Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions

We perform a mixed coarse-graining approach in a normal mode analysis of protein motions, which enables the modeling of a protein's native conformation with different regions having low and high resolution. As a result, the dynamics of the interesting functional parts within a supramolecular assemblage can be analyzed at high resolution, while the remainder of the structure is represented at poorer resolution, thus keeping the total number of nodes in the system sufficiently low for computational tractability. Our results indicate that the vibrational dynamics of specific components in a large multi-subunit protein are best described by retaining all the components of the structure, whether at higher or lower resolution. It is also shown that similar frequency distributions are obtained for different proteins and at different levels of coarse-graining, at the lower end of the spectrum, where the most significant slowest motions occur.     

Conductivity hysteresis in polymer electrolytes incorporating poly(tetrahydrofuran)

Conductivity hysteresis and room temperature ionic conductivities >10⁻³ S/cm were recently reported for electrolytes prepared from blends of an amphiphilic comb copolymer, poly[2,5,8,11,14-pentaoxapentadecamethylene (5-hexadecyloxy-1,3-phenylene)] (polymer I), and a linear multiblock copolymer, poly(oligotetrahydrofuran-co-dodecamethylene) (polymer II), following thermal treatment [F. Chia, Y. Zheng, J. Liu, N. Reeves, G. Ungar, P.V. Wright, Electrochim. Acta 43 (2003) 1939]. To investigate the origin of these effects, polymers I and II were synthesized in this work, and the conductivity and thermal properties of the individual polymers were investigated. AC impedance measurements were conducted on I and II doped with LiBF₄ or LiClO₄ during gradual heating to 110 °C and slow cooling to room temperature. Significant conductivity hysteresis was seen for polymer II, and was similarly observed for poly(tetrahydrofuran) (PTHF) homopolymer at equivalent doping levels. From thermogravimetic analysis (TGA), gel permeation chromatography (GPC) and ¹H NMR spectroscopy, both polymer II and PTHF were found to partially decompose to THF during heat treatment, resulting in a self-plasticizing effect on conductivity.     

Effects of infill walls on base responses and roof drift of reinforced concrete buildings under time‐history loading

In this study, the effects of infill walls on base reaction and roof drift of reinforced concrete frames were investigated. These effects were studied using 3D finite element method on 216 building models. Number of floors, number of bays, ratio of shear walls and ratio of infilled bays were selected as parameters. Sensitivity analysis was performed to determine the effect of each parameter on base shear, normal base reaction and roof drift. Based on the sensitivity analysis, the percentage of shear walls was the most important parameter affecting base shear, normal base reaction and roof drift. The effect of infill walls on base shear, normal base reaction and roof drift decreased when the percentage of the shear walls increased. The models without any infill walls had minimal normal base reaction under time‐history loading. However, an increase in the percentage of infill walls led to an increase in normal base reaction. The roof drift of the models was not critical. Copyright © 2009 John Wiley & Sons, Ltd.     

Effect of laser etching on the fracture strength of the monolithic zirconia and fiber-reinforced composite inlay-retained fixed partial dentures

Aim: The aim of this study was to evaluate the fracture strength of monolithic zirconia and fiber-reinforced composite (FRC) inlay-retained FPDs, both of which are cemented to the laser-etched cavity surfaces.

Materials and Methods: Eighty freshly extracted sound human teeth were used. A premolar and a molar tooth were embedded in an autopolymerizing acrylic resin. Forty acrylic resin models were randomly divided into two groups including monolithic zirconia and FRC inlay-retained FPDs (n = 20). Then, these groups were divided into two subgroups according to conditioning of the cavity surfaces with or without Er:YAG laser etching. Monolithic zirconia inlay-retained FPDs were produced by an inLab MC XL milling device using monolithic zirconia blocks. Tescera? Fiber Reinforcement Materials were used for the FRC inlay-retained FPDs. After 10.000 thermal cycles, fracture strength test was applied to the specimens.

Results: The monolithic zirconia inlay-retained FPDs exhibited the highest fracture strength than the FRC inlay-retained FPDs. Fracture strength was increased with laser etching for both restorative materials (p < 0.05).

Conclusion: Laser etching had positively effect on the fracture strength of the inlay-retained FDPs.     

A Study on Degree of Starch Gelatinization in Cakes Baked in Three Different Ovens

The main objective of the study was to determine the effects of different baking ovens and different cake formulations on the degree of starch gelatinization during cake baking. Baking was performed in microwave, infrared–microwave combination, and conventional ovens. Starch gelatinization levels of fat free, 25% fat, and 25% Simplesse™-containing cake samples were examined using differential scanning calorimeter (DSC) and rapid visco analyzer (RVA). Both DSC and RVA results showed that increasing baking time increased gelatinization level for all baking types significantly. It was also found that the effect of fat content on starch gelatinization was different depending on the type of baking. Addition of fat reduced the degree of starch gelatinization in conventional baking. However, fat enhanced the gelatinization in microwave and infrared–microwave combination ovens. Usage of Simplesse™ as a fat replacer decreased the starch gelatinization in all types of baking significantly. There was insufficient starch gelatinization in microwave-baked cakes in which the degree of gelatinization ranged from 55% to 78% depending on formulation. On the other hand, it ranged from 85% to 93% in conventionally baked cakes. Combining infrared with microwaves increased degree of starch gelatinization (70–90%).     

Functional properties of microwave-treated wheat gluten

In this study, the effects of microwave treatments on solubility, foaming and emulsifying properties of gluten were investigated. The solubility of microwave-heated gluten proteins gradually decreased as the treatment time increased, at all power levels applied. The highest solubility values were obtained for gluten samples microwave treated at 50% power level. The lowest emulsifying capacity values were obtained with the samples heated at 100% power level at all treatment times. The emulsifying stability values of microwave-heated gluten samples were found to be slightly higher than those of the control sample. However, there were no significant differences among the microwave power levels at all treatment times in terms of the emulsifying stability values. The foam volumes of the samples treated at 80 and 100% energy levels were slightly higher than those of the control gluten. The foam stability values of microwave-heated gluten samples gradually increased with treatment time at all power levels, which were more pronounced at 100% power level. Generally, microwave treatment did not cause major changes on the protein electrophoretic patterns of gluten samples at the power levels used.     

The effects of gums on macro and micro-structure of breads baked in different ovens

In this study, the effects of gums on macro and micro-structure of breads baked in different ovens (infrared (IR)-microwave combination and conventional) were investigated by the help of image and SEM analysis, respectively. The gums used were xanthan, guar, κ-carrageenan and xanthan-guar blend. The gums were added to the formulation at 0.5% concentration. As a control, no gum added formulations were used. Results of Image analysis demonstrated that xanthan-guar gum blend addition improved bread quality with increasing pore area fractions. It was seen that about 75% of the pores of control breads baked in infrared-microwave combination oven and about 63% of the pores of control breads baked in conventional oven had diameters of above 1000 μm. According to SEM analysis, pores in control breads baked in conventional oven were found to be smaller, and had spherical, oval-like shape as compared to the ones baked in IR-microwave combination oven. Moreover, more homogeneous closed-cell structure was observed for conventionally baked control breads. The pores of breads baked in IR-microwave combination oven were so close to each other which resulted in coalescence of the gas cells to form channels, then the pores were no longer spherical. The starch granules in conventionally baked breads were more distorted and seen as a continuous sheet of gelatinized starch. On the other hand, granular residues and continuous starch structure was observed together in IR-microwave combination heating.     

Investigation of physicochemical properties of breads baked in microwave and infrared-microwave combination ovens during storage

Staling of breads baked in different ovens (microwave, infrared-microwave combination and conventional) was investigated with the help of mechanical (compression measurements), physicochemical (DSC, X-ray, FTIR) and rheological (RVA) methods. The effect of xanthan-guar gum blend addition on bread staling was also studied. Xanthan-guar gum blend at 0.5% concentration was used in bread formulation. The gums were mixed at equal concentrations to obtain the blend. After baking, the staling parameters of breads were monitored over 5 days storage. During storage, it was seen that hardness, retrogradation enthalpies, setback viscosity, crystallinity values, and FTIR outputs related to starch retrogradation of bread samples increased, whereas FTIR outputs related to moisture content of samples decreased significantly with time. The hardness, retrogradation enthalpy, setback viscosity, and crystallinity values of microwave-baked samples were found to be highest among other heating modes. Using IR-microwave combination heating made it possible to produce breads with similar staling degrees as conventionally baked ones in terms of retrogradation enthalpy and FTIR outputs related to starch retrogradation. Addition of xanthan-guar gum blend decreased hardness, retrogradation enthalpy and total mass crystallinity values of bread samples showing that staling was delayed.     

A computational and experimental approach to develop minocycline-imprinted hydrogels and determination of their drug delivery performances

In this study, minocycline-imprinted hydrogels are developed for controlled drug delivery in ocular disease treatments. An integrated computational and experimental study are conducted for investigating the relationship between design parameters and the drug loading/release performance of hydrogels. First, suitable functional monomers are determined for successful drug-imprinting by studying pre-polymerization conditions with full-atom molecular dynamics (MD) simulations. MD simulations suggest that acrylic acid and itaconic acid are suitable monomers for imprinting minocycline. Then, minocycline-imprinted hydrogels are synthesized with acrylic acid, commonly used in hydrogels, and three different amounts of cross-linker ethylene glycol dimethacrylate, 1, 2 and 3 mol%. All hydrogels are characterized and their drug loading and release performances are determined. Our computational and experimental calculations indicate an optimum cross-linker amount of 2 mol% for controlled minocycline release from imprinted hydrogels with an imprinting factor of almost 3. Finally, the drug release kinetics are determined by Korsmeyer-Peppas model.