Modeling signal transduction networks: a comparison of two stochastic kinetic simulation algorithms

Computational efficiency of stochastic kinetic algorithms depend on factors such as the overall species population, the total number of reactions, and the average number of nodal interactions or connectivity in a network. These size measures of the network model can have a significant impact on computational efficiency. In this study, two scalable biological networks are used to compare the size scaling efficiencies of two popular and conceptually distinct stochastic kinetic simulation algorithms--the random substrate method of Firth and Bray (FB), and the Gillespie algorithm as implemented using the Gibson-Bruck method (GGB). The arithmetic computational efficiencies of these two algorithms, respectively, scale with the square of the total species population and the logarithm of the total number of active reactions. The two scalable models considered are the size scalable model (SSM), a four compartment reaction model for a signal transduction network involving receptors with single phosphorylation binding sites, and the variable connectivity model (VCM), a single compartment model where receptors possess multiple phosphorylation binding sites. The SSM has fixed species connectivity while the connectivity between species in VCM increases with the number of phosphorylation sites. For SSM, we find that, as the total species population is increased over four orders of magnitude, the GGB algorithm performs significantly better than FB for all three SSM compartment models considered. In contrast, for VCM, we find that as the overall species population decreases while the number of phosphorylation sites increases (implying an increase in network linkage) there exists a crossover point where the computational demands of the GGB method exceed that of the FB.     

Room temperature solution synthesis of alkyl-capped tetrahedral shaped silicon nanocrystals

We report the room temperature solution synthesis of alkyl protected silicon nanocrystals. The nanocrystals are of unusually uniform tetrahedral morphology and of a limited size distribution. The nanocrystals were characterized by transmission and scanning electron microscopy as well as atomic force microscopy.     

Disruption of spinal cord white matter and sciatic nerve geometry inhibits axonal growth in vitro in the absence of glial scarring

Background  

Axons within the mature mammalian central nervous system fail to regenerate following injury, usually resulting in long-lasting motor and sensory deficits. Studies involving transplantation of adult neurons into white matter implicate glial scar-associated factors in regeneration failure. However, these studies cannot distinguish between the effects of these factors and disruption of the spatial organization of cells and molecular factors (disrupted geometry). Since white matter can support or inhibit neurite growth depending on the geometry of the fiber tract, the present study sought to determine whether disrupted geometry is sufficient to inhibit neurite growth.     

Development of models correlating vibration excitation forces to dynamic characteristics of two-phase flow in a tube bundle

Recent experiments revealed significant quasi-periodic forces in both the drag and lift directions in a rotated triangular tube bundle subjected to two-phase cross-flow. The quasi-periodic drag forces were found to be related to the momentum flux fluctuations in the main flow path between the cylinders. The quasi-periodic lift forces, on the other hand, are mostly correlated to the oscillation in the wake of the cylinders. In this paper, we develop semi-analytical models for correlating vibration excitation forces to dynamic characteristics of two-phase flow in a rotated triangular tube bundle for a better understanding of the nature of vibration excitation forces. The relationships between the lift or drag forces and the dynamic characteristics of two-phase flow are established through fluid mechanics momentum equations. A model has been developed to correlate the void fraction fluctuation in the main flow path and the dynamic drag forces. A second model has been developed for correlating the oscillation in the wake of the cylinders and the dynamic lift forces. Although still preliminary, each model can predict the corresponding forces relatively well.     

A simple synthesis of catalytically active,high surface area ceria aerogels

A simple synthetic route for preparing high surface area, structurally stable ceria aerogels is presented. Ceria aerogels were doped with 1% palladium: a water-gas shift (WGS) active metal. A reduced Pd/ceria aerogel and an as-prepared Pd/ceria aerogel are compared to determine the effect of pretreatment conditions on WGS activity. The BET surface area of the as-prepared ceria aerogel was 345 m²/g. CO chemisorption data and high-resolution TEM images indicate that the particle size of palladium on the reduced Pd/ceria sample was approximately 15 nm. X-ray photoelectron spectroscopy (XPS) data establish that the fraction of Ce³⁺ from Ce₂O₃ was approximately the same for both reduced and as-prepared samples. XPS data also indicate that approximately 44% of the palladium on the reduced Pd/ceria sample was converted to the metallic form. Each catalyst was tested for WGS activity. The reduced Pd/ceria sample exhibited the greatest WGS activity as compared with the other samples used in this study.     

谈谈量子力学中的状态叠加原理

以对话的形式,介绍并评论了布洛欣采夫、狄拉克以及朗道和栗弗席茨关于状态叠加原理的不同表述.     

Phenylboronic acid mediated triple condensation reactions of phloroglucinol and unsaturated carbonyl compounds

[reaction: see text] A remarkable phenylboronic acid mediated triple condensation reaction of phloroglucinol (1,3,5-trihydroxybenzene) with a series of alpha,beta-unsaturated carbonyl compounds is reported. This experimentally simple reaction afforded novel C3-symmetric 2H-chromene derivatives. These derivatives represent structural analogues of the natural product xyloketal A, which has been reported to be a potent inhibitor of acetylcholine esterase.