Using genetic algorithm to design protein sequence

In this work, genetic algorithms concepts along with a rotamer library for proteins side chains are used to optimize the tertiary structure of the hydrophobic core of Cytochrome b(562) starting from the known PDB structure of its backbone which is kept fixed while the side chains of the hydrophobic core are allowed to adopt the conformations present in the rotamer library. The atoms of the side chains forming the core interact via van der Waals energy. Besides the prediction of the native core structure, it is also suggested a set of different amino acid sequences for this core. Comparison between these new cores and the native are made in terms of their volumes, van der Waals energies values and the numbers of contacts made by the side chains forming the cores. This paper proves that genetic algorithms area efficient to design new sequence for the protein core. (C) 2007 Elsevier B.V. All rights reserved.

Predicting peptides structure with solvation potential and rotamer library dependent of the backbone

In this work, genetic algorithms concepts along with a rotamer library dependent of backbone and implicit solvation potential are used to study the tertiary structure of peptides. We starting from known primary sequence and optimize the structure of the backbone while the side chains allowed adopting the conformations present in a rotamer library. The GA, implemented with two force fields with a growing complexity, was used predict the structure of a polyalanine and a poly-isolueucine. This paper presents good and interesting results about the study of peptides structures and about the development of computational tools to study peptides structures. (C) 2007 Elsevier B.V. All rights reserved.

A fluorescence probe study of gemini surfactants in aqueous solution: a comparison between n-2-n and n-6-n series of the alkanediyl-a,w-bis (dimethylalkylammonium bromides)

Two series of alkanediyl-a,w-bis (dimethylalkylammonium bromide (n-2-n and n-6-n; n=8, 10,12, and 16) have been synthesized and their micelles properties studied in aqueous solution using pyrene, pyrenecarboxaldehyde (PCA) and 1,8 anilinonaphtalene sulfonic acid sodium salt (ANS) as fluorescent probes. The micelles from these surfactants have been characterized on the basis of the information provided by micelle-solubilized fluorescent probes. The obtained results indicated that the surfactant concentration at which a marked decrease in l max parameter of pyrenecarboxaldehyde (PCA) occurs corresponds to the CMC determined by conductimetric measurements. Changes in the emission spectra of ANS and PCA observed in the submicellar range for both surfactants series (n-2-n and n-6-n) were interpreted as formation of pre-aggregates. It was found that the dimeric surfactants with long spacer (s= 6) form more hydrated aggregates when compared with those formed by the n-2-n and CnTAB surfactants series. This was attributed to a more difficult packing of n-6-n surfactant molecules to form micelles.

The equivalence principle revisited

A precise fomulation of the strong Equivalence Principle is essential to the understanding of the relationship between gravitation and quantum mechanics. The relevant aspects are reviewed in a context including General Relativity but allowing for the presence of torsion. For the sake of brevity, a concise statement is proposed for the Principle: An ideal observer immersed in a gravitational field can choose a reference frame in which gravitation goes unnoticed. This statement is given a clear mathematical meaning through an accurate discussion of its terms. It holds for ideal observers (time-like smooth non-intersecting curves), but not for real, spatially extended observers. Analogous results hold for gauge fields. The difference between gravitation and the other fundamental interactions comes from their distinct roles in the equation of force.

Electromagnetic hadron form factors and higher Fock components

Investigation of the spacelike and timelike electromagnetic form factors of hadrons, within a relativistic microscopical model characterized by a small set of hypothesis, could shed light on the components of hadron states beyond the valence one. Our relativistic approach has been successfully applied first to the pion and then the extension to the nucleon has been undertaken. The pion case is shortly reviewed as an illustrative example for introducing the main ingredients of our approach, and preliminary results for the nucleon in the spacelike range -10 (GeV/c)(2) <= q(2) <= 0 are evaluated.

Electromagnetic structure and weak decay of meson K in a light-front QCD-inspired model

The kaon electromagnetic (e.m.) form factor is reviewed considering a light-front constituent quark model. In this approach, it is discussed the relevance of the quark-antiquark pair terms for the full covariance of the e.m. current. It is also verified, by considering a QCD dynamical model, that a good agreement with experimental data can be obtained for the kaon weak decay constant once a probability of about 80% of the valence component is taken into account.

Timelike and spacelike hadron form factors, Fock state components and light-front dynamics

A unified description of spacelike and timelike hadron form factors within a light-front model was successfully applied to the pion. The model is extended to the nucleon to study the role of qq pair production and of nonvalence components in the nucleon form factors. Preliminary results in the spacelike range 0 <= Q(2) <= 10 (GeV/c)(2) are presented.

Evolution of magnetic field and spin period in accreting neutron stars

Based on the accretion-induced magnetic field decay model, in which a frozen field and an incompressible fluid are assumed, we obtain the following results: (1) an analytic relation between the magnetic field and spin period, if the fastness parameter of the accretion disk is neglected (The evolutionary tracks of accreting neutron stars in the P-B diagram in our model are different from the equilibrium period lines when the influence of the fastness parameter is taken into account.); (2) the theoretical minimum spin period of an accreting neutron star is max(1.1ms (DeltaM/M(circle dot))(-1)R(6)(-5/14) I(45)(M/M(circle dot))(-1/2),1.1ms (M/M(circle dot))(-1/2) R(6)(17/14)), independent of the accretion rate (X-ray luminosity) but dependent on the total accretion mass, DeltaM; however, the minimum magnetic field depends on the accretion rate; (3) the magnetic field strength decreases faster with time than does the period.

Gravitation as anholonomy

A gravitational field can be seen as the anholonomy of the tetrad fields. This is more explicit in the teleparallel approach, in which the gravitational field-strength is the torsion of the ensuing Weitzenbock connection. In a tetrad frame, that torsion is just the anholonomy of that frame. The infinitely many tetrad fields taking the Lorentz metric into a given Riemannian metric differ by point-dependent Lorentz transformations. Inertial frames constitute a smaller infinity of them, differing by fixed-point Lorentz transformations. Holonomic tetrads take the Lorentz metric into itself, and correspond to Minkowski flat spacetime. An accelerated frame is necessarily anholonomic and sees the electromagnetic field strength with an additional term.

Kaon and Pion Electromagnetic Form Factor Ratios in the Light-Front

We have applied the light-front formalism to calculate the electromagnetic form factors for the pion and the kaon from two models at low and high energies in order to explore the differences between such models. We have also compared the results for the ratio F(K)(Q(2))/F(pi)(Q(2)) with the experimental data, up to 10 [GeV/c](2) and we have observed that the theoretical results are in good concordance for low energies, but they are very different at higher energy scales.

Light-Front model of transition form-factors in heavy meson decay

Electroweak transition form factors of heavy meson decays are important ingredients in the extraction of the Cabibbo-Kobayashi-Maskawa (CKM) matrix elements from experimental data. In this work, within a. light-front framework, we calculate electroweak transition form factor for the semileptonic decay of D mesons into a pion or a kaon. The model results underestimate in both cases the new data of CLEO for the larger momentum transfers accessible in the experiment. We discuss possible reasons for that in order to improve the model.

Frame dependence of the pair contribution to the pion electromagnetic form factor in a light-front approach

The frame dependence of the pair-term contribution to the electromagnetic form factor of the pion is studied within the Light Front approach. A symmetric ansatz for the pion Bethe-Salpeter amplitude with a pseudo scalar coupling of the constituent to the pion field is used. In this model, the pair term vanishes for the Drell-Yan condition, while it is dominant for momentum transfer along the light-front direction.

Weak decay constant of pseudoscalar mesons in a QCD-inspired model

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

On the unzipping of multiwalled carbon nanotubes

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Nonzero Gap Two-Dimensional Carbon Allotrope from Porous Graphene

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)