On the modelling of wave breaking and set-up on coral reefs

An extended refraction-diffraction equation [Massel, S.R., 1993. Extended refraction-diffraction equation for surface waves. Coastal Eng. 19, 97-126] has been applied to predict wave transformation and breaking as well as wave-induced set-up on two-dimensional reef profiles of various shapes. A free empirical coefficient alpha in a formula for the average rate of energy dissipation [epsilon(b)] = (alpha rho g omega/8 pi)(root gh/C)(H-3/h) in the modified periodic bore model was found to be a function of the dimensionless parameter F-c0 = (g(1.25)H(0)(0.5)T(2.5))/h(r)(1.75), proposed by Gourlay [Gourlayl M.R., 1994. Wave transformation on a coral reef. Coastal Eng. 23, 17-42]. The applicability of the developed model has been demonstrated for reefs of various shapes subjected to various incident wave conditions. Assuming proposed relationships of the coefficient alpha and F-c0, the model provides results on wave height attenuation and set-up elevation which compare well with experimental data. (C) 2000 Elsevier Science B.V. All rights reserved.

The role of Ti as a catalyst for the dissociation of hydrogen on a Mg(0001) surface

In this paper, the dissociative chemisorption of hydrogen on both pure and Ti-incorporated Mg(0001) surfaces are studied by ab initio density functional theory (DFT) calculations. The calculated dissociation barrier of hydrogen molecule on a pure Mg(0001) surface (1.05 eV) is in good agreement with comparable theoretical studies. For the Ti-incorporated Mg(0001) surface, the activated barrier decreases to 0.103 eV due to the strong interaction between the molecular orbital of hydrogen and the d metal state of Ti. This could explain the experimentally observed improvement in absorption kinetics of hydrogen when transition metals have been introduced into the magnesium materials.

Properties of the stochastic Gross-Pitaevskii equation: finite temperature Ehrenfest relations and the optimal plane wave representation

We present Ehrenfest relations for the high temperature stochastic Gross-Pitaevskii equation description of a trapped Bose gas, including the effect of growth noise and the energy cutoff. A condition for neglecting the cutoff terms in the Ehrenfest relations is found which is more stringent than the usual validity condition of the truncated Wigner or classical field method-that all modes are highly occupied. The condition requires a small overlap of the nonlinear interaction term with the lowest energy single particle state of the noncondensate band, and gives a means to constrain dynamical artefacts arising from the energy cutoff in numerical simulations. We apply the formalism to two simple test problems: (i) simulation of the Kohn mode oscillation for a trapped Bose gas at zero temperature, and (ii) computing the equilibrium properties of a finite temperature Bose gas within the classical field method. The examples indicate ways to control the effects of the cutoff, and that there is an optimal choice of plane wave basis for a given cutoff energy. This basis gives the best reproduction of the single particle spectrum, the condensate fraction and the position and momentum densities.

Ab initio studies of hydrogen desorption from low index magnesium hydride surface

The low index Magnesium hydride surfaces, MgH2(001) and MgH2(110), have been studied by ab intio Density Functional Theory (DFT) calculations. It was found that the MgH2(110) surface is more stable than MgH2(001) surface, which is in good agreement with the experimental observation. The H-2 desorption barriers vary depending on the crystalline surfaces that are exposed and also the specific H atom sites involved-they are found to be generally high, due to the thermodynamic stability of the MgH2, system, and are larger for the MgH2(001) surface. The pathway for recombinative desorption of one in-plane and one bridging H atom from the MgH2(110) surface was found to be the lowest energy barrier amongst those computed (172 KJ/mol) and is in good agreement with the experimental estimates. (c) 2006 Elsevier B.V. All rights reserved.

Catalytic effects of subsurface carbon in the chemisorption of hydrogen on a Mg(0001) surface: an ab-initio study

Ab initio density functional theory (DFT) calculations are performed to explore possible catalytic effects on the dissociative chemisorption of hydrogen on a Mg(0001) surface when carbon is incorporated into Mg materials. The computational results imply that a C atom located initially on a Mg(0001) surface can migrate into the subsurface and occupy an fcc interstitial site, with charge transfer to the C atom from neighboring Mg atoms. The effect of subsurface C on the dissociation of H-2 on the Mg(0001) surface is found to be relatively marginal: a perfect sublayer of interstitial C is calculated to lower the barrier by 0.16 eV compared with that on a pure Mg(0001) surface. Further calculations reveal, however, that sublayer C may have a significant effect in enhancing the diffusion of atomic hydrogen into the sublayers through fcc channels. This contributes new physical understanding toward rationalizing the experimentally observed improvement in absorption kinetics of H2 when graphite or single walled carbon nanotubes (SWCNT) are introduced into the Mg powder during ball milling.

First-principle study of adsorption of hydrogen on Ti-doped Mg(0001) surface

Ab initio density functional theory (DFT) calculations are performed to study the adsorption of H-2 molecules on a Ti-doped Mg(0001) surface. We find that two hydrogen molecules are able to dissociate on top of the Ti atom with very small activation barriers (0.103 and 0.145 eV for the first and second H-2 molecules, respectively). Additionally, a molecular adsorption state of H-2 above the Ti atom is observed for the first time and is attributed to the polarization of the H-2 molecule by the Ti cation. Our results parallel recent findings for H-2 adsorption on Ti-doped carbon nanotubes or fullerenes. They provide new insight into the preliminary stages of hydrogen adsorption onto Ti-incorporated Mg surfaces.

Transition-state-theory calculations for reactions of O(3P) with halogenated olefins

The potential energy surfaces for the reactions of atomic oxygen in its ground electronic state, O(P-3), with the olefins: CF2=CCl2 and CF2=CF - CF3, have been characterized using ab initio molecular orbital calculations. Geometry optimization and vibrational frequency calculations were performed for reactants, transition states and products at the MP2 and QCISD levels of theory using the 6-31G(d) basis set. This database was then used to calculate the rate constants by means of Transition-State-Theory. To obtain a better reference and to test the reliability of the activation barriers we have also carried out computations using the CCSD(T)(fc)/6-311Gdagger, MP4(SDQ)(fc)/CBSB4 and MP2(fc)/CBSB3 single point energy calculations at both of the above levels of theory, as well as with the composite CBS-RAD procedure ( P. M. Mayer, C. J. Parkinson, D. M. Smith and L. Radom, J. Chem. Phys., 1998, 108, 604) and a modi. cation of this approach, called: CBS-RAD( MP2, MP2). It was found that the kinetic parameters obtained in this work particularly with the CBS-RAD ( MP2, MP2) procedure are in reasonable agreement with the experimental values. For both reactions it is found that the channels leading to the olefin double-bond addition predominates with respect to any other reaction pathway. However, on account of the different substituents in the alkenes we have located, at all levels of theory, two transition states for each reaction. Moreover, we have found that, for the reactions studied, a correlation exists between the activation energies and the electronic structure of the transition states which can explain the influence of the substituent effect on the reactivity of the halo-olefins.

Theory of strongly correlated electron systems. I. Intersite coulomb interaction and the approximation of renormalized fermions in total energy calculations

The diagrammatic strong-coupling perturbation theory (SCPT) for correlated electron systems is developed for intersite Coulomb interaction and for a nonorthogonal basis set. The construction is based on iterations of exact closed equations for many - electron Green functions (GFs) for Hubbard operators in terms of functional derivatives with respect to external sources. The graphs, which do not contain the contributions from the fluctuations of the local population numbers of the ion states, play a special role: a one-to-one correspondence is found between the subset of such graphs for the many - electron GFs and the complete set of Feynman graphs of weak-coupling perturbation theory (WCPT) for single-electron GFs. This fact is used for formulation of the approximation of renormalized Fermions (ARF) in which the many-electron quasi-particles behave analogously to normal Fermions. Then, by analyzing: (a) Sham's equation, which connects the self-energy and the exchange- correlation potential in density functional theory (DFT); and (b) the Galitskii and Migdal expressions for the total energy, written within WCPT and within ARF SCPT, a way we suggest a method to improve the description of the systems with correlated electrons within the local density approximation (LDA) to DFT. The formulation, in terms of renormalized Fermions LIDA (RF LDA), is obtained by introducing the spectral weights of the many electron GFs into the definitions of the charge density, the overlap matrices, effective mixing and hopping matrix elements, into existing electronic structure codes, whereas the weights themselves have to be found from an additional set of equations. Compared with LDA+U and self-interaction correction (SIC) methods, RF LDA has the advantage of taking into account the transfer of spectral weights, and, when formulated in terms of GFs, also allows for consideration of excitations and nonzero temperature. Going beyond the ARF SCPT, as well as RF LIDA, and taking into account the fluctuations of ion population numbers would require writing completely new codes for ab initio calculations. The application of RF LDA for ab initio band structure calculations for rare earth metals is presented in part 11 of this study (this issue). (c) 2005 Wiley Periodicals, Inc.

Wave-generated flow on coral reefs - an analysis for two-dimensional horizontal reef-tops with steep faces

Waves breaking on the seaward rim of a coral reef generate a flow of water from the exposed side of the reef to the sheltered side and/or to either channels through the reef-rim or lower sections of the latter. This wave-generated flow is driven by the water surface gradient resulting from the wave set-up created by the breaking waves. This paper reviews previous approaches to modelling wave-generated flows across coral reefs and discusses the influence of reef morphology and roughness upon these flows. Laboratory measurements upon a two-dimensional horizontal reef platform with a steep reef face provide the basis for extending a previous theoretical analysis for wave set-up on a reef in the absence of a flow [Gourlay, M.R., 1996b. Wave set-up on coral reefs. 2. Set-up on reefs with various profiles. Coastal Engineering 28, 1755] to include the interaction between a unidirectional flow and the wave set-up. The laboratory model results are then used to demonstrate that there are two basic reef-top flow regimes-reef-top control and reef-rim control. Using open channel flow theory, analytical relationships are derived for the reef-top current velocity in terms of the offreef wave conditions, the reef-top water depth and the physical characteristics of the reef-top topography. The wave set-up and wave-generated flow relationships are found to predict experimental values with reasonable accuracy in most cases. The analytical relationships are used to investigate wave-generated flows into a boat harbour channel on Heron Reef in the southern Great Barrier Reef. (c) 2005 Elsevier B.V. All rights reserved.

Structural basis and prediction of substrate specificity in protein serine/threonine kinases

The large number of protein kinases makes it impractical to determine their specificities and substrates experimentally. Using the available crystal structures, molecular modeling, and sequence analyses of kinases and substrates, we developed a set of rules governing the binding of a heptapeptide substrate motif (surrounding the phosphorylation site) to the kinase and implemented these rules in a web-interfaced program for automated prediction of optimal substrate peptides, taking only the amino acid sequence of a protein kinase as input. We show the utility of the method by analyzing yeast cell cycle control and DNA damage checkpoint pathways. Our method is the only available predictive method generally applicable for identifying possible substrate proteins for protein serine/threonine kinases and helps in silico construction of signaling pathways. The accuracy of prediction is comparable to the accuracy of data from systematic large-scale experimental approaches.

Response of the salt-freshwater interface in a coastal aquifer to a wave-induced groundwater pulse: field observations and modelling

Field observations on an unconfined coastal aquifer showed that a groundwater pulse, generated by it moderate (significant wave height, H-sig similar to 4.5 m) wave/storm event, induced significant oscillations in the salt-freshwater interface of the order of several metres in the horizontal direction. A dynamic sharp-interface model is developed to quantify the mechanism of these interface oscillations. The model uses the 50% seawater salinity contour as the location of the equivalent sharp-interface. The model was calibrated against the observed groundwater table fluctuations. It predicted reasonably well the interface oscillations with a slight over-prediction of the oscillation magnitude and a steepening of the interface. The neglect of mixing in the salt-freshwater mixing zone by the sharp-interface model is suggested as a possible contributor to the discrepancies between the model predictions and observations. In contrast with the significant wave effects, there was no observable response of the interface to diurnal or semidiurnal tides. (C) 2004 Elsevier Ltd. All rights reserved.

OMERACT-OARSI Initiative: Osteoarthritis Research Society International set of responder criteria for osteoarthritis clinical trials revisited.

Background: The OARSI Standing Committee for Clinical Trials Response Criteria Initiative had developed two sets of responder criteria to present the results of changes after treatment in three symptomatic domains (pain, function, and patient's global assessment) as a single variable for clinical trials (1). For each domain, a response was defined by both a relative and an absolute change, with different cut-offs with regard to the drug, the route of administration and the OA localization. Objective: To propose a simplified set of responder criteria with a similar cut-off, whatever the drug, the route or the OA localization. Methods: Data driven approach: (1) Two databases were considered The 'elaboration' database with which the formal OARSI sets of responder criteria were elaborated and The 'revisit' database. (2) Six different scenarios were evaluated: The two formal OARSI sets of criteria Four proposed scenarios of simplified sets of criteria Data from clinical randomized blinded placebo controlled trials were used to evaluate the performances of the two formal scenarios with two different databases ('elaboration' versus 'revisit') and those of the four proposed simplified scenarios within the 'revisit' database. The placebo effect, active effect, treatment effect, and the required sample arm size to obtain the placebo effect and the active treatment effect observed were the performances evaluated for each of the six scenarios. Experts' opinion approach: Results were discussed among the participants of the OMERACT VI meeting, who voted to select the definite OMERACT-OARSI set of criteria (one of the six evaluated scenarios). Results: Data driven approach: Fourteen trials totaling 1886 CA patients and fifteen studies involving 8164 CA patients were evaluated in the 'elaboration' and the 'revisit' databases respectively. The variability of the performances observed in the 'revisit' database when using the different simplified scenarios was similar to that observed between the two databases ('elaboration' versus 'revisit') when using the formal scenarios. The treatment effect and the required sample arm size were similar for each set of criteria. Experts' opinion approach: According to the experts, these two previous performances were the most important of an optimal set of responder criteria. They chose the set of criteria considering both pain and function as evaluation domain and requiring an absolute change and a relative change from baseline to define a response, with similar cut-offs whatever the drug, the route of administration or the CA localization. Conclusion: This data driven and experts' opinion approach is the basis for proposing an optimal simplified set of responder criteria for CA clinical trials. Other studies, using other sets of CA patients, are required in order to further validate this proposed OMERACT - OARSI set of criteria. (C) 2004 OsteoArthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Coral mortality increases wave energy reaching shores protected by reef flats: Examples from the Seychelles

In the granitic Seychelles, many shores and beaches are fringed by coral reef flats which provide protection to shores from erosion by waves. The surfaces of these reef flats support a complex ecology. About 10 years ago their seaward zones were extensively covered by a rich coral growth, which reached approximately to mean low water level, but in 1998 this was largely killed by seawater warming. The resulting large expanses of dead coral skeletons in these locations are now disintegrating, and much of the subsequent modest recovery by new coral recruitment was set back by further mortalities. A mathematical model of wave energy reaching shorelines protected by coral reef flats has been applied to 14 Seychelles reefs. It is derived from equations which predict: (1) the raised water level, or wave set-up, on reef flats resulting from wave breaking, which depends upon offshore wave height and period, depth of still water over the reef flat and the reef crest profile, and (2) the decay of energy from reef edge to shoreline that is affected by width of reef flat, surface roughness, sea level rise and 'pseudo-sea level rise' created by increased depth resulting from disintegration of coral colonies. The model treats each reef as one entity, but because biota and zonation on reef flats are not homogenous, all reefs are divided into four zones. In each, cover by both living and dead biota was estimated for calculation of parameters, and then averaged to obtain input data for the model. All possible biological factors were taken into account, such as the ability of seagrass beds to grow upwards to match expected sea level rise, reduction in height of the reef flat in relation to sea level as zones of dead corals decay, and the observed 'rounding' of reef crests as erosion removes corals from those areas. Estimates were also made of all these factors for a time approximately a decade ago, representing a time before the mass coral mortality, and for approximately a decade in the future when the observed rapid state of dead coral colony disintegration is assumed to have reached an end point. Results of increased energy over the past decade explain observations of erosion in some sites in the Seychelles. Most importantly, it is estimated that the rise in energy reaching shores protected by fringing reefs will now accelerate more rapidly, such that the increase expected over the next decade will be approximately double than that seen over the past decade. (c) 2005 Elsevier Ltd. All rights reserved.

Slowing down a pine invasion despite uncertainty in demography and dispersal

1. Management decisions regarding invasive plants often have to be made quickly and in the face of fragmentary knowledge of their population dynamics. However, recommendations are commonly made on the basis of only a restricted set of parameters. Without addressing uncertainty and variability in model parameters we risk ineffective management, resulting in wasted resources and an escalating problem if early chances to control spread are missed. 2. Using available data for Pinus nigra in ungrazed and grazed grassland and shrubland in New Zealand, we parameterized a stage-structured spread model to calculate invasion wave speed, population growth rate and their sensitivities and elasticities to population parameters. Uncertainty distributions of parameters were used with the model to generate confidence intervals (CI) about the model predictions. 3. Ungrazed grassland environments were most vulnerable to invasion and the highest elasticities and sensitivities of invasion speed were to long-distance dispersal parameters. However, there was overlap between the elasticity and sensitivity CI on juvenile survival, seedling establishment and long-distance dispersal parameters, indicating overlap in their effects on invasion speed. 4. While elasticity of invasion speed to long-distance dispersal was highest in shrubland environments, there was overlap with the CI of elasticity to juvenile survival. In shrubland invasion speed was most sensitive to the probability of establishment, especially when establishment was low. In the grazed environment elasticity and sensitivity of invasion speed to the severity of grazing were consistently highest. Management recommendations based on elasticities and sensitivities depend on the vulnerability of the habitat. 5. Synthesis and applications. Despite considerable uncertainty in demography and dispersal, robust management recommendations emerged from the model. Proportional or absolute reductions in long-distance dispersal, juvenile survival and seedling establishment parameters have the potential to reduce wave speed substantially. Plantations of wind-dispersed invasive conifers should not be sited on exposed sites vulnerable to long-distance dispersal events, and trees in these sites should be removed. Invasion speed can also be reduced by removing seedlings, establishing competitive shrubs and grazing. Incorporating uncertainty into the modelling process increases our confidence in the wide applicability of the management strategies recommended here.

A wave equation technique for designing compact gradient coils

A primary purpose of this research is to design a gradient coil that is planar in construction and can be inserted within existing infrastructure. The proposed wave equation method for the design of gradient coils is novel within the field. it is comprehensively shown how this method can be used to design the planar x-, y-, and z-gradient wire windings to produce the required magnetic fields within a certain domain. The solution for the cylindrical gradient coil set is also elucidated. The wave equation technique is compared with the well-known target held method to gauge the quality of resultant design. In the case of the planar gradient coil design, it is shown that using the new method, a set of compact gradient coils with large field of view can be produced. The final design is considerably smaller in dimension when compared with the design obtained using the target field method, and therefore the manufacturing costs and materials required are somewhat reduced.