Parameter optimization for the Gaussian model of protein folding

Computational models of protein folding and ligand docking are large and complex. Few systematic methods have yet been developed to optimize the parameters in such models. We describe here an iterative parameter optimization strategy that is based on minimizing a structural error measure by descent in parameter space. At the start, we know the ‘correct’ native structure that we want the model to produce, and an initial set of parameters representing the relative strengths of interactions between the amino acids. The parameters are changed systematically until the model native structure converges as closely as possible to the correct native structure. As a test, we apply this parameter optimization method to the recently developed Gaussian model of protein folding: each amino acid is represented as a bead and all bonds, covalent and noncovalent, are represented by Hooke's law springs. We show that even though the Gaussian model has continuous degrees of freedom, parameters can be chosen to cause its ground state to be identical to that of Go-type lattice models, for which the global ground states are known. Parameters for a more realistic protein model can also be obtained to produce structures close to the real native structures in the protein database.     

Developmental, Gustatory, and Behavioral Responses of Leafroller Larvae, Choristoneura rosaceana, to Tannic Acid and Glucose

Soluble sugars are essential nutrients generally perceived as phagostimulants to most insects studied. However, tannins are known as digestibility reducers, hence deleterious to caterpillar development, and as deterrents as well. Previous work demonstrated that larvae of the polyphagous oblique-banded leafroller, Choristoneura rosaceana, performed better when reared on a control + 0.5% tannic acid diet than on the standard control diet and that larvae reared on a control + 5% glucose diet had slower development and reduced survival. This study was designed to elucidate the behavioral and neurophysiological components of the larval responses to tannic acid and glucose. C. rosaceana larvae were reared individually from the first to the sixth instar on one of four different artificial diets: (1) control; (2) control + 5% glucose; (3) control + 0.5% tannic acid; (4) control + 5% glucose + 0.5% tannic acid. After 14 days, larvae reared on the control + 5% glucose diet had not developed past the fourth instar, whereas a considerable proportion of larvae reared on the control + 0.5% tannic acid diet had already attained the pupal stage. Insects reared on the control or the control + 5% glucose + 0.5% tannic acid diet had intermediate development, with most larvae in the fifth instar. In addition, once the mid-sixth instar was reached, the feeding preferences to 25 and 300 mM glucose, 25 mM tannic acid, and 25 mM glucose + 25 mM tannic acid over water were assessed in two-choice tests. Feeding affected preference. Control-reared insects preferred feeding on treatments containing glucose and were not deterred by tannic acid. However, larvae that had been exposed to tannic acid during their development were deterred by tannic acid and their glucose discrimination was impaired. The sensitivity to glucose was also examined from neurophysiological recordings by stimulating the sugar-sensitive cell (cell 1) on the lateral styloconic sensillum of the maxillary galea with increasing concentrations of glucose (1, 10, 25, 50, 100, 200, 300, and 500 mM). We also determined whether tannic acid was phagostimulatory, since insects develop relatively quickly on a diet containing this compound, by testing 1 mM tannic acid, 1 mM tannic acid + 300 mM glucose, and 300 mM glucose on the lateral styloconic sensilla. The traces indicated that 1 mM tannic acid was not detected by any of the four chemosensory cells in these sensilla. The combination of tannic acid and glucose produced no spikes from the sugar-sensitive cell, whereas a prominent spike activity resulted with 300 mM glucose. We concluded that, although C. rosaceana larvae develop faster on a tannic acid diet, this compound is not a phagostimulant. The converse is true for glucose; i.e., it stimulates the sugar-sensitive cell in the lateral styloconica in a concentration-dependent fashion. Previous dietary experience changes the sensory and behavioral responses of C. rosaceana to glucose. Our findings imply that not all compounds that are phagostimulatory are necessarily beneficial to an insect's fitness. Therefore, developmental studies should be interpreted in conjunction with behavioral and physiological data.     

Dynamic Fracture Characterization of Al2O3 and SiCw/Al2O3

The dynamic stress intensity factors, which were determined with newly developed bar impact facilities and a new data reduction procedure, for an Al₂O₃ ceramic and 29 vol% SiC_w/Al₂O₃ composite were virtually identical, thus indicating that the short SiC whiskers were ineffective under dynamic fracture. SEM studies revealed five distinct fracture morphologies with increased percentage area of transgranular fracture in both materials with rapid crack propagation. Also, the high dynamic stress intensity factor caused multiple microscopic crack planes to form and then join as the crack advanced.     

Modeling nonisothermal impregnation of fibrous media with reactive polymer resin

The manufacture of polymer composites through resin transfer molding (RTM) or structural reaction injection molding (SRIM) involves the impregnation of a fibrous reinforcement in a mold cavity with a reactive polymer resin. The design of RTM and SRIM operations requires an understanding of the various parameters, such as materials properties, mold geometry, and mold filling conditions, that affect the resin impregnation process. Modeling provides a potential tool for analyzing the relationships among the important parameters. The present work provides the physical model and finite element formulations for simulating the mold filling stage. Resin flow through the fibers is modeled using two-dimensional Darcian flow. Simultaneous resin reaction and heat transfer among resin, mold walls, and fibers are considered in the model. The proposed technique emphasizes the use of the least squares finite element method to solve the convection dominated mass and energy equations for the resin. Excellent numerical stability of the proposed technique provides a powerful numerical method for the modeling of polymer processing systems characterized by convection dominated transport equations. Results from example numerical studies for SRIM of polyurethane/glass fiber composites were presented to illustrate the application of the proposed model and numerical scheme.     

Uncertainties in the fate of nitrogen I: An overview of sources of uncertainty illustrated with a Dutch case study

This study focuses on the uncertainties in the fate of nitrogen (N) in the Netherlands. Nitrogen inputs into the Netherlands in products, by rivers, and by atmospheric deposition, and microbial and industrial fixation of atmospheric N₂ amount to about 4450 Gg N y^–1. About 60% of this N is transported out of the Netherlands in products. The fate of the remaining 40%, however, is less clear. We discuss uncertainties in losses to the atmosphere (as ammonia or through denitrification), by leaching and runoff, and in N accumulation in biomass and soils. These processes may account for the fate of about 40% of the N in the Netherlands, and for the fate of about 60% of the N in Dutch agricultural soils. Reducing uncertainties in the estimates of these fluxes is necessary for reducing the impact of excess N in the environment. In particular, monitoring the environmental effects of ammonia emissions and nitrate leaching to groundwater and aquatic systems requires an increased understanding of the fate of N. Uncertainties arise because (1) some N fluxes cannot be measured directly and are usually quantified indirectly as the balance in N budgets, (2) direct measurements of N fluxes have inevitable inaccuracies, (3) lack of experimental data and other information (e.g. statistics) needed for upscaling, (4) large spatial and temporal variability of fluxes, and (5) poor understanding of the processes involved. These uncertainties can be reduced by additional experimental studies and by further development of process-based models and N budget studies. We prioritize these future research needs according to a range of different criteria.     

Carbon nanotubes and onions from carbon monoxide using Ni(acac)2 and Cu(acac)2 as catalyst precursors

New catalyst precursors (copper and nickel acetylacetonates) have been used successfully for the synthesis of carbon nanotubes and onion particles from carbon monoxide. Catalyst nanoparticles and carbon products were produced by metal-organic precursor vapour decomposition and catalytic disproportionation of carbon monoxide in a laminar flow reactor at temperatures between 705 and 1216 °C. Carbon nanotubes (CNTs) were formed in the presence of nickel particles at 923-1216 °C. The CNTs were single-walled, 1-3 nm in diameter and up to 90 nm long. Hollow carbon onion particles (COPs) were produced in the presence of copper particles at 1216 °C. The COPs were from 5 to 30 nm in diameter and consisted of several concentric carbon layers surrounding a hollow core. The results of computational fluid dynamics calculations to determine the temperature and velocity profiles and mixing conditions of the species in the reactor are presented. The mechanisms for the formation of both CNTs and COPs are discussed on the basis of the experimental and computational results.     

Dietary diversity and associated factors among beneficiaries of 77 child care centers: Central Regional,Venezuela

The aim of this study was to estimate household measure diet quality, using a dietary diversity score, and its associated demographic and socio-economic factors. One hundred fifty three households representatives of the Capital District and Miranda State belonging of seventy seven day care children centers were studied. To gather data on dietary diversity, we used the food register method, collecting data on household food availability during a month. Dietary diversity at day care centers of the Capital District was 46 foods differed from that found, in Miranda State was 39 foods (p = 0.005). Likewise it differed in beneficiaries' households of the Capital District was 33 foods compared to those in Miranda State was 25 foods (p = 0.000). There were 13 and 14 foods more between day care centers and the households in both states. State (Capital District or Miranda), money spent on food per person, households size and social level were variables that explained 28.9% of dietary diversity variation in households studied. Households in the Capital District had less members, spent more money on food, and a greater proportion were non-poor compared to those in Miranda. These factors could partially explain differences in diet quality among households in the two States. Whatever perspective studied indicates that the dietary diversity had a statistically significant difference between day care centers and households in states studied. Miranda State was more deficiency than Capital District. Higher dietary diversity reflects a better quality diet at day care centers compared to households studied.     

Stress relaxation in low‐shrink‐force polyolefin films

The morphology and stress relaxation of coextruded five‐layer LLDPE (linear low‐density polyethylene)/EVA (ethylene‐vinyl‐acetate) copolymer films were studied. Increasing VA (vinyl acetate) content in EVA causes a decrease of shrink tension in the films, which can be explained by a decrease in amount of crystallinity. The relaxation time spectrum of the coextruded crosslinked LLDPE/EVA films is similar to the relaxation time spectrum of crosslinked LLDPE film at room temperature. However, at elevated temperatures, an additional peak appears on the spectrum of coextruded film. The cause of this peak is temperature‐ and stress‐induced recrystallization of EVA during the relaxation test. This recrystallization was confirmed with DSC and wide angle X‐ray analysis. Polym. Eng. Sci. 44:1716–1720, 2004. © 2004 Society of Plastics Engineers.     

Long-term stability of PEG-based antifouling surfaces in seawater

Poly(ethylene glycol) (PEG) is a hydrophilic polymer that has been extensively used in the biomedical and marine environment due to its antifouling properties. In the biomedical field, PEG has been successfully used to functionalize surfaces due to its resistance to cell and nonspecific protein adsorption. However, the long-term stability of PEG has limited its use in some areas. In the shipping industry, there is a great need for long-term solutions to keep the hulls of the ships fouling-free. The long-term stability of PEG in polydimethylsiloxane (PDMS) fouling-release coatings is studied here, in both accelerated laboratory tests and real seawater conditions. This article shows how PEG-based copolymers, which have been exposed in fouling-release coatings to real-life seawater conditions, are isolated and compared to those exposed to accelerated laboratory testing with successful results. The influence of the chemistry of the PEG compounds, the chosen laboratory degrading agents, and the possible degradation pathways and products are discussed.