Convergence acceleration of preconditioned conjugate gradient solver based on error vector sampling for a sequence of linear systems

In this article, we focus on solving a sequence of linear systems that have identical (or similar) coefficient matrices. For this type of problem, we investigate subspace correction (SC) and deflation methods, which use an auxiliary matrix (subspace) to accelerate the convergence of the iterative method. In practical simulations, these acceleration methods typically work well when the range of the auxiliary matrix contains eigenspaces corresponding to small eigenvalues of the coefficient matrix. We develop a new algebraic auxiliary matrix construction method based on error vector sampling in which eigenvectors with small eigenvalues are efficiently identified in the solution process. We use the generated auxiliary matrix for convergence acceleration in the following solution step. Numerical tests confirm that both SC and deflation methods with the auxiliary matrix can accelerate the solution process of the iterative solver. Furthermore, we examine the applicability of our technique to the estimation of the condition number of the coefficient matrix. We also present the algorithm of the preconditioned conjugate gradient method with condition number estimation.     

Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator

Many cellular functions necessary for life are tightly regulated by protein allosteric conformational change, and correlated dynamics between protein regions has been found to contribute to the function of proteins not previously considered allosteric. The ability to map and control such dynamic coupling would thus create opportunities for the extension of current therapeutic design strategy. Here, we present an approach to determine the networks of residues involved in the transfer of correlated motion across a protein, and apply our approach to rescue disease-causative mutant cystic fibrosis transmembrane regulator (CFTR) ion channels, ΔF508 and ΔI507, which together constitute over 90% of cystic fibrosis cases. We show that these mutations perturb dynamic coupling within the first nucleotide-binding domain (NBD1), and uncover a critical residue that mediates trans-domain coupled dynamics. By rationally designing a mutation to this residue, we improve aberrant dynamics of mutant CFTR as well as enhance surface expression and function of both mutants, demonstrating the rescue of a disease mutation by rational correction of aberrant protein dynamics.     

Influence of exchange coupling on current-driven domain wall motion in a nanowire

In this study, the effect of exchange stiffness constant on current-driven domain wall motion in nanowires with in-plane magnetic anisotropy (IMA) and perpendicular magnetic anisotropy (PMA) has been investigated using micromagnetic simulation. The critical current density in a nanowire with IMA decreases as the exchange stiffness constant decreases because the domain wall width at the upper edge of the nanowire narrows according to the decrease of the exchange stiffness constant. On the other hand, the critical current density in a nanowire with PMA slightly decreases contrary to that of IMA although the domain wall width reasonably decreases as the exchange stiffness constant decreases. The slight reduction rate of the critical current density is due to the increase of the effective hard-axis anisotropy of PMA nanowire.     

A novel route for immobilization of oligonucleotides onto modified silica nanoparticles

A novel approach for immobilization of probe oligonucleotides that uses zirconium phosphate modified silica nanoparticles is proposed. The surface modification of nanoparticles was carried out in two stages. Initially binding of Zr4+ to the surface of silica nanoparticles and later treated with phosphoric acid for terminal phosphate groups. Oligonucleotide probes modified with amine group at 5'-end were strongly binds to the phosphate terminated silica nanoparticles with imidazole in presence of 0.1 mol L(-1) EDC [N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide], as phosphate groups are more reactive towards amine group. Various studies, i.e., synthesis of silica nanoparticles, their surface modification, probe immobilization, measurement of hybridization and effect of bovine serum albumin (BSA) were carried out during optimization of reaction conditions. The significant reduction in the background signal was observed by treating the probe modified silica nanoparticles with bovine serum albumin prior to hybridization. The probe modified silica nanoparticles were retained their properties and the hybridization was induced by exposure of single-stranded DNA (ssDNA) containing silica nanoparticles to the complementary DNA in solution. The decrease in the fluorescence signal for one mismatch and three mismatch was observed upon hybridization of probe with target DNAs, while there was no response for the random target ssDNA under the same experimental conditions. The intensity of fluorescence signal was linear to the concentration of target DNA ranging from 3.9 x 10(-9) to 3.0 x 10(-6)mol L(-1). A detection limit of 1.22 x 10(-9) mol L(-1) of oligonucleotides can be estimated. The proposed hybridization assay is simple and possesses good analytical characteristics and it can provide an effective and efficient route in the development of DNA biosensors and biochips.     

A system of evolution equations for non-isothermal phase transitions

We propose and study a system of evolution equations. This is an abstract formulation of problems arising in non-isothermal phase transitions. We consider time-dependent constraints on the unknown functions. Thus the problem yields a system of parabolic variational inequalities. We prove the existence of a solution in a general framework, and then apply the abstract result to some models of phase transitions.     

Spectral, structural and DFT studies of platinum group metal 3,6-bis(2-pyridyl)-4-phenylpyridazine complexes and their ligand bonding modes

Reactions of 3,6-bis(2-pyridyl)-4-phenylpyridazine (L^ph) with [(η⁶-arene)Ru(μ-Cl)Cl]₂ (arene = C₆H₆, p-ⁱPrC₆H₄Me and C₆Me₆), [(η⁵-C₅Me₅)M(μ-Cl)Cl]₂, (M = Rh and Ir) and [(η⁵-Cp)Ru(PPh₃)₂Cl] (Cp = C₅H₅, C₅Me₅ and C₉H₇) afford mononuclear complexes of the type [(η⁶-arene)Ru(L^ph)Cl]PF₆, [(η⁵-C₅Me₅)M(L^ph)Cl]PF₆ and [(Cp)Ru(L^ph)(PPh₃)]PF₆ with different structural motifs depending on the π-acidity of the ligand, electronic properties of the central metal atom and nature of the co-ligands. Complexes [(η⁶-C₆H₆)Ru(L^ph)Cl]PF₆1, [(η⁶-p-ⁱPrC₆H₄Me)Ru(L^ph)Cl]PF₆2, [(η⁵-C₅Me₅)Ir(L^ph)Cl]PF₆5, [(η⁵-Cp)Ru(PPh₃)(L^ph)]PF₆, (Cp = C₅H₅, 6; C₅Me₅, 7; C₉H₇, 8) show the type-A binding mode (see text), while complexes [(η⁶-C₆Me₆)Ru(L^ph)Cl]PF₆3 and [(η⁵-C₅Me₅)Rh(L^ph)Cl]PF₆4 show the type-B binding mode (see text). These differences reflect the more electron-rich character of the [(η⁶-C₆Me₆)Ru(μ-Cl)Cl]₂ and [(η⁵-C₅Me₅)Rh(μ-Cl)Cl]₂ complexes compared to the other starting precursor complexes. Binding modes of the ligand L^ph are determined by ¹H NMR spectroscopy, single-crystal X-ray analysis as well as evidence obtained from the solid-state structures and corroborated by density functional theory calculations. From the systems studied here, it is concluded that the electron density on the central metal atom of these complexes plays an important role in deciding the ligand binding sites.     

(-)-Axinyssene: a novel cytotoxic diterpene from a Japanese marine sponge Axinyssa sp

[structure: see text] A novel diterpene, (-)-axinyssene, was isolated from the Japanese marine sponge Axinyssa sp. The structure of (-)-axinyssene was determined on the basis of spectroscopic and synthetic evidence to be 1-methyl-4-[(4E)-5',9'-dimethyl-1'-methylene-4',8'-decadienyl]-(4S)-cyclohexene. (-)- and (+)-axinyssene showed mild cytotoxicity against acute promyelocytic leukemia, HL-60 cells.     

A novel method for synthesis of silica nanoparticles

A sequential method has been used, for the first time, to prepare monodisperse and uniform-size silica nanoparticles using ultrasonication by sol-gel process. The silica particles were obtained by hydrolysis of tetraethyl orthosilicate (TEOS) in ethanol medium and a detailed study was carried out on the effect of different reagents on particle sizes. Various-sized particles in the range 20-460 nm were synthesized. The reagents ammonia (2.8-28 mol L(-1)), ethanol (1-8 mol L(-1)), water (3-14 mol L(-1)), and TEOS (0.012-0.12 mol L(-1)) were used and particle size was examined under scanning electron microscopy and transmission electron microscopy. In addition to the above observations, the effect of temperature on particle size was studied. The results obtained in the present study are in agreement with the results observed for the electronic absorption behavior of silica particles, which was measured by UV-vis spectrophotometry.     

Four-color hole burning spectra of phenol/ammonia 1:3 and 1:4 clusters

The hole burning spectra of phenol/ammonia (1:3 and 1:4) clusters were measured by a newly developed four-color (UV-near-IR-UV-UV) hole burning spectroscopy, which is a kind of population labeling spectroscopy. From the hole burning spectra, it was found that single species is observed in an n = 3 cluster, while three isomers are observed simultaneously for n = 4. A possibility was suggested that the reaction efficiency of the hydrogen transfer from the electronically excited phenol/ammonia clusters, which was measured by a comparison with the action spectra of the corresponding cluster, depends on the initial vibronic levels.     

T = 0 versusT = 1 pairing in 0(36) limit of IBM-4 for heavyN = Z nuclei

In theO(36) limit of the interacting boson model including spin-isospin degrees of freedom (IBM-4), starting with a group chain that preservess andd boson spins and isospins together with a simple mixing hamiltonian, it is shown that the model generates, for heavyN =Z nuclei, even-even to odd-odd staggering in the number ofT = 0 pairs in the ground states for moderate difference in the basicT = 0 andT = 1s-boson pair energies; the staggering disappears when the energy difference is large.