Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach which is a combination of an heterogeneity sensitive spatial domain decomposition with an \textit{a priori} rearrangement of subdomain-walls. Within this approach, the theoretical modeling and scaling-laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase separated binary Lennard-Jones fluid.Comment: 14 pages, 12 figure

Total Photoabsorption Cross Sections of A=6 Nuclei with Complete Final State Interaction

The total photoabsorption cross sections of 6He and 6Li are calculated microscopically with full inclusion of the six-nucleon final state interaction using semirealistic nucleon-nucleon potentials. The Lorentz Integral Transform (LIT) method and the effective interaction approach for the hyperspherical formalism are employed. While 6Li has a single broad giant resonance peak, there are two well separated peaks for 6He corresponding to the breakup of the neutron halo and the alpha core, respectively. The comparison with the few available experimental data is discussed.Comment: LaTeX, 8 pages, 3 ps figure

Experimental study of fragmentation products in the reactions 112Sn + 112Sn and 124Sn + 124Sn at 1 AGeV

Production cross-sections and longitudinal velocity distributions of the projectile-like residues produced in the reactions 112Sn + 112Sn and 124Sn + 124Sn both at an incident beam energy of 1 AGeV were measured with the high-resolution magnetic spectrometer, the Fragment Separator (FRS) of GSI. For both reactions the characteristics of the velocity distributions and nuclide production cross sections were determined for residues with atomic number Z $\geq$ 10. A comparison of the results of the two reactions is presented.Comment: 14 pages, 12 figure

Physical and chemical evaluation of cultivars and new hybrids of pineapple.

The Embrapa Cassava & Fruits develops pineapple cultivars resistant to Fusariosis with equal or better characteristics of Pérola and Smooth Cayenne varieties

Cultivo de meristemas apicais de plantas in vitro para limpeza viral em abacaxi.

O abacaxi é uma das frutas tropicais mais apreciadas em todo mundo. O Brasil, como um dos centros de origem e diversidade genética da espécie, tem se destacado no melhoramento genético e na conservação de germoplasma desta importante fruteira (Cabral et al.,2004). Dentre as doenças de maior impacto na abacaxicultura brasileira destaca-se a fusariose, para a qual várias ações estão sendo desenvolvidas, incluindo o lançamento de híbridos resistentes. O programa de melhoramento da Embrapa Mandioca e Fruticultura Tropical (CNPMF) já lançou os abacaxis Imperial, Vitória e Ajubá, com excelentes características organolépticas, alta produtividade e resistentes à fusariose (Cabral e Matos, 2005; Ventura et al., 2007; Cabral e Matos, 2008).pdf 70

Situação e perspectivas da abacaxicultura no Amazonas.

Na região Amazônica ocorrem muitos tipos silvestres de abacaxizeiro em habitats naturais e diversas cultivares locais são plantadas em pequena escala por agricultores familiares para consumo e comercialização local. No Amazonas, a variedade denominada Turiaçu é predominante nos cultivos. Presume-se que esta variedade tenha sido trazida da região de Turiaçu, no Maranhão. As características botânicas e agronômicas são muito semelhantes entre as populações de abacaxizeiro cultivadas nos municípios de Turiaçu, MA e Itacoatiara, AM. Até o momento, sintomas de fusariose (Fusarium guttiforme), a principal doença do abacaxizeiro, não foram observados para a variedade Turiaçu, no Amazonas e Maranhão. Esta variedade ainda foi pouco estudada em seus aspectos agronômicos, como exigências nutricionais, indução floral e produção de mudas. No Amazonas, o cultivo do abacaxi Turiaçu já tem sido feito com uso de tecnologias básicas, tais como, plantio em fileiras duplas, aplicação de indutores florais, preparo do solo e adubação química, baseando-se no sistema de produção já estabelecido para a cultivar Pérola. Estima-se que em 80 a 85% da área cultivada no estado do Amazonas seja utilizada a variedade Turiaçu. A produção de abacaxi no Amazonas cresceu em 63% de 2004 para 2011, e atualmente o estado é o oitavo maior produtor do país. Esta produção se concentra no município de Itacoatiara, sobretudo nas regiões de Novo Remanso e Vila do Engenho

Caracterização física e físico-química de cultivares e de híbridos de abacaxi desenvolvidos pela Embrapa.

O abacaxi (Ananas comosus var. comosus) é uma autêntica fruta das regiões tropicais, cultivado também sob condições subtropicais. É muito consumido in natura e utilizado na indústria para obtenção de geleias, doces em calda, produtos minimamente processados, sucos, dentre outros. O objetivo desse trabalho foi avaliar a cor e as características físico- químicas de nove genótipos de abacaxi, sendo cinco variedades cultivadas (Gold ou MD2, Pérola, Smooth Cayenne, Vitória e Imperial) e quatro novos híbridos desenvolvidos pela Embrapa Mandioca e Fruticultura (SC x PRI-21, SC 48 x PRI-02, PE x SC-73 e PA x PE-01).1 CD-ROM

Temperature quenching in LAB based liquid scintillator

The effect of temperature changes on the light output of LAB based liquid scintillator is investigated in a range from $-5$ to 30\,^{\circ } C with $\alpha$ -particles and electrons in a small scale setup. Two PMTs observe the scintillator liquid inside a cylindrically shaped aluminum cuvette that is heated or cooled and the temperature dependent PMT sensitivity is monitored and corrected. The $\alpha$ -emitting isotopes in dissolved radon gas and in natural Samarium (bound to a LAB solution) excite the liquid scintillator mixtures and changes in light output with temperature variation are observed by fitting light output spectra. Furthermore, also changes in light output by compton electrons, which are generated from external calibration $\gamma$ -ray sources, is analysed with varying temperature. Assuming a linear behaviour, a combined negative temperature coefficient of ${(-0.29 \pm 0.01)}{\,\%/^{\circ }}\hbox {C}$ is found. Considering hints for a particle type dependency, electrons show ${(-0.17 \pm 0.02)}{\,\%/^{\circ }}\hbox {C}$ , whereas the temperature dependency seems stronger for $\alpha$ -particles, with ${(-0.35 \pm 0.03)}{\,\%/^{\circ }}\hbox {C}$ . Due to a high sampling rate, a pulse shape analysis can be performed and shows an enhanced slow decay component at lower temperatures, pointing to reduced non-radiative triplet state de-excitations.Peer Reviewe

(Anti-)Brane backreaction beyond perturbation theory

We improve on the understanding of the backreaction of anti-D6-branes in a flux background that is mutually BPS with D6-branes. This setup is analogous to the study of the backreaction of anti-D3-branes inserted in the KS throat, but does not require us to smear the anti-branes or do a perturbative analysis around the BPS background. We solve the full equations of motion near the anti-D6-branes and show that only two boundary conditions are consistent with the equations of motion. Upon invoking a topological argument we eliminate the boundary condition with regular H flux since it cannot lead to a solution that approaches the right kind of flux away from the anti-D6-brane. This leaves us with a boundary condition which has singular, but integrable, H flux energy density.Comment: 12 pages + appendices, 1 figure; v2: minor changes, version published in JHE