An open source massively parallel solver for Richards equation: Mechanistic modelling of water fluxes at the watershed scale

In this paper we present a massively parallel open source solver for Richards equation, named the RichardsFOAM solver. This solver has been developed in the framework of the open source generalist computational fluid dynamics tool box OpenFOAM (R) and is capable to deal with large scale problems in both space and time. The source code for RichardsFOAM may be downloaded from the CPC program library website. It exhibits good parallel performances (up to similar to 90% parallel efficiency with 1024 processors both in strong and weak scaling), and the conditions required for obtaining such performances are analysed and discussed. These performances enable the mechanistic modelling of water fluxes at the scale of experimental watersheds (up to few square kilometres of surface area), and on time scales of decades to a century. Such a solver can be useful in various applications, such as environmental engineering for long term transport of pollutants in soils, water engineering for assessing the impact of land settlement on water resources, or in the study of weathering processes on the watersheds. (C) 2014 Elsevier B.V. All rights reserved.

Surface Freshwater Storage Variations in the Orinoco Floodplains Using Multi-Satellite Observations

Variations in surface water extent and storage are poorly characterized from regional to global scales. In this study, a multi-satellite approach is proposed to estimate the water stored in the floodplains of the Orinoco Basin at a monthly time-scale using remotely-sensed observations of surface water from the Global Inundation Extent Multi-Satellite (GIEMS) and stages from Envisat radar altimetry. Surface water storage variations over 2003-2007 exhibit large interannual variability and a strong seasonal signal, peaking during summer, and associated with the flood pulse. The volume of surface water storage in the Orinoco Basin was highly correlated with the river discharge at Ciudad Bolivar (R = 0.95), the closest station to the mouth where discharge was estimated, although discharge lagged one month behind storage. The correlation remained high (R = 0.73) after removing seasonal effects. Mean annual variations in surface water volume represented similar to 170 km(3), contributing to similar to 45% of the Gravity Recovery and Climate Experiment (GRACE)-derived total water storage variations and representing similar to 13% of the total volume of water that flowed out of the Orinoco Basin to the Atlantic Ocean.

Development of a global inundation map at high spatial resolution from topographic downscaling of coarse-scale remote sensing data

Large-scale estimates of the area of terrestrial surface waters have greatly improved over time, in particular through the development of multi-satellite methodologies, but the generally coarse spatial resolution (tens of kms) of global observations is still inadequate for many ecological applications. The goal of this study is to introduce a new, globally applicable downscaling method and to demonstrate its applicability to derive fine resolution results from coarse global inundation estimates. The downscaling procedure predicts the location of surface water cover with an inundation probability map that was generated by bagged derision trees using globally available topographic and hydrographic information from the SRTM-derived HydroSHEDS database and trained on the wetland extent of the GLC2000 global land cover map. We applied the downscaling technique to the Global Inundation Extent from Multi-Satellites (GIEMS) dataset to produce a new high-resolution inundation map at a pixel size of 15 arc-seconds, termed GIEMS-D15. GIEMS-D15 represents three states of land surface inundation extents: mean annual minimum (total area, 6.5 x 10(6) km(2)), mean annual maximum (12.1 x 10(6) km(2)), and long-term maximum (173 x 10(6) km(2)); the latter depicts the largest surface water area of any global map to date. While the accuracy of GIEMS-D15 reflects distribution errors introduced by the downscaling process as well as errors from the original satellite estimates, overall accuracy is good yet spatially variable. A comparison against regional wetland cover maps generated by independent observations shows that the results adequately represent large floodplains and wetlands. GIEMS-D15 offers a higher resolution delineation of inundated areas than previously available for the assessment of global freshwater resources and the study of large floodplain and wetland ecosystems. The technique of applying inundation probabilities also allows for coupling with coarse-scale hydro-climatological model simulations. (C) 2014 Elsevier Inc All rights reserved.

Retrieval and Multi-scale Validation of Soil Moisture from Multi-temporal SAR Data in a Semi-Arid Tropical Region

The current study presents an algorithm to retrieve surface Soil Moisture (SM) from multi-temporal Synthetic Aperture Radar (SAR) data. The developed algorithm is based on the Cumulative Density Function (CDF) transformation of multi-temporal RADARSAT-2 backscatter coefficient (BC) to obtain relative SM values, and then converts relative SM values into absolute SM values using soil information. The algorithm is tested in a semi-arid tropical region in South India using 30 satellite images of RADARSAT-2, SMOS L2 SM products, and 1262 SM field measurements in 50 plots spanning over 4 years. The validation with the field data showed the ability of the developed algorithm to retrieve SM with RMSE ranging from 0.02 to 0.06 m(3)/m(3) for the majority of plots. Comparison with the SMOS SM showed a good temporal behaviour with RMSE of approximately 0.05 m(3)/m(3) and a correlation coefficient of approximately 0.9. The developed model is compared and found to be better than the change detection and delta index model. The approach does not require calibration of any parameter to obtain relative SM and hence can easily be extended to any region having time series of SAR data available.

A novel interferometric technique to estimate thermal diffusivity of `optically transparent solid' using `Isothermal surface velocimetry'

One-dimensional transient heat flow is interpreted as a procession of `macro-scale translatory motion of indexed isothermal surfaces'. A new analytical model is proposed by introducing velocity of isothermal surface in Fourier heat diffusion equation. The velocity dependent function is extracted by revisiting `the concept of thermal layer of heat conduction in solid' and `exact solution' to estimate thermal diffusivity. The experimental approach involves establishment of 1 D unsteady heat flow inside the sample through Step-temperature excitation. A novel self-reference interferometer is utilized to separate a `unique isothermal surface' in time-varying temperature field. The translatory motion of the said isothermal surface is recorded using digital camera to estimate its velocity. From the knowledge of thermo-optic coefficient, temperature of the said isothermal surface is predicted. The performance of proposed method is evaluated for Quartz sample and compared with literature.

MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature

Background: Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily constructed from various forms of molecular data such as 3D atomic coordinates (PDB) and Electron Microscopy (EM) data. Methods: We present a Multi-Scale Morse-Smale Molecular-Surface Alignment tool, MS3ALIGN, which aligns molecular surfaces based on significant protrusions on the molecular surface. The input is a pair of molecular surfaces represented as triangle meshes. A key advantage of MS3ALIGN is computational efficiency that is achieved because it processes only a few carefully chosen protrusions on the molecular surface. Furthermore, the alignments are partial in nature and therefore allows for inexact surfaces to be aligned. Results: The method is evaluated in four settings. First, we establish performance using known alignments with varying overlap and noise values. Second, we compare the method with SurfComp, an existing surface alignment method. We show that we are able to determine alignments reported by SurfComp, as well as report relevant alignments not found by SurfComp. Third, we validate the ability of MS3ALIGN to determine alignments in the case of structurally dissimilar binding sites. Fourth, we demonstrate the ability of MS3ALIGN to align iso-surfaces derived from cryo-electron microscopy scans. Conclusions: We have presented an algorithm that aligns Molecular Surfaces based on the topology of surface curvature. Awebserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet. in/ms3align.

Capillary Effect on Vertically Excited Surface Wave in Circular Cylindrical Vessel

In a vertically oscillating circular cylindrical container, singular perturbation theory of two-time scale expansions was developed in inviscid fluids to investigate the motion of single free surface standing wave including the effect of surface tension.

Instability Analysis of Nonlinear Surface Waves in a Circular Cylindrical Container Subjected to a Vertical Excitation

Singular perturbation theory of two-time scale expansions was developed both in inviscid and weak viscous fluids to investigate the motion of single surface standing wave in a liquid-filled circular cylindrical vessel, which is subject to a vertical periodical oscillation. Firstly, it is assumed that the fluid in the circular cylindrical vessel is inviscid, incompressible and the motion is irrotational, a nonlinear evolution equation of slowly varying complex amplitude, which incorporates cubic nonlinear term, external excitation and the influence of surface tension, was derived from solvability condition of high-order approximation. It shows that when forced frequency is low, the effect of surface tension on mode selection of surface wave is not important. However, when forced frequency is high, the influence of surface tension is significant, and can not be neglected. This proved that the surface tension has the function, which causes free surface returning to equilibrium location. Theoretical results much close to experimental results when the surface tension is considered. In fact, the damping will appear in actual physical system due to dissipation of viscosity of fluid. Based upon weakly viscous fluids assumption, the fluid field was divided into an outer potential flow region and an inner boundary layer region. A linear amplitude equation of slowly varying complex amplitude, which incorporates damping term and external excitation, was derived from linearized Navier-Stokes equation. The analytical expression of damping coefficient was determined and the relation between damping and other related parameters (such as viscosity, forced amplitude and depth of fluid) was presented. The nonlinear amplitude equation and a dispersion, which had been derived from the inviscid fluid approximation, were modified by adding linear damping. It was found that the modified results much reasonably close to experimental results. Moreover, the influence both of the surface tension and the weak viscosity on the mode formation was described by comparing theoretical and experimental results. The results show that when the forcing frequency is low, the viscosity of the fluid is prominent for the mode selection. However, when the forcing frequency is high, the surface tension of the fluid is prominent. Finally, instability of the surface wave is analyzed and properties of the solutions of the modified amplitude equation are determined together with phase-plane trajectories. A necessary condition of forming stable surface wave is obtained and unstable regions are illustrated. (c) 2005 Elsevier SAS. All rights reserved.

Damping of Vertically Excited Surface Wave in Weakly Viscous Fluid

In a vertically oscillating circular cylindrical container, singular perturbation theory of two-time scale expansions is developed in weakly viscous fluids to investigate the motion of single free surface standing wave by linearizing the Navier-Stokes equation. The fluid field is divided into an outer potential flow region and an inner boundary layer region. The solutions of both two regions are obtained and a linear amplitude equation incorporating damping term and external excitation is derived. The condition to appear stable surface wave is obtained and the critical curve is determined. In addition, an analytical expression of damping coefficient is determined. Finally, the dispersion relation, which has been derived from the inviscid fluid approximation, is modified by adding linear damping. It is found that the modified results are reasonably closer to experimental results than former theory. Result shows that when forcing frequency is low, the viscosity of the fluid is prominent for the mode selection. However, when forcing frequency is high, the surface tension of the fluid is prominent.

Combined effect of surface tension, gravity and van der Waals force induced by a non-contact probe tip on the shape of liquid surface

Aiming at understanding how a liquid film on a substrate affects the atomic force microscopic image in experiments, we present an analytical representation of the shape of liquid surface under van der Waals interaction induced by a non-contact probe tip. The analytical expression shows good consistence with the corresponding numerical results. According to the expression, we find that the vertical scale of the liquid dome is mainly governed by a combination of van der Waals force, surface tension and probe tip radius, and is weekly related to gravity. However, its horizontal extension is determined by the capillary length.

Influence of Surface Stress on Frequency of Microcantilever-Based Biosensors (vol 10, pg 307, 2004)

Microcantilever-based biosensors have been found increasing applications in physical, chemical, and biological fields in recent years. When biosensors are used in those fields, surface stress and mass variations due to bio-molecular binding can cause the microcantilever deform or the shift of frequency. These simple biosensors allow biologists to study surface biochemistry on a micro or nano scale and offer new opportunities in developing microscopic biomedical analysis with unique characteristics. To compare and illustrate the influence of the surface stress on the frequency and avoid unnecessary and complicated numerical solution of the resonance frequency, some dimensionless numbers are derived in this paper by making governing equations dimensionless. Meanwhile, in order to analyze the influence of the general surface stress on the frequency, a new model is put forward, and the frequency of the microcantilever is calculated by using the subspace iteration method and the Rayleigh method. The sensitivity of microcantilever is also discussed. (19 refs.)

Strain-Induced Grain Refinement of Cobalt During Surface Mechanical Attrition Treatment

The microstructural evolution during surface mechanical attrition treatment of cobalt (a mixture of hexagonal close packed (hep) and face-centered cubic (fcc) phases) was investigated. In order to reveal the mechanism of grain refinement and strain accommodation. The microstructure was systematically characterized by both cross-sectional and planar-view transmission electron microscopy. In the hcp phase, the process of grain refinement. Accompanied by an increase in strain imposed in the surface layer. Involved: (1) the onset of 110 111 deformation twinning, (2) the operation of (1 120) 110 1 0} prismatic and (1 120) (000 1) basal slip, leading to the formation of low-angle dislocation boundaries, and (3) the successive subdivision of grains to a finer and finer scale. Ressulting in the formation of highly misoriented nanocrystalline grains. Moreover. The formation of nanocrystalliies at the grain boundary and triple junction was also observed to occur concurrently with straining. By contrast. The fec phase accommodated strain in a sequence as follows: (1) slip of dislocations by forming intersecting planar arrays of dislocations, (2) {1 1 1} deformation twinning, and (3) the gamma(fcc) --> epsilon(hcp) martensitic phase transformation. The mechanism of grain refinement was interpreted in terms of the structural subdivision of grains together with dynamic recrystallization occurring in the hep phase and the gamma --> E: martensitic transformation in the fcc phase as well.

Effect of surface tension on the mode selection of vertically excited surface waves in a circular cylindrical vessel

Singular perturbation theory of two-time-scale expansions was developed in inviscid fluids to investigate patternforming, structure of the single surface standing wave, and its evolution with time in a circular cylindrical vessel subject to a vertical oscillation. A nonlinear slowly varying complex amplitude equation, which involves a cubic nonlinear term, an external excitation and the influence of surface tension, was derived from the potential flow equation. Surface tension was introduced by the boundary condition of the free surface in an ideal and incompressible fluid. The results show that when forced frequency is low, the effect of surface tension on the mode selection of surface waves is not important. However, when the forced frequency is high, the surface tension cannot be neglected. This manifests that the function of surface tension is to cause the free surface to return to its equilibrium configuration. In addition, the effect of surface tension seems to make the theoretical results much closer to experimental results.

Vertically forced surface wave in weakly viscous fluids bounded in a circular cylindrical vessel

Two-time scale perturbation expansions were developed in weakly viscous fluids to investigate surface wave motions by linearizing the Navier-Stokes equation in a circular cylindrical vessel which is subject to a vertical oscillation. The fluid field was divided into an outer potential flow region and an inner boundary layer region. A linear amplitude equation of slowly varying complex amplitude, which incorporates a damping term and external excitation, was derived for the weakly viscid fluids. The condition for the appearance of stable surface waves was obtained and the critical curve was determined. In addition, an analytical expression for the damping coefficient was determined and the relationship between damping and other related parameters (such as viscosity, forced amplitude, forced frequency and the depth of fluid, etc.) was presented. Finally, the influence both of the surface tension and the weak viscosity on the mode formation was described by comparing theoretical and experimental results. The results show that when the forcing frequency is low, the viscosity of the fluid is prominent for the mode selection. However, when the forcing frequency is high, the surface tension of the fluid is prominent.

Study of the surface structure of butterfly wings using the scanning electron microscopic moire method

Scanning electron microscopic (SEM) moire method was used to study the surface structure of three kinds of butterfly wings: Papilio maackii Menetries, Euploea midamus (Linnaeus), and Stichophthalma how-qua (Westwood). Gratings composed of curves with different orientations were found on scales. The planar characteristics of gratings and some other planar features of the surface structure of these wings were revealed, respectively, in terms of virtual strain. Experimental results demonstrate that SEM moire method is a simple, nonlocal, economical, effective technique for determining which grating exists on one whole scale, measuring the dimension and the whole planar structural character of the grating on each scale, as well as characterizing the relationship between gratings on different scales of each butterfly wing. Thus, the SEM moire method is a useful tool to assist with characterizing the structure of butterfly wings and explaining their excellent properties. (c) 2007 Optical Society of America.