A hybrid approach to protein folding problem integrating constraint programming with local search

<p>Abstract</p> <p>Background</p> <p>The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint programming are two common techniques to approach this problem. The present study introduces a novel hybrid approach to simulate the protein folding problem using constraint programming technique integrated within local search.</p> <p>Results</p> <p>Using the face-centered-cubic lattice model and 20 amino acid pairwise interactions energy function for the protein folding problem, a constraint programming technique has been applied to generate the neighbourhood conformations that are to be used in generic local search procedure. Experiments have been conducted for a few small and medium sized proteins. Results have been compared with both pure constraint programming approach and local search using well-established local move set. Substantial improvements have been observed in terms of final energy values within acceptable runtime using the hybrid approach.</p> <p>Conclusion</p> <p>Constraint programming approaches usually provide optimal results but become slow as the problem size grows. Local search approaches are usually faster but do not guarantee optimal solutions and tend to stuck in local minima. The encouraging results obtained on the small proteins show that these two approaches can be combined efficiently to obtain better quality solutions within acceptable time. It also encourages future researchers on adopting hybrid techniques to solve other hard optimization problems.</p

The apicomplexan plastid and its evolution

Protistan species belonging to the phylum Apicomplexa have a non-photosynthetic secondary plastid—the apicoplast. Although its tiny genome and even the entire nuclear genome has been sequenced for several organisms bearing the organelle, the reason for its existence remains largely obscure. Some of the functions of the apicoplast, including housekeeping ones, are significantly different from those of other plastids, possibly due to the organelle’s unique symbiotic origin

J/psi production from proton-proton collisions at sqrt(s) = 200 GeV

J/psi production has been measured in proton-proton collisions at sqrt(s)= 200 GeV over a wide rapidity and transverse momentum range by the PHENIX experiment at RHIC. Distributions of the rapidity and transverse momentum, along with measurements of the mean transverse momentum and total production cross section are presented and compared to available theoretical calculations. The total J/psi cross section is 3.99 +/- 0.61(stat) +/- 0.58(sys) +/- 0.40(abs) micro barns. The mean transverse momentum is 1.80 +/- 0.23(stat) +/- 0.16(sys) GeV/c.Comment: 326 authors, 6 pages text, 4 figures, 1 table, RevTeX 4. To be submitted to PRL. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Measurement of Single Electron Event Anisotropy in Au+Au Collisions at sqrt(s_NN) = 200 GeV

The transverse momentum dependence of the azimuthal anisotropy parameter v_2, the second harmonic of the azimuthal distribution, for electrons at mid-rapidity (|eta| < 0.35) has been measured with the PHENIX detector in Au+Au collisions at sqrt(s_NN) = 200 GeV. The measurement was made with respect to the reaction plane defined at high rapidities (|eta| = 3.1 -- 3.9). From the result we have measured the v_2 of electrons from heavy flavor decay after subtraction of the v_2 of electrons from other sources such as photon conversions and Dalitz decay from light neutral mesons. We observe a non-zero single electron v_2 with a 90% confidence level in the intermediate p_T region.Comment: 330 authors, 11 pages text, RevTeX4, 9 figures, 1 tables. Submitted to Physical Review C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Seaweeds and their communities in polar regions

Polar seaweeds typically begin to grow in late winter-spring, around the time of sea-ice break up. They can grow under very low light enabling distributions to depths of ≥40 m. Moreover, they are physiologically adapted to low temperatures. Intertidal species exhibit a remarkable stress tolerance against freezing, desiccation and salinity changes. Endemism is much greater in the Antarctic compared to the Arctic species. On rocky shores of the Antarctic Peninsula and of Spitsbergen >80% of the bottom can be covered by seaweeds with standing biomass levels ≥20 kg wet wt m-2. Species richness and biomass declines, however, towards higher latitudes. Seaweeds are the dominant organisms in coastal waters and thus play important roles in benthic food webs and are likely to be of particular importance to benthic detrital food chains. Chemical defenses against herbivores are common in Antarctic, but not in Arctic seaweeds. More research is needed especially to study the effects of global climate changes

Respostas metabólicas à suplementação com frutose em exercício de força de membros inferiores Metabolic responses to fructose supplementation in strength exercise of lower limbs

A frutose, por seu metabolismo independente da insulina, realiza significativas alterações no metabolismo hepático, promovendo um entorno metabólico favorável ao metabolismo tanto da glicose como dos lipídios, durante o exercício. Essa condição tem sido bastante estudada em exercício de endurance; no entanto, nenhum estudo sobre a suplementação com frutose no exercício de força (EF) foi encontrado. O objetivo do presente estudo foi avaliar os efeitos agudos da adição de frutose a um suplemento de glicose sobre o metabolismo de lipídios em EF. Vinte homens treinados ingeriram suplemento de glicose (G) ou glicose mais frutose (G+F), 15 minutos antes de realizar exercício de força (10 séries de 10 repetições). Os sujeitos foram testados em ordem randômica em um desenho cruzado e com uma semana de intervalo em duas condições experimentais: EF+(G) e EF+(G+F). A análise dos resultados mostrou que os valores de triglicérides durante o exercício foram maiores (p < 0,05) quando os sujeitos foram suplementados com G+F do que quando suplementados apenas com G. Ao final do exercício, os valores de ácidos graxos livres foram maiores quando os sujeitos foram suplementados G+F (p < 0,05). A glicemia foi menor durante o exercício e maior na recuperação (p < 0,05) para essa condição. O comportamento da insulina não diferiu entre os experimentos durante o exercício de força (p > 0,05), mas foi maior em G+F que em G (p < 0,05) durante a recuperação. A percepção subjetiva de esforço (PSE) foi menor (p < 0,05) para a suplementação com G+F do que com G. Em conclusão, a suplementação com G+F afeta positivamente o metabolismo de lipídios durante o exercício de força e favorece seu metabolismo imediatamente após o esforço, proporcionando condição metabólica que reflete em uma condição que afeta favoravelmente a PSE.<br>Due to its insulin-independent metabolism, fructose promotes significant changes in liver metabolism, promoting a metabolic surrounding favorable to the glucose as well as lipids metabolism during the exercise. This condition has been widely studied in endurance exercises; however, none study about fructose supplementation in strength exercise (SE) was found. This study aimed to assess the acute effects of the fructose addition to a glucose supplement on lipid metabolism in strength exercise. Twenty trained male subjects ingested a glucose (G) or glucose plus fuctose (G+F) supplement, 15 minutes before practicing a strength exercise (10 sets of 10 repetitions). The subjects were tested randomly in a crossover design and with a week of pause in two experimental conditions: SE+(G) and SE+(G+F). The analysis of the results showed that values of triglycerides during the exercise were higher (p < 0.05) when the subjects were supplemented with G+F than when they were supplemented only with G. By the end of the exercise the values of free fatty acid were higher when in G+F (p < 0.05). Glycemia was lower during the exercise and higher in the recovery (p < 0.05) in this condition. Insulin values did not differ among the experiments during strength exercises (p > 0.05), but they were higher in G+F than in G (p < 0.05) during recovery. Perceived exertion (PE) was lower (p < 0.05) in G+F than in G. It can be concluded that the G+F supplementation positively affects the lipid metabolism during the strength exercise and favors its metabolism immediately after the effort, promoting a metabolic condition that reflects on a condition that favorably affects the PE