Statistical physics approach to dendritic computation: The excitable-wave mean-field approximation

We analytically study the input-output properties of a neuron whose active dendritic tree, modeled as a Cayley tree of excitable elements, is subjected to Poisson stimulus. Both single-site and two-site mean-field approximations incorrectly predict a nonequilibrium phase transition which is not allowed in the model. We propose an excitable-wave mean-field approximation which shows good agreement with previously published simulation results [Gollo et al., PLoS Comput. Biol. 5, e1000402 (2009)] and accounts for finite-size effects. We also discuss the relevance of our results to experiments in neuroscience, emphasizing the role of active dendrites in the enhancement of dynamic range and in gain control modulation.

Beyond the diffraction limit of optical/IR interferometers I. Angular diameter and rotation parameters of Achernar from differential phases

Context. Spectrally resolved long-baseline optical/IR interferometry of rotating stars opens perspectives to investigate their fundamental parameters and the physical mechanisms that govern their interior, photosphere, and circumstellar envelope structures. Aims. Based on the signatures of stellar rotation on observed interferometric wavelength-differential phases, we aim to measure angular diameters, rotation velocities, and orientation of stellar rotation axes. Methods. We used the AMBER focal instrument at ESO-VLTI in its high-spectral resolution mode to record interferometric data on the fast rotator Achernar. Differential phases centered on the hydrogen Br gamma line (K band) were obtained during four almost consecutive nights with a continuous Earth-rotation synthesis during similar to 5h/night, corresponding to similar to 60 degrees position angle coverage per baseline. These observations were interpreted with our numerical code dedicated to long-baseline interferometry of rotating stars. Results. By fitting our model to Achernar's differential phases from AMBER, we could measure its equatorial radius R-eq = 11.6 +/- 0.3 R-circle dot, equatorial rotation velocity V-eq = 298 +/- 9 km s(-1), rotation axis inclination angle i = 101.5 +/- 5.2 degrees, and rotation axis position angle (from North to East) PA(rot) = 34.9 +/- 1.6 degrees. From these parameters and the stellar distance, the equatorial angular diameter circle divide(eq) of Achernar is found to be 2.45 +/- 0.09 mas, which is compatible with previous values derived from the commonly used visibility amplitude. In particular, circle divide(eq) and PA(rot) measured in this work with VLTI/AMBER are compatible with the values previously obtained with VLTI/VINCI. Conclusions. The present paper, based on real data, demonstrates the super-resolution potential of differential interferometry for measuring sizes, rotation velocities, and orientation of rotating stars in cases where visibility amplitudes are unavailable and/or when the star is partially or poorly resolved. In particular, we showed that differential phases allow the measurement of sizes up to similar to 4 times smaller than the diffraction-limited angular resolution of the interferometer.

Carlosbarbosaite, ideally (UO2)(2)Nb2O6(OH)(2)center dot 2H(2)O, a new hydrated uranyl niobate mineral with tunnels from Jaguaracu, Minas Gerais, Brazil: description and crystal structure

Carlosbarbosaite, ideally (UO2)(2)Nb2O6(OH)(2)center dot 2H(2)O, is a new mineral which occurs as a late cavity filling in albite in the Jaguaracu pegmatite, Jaguaracu municipality, Minas Gerais, Brazil. The name honours Carlos do Prado Barbosa (1917-2003). Carlosbarbosaite forms long flattened lath-like crystals with a very simple orthorhombic morphology. The crystals are elongated along [001] and flattened on (100); they are up to 120 mu m long and 2-5 mu m thick. The colour is cream to pale yellow, the streak yellowish white and the lustre vitreous. The mineral is transparent (as individual crystals) to translucent (massive). It is not fluorescent under either long-wave or short-wave ultraviolet radiation. Carlosbarbosaite is biaxial(+) with alpha = 1.760(5), beta = 1.775(5), gamma = 1.795(5), 2V(meas) = 70(1)degrees, 2V(calc) = 83 degrees. The orientation is X parallel to a, Y parallel to b, Z parallel to c. Pleochroism is weak, in yellowish green shades, which are most intense in the Z direction. Two samples were analysed. For sample I, the composition is: UO3 54.52, CaO 2.07, Ce2O3 0.33, Nd2O3 0.49, Nb2O5 14.11, Ta2O5 15.25, TiO2 2.20, SiO2 2.14, Fe2O3 1.08, Al2O3 0.73, H2O (calc.) 11.49, total 104.41 wt.%; the empirical formula is (square 0.68Ca0.28Nd0.02Ce0.02)(Sigma=1.00)[U-1.44 square O-0.56(2.88)(H2O)(1.12)](Nb0.80Ta0.52Si0.27Ti0.21Al0.11Fe0.10)(Sigma=2.01) O-4.72(OH)(3.20)(H2O)(2.08). For sample 2, the composition is: UO3 41.83, CaO 2.10, Ce2O3 0.31, Nd2O3 1.12, Nb2O5 14.64, Ta2O5 16.34, TiO2 0.95, SiO2 3.55, Fe2O3 0.89, Al2O3 0.71, H2O (calc.) 14.99, total 97.43 wt.%; the empirical formula is (square 0.67Ca0.27Nd0.05Ce0.01)(Sigma=1.00)[U-1.04 square O-0.96(2.08)(H2O)(1.92)] (Nb0.79Ta0.53Si0.42Ti0.08Al0.10Fe0.08)(Sigma=2.00)O-4.00(OH)(3.96)(H2O)(2.04). The ideal endmember formula is (UO2)(2)Nb2O6(OH)(2)center dot 2H(2)O. Calculated densities are 4.713 g cm(-3) (sample 1) and 4.172 g cm(-3) (sample 2). Infrared spectra show that both (OH) and H2O are present. The strongest eight X-ray powder-diffraction lines [listed as d in angstrom(I)(hkl)] are: 8.405(8)(110), 7.081(10)(200), 4.201(9)(220), 3.333(6)(202), 3.053(8)(022), 2.931(7)(420), 2.803(6)(222) and 2.589(5)(040,402). The crystal structure was solved using single-crystal X-ray diffraction (R = 0.037) which gave the following data: orthorhombic, Cmem, a = 14.150(6), b = 10.395(4), c = 7.529(3) angstrom, V = 1107(1) angstrom(3), Z = 4. The crystal structure contains a single U site with an appreciable deficiency in electron scattering, which is populated by U atoms and vacancies. The U site is surrounded by seven 0 atoms in a pentagonal bipyramidal arrangemet. The Nb site is coordinated by four 0 atoms and two OH groups in an octahedral arrangement. The half-occupied tunnel Ca site is coordinated by four 0 atoms and four H2O groups. Octahedrally coordinated Nb polyhedra share edges and comers to form Nb2O6(OH)(2) double chains, and edge-sharing pentagonal bipyramidal U polyhedra form UO5 chains. The Nb2O6(OH)(2) and UO5 chains share edges to form an open U-Nb-phi framework with tunnels along [001] that contain Ca(H2O)(4) clusters. Carlosbarbosaite is closely related to a family of synthetic U-Nb-O framework tunnel structures, it differs in that is has an (OH)-bearing framework and Ca(H2O)(4) tunnel occupant. The structure of carlosbarbosaite resembles that of holfertite.

Exploring the coordination chemistry of isomerizable terpyridine derivatives for successful analyses of cis and trans isomers by travelling wave ion mobility mass spectrometry

The photochemical cis-trans isomerization of the 4-{4-[2-(pyridin-4-yl)ethenyl]phenyl}-2,2': 6',2''-terpyridine ligand (vpytpy) was investigated by UV-vis, NMR and TWIM-MS. Ion mobility mass spectrometry was performed pursuing the quantification of the isomeric composition during photolysis, however an in-source trans-to-cis isomerization process was observed. In order to overcome this inherent phenomenon, the isomerization of the vpytpy species was suppressed by complexation, reacting with iron(II) ions, and forming the [Fe(vpytpy)(2)](2+) complex. The strategy of "freezing" the cis-trans isomerizable ligand at a given geometric conformation was effective, preventing further isomerization, thus allowing the distinction of each one of the isomers in the photolysed mixture. In addition, the experimental drift times were related to the calculated surface areas of the three possible cis-cis, cis-trans and trans-trans iron(II) complex isomers. The stabilization of the ligand in a given conformation also allows us to obtain the cis-cis and cis-trans complexes exhibiting the ligand in the metastable cis-conformation, as well as in the thermodynamically stable trans-conformation.

X-ray diffraction and theoretical investigation of the Gedunin crystal structure

The Gedunin compound (C28H34O6) is a natural product extracted from Trichilia pallida that has shown a wide activity. The crystallographic structure shows two conformers in the asymmetric unit, which differ in a rotation of the furan group. To understand this molecular arrangement, the density functional calculations. Molecular Electrostatic Potential (MEP) and thermodynamic function calculation have been performed at the B3LYP/6-311++g(d,p) level. Both conformers were optimized and the agreement with the experimental structure was very good, making possible further theoretical analysis of the structure. The inter-conversion between two conformers depends on the energy barrier. This process is studied in the vacuum and shows two transition states with a low energetic barrier for a potential energy curve scanning rigid around furan group: 4.37 kcal/mol and 16.52 kcal/mol. As the first transition state has a notably lower energetic barrier, the preferred inter-conversion pathway between the conformers involves the first rather than the second transition state. Understanding this transition state in detail led us to perform its optimization, showing an energetic barrier around 3.66 kcal/mol. The negative free energy and low enthalpy confirm that the process is spontaneous and exothermic. The results show that this requirement makes the existence of the two conformers in the asymmetric unit possible. The structure of molecules in the asymmetric unit is better understood when the MEP is used on the interaction between molecules. For Gedunin, both molecules have shown MEP with well-defined regions, and this behavior contributes to the observed link between molecules and for the negative regions complementing positive regions of another molecule. (C) 2011 Elsevier B.V. All rights reserved.

Crystallization and preliminary X-ray diffraction of malate dehydrogenase from Plasmodium falciparum

The expression, purification, crystallization and preliminary X-ray diffraction characterization of malate dehydrogenase (MDH) from the malarial parasite Plasmodium falciparum (PfMDH) are reported. In order to gain a deeper understanding of the function and role of PfMDH, the protein was purified to homogeneity. The purified protein crystallized in space group P1, with unit-cell parameters a = 72, b = 157, c = 159 angstrom, a = 105, beta = 101, ? = 95 degrees. The resulting crystals diffracted to a maximal resolution of 2.24 angstrom and the structure has been solved by molecular replacement, with 16 monomers in the asymmetric unit. The 16 monomers are arranged into four independent tetramers, in agreement with previous reports demonstrating the tetrameric solution state of PfMDH. The X-ray structure of PfMDH is expected to clarify the differences in catalysis by PfMDH compared with other MDH family members and to provide a basis for the structure-based design of specific PfMDH inhibitors as well as general MDH inhibitors.

Protomers: formation, separation and characterization via travelling wave ion mobility mass spectrometry

Travelling wave ion mobility mass spectrometry (TWIM-MS) with post-TWIM and pre-TWIM collision-induced dissociation (CID) experiments were used to form, separate and characterize protomers sampled directly from solutions or generated in the gas phase via CID. When in solution equilibria, these species were transferred to the gas phase via electrospray ionization, and then separated by TWIM-MS. CID performed after TWIM separation (post-TWIM) allowed the characterization of both protomers via structurally diagnostic fragments. Protonated aniline (1) sampled from solution was found to be constituted of a ca. 5:1 mixture of two gaseous protomers, that is, the N-protonated (1a) and ring protonated (1b) molecules, respectively. When dissociated, 1a nearly exclusively loses NH3, whereas 1b displays a much diverse set of fragments. When formed via CID, varying populations of 1a and 1b were detected. Two co-existing protomers of two isomeric porphyrins were also separated and characterized via post-TWIM CID. A deprotonated porphyrin sampled from a basic methanolic solution was found to be constituted predominantly of the protomer arising from deprotonation at the carboxyl group, which dissociates promptly by CO2 loss, but a CID-resistant protomer arising from deprotonation at a porphyrinic ring NH was also detected and characterized. The doubly deprotonated porphyrin was found to be constituted predominantly of a single protomer arising from deprotonation of two carboxyl groups. Copyright (C) 2012 John Wiley & Sons, Ltd.

Crystallization and preliminary X-ray diffraction analysis of three myotoxic phospholipases A2 from Bothrops brazili venom

Two myotoxic and noncatalytic Lys49-phospholipases A2 (braziliantoxin-II and MT-II) and a myotoxic and catalytic phospholipase A2 (braziliantoxin-III) from the venom of the Amazonian snake Bothrops brazili were crystallized. The crystals diffracted to resolutions in the range 2.562.05 angstrom and belonged to space groups P3121 (braziliantoxin-II), P6522 (braziliantoxin-III) and P21 (MT-II). The structures were solved by molecular-replacement techniques. Both of the Lys49-phospholipases A2 (braziliantoxin-II and MT-II) contained a dimer in the asymmetric unit, while the Asp49-phospholipase A2 braziliantoxin-III contained a monomer in its asymmetric unit. Analysis of the quaternary assemblies of the braziliantoxin-II and MT-II structures using the PISA program indicated that both models have a dimeric conformation in solution. The same analysis of the braziliantoxin-III structure indicated that this protein does not dimerize in solution and probably acts as a monomer in vivo, similar to other snake-venom Asp49-phospholipases A2.

Aortic distensibility measured by pulse-wave velocity is not modified in patients with Chagas' disease

Abstract Background Experimental studies demonstrate that infection with trypanosoma cruzi causes vasculitis. The inflammatory lesion process could hypothetically lead to decreased distensibility of large and small arteries in advanced Chagas' disease. We tested this hypothesis. Methods and results We evaluated carotid-femoral pulse-wave velocity (PWV) in 53 Chagas' disease patients compared with 31 healthy volunteers (control group). The 53 patients were classified into 3 groups: 1) 16 with indeterminate form of Chagas' disease; 2) 18 with Chagas' disease, electrocardiographic abnormalities, and normal systolic function; 3) 19 with Chagas' disease, systolic dysfunction, and mild-to-moderate congestive heart failure. No difference was noted between the 4 groups regarding carotid-femoral PWV (8.4 ± 1.1 vs 8.2 ± 1.5 vs 8.2 ± 1.4 vs 8.7 ± 1.6 m/s, P = 0.6) or pulse pressure (39.5 ± 7.6 vs 39.3 ± 8.1 vs 39.5 ± 7.4 vs 39.7 ± 6.9 mm Hg, P = 0.9). A positive, significant, similar correlation occurred between PWV and age in patients with Chagas' disease (r = 0.42, P = 0.002), in controls (r = 0.48, P = 0.006), and also between PWV and systolic blood pressure in both groups (patients with Chagas' disease, r = 0.38, P = 0.005; healthy subjects, r = 0.36, P = 0.043). Conclusion Carotid femoral pulse-wave velocity is not modified in patients with Chagas' disease, suggesting that elastic properties of large arteries are not affected in this disorder.

A control and automation system for wave basins

This paper presents the new active absorption wave basin, named Hydrodynamic Calibrator (HC), constructed at the University of São Paulo (USP), in the Laboratory facilities of the Numerical Offshore Tank (TPN). The square (14 m 14 m) tank is able to generate and absorb waves from 0.5 Hz to 2.0 Hz, by means of 148 active hinged flap wave makers. An independent mechanical system drives each flap by means of a 1HP servo-motor and a ball-screw based transmission system. A customized ultrasonic wave probe is installed in each flap, and is responsible for measuring wave elevation in the flap. A complex automation architecture was implemented, with three Programmable Logic Computers (PLCs), and a low-level software is responsible for all the interlocks and maintenance functions of the tank. Furthermore, all the control algorithms for the generation and absorption are implemented using higher level software (MATLAB /Simulink block diagrams). These algorithms calculate the motions of the wave makers both to generate and absorb the required wave field by taking into account the layout of the flaps and the limits of wave generation. The experimental transfer function that relates the flap amplitude to the wave elevation amplitude is used for the calculation of the motion of each flap. This paper describes the main features of the tank, followed by a detailed presentation of the whole automation system. It includes the measuring devices, signal conditioning, PLC and network architecture, real-time and synchronizing software and motor control loop. Finally, a validation of the whole automation system is presented, by means of the experimental analysis of the transfer function of the waves generated and the calculation of all the delays introduced by the automation system.

Reactive sputter magnetron reactor for preparation of thin films and simultaneous in-situ structural study by X-ray diffraction.

Reactive Sputter Magnetron (RSM) is a widely used technique to thin films growing of compounds both, in research laboratories and in industrial processes. The nature of the deposited compound will depend then on the nature of the magnetron target and the nature of the ions generated in the plasma. One important aspect of the problem is the knowledge of the evolution of the film during the process of growing itself. In this work, we present the design, construction of a chamber to be installed in the Huber goniometer in the XRD2 line of LNLS in Campinas, which allows in situ growing kinetic studies of thin films.

Crystallization and preliminary X-ray diffraction analysis of selenophosphate synthetases from Trypanosoma brucei and Leishmania major

Selenophosphate synthetase (SPS) plays an indispensable role in selenium metabolism, being responsible for catalyzing the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential selenium donor for selenocysteine synthesis. Recombinant full-length Leishmania major SPS (LmSPS2) was recalcitrant to crystallization. Therefore, a limited proteolysis technique was used and a stable N-terminal truncated construct (ΔN-LmSPS2) yielded suitable crystals. The Trypanosoma brucei SPS orthologue (TbSPS2) was crystallized by the microbatch method using paraffin oil. X-ray diffraction data were collected to resolutions of 1.9 Å for ΔN-LmSPS2 and 3.4 Å for TbSPS2.

Studies of Inorganic Layer and Framework Structures Using Time-, Temperature- and Pressure-Resolved Powder Diffraction Techniques

This thesis is concerned with in-situ time-, temperature- and pressure-resolved synchrotron X-ray powder diffraction investigations of a variety of inorganic compounds with twodimensional layer structures and three-dimensional framework structures. In particular, phase stability, reaction kinetics, thermal expansion and compressibility at non-ambient conditions has been studied for 1) Phosphates with composition MIV(HPO4)2·nH2O (MIV = Ti, Zr); 2) Pyrophosphates and pyrovanadates with composition MIVX2O7 (MIV = Ti, Zr and X = P, V); 3) Molybdates with composition ZrMo2O8. The results are compiled in seven published papers and two manuscripts. Reaction kinetics for the hydrothermal synthesis of α-Ti(HPO4)2·H2O and intercalation of alkane diamines in α-Zr(HPO4)2·H2O was studied using time-resolved experiments. In the high-temperature transformation of γ-Ti(PO4)(H2PO4)·2H2O to TiP2O7 three intermediate phases, γ'-Ti(PO4)(H2PO4)·(2-x)H2O, β-Ti(PO4)(H2PO4) and Ti(PO4)(H2P2O7)0.5 were found to crystallise at 323, 373 and 748 K, respectively. A new tetragonal three-dimensional phosphate phase called τ-Zr(HPO4)2 was prepared, and subsequently its structure was determined and refined using the Rietveld method. In the high-temperature transformation from τ-Zr(HPO4)2 to cubic α-ZrP2O7 two new orthorhombic intermediate phases were found. The first intermediate phase, ρ-Zr(HPO4)2, forms at 598 K, and the second phase, β-ZrP2O7, at 688 K. Their respective structures were solved using direct methods and refined using the Rietveld method. In-situ high-pressure studies of τ-Zr(HPO4)2 revealed two new phases, tetragonal ν-Zr(HPO4)2 and orthorhombic ω-Zr(HPO4)2 that crystallise at 1.1 and 8.2 GPa. The structure of ν-Zr(HPO4)2 was solved and refined using the Rietveld method. The high-pressure properties of the pyrophosphates ZrP2O7 and TiP2O7, and the pyrovanadate ZrV2O7 were studied up to 40 GPa. Both pyrophosphates display smooth compression up to the highest pressures, while ZrV2O7 has a phase transformation at 1.38 GPa from cubic to pseudo-tetragonal β-ZrV2O7 and becomes X-ray amorphous at pressures above 4 GPa. In-situ high-pressure studies of trigonal α-ZrMo2O8 revealed the existence of two new phases, monoclinic δ-ZrMo2O8 and triclinic ε-ZrMo2O8 that crystallises at 1.1 and 2.5 GPa, respectively. The structure of δ-ZrMo2O8 was solved by direct methods and refined using the Rietveld method.

Potential vorticity conserving flows and vortex-wave interaction : the role of vertical velocity and isopycnal diffusion on plankton heterogeneity

Programa de doctorado de oceanografía