Experiences with Mesh-like computations using Prediction Binary Trees

In this paper we aim at exploiting the temporal coherence among successive phases of a computation, in order to implement a load-balancing technique in mesh-like computations to be mapped on a cluster of processors. A key concept, on which the load balancing schema is built on, is the use of a Predictor component that is in charge of providing an estimation of the unbalancing between successive phases. By using this information, our method partitions the computation in balanced tasks through the Prediction Binary Tree (PBT). At each new phase, current PBT is updated by using previous phase computing time for each task as next phase's cost estimate. The PBT is designed so that it balances the load across the tasks as well as reduces {\em dependency} among processors for higher performances. Reducing dependency is obtained by using rectangular tiles of the mesh, of almost-square shape (i. e. one dimension is at most twice the other). By reducing dependency, one can reduce inter-processors communication or exploit local dependencies among tasks (such as data locality). Furthermore, we also provide two heuristics which take advantage of data-locality. Our strategy has been assessed on a significant problem, Parallel Ray Tracing. Our implementation shows a good scalability, and improves performance in both cheaper commodity cluster and high performance clusters with low latency networks. We report different measurements showing that tasks granularity is a key point for the performances of our decomposition/mapping strategy

Snazer: the simulations and networks analyzer

<p>Abstract</p> <p>Background</p> <p>Networks are widely recognized as key determinants of structure and function in systems that span the biological, physical, and social sciences. They are static pictures of the interactions among the components of complex systems. Often, much effort is required to identify networks as part of particular patterns as well as to visualize and interpret them.</p> <p>From a pure dynamical perspective, simulation represents a relevant <it>way</it>-<it>out</it>. Many simulator tools capitalized on the "noisy" behavior of some systems and used formal models to represent cellular activities as temporal trajectories. Statistical methods have been applied to a fairly large number of replicated trajectories in order to infer knowledge.</p> <p>A tool which both graphically manipulates reactive models and deals with sets of simulation time-course data by aggregation, interpretation and statistical analysis is missing and could add value to simulators.</p> <p>Results</p> <p>We designed and implemented <it>Snazer</it>, the simulations and networks analyzer. Its goal is to aid the processes of visualizing and manipulating reactive models, as well as to share and interpret time-course data produced by stochastic simulators or by any other means.</p> <p>Conclusions</p> <p><it>Snazer </it>is a solid prototype that integrates biological network and simulation time-course data analysis techniques.</p

Synthetic Mimic of Antimicrobial Peptide with Nonmembrane-Disrupting Antibacterial Properties

Proteolysis in dairy lactic acid bacteria has been studied in great detail by genetic, biochemical and ultrastructural methods. From these studies the picture emerges that the proteolytic systems of lactococci and lactobacilli are remarkably similar in their components and mode of action. The proteolytic system consists of an extracellularly located serine-proteinase, transport systems specific for di-tripeptides and oligopeptides (> 3 residues), and a multitude of intracellular peptidases. This review describes the properties and regulation of individual components as well as studies that have led to identification of their cellular localization. Targeted mutational techniques developed in recent years have made it possible to investigate the role of individual and combinations of enzymes in vivo. Based on these results as well as in vitro studies of the enzymes and transporters, a model for the proteolytic pathway is proposed. The main features are: (i) proteinases have a broad specificity and are capable of releasing a large number of different oligopeptides, of which a large fraction falls in the range of 4 to 8 amino acid residues; (ii) oligopeptide transport is the main route for nitrogen entry into the cell; (iii) all peptidases are located intracellularly and concerted action of peptidases is required for complete degradation of accumulated peptides.

GPU cost estimation for load balancing in parallel ray tracing

Interactive ray tracing has seen enormous progress in recent years. However, advanced rendering techniques requiring many million rays per second are still not feasible at interactive speed, and are only possible by means of highly parallel ray tracing. When using compute clusters, good load balancing is crucial in order to fully exploit the available computational power, and to not suffer from the overhead involved by synchronization barriers. In this paper, we present a novel GPU method to compute a costmap: a per-pixel cost estimate of the ray tracing rendering process. We show that the cost map is a powerful tool to improve load balancing in parallel ray tracing, and it can be used for adaptive task partitioning and enhanced dynamic load balancing. Its effectiveness has been proven in a parallel ray tracer implementation tailored for a cluster of workstations

PENGARUH LAMA PEMASAKAN BIJI TERHADAP RENDEMEN DAN SIFAT FISIKO-KIMIA MINYAK KEMIRI

Kemiri (Aleuritus mollucana Willd) plants are widely distributed in the tropical and sub tropical regions. Meanwhile, kemiri plant grows vastly almost anywhere in Indonesia. Kemiri nut meg can be used not only as food-seasoning, ingredients but also as a traditional medicine. The kernel portion of kemiri nut has high nutrition and energy (calorific) values, and so does its oil. The nut, is the meat part after removing the kemiri thell, could is further produced oil after having undergone certains extractions process. Kemiri nut oil has such specific characteristics that being easily dried under open air. Therefore, this oil can be used as volatilizing agent in the manufactures of paint and varnish. In addition, the properties of kemiri nut oil are affected by its extraction methods and quality of its raw material (kemiri nut). In this regard, the study is conducted to learn the effect of cooking duration on the yield and physico-chemical propertiesof the resulting oil. The aim of this study is to find out the optimal cooking duration capable of producing oil with satisfactory qualities. The results reveal that increase in the cooking duration are affected significantly the yield, specific gravity, light transmittion, free fatty acid (FFA) content, and iod number of the oil. Cooking duration for 30 minutes turned out to give optimum condition with respect to oil properties, i.e. yield at 49,94%, iod number = 158.657; FFA = 1.1399; specific gravity = 0.9211, and transmittion = 70.43. Keywords : yield, physico-chemical properties, cooking duration

Pengaruh Lama Pemasakan Biji terhadap Rendemen dan Sifat Fisiko-kimia Minyak Kemiri

Kemiri (Aleuritus mollucana Willd) plants are widely distributed in the tropical and sub tropical regions. Meanwhile, kemiri plant grows vastly almost anywhere in Indonesia. Kemiri nut meg can be used not only as food-seasoning, ingredients but also as a traditional medicine. The kernel portion of kemiri nut has high nutrition and energy (calorific) values, and so does its oil. The nut, is the meat part after removing the kemiri thell, could is further produced oil after having undergone certains extractions process.Kemiri nut oil has such specific characteristics that being easily dried under open air. Therefore, this oil can be used as volatilizing agent in the manufactures of paint and varnish.In addition, the properties of kemiri nut oil are affected by its extraction methods and quality of its raw material (kemiri nut). In this regard, the study is conducted to learn the effect of cooking duration on the yield and physico-chemical propertiesof the resulting oil. The aim of this study is to find out the optimal cooking duration capable of producing oil with satisfactory qualities.The results reveal that increase in the cooking duration are affected significantly the yield, specific gravity, light transmittion, free fatty acid (FFA) content, and iod number of the oil. Cooking duration for 30 minutes turned out to give optimum condition with respect to oil properties, i.e. yield at 49,94%, iod number = 158.657; FFA = 1.1399; specific gravity = 0.9211, and transmittion = 70.43

Pengaruh Suhu dan Waktu Pemasakan Biji Kemiri terhadap Sifat Minyaknya

Penelitian ini bertujuan untuk mempelajari pengaruh suhu dan waktu pemasakan biji kemiri terhadap sifat fisiko - kimia minyak kemiri, sehingga didapat kondisi pemasakan biji yang terbaik : Rancangan percobaan yang dipergunakan adalah Acak Lengkap Faktorial,yang terdiri dari dua faktor, yaitu suhu pemasakan (A) dan waktu pemasakan (B). Faktor A dalam 3 taraf yaitu 950C, 1050C, 1150C, sedangkan faktor B dalam 4 taraf yaitu 20, 30, 40, 50 menit.Hasil analisis keragaman menunjukkan bahwa suhu dan waktu pemasakan tidak memberikan pengaruh yang nyata terhadap rendemen, bobot jenis, indeks bias dan bilangan peroksida minyak kemiri. Waktu pemasakan berpengaruh nyata pada viskositas dan kadar asam lemak bebas, tetapi berpengaruh sangat nyata pada bilangan iod. Juga didapatkan bahwa suhu dan waktu pemasakan, serta interaksi kedua faktor berpengaruh sangat nyata pada bilangan penyabunan minyak kemiri. Interaksi kedua faktor hanya berpengaruh terhadap kejemihan (transmisi).Hasil menunjukkan bahwa rendemen minyak kemiri yang tinggi dengan sifat fisiko kimia yang baik diperoleh dari kombinasi suhu 950C dan waktu pemasakan 30 menit, yaitu 52,72 %, dengan sifat fisiko kimia yang dapat bersaing dengan minyak biji rami yaitu : bobot jenis 0,9268, indeks bias 1,4739, viskositas 50,37 cp, transmisi 79,30 %, kadar asam lemak bebas 1,6380%, bilangan iod 158,75, bilangan peroksida 1,1572 mg 02 per 100 gr, dan bilangan penyabunan 191.12. Altematif lain kombinasi suhu dan waktu pemasakan adalah pada suhu 105°C dan waktupemasakan 20 menit