Aperiodic Variability in the Cane-Zebiak Model: A Diagnostic Study

The finite predictability of the coupled ocean-atmosphere system is determined by its aperiodic variability. To gain insight regarding the predictability of such a system, a series of diagnostic studies has been carried out to investigate the role of convergence feedback in producing the aperiodic behavior of the standard version of the Cane-Zebiak model. In this model, an increase in sea surface temperature (SST) increases atmospheric heating by enhancing local evaporation (SST anomaly feedback) and low-level convergence (convergence feedback). The convergence feedback is a nonlinear function of the background mean convergence field. For the set of standard parameters used in the model, it is shown that the convergence feedback contributes importantly to the aperiodic behaviour of the model. As the strength of the convergence feedback is increased from zero to its standard value, the model variability goes from a periodic regime to an aperiodic regime through a broadening of the frequency spectrum around the basic periodicity of about 4 years. Examination of the forcing associated with the convergence feedback reveals that it is intermittent, with relatively large amplitude only during 2 or 3 months in the early part of the calendar year. This seasonality in the efficiency of the convergence feedback is related to the strong seasonality of the mean convergence over the eastern Pacific. It is shown that if the mean convergence field is fixed at its March value, aperiodic behavior is produced even in the absence of annual cycles in the other mean fields. On the, other hand, if the mean convergence field is fixed at its September value, the coupled model evolution remains close to periodic, even in the presence of the annual cycle in the other fields. The role of convergence feedback on the aperiodic variability of the model for other parameter regimes is also examined. It is shown that a range exists in the strength of the SST anomaly feedback for which the model variability is aperiodic even without the convergence feedback. It appears that in the absence of convergence feedback, enhancement of the strength of the air-sea coupling in the model through other physical processes also results in aperiodicity in the model.

Parametric instability of stochastic columns

Columns which have stochastically distributed Young's modulus and mass density and are subjected to deterministic periodic axial loadings are considered. The general case of a column supported on a Winkler elastic foundation of random stiffness and also on discrete elastic supports which are also random is considered. Material property fluctuations are modeled as independent one-dimensional univariate homogeneous real random fields in space. In addition to autocorrelation functions or their equivalent power spectral density functions, the input random fields are characterized by scale of fluctuations or variance functions for their second order properties. The foundation stiffness coefficient and the stiffnesses of discrete elastic supports are treated to constitute independent random variables. The system equations of boundary frequencies are obtained using Bolotin's method for deterministic systems. Stochastic FEM is used to obtain the discrete system with random as well as periodic coefficients. Statistical properties of boundary frequencies are derived in terms of input parameter statistics. A complete covariance structure is obtained. The equations developed are illustrated using a numerical example employing a practical correlation structure.

Conformational analysis and design of cross-strand disulfides in antiparallel beta-sheets

Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel beta-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive chi(1) value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1 degrees C in T-m. All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (Delta Delta G(0) = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity. Proteins 2011; 79: 244-260. (C) 2010 Wiley-Liss, Inc.

Decoupled three-dimensional finite element computation of thermoelastic damping using Zener's approximation

We consider three dimensional finite element computations of thermoelastic damping ratios of arbitrary bodies using Zener's approach. In our small-damping formulation, unlike existing fully coupled formulations, the calculation is split into three smaller parts. Of these, the first sub-calculation involves routine undamped modal analysis using ANSYS. The second sub-calculation takes the mode shape, and solves on the same mesh a periodic heat conduction problem. Finally, the damping coefficient is a volume integral, evaluated elementwise. In the only other decoupled three dimensional computation of thermoelastic damping reported in the literature, the heat conduction problem is solved much less efficiently, using a modal expansion. We provide numerical examples using some beam-like geometries, for which Zener's and similar formulas are valid. Among these we examine tapered beams, including the limiting case of a sharp tip. The latter's higher-mode damping ratios dramatically exceed those of a comparable uniform beam.

Contraceptive vaccines: current status and problems in mass application

Progress in the development of contraceptive vaccines for males and females is reviewed. Based on the criteria which need to be met with, none of the proposed candidate antigens meets the requirements for use as a contraceptive vaccine for human application. One of the major problems is the need for periodic injections to maintain required titre and use of an alternate method until effective titres are obtained. Some of the problems associated with active immunization approach can be overcome by the use of preformed, highly specific, potent antibodies. Some progress has been achieved in this direction by the use of humanized single chain monoclonal antibodies to human chorionic gonadotropin.

One protein�many functions

The concept of one enzyme-one activity had influenced biochemistry for over half a century. Over 1000 enzymes are now described. Many of them are highly 'specific'. Some of them are crystallized and their three-dimensional structures determined. They range from 12 to 1000 kDa in molecular weight and possess 124 to several hundreds of amino acids. They occur as single polypeptides or multiple-subunit proteins. The active sites are assembled on these by appropriate tertiary folding of the polypeptide chain, or by interaction of the constituent subunits. The substrate is held by the side-chains of a few amino acids at the active site on the surface, occupying a tiny fraction of the total area. What is the bulk of the protein behind the active site doing? Do all proteins have only one function each? Why not a protein have more than one active site on its large surface? Will we discover more than one activity for some proteins? These newer possibilities are emerging and are finding experimental support. Some proteins purified to homogeneity using assay methods for different activities are now recognized to have the same molecular weight and a high degree of homology of amino acid sequence. Obviously they are identical. They represent the phenomenon of one protein-many functions.

Propagating intensity disturbances in polar corona as seen from AIA/SDO

Context. Polar corona is often explored to find the energy source for the acceleration of the fast solar wind. Earlier observations show omni-presence of quasi-periodic disturbances, traveling outward, which is believed to be caused by the ubiquitous presence of outward propagating waves. These waves, mostly of compressional type, might provide the additional momentum and heat required for the fast solar wind acceleration. It has been conjectured that these disturbances are not due to waves but high speed plasma outflows, which are difficult to distinguish using the current available techniques. Aims. With the unprecedented high spatial and temporal resolution of AIA/SDO, we search for these quasi-periodic disturbances in both plume and interplume regions of the polar corona. We investigate their nature of propagation and search for a plausible interpretation. We also aim to study their multi-thermal nature by using three different coronal passbands of AIA. Methods. We chose several clean plume and interplume structures and studied the time evolution of specific channels by making artificial slits along them. Taking the average across the slits, space-time maps are constructed and then filtration techniques are applied to amplify the low-amplitude oscillations. To suppress the effect of fainter jets, we chose wider slits than usual. Results. In almost all the locations chosen, in both plume and interplume regions we find the presence of propagating quasi-periodic disturbances, of periodicities ranging from 10-30 min. These are clearly seen in two channels and in a few cases out to very large distances (approximate to 250 `') off-limb, almost to the edge of the AIA field of view. The propagation speeds are in the range of 100-170 km s(-1). The average speeds are different for different passbands and higher in interplume regions. Conclusions. Propagating disturbances are observed, even after removing the effects of jets and are insensitive to changes in slit width. This indicates that a coherent mechanism is involved. In addition, the observed propagation speed varies between the different passpands, implying that these quasi-periodic intensity disturbances are possibly due to magneto-acoustic waves. The propagation speeds in interplume region are higher than in the plume region.

Charge Density Analysis of Heterohalogen (Cl center dot center dot center dot F) and Homohalogen (F center dot center dot center dot F) Intermolecular Interactions

Experimental charge density distribution in 2-chloro-4-fluorobenzoic acid and 4-fluorobenzamide has been carried out using high resolution X-ray diffraction data collected at 100 K using Hansen-Coppens multipolar formalism of electron density. These compounds display short Cl center dot center dot center dot F and F center dot center dot center dot F interactions, respectively. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculation at the B3LYP/6-31G** level. The topological features were derived from Bader's ``atoms in molecules'' (AIM) approach. Intermolecular Cl center dot center dot center dot F interaction in 2-chloro-4-fluorobenzoic acid is attractive in nature (type II interaction) while the nature of F center dot center dot center dot F interactions in 4-fluorobenzamide shows indication of a minor decrease in repulsion (type I interaction), though the extent of polarization on the fluorine atom is arguably small.

Scroll-Wave Dynamics in Human Cardiac Tissue: Lessons from a Mathematical Model with Inhomogeneities and Fiber Architecture

Cardiac arrhythmias, such as ventricular tachycardia (VT) and ventricular fibrillation (VF), are among the leading causes of death in the industrialized world. These are associated with the formation of spiral and scroll waves of electrical activation in cardiac tissue; single spiral and scroll waves are believed to be associated with VT whereas their turbulent analogs are associated with VF. Thus, the study of these waves is an important biophysical problem. We present a systematic study of the combined effects of muscle-fiber rotation and inhomogeneities on scroll-wave dynamics in the TNNP (ten Tusscher Noble Noble Panfilov) model for human cardiac tissue. In particular, we use the three-dimensional TNNP model with fiber rotation and consider both conduction and ionic inhomogeneities. We find that, in addition to displaying a sensitive dependence on the positions, sizes, and types of inhomogeneities, scroll-wave dynamics also depends delicately upon the degree of fiber rotation. We find that the tendency of scroll waves to anchor to cylindrical conduction inhomogeneities increases with the radius of the inhomogeneity. Furthermore, the filament of the scroll wave can exhibit drift or meandering, transmural bending, twisting, and break-up. If the scroll-wave filament exhibits weak meandering, then there is a fine balance between the anchoring of this wave at the inhomogeneity and a disruption of wave-pinning by fiber rotation. If this filament displays strong meandering, then again the anchoring is suppressed by fiber rotation; also, the scroll wave can be eliminated from most of the layers only to be regenerated by a seed wave. Ionic inhomogeneities can also lead to an anchoring of the scroll wave; scroll waves can now enter the region inside an ionic inhomogeneity and can display a coexistence of spatiotemporal chaos and quasi-periodic behavior in different parts of the simulation domain. We discuss the experimental implications of our study.

Flap-lag-torsion stability in hover and forward flight with three-dimensional wake

The contributions of full-wake dynamics in trim analysis are demonstrated for finding the control inputs and periodic responses simultaneously, as well as in Floquet eigenanalysis for finding the damping levels. The equations of flap bending, lag bending, and torsion are coupled with a three-dimensional, finite state wake, and low-frequency (<1/rev) to high frequency (>1/rev) multiblade modes are considered. Full blade-wake dynamics is used in trim analysis and Floquet eigenanalysis. A uniform cantilever blade in trimmed flight is investigated over a range of thrust levels, advance ratios, number of blades, and blade torsional frequencies. The investigation includes the convergence characteristics of control inputs, periodic responses, and damping levels with respect to the number of spatial azimuthal harmonics and radial shape functions in the wake representation. It also includes correlation with the measured lag damping of a three-bladed untrimmed rotor. The parametric study shows the dominant influence of wake dynamics on control inputs, periodic responses, and damping levels, and wake theory generally improves the correlation.

Neural network modeling of associative memory: Beyond the Hopfield model

A number of neural network models, in which fixed-point and limit-cycle attractors of the underlying dynamics are used to store and associatively recall information, are described. In the first class of models, a hierarchical structure is used to store an exponentially large number of strongly correlated memories. The second class of models uses limit cycles to store and retrieve individual memories. A neurobiologically plausible network that generates low-amplitude periodic variations of activity, similar to the oscillations observed in electroencephalographic recordings, is also described. Results obtained from analytic and numerical studies of the properties of these networks are discussed.

Parallel computing concepts and methods for floquet analysis of helicopter trim and stability

Floquet analysis is widely used for small-order systems (say, order M < 100) to find trim results of control inputs and periodic responses, and stability results of damping levels and frequencies, Presently, however, it is practical neither for design applications nor for comprehensive analysis models that lead to large systems (M > 100); the run time on a sequential computer is simply prohibitive, Accordingly, a massively parallel Floquet analysis is developed with emphasis on large systems, and it is implemented on two SIMD or single-instruction, multiple-data computers with 4096 and 8192 processors, The focus of this development is a parallel shooting method with damped Newton iteration to generate trim results; the Floquet transition matrix (FTM) comes out as a byproduct, The eigenvalues and eigenvectors of the FTM are computed by a parallel QR method, and thereby stability results are generated, For illustration, flap and flap-lag stability of isolated rotors are treated by the parallel analysis and by a corresponding sequential analysis with the conventional shooting and QR methods; linear quasisteady airfoil aerodynamics and a finite-state three-dimensional wake model are used, Computational reliability is quantified by the condition numbers of the Jacobian matrices in Newton iteration, the condition numbers of the eigenvalues and the residual errors of the eigenpairs, and reliability figures are comparable in both the parallel and sequential analyses, Compared to the sequential analysis, the parallel analysis reduces the run time of large systems dramatically, and the reduction increases with increasing system order; this finding offers considerable promise for design and comprehensive-analysis applications.

Singularity structure and chaotic behavior of the homopolar disk dynamo

We study in great detail a system of three first-order ordinary differential equations describing a homopolar disk dynamo (HDD). This system displays a large variety of behaviors, both regular and chaotic. Existence of periodic solutions is proved for certain ranges of parameters. Stability criteria for periodic solutions are given. The nonintegrability aspects of the HDD system are studied by investigating analytically the singularity structure of the system in the complex domain. Coexisting attractors (including period-doubling sequence) and coexisting strange attractors appear in some parametric regimes. The gluing of strange attractors and the ungluing of a strange attractor are also shown to occur. A period of bifurcation leading to chaos, not observed for other chaotic systems, is shown to characterize the chaotic behavior in some parametric ranges. The limiting case of the Lorenz system is also studied and is related to HDD.

Time-Resolved Photoluminescence and Microwave Conductivity at Semiconductor Electrodes: Depletion Layer Effects

Analytical expressions which include depletion layer effects on low-injection carrier relaxation are being presented for the first time here. Starting from the continuity equation for the minority carriers, we derive expressions for the output signal pertinent to time-resolved microwave and luminescence experiments. These are valid for the time domain that usually overlaps with the time scales of surface processes, such as charge transfer and trapping. Apart from the usual pulse form of illumination, theoretical expressions pertaining to other forms of illumination such as switch-on and switch-off transient modes, a periodic mode, and a steady state and their various inter-relationships are derived here. The expressions obtained are seen to be generalizations of existing flat-band low-injection results in the Limit of early or initial band bendings. The importance of the depletion layer as an experimental parameter is clearly seen in the limit of larger band bendings wherein it is shown, unlike the flat-band case, to exhibit pure exponential forms of carrier relaxation. Our results are consistent with the main conclusions of the numerical and experimental work published recently. Furthermore, this work provides the actual functional relationships between the applied potential and observed carrier decay. This should enable one to extract the surface kinetic parameters, after deciding on the dominant mode of carrier relaxation at the interface, whether charge transfer or trapping, by studying the potential dependence of the fate of relaxation.

Purification and characterization of DNA-dependent RNA polymerase II from Candida utilis

DNA-dependent RNA polymerase II from Candida utilis has been purified to near homogeneity. The purified enzyme resolved into three subforms, viz. IIO, IIA and IIB. On SDS-PAGE the enzyme showed ten polypeptides with molecular weights in the range of 205 kDa to 14 kDa. By two dimensional electrophoresis (IEF followed by SDS-PAGE) the presence of basic and acidic polypeptides has been demonstrated. The enzyme showed Km values of 5, 5.6 and 8 mu M for GTP, CTP and ATP, respectively, and the activity was inhibited by low levels of oc-amanitin and antibodies raised against bovine RNA polymerase II. By Western blot analysis the enzyme was found to cross-react with antibodies to bovine RNA polymerase II. RNA polymerase II from G. utilis is a phosphoprotein, the subunits RPB1 and RPB10 were found to be phosphorylated. Analysis of carboxy-terminal domain indicated that it was functionally redundant at least in case of nonspecific transcription, implicating its role in other nuclear processes, such as promoter specific initiation or transcription activation or RNA processing.