Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

All-atom force fields are important for predicting thermodynamic, structural, and dynamic properties of RNA. In this paper, results are reported for thermodynamic integration calculations of free energy differences of duplex formation when CG pairs in the RNA duplexes r(CCGG)(2), r(GGCC)(2), r(GCGC)(2), and r(CGCG)(2) are replaced by isocytidine-isoguanosine (iCiG) pairs. Agreement with experiment was improved when ε/ζ, α/γ, β, and χ torsional parameters in the AMBER99 force field were revised on the basis of quantum mechanical calculations. The revised force field, AMBER99TOR, brings free energy difference predictions to within 1.3, 1.4, 2.3, and 2.6 kcal/mol at 300 K, respectively, compared to experimental results for the thermodynamic cycles of CCGG → iCiCiGiG, GGCC → iGiGiCiC, GCGC → iGiCiGiC, and CGCG → iCiGiCiG. In contrast, unmodified AMBER99 predictions for GGCC → iGiGiCiC and GCGC → iGiCiGiC differ from experiment by 11.7 and 12.6 kcal/mol, respectively. In order to test the dynamic stability of the above duplexes with AMBER99TOR, four individual 50 ns molecular dynamics (MD) simulations in explicit solvent were run. All except r(CCGG)(2) retained A-form conformation for ≥82% of the time. This is consistent with NMR spectra of r(iGiGiCiC)(2), which reveal an A-form conformation. In MD simulations, r(CCGG)(2) retained A-form conformation 52% of the time, suggesting that its terminal base pairs may fray. The results indicate that revised backbone parameters improve predictions of RNA properties and that comparisons to measured sequence dependent thermodynamics provide useful benchmarks for testing force fields and computational methods.     

Analysis of differential equations of fractional order

This paper provides a robust convergence checking method for nonlinear differential equations of fractional order with consideration of homotopy perturbation technique. The differential operators are taken in the Caputo sense. Some theorems to prove the existence and uniqueness of the series solutions are presented. Results show that the proposed theoretical analysis is accurate.     

On generalized statistical convergence of double sequences via ideals

The concept of statistical convergence is one of the most active area of research in the field of summability. Most of the new summability methods have relation with this popular method. In this paper we generalize the notions of statistical convergence, (λ, μ)-statistical convergence, (V, λ, μ) summability and (C, 1, 1) summability for a double sequence x = (x _jk ) via ideals. We also establish the relation between our new methods.     

Labeling of acetaminophen with I-131 and biodistribution in rats

The aim of the present study was to label acetaminophen (APAP) with I-131 and to determine its radiopharmaceutical potential in rats. Acetaminophen was labeled with I-131 using the iodogen method. The radiochemical purity of (131)I-APAP was determined by RTLC and paper electrophoresis. The labeling yield was 94 +/- 4%. The biodistribution studies of the labeled compound (specific activity; 56.60 GBq/mmol) were performed in male Albino Wistar rats. The uptake of (131)I-APAP in some organs were determined at different time after injection to the rats. The radioactivity in each organ was counted and the percentage of injected activity per gram of tissue weight (%ID/g) for each organ and blood was calculated. (131)I-APAP uptake in the lung, liver, kidneys, pancreas, blood, stomach and some brain region, were observed. Thus, (131)I-APAP may be radiopharmaceutical for the imaging of the brain.     

On stable implicit difference scheme for hyperbolic–parabolic equations in a Hilbert space

The first‐order of accuracy difference scheme for approximately solving the multipoint nonlocal boundary value problem for the differential equation in a Hilbert space H, with self‐adjoint positive definite operator A is presented. The stability estimates for the solution of this difference scheme are established. In applications, the stability estimates for the solution of difference schemes of the mixed type boundary value problems for hyperbolic–parabolic equations are obtained. © 2008 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2009     

Structure and electrochemical behaviour of Bis[N‐(4‐methylphenyl)salicylaldimine]copper(II) N,N′dimethylformamide solvate

The molecular model of mononuclear complex formed, through a reaction between N‐(4‐methylphenyl)salicylaldimine and Cu^II ion was determined using x‐ray diffraction method. The Cu^II coordination was found to have a distorted square‐planar structure and a cis coordination geometry was observed within the surrounding of the copper. The electro chemical behaviour of the mononuclear copper complex was studied with cyclic voltammetry.     

Hydrolytic Degradation of Polylactic Acid Fibers as a Function of pH and Exposure Time

Polylactic acid (PLA) is a widely used bioresorbable polymer in medical devices owing to its biocompatibility, bioresorbability, and biodegradability. It is also considered a sustainable solution for a wide variety of other applications, including packaging. Because of its widespread use, there have been many studies evaluating this polymer. However, gaps still exist in our understanding of the hydrolytic degradation in extreme pH environments and its impact on physical and mechanical properties, especially in fibrous materials. The goal of this work is to explore the hydrolytic degradation of PLA fibers as a function of a wide range of pH values and exposure times. To complement the experimental measurements, molecular-level details were obtained using both molecular dynamics (MD) simulations with ReaxFF and density functional theory (DFT) calculations. The hydrolytic degradation of PLA fibers from both experiments and simulations was observed to have a faster rate of degradation in alkaline conditions, with 40% of strength loss of the fibers in just 25 days together with an increase in the percent crystallinity of the degraded samples. Additionally, surface erosion was observed in these PLA fibers, especially in extreme alkaline environments, in contrast to bulk erosion observed in molded PLA grafts and other materials, which is attributed to the increased crystallinity induced during the fiber spinning process. These results indicate that spun PLA fibers function in a predictable manner as a bioresorbable medical device when totally degraded at end-of-life in more alkaline conditions.