiltonian in Coulomb gauge. Constituent quark masses are obtained by solving a gap equation, and baryon and meson bound-state wave functions are obtained using a variational method. We derive a low-energy meson-nucleon potential from a quark-interchange mechanism whose ingredients are the quark-quark and quark-antiquark interactions and baryon and meson wave functions, all derived from the same microscopic Hamiltonian. The model is supplemented with (σ, ρ, ω, a0) single-meson exchanges to describe the long-range part of the interaction. Cross sections and phase shifts are obtained by iterating the quark-interchange plus meson-exchange potentials in a Lippmann-Schwinger equation. Once coupling constants of long-range scalar σ and a0 meson exchanges are adjusted to describe experimental phase shifts of the K+N and K0N reactions, predictions for cross sections and s-wave phase shifts for the D̄0N and D-N reactions are obtained without introducing new parameters. © 2013 American Physical Society.

Interaction between GIS and hydrologic model: a preliminary approach using ArcHydro Framework Data Model

In different regions of Brazil, population growth and economic development can degrade water quality, compromising watershed health and human supply. Because of its ability to combine spatial and temporal data in the same environment and to create water resources management (WRM) models, the Geographical Information System (GIS) is a powerful tool for managing water resources, preventing floods and estimating water supply. This paper discusses the integration between GIS and hydrological models and presents a case study relating to the upper section of the Paraíba do Sul Basin (Sao Paulo State portion), situated in the Southeast of Brazil. The case study presented in this paper has a database suitable for the basin's dimensions, including digitized topographic maps at a 50,000 scale. From an ArcGIS®/ArcHydro Framework Data Model, a geometric network was created to produce different raster products. This first grid derived from the digital elevation model grid (DEM) is the flow direction map followed by flow accumulation, stream and catchment maps. The next steps in this research are to include the different multipurpose reservoirs situated along the Paraíba do Sul River and to incorporate rainfall time series data in ArcHydro to build a hydrologic data model within a GIS environment in order to produce a comprehensive spatial-temporal model.

Interaction of a synthetic antimicrobial peptide with model membrane by fluorescence spectroscopy

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

Interaction of biologically-relevant peptides with membrane model systems

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

Interaction between fiscal and monetary policy in a dynamic nonlinear model

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