Protein structure prediction aided by geometrical and probabilistic constraints

Database-assisted ab initio protein structure prediction methods have exhibited considerable promise in the recent past, with several implementations being successful in community-wide experiments (CASP). We have employed combinatorial optimization techniques toward solving the protein structure prediction problem. A Monte Carlo minimization algorithm has been employed on a constrained search space to identify minimum energy configurations. The search space is constrained by using radius of gyration cutoffs, the loop backbone dihedral probability distributions, and various secondary structure packing conformations. Simulations have been carried out on several sequences and 1000 conformations have been initially generated. Of these, 50 best candidates have then been selected as probable conformations. The search for the optimum has been simplified by incorporating various geometrical constraints on secondary structural elements using distance restraint potential functions. The advantages of the reported methodology are its simplicity, and modifiability to include other geometric and probabilistic restraints.     

A C0 interior penalty method for a fourth‐order variational inequality of the second kind

In this article, we propose a C⁰ interior penalty method for the frictional plate contact problem and derive both a priori and a posteriori error estimates. We derive an abstract error estimate in the energy norm without additional regularity assumption on the exact solution. The a priori error estimate is of optimal order whenever the solution is regular. Further, we derive a reliable and efficient a posteriori error estimator. Numerical experiments are presented to illustrate the theoretical results. © 2015 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 32: 36–59, 2016     

Synthesis of gold nanoparticles by <Emphasis Type=Italic>Cacumen Platycladi</Emphasis> leaf extract and its simulated solution: toward the plant-mediated biosynthetic mechanism

In this study, biogenic fabrication of gold nanoparticles (AuNPs), respectively, by Cacumen Platycladi leaf extract and the simulation of its active components were thoroughly investigated. The simulated solution was prepared based on components measurement and Fourier-transform infrared spectroscopy analysis of Cacumen Platycladi leaf extract before and after reaction. Several analytic methods such as UV–Vis spectrophotometry, X-ray diffraction, transmission electron microscopy, and thermogravimetric study were adopted to characterize the AuNPs. The results showed that flavonoid and reducing sugar were the main reductive and protective components in the extract vital in the biosynthesis of the AuNPs. In addition, pH of the reaction solution was proved to be the most significant factor upon the synthesis process. The bioreduction mechanism of chloroaurate ions and the formation mechanism of AuNPs were also discussed. To the best of our knowledge, this is the first report on plausible elucidation of the biosynthetic mechanism through comparative study between a plant extract and its simulated solution.     

Extending the Scope of the B(C6F5)3‐Catalyzed CN Bond Reduction: Hydrogenation of Oxime Ethers and Hydrazones

The B(C₆F₅)₃‐catalyzed hydrogenation is applied to aldoxime triisopropylsilyl ethers and hydrazones bearing an easily removable phthaloyl protective group. The C?N reduction of aldehyde‐derived substrates (oxime ethers and hydrazones) is enabled by using 1,4‐dioxane as the solvent known to participate as the Lewis‐basic component in FLP‐type heterolytic dihydrogen splitting. More basic ketone‐derived hydrazones act as Lewis bases themselves in the FLP‐type dihydrogen activation and are therefore successfully hydrogenated in nondonating toluene. The difference in reactivity between aldehyde‐ and ketone‐derived substrates is also reflected in the required catalyst loading and dihydrogen pressure.     

Understanding the problems in pharmaceutical procurement with special reference to active pharmaceutical ingredients and excipients

Accreditation and Quality Assurance - Procurement of raw materials, key intermediates and excipients for the preparation of finished pharmaceutical preparation is considered to be complex process...     

Topologically driven tandem radical cyclization-based strategy for the synthesis of oxa- and aza-cages

Tandem radical cyclization-based strategy for the synthesis of oxa- and aza-cage compounds is described. The aryl iodides 1 and N-tosyl propargylated amine 8 lead to oxa- and aza-cages, respectively, after two tandem 5-exo-trig radical cyclizations. The alcohols 11 on reaction with ⁿBu₃SnH and AIBN give rise to the oxa-cages 14 bearing the tributyltin moiety after three tandem 5-exo-trig cyclizations. On the other hand, reaction of the propargyl ether 16 under similar conditions furnishes the oxa-cage 17 by a 5-exo-trig, 4-exo-trig, 5-exo-trig tandem radical cyclization sequence.     

Damped quadratic and mixed-parity oscillator response using Krylov–Bogoliubov method and energy balance

Approximate analytic solutions of linearly damped quadratic and mixed parity nonlinear oscillators are obtained using the Krylov–Bogoliubov method and considering energy balance during the oscillatory motion. Difference in the system characteristic during the positive and negative half cycles of the oscillations is incorporated by considering two equivalent auxiliary equations of the system. The amplitudes of oscillations during the positive motion and negative motion are obtained using principle of energy balance. Solutions obtained through numerical simulation of the system are compared with the analytic expressions.     

Trace metal assay of thorium oxide by atomic emission spectrometry

Summary An Atomic Emission Spectrometric (AES) method has been developed for the direct determination of twenty-two metallic elements at trace concentrations in thorium oxide. The method is based on the use of a d.c. arc — carrier distillation technique with 12% composition of a mixed carrier, viz. AgCl+SrF₂ in 5:1 proportion, and is equally applicable to both volatile and refractory analytes. A direct reading emission spectrometer with computerised data acquisition and processing facility has been used in these studies. The standardisation procedure includes study of volatilisation/excitation characteristics of the analyte elements to optimise choice and proportion of the carrier and signal integration time apart from optimisation of other experimental parameters such as arc current, viewing position of the arc plasma, sample charge etc. The detection limits for the analytes lie in the range 0.1–50 ppm while the precision of determinations is better than 15% for most of the elements as evaluated from the repetitive analyses of spiked samples.     

Solvent-exfoliated graphene at extremely high concentration

We describe three related methods to disperse graphene in solvents with concentrations from 2 to 63 mg/mL. Simply sonicating graphite in N-methyl-2-pyrrolidinone, followed by centrifugation, gives dispersed graphene at concentrations of up to 2 mg/mL. Filtration of a sonicated but uncentrifuged dispersion gives a partially exfoliated powder that can be redispersed at concentrations of up to 20 mg/mL. However, this process can be significantly improved by removing any unexfolaited graphite from the starting dispersion by centrifugation. The centrifuged dispersion can be filtered to give a powder of exfoliated few-layer graphene. This powder can be redispersed at concentrations of at least 63 mg/mL. The dispersed flakes are ~1 μm long and ~3 to 4 layers thick on average. Although some sedimentation occurs, ~26-28 mg/mL of the dispersed graphene appears to be indefinitely stable.