Dynamics of meso and thermo citrate synthases with implicit solvation

The dynamics of hydration of meso and thermo citrate synthases has been investigated using the EEF1 methodology implemented with the CHARNM program. The native enzymes are composed of two identical subunits, each divided into a small and large domain. The dynamics behavior of both enzymes at 30 degrees C and 60 degrees C has been compared. The results of simulations show that during the hydration process, each subunit follows a different pathway of hydration, in spite of the identical sequence. The hydrated structures were compared with the crystalline structure, and the root mean square deviation (RMSD) of each residue along the trajectory was calculated. The regions with larger and smaller mobility were identified. In particular, helices belonging to the small domain are more mobile than those of the large domain. In contrast, the residues that constitute the active site show a much lower displacement compared with the crystalline structure. Hydration free energy calculations point out that Thermoplasma acidophilum citrate synthase (TCS) is more stable than chicken citrate synthase (CCS), at high temperatures. Such result has been ascribed to the higher number of superficial charges in the thermophilic homologue, which stabilizes the enzyme, while the mesophilic homologue denatures. These results are in accord with the experimental found that TCS keeps activity at temperatures farther apart from the catalysis regular temperature than the CCS. (c) 2005 Wiley Periodicals, Inc.

Morphological characterization of the ovary and vitellogenesis dynamics in the tick Amblyomma cajennense (Acari : Ixodidae)

In this work we describe the internal morphology of the female reproductive system of the cayenne tick Amblyomma cajennense. This system is represented by a panoistic ovary, which lacks nurse cells in the germarium. This ovary consists of a single tube, in which a large number of oocytes develop asynchronously, thus accompanying the processes of yolk deposition in the oocytes. The oocytes were classified into stages that varied from I to V, according to: cytoplasm appearance, presence of the germ vesicle, presence of yolk granules, and presence of chorion. The study of vitellogenesis dynamics suggest that the yolk elements are deposited in the oocyte following a preferencial sequence, in which the lipids are the first to appear, followed by proteins an finally by the carbohydrates. In this way the yolk of A. cajennense ticks have these three elements that may be free in the cytoplasm or chemically bounded forming glycoprotein or lipoprotein complexes. (C) 2004 Elsevier B.V. All rights reserved.

Tree population and community dynamics in a Brazilian tropical semideciduous forest

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Dynamics of the deconfinement transition of quarks and gluons in a finite volume

We employ finite elements methods for the approximation of solutions of the Ginzburg-Landau equations describing the deconfinement transition in quantum chromodynamics. These methods seem appropriate for situations where the deconfining transition occurs over a finite volume as in relativistic heavy ion collisions. where in addition expansion of the system and flow of matter are important. Simulation results employing finite elements are presented for a Ginzburg-Landau equation based on a model free energy describing the deconfining transition in pure gauge SU(2) theory. Results for finite and infinite system are compared. (C) 2009 Elsevier B.V. All rights reserved.

Interfacial surface charge and free accessibility to the PLA(2)-active site-like region are essential requirements for the activity of Lys49 PLA(2) homologues

Lys49 phospholipase A(2) homologues are highly myotoxic and cause extensive tissue damage but do not display hydrolytic activity towards natural phospholipids. The binding of heparin, heparin derivatives and polyanionic compounds such as suramin result in partial inhibition (up to 60%) of the myotoxic effects due to a change in the overall charge of the interfacial surface. In vivo experiments demonstrate that polyethylene glycol inhibits more than 90% of the myotoxic effects without exhibiting secondary toxic effects. The crystal structure of bothropstoxin-I complexed with polyethylene glycol reveals that this inhibition is due to steric hindrance of the access to the PLA(2)-active site-like region. These two inhibitory pathways indicate the roles of the overall surface charge and free accessibility to the PLA2-active site-like region in the functioning of Lys49 phospholipases A(2) homologues. Molecular dynamics simulations, small angle X-ray scattering and structural analysis indicate that the oligomeric states both in solution and in the crystalline states of Lys49 phospholipases A2 are principally mediated by hydrophobic contacts formed between the interfacial surfaces. These results provide the framework for the potential application of both clinically approved drugs for the treatment of Viperidae snakebites. (c) 2006 Elsevier Ltd. All rights reserved.

Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Configuration-Dependent Diffusion Dynamics of Downhill and Two-State Protein Folding

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

Infrared dynamics in (2+1) dimensions

In this work we study the asymptotic behavior of (2+1)-dimensional quantum electrodynamics in the infrared region. We show that an appropriate redefinition of the fermion current operator leads to an asymptotic evolution operator that contains a divergent Coulomb phase factor and a contribution from the electromagnetic field at large distances, factored from the evolution operator for free fields, and we conclude that the modified scattering operator maps two spaces of coherent states of the electromagnetic field, as in the Kulish-Faddeev model for QED (quantum electrodynamics) in four space-time dimensions.

PP-wave light-cone free string field theory at finite temperature

In this paper, a real-time formulation of light-cone pp-wave string field theory at finite temperature is presented. This is achieved by developing the thermo field dynamics (TFD) formalism in a second quantized string scenario. The equilibrium thermodynamic quantities for a pp-wave ideal string gas are derived directly from expectation values on the second quantized string thermal vacuum. Also, we derive the real-time thermal pp-wave closed string propagator. In the flat space limit it is shown that this propagator can be written in terms of Theta functions, exactly as the zero temperature one. At the end, we show how superstrings interactions can be introduced, making this approach suitable to study the BMN dictionary at finite temperature.

Solitary waves on a free surface of a heated Maxwell fluid

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Analytical study of the nonlinear behavior of a shape memory oscillator: Part I-primary resonance and free response at low temperatures

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Magnetic Field Line Escape: Comparison with Mean Free Path

In the present work, we determine the fraction of magnetic field lines that reach the tokamak wall leaving the plasma surrounded by a chaotic layer created by resonant perturbations at the plasma edge. The chaotic layer arises in a scenario where an integrable magnetic field with reversed magnetic shear is perturbed by an ergodic magnetic limiter. For each considered line, we calculate its connection length, i.e. the number of toroidal turns that the field lines complete before reaching the wall. We represent the results in the poloidal section in which the initial coordinates are chosen. We also estimate the radial profile of the fraction of field lines, for different temperatures, whose connection lengths are smaller than the electron collisional mean free path.

The Role of the Korteweg-de Vries Hierarchy in the N-Soliton Dynamics of the Shallow Water Wave Equation

We apply a multiple-time version of the reductive perturbation method to study long waves as governed by the shallow water wave model equation. As a consequence of the requirement of a secularity-free perturbation theory, we show that the well known N-soliton dynamics of the shallow water wave equation, in the particular case of α = 2β, can be reduced to the N-soliton solution that satisfies simultaneously all equations of the Korteweg-de Vries hierarchy.

Constraining the free parameter of the high parton density effects

The high parton density effects are strongly dependent of the spatial gluon distribution within the proton, with radius R, which cannot be derived from perturbative QCD. In this paper we assume that the unitarity corrections are present in the HERA kinematical region and constrain the value of R using the data for the proton structure function and its slope. We obtain that the gluons are not distributed uniformly in the whole proton disc, but behave as concentrated in smaller regions. (C) 2000 Elsevier Science B.V.

Free expansion of attractive and repulsive Bose-Einstein condensed vortex states

A numerical study of the time-dependent Gross-Pitaevskii equation for an axially symmetric trap to obtain insight into the free expansion of vortex states of BEC is presented. As such, the ratio of vortex-core radius to radia rms radius xc/xrms(<1) is found to play an interesting role in the free expansion of condensed vortex states. the larger this ratio, the more prominent is the vortex core and the easier is the possibility of experimental detection of vortex states.