Investigation of the signaling mechanism and verification of the performance of an electrochemical real-time PCR system based on the interaction of methylene blue with DNA

The operation of an electrochemical real-time PCR system, based on intercalative binding of methylene blue (MB) with dsDNA, has been demonstrated. PCR was performed on a fabricated electrode-patterned glass chip containing MB while recording the cathodic current peak by measuring the square wave voltammogram (SWV). The current peak signal was found to decrease with an increase in the PCR cycle number. This phenomenon was found to be mainly a consequence of the lower apparent diffusion rate of the MB-DNA complex (D(b) = 6.82 × 10(-6) cm(2) s(-1) with 612 bp dsDNA) as compared to that of free MB (D(f) = 5.06 × 10(-5) cm(2) s(-1)). Utilizing this signal changing mechanism, we successfully demonstrated the feasibility of an electrochemical real-time PCR system by accurately quantifying initial copy numbers of Chlamydia trachomatis DNA templates on a direct electrode chip. A standard calibration plot of the threshold cycle (C(t)) value versus the log of the input template quantity demonstrated reliable linearity and a good PCR efficiency (106%) that is comparable to that of a conventional TaqMan probe-based real time PCR. Finally, the system developed in this effort can be employed as a key technology for the achievement of point-of-care genetic diagnosis based on the electrochemical real-time PCR.     

Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water

We report the development of an atomic decomposition method of the protein solvation free energy in water, which ascribes global change in the solvation free energy to local changes in protein conformation as well as in hydration structure. So far, empirical decomposition analyses based on simple continuum solvation models have prevailed in the study of protein-protein interactions, protein-ligand interactions, as well as in developing scoring functions for computer-aided drug design. However, the use of continuum solvation model suffers serious drawbacks since it yields the protein free energy landscape which is quite different from that of the explicit solvent model and since it does not properly account for the non-polar hydrophobic effects which play a crucial role in biological processes in water. Herein, we develop an exact and general decomposition method of the solvation free energy that overcomes these hindrances. We then apply this method to elucidate the molecular origin for the solvation free energy change upon the conformational transitions of 42-residue amyloid-beta protein (Aβ42) in water, whose aggregation has been implicated as a primary cause of Alzheimer's disease. We address why Aβ42 protein exhibits a great propensity to aggregate when transferred from organic phase to aqueous phase.     

Predictive modeling and analysis of HfO2 thin film process based on Bayesian information criterion using PCA‐based neural networks

Principal component analysis (PCA)‐based neural network (NNet) models of HfO₂ thin films are used to study the process of efficient model selection and develop an improved model by using multivariate functional data such as X‐ray diffraction data (XRD). The accumulation capacitance and the hysteresis index input parameters, both characteristic of HfO₂ dielectric films, were selected for the inclusion in the model by analyzing the process conditions. Standardized XRD were used to analyze the characteristic variations for different process conditions; the responses and the electrical properties were predicted by NNet modeling using crystallinity‐based measurement data. A Bayesian information criterion (BIC) was used to compare the model efficiency and to select an improved model for response prediction. Two conclusions summarize the results of the research documented in this paper: (i) physical or material properties can be predicted by the PCA‐based NNet model using large‐dimension data, and (ii) BIC can be used for the selection and evaluation of predictive models in semiconductor manufacturing processes. Copyright © 2013 John Wiley & Sons, Ltd.     

Azeotropy in Terpolymerization

Abstract

A number of polyurethanes were synthesized by reacting castor oil with isophorone diisocyanate while varying the NCO/OH ratio. All these polyurethanes were reacted with such acrylic monomers as acrylamide and methacrylamide by using ethylene glycol dimethacrylate as a crosslinker and benzoyl peroxide as the initiator. The physicochemical properties of interpenetrating polymer networks (IPNs) are reported. The durability, solvent absorption, outdoor weathering, and aging properties of IPNs have been studied. Thermogravimetric analysis was used to study the thermal behavior of IPNs and the evaluation of kinetic parameters. A number of equations, such as those of Freeman-Anderson, Broido, Piloyan-Novikova, Horowitz-Mitzger, and Coats-Redfern, have been used to determine the kinetic parameters. The degradation mechanism is discussed.     

Multiple semi‐coarsened multigrid method with application to large eddy simulation

The Multiple Semi‐coarsened Grid (MSG) multigrid method of Mulder (J. Comput. Phys. 1989; 83 :303–323) is developed as a solver for fully implicit discretizations of the time‐dependent incompressible Navier–Stokes equations. The method is combined with the Symmetric Coupled Gauss–Seidel (SCGS) smoother of Vanka (Comput. Methods Appl. Mech. Eng. 1986; 55 :321–338) and its robustness demonstrated by performing a number of large‐eddy simulations, including bypass transition on a flat plate and the turbulent thermally‐driven cavity flow. The method is consistently able to reduce the non‐linear residual by 5 orders of magnitude in 40–80 work units for problems with significant and varying coefficient anisotropy. Some discussion of the parallel implementation of the method is also included. Copyright © 2005 John Wiley & Sons, Ltd.     

He(I) and He(II) photoelectron spectra of glycine and related molecules

Photoelectron spectra obtained by He(I) and He(II) excitation of glycine, sarcosine and glycine methyl ester are presented. The p-type bands in the He(I) spectrum of glycine are interpreted in terms of localized molecular orbitals; the C 2s bands are identified in the He(II) spectrum. He(I) spectra of some N-acetylamino acids and of a variety of α-and ω-substituted amino acids are also reported.     

Ratiometry of monomer/excimer emissions of dipyrenyl calix[4]arene in aqueous media

Variations in the ratio of monomer/excimer emissions from pyrenyl groups bound to a calix[4]arene through facing carboxamidomethyl substituents have been investigated in H₂O/CH₃CN mixtures. Above a level of 50% H₂O, monomer emission declines and the excimer emission concomitantly increases. DFT calculations support the argument that disruption of intramolecular NHO bonds by water results in a geometry, which favors contact of the pyrene units and thus a strong excimer emission. Addition of Fe(III) to a H₂O/CH₃CN (4:1, v/v) solution of 1 at pH 6.1 quenches both monomer and excimer emissions through electron transfer (eT) from excited pyrene to the metal ion.     

Facile one-step synthesis of Ru doped NiCoP nanoparticles as highly efficient electrocatalysts for oxygen evolution reaction

Transition metal phosphides (TMPs) as ever-evolving electrocatalytic materials have attracted increasing attention in water splitting reactions owing to their cost-effective, highly active and stable catalytic properties. This work presents a facile synthetic route to NiCoP nanoparticles with Ru dopants which function as highly efficient electrocatalysts for oxygen evolution reaction (OER) in alkaline media. The Ru dopants induced a high content of Ni and Co vacancies in NiCoP nanoparticles, and the more defective Ru doped NiCoP phase than undoped NiCoP ones led to a greater number of catalytically active sites and improved electrical conductivity after undergoing electrochemical activation. The Ru doped NiCoP catalyst exhibited high OER catalytic performance in alkaline media with a low overpotential of 281 mV at 10 mA cm⁻² and a Tafel slope of 42.7 mV dec⁻¹.