Finite element discretization of a biological network formation system: a preliminary study

A finite element discretization is developed for the Cai-Hu model, describing the formation of biological networks. The model consists of a non linear elliptic equation for the pressure $p$ and a non linear reaction-diffusion equation for the conductivity tensor $\mathbb{C}$. The problem requires high resolution due to the presence of multiple scales, the stiffness in all its components and the non linearities. We propose a low order finite element discretization in space coupled with a semi-implicit time advancing scheme. The code is {verified} with several numerical tests performed with various choices for the parameters involved in the system. In absence of the exact solution, we apply Richardson extrapolation technique to estimate the order of the method.Comment: 11 pages, 3 figures, 18 plots, 2 table

A parallel solver for FSI problems with fictitious domain approach

We present and analyze a parallel solver for the solution of fluid structure interaction problems described by a fictitious domain approach. In particular, the fluid is modeled by the non-stationary incompressible Navier-Stokes equations, while the solid evolution is represented by the elasticity equations. The parallel implementation is based on the PETSc library and the solver has been tested in terms of robustness with respect to mesh refinement and weak scalability by running simulations on a Linux cluster.Comment: Contribution to the 5th African Conference on Computational Mechanic

A parallel solver for fluid structure interaction problems with Lagrange multiplier

The aim of this work is to present a parallel solver for a formulation of fluid-structure interaction (FSI) problems which makes use of a distributed Lagrange multiplier in the spirit of the fictitious domain method. The fluid subproblem, consisting of the non-stationary Stokes equations, is discretized in space by $\mathcal{Q}_2$-$\mathcal{P}_1$ finite elements, whereas the structure subproblem, consisting of the linear or finite incompressible elasticity equations, is discretized in space by $\mathcal{Q}_1$ finite elements. A first order semi-implicit finite difference scheme is employed for time discretization. The resulting linear system at each time step is solved by a parallel GMRES solver, accelerated by block diagonal or triangular preconditioners. The parallel implementation is based on the PETSc library. Several numerical tests have been performed on Linux clusters to investigate the effectiveness of the proposed FSI solver.Comment: 27 pages, 8 figures, 14 table

Genes for asparagine metabolism in Lotus japonicus : differential expression and interconnection with photorespiration

Background: Asparagine is a very important nitrogen transport and storage compound in plants due to its high nitrogen/carbon ratio and stability. Asparagine intracellu lar concentration depends on a balance between asparagine biosynthesis and degradation. The main enzymes involved in asparagine metabolism are as paragine synthetase (ASN), asparaginase (NSE) and serine-glyoxylate aminotransfera se (SGAT). The study of the genes encoding for these enzymes in the model legume Lotus japonicus is of particular interest since it has been proposed that asparagine is the principal molecule used to transport reduced nitrogen within the plant in most temperate legumes. Results: A differential expression of genes encoding for seve ral enzymes involved in asparagine metabolism was detected in L. japonicus . ASN is encoded by three genes, LjASN1 was the most highly expressed in mature leaves while LjASN2 expression was negligible and LjASN3 showed a low expression in this organ, suggesting that LjASN1 is the main gene responsible for asparagine synthesis in mature leaves. In young leaves, LjASN3 was the only ASN gene expressed although at low levels, while all the three genes encoding for NSE were highly expressed, especially LjNSE1 .Innodules, LjASN2 and LjNSE2 were the most highly expressed genes, suggesting an important role for these genes in this organ. Several lines of evidence support the connection between asparagine metabolic genes and photorespiration in L. japonicus : a) a mutant plant deficient in LjNSE1 showed a dramatic decrease in the expression of the two genes encoding for SGAT; b) expression of the genes involved in asparagine metabolism is altered in a photorespiratory mutant lacking plastidic glutamine synthetase; c) a clustering analysis indicated a similar pattern of expression among several genes involved in photorespiratory and asparagine metabolism, indicating a clear link between LjASN1 and LjSGAT genes and photorespiration. Conclusions: The results obtained in this paper indicate the exis tence of a differential expression of asparagine metabolic genes in L. japonicus and point out the crucial relevance of particular genes in different organs. Moreover, the data presented establish clear links betw een asparagine and photorespiratory metabolic genes in this plant.Junta de Andalucía (P10-CVI- 6368)FEDER-Ministerio de Economía y Competitividad (AGL 2014 – 54413-R

Local conformational changes in the 8–17 deoxyribozyme core induced by activating and inactivating divalent metal ions

The 8-17 deoxyribozyme (DNAzyme) is a catalytic DNA molecule capable of cleaving specific RNA substrates. The deoxyribozyme is activated by a wide variety of divalent metal ions, from Mg2+ to Pb2+, with just a few exceptions. It is not clear if metal ions are directly involved in catalysis, or are required to attain an active conformation, or both. In particular, the connection between metal-induced global structural rearrangements and catalysis is not straightforward. To gain more information on the local structural changes induced by metal ions, we introduced fluorescent 2-aminopurine (2-Ap) residues at different positions of the 8-17 'core'. We found that a construct containing 2-Ap at position 15 was best suited to monitor conformational changes in the presence of Mg2+, Ca2+ or Mn2+. Binding of these activating metal ions caused a local rearrangement at position 15, apparently entailing decreased stacking of the 2-Ap base. The metal dependence for such conformational change was generally hyperbolic (suggesting it mirrored the binding by a single metal ion) and yielded apparent dissociation constants close to those required for activation. In contrast, Cu2+, a divalent metal ion which does not support catalysis, caused in the deoxyribozyme a slow, reversible inactivation, which correlated with a very distinct conformational change at position 15

Nuevos desarrollos en la aplicación de materiales compósitos en construcciones: sistemas de resinas a base acuosa "bet on tex ipn" y su aplicación en tecnologías FRP y FRCM

Composite materials mainly based on carbon fibers and epoxy resins matrices are used in constructions since 30 years and have reached in a very short time a high technical level in all the world. Besides this extraordinary result, some lack of properties of epoxy resins have being criticized, bringing some limitations in applications and in the definition of designing solutions. Restrictions in applications of epoxy-based technologies are due to absence of resins’ moisture permeability, high sensitivity to humidity during application, low thermal properties with a Tg. value of 100 °C and a lack of fire resistance. As Ardea Company, we have developed a long research work on this topic and a new water resin system, Betontex IPN, based on interpenetrated polymer network structures, has been introduced on the construction market. Betontex IPN are a two components resin system: Component A, a polymeric substance in water emulsion and component B, a second polymer phase supported on active inorganic micro crystals filler. After mixing and hardening, the resulting material is permeable to water moisture and resistant to fire (according to UNI 9177), with a thermal resistance over 180° C and ultimate degradation temperature over 600°C. The properties of the resins in combination with carbon, aramide and glass fiber reinforcements have been tested in masonry and concrete structures. IPN resins show a large range of many interesting properties and may be used as FRP technology, in place of epoxy resins, or as FRCM technology, where IPN acts as adhesion promoter between fibers and mortar. Other properties of IPN resins are: high mechanical properties; good adhesion to fibers, high compatibility and good adhesion to lime mortar, concrete, masonry, wood and marble. The IPN resin system may be used also in humid conditions and applied over wet surface. In the last years the new IPN technologies have been largely applied for rehabilitation of damaged structures after earthquakes of 2009 (L’Aquila) and 2012 (Emilia Romagna-Italy).Los materiales compósitos formados principalmente por fibras de carbón y matrices de resinas poliméricas epoxi han sido utilizados por más de 30 años, alcanzando un alto nivel técnico en todo el mundo. A pesar de los extraordinarios resultados obtenidos con este tipo de resinas, algunas de sus características han sido fuertemente criticadas, teniendo como consecuencia algunas limitaciones en su aplicación y en la definición de soluciones de diseño. Las restricciones de las aplicaciones de las tecnologías basadas en resinas epoxi se deben principalmente a su ausencia de permeabilidad a la humedad, su alta sensibilidad a la humedad durante la aplicación, sus escasas propiedades térmicas con un valor de T.g. de 100 °C y su falta de resistencia a la quema.En nuestra empresa Ardea, hemos llevado a cabo una larga investigación sobre este tema y hemos introducido en el mercado de la construcción un nuevo sistema de resinas a base acuosa, Betontex IPN, los cuales están basados en estructuras poliméricas interpenetradas. Betontex IPN es un sistema de resinas de dos componenes: el Componente A es una sustancia polimérica emulsionada en agua y el Componente B es una segunda fase polimérica presente en un relleno inorgánico microcristalino. Después del mezclado e homogenizado, el material resultante es permeable a la humedad y resistente a la quema (de acuerdo a la normativa UNI 9177), con una resistencia térmica más allá de los 180 °C y una temperatura de degradación mayor a 600 °C.Las propiedades de éstas resinas en combinación con refuerzos de fibras de carbón, aramida y vidrio han sido evaluadas en estructuras de mampostería y concreto. Las resinas IPN muestran una gran gama de propiedades interesantes y pueden ser usadas como tecnología FRP en lugar de las resinas epoxi, o como tecnología FRCM, en donde el IPN actúa como promotor de adhesión entre las fibras y el mortero. Otras propiedades de las resinas IPN incluyen buenas propiedades mecánicas, buena adhesión a las fibras, alta compatibilidad y buena adhesión a morteros de cal, concreto, mampostería, madera y mármol. El sistema de resinas IPN puede también ser usado en condiciones húmedas y aplicado sobre superficies mojadas. En los últimos años, las nuevas tecnologías IPN han sido ampliamente usadas para la rehabilitación de estructuras dañadas como consecuencia de los terremotos de 2009 (L’Aquila, Italia) y 2012 (Emilia Romagna, Italia)

Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme

The 8-17 deoxyribozyme is a small DNA catalyst of significant applicative interest. We have analyzed the kinetic features of a well behaved 8-17 construct and determined the influence of several reaction conditions on such features, providing a basis for further exploration of the deoxyribozyme mechanism. The 8-17 bound its substrate with a rate constant ∼10-fold lower than those typical for the annealing of short complementary oligonucleotides. The observed free energy of substrate binding indicates that an energetic penalty near to +7 kcal/mol is attributable to the deoxyribozyme core. Substrate cleavage required divalent metal ion cofactors, and the dependence of activity on the concentration of Mg(2+), Ca(2+) or Mn(2+) suggests the occurrence of a single, low-specificity binding site for activating ions. The efficiency of activation correlated with the Lewis acidity of the ion cofactor, compatible with a metal-assisted deprotonation of the reactive 2′-hydroxyl group. However, alternative roles of the metal ions cannot be excluded, because those ions that are stronger Lewis acids are also capable of forming stronger interactions with ligands such as the phosphate oxygens. The apparent enthalpy of activation for the 8-17 reaction was close to the values observed for hydroxide-catalyzed and hammerhead ribozyme-catalyzed RNA cleavage

On the interface matrix for fluid-structure interaction problems with fictitious domain approach

We study a recent formulation for fluid-structure interaction problems based on the use of a distributed Lagrange multiplier in the spirit of the fictitious domain approach. In this paper, we focus our attention on a crucial computational aspect regarding the interface matrix for the finite element discretization: it involves integration of functions supported on two different meshes. Several numerical tests show that accurate computation of the interface matrix has to be performed in order to ensure the optimal convergence of the method