A preconditioned domain decomposition algorithm for the solution of the elliptic Neumann problem

A new preconditioned conjugate gradient (PCG)-based domain decomposition method is given for the solution of linear equations arising in the finite element method applied to the elliptic Neumann problem. The novelty of the proposed method is in the recommended preconditioner which is constructed by using cyclic matrix. The resulting preconditioned algorithms are well suited to parallel computation.     

GENETIC VARIATIONS AND LINOLENIC ACID INDUCED CHANGES IN THE ORIENTATION PATTERN OF CHLOROPHYLL a IN THYLAKOID MEMBRANES

Abstract Orientation pattern of the Q_y absorption and emission dipoles of chlorophyll a were studied in wild type Scenedesmus obliquus and in mutants deficient in chlorophyll b and carotenoids. Fluorescence polarization ratio at –140°C and linear dichroism at 25°C were measured in whole cells and thylakoids aligned in polyacrylamide gel. Unlike normal thylakoids, mutants displayed fluorescence polarization ratios significantly lower than 1.0 and showed a negative LD signal around 672 nm, indicating the tendency of the Q_y dipoles to tilt out from the membrane plane. Such an orientation pattern can also be artificially induced by treating normal thylakoids with linolenic acid.     

Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide

Non‐equilibrium molecular dynamics simulations of a solvated 21‐residue polyalanine (A21) peptide, featuring a high propensity for helix formation, have been performed at 300 K and 1 bar in the presence of external electromagnetic (e/m) fields in the microwave region (2.45 GHz) and an r.m.s. electric field intensity range of 0.01–0.05 V/Å. To investigate how the field presence affects transitions between the conformational states of a protein, we report 16 independent 40 ns‐trajectories of A21 starting from both extended and fully folded states. We observe folding‐behavior of the peptide consistent with prior simulation and experimental studies. The peptide displays a natural tendency to form stable elements of secondary structure which are stabilized by tertiary interactions with proximate regions of the peptide. Consistent with our earlier work, the presence of external e/m fields disrupts this behavior, involving a mechanism of localized dipolar alignment which serves to enhance intra‐protein perturbations in hydrogen bonds (English, et al., J. Chem. Phys. 2010 , 133, 091105), leading to more frequent transitions between shorter‐lifetime states. © 2012 Wiley Periodicals, Inc.     

Thermocapillary Flow and Aggregation of Bubbles on a Solid Wall

Theory suggests that thermocapillary flow about neighboring bubbles in liquids on hot walls pulls the bubbles together. A temperature gradient perpendicular to the wall establishes a surface tension gradient at the bubble-liquid interface, which in turn sustains a shear stress gradient that pumps adjacent fluid away from the wall. Neighboring bubbles are mutually entrained in this flow and also respond thermophoretically to lateral temperature gradients in the temperature near field. The theory predicts that the aggregation velocity scales with the temperature gradient, the radius of the bubbles, the derivative of the surface tension with respect to temperature, and the reciprocal of the liquid's viscosity. Bubble aggregation experiments under controlled conditions were performed to test the theory. Scaling the experimental bubble trajectories according to the theory substantially collapses all of the data onto a master curve when the interbubble separation is greater than 3 radii, which suggests that the theory is correct. Calculated velocities agree with the experimental results when hindrance of bubble motion due to the wall is included. Values for the parameter that describes the hindrance effect are obtained from fitting the data to the theory, from independent measurements, and from direct hydrodynamic calculation. The results of the three determinations agree within 15% of the possible range of the value of the parameter. Copyright 2000 Academic Press.     

A two-dimensional laser diameter gauge

A two-dimensional diameter control apparatus has been devised and constructed on the laser scanning principle, which uses a reference grating to determine the outer diameter of an object as well as the position of the scanning beam.     

Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: a nonequilibrium molecular dynamics study

Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V ?(-1). A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-á-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.