Select-divide-and-conquer method for large-scale configuration interaction

A select-divide-and-conquer variational method to approximate configuration interaction (CI) is presented. Given an orthonormal set made up of occupied orbitals (Hartree-Fock or similar) and suitable correlation orbitals (natural or localized orbitals), a large N-electron target space S is split into subspaces S0,S1,S2,...,SR. S0, of dimension d0, contains all configurations K with attributes (energy contributions, etc.) above thresholds T0={T0egy, T0etc.}; the CI coefficients in S0 remain always free to vary. S1 accommodates KS with attributes above T1≤T0. An eigenproblem of dimension d0+d1 for S0+S 1 is solved first, after which the last d1 rows and columns are contracted into a single row and column, thus freezing the last d1 CI coefficients hereinafter. The process is repeated with successive Sj(j≥2) chosen so that corresponding CI matrices fit random access memory (RAM). Davidson's eigensolver is used R times. The final energy eigenvalue (lowest or excited one) is always above the corresponding exact eigenvalue in S. Threshold values {Tj;j=0, 1, 2,...,R} regulate accuracy; for large-dimensional S, high accuracy requires S 0+S1 to be solved outside RAM. From there on, however, usually a few Davidson iterations in RAM are needed for each step, so that Hamiltonian matrix-element evaluation becomes rate determining. One μhartree accuracy is achieved for an eigenproblem of order 24 × 106, involving 1.2 × 1012 nonzero matrix elements, and 8.4×109 Slater determinants

The M1 matrix protein controls the filamentous phenotype of influenza A virus

We show that most isolates of influenza A induce filamentous changes in infected cells in contrast to A/WSN/33 and A/PR8/34 strains which have undergone extensive laboratory passage and are mouse-adapted. Using reverse genetics, we created recombinant viruses in the naturally filamentous genetic background of A/Victoria/3/75 and established that this property is regulated by the M1 protein sequence, but that the phenotype is complex and several residues are involved. The filamentous phenotype was lost when the amino acid at position 41 was switched from A to V, at the same time, this recombinant virus also became insensitive to the antibody 14C2. On the other hand, the filamentous phenotype could be fully transferred to a virus containing RNA segment 7 of the A/WSN/33 virus by a combination of three mutations in both the amino and carboxy regions of the M1 protein. This observation suggests that an interaction among these regions of M1 may occur during assembly. (C) 2004 Elsevier Inc. All rights reserved.

The interaction of flexural-gravity waves with periodic geometries

A periodic structure of finite extent is embedded within an otherwise uniform two-dimensional system consisting of finite-depth fluid covered by a thin elastic plate. An incident harmonic flexural-gravity wave is scattered by the structure. By using an approximation to the corresponding linearised boundary value problem that is based on a slowly varying structure in conjunction with a transfer matrix formulation, a method is developed that generates the whole solution from that for just one cycle of the structure, providing both computational savings and insight into the scattering process. Numerical results show that variations in the plate produce strong resonances about the ‘Bragg frequencies’ for relatively few periods. We find that certain geometrical variations in the plate generate these resonances above the Bragg value, whereas other geometries produce the resonance below the Bragg value. The familiar resonances due to periodic bed undulations tend to be damped by the plate.

Delayed local inflammatory response induced by Thalassophryne nattereri venom is related to extracellular matrix degradation

Symptoms evoked by Thalassophryne nattereri fish envenomation include local oedema, severe pain and intense necrosis with strikingly inefficient healing, continuing for several weeks or months. Investigations carried out in our laboratory showed that, in the venom-induced acute inflammation, thrombosis in venules and constrictions in arterioles were highly visible, in contrast to a notable lack of inflammatory cell. Nevertheless, the reason that the venom toxins favour delayed local inflammatory response is poorly defined. In this study, we analysed the movement of leucocytes after T. nattereri venom injection in the intraplantar region of Swiss mice, the production of pro-inflammatory mediators and the venom potential to elicit matrix metalloproteinase production and extracellular matrix degradation. Total absence of mononuclear and neutrophil influx was observed until 14 days, but the venom stimulates pro-inflammatory mediator secretion. Matrix metalloproteinases (MMP)-2 and MMP-9 were detected in greater quantities, accompanied by tissue degradation of collagenous fibre. An influx of mononuclear cells was noted very late and at this time the levels of IL-6, IL-1 beta and MMP-2 remained high. Additionally, the action of venom on the cytoskeletal organization was assessed in vitro. Swift F-actin disruption and subsequent loss of focal adhesion was noted. Collectively these findings show that the altered specific interaction cell-matrix during the inflammatory process creates an inadequate environment for infiltration of inflammatory cells.

On S-matrix factorization of the Landau-Lifshitz model

We consider the three-particle scattering S-matrix for the Landau-Lifshitz model by directly computing the set of the Feynman diagrams up to the second order. We show, following the analogous computations for the non-linear Schrdinger model [1, 2], that the three-particle S-matrix is factorizable in the first non-trivial order.

Columnar joints in the Patino Formation sandstones, Eastern Paraguay: a dynamic interaction between dyke intrusion, quartz dissolution and cooling-induced fractures

The Patino Formation sandstones, which crop out in Aregua neighborhood in Eastern Paraguay and show columnar joints near the contact zone with a nephelinite dyke, have as their main characteristics the high proportion of syntaxial quartz overgrowth and a porosity originated from different processes, initially by dissolution and later by partial filling and fracturing. Features like the presence of floating grains in the syntaxial cement, the transitional interpenetrative contact between the silica-rich cement and grains as well as the intense fracture porosity are strong indications that the cement has been formed by dissolution and reprecipitation of quartz from the framework under the effect of thermal expansion followed by rapid contraction. The increase of the silica-rich cement towards the dyke in association with the orthogonal disposition of the columns relative to dyke walls are indicative that the igneous body may represent the main heat source for the interstitial aqueous solutions previously existing in the sediments. At macroscopic scale, the increasing of internal tensions in the sandstones is responsible for the nucleation of polygons, leading to the individualization of prisms, which are interconnected by a system of joints, formed firstly on isotherm surfaces of low temperature and later on successive adjacent planes towards the dyke heat source.

Incorporation of Ag nanoparticles into membrane mimetic systems composed by phospholipid layer-by-layer (LbL) films to achieve surface-enhanced Raman scattering as a tool in drug interaction studies

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

Pathogenesis II: Fungal responses to host responses: interaction of host cells with fungi

Most of our knowledge concerning the virulence determinants of pathogenic fungi comes from the infected host, mainly from animal models and more recently from in vitro studies with cell cultures. The fungi usually present intra- and/or extracellular host-parasite interfaces, with the parasitism phenomenon dependent on complementary surface molecules. Among living organisms, this has been characterized as a cohabitation event, where the fungus is able to recognize specific host tissues acting as an attractant, creating stable conditions for its survival. Several fungi pathogenic for humans and animals have evolved special strategies to deliver elements to their cellular targets that may be relevant to their pathogenicity. Most of these pathogens express surface factors that mediate binding to host cells either directly or indirectly, in the latter case binding to host adhesion components such as extracellular matrix (ECM) proteins, which act as 'interlinking' molecules. The entry of the pathogen into the host cell is initiated by fungal adherence to the cell surface, which generates an uptake signal that may induce its cytoplasmic internalization. Once this is accomplished, some fungi are able to alter the host cytoskeletal architecture, as manifested by a rearrangement of microtubule and microfilament proteins, and this can also induce epithelial host cells to become apoptotic. It is possible that fungal pathogens induce modulation of different host cell pathways in order to evade host defences and to foster their own proliferation. For a number of pathogens, the ability to bind ECM glycoproteins, the capability of internalization and the induction of apoptosis are considered important factors in virulence. Furthermore, specific recognition between fungal parasites and their host cell targets may be mediated by the interaction of carbohydrate-binding proteins, e.g., lectins on the surface of one type of cell, probably a parasite, that combine with complementary sugars on the surface of host-cell. These interactions supply precise models to study putative adhesins and receptor-containing molecules in the context of the fungus-host interface. The recognition of the host molecules by fungi such as Aspergillus fumigatus, Paracoccidioides brasiliensis and Histoplasma capsulatum, and their molecular mechanisms of adhesion and invasion, are reviewed in this paper.

Binding of extracellular matrix proteins to Paracoccidioides brasiliensis

Adhesion to extracellular matrix (ECM) proteins plays a crucial role in invasive fungal diseases. ECM proteins bind to the surface of Paracoccidioides brasiliensis yeast cells in distinct qualitative patterns. Extracts from Pb18 strain, before (18a) and after animal inoculation (18b), exhibited differential adhesion to ECM components. Pb18b extract had a higher capacity for binding to ECM components than Pb18a. Laminin was the most adherent component for both samples, followed by type I collagen, fibronectin, and type IV collagen for Pb18b. A remarkable difference was seen in the interaction of the two extracts with fibronectin and their fragments. Pb18b extract interacted significantly with the 120-kDa fragment. Ligand affinity binding assays showed that type I collagen recognized two components (47 and 80 kDa) and gp43 bound both fibronectin and laminin. The peptide 1 (NLGRDAKRHL) from gp43, with several positively charged amino acids, contributed most to the adhesion of P. brasiliensis to Vero cells. Synthetic peptides derived from peptide YIGRS of laminin or from RGD of both laminin and fibronectin showed the greatest inhibition of adhesion of gp43 to Vero cells. In conclusion, this work provided new molecular details on the interaction between P. brasiliensis and ECNI components. (c) 2006 Elsevier SAS. All rights reserved.

Diffusion of Interstitial Elements in Ti Alloys used as Biomaterials

Titanium alloys are excellent implant materials for orthopedic applications due to their desirable properties, such as good corrosion resistance, low elasticity modulus, and excellent biocompatibility. The presence of interstitial elements (such as oxygen and nitrogen) causes strong changes in the material's mechanical properties, mainly in its elastic properties. Study of the interaction among interstitial elements present in metals began with Snoek's postulate, that a stress-induced ordering of interstitials gives rise to a peak in the mechanical relaxation (internal friction) spectra. In the mechanical relaxation spectra, each species of interstitial solute atom gives rise to a distinct Snoek's peak, whose temperature and position depend on the measurement frequency. This effect is very interesting because its peculiar parameters are directly related to the diffusion coefficient (D) for the interstitial solute. This paper presents a study of diffusion of heavy interstitial elements in Ti-35Nb-7Zr-5Ta alloys using mechanical spectroscopy. Pre-exponential factors and activation energies are calculated for oxygen and nitrogen in theses alloys.

Diffusion of Interstitial Solutes in Nb-46wt% Ti Alloys Measured by Mechanical Spectroscopy

The mechanical properties of metals with a body-centered cubic (bcc) structure, such as Nb, Ta, V, and their alloys, are modified with the introduction of interstitial impurities, such as O, N, C, or H. These metals can dissolve great amounts of O and N, for example, to form solid solutions. The interstitial solute atoms (ISA) in metals with a bcc structure occupy octahedral sites and cause local distortion with tetragonal symmetry. So ISA in these metals forms an elastic dipole that can align along one of the three cubic axis of the crystal. In the present paper, the torsion pendulum technique was employed for the investigation of various interactions among the metallic matrix and different interstitial solutes in the Nb-46wt%Ti alloy. From the relaxation spectra, we obtained the diffusion coefficients, pre-exponential factors, and activation energies for nitrogen in the Nb-46wt%Ti alloy.

Diffusion of Oxygen and Nitrogen in the Ti-15Mo Alloy used for Biomedical Applications

The Ti-15Mo alloy is a promising material for use as a biomaterial because of its excellent corrosion resistance and its good combination of mechanical properties, such as fatigue, hardness, and wears resistance. This alloy has a body-centered predominantly cubic crystalline structure and the addition of interstitial atoms, such as oxygen and nitrogen, strongly alters its mechanical properties. Mechanical spectroscopy is a powerful tool to study the interaction of interstitial elements with the matrix metal or substitutional solutes, providing information such as the distribution and the concentration of interstitial elements. The objective of this paper is to study of the effects of heavy interstitial elements, such as oxygen and nitrogen, on the anelastic properties of the Ti-15Mo alloy by using mechanical spectroscopy measurements. In this study, the diffusion coefficients, pre-exponential factors, and activation energies were calculated for the oxygen in the Ti-15Mo alloy.

Long-term effect of carbodiimide on dentin matrix and resin-dentin bonds

Objectives: To characterize the interaction of 1-Ethyl-3-[3-dimethylaminopropyl] carbodiimide Hydrochloride (EDC) with dentin matrix and its effect on the resin-dentin bond. Methods: Changes to the stiffness of demineralized dentin fragments treated with EDC/N-hydroxysuccinimide (NHS) in different solutions were evaluated at different time points. The resistance against enzymatic degradation was indirectly evaluated by ultimate tensile strength (UTS) test of demineralized dentin treated or not with EDC/NHS and subjected to collagenase digestion. Short- and long-term evaluations of the strength of resin-dentin interfaces treated with EDC/NHS for 1 h were performed using microtensile bond strength (mu TBS) test. All data (MPa) were individually analyzed using ANOVA and Tukey HSD tests (alpha = 0.05). Results: The different exposure times significantly increased the stiffness of dentin (p < 0.0001, control-5.15 and EDC/NHS-29.50), while no differences were observed among the different solutions of EDC/NHS (p = 0.063). Collagenase challenge did not affect the UTS values of EDC/NHS group (6.08) (p > 0.05), while complete degradation was observed for the control group (p = 0.0008, control-20.84 and EDC/NHS-43.15). EDC/NHS treatment did not significantly increase resin-dentin mu TBS, but the values remained stable after 12 months water storage (p < 0.05). Conclusions: Biomimetic use of EDC/NHS to induce exogenous collagen cross-links resulted in increased mechanical properties and stability of dentin matrix and dentin-resin interfaces. (C) 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 94B: 250-255, 2010.

Bioinformatical and in vitro approaches to essential oil-induced matrix metalloproteinase inhibition

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Interaction of the Anti-Inflammatory Annexin A1 Protein and Tacrolimus Immunosuppressant in the Renal Function of Rats

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)