14-3-3: Defense and regulatory proteins coding by Eucalyptus genome

The data mining of Eucalyptus ESTs genome finds four clusters (EGCEST2257E11.g, EGBGRT3213F11.g, and EGCCFB1223H11.g) from highly conservative 14-3-3 protein family which modulates a wide variety of cellular processes. Multiple alignments were built from twenty four sequences of 14-3-3 proteins searched into the GenBank databases and into the four pools of Eucalyptus genome programs. The alignment has shown two regions highly conservative on the sequences corresponding to the motifs of protein phosphorylation and nine highly conservative regions on the sequence corresponding to the linkage regions of alpha helices structure based on three dimensional of dimer functional structure. The differences of amino acid into the structural and functional domains of 14-3-3 plant protein were identified and can explain the functional diversity of different isoforms. The phylogenic protein trees were built by the maximum parsimony and neighborjoining procedures of Clustal X alignments and PAUP software for phylogenic analysis.

Three-dimensional structure of ribonuclease T-1 complexed with an isosteric phosphonate substrate analogue of GpU: Alternate substrate binding modes and catalysis

The X-ray crystal structure of a complex between ribonuclease T-1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2.0 Angstrom resolution. This Ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. on the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T-1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(S-p)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [:Steyaert, J., and Engleborghs (1995) fur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T-1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.

Thermodynamics of a Peyrard-Bishop One-Dimensional Lattice with On-site Hump Potential

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Three-Dimensional Modelling of Honeybee Venom Allergenic Proteases: Relation to Allergenicity

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

Mean-field model for Josephson oscillation in a Bose-Einstein condensate on an one-dimensional optical trap

Using the axially-symmetric time-dependent Gross-Pitaevskii equation we study the phase coherence in a repulsive Bose-Einstein condensate (BEC) trapped by a harmonic and an one-dimensional optical lattice potential to describe the experiment by Cataliotti et al. on atomic Josephson oscillation [Science 293, 843 (2001)]. The phase coherence is maintained after the BEC is set into oscillation by a small displacement of the magnetic trap along the optical lattice. The phase coherence in the presence of oscillating neutral current across an array of Josephson junctions manifests in an interference pattern formed upon free expansion of the BEC. The numerical response of the system to a large displacement of the magnetic trap is a classical transition from a coherent superfluid to an insulator regime and a subsequent destruction of the interference pattern in agreement With the more recent experiment by Cataliotti et al. [New J. Phys. 5, 71 (2003)].

Black soliton in a quasi-one-dimensional trapped fermion-fermion mixture

Employing a time dependent mean-field-hydrodynamic model we study the generation of black solitons in a degenerate fermion-fermion mixture in a cigar-shaped geometry using variational and numerical solutions. The black soliton is found to be the first stationary vibrational excitation of the system and is considered to be a nonlinear continuation of the vibrational excitation of the harmonic oscillator state. We illustrate the stationary nature of the black soliton, by studying different perturbations on it after its formation.

A model for Hopfions on the space-time S(3)xR

We construct static and time dependent exact soliton solutions for a theory of scalar fields taking values on a wide class of two dimensional target spaces, and defined on the four dimensional space-time S-3 X R. The construction is based on an ansatz built out of special coordinates on S3. The requirement for finite energy introduce boundary conditions that determine an infinite discrete spectrum of frequencies for the oscillating solutions. For the case where the target space is the sphere S-2, we obtain static soliton solutions with nontrivial Hopf topological charges. In addition, such Hopfions can oscillate in time, preserving their topological Hopf charge, with any of the frequencies belonging to that infinite discrete spectrum. (C) 2005 American Institute of Physics.

Dissipation-managed soliton in a quasi-one-dimensional Bose-Einstein condensate

We use the time-dependent mean-field Cross-Pitaevskii equation to study the formation of a dynamically-stabilized dissipation managed bright soliton in a quasi-one dimensional Bose-Einstein condensate (BEC). Because of three-body recombination of bosonic atoms to molecules, atoms are lost (dissipated) from a BEC. Such dissipation leads to the decay of a BEC soliton. We demonstrate by a perturbation procedure that an alimentation of atoms from an external source to the BEC may compensate for the dissipation loss and lead to a dynamically-stabilized soliton. The result of the analytical perturbation method is in excellent agreement with mean-field numerics. It seems possible to obtain such a dynamically stabilized BEC soliton without dissipation in laboratory.

Lie symmetry analysis and reductions of a two-dimensional integrable generalization of the Camassa-Holm equation

In this Letter we investigate Lie symmetries of a (2 + 1)-dimensional integrable generalization of the Camassa-Holm (CH) equation. Through the similarity reductions we obtain four different (1 + 1)-dimensional systems of partial differential equations in which one of them turns out to be a (1 + 1)-dimensional CH equation. We establish their integrability by providing the Lax pair for all of them. Further, we present a brief analysis for some types of particular solutions which include the cuspon, peakon and soliton solutions for the two-dimensional generalization of the CH equation. (C) 2000 Published by Elsevier B.V. B.V.

Propagator, tree-level unitarity and effective nonrelativistic potential for three-dimensional higher-derivative gravity augmented by a gravitational Chern-Simons term

An algorithm for computing the propagator for three-dimensional quadratic gravity with a gravitational Chern-Simons term, based on an extension of the three-dimensional Barnes-Rivers operators, is proposed. A systematic study of the tree-level unitarity of this theory is developed and its agreement with Newton's law is investigated by computing the effective nonrelativistic potential. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Is it physically sound to add a topologically massive term to three-dimensional massive electromagnetic or gravitational models?

The addition of a topologically massive term to an admittedly nonunitary three-dimensional massive model, be it an electromagnetic system or a gravitational one, does not cure its nonunitarity. What about the enlargement of avowedly unitary massive models by way of a topologically massive term? the electromagnetic models remain unitary after the topological augmentation but, surprisingly enough, the gravitational ones have their unitarity spoiled. Here we analyze these issues and present the explanation why unitary massive gravitational models, unlike unitary massive electromagnetic ones, cannot coexist from the viewpoint of unitarity with topologically massive terms. We also discuss the novel features of the three-term effective field models that are gauge-invariant.

Spinning Hopf solitons on S-3 x R

We consider a field theory with target space being the two dimensional sphere S-2 and defined on the space-time S-3 x R. The Lagrangean is the square of the pull-back of the area form on S-2. It is invariant under the conformal group SO(4, 2) and the infinite dimensional group of area preserving diffeomorphisms of S-2. We construct an infinite number of exact soliton solutions with non-trivial Hopf topological charges. The solutions spin with a frequency which is bounded above by a quantity proportional to the inverse of the radius of S-3. The construction of the solutions is made possible by an ansatz which explores the conformal symmetry and a U(1) subgroup of the area preserving diffeomorphism group.

Higher-derivative theory of (2+1)-dimensional gravity

Higher-derivative gravity in 2 + 1 dimensions is considered. The general solution of the linearized field equations in a three-dimensional version of the Teyssandier gauge is obtained, and from that the solution for a static pointlike source is found. The deflection of light rays is also analysed. (C) 2001 Elsevier B.V. B.V. All rights reserved.

Mean-field model for the interference of matter-waves from a three-dimensional optical trap

Using the mean-field time-dependent Gross-Pitaevskii equation we study the formation of a repulsive Bose-Einstein condensate on a combined optical and harmonic traps in two and three dimensions and subsequent generation of the interference pattern upon the removal of the combined traps as in the experiment by, Greiner et al. [Nature (London 415 (2002) 39]. For optical traps of moderate strength, interference pattern of 27 (9) prominent bright spots is found to be formed in three. (two) dimensions on a cubic (square) lattice in agreement with experiment. Similar interference pattern can also be formed upon removal of the optical lattice trap only. The pattern so formed can oscillate for a long time in the harmonic trap which can be observed experimentally. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Formation of soliton trains in Bose-Einstein condensates as a nonlinear Fresnel diffraction of matter waves

The problem of generation of atomic soliton trains in elongated Bose-Einstein condensates is considered in framework of Whitham theory of modulations of nonlinear waves. Complete analytical solution is presented for the case when the initial density distribution has sharp enough boundaries. In this case the process of soliton train formation can be viewed as a nonlinear Fresnel diffraction of matter waves. Theoretical predictions are compared with results of numerical simulations of one- and three-dimensional Gross-Pitaevskii equation and with experimental data on formation of Bose-Einstein bright solitons in cigar-shaped traps. (C) 2003 Elsevier B.V. All rights reserved.