Phase transitions in gene networks evolved under different selection rules

Mathematical models of gene regulation are a powerful tool for understanding the complex features of genetic control. While various modeling efforts have been successful at explaining gene expression dynamics, much less is known about how evolution shapes the structure of these networks. An important feature of gene regulatory networks is their stability in response to environmental perturbations. Regulatory systems are thought to have evolved to exist near the transition between stability and instability, in order to have the required stability to environmental fluctuations while also being able to achieve a wide variety of functions (corresponding to different dynamical patterns). We study a simplified model of gene network evolution in which links are added via different selection rules. These growth models are inspired by recent work on `explosive' percolation which shows that when network links are added through competitive rather than random processes, the connectivity phase transition can be significantly delayed, and when it is reached, it appears to be first order (discontinuous, e.g., going from no failure at all to large expected failure) instead of second order (continuous, e.g., going from no failure at all to very small expected failure). We find that by modifying the traditional framework for networks grown via competitive link addition to capture how gene networks evolve to avoid damage propagation, we also see significant delays in the transition that depend on the selection rules, but the transitions always appear continuous rather than `explosive'.

Irrigacao por sulco com e sem utilizacao da agua de escoamento superficial.

Compararam-se dois sistemas de irrigacao por sulcos. Um deles constou da aplicacao de vazoes constantes, atraves de sifoes, para valores de R iguais a 0,26; 1 e 2. O outro constou de reutilizacao da agua escoada para valores de R iguaia a 0,5, 1 e 2. Observaram-se decrescimos nas perdas por percolacao, enquanto as eficiencias de aplicaca oe de distribuicao aumentaram, o mesmo acontecendo com as perdas por escoamento em ambos os sistemas de irrigacao, quando o valor de R aumentou. A eficiencia de irrigacao cresceu com o valor de R, quando se reutilizou a agua de escoamento, ocorrendo o inverso quando nao se reutilizou esta agua. Foram feitas determinacoes quanto a flutuacao da vazao de escoamento disponivel durante a irrigacao de cinco setores consecutivos, visando o dimensionamento de sistemas de irrigacao com reutilizacao desta agua.

Mensuração de perdas de sedimentos por escoamento superficial em encostas, com uso de parcelas de erosão, em diferentes usos e coberturas do solo no Bioma Cerrado : Bacia Hidrográfica do Ribeirão do Gama/DF

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Humanas, Departamento de Geografia, 2015.

Efecto antiinflamatorio de extractos metanólicos de plantas de Azuay y Loja (Ecuador) a través del modelo de peces cebra

Los peces cebra son utilizados como modelo biológico para screening primario de extractos de plantas con potencial bioactividad, aprovechando sus similitudes: genética, fisiológica y respuesta farmacológica con los mamíferos. En el estudio se empleó este modelo para valorar la actividad antiinflamatoria de 36 extractos metanólicos de plantas medicinales utilizadas en las provincias de Azuay y Loja (Ecuador). Parte del material vegetal fue recolectado con el aporte de una hierbatera de etnia Saraguro. Los extractos fueron preparados por percolación y su toxicidad fue evaluada en peces cebra en concentraciones variables de 400 a 3,125 μg/ml, determinándose la máxima concentración tolerada para cada uno de ´estos. La actividad antiinflamatoria se evaluó a través del ensayo de migración leucocitaria inducida por lipopolisacárido de Sallmonella typhi. Los extractos de: Cestrum aff. peruvianum, Galinsoga parviflora, Galium sp., Oenothera tetraptera, Peperomia aff. galioides , Passiflora ampullaceae y Ambrosia arborescens, correspondientes al 18,92% de los analizados, mostraron un potencial antiinflamatorio comparable con indometacina y dexametasona; siendo el extracto metanólico de Cestrum aff. peruvianum el más relevante a 50 g/ml. El análisis fitoquímico básico de los extractos se realizó por cromatografía de capa fina, evidenciándose la presencia de saponinas y terpenoidoes como compuestos principales en la mayoría de los extractos.

Análise de modelos geológicos utilizando percolação dinâmica

In the present study we elaborated algorithms by using concepts from percolation theory which analyze the connectivity conditions in geological models of petroleum reservoirs. From the petrophysical parameters such as permeability, porosity, transmittivity and others, which may be generated by any statistical process, it is possible to determine the portion of the model with more connected cells, what the interconnected wells are, and the critical path between injector and source wells. This allows to classify the reservoir according to the modeled petrophysical parameters. This also make it possible to determine the percentage of the reservoir to which each well is connected. Generally, the connected regions and the respective minima and/or maxima in the occurrence of the petrophysical parameters studied constitute a good manner to characterize a reservoir volumetrically. Therefore, the algorithms allow to optimize the positioning of wells, offering a preview of the general conditions of the given model s connectivity. The intent is not to evaluate geological models, but to show how to interpret the deposits, how their petrophysical characteristics are spatially distributed, and how the connections between the several parts of the system are resolved, showing their critical paths and backbones. The execution of these algorithms allows us to know the properties of the model s connectivity before the work on reservoir flux simulation is started

Leishmanicidal and cytotoxic activity of extracts and saponins from Ilex laurina (Aquifoliaceae)

Purpose: To evaluate the leishmanicidal and cytotoxic activity of alcohol and non-alcohol extracts and saponins from Ilex laurina . Methods: Extracts were obtained by percolation with solvents of different polarities: hexane, dichloromethane, ethyl acetate and ethanol. The ethyl acetate extract was subjected to silica gel column chromatography eluting with a step gradient of dichloromethane-methanol. All products were evaluated in vitro for leishmanicidal activity against amastigotes of leishmania panamensis and cytotoxicity on U- 937 cells. Results: Two saponins were isolated from the ethyl acetate extract. The ethyl acetate extract showed high leishmanicidal activity against intracellular amastigotes of L. panamensis (EC50, 7.5 ± 1.5 μg/mL) and low activity against axenic amastigotes (EC50, 52.8 ±1.6 μg/mL); this extract showed also high cytotoxicity (LC50, 57.7 ± 12.1 μg/mL). Saponin 2 exhibited high activity against intracellular amastigotes (EC50, 5.9 ± 0.5 μg/mL) but also showed high cytotoxicity on U-937 cells (EC50, 25.7 ± 6.1 μg/mL). This compound showed similar leishmanicidal activity and cytotoxicity to meglumine antimoniate and amphotericin B, respectively, drugs currently used for the treatment of leishmaniasis. Conclusions: Based on these results, Ilex laurina is a potential source of compounds that can lead to the development of new therapeutic alternatives against leishmaniasis.

Estudo de adsorvente obtido de terras diatomáceas para remoção de metais pesados em águas produzidas: processamento, caracterização e dinâmica em leito fixo

The acceleration of industrial growth in recent decades on all continents aroused the interest of the companies to counter the impacts produced on the environment, spurred primarily by major disasters in the petroleum industry. In this context, the water produced is responsible for the largest volume of effluent from the production and extraction of oil and natural gas. This effluent has in its composition some critical components such as inorganic salts, heavy metals (Fe, Cu, Zn, Pb, Cd, ), presence of oil and chemicals added in the various production processes. In response to impact, have been triggered by research alternative adsorbent materials for water treatment and water produced, in order to removing oils and acids and heavy metals. Many surveys of diatomaceous earth (diatomite) in Brazil involve studies on the physico-chemical, mineral deposits, extraction, processing and applications. The official estimated Jazi are around 2.5 million tonnes, the main located in the states of Bahia (44%) and Rio Grande do Norte (37,4%). Moreover, these two states appear as large offshore producers, earning a prominent role in research of adsorbents such as diatomite for treatment of water produced. Its main applications are as an agent of filtration, adsorption of oils and greases, industrial load and thermal insulator. The objective of this work was the processing and characterization of diatomite diatomaceous earth obtained from the municipality of Macaíba-RN (known locally as tabatinga) as a low cost regenerative adsorbent for removal of heavy metals in the application of water produced treatment. In this work we adopted a methodology for batch processing, practiced by small businesses located in producing regions of Brazil. The characterization was made by X-ray diffraction (XRD), scanning electron microscopy (SEM) and specific surface area (BET). Research conducted showed that the improvement process used was effective for small volume production of diatomite concentrated. The diatomite obtained was treated by calcination at temperature of 900 oC for 2 hours, with and without fluxing Na2CO3 (4%), according to optimal results in the literature. Column adsorption experiments were conducted to percolation of the in nature, calcined and calcined fluxing diatomites. Effluent was used as a saline solution containing ions of Cu, Zn, Na, Ca and Mg simulating the composition of produced waters in the state of Rio Grande do Norte, Brazil. The breakthrough curves for simultaneous removal of copper ions and zinc as a result, 84.3% for calcined diatomite and diatomite with 97.3 % for fluxing. The calcined fluxing diatomite was more efficient permeability through the bed and removal of copper and zinc ions. The fresh diatomite had trouble with the permeability through the bed under the conditions tested, compared with the other obtained diatomite. The results are presented as promising for application in the petroleum industry

Atomic-level structure and deformation in metallic glasses

Metallic glasses (MGs) are a relatively new class of materials discovered in 1960 and lauded for its high strengths and superior elastic properties. Three major obstacles prevent their widespread use as engineering materials for nanotechnology and industry: 1) their lack of plasticity mechanisms for deformation beyond the elastic limit, 2) their disordered atomic structure, which prevents effective study of their structure-to-property relationships, and 3) their poor glass forming ability, which limits bulk metallic glasses to sizes on the order of centimeters. We focused on understanding the first two major challenges by observing the mechanical properties of nanoscale metallic glasses in order to gain insight into its atomic-level structure and deformation mechanisms. We found that anomalous stable plastic flow emerges in room-temperature MGs at the nanoscale in wires as little as ~100 nanometers wide regardless of fabrication route (ion-irradiated or not). To circumvent experimental challenges in characterizing the atomic-level structure, extensive molecular dynamics simulations were conducted using approximated (embedded atom method) potentials to probe the underlying processes that give rise to plasticity in nanowires. Simulated results showed that mechanisms of relaxation via the sample free surfaces contribute to tensile ductility in these nanowires. Continuing with characterizing nanoscale properties, we studied the fracture properties of nano-notched MGnanowires and the compressive response of MG nanolattices at cryogenic (~130 K) temperatures. We learned from these experiments that nanowires are sensitive to flaws when the (amorphous) microstructure does not contribute stress concentrations, and that nano-architected structures with MG nanoribbons are brittle at low temperatures except when elastic shell buckling mechanisms dominate at low ribbon thicknesses (~20 nm), which instead gives rise to fully recoverable nanostructures regardless of temperature. Finally, motivated by understanding structure-to-property relationships in MGs, we studied the disordered atomic structure using a combination of in-situ X-ray tomography and X-ray diffraction in a diamond anvil cell and molecular dynamics simulations. Synchrotron X-ray experiments showed the progression of the atomic-level structure (in momentum space) and macroscale volume under increasing hydrostatic pressures. Corresponding simulations provided information on the real space structure, and we found that the samples displayed fractal scaling (r^d ∝ V, d < 3) at short length scales (< ~8 Å), and exhibited a crossover to a homogeneous scaling (d = 3) at long length scales. We examined this underlying fractal structure of MGs with parallels to percolation clusters and discuss the implications of this structural analogy to MG properties and the glass transition phenomenon.

Estudo das propriedades críticas do processo epidêmico por par com difusão de pares

The pair contact process - PCP is a nonequilibrium stochastic model which, like the basic contact process - CP, exhibits a phase transition to an absorbing state. While the absorbing state CP corresponds to a unique configuration (empty lattice), the PCP process infinitely many. Numerical and theoretical studies, nevertheless, indicate that the PCP belongs to the same universality class as the CP (direct percolation class), but with anomalies in the critical spreading dynamics. An infinite number of absorbing configurations arise in the PCP because all process (creation and annihilation) require a nearest-neighbor pair of particles. The diffusive pair contact process - PCPD) was proposed by Grassberger in 1982. But the interest in the problem follows its rediscovery by the Langevin description. On the basis of numerical results and renormalization group arguments, Carlon, Henkel and Schollwöck (2001), suggested that certain critical exponents in the PCPD had values similar to those of the party-conserving - PC class. On the other hand, Hinrichsen (2001), reported simulation results inconsistent with the PC class, and proposed that the PCPD belongs to a new universality class. The controversy regarding the universality of the PCPD remains unresolved. In the PCPD, a nearest-neighbor pair of particles is necessary for the process of creation and annihilation, but the particles to diffuse individually. In this work we study the PCPD with diffusion of pair, in which isolated particles cannot move; a nearest-neighbor pair diffuses as a unit. Using quasistationary simulation, we determined with good precision the critical point and critical exponents for three values of the diffusive probability: D=0.5 and D=0.1. For D=0.5: PC=0.89007(3), β/v=0.252(9), z=1.573(1), =1.10(2), m=1.1758(24). For D=0.1: PC=0.9172(1), β/v=0.252(9), z=1.579(11), =1.11(4), m=1.173(4)

Compositional effects of large graphene oxide sheets on the spinnability and properties of polyurethane composite fibers

Recent advances in wearable electronics, technical textiles, and wearable strain sensing devices have resulted in extensive research on stretchable electrically conductive fibers. Addressing these areas require the development of efficient fiber processing methodologies that do not compromise the mechanical properties of the polymer (typically an elastomer) when nanomaterials are added as conductive fillers. It is highly desirable that the addition of conductive fillers provides not only electrical conductivity, but that these fillers also enhance the stiffness, strength, stretchability, and toughness of the polymer. Here, the compatibility of polyurethane (PU) and graphene oxide (GO) is utilized for the study of the properties of elastomeric conductive fibers prepared by wet-spinning. The GO-reinforced PU fibers demonstrate outstanding mechanical properties with a 200-fold and a threefold enhancement in Young's modulus and toughness, respectively. Postspinning thermal annealing of the fibers results in electrically conductive fibers with a low percolation threshold (≈0.37 wt% GO). An investigation into optimized fiber's electromechanical behavior reveals linear strain sensing abilities up to 70%. Results presented here provide practical insights on how to simultaneously maintain or improve electrical, mechanical, and electromechanical properties in conductive elastomer fibers.

Small cluster in cyber physical systems: network topology, interdependence and cascading failures

In cyber physical system (CPS), computational resources and physical resources are strongly correlated and mutually dependent. Cascading failures occur between coupled networks, cause the system more fragile than single network. Besides widely used metric giant component, we study small cluster (small component) in interdependent networks after cascading failures occur. We first introduce an overview on how small clusters distribute in various single networks. Then we propose a percolation theory based mathematical method to study how small clusters be affected by the interdependence between two coupled networks. We prove that the upper bounds exist for both the fraction and the number of operating small clusters. Without loss of generality, we apply both synthetic network and real network data in simulation to study small clusters under different interdependence models and network topologies. The extensive simulations highlight our findings: except the giant component, considerable proportion of small clusters exists, with the remaining part fragmenting to very tiny pieces or even massive isolated single vertex; no matter how the two networks are tightly coupled, an upper bound exists for the size of small clusters. We also discover that the interdependent small-world networks generally have the highest fractions of operating small clusters. Three attack strategies are compared: Inter Degree Priority Attack, Intra Degree Priority Attack and Random Attack. We observe that the fraction of functioning small clusters keeps stable and is independent from the attack strategies.

Effect of back pressure during equal-channel angular pressing on deformation-induced porosity in copper

The effect of back pressure during equal channel angular pressing (ECAP) on deformation-induced porosity is investigated. While percolating porosity was found after 4 ECAP passes in the absence of back pressure, no percolation was detected when a back pressure of 200 MPa was applied. However, after ECAP with back pressure continued to 8 passes, percolating porosity did appear. The nature of the percolating porosity developed in severely deformed materials is discussed.

Procesos hopping a través del modelo difusional en materiales nanocristalinos usados para aplicaciones fotovoltaicas

Se presentan los modelos de hopping de rango variable (variable range hopping; VRH), vecinos cercanos (nearest neighbor hopping; NNH) y barreras de potencial presentes en las fronteras de grano; como mecanismos de transporte eléctrico predominantes en los materiales semiconductores para aplicaciones fotovoltaicas. Las medidas de conductividad a oscuras en función de temperatura fueron realizadas para región de bajas temperaturas entre 120 y 400 K con Si y compuestos Cu3BiS2 y Cu2ZnSnSe4. Siguiendo la teoría de percolación, se obtuvieron parámetros hopping y la densidad de estados cerca del nivel de Fermi, N(EF), para todas las muestras. A partir de los planteamientos dados por Mott para VRH, se presentó el modelo difusional, que permitió establecer la relación entre la conductividad y la densidad de estados de defecto o estados localizados en el gap del material. El análisis comparativo entre modelos, evidenció, que es posible obtener mejora hasta de un orden de magnitud en valores para cada uno de los parámetros hopping que caracterizan el material.