Automated RNA tertiary structure prediction from secondary structure and low‐resolution restraints

A novel protocol for all‐atom RNA tertiary structure prediction is presented that uses restrained molecular mechanics and simulated annealing. The restraints are from secondary structure, covariation analysis, coaxial stacking predictions for helices in junctions, and, when available, cross‐linking data. Results are demonstrated on the Alu domain of the mammalian signal recognition particle RNA, the Saccharomyces cerevisiae phenylalanine tRNA, the hammerhead ribozyme, the hepatitis C virus internal ribosomal entry site, and the P4–P6 domain of the Tetrahymena thermophila group I intron. The predicted structure is selected from a pool of decoy structures with a score that maximizes radius of gyration and base–base contacts, which was empirically found to select higher quality decoys. This simple ab initio approach is sufficient to make good predictions of the structure of RNAs compared to current crystal structures using both root mean square deviation and the accuracy of base–base contacts. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Synthesis and characterization of soluble polyimides functionalized with carbazole moieties

Here, we report the synthesis and characterization of new soluble polyimides that are functionalized using carbazole moieties in their side chain. As a monomer for synthesizing the polyimides, 4″‐carbazole‐9‐yl‐[1,1′;2′,1″] terphenyl‐4‐4′‐diamine and 2‐(3‐carbazol‐9‐yl‐propyl)‐biphenyl‐4,4′‐diamine were synthesized and then characterized using ¹H NMR, ¹³C NMR, FTIR, UV–visible and photoluminescence spectroscopy, differential scanning calorimetry (DSC), and elemental analysis. The polyimides synthesized via chemical imidization processes were characterized with X‐ray photoelectron spectroscopy, gel permeation chromatography, wide angle X‐ray diffraction, thermogravimetric analysis, DSC, tensile strength measurement, and dielectric property measurement. Results showed that the synthesized polyimides were soluble in a variety of organic solvents, optically transparent in a visible range, thermally stable, mechanically strong, and considerably low dielectric. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 8117–8130, 2008     

On the problem of constraints in minimally coupled relativistic wave equations for particles of unique mass

We study the problem of a possible change in the number of constraints in linear relativistic wave equations (-iβ _μ ∂ ^μ +m)ψ=0 for particles of unique mass, on introduction of minimal coupling to an external electromagnetic field. Complementing our earlier work in which we obtained conditions for non-loss of constraints in equations characterised by the minimalβ-algebraβ ₀ ⁵ =β ₀ ³ we derive here the conditions for such theories not to generate more constraints than in the free case. The results are illustrated by considering specific equations and a fallacy in certain conclusions of Kobayashi and Shamaly on this problem is pointed out.     

Trace analysis of mercury by a radiochemical displacement method using cobalt(III) diethyldithiocarbamate

A radiochemical displacement method was utilized for the determination of traces of mercury in water taking advantage of its ability to displace cobalt from cobalt(III) diethyldithiocarbamate tagged with⁶⁰Co. The method is found to be applicable in the concentration range of 50–200 g/ml mercury. The interfernces from various cations like Fe(III), Co(II), Cu(II), Pb(II) and Ag(I) ions were studied.     

Ordinary linear differential equations involving random functions

Physical processes which can be represented by symbolic differential equations involving random functions are cited and studied. The solutions of these equations are obtained using Ramakrishnan’s recent phenomenological interpretation of integrals of random functions.     

The electronic states of carbon monofluoride: Rydberg states

Hartree-Fock and multiconfiguration Hartree-Fock calculations are reported on some low-lying Rydberg states of CF and the ground state of CF⁺. For the CF⁺ ground state, ¹Σ⁺, the calculations give a bond length of 1.55 Å, a fundamental frequency of 1821 cm^?1, and a dissociation energy of 6.9 eV. Many interactions between the valence and Rydberg state manifolds are revealed. Also a strong mixing of the 3dσ and 4sσ components due to an accidental degeneracy is described.     

Reactive Pulsed Laser Deposition of titanium nitride thin film: Optimization of process parameters using Secondary Ion Mass Spectrometry

Reactive Pulsed Laser Deposition is a single step process wherein the ablated elemental metal reacts with a low pressure ambient gas to form a compound. We report here a Secondary Ion Mass Spectrometry based analytical methodology to conduct minimum number of experiments to arrive at optimal process parameters to obtain high quality TiN thin film. Quality of these films was confirmed by electron microscopic analysis. This methodology can be extended for optimization of other process parameters and materials.