Parallel Fully-Implicit Computation of MHD Acceleration Experiments

A three-dimensional MHD solver is described in the paper. The solver simulates reacting flows with nonequilibrium between translational-rotational, vibrational and electron translational modes. The conservation equations are discretized with implicit time marching and the second-order modified Steger-Warming scheme, and the resulted linear system is solved iteratively with Newton-Krylov-Schwarz method that is implemented by PETSc package. The results of convergence tests are plotted, which show good scalability and convergence around twice faster when compared with the DPLR method. Then five test runs are conducted simulating the experiments done at the NASA Ames MHD channel, and the calculated pressures, temperatures, electrical conductivity, back EMF, load factors and flow accelerations are shown to agree with the experimental data. Our computation shows that the electrical conductivity distribution is not uniform in the powered section of the MHD channel, and that it is important to include Joule heating in order to calculate the correct conductivity and the MHD acceleration.

A block SPP algorithm for multidimensional tridiagonal equations with optimal message vector length

A parallel strategy for solving multidimensional tridiagonal equations is investigated in this paper. We present in detail an improved version of single parallel partition (SPP) algorithm in conjunction with message vectorization, which aggregates several communication messages into one to reduce the communication cost. We show the resulting block SPP can achieve good speedup for a wide range of message vector length (MVL), especially when the number of grid points in the divided direction is large. Instead of only using the largest possible MVL, we adopt numerical tests and modeling analysis to determine an optimal MVL so that significant improvement in speedup can be obtained.

On optimal message vector length for block single parallel partition algorithm in a three-dimensional ADI solver

It has long been recognized that many direct parallel tridiagonal solvers are only efficient for solving a single tridiagonal equation of large sizes, and they become inefficient when naively used in a three-dimensional ADI solver. In order to improve the parallel efficiency of an ADI solver using a direct parallel solver, we implement the single parallel partition (SPP) algorithm in conjunction with message vectorization, which aggregates several communication messages into one to reduce the communication costs. The measured performances show that the longest allowable message vector length (MVL) is not necessarily the best choice. To understand this observation and optimize the performance, we propose an improved model that takes the cache effect into consideration. The optimal MVL for achieving the best performance is shown to depend on number of processors and grid sizes. Similar dependence of the optimal MVL is also found for the popular block pipelined method.

Molecular Modeling and Affinity Determination of scFv Antibody: Proper Linker Peptide Enhances Its Activity

One of existing strategies to engineer active antibody is to link VH and VL domains via a linker peptide. How the composition, length, and conformation of the linker affect antibody activity, however, remains poorly understood. In this study, a dual approach that coordinates molecule modeling, biological measurements, and affinity evaluation was developed to quantify the binding activity of a novel stable miniaturized anti-CD20 antibody or singlechain fragment variable (scFv) with a linker peptide. Upon computer-guided homology modeling, distance geometry analysis, and molecular superimposition and optimization, three new linker peptides PT1, PT2, and PT3 with respective 7, 10, and 15 residues were proposed and three engineered antibodies were then constructed by linking the cloned VH and VL domains and fusing to a derivative of human IgG1. The binding stability and activity of scFv-Fc chimera to CD20 antigen was quantified using a micropipette adhesion frequency assay and a Scatchard analysis. Our data indicated that the binding affinity was similar for the chimera with PT2 or PT3 and ~24-fold higher than that for the chimera with PT1, supporting theoretical predictions in molecular modeling. These results further the understanding in the impact of linker peptide on antibody structure and activity.

Physical Modeling And Parametric Study On Two-Degree-Of-Freedom Viv Of A Cylinder Near Rigid Wall

Unlike most previous studies on the transverse vortex-induced vibration(VIV) of a cylinder mainly under the wallfree condition (Williamson & Govardhan,2004),this paper experimentally investigates the vortex-induced vibration of a cylinder with two degrees of freedom near a rigid wall exposed to steady flow.The amplitude and frequency responses of the cylinder are discussed.The lee wake flow patterns of the cylinder undergoing VIV were visualized by employing the hydrogen bubble technique.The effects of the gap-to-diameter ratio (e0/D) and the mass ratio on the vibration amplitude and frequency are analyzed.Comparisons of VIV response of the cylinder are made between one degree (only transverse) and two degrees of freedom (streamwise and transverse) and those between the present study and previous ones.The experimental observation indicates that there are two types of streamwise vibration,i.e.the first streamwise vibration (FSV) with small amplitude and the second streamwise vibration (SSV) which coexists with transverse vibration.The vortex shedding pattem for the FSV is approximately symmetric and that for the SSV is alternate.The first streamwise vibration tends to disappear with the decrease of e0/D.For the case of large gap-to-diameter ratios (e.g.e0/D = 0.54～1.58),the maximum amplitudes of the second streamwise vibration and transverse one increase with the increasing gapto-diameter ratio.But for the case of small gap-to-diameter ratios (e.g.e0/D = 0.16,0.23),the vibration amplitude of the cylinder increases slowly at the initial stage (i.e.at small reduced velocity V,),and across the maximum amplitude it decreases quickly at the last stage (i.e.at large Vr).Within the range ofthe examined small mass ratio (m＜4),both streamwise and transverse vibration amplitude of the cylinder decrease with the increase of mass ratio for the fixed value of V,.The vibration range (in terms of Vr ) tends to widen with the decrease of the mass ratio.In the second streamwise vibration region,the vibration frequency of the cylinder with a small mass ratio (e.g.mx = 1.44) undergoes a jump at a certain Vr,.The maximum amplitudes of the transverse vibration for two-degree-of-freedom case is larger than that for one-degree-of-freedom case,but the transverse vibration frequency of the cylinder with two degrees of freedom is lower than that with one degree of freedom (transverse).

MODELING EVOLUTION OF INTERNAL WAVES IN SOUTH CHINA SEA

Internal waves are an important factor in the design of drill operations and production in deep water, because the waves have very large amplitude and may induce large horizontal velocity. How the internal waves occur and propagate over benthal terrain is of great concern for ocean engineers. In the present paper, we have formulated a mathematical model of internal wave propagation in a two-layer deep water, which involves the effects of friction, dissipation and shoaling, and is capable of manifesting the variation of the amplitude and the velocity pattern. After calibration by field data measured at the Continental Slope in the Northern South China Sea, we have applied the model to the South China Sea, investigating the westward propagation of internal waves from the Luzon Strait, where internal waves originate due to the interaction of benthal ridge and tides. We find that the internal wave induced velocity profile is obviously characterized by the opposite flow below and above the pycnocline, which results in a strong shear, threatening safety of ocean structures, such as mooring system of oil platform, risers, etc. When internal waves propagate westwards, the amplitude attenuates due to the effects of friction and dissipation. The preliminary results show that the amplitude is likely to become half of its initial value at Luzon Strait when the internal waves propagate about 400 kilometers westwards.

Modeling on Runoff and Sediment Yield in Small Watersheds

The prediction and estimate of water and soil loss is fundamental important for understanding the effect of the spatial heterogeneity of underlying surfaces and preventing ecological environment deterioration. In this paper, a dynamic model of runoff and sediment yield in small watersheds is established. The proposed model includes three components: runoff generation caused by rainfall, soil erosion on hillslopes by overland flow, and runoff concentration and sediment transport on watersheds. Applying the proposed model, the runoff and sediment yield processes in a typical catchment on the loess plateau was estimated, which exhibited a good agreement between predicted results and observation.

Movement of a Spherical Brownian Particle Between Infinite Parallel Plates: Hindered Dispersion and Sedimentation

The dispersion of an isolated, spherical, Brownian particle immersed in a Newtonian fluid between infinite parallel plates is investigated. Expressions are developed for both a 'molecular' contribution to dispersion, which arises from random thermal fluctuations, and a 'convective' contribution, arising when a shear flow is applied between the plates. These expressions are evaluated numerically for all sizes of the particle relative to the bounding plates, and the method of matched asymptotic expansions is used to develop analytical expressions for the dispersion coefficients as a function of particle size to plate spacing ratio for small values of this parameter.

It is shown that both the molecular and convective dispersion coefficients decrease as the size of the particle relative to the bounding plates increase. When the particle is small compared to the plate spacing, the coefficients decrease roughly proportional to the particle size to plate spacing ratio. When the particle closely fills the space between the plates, the molecular dispersion coefficient approaches zero slowly as an inverse logarithmic function of the particle size to plate spacing ratio, and the convective dispersion coefficent approaches zero approximately proportional to the width of the gap between the edges of the sphere and the bounding plates.

Stormwater runoff - modeling impacts of urbanization and climate change

Development pressure throughout the coastal areas of the United States continues to build, particularly in the southeast (Allen and Lu 2003, Crossett et al. 2004). It is well known that development alters watershed hydrology: as land becomes covered with surfaces impervious to rain, water is redirected from groundwater recharge and evapotranspiration to stormwater runoff, and as the area of impervious cover increases, so does the volume and rate of runoff (Schueler 1994, Corbett et al. 1997). Pollutants accumulate on impervious surfaces, and the increased runoff with urbanization is a leading cause of nonpoint source pollution (USEPA 2002). Sediment, chemicals, bacteria, viruses, and other pollutants are carried into receiving water bodies, resulting in degraded water quality (Holland et al. 2004, Sanger et al. 2008). (PDF contains 5 pages)

Nuclear Hartree-Fock calculations on parallel computers

Hartree-Fock (HF) calculations have had remarkable success in describing large nuclei at high spin, temperature and deformation. To allow full range of possible deformations, the Skyrme HF equations can be discretized on a three-dimensional mesh. However, such calculations are currently limited by the computational resources provided by traditional supercomputers. To take advantage of recent developments in massively parallel computing technology, we have implemented the LLNL Skyrme-force static and rotational HF codes on Intel's DELTA and GAMMA systems at Caltech.

We decomposed the HF code by assigning a portion of the mesh to each node, with nearest neighbor meshes assigned to nodes connected by communication· channels. This kind of decomposition is well-suited for the DELTA and the GAMMA architecture because the only non-local operations are wave function orthogonalization and the boundary conditions of the Poisson equation for the Coulomb field.

Our first application of the HF code on parallel computers has been the study of identical superdeformed (SD) rotational bands in the Hg region. In the last ten years, many SD rotational bands have been found experimentally. One very surprising feature found in these SD rotational bands is that many pairs of bands in nuclei that differ by one or two mass units have nearly identical deexcitation gamma-ray energies. Our calculations of the five rotational bands in ^(192)Hg and ^(194)Pb show that the filling of specific orbitals can lead to bands with deexcitation gamma-ray energies differing by at most 2 keV in nuclei differing by two mass units and over a range of angular momenta comparable to that observed experimentally. Our calculations of SD rotational bands in the Dy region also show that twinning can be achieved by filling or emptying some specific orbitals.

The interpretation of future precise experiments on atomic parity nonconservation (PNC) in terms of parameters of the Standard Model could be hampered by uncertainties in the atomic and nuclear structure. As a further application of the massively parallel HF calculations, we calculated the proton and neutron densities of the Cesium isotopes from A = 125 to A = 139. Based on our good agreement with experimental charge radii, binding energies, and ground state spins, we conclude that the uncertainties in the ratios of weak charges are less than 10^(-3), comfortably smaller than the anticipated experimental error.

Asymptotic scaling in the two-dimensional O(3) Nonlinear sigma model: a Monte Carlo study on parallel computers

We investigate the 2d O(3) model with the standard action by Monte Carlo simulation at couplings β up to 2.05. We measure the energy density, mass gap and susceptibility of the model, and gather high statistics on lattices of size L ≤ 1024 using the Floating Point Systems T-series vector hypercube and the Thinking Machines Corp.'s Connection Machine 2. Asymptotic scaling does not appear to set in for this action, even at β = 2.10, where the correlation length is 420. We observe a 20% difference between our estimate m/Λ^─_(Ms) = 3.52(6) at this β and the recent exact analytical result . We use the overrelaxation algorithm interleaved with Metropolis updates and show that decorrelation time scales with the correlation length and the number of overrelaxation steps per sweep. We determine its effective dynamical critical exponent to be z' = 1.079(10); thus critical slowing down is reduced significantly for this local algorithm that is vectorizable and parallelizable.

We also use the cluster Monte Carlo algorithms, which are non-local Monte Carlo update schemes which can greatly increase the efficiency of computer simulations of spin models. The major computational task in these algorithms is connected component labeling, to identify clusters of connected sites on a lattice. We have devised some new SIMD component labeling algorithms, and implemented them on the Connection Machine. We investigate their performance when applied to the cluster update of the two dimensional Ising spin model.

Finally we use a Monte Carlo Renormalization Group method to directly measure the couplings of block Hamiltonians at different blocking levels. For the usual averaging block transformation we confirm the renormalized trajectory (RT) observed by Okawa. For another improved probabilistic block transformation we find the RT, showing that it is much closer to the Standard Action. We then use this block transformation to obtain the discrete β-function of the model which we compare to the perturbative result. We do not see convergence, except when using a rescaled coupling β_E to effectively resum the series. For the latter case we see agreement for m/ Λ^─_(Ms) at , β = 2.14, 2.26, 2.38 and 2.50. To three loops m/Λ^─_(Ms) = 3.047(35) at β = 2.50, which is very close to the exact value m/ Λ^─_(Ms) = 2.943. Our last point at β = 2.62 disagrees with this estimate however.

Panel discussion: U.S. EPA using modeling and ecosystem services to enhance coastal decision making

This panel will discuss the research being conducted, and the models being used in three current coastal EPA studies being conducted on ecosystem services in Tampa Bay, the Chesapeake Bay and the Coastal Carolinas. These studies are intended to provide a broader and more comprehensive approach to policy and decision-making affecting coastal ecosystems as well as provide an account of valued services that have heretofore been largely unrecognized. Interim research products, including updated and integrated spatial data, models and model frameworks, and interactive decision support systems will be demonstrated to engage potential users and to elicit feedback. It is anticipated that the near-term impact of the projects will be to increase the awareness by coastal communities and coastal managers of the implications of their actions and to foster partnerships for ecosystem services research and applications. (PDF contains 4 pages)

Watershed monitoring and the TMDL modeling to assess bacterial loading in estuarine environments to improve management

Shellfish bed closures along the North Carolina coast have increased over the years seemingly concurrent with increases in population (Mallin 2000). More and faster flowing storm water has come to mean more bacteria, and fecal indicator bacterial (FIB) standards for shellfish harvesting are often exceeded when no source of contamination is readily apparent (Kator and Rhodes, 1994). Could management reduce bacterial loads if the source of the bacteria where known? Several potentially useful methods for differentiating human versus animal pollution sources have emerged including Ribotyping and Multiple Antibiotic Resistance (MAR) (US EPA, 2005). Total Maximum Daily Load (TMDL) studies on bacterial sources have been conducted for streams in NC mountain and Piedmont areas (U.S. EPA, 1991 and 2005) and are likely to be mandated for coastal waters. TMDL analysis estimates allowable pollutant loads and allocates them to known sources so management actions may be taken to restore water to its intended uses (U.S. EPA, 1991 and 2005). This project sought first to quantify and compare fecal contamination levels for three different types of land use on the coast, and second, to apply MAR and ribotyping techniques and assess their effectiveness for indentifying bacterial sources. Third, results from these studies would be applied to one watershed to develop a case study coastal TMDL. All three watershed study areas are within Carteret County, North Carolina. Jumping Run Creek and Pettiford Creek are within the White Oak River Basin management unit whereas the South River falls within the Neuse River Basin. Jumping Run Creek watershed encompasses approximately 320 ha. Its watershed was a dense, coastal pocosin on sandy, relic dune ridges, but current land uses are primarily medium density residential. Pettiford Creek is in the Croatan National Forest, is 1133 ha. and is basically undeveloped. The third study area is on Open Grounds Farm in the South River watershed. Half of the 630 ha. watershed is under cultivation with most under active water control (flashboard risers). The remaining portion is forested silviculture.(PDF contains 4 pages)