Black-box decomposition approach for computational hemodynamics: One-dimensional models

Increasing efforts exist in integrating different levels of detail in models of the cardiovascular system. For instance, one-dimensional representations are employed to model the systemic circulation. In this context, effective and black-box-type decomposition strategies for one-dimensional networks are needed, so as to: (i) employ domain decomposition strategies for large systemic models (1D-1D coupling) and (ii) provide the conceptual basis for dimensionally-heterogeneous representations (1D-3D coupling, among various possibilities). The strategy proposed in this article works for both of these two scenarios, though the several applications shown to illustrate its performance focus on the 1D-1D coupling case. A one-dimensional network is decomposed in such a way that each coupling point connects two (and not more) of the sub-networks. At each of the M connection points two unknowns are defined: the flow rate and pressure. These 2M unknowns are determined by 2M equations, since each sub-network provides one (non-linear) equation per coupling point. It is shown how to build the 2M x 2M non-linear system with arbitrary and independent choice of boundary conditions for each of the sub-networks. The idea is then to solve this non-linear system until convergence, which guarantees strong coupling of the complete network. In other words, if the non-linear solver converges at each time step, the solution coincides with what would be obtained by monolithically modeling the whole network. The decomposition thus imposes no stability restriction on the choice of the time step size. Effective iterative strategies for the non-linear system that preserve the black-box character of the decomposition are then explored. Several variants of matrix-free Broyden`s and Newton-GMRES algorithms are assessed as numerical solvers by comparing their performance on sub-critical wave propagation problems which range from academic test cases to realistic cardiovascular applications. A specific variant of Broyden`s algorithm is identified and recommended on the basis of its computer cost and reliability. (C) 2010 Elsevier B.V. All rights reserved.

Numerical solution of the PTT constitutive equation for unsteady three-dimensional free surface flows

This work deals with the development of a numerical technique for simulating three-dimensional viscoelastic free surface flows using the PTT (Phan-Thien-Tanner) nonlinear constitutive equation. In particular, we are interested in flows possessing moving free surfaces. The equations describing the numerical technique are solved by the finite difference method on a staggered grid. The fluid is modelled by a Marker-and-Cell type method and an accurate representation of the fluid surface is employed. The full free surface stress conditions are considered. The PTT equation is solved by a high order method, which requires the calculation of the extra-stress tensor on the mesh contours. To validate the numerical technique developed in this work flow predictions for fully developed pipe flow are compared with an analytic solution from the literature. Then, results of complex free surface flows using the FIT equation such as the transient extrudate swell problem and a jet flowing onto a rigid plate are presented. An investigation of the effects of the parameters epsilon and xi on the extrudate swell and jet buckling problems is reported. (C) 2010 Elsevier B.V. All rights reserved.

Numerical Solution of the Upper-Convected Maxwell Model for Three-Dimensional Free Surface Flows

This work presents a finite difference technique for simulating three-dimensional free surface flows governed by the Upper-Convected Maxwell (UCM) constitutive equation. A Marker-and-Cell approach is employed to represent the fluid free surface and formulations for calculating the non-Newtonian stress tensor on solid boundaries are developed. The complete free surface stress conditions are employed. The momentum equation is solved by an implicit technique while the UCM constitutive equation is integrated by the explicit Euler method. The resulting equations are solved by the finite difference method on a 3D-staggered grid. By using an exact solution for fully developed flow inside a pipe, validation and convergence results are provided. Numerical results include the simulation of the transient extrudate swell and the comparison between jet buckling of UCM and Newtonian fluids.

Thermodynamic characterization of the palm tree Roystonea regia peroxidase stability

The structural stability of a peroxidase, a dimeric protein from royal palm tree (Roystonea regia) leaves, has been characterized by high-sensitivity differential scanning calorimetry, circular dichroism, steady-state tryptophan fluorescence and analytical ultracentifugation under different solvent conditions. It is shown that the thermal and chemical (using guanidine hydrochloride (Gdn-HCl)) folding/unfolding of royal palm tree peroxidase (RPTP) at pH 7 is a reversible process involving a highly cooperative transition between the folded dimer and unfolded monomers, with a free stabilization energy of about 23 kcal per mol of monomer at 25 degrees C. The structural stability of RPTP is pH-dependent. At pH 3, where ion pairs have disappeared due to protonation, the thermally induced denaturation of RPTP is irreversible and strongly dependent upon the scan rate, suggesting that this process is under kinetic control. Moreover, thermally induced transitions at this pH value are dependent on the protein concentration, allowing it to be concluded that in solution RPTP behaves as dimer, which undergoes thermal denaturation coupled with dissociation. Analysis of the kinetic parameters of RPTP denaturation at pH 3 was accomplished on the basis of the simple kinetic scheme N ->(k) D, where k is a first-order kinetic constant that changes with temperature, as given by the Arrhenius equation; N is the native state, and D is the denatured state, and thermodynamic information was obtained by extrapolation of the kinetic transition parameters to an infinite heating rate. Obtained in this way, the value of RPTP stability at 25 degrees C is ca. 8 kcal per mole of monomer lower than at pH 7. In all probability, this quantity reflects the contribution of ion pair interactions to the structural stability of RPTP. From a comparison of the stability of RPTP with other plant peroxidases it is proposed that one of the main factors responsible for the unusually high stability of RPTP which enhances its potential use for biotechnological purposes, is its dimerization. (c) 2008 Elsevier Masson SAS. All rights reserved.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Resprouting from roots in four Brazilian tree species

Previous studies pointed out that species richness and high density values within the Leguminosae in Brazilian forest fragments affected by fire could be due, at least partially, to the high incidence of root sprouting in this family. However, there are few Studies of the factors that induce root sprouting in woody plants after disturbance. We investigated the bud formation on root cuttings, and considered a man-made disturbance that isolates the root from the shoot apical dominance of three Leguminosae (Bauhinia forficata Link., Centrolobium tomentosum Guill. ex Benth, and Inga laurina (Sw.) Willd) and one Rutaceae (Esenbeckia febrifuga (St. Hit.) Juss. ex Mart.). All these species resprout frequently after fire. We also attempted to induce bud formation on root systems by removing the main trunk, girdling or sectioning the shallow lateral roots from forest tree species Esenbeckia febrifuga and Hymenaea courbaril L. We identified the origin of shoot primordia and their early development by fixing the samples in Karnovsky solution, dehydrating in ethyl alcohol series and embedding in plastic resin. Serial sections were cut on a rotary microtome and stained with toluidine blue O. Permanent slides were mounted in synthetic resin. We observed different modes of bud origin on root cuttings: close to the vascular cambium (C. tomentosum), from the callus (B. forficata and E febrifuga) and from the phloematic parenchyma proliferation (L laurina). Fragments of B. forficala root bark were also capable of forming reparative buds from healing phellogen formed in callus in the bark's inner side. In the attempt of bud induction on root systems, Hymenaea courbaril did not respond to any of the induction tests, probably because of plant age. However, Esenbeckia febrifuga roots formed suckers when the main trunk was removed or their roots were sectioned and isolated from the original plant. We experimentally demonstrated the ability of four tree species to resprout from roots after disturbance. Our results suggest that the release of apical dominance enables root resprouting in the studied species. Rev. Biol. Trop. 57 (3): 789-800. Epub 2009 September 30.

Crossover between the extended and localized regimes in stochastic partially self-avoiding walks in one-dimensional disordered systems

Consider N sites randomly and uniformly distributed in a d-dimensional hypercube. A walker explores this disordered medium going to the nearest site, which has not been visited in the last mu (memory) steps. The walker trajectory is composed of a transient part and a periodic part (cycle). For one-dimensional systems, travelers can or cannot explore all available space, giving rise to a crossover between localized and extended regimes at the critical memory mu(1) = log(2) N. The deterministic rule can be softened to consider more realistic situations with the inclusion of a stochastic parameter T (temperature). In this case, the walker movement is driven by a probability density function parameterized by T and a cost function. The cost function increases as the distance between two sites and favors hops to closer sites. As the temperature increases, the walker can escape from cycles that are reminiscent of the deterministic nature and extend the exploration. Here, we report an analytical model and numerical studies of the influence of the temperature and the critical memory in the exploration of one-dimensional disordered systems.

Three-dimensional visualization of human hemoglobin phenotypes with HPLC

Hemoglobinopathies were included in the Brazilian Neonatal Screening Program on June 6, 2001. Automated high-performance liquid chromatography (HPLC) was indicated as one of the diagnostic methods. The amount of information generated by these systems is immense, and the behavior of groups cannot always be observed in individual analyses. Three-dimensional (3-D) visualization techniques can be applied to extract this information, for extracting patterns, trends or relations from the results stored in databases. We applied the 3-D visualization tool to analyze patterns in the results of hemoglobinopathy based on neonatal diagnosis by HPLC. The laboratory results of 2520 newborn analyses carried out in 2001 and 2002 were used. The ""Fast"", ""F1"", ""F"" and ""A"" peaks, which were detected by the analytical system, were chosen as attributes for mapping. To establish a behavior pattern, the results were classified into groups according to hemoglobin phenotype: normal (N = 2169), variant (N = 73) and thalassemia (N = 279). 3-D visualization was made with the FastMap DB tool; there were two distribution patterns in the normal group, due to variation in the amplitude of the values obtained by HPLC for the F1 window. It allowed separation of the samples with normal Hb from those with alpha thalassemia, based on a significant difference (P < 0.05) between the mean values of the ""Fast"" and ""A"" peaks, demonstrating the need for better evaluation of chromatograms; this method could be used to help diagnose alpha thalassemia in newborns.

Analytical solutions for Tokamak equilibria with reversed toroidal current

In tokamaks, an advanced plasma confinement regime has been investigated with a central hollow electric current with negative density which gives rise to non-nested magnetic surfaces. We present analytical solutions for the magnetohydrodynamic equilibria of this regime in terms of non-orthogonal toroidal polar coordinates. These solutions are obtained for large aspect ratio tokamaks and they are valid for any kind of reversed hollow current density profiles. The zero order solution of the poloidal magnetic flux function describes nested toroidal magnetic surfaces with a magnetic axis displaced due to the toroidal geometry. The first order correction introduces a poloidal field asymmetry and, consequently, magnetic islands arise around the zero order surface with null poloidal magnetic flux gradient. An analytic expression for the magnetic island width is deduced in terms of the equilibrium parameters. We give examples of the equilibrium plasma profiles and islands obtained for a class of current density profile. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3624551]

Localized modes of binary mixtures of Bose-Einstein condensates in nonlinear optical lattices

The properties of the localized states of a two-component Bose-Einstein condensate confined in a nonlinear periodic potential (nonlinear optical lattice) are investigated. We discuss the existence of different types of solitons and study their stability by means of analytical and numerical approaches. The symmetry properties of the localized states with respect to nonlinear optical lattices are also investigated. We show that nonlinear optical lattices allow the existence of bright soliton modes with equal symmetry in both components and bright localized modes of mixed symmetry type, as well as dark-bright bound states and bright modes on periodic backgrounds. In spite of the quasi-one-dimensional nature of the problem, the fundamental symmetric localized modes undergo a delocalizing transition when the strength of the nonlinear optical lattice is varied. This transition is associated with the existence of an unstable solution, which exhibits a shrinking (decaying) behavior for slightly overcritical (undercritical) variations in the number of atoms.

Orbital multicriticality in spin-gapped quasi-one-dimensional antiferromagnets

Motivated by the quasi-one-dimensional antiferromagnet CaV(2)O(4), we explore spin-orbital systems in which the spin modes are gapped but orbitals are near a macroscopically degenerate classical transition. Within a simplified model we show that gapless orbital liquid phases possessing power-law correlations may occur without the strict condition of a continuous orbital symmetry. For the model proposed for CaV(2)O(4), we find that an orbital phase with coexisting order parameters emerges from a multicritical point. The effective orbital model consists of zigzag-coupled transverse field Ising chains. The corresponding global phase diagram is constructed using field theory methods and analyzed near the multicritical point with the aid of an exact solution of a zigzag XXZ model.

Energy spectra for quantum wires and two-dimensional electron gases in magnetic fields with Rashba and Dresselhaus spin-orbit interactions

We introduce an analytical approximation scheme to diagonalize parabolically confined two-dimensional (2D) electron systems with both the Rashba and Dresselhaus spin-orbit interactions. The starting point of our perturbative expansion is a zeroth-order Hamiltonian for an electron confined in a quantum wire with an effective spin-orbit induced magnetic field along the wire, obtained by properly rotating the usual spin-orbit Hamiltonian. We find that the spin-orbit-related transverse coupling terms can be recast into two parts W and V, which couple crossing and noncrossing adjacent transverse modes, respectively. Interestingly, the zeroth-order Hamiltonian together with W can be solved exactly, as it maps onto the Jaynes-Cummings model of quantum optics. We treat the V coupling by performing a Schrieffer-Wolff transformation. This allows us to obtain an effective Hamiltonian to third order in the coupling strength k(R)l of V, which can be straightforwardly diagonalized via an additional unitary transformation. We also apply our approach to other types of effective parabolic confinement, e. g., 2D electrons in a perpendicular magnetic field. To demonstrate the usefulness of our approximate eigensolutions, we obtain analytical expressions for the nth Landau-level g(n) factors in the presence of both Rashba and Dresselhaus couplings. For small values of the bulk g factors, we find that spin-orbit effects cancel out entirely for particular values of the spin-orbit couplings. By solving simple transcendental equations we also obtain the band minima of a Rashba-coupled quantum wire as a function of an external magnetic field. These can be used to describe Shubnikov-de Haas oscillations. This procedure makes it easier to extract the strength of the spin-orbit interaction in these systems via proper fitting of the data.

Contribution of the second Landau level to the exchange energy of the three-dimensional electron gas in a high magnetic field

We derive a closed analytical expression for the exchange energy of the three-dimensional interacting electron gas in strong magnetic fields, which goes beyond the quantum limit (L=0) by explicitly including the effect of the second, L=1, Landau level and arbitrary spin polarization. The inclusion of the L=1 level brings the fields to which the formula applies closer to the laboratory range, as compared to previous expressions, valid only for L=0 and complete spin polarization. We identify and explain two distinct regimes separated by a critical density n(c). Below n(c), the per particle exchange energy is lowered by the contribution of L=1, whereas above n(c) it is increased. As special cases of our general equation we recover various known more limited results for higher fields, and we identify and correct a few inconsistencies in some of these earlier expressions.

Solution structure of the human signaling protein RACK1

Background: The adaptor protein RACK1 (receptor of activated kinase 1) was originally identified as an anchoring protein for protein kinase C. RACK1 is a 36 kDa protein, and is composed of seven WD repeats which mediate its protein-protein interactions. RACK1 is ubiquitously expressed and has been implicated in diverse cellular processes involving: protein translation regulation, neuropathological processes, cellular stress, and tissue development. Results: In this study we performed a biophysical analysis of human RACK1 with the aim of obtaining low resolution structural information. Small angle X-ray scattering (SAXS) experiments demonstrated that human RACK1 is globular and monomeric in solution and its low resolution structure is strikingly similar to that of an homology model previously calculated by us and to the crystallographic structure of RACK1 isoform A from Arabidopsis thaliana. Both sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation techniques showed that RACK1 is predominantly a monomer of around 37 kDa in solution, but also presents small amounts of oligomeric species. Moreover, hydrodynamic data suggested that RACK1 has a slightly asymmetric shape. The interaction of RACK1 and Ki1/57 was tested by sedimentation equilibrium. The results suggested that the association between RACK1 and Ki-1/57(122-413) follows a stoichiometry of 1:1. The binding constant (KB) observed for RACK1-Ki-1/57(122-413) interaction was of around (1.5 +/- 0.2) x 10(6) M(-1) and resulted in a dissociation constant (KD) of (0.7 +/- 0.1) x 10(-6) M. Moreover, the fluorescence data also suggests that the interaction may occur in a cooperative fashion. Conclusion: Our SAXS and analytical ultracentrifugation experiments indicated that RACK1 is predominantly a monomer in solution. RACK1 and Ki-1/57(122-413) interact strongly under the tested conditions.

Green Chemistry-Sensitive Analytical Procedure for Photometric Determination of Orthophosphate in River and Tap Water by Use of a Simple LED-Based Photometer

In the current work a Green Analytical Chemistry (GAC) procedure for photometric determination of orthophosphate in river water at mu g L-1 concentration level is described. The flow system module and the LED-based photometer were assembled together to constitute a compact unit in order to allow that a flow cell with optical path-length of 100mm was coupled to them. The photometric procedure based on the molybdenum blue method was implemented employing the multicommuted flow injection analysis approach, which provided facilities to allow reduction of reagent consumption and as well as waste generation. Aiming to prove the usefulness of the system, orthophosphate in river and tap waters was determined. Accuracy was ascertained by spiking samples with orthophosphate solution yielding recoveries ranging from 96% up to 107%. Other profitable features such as a wide linear response range between 10 to 800 mu g L-1 [image omitted]; a detection limit (3 sigma criterion) of 2.4 mu g L-1 [image omitted]; a relative standard deviation (n=7) of 2% using a typical water sample with concentration of 120 mu g L-1 [image omitted]; reagent consumption of 3.0mg ammonium molybdate, 0.3mg hydrazine sulfate, and 0.03mg stannous chloride per determination; a waste generation of 2.4mL per determination; and a sampling throughput of 20 determination per hours were also achieved.