Schur complement preconditioners for anisotropic problems

We present two new variants of Schur complement domain decompositionpreconditioners suitable for 2D anisotropic problems. Thesevariants are based on adaptations of the probing idea, describedby Chan et al (1992 Fifth Int. Symp. on Domain DecompositionMethods for Partial Differential Equations, Philadelphia: SIAM,pp 236-249), used in conjunction with a coarse grid approximationas introduced by Bramble et al (1986 Math. Comput. 47, 103-134).The new methods are specifically designed for situations wherethe coupling between neighbouring interfaces is stronger thanthe coupling within an interface. Taking into account this strongcoupling, one variant uses a multicolour probing technique toavoid distortion in the probe approximations that appear whenusing the method proposed by Chan et al. The second techniqueuses additional probe matrices to approximate not only the couplingwithin the interfaces but also the coupling between interfacepoints across the subdomains. This latter procedure looks somewhatlike an alternating line relaxation method for anisotropic problems,see Brandt (1977 Math. Comput.. 31, 333-390). To assess therelevance of the new preconditioners, we compare their numericalbehaviour with well known robust preconditioners such as thebalanced Neumann-Neumann method proposed by Mandel (1993 Commun.Numer. Methods Eng.. 9, 233-241).     

A theoretical model for the critical micelle concentration of bile salts

Critical micelle concentration (CMC) is a fundamental parameter in the evaluation of the biological activity of natural and synthetic bile salts. The CMC is logarithmically related to the free energy of solute micellization in aqueous solution. Hydrophobic and hydrogen bonding interaction energies were identified as the primary contributors to this free energy and the logarithm of the CMC was modeled as a linear function of relevant chemical group contributions to the solvent accessible molecular surface area of the solute. The structures (three-dimensional atomic coordinates) of 23 mono-, di-, and tri-hydroxyl bile acids were generated and optimized by energy minimization. The accessible surface area for each structure was computed and partitioned according to calculated charge distribution and polar group orientation. Experimental CMC values were fitted to these computed quantities by least squares multiple linear regression. Two regression equations, based on slightly different surface area partition schemes, were derived and compared. Their significance in explaining the aggregation process and in predicting the CMC of new bile salts is discussed.     

评《马氏决策过程》

（《马氏决策过程》,侯振挺、郭先平著,长沙,湖南科技出版社,1997,中文版,386页,定价：28元）马尔可夫决策过程是概率论的运筹学的理论研究和实际应用中极其重要的领域之一．随着中国和国际上对马尔可夫决策过程（MarkovDecisionProcesses,简记为MDP）研究的新进展,许     

High-affinity interactions of ligands at recombinant Guinea pig 5HT7 receptors

The serotonin 5HT₇ receptor has been implicated in numerous physiological and pathological processes from circadian rhythms [1] to depression and schizophrenia. Clonal cell lines heterologously expressing recombinant receptors offer good models for understanding drug-receptor interactions and development of quantitative structure-activity relationships (QSAR). Comparative Molecular Field Analysis (CoMFA) is an important modern QSAR procedure that relates the steric and electrostatic fields of a set of aligned compounds to affinity. Here, we utilized CoMFA to predict affinity for a number of high-affinity ligands at the recombinant guinea pig 5HT₇ receptor. Using R-lisuride as the template, a final CoMFA model was derived using procedures similar to those of our recent papers [2, 3, 4] The final cross-validated model accounted for >85% of the variance in the compound affinity data, while the final non-cross validated model accounted for >99% of the variance. Model evaluation was done using cross-validation methods with groups of 5 ligands. Twenty cross-validation runs yielded an average predictive r²(q²) of 0.779 ± 0.015 (range: 0.669–0.867). Furthermore, 3D-chemical database search queries derived from the model yielded hit lists of promising agents with high structural similarity to the template. Together, these results suggest a possible basis for high-affinity drug action at 5HT₇ receptors.     

Simulation model for anomalous precession of the perihelion of mercury's orbit

The ‘anomalous perihelion precession’ of Mercury, announced by Le Verrier in 1859, was a highly controversial topic for more than half a century and invoked many alternative theories until 1916, when Einstein presented his theory of general relativity as an alternative theory of gravitation and showed perihelion precession to be one of its potential manifestations. As perihelion precession was a directly derived result of the full General Theory and not just the Equivalence Principle, Einstein viewed it as the most critical test of his theory. This paper presents the computed value of the anomalous perihelion precession of Mercury's orbit using a new relativistic simulation model that employs a simple transformation factor for mass and time, proposed in an earlier paper. This computed value compares well with the prediction of general relativity and is, also, in complete agreement with the observed value within its range of uncertainty. No general relativistic equations have been used for computing the results presented in this paper.     

Coupled axial–torsional behavior of cylindrical elastomer bushings

Elastomer bushings are important components in a vehicle suspension system to isolate vibration. The purpose of the work is to present experimental and computational studies of cylindrical bushings subjected to axial, torsional and coupled axial-torsional deformation modes. The experimental results show that the relationship between the forces and moments and their corresponding displacements and rotations are nonlinear due to the nature of the elastomer material. When an axial deformation is superimposed on a torsional deformation, a nonlinear coupled response exists; the torsional moment initially decreases and then increases with increasing axial deformation. This nonlinear coupling effect for small superimposed deformations is not well predicted computationally when modeling the bushing using common constitutive material laws in a commercial finite element package.     

EXCISION REPAIR IN TETRAHYMENA: EVENTS FOLLOWING REFEEDING OF STARVED UV-IRRADIATED CELLS

Abstract —Starvation of early-log-phase Tetrahymena pyriformis in non-nutrient phosphate buffer for 24 h results in a 40 per cent increase in cell number, as well as a complete cessation of DNA synthesis. Low levels of DNA synthesis are detectable between 1 and 2h after starved cells are transferred to a nutrient medium. Larger amounts of DNA synthesis are detected after the first 2 h of refeeding, and one round of replication is complete 4.5 h after refeeding. Damage, caused by sublethal doses of UV radiation (254 nm) administered just prior to refeeding, to the DNA of starved Tetrahymena appears to be corrected by an excision-repair process after refeeding of starved, irradiated cells. Changes in buoyant density of DNA synthesized, rate of DNA synthesis, and the chromatographic distribution of photoproducts were investigated following refeeding of starved, irradiated cells. Excision repair begins 1 h after refeeding and appears to be essentially complete within 7 h. During this time, thymine dimers produced by irradiation are removed. Semiconservative DNA synthesis commences 2–3 h after the first appearance of excision repair. In addition, between 3 and 8 h after refeeding, the rate of DNA synthesis in irradiated, refed cultures is much lower than the rate of DNA synthesis in unirradiated, refed cultures. Also, the specific activity in vitro of DNA polymerase from irradiated refed cells is very much greater than that of polymerase from unirradiated, refed cells.     

Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup

A coarse-grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations ΔΔG_aq(Li⁺ Δ Cs⁺), and for the zero-sum ethane-to-ethane′ perturbation ΔΔG_aq(CH₃? methyl? X → X? methyl? CH₃), where X is a ghost methyl. The difference in binding free energy for a docked HIV-1 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, ΔG(CO? NH → CH?CH). A potassium ion (K⁺) is driven outward from the center of mass of ionophore salinomycin (SAL^?) in a potential of mean force calculation ΔG_MeOH(SAL^? · K⁺) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, ΔΔG_oct(phenol → benzene), is determined in water-saturated octanol and then expressed in terms of relative partition coefficients, Δ log(P_o/w). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y-MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. © 1994 by John Wiley & Sons, Inc.     

Simultaneous quantitation of IC87114, roflumilast and its active metabolite roflumilast N‐oxide in plasma by LC‐MS/MS: application for a pharmacokinetic study

A sensitive and reliable high‐performance liquid chromatography–mass spectrometry (LC–MS/MS) was developed and validated for simultaneous quantification IC87114, roflumilast (RFM), and its active metabolite roflumilast N‐oxide (RFN) using tolbutamide as an internal standard. The analytes were extracted by using liquid–liquid extraction and separated on a reverse phase C₁₈ column (50 mm × 3 mm i.d., 4.6 µ) using methanol: 2 mM ammonium acetate buffer, pH 4.0 as mobile phase at a flow rate 1 mL/min in gradient mode. Selective reaction monitoring was performed using the transitions m/z 398.3 > 145.9, 403.1 >186.9, 419.1 > 187.0 and 271.1 > 155.0 to quantify quantification IC87114, RFM, RFN and tolbutamide, respectively. The method was validated over the concentration range of 0.1–60 ng.mL^?1 for RFM and RFN and 6 to 2980 ng.mL^?1 for IC87114. Intra‐ and inter‐day accuracy and precision of validated method were within the acceptable limits of <15% at all concentrations. Coefficients of correlation (r²) for the calibration curves were >0.99 for all analytes. The quantitation method was successfully applied for simultaneous estimation of IC87114, RFM and RFN in a pharmacokinetic drug–drug interaction study in Wistar rats. Copyright © 2012 John Wiley & Sons, Ltd.