Numerical modeling of water wave interaction with a soft mud bed

A vertical 2-D numerical model is presented for simulating the interaction between water waves and a soft mud bed. Taking into account nonlinear rheology, a semi-empirical rheological model is applied to this water-mud model, reflecting the combined visco-elasto-plastic properties of soft mud under such oscillatory external forces as water waves. In order to increase the resolution of the flow in the neighborhood of both sides of the inter-surface, a logarithmic grid in the vertical direction is employed for numerical treatment. Model verifications are given through comparisons between the calculated and the measured mud mass transport velocities as well as wave height changes.

Modeling gross primary production of alpine ecosystems in the Tibetan Plateau using MODIS images and climate data

The eddy covariance technique provides measurements of net ecosystem exchange (NEE) Of CO2 between the atmosphere and terrestrial ecosystems, which is widely used to estimate ecosystem respiration and gross primary production (GPP) at a number Of CO2 eddy flux tower sites. In this paper, canopy-level maximum light use efficiency, a key parameter in the satellite-based Vegetation Photosynthesis Model (VPM), was estimated by using the observed CO2 flux data and photosynthetically active radiation (PAR) data from eddy flux tower sites in an alpine swamp ecosystem, an alpine shrub ecosystem and an alpine meadow ecosystem in Qinghai-Tibetan Plateau, China. The VPM model uses two improved vegetation indices (Enhanced Vegetation Index (EVI), Land Surface Water Index (LSWI)) derived from the Moderate Resolution Imaging Spectral radiometer (MODIS) data and climate data at the flux tower sites, and estimated the seasonal dynamics of GPP of the three alpine grassland ecosystems in Qinghai-Tibetan Plateau. The seasonal dynamics of GPP predicted by the VPM model agreed well with estimated GPP from eddy flux towers. These results demonstrated the potential of the satellite-driven VPM model for scaling-up GPP of alpine grassland ecosystems, a key component for the study of the carbon cycle at regional and global scales. (c) 2006 Elsevier Inc. All rights reserved.

Modeling trophic positions of the alpine meadow ecosystem combining stable carbon and nitrogen isotope ratios

Stable carbon and nitrogen isotope ratios of single tissues or whole bodies were analyzed to establish trophic positions of main consumers living at the alpine meadow ecosystem in the Tibetan Plateau. The results demonstrated that delta C-13 and delta N-15 values of vertebrates showed great variations and ranged from -26.83 to -22.51 parts per thousand and from 2.33 to 8.44 parts per thousand, respectively. Plateau pika, root vole, plateau hare, infants of rodents and hatchlings of passerine bird species had the lowest delta C-13 and delta N-15 values. delta C-13 and delta N-15 values of omnivorous and insectivorous birds and amphibians showed intermediate. Carnivorous species, steppe polecat and Upland buzzard, and omnivorous Robin accentor and White wagtail possessed extremely higher VC and delta N-15 values. Omnivorous birds captured in earlier year had significantly less negative delta C-13 and greater delta N-15 values than those captured later. Based on steady angular enrichment between trophic levels, an "alpha and vector model" combing delta C-13 and delta N-15 values was introduced to reveal trophic positions, the results indicated that Tibetan sheep, Tibetan yak, plateau pika, root vole, plateau hare, infants of small rodents showed the lowest trophic positions (TP 1.81-2.38). While omnivorous and insectivorous birds, their hatchlings and amphibians showed intermediate trophic positions (TP 2.06-2.89), carnivorous species steppe polecat and Upland buzzard, migrant birds possessed extremely higher trophic positions (TP 2.89-3.05). The isotopic investigation of organisms and the introduced "alpha and vector model" successfully demonstrated the same trophic positions and diet prediction of consumers as nitrogen enrichment model at the alpine meadow ecosystem. Besides of this information, the "alpha and vector model" can also be incorporated into multiple isotope signatures to infer trophic relationships. This angular enrichment model has the potential to address basic ecological questions, such as trophic structure, trophic dynamics, and energy flow in other terrestrial ecosystems of properly handled. (C) 2005 Elsevier B.V. All rights reserved.

Observation and modeling for terrestrial processes in alpine meadow

The water-heat transfer process between land and atmosphere in Haibei alpine meadow area has been systematically observed. A multi-layer coupling model for land-atmosphere interaction was presented with special attention paid to the moisture transfer in leaf stomata under unsaturated condition. A profound investigation on the physical process of turbulent transfer inside the vegetation has been performed with a revised formula of water absorption for root system. The present model facilitates the study of vertically distributed physical variables in detail. Numerical simulation was conducted according to the transfer process of Kinesia humility meadow in the area of Haibei Alpine Meadow Ecosystem Station, CAS. The calculated results agree well with observation.

A Perturbation Scheme for Spherical Arrangements with Application to Molecular Modeling

We describe a software package for computing and manipulating the subdivision of a sphere by a collection of (not necessarily great) circles and for computing the boundary surface of the union of spheres. We present problems that arise in the implementation of the software and the solutions that we have found for them. At the core of the paper is a novel perturbation scheme to overcome degeneracies and precision problems in computing spherical arrangements while using floating point arithmetic. The scheme is relatively simple, it balances between the efficiency of computation and the magnitude of the perturbation, and it performs well in practice. In one O(n) time pass through the data, it perturbs the inputs necessary to insure no potential degeneracies and then passes the perturbed inputs on to the geometric algorithm. We report and discuss experimental results. Our package is a major component in a larger package aimed to support geometric queries on molecular models; it is currently employed by chemists working in "rational drug design." The spherical subdivisions are used to construct a geometric model of a molecule where each sphere represents an atom. We also give an overview of the molecular modeling package and detail additional features and implementation issues.

Automatic Qualitative Modeling of Dynamic Physical Systems

This report describes MM, a computer program that can model a variety of mechanical and fluid systems. Given a system's structure and qualitative behavior, MM searches for models using an energy-based modeling framework. MM uses general facts about physical systems to relate behavioral and model properties. These facts enable a more focussed search for models than would be obtained by mere comparison of desired and predicted behaviors. When these facts do not apply, MM uses behavior-constrained qualitative simulation to verify candidate models efficiently. MM can also design experiments to distinguish among multiple candidate models.

Understanding and Modeling the Behavior of a Harmonic Drive Gear Transmission

In my research, I have performed an extensive experimental investigation of harmonic-drive properties such as stiffness, friction, and kinematic error. From my experimental results, I have found that these properties can be sharply non-linear and highly dependent on operating conditions. Due to the complex interaction of these poorly behaved transmission properties, dynamic response measurements showed surprisingly agitated behavior, especially around system resonance. Theoretical models developed to mimic the observed response illustrated that non-linear frictional effects cannot be ignored in any accurate harmonic-drive representation. Additionally, if behavior around system resonance must be replicated, kinematic error and transmission compliance as well as frictional dissipation from gear-tooth rubbing must all be incorporated into the model.

Modeling of protein adsorption in membrane affinity chromatography

For the design of affinity membranes, protein adsorption in membrane affinity chromatography (MAC) was studied by frontal analysis. According to fast mass transfer, small thickness of affinity membranes and high affinity between the protein and the ligand, an ideal adsorption (IA) model was proposed for MAC and was used together with equilibrium-dispersive (E-D) model to describe the adsorption of bovine serum albumin (BSA) onto cellulose diacetate/polyethyleneimine (CA/PEI) blend membranes with and without Cu2+ chelating. E-D model was found to better describe the initial region of experimental breakthrough curves. The influence of axial dispersion was revealed and it showed the importance of design of the module to homogenously distribute feed solution. IA model was found to be better for the whole experimental breakthrough curve. According to it, the capacity of affinity membranes and the specificity of the interaction are of equal importance for the design of affinity membranes. An optimum feed concentration was also found in the operation of MAC. The discrepancy between experimental optimum feed concentrations and predicted ones from IA model may be due to the ignorance of some experimental effects such as axial dispersion.

Modeling of a compact plate-fin reformer for methanol steam reforming in fuel cell systems

The characteristics of a compact plate-fin reformer (PFR) which integrates endothermic and exothermic reactions into one unit have been investigated by experiment as well as by numerical simulation. One reforming chamber was integrated with two vaporization chambers and two combustion chambers to constitute a single unit of PFR. In the PFR, which is based on a plate-fin beat exchanger, catalytic combustion of the reforming gas is used to simulate the fuel cell anode off gas (AOG) which supplies the necessary heat for the methanol steam reforming. Temperature distributions in all chambers and composition distribution in reforming chamber have been studied, and the effect of the ratio of H2O/CH3OH on the performance of the PFR has also been investigated. A model of the PFR was derived using a three-dimensional numerical model for a cross-current flow arrangement. Theoretical predictions of the temperature distributions in the PFR were in good agreement with experimental values. In addition, the numerical model was able to accurately predict the methanol conversion and the reformate composition in reforming chamber. © 2005 Elsevier B.V. All rights reserved.

Modeling subauroral polarization streams equatorward of the plasmapause footprints

Pint?r, B.; Thom, S. D.; Balthazor, R.; Vo, H.; Bailey, G. J., Modeling subauroral polarization streams equatorward of the plasmapause footprints, Journal of Geophysical Research, Volume 111, Issue A10, CiteID A10306 RAE2008

APPLICATION OF THE KHOKHLOV-ZABOLOTSKAYA-KUZNETSOV EQUATION TO MODELING HIGH-INTENSITY FOCUSED ULTRASOUND BEAMS

High-intensity focused ultrasound is a form of therapeutic ultrasound which uses high amplitude acoustic waves to heat and ablate tissue. HIFU employs acoustic amplitudes that are high enough that nonlinear propagation effects are important in the evolution of the sound field. A common model for HIFU beams is the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation which accounts for nonlinearity, diffraction, and absorption. The KZK equation models diffraction using the parabolic or paraxial approximation. Many HIFU sources have an aperture diameter similar to the focal length and the paraxial approximation may not be appropriate. Here, results obtained using the “Texas code,” a time-domain numerical solution to the KZK equation, were used to assess when the KZK equation can be employed. In a linear water case comparison with the O’Neil solution, the KZK equation accurately predicts the pressure field in the focal region. The KZK equation was also compared to simulations of the exact fluid dynamics equations (no paraxial approximation). The exact equations were solved using the Fourier-Continuation (FC) method to approximate derivatives in the equations. Results have been obtained for a focused HIFU source in tissue. For a low focusing gain transducer (focal length 50λ and radius 10λ), the KZK and FC models showed excellent agreement, however, as the source radius was increased to 30λ, discrepancies started to appear. Modeling was extended to the case of tissue with the appropriate power law using a relaxation model. The relaxation model resulted in a higher peak pressure and a shift in the location of the peak pressure, highlighting the importance of employing the correct attenuation model. Simulations from the code that were compared to experimental data in water showed good agreement through the focal plane.

Iterative Linearized Density Matrix Propagation for Modeling Coherent Energy Transfer in Photosynthetic Light Harvesting

We present results of calculations [1] that employ a new mixed quantum classical iterative density matrix propagation approach (ILDM , or so called Is‐Landmap) [2] to explore the survival of coherence in different photo synthetic models. Our model studies confirm the long lived quantum coherence , while conventional theoretical tools (such as Redfield equation) fail to describe these phenomenon [3,4]. Our ILDM method is a numerical exactly propagation scheme and can be served as a bench mark calculation tools[2]. Result get from ILDM and from other recent methods have been compared and show agreement with each other[4,5]. Long lived coherence plateau has been attribute to the shift of harmonic potential due to the system bath interaction, and the harvesting efficiency is a balance between the coherence and dissipation[1]. We use this approach to investigate the excitation energy transfer dynamics in various light harvesting complex include Fenna‐Matthews‐Olsen light harvesting complex[1] and Cryptophyte Phycocyanin 645 [6]. [1] P.Huo and D.F.Coker ,J. Chem. Phys. 133, 184108 (2010) . [2] E.R. Dunkel, S. Bonella, and D.F. Coker, J. Chem. Phys. 129, 114106 (2008). [3] A. Ishizaki and G.R. Fleming, J. Chem. Phys. 130, 234111 (2009). [4] A. Ishizaki and G.R. Fleming, Proc. Natl. Acad. Sci. 106, 17255 (2009). [5] G. Tao and W.H. Miller, J. Phys. Chem. Lett. 1, 891 (2010). [6] P.Huo and D.F.Coker in preparation