Efficiency of pseudo-spectral algorithms with Anderson mixing for the SCFT of periodic block-copolymer phases

This study examines the numerical accuracy, computational cost, and memory requirements of self-consistent field theory (SCFT) calculations when the diffusion equations are solved with various pseudo-spectral methods and the mean field equations are iterated with Anderson mixing. The different methods are tested on the triply-periodic gyroid and spherical phases of a diblock-copolymer melt over a range of intermediate segregations. Anderson mixing is found to be somewhat less effective than when combined with the full-spectral method, but it nevertheless functions admirably well provided that a large number of histories is used. Of the different pseudo-spectral algorithms, the 4th-order one of Ranjan, Qin and Morse performs best, although not quite as efficiently as the full-spectral method.

A high-order arbitrarily unstructured finite-volume model of the global atmosphere: tests solving the shallow-water equations

Simulations of the global atmosphere for weather and climate forecasting require fast and accurate solutions and so operational models use high-order finite differences on regular structured grids. This precludes the use of local refinement; techniques allowing local refinement are either expensive (eg. high-order finite element techniques) or have reduced accuracy at changes in resolution (eg. unstructured finite-volume with linear differencing). We present solutions of the shallow-water equations for westerly flow over a mid-latitude mountain from a finite-volume model written using OpenFOAM. A second/third-order accurate differencing scheme is applied on arbitrarily unstructured meshes made up of various shapes and refinement patterns. The results are as accurate as equivalent resolution spectral methods. Using lower order differencing reduces accuracy at a refinement pattern which allows errors from refinement of the mountain to accumulate and reduces the global accuracy over a 15 day simulation. We have therefore introduced a scheme which fits a 2D cubic polynomial approximately on a stencil around each cell. Using this scheme means that refinement of the mountain improves the accuracy after a 15 day simulation. This is a more severe test of local mesh refinement for global simulations than has been presented but a realistic test if these techniques are to be used operationally. These efficient, high-order schemes may make it possible for local mesh refinement to be used by weather and climate forecast models.

An integrated model of soil-canopy spectral radiances, photosynthesis, fluorescence, temperature and energy balance

This paper presents the model SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes), which is a vertical (1-D) integrated radiative transfer and energy balance model. The model links visible to thermal infrared radiance spectra (0.4 to 50 μm) as observed above the canopy to the fluxes of water, heat and carbon dioxide, as a function of vegetation structure, and the vertical profiles of temperature. Output of the model is the spectrum of outgoing radiation in the viewing direction and the turbulent heat fluxes, photosynthesis and chlorophyll fluorescence. A special routine is dedicated to the calculation of photosynthesis rate and chlorophyll fluorescence at the leaf level as a function of net radiation and leaf temperature. The fluorescence contributions from individual leaves are integrated over the canopy layer to calculate top-of-canopy fluorescence. The calculation of radiative transfer and the energy balance is fully integrated, allowing for feedback between leaf temperatures, leaf chlorophyll fluorescence and radiative fluxes. Leaf temperatures are calculated on the basis of energy balance closure. Model simulations were evaluated against observations reported in the literature and against data collected during field campaigns. These evaluations showed that SCOPE is able to reproduce realistic radiance spectra, directional radiance and energy balance fluxes. The model may be applied for the design of algorithms for the retrieval of evapotranspiration from optical and thermal earth observation data, for validation of existing methods to monitor vegetation functioning, to help interpret canopy fluorescence measurements, and to study the relationships between synoptic observations with diurnally integrated quantities. The model has been implemented in Matlab and has a modular design, thus allowing for great flexibility and scalability.

On integral equation and least squares methods for scattering by diffraction gratings

In this paper we consider the scattering of a plane acoustic or electromagnetic wave by a one-dimensional, periodic rough surface. We restrict the discussion to the case when the boundary is sound soft in the acoustic case, perfectly reflecting with TE polarization in the EM case, so that the total field vanishes on the boundary. We propose a uniquely solvable first kind integral equation formulation of the problem, which amounts to a requirement that the normal derivative of the Green's representation formula for the total field vanish on a horizontal line below the scattering surface. We then discuss the numerical solution by Galerkin's method of this (ill-posed) integral equation. We point out that, with two particular choices of the trial and test spaces, we recover the so-called SC (spectral-coordinate) and SS (spectral-spectral) numerical schemes of DeSanto et al., Waves Random Media, 8, 315-414 1998. We next propose a new Galerkin scheme, a modification of the SS method that we term the SS* method, which is an instance of the well-known dual least squares Galerkin method. We show that the SS* method is always well-defined and is optimally convergent as the size of the approximation space increases. Moreover, we make a connection with the classical least squares method, in which the coefficients in the Rayleigh expansion of the solution are determined by enforcing the boundary condition in a least squares sense, pointing out that the linear system to be solved in the SS* method is identical to that in the least squares method. Using this connection we show that (reflecting the ill-posed nature of the integral equation solved) the condition number of the linear system in the SS* and least squares methods approaches infinity as the approximation space increases in size. We also provide theoretical error bounds on the condition number and on the errors induced in the numerical solution computed as a result of ill-conditioning. Numerical results confirm the convergence of the SS* method and illustrate the ill-conditioning that arises.

A novel spectral representation of electromyographic signals

Time/frequency and temporal analyses have been widely used in biomedical signal processing. These methods represent important characteristics of a signal in both time and frequency domain. In this way, essential features of the signal can be viewed and analysed in order to understand or model the physiological system. Historically, Fourier spectral analyses have provided a general method for examining the global energy/frequency distributions. However, an assumption inherent to these methods is the stationarity of the signal. As a result, Fourier methods are not generally an appropriate approach in the investigation of signals with transient components. This work presents the application of a new signal processing technique, empirical mode decomposition and the Hilbert spectrum, in the analysis of electromyographic signals. The results show that this method may provide not only an increase in the spectral resolution but also an insight into the underlying process of the muscle contraction.

Fast and accurate SCFT calculations for periodic block-copolymer morphologies using the spectral method with Anderson mixing

We study the numerical efficiency of solving the self-consistent field theory (SCFT) for periodic block-copolymer morphologies by combining the spectral method with Anderson mixing. Using AB diblock-copolymer melts as an example, we demonstrate that this approach can be orders of magnitude faster than competing methods, permitting precise calculations with relatively little computational cost. Moreover, our results raise significant doubts that the gyroid (G) phase extends to infinite $\chi N$. With the increased precision, we are also able to resolve subtle free-energy differences, allowing us to investigate the layer stacking in the perforated-lamellar (PL) phase and the lattice arrangement of the close-packed spherical (S$_{cp}$) phase. Furthermore, our study sheds light on the existence of the newly discovered Fddd (O$^{70}$) morphology, showing that conformational asymmetry has a significant effect on its stability.

Was UV spectral solar irradiance lower during the recent low sunspot minimum?

A detailed analysis is presented of solar UV spectral irradiance for the period between May 2003 and August 2005, when data are available from both the Solar Ultraviolet pectral Irradiance Monitor (SUSIM) instrument (on board the pper Atmosphere Research Satellite (UARS) spacecraft) and the Solar Stellar Irradiance Comparison Experiment (SOLSTICE) instrument (on board the Solar Radiation and Climate Experiment (SORCE) satellite). The ultimate aim is to develop a data composite that can be used to accurately determine any differences between the “exceptional” solar minimum at the end of solar cycle 23 and the previous minimum at the end of solar cycle 22 without having to rely on proxy data to set the long‐term change. SUSIM data are studied because they are the only data available in the “SOLSTICE gap” between the end of available UARS SOLSTICE data and the start of the SORCE data. At any one wavelength the two data sets are considered too dissimilar to be combined into a meaningful composite if any one of three correlations does not exceed a threshold of 0.8. This criterion removes all wavelengths except those in a small range between 156 nm and 208 nm, the longer wavelengths of which influence ozone production and heating in the lower stratosphere. Eight different methods are employed to intercalibrate the two data sequences. All methods give smaller changes between the minima than are seen when the data are not adjusted; however, correcting the SUSIM data to allow for an exponentially decaying offset drift gives a composite that is largely consistent with the unadjusted data from the SOLSTICE instruments on both UARS and SORCE and in which the recent minimum is consistently lower in the wave band studied.

Can we measure terrestrial photosynthesis from space directly, using spectral reflectance and fluorescence?

Attempts to estimate photosynthetic rate or gross primary productivity from remotely sensed absorbed solar radiation depend on knowledge of the light use efficiency (LUE). Early models assumed LUE to be constant, but now most researchers try to adjust it for variations in temperature and moisture stress. However, more exact methods are now required. Hyperspectral remote sensing offers the possibility of sensing the changes in the xanthophyll cycle, which is closely coupled to photosynthesis. Several studies have shown that an index (the photochemical reflectance index) based on the reflectance at 531 nm is strongly correlated with the LUE over hours, days and months. A second hyperspectral approach relies on the remote detection of fluorescence, which is a directly related to the efficiency of photosynthesis. We discuss the state of the art of the two approaches. Both have been demonstrated to be effective, but we specify seven conditions required before the methods can become operational.

Spectral analysis of diffusions with jump boundary

In this paper we consider one-dimensional diffusions with constant coefficients in a finite interval with jump boundary and a certain deterministic jump distribution. We use coupling methods in order to identify the spectral gap in the case of a large drift and prove that there is a threshold drift above which the bottom of the spectrum no longer depends on the drift. As a corollary to our result we are able to answer two questions concerning elliptic eigenvalue problems with non-local boundary conditions formulated previously by Iddo Ben-Ari and Ross Pinsky.

On the spectral gap of Brownian motion with jump boundary

In this paper we consider the Brownian motion with jump boundary and present a new proof of a recent result of Li, Leung and Rakesh concerning the exact convergence rate in the one-dimensional case. Our methods are dierent and mainly probabilistic relying on coupling methods adapted to the special situation under investigation. Moreover we answer a question raised by Ben-Ari and Pinsky concerning the dependence of the spectral gap from the jump distribution in a multi-dimensional setting.

Modeling ocean primary production: sensitivity to spectral resolution of attenuation and absorption of light

Modeling the vertical penetration of photosynthetically active radiation (PAR) through the ocean, and its utilization by phytoplankton, is fundamental to simulating marine primary production. The variation of attenuation and absorption of light with wavelength suggests that photosynthesis should be modeled at high spectral resolution, but this is computationally expensive. To model primary production in global 3d models, a balance between computer time and accuracy is necessary. We investigate the effects of varying the spectral resolution of the underwater light field and the photosynthetic efficiency of phytoplankton (α∗), on primary production using a 1d coupled ecosystem ocean turbulence model. The model is applied at three sites in the Atlantic Ocean (CIS (∼60°N), PAP (∼50°N) and ESTOC (∼30°N)) to include the effect of different meteorological forcing and parameter sets. We also investigate three different methods for modeling α∗ – as a fixed constant, varying with both wavelength and chlorophyll concentration [Bricaud, A., Morel, A., Babin, M., Allali, K., Claustre, H., 1998. Variations of light absorption by suspended particles with chlorophyll a concentration in oceanic (case 1) waters. Analysis and implications for bio-optical models. J. Geophys. Res. 103, 31033–31044], and using a non-spectral parameterization [Anderson, T.R., 1993. A spectrally averaged model of light penetration and photosynthesis. Limnol. Oceanogr. 38, 1403–1419]. After selecting the appropriate ecosystem parameters for each of the three sites we vary the spectral resolution of light and α∗ from 1 to 61 wavebands and study the results in conjunction with the three different α∗ estimation methods. The results show modeled estimates of ocean primary productivity are highly sensitive to the degree of spectral resolution and α∗. For accurate simulations of primary production and chlorophyll distribution we recommend a spectral resolution of at least six wavebands if α∗ is a function of wavelength and chlorophyll, and three wavebands if α∗ is a fixed value.