A simplified homology‐model builder toward highly protein‐like structures: An inspection of restraining potentials

A homology model builder using simple restraining potentials based on spline‐interpolated quadratic functions is developed and interfaced with CHARMM package. The continuity and stability of the potential function were validated, and the parameters were optimized using the CASP7 targets. The performance of the model builder was benchmarked to the Modeller program using the template‐based modeling targets in CASP9. The benchmark results show that, while our builder yields the structures with slightly lower packing, backbone, and template modeling scores, our models show much better protein‐like scores in terms of normalized discrete optimized protein energy, dipolar distance‐scaled finite‐ideal gas reference, Molprobity clash, Ramachandran appearance Z‐score, and rotamer Z‐score. As our model builder is interfaced with CHARMM, it is advantageous to directly use other CHARMM functionality and energy functions to refine the model structures or to use the models for other computational studies using CHARMM. © 2012 Wiley Periodicals, Inc.     

Joint optimization of process target mean and tolerance limits with measurement errors under multi-decision alternatives

Determining the optimal target mean for a process has been identified as an important research area and a number of models have been proposed in the literature. This paper differs from previous studies of this problem in two ways. First, most previous studies address the process target problem through models seeking the optimal process mean using fixed tolerance settings of a process. Second, in real-world industrial settings, there are several markets often available with different price/cost structures. In this paper, we develop a model for jointly determining both the optimal process target mean and the optimal tolerance limits under the situation where there are several markets available with different price/cost structures. We then investigate the effects of measurement errors on the optimum process target and tolerance limits with multi-decision alternatives. A numerical example is given, and sensitivity analyses are also performed to study the effects of measurement errors on this model.     

Synthesis and Characterization of Polymeric Acid‐Doped Polyaniline Interpenetrating Polymer Networks

Polyaniline (PANI)/poly(2‐acrylamido‐2‐methylpropane sulfonic acid) (PAMPS) semi‐interpenetrating network polymers (semi‐IPNs) were prepared using the simultaneous method. The formation and properties of the interpenetrating PANI/PAMPS semi‐IPNs were investigated using Fourier transform infrared spectroscopy, X‐ray diffraction, solid‐state ¹³C‐NMR, differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The interaction of PAMPS with PANI as a polymeric acid dopant was also investigated. These semi‐IPNs had a different microstructure compared to that of pure PANI. Packing structures and several decomposition steps were ordered for each semi‐IPN, while pure PANI exhibits a single amorphous peak and one decomposition step. The NMR spectra show that these peaks broaden and shifted downfield in the semi‐IPNs. A thermal reaction between PANI and PAMPS was observed using DSC and TGA, and the data from the two techniques are in agreement.     

Ratiometric detection of mitochondrial thiols with a two-photon fluorescent probe

We report a ratiometric two-photon probe (SSH-Mito) for mitochondrial thiols. This probe shows a marked blue-to-yellow emission color change in response to RSH, a significant two-photon cross section, good mitochondrial thiol selectivity, low cytotoxicity, and insensitivity to pH over the biologically relevant pH range, allowing the direct visualization of RSH levels in live cells as well as in living tissues at 90-190 μm depth without interference from other biologically relevant species through the use of two-photon microscopy.     

On the precipitation of delta phase in ALLVAC® 718Plus

ALLVAC 718Plus is a new commercial superalloy derived from Inconel 718, but possessing a higher temperature capability whilst employing the same philosophy regarding the microstructure. Many articles have been published describing various heat treatments exploiting the precipitation of intermetallic phases at grain boundaries to optimize the mechanical properties over a range of testing conditions. The requirement to further improve the mechanical properties of this alloy drives our interest in the precipitation mechanism of the delta and eta phases found in this alloy. We report the presence of finely layered structures composed of two phases, delta and eta, with distinct structures and chemistries. Possible pathways to explain this precipitation in 718Plus are considered as follows: (i) the sequential formation of the delta from eta phase and (ii) the simultaneous precipitation of both eta and delta facilitated via solute rejection. Both can result in the formation of those small delta layers observed in HRSTEM. We discuss which is most likely by comparing the relative alignment of the phases by image processing and the analysis of the HRSTEM images, and propose formation mechanisms consistent with the distinctive dislocation structures observed at the interface.     

The quality of non-textual elements in mathematics textbooks: an exploratory comparison between South Korea and the United States

As an exploratory investigation, this study aims to analyze non-textual elements in some Korean and US mathematics textbooks using a conceptual framework whose components include accuracy, connectivity, contextuality, and conciseness. By analyzing three US textbooks and three Korean ones, the study not only shows patterns in the use of non-textual elements in mathematics textbooks in different contexts but also provides insights into how to assess the quality of non-textual elements in mathematics textbooks, which I hope will contribute to the provision of more meaningful and productive learning opportunities to school children. Overall, the results from this study show that there is significant difference across topics and textbooks, which implies different opportunities to learn through non-textual elements. This study makes a unique contribution to the conceptualization of non-textual elements in mathematics education and has implications for textbook analysis and curriculum development.     

Approximately dual Gabor frames and almost perfect reconstruction based on a class of window functions

It is a well-known problem in Gabor analysis how to construct explicitly given dual frames associated with a given frame. In this paper we will consider a class of window functions for which approximately dual windows can be calculated explicitly. The method makes it possible to get arbitrarily close to perfect reconstruction by allowing the modulation parameter to vary. Explicit estimates for the deviation from perfect reconstruction are provided for some of the standard functions in Gabor analysis, e.g., the Gaussian and the two-sided exponential function.     

A study of three-nucleon transfer reactions on 18O

The reactions ¹⁸O¹¹B, ⁸Li)²¹Ne, ¹⁸O(¹²C, ⁹Be)²¹Ne and ¹⁸O(¹³C, ¹⁰B)²¹F have been studied, using beams of 115 MeV ¹¹B and ¹²C and 105 MeV ¹³C incident on a gas target. Shell-model calculations have been performed for ²¹Ne and ²¹F, for comparison with the experimental data. It is found that the data can be interpreted using the shell-model spectroscopic factors and a semiclassical reaction theory. Assignments are suggested for several previously unidentified high-spin states in ²¹Ne and ²¹F.