Science.gov

Sample records for adaptive local grid

  1. An Adaptive Unstructured Grid Method by Grid Subdivision, Local Remeshing, and Grid Movement

    NASA Technical Reports Server (NTRS)

    Pirzadeh, Shahyar Z.

    1999-01-01

    An unstructured grid adaptation technique has been developed and successfully applied to several three dimensional inviscid flow test cases. The approach is based on a combination of grid subdivision, local remeshing, and grid movement. For solution adaptive grids, the surface triangulation is locally refined by grid subdivision, and the tetrahedral grid in the field is partially remeshed at locations of dominant flow features. A grid redistribution strategy is employed for geometric adaptation of volume grids to moving or deforming surfaces. The method is automatic and fast and is designed for modular coupling with different solvers. Several steady state test cases with different inviscid flow features were tested for grid/solution adaptation. In all cases, the dominant flow features, such as shocks and vortices, were accurately and efficiently predicted with the present approach. A new and robust method of moving tetrahedral "viscous" grids is also presented and demonstrated on a three-dimensional example.

  2. Hierarchy-Direction Selective Approach for Locally Adaptive Sparse Grids

    SciTech Connect

    Stoyanov, Miroslav K

    2013-09-01

    We consider the problem of multidimensional adaptive hierarchical interpolation. We use sparse grids points and functions that are induced from a one dimensional hierarchical rule via tensor products. The classical locally adaptive sparse grid algorithm uses an isotropic refinement from the coarser to the denser levels of the hierarchy. However, the multidimensional hierarchy provides a more complex structure that allows for various anisotropic and hierarchy selective refinement techniques. We consider the more advanced refinement techniques and apply them to a number of simple test functions chosen to demonstrate the various advantages and disadvantages of each method. While there is no refinement scheme that is optimal for all functions, the fully adaptive family-direction-selective technique is usually more stable and requires fewer samples.

  3. Cosmos++: Relativistic Magnetohydrodynamics on Unstructured Grids with Local Adaptive Refinement

    SciTech Connect

    Anninos, P; Fragile, P C; Salmonson, J D

    2005-05-06

    A new code and methodology are introduced for solving the fully general relativistic magnetohydrodynamic (GRMHD) equations using time-explicit, finite-volume discretization. The code has options for solving the GRMHD equations using traditional artificial-viscosity (AV) or non-oscillatory central difference (NOCD) methods, or a new extended AV (eAV) scheme using artificial-viscosity together with a dual energy-flux-conserving formulation. The dual energy approach allows for accurate modeling of highly relativistic flows at boost factors well beyond what has been achieved to date by standard artificial viscosity methods. it provides the benefit of Godunov methods in capturing high Lorentz boosted flows but without complicated Riemann solvers, and the advantages of traditional artificial viscosity methods in their speed and flexibility. Additionally, the GRMHD equations are solved on an unstructured grid that supports local adaptive mesh refinement using a fully threated oct-tree (in three dimensions) network to traverse the grid hierarchy across levels and immediate neighbors. A number of tests are presented to demonstrate robustness of the numerical algorithms and adaptive mesh framework over a wide spectrum of problems, boosts, and astrophysical applications, including relativistic shock tubes, shock collisions, magnetosonic shocks, Alfven wave propagation, blast waves, magnetized Bondi flow, and the magneto-rotational instability in Kerr black hole spacetimes.

  4. AN OPTIMAL ADAPTIVE LOCAL GRID REFINEMENT APPROACH TO MODELING CONTAMINANT TRANSPORT

    EPA Science Inventory

    A Lagrangian-Eulerian method with an optimal adaptive local grid refinement is used to model contaminant transport equations. pplication of this approach to two bench-mark problems indicates that it completely resolves difficulties of peak clipping, numerical diffusion, and spuri...

  5. Interactive solution-adaptive grid generation

    NASA Technical Reports Server (NTRS)

    Choo, Yung K.; Henderson, Todd L.

    1992-01-01

    TURBO-AD is an interactive solution-adaptive grid generation program under development. The program combines an interactive algebraic grid generation technique and a solution-adaptive grid generation technique into a single interactive solution-adaptive grid generation package. The control point form uses a sparse collection of control points to algebraically generate a field grid. This technique provides local grid control capability and is well suited to interactive work due to its speed and efficiency. A mapping from the physical domain to a parametric domain was used to improve difficulties that had been encountered near outwardly concave boundaries in the control point technique. Therefore, all grid modifications are performed on a unit square in the parametric domain, and the new adapted grid in the parametric domain is then mapped back to the physical domain. The grid adaptation is achieved by first adapting the control points to a numerical solution in the parametric domain using control sources obtained from flow properties. Then a new modified grid is generated from the adapted control net. This solution-adaptive grid generation process is efficient because the number of control points is much less than the number of grid points and the generation of a new grid from the adapted control net is an efficient algebraic process. TURBO-AD provides the user with both local and global grid controls.

  6. Interactive solution-adaptive grid generation procedure

    NASA Technical Reports Server (NTRS)

    Henderson, Todd L.; Choo, Yung K.; Lee, Ki D.

    1992-01-01

    TURBO-AD is an interactive solution adaptive grid generation program under development. The program combines an interactive algebraic grid generation technique and a solution adaptive grid generation technique into a single interactive package. The control point form uses a sparse collection of control points to algebraically generate a field grid. This technique provides local grid control capability and is well suited to interactive work due to its speed and efficiency. A mapping from the physical domain to a parametric domain was used to improve difficulties encountered near outwardly concave boundaries in the control point technique. Therefore, all grid modifications are performed on the unit square in the parametric domain, and the new adapted grid is then mapped back to the physical domain. The grid adaption is achieved by adapting the control points to a numerical solution in the parametric domain using control sources obtained from the flow properties. Then a new modified grid is generated from the adapted control net. This process is efficient because the number of control points is much less than the number of grid points and the generation of the grid is an efficient algebraic process. TURBO-AD provides the user with both local and global controls.

  7. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

    Banks, D. W.; Hafez, M. M.

    1996-01-01

    Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.

  8. Grid quality improvement by a grid adaptation technique

    NASA Technical Reports Server (NTRS)

    Lee, K. D.; Henderson, T. L.; Choo, Y. K.

    1991-01-01

    A grid adaptation technique is presented which improves grid quality. The method begins with an assessment of grid quality by defining an appropriate grid quality measure. Then, undesirable grid properties are eliminated by a grid-quality-adaptive grid generation procedure. The same concept has been used for geometry-adaptive and solution-adaptive grid generation. The difference lies in the definition of the grid control sources; here, they are extracted from the distribution of a particular grid property. Several examples are presented to demonstrate the versatility and effectiveness of the method.

  9. Structured adaptive grid generation using algebraic methods

    NASA Technical Reports Server (NTRS)

    Yang, Jiann-Cherng; Soni, Bharat K.; Roger, R. P.; Chan, Stephen C.

    1993-01-01

    The accuracy of the numerical algorithm depends not only on the formal order of approximation but also on the distribution of grid points in the computational domain. Grid adaptation is a procedure which allows optimal grid redistribution as the solution progresses. It offers the prospect of accurate flow field simulations without the use of an excessively timely, computationally expensive, grid. Grid adaptive schemes are divided into two basic categories: differential and algebraic. The differential method is based on a variational approach where a function which contains a measure of grid smoothness, orthogonality and volume variation is minimized by using a variational principle. This approach provided a solid mathematical basis for the adaptive method, but the Euler-Lagrange equations must be solved in addition to the original governing equations. On the other hand, the algebraic method requires much less computational effort, but the grid may not be smooth. The algebraic techniques are based on devising an algorithm where the grid movement is governed by estimates of the local error in the numerical solution. This is achieved by requiring the points in the large error regions to attract other points and points in the low error region to repel other points. The development of a fast, efficient, and robust algebraic adaptive algorithm for structured flow simulation applications is presented. This development is accomplished in a three step process. The first step is to define an adaptive weighting mesh (distribution mesh) on the basis of the equidistribution law applied to the flow field solution. The second, and probably the most crucial step, is to redistribute grid points in the computational domain according to the aforementioned weighting mesh. The third and the last step is to reevaluate the flow property by an appropriate search/interpolate scheme at the new grid locations. The adaptive weighting mesh provides the information on the desired concentration

  10. Dynamic Load Balancing for Adaptive Unstructured Grids

    NASA Technical Reports Server (NTRS)

    Biswas, Rupak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Dynamic mesh adaptation on unstructured grids is a powerful tool for computing unsteady three-dimensional problems that require grid modifications to efficiently resolve solution features. By locally refining and coarsening the mesh to capture phenomena of interest, such procedures make standard computational methods more cost effective. Highly refined meshes are required to accurately capture shock waves, contact discontinuities, vortices, and shear layers in fluid flow problems. Adaptive meshes have also proved to be useful in several other areas of computational science and engineering like computer vision and graphics, semiconductor device modeling, and structural mechanics. Local mesh adaptation provides the opportunity to obtain solutions that are comparable to those obtained on globally-refined grids but at a much lower cost. Additional information is contained in the original extended abstract.

  11. LAPS Grid generation and adaptation

    NASA Astrophysics Data System (ADS)

    Pagliantini, Cecilia; Delzanno, Gia Luca; Guo, Zehua; Srinivasan, Bhuvana; Tang, Xianzhu; Chacon, Luis

    2011-10-01

    LAPS uses a common-data framework in which a general purpose grid generation and adaptation package in toroidal and simply connected domains is implemented. The initial focus is on implementing the Winslow/Laplace-Beltrami method for generating non-overlapping block structured grids. This is to be followed by a grid adaptation scheme based on Monge-Kantorovich optimal transport method [Delzanno et al., J. Comput. Phys,227 (2008), 9841-9864], that equidistributes application-specified error. As an initial set of applications, we will lay out grids for an axisymmetric mirror, a field reversed configuration, and an entire poloidal cross section of a tokamak plasma reconstructed from a CMOD experimental shot. These grids will then be used for computing the plasma equilibrium and transport in accompanying presentations. A key issue for Monge-Kantorovich grid optimization is the choice of error or monitor function for equi-distribution. We will compare the Operator Recovery Error Source Detector (ORESD) [Lapenta, Int. J. Num. Meth. Eng,59 (2004) 2065-2087], the Tau method and a strategy based on the grid coarsening [Zhang et al., AIAA J,39 (2001) 1706-1715] to find an ``optimal'' grid. Work supported by DOE OFES.

  12. SAGE - MULTIDIMENSIONAL SELF-ADAPTIVE GRID CODE

    NASA Technical Reports Server (NTRS)

    Davies, C. B.

    1994-01-01

    SAGE, Self Adaptive Grid codE, is a flexible tool for adapting and restructuring both 2D and 3D grids. Solution-adaptive grid methods are useful tools for efficient and accurate flow predictions. In supersonic and hypersonic flows, strong gradient regions such as shocks, contact discontinuities, shear layers, etc., require careful distribution of grid points to minimize grid error and produce accurate flow-field predictions. SAGE helps the user obtain more accurate solutions by intelligently redistributing (i.e. adapting) the original grid points based on an initial or interim flow-field solution. The user then computes a new solution using the adapted grid as input to the flow solver. The adaptive-grid methodology poses the problem in an algebraic, unidirectional manner for multi-dimensional adaptations. The procedure is analogous to applying tension and torsion spring forces proportional to the local flow gradient at every grid point and finding the equilibrium position of the resulting system of grid points. The multi-dimensional problem of grid adaption is split into a series of one-dimensional problems along the computational coordinate lines. The reduced one dimensional problem then requires a tridiagonal solver to find the location of grid points along a coordinate line. Multi-directional adaption is achieved by the sequential application of the method in each coordinate direction. The tension forces direct the redistribution of points to the strong gradient region. To maintain smoothness and a measure of orthogonality of grid lines, torsional forces are introduced that relate information between the family of lines adjacent to one another. The smoothness and orthogonality constraints are direction-dependent, since they relate only the coordinate lines that are being adapted to the neighboring lines that have already been adapted. Therefore the solutions are non-unique and depend on the order and direction of adaption. Non-uniqueness of the adapted grid is

  13. Near-Body Grid Adaption for Overset Grids

    NASA Technical Reports Server (NTRS)

    Buning, Pieter G.; Pulliam, Thomas H.

    2016-01-01

    A solution adaption capability for curvilinear near-body grids has been implemented in the OVERFLOW overset grid computational fluid dynamics code. The approach follows closely that used for the Cartesian off-body grids, but inserts refined grids in the computational space of original near-body grids. Refined curvilinear grids are generated using parametric cubic interpolation, with one-sided biasing based on curvature and stretching ratio of the original grid. Sensor functions, grid marking, and solution interpolation tasks are implemented in the same fashion as for off-body grids. A goal-oriented procedure, based on largest error first, is included for controlling growth rate and maximum size of the adapted grid system. The adaption process is almost entirely parallelized using MPI, resulting in a capability suitable for viscous, moving body simulations. Two- and three-dimensional examples are presented.

  14. Adaptive EAGLE dynamic solution adaptation and grid quality enhancement

    NASA Technical Reports Server (NTRS)

    Luong, Phu Vinh; Thompson, J. F.; Gatlin, B.; Mastin, C. W.; Kim, H. J.

    1992-01-01

    In the effort described here, the elliptic grid generation procedure in the EAGLE grid code was separated from the main code into a subroutine, and a new subroutine which evaluates several grid quality measures at each grid point was added. The elliptic grid routine can now be called, either by a computational fluid dynamics (CFD) code to generate a new adaptive grid based on flow variables and quality measures through multiple adaptation, or by the EAGLE main code to generate a grid based on quality measure variables through static adaptation. Arrays of flow variables can be read into the EAGLE grid code for use in static adaptation as well. These major changes in the EAGLE adaptive grid system make it easier to convert any CFD code that operates on a block-structured grid (or single-block grid) into a multiple adaptive code.

  15. On Accuracy of Adaptive Grid Methods for Captured Shocks

    NASA Technical Reports Server (NTRS)

    Yamaleev, Nail K.; Carpenter, Mark H.

    2002-01-01

    The accuracy of two grid adaptation strategies, grid redistribution and local grid refinement, is examined by solving the 2-D Euler equations for the supersonic steady flow around a cylinder. Second- and fourth-order linear finite difference shock-capturing schemes, based on the Lax-Friedrichs flux splitting, are used to discretize the governing equations. The grid refinement study shows that for the second-order scheme, neither grid adaptation strategy improves the numerical solution accuracy compared to that calculated on a uniform grid with the same number of grid points. For the fourth-order scheme, the dominant first-order error component is reduced by the grid adaptation, while the design-order error component drastically increases because of the grid nonuniformity. As a result, both grid adaptation techniques improve the numerical solution accuracy only on the coarsest mesh or on very fine grids that are seldom found in practical applications because of the computational cost involved. Similar error behavior has been obtained for the pressure integral across the shock. A simple analysis shows that both grid adaptation strategies are not without penalties in the numerical solution accuracy. Based on these results, a new grid adaptation criterion for captured shocks is proposed.

  16. Discontinuous finite element solution of the radiation diffusion equation on arbitrary polygonal meshes and locally adapted quadrilateral grids

    SciTech Connect

    Ragusa, Jean C.

    2015-01-01

    In this paper, we propose a piece-wise linear discontinuous (PWLD) finite element discretization of the diffusion equation for arbitrary polygonal meshes. It is based on the standard diffusion form and uses the symmetric interior penalty technique, which yields a symmetric positive definite linear system matrix. A preconditioned conjugate gradient algorithm is employed to solve the linear system. Piece-wise linear approximations also allow a straightforward implementation of local mesh adaptation by allowing unrefined cells to be interpreted as polygons with an increased number of vertices. Several test cases, taken from the literature on the discretization of the radiation diffusion equation, are presented: random, sinusoidal, Shestakov, and Z meshes are used. The last numerical example demonstrates the application of the PWLD discretization to adaptive mesh refinement.

  17. An adaptive grid with directional control

    NASA Technical Reports Server (NTRS)

    Brackbill, J. U.

    1993-01-01

    An adaptive grid generator for adaptive node movement is here derived by combining a variational formulation of Winslow's (1981) variable-diffusion method with a directional control functional. By applying harmonic-function theory, it becomes possible to define conditions under which there exist unique solutions of the resulting elliptic equations. The results obtained for the grid generator's application to the complex problem posed by the fluid instability-driven magnetic field reconnection demonstrate one-tenth the computational cost of either a Eulerian grid or an adaptive grid without directional control.

  18. Coupling a local adaptive grid refinement technique with an interface sharpening scheme for the simulation of two-phase flow and free-surface flows using VOF methodology

    NASA Astrophysics Data System (ADS)

    Malgarinos, Ilias; Nikolopoulos, Nikolaos; Gavaises, Manolis

    2015-11-01

    This study presents the implementation of an interface sharpening scheme on the basis of the Volume of Fluid (VOF) method, as well as its application in a number of theoretical and real cases usually modelled in literature. More specifically, the solution of an additional sharpening equation along with the standard VOF model equations is proposed, offering the advantage of "restraining" interface numerical diffusion, while also keeping a quite smooth induced velocity field around the interface. This sharpening equation is solved right after volume fraction advection; however a novel method for its coupling with the momentum equation has been applied in order to save computational time. The advantages of the proposed sharpening scheme lie on the facts that a) it is mass conservative thus its application does not have a negative impact on one of the most important benefits of VOF method and b) it can be used in coarser grids as now the suppression of the numerical diffusion is grid independent. The coupling of the solved equation with an adaptive local grid refinement technique is used for further decrease of computational time, while keeping high levels of accuracy at the area of maximum interest (interface). The numerical algorithm is initially tested against two theoretical benchmark cases for interface tracking methodologies followed by its validation for the case of a free-falling water droplet accelerated by gravity, as well as the normal liquid droplet impingement onto a flat substrate. Results indicate that the coupling of the interface sharpening equation with the HRIC discretization scheme used for volume fraction flux term, not only decreases the interface numerical diffusion, but also allows the induced velocity field to be less perturbed owed to spurious velocities across the liquid-gas interface. With the use of the proposed algorithmic flow path, coarser grids can replace finer ones at the slight expense of accuracy.

  19. An Adaptive VOF Method on Unstructured Grid

    NASA Astrophysics Data System (ADS)

    Wu, L. L.; Huang, M.; Chen, B.

    2011-09-01

    In order to improve the accuracy of interface capturing and keeping the computational efficiency, an adaptive VOF method on unstructured grid is proposed in this paper. The volume fraction in each cell is regarded as the criterion to locally refine the interface cell. With the movement of interface, new interface cells (0 ≤ f ≤ 1) are subdivided into child cells, while those child cells that no longer contain interface will be merged back into the original parent cell. In order to avoid the complicated redistribution of volume fraction during the subdivision and amalgamation procedure, a predictor-corrector algorithm is proposed to implement the subdivision and amalgamation procedures only in empty or full cell ( f = 0 or 1). Thus volume fraction in the new cell can take the value from the original cell directly, and the interpolation of the interface is avoided. The advantage of this method is that the re-generation of the whole grid system is not necessary, so its implementation is very efficient. Moreover, an advection flow test of a hollow square was performed, and the relative shape error of the result obtained by adaptive mesh is smaller than those by non-refined grid, which verifies the validation of our method.

  20. The fundamentals of adaptive grid movement

    NASA Technical Reports Server (NTRS)

    Eiseman, Peter R.

    1990-01-01

    Basic grid point movement schemes are studied. The schemes are referred to as adaptive grids. Weight functions and equidistribution in one dimension are treated. The specification of coefficients in the linear weight, attraction to a given grid or a curve, and evolutionary forces are considered. Curve by curve and finite volume methods are described. The temporal coupling of partial differential equations solvers and grid generators was discussed.

  1. Grid adaptation using chimera composite overlapping meshes

    NASA Technical Reports Server (NTRS)

    Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen

    1994-01-01

    The objective of this paper is to perform grid adaptation using composite overlapping meshes in regions of large gradient to accurately capture the salient features during computation. The chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using trilinear interpolation. Application to the Euler equations for shock reflections and to shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well-resolved.

  2. Grid adaptation using Chimera composite overlapping meshes

    NASA Technical Reports Server (NTRS)

    Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen

    1993-01-01

    The objective of this paper is to perform grid adaptation using composite over-lapping meshes in regions of large gradient to capture the salient features accurately during computation. The Chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using tri-linear interpolation. Applications to the Euler equations for shock reflections and to a shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well resolved.

  3. Grid adaption using Chimera composite overlapping meshes

    NASA Technical Reports Server (NTRS)

    Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen

    1993-01-01

    The objective of this paper is to perform grid adaptation using composite over-lapping meshes in regions of large gradient to capture the salient features accurately during computation. The Chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using tri-linear interpolation. Applications to the Euler equations for shock reflections and to a shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well resolved.

  4. Adaptive grid generation in a patient-specific cerebral aneurysm.

    PubMed

    Hodis, Simona; Kallmes, David F; Dragomir-Daescu, Dan

    2013-11-01

    Adapting grid density to flow behavior provides the advantage of increasing solution accuracy while decreasing the number of grid elements in the simulation domain, therefore reducing the computational time. One method for grid adaptation requires successive refinement of grid density based on observed solution behavior until the numerical errors between successive grids are negligible. However, such an approach is time consuming and it is often neglected by the researchers. We present a technique to calculate the grid size distribution of an adaptive grid for computational fluid dynamics (CFD) simulations in a complex cerebral aneurysm geometry based on the kinematic curvature and torsion calculated from the velocity field. The relationship between the kinematic characteristics of the flow and the element size of the adaptive grid leads to a mathematical equation to calculate the grid size in different regions of the flow. The adaptive grid density is obtained such that it captures the more complex details of the flow with locally smaller grid size, while less complex flow characteristics are calculated on locally larger grid size. The current study shows that kinematic curvature and torsion calculated from the velocity field in a cerebral aneurysm can be used to find the locations of complex flow where the computational grid needs to be refined in order to obtain an accurate solution. We found that the complexity of the flow can be adequately described by velocity and vorticity and the angle between the two vectors. For example, inside the aneurysm bleb, at the bifurcation, and at the major arterial turns the element size in the lumen needs to be less than 10% of the artery radius, while at the boundary layer, the element size should be smaller than 1% of the artery radius, for accurate results within a 0.5% relative approximation error. This technique of quantifying flow complexity and adaptive remeshing has the potential to improve results accuracy and reduce

  5. Adaptive grid generation in a patient-specific cerebral aneurysm

    NASA Astrophysics Data System (ADS)

    Hodis, Simona; Kallmes, David F.; Dragomir-Daescu, Dan

    2013-11-01

    Adapting grid density to flow behavior provides the advantage of increasing solution accuracy while decreasing the number of grid elements in the simulation domain, therefore reducing the computational time. One method for grid adaptation requires successive refinement of grid density based on observed solution behavior until the numerical errors between successive grids are negligible. However, such an approach is time consuming and it is often neglected by the researchers. We present a technique to calculate the grid size distribution of an adaptive grid for computational fluid dynamics (CFD) simulations in a complex cerebral aneurysm geometry based on the kinematic curvature and torsion calculated from the velocity field. The relationship between the kinematic characteristics of the flow and the element size of the adaptive grid leads to a mathematical equation to calculate the grid size in different regions of the flow. The adaptive grid density is obtained such that it captures the more complex details of the flow with locally smaller grid size, while less complex flow characteristics are calculated on locally larger grid size. The current study shows that kinematic curvature and torsion calculated from the velocity field in a cerebral aneurysm can be used to find the locations of complex flow where the computational grid needs to be refined in order to obtain an accurate solution. We found that the complexity of the flow can be adequately described by velocity and vorticity and the angle between the two vectors. For example, inside the aneurysm bleb, at the bifurcation, and at the major arterial turns the element size in the lumen needs to be less than 10% of the artery radius, while at the boundary layer, the element size should be smaller than 1% of the artery radius, for accurate results within a 0.5% relative approximation error. This technique of quantifying flow complexity and adaptive remeshing has the potential to improve results accuracy and reduce

  6. Adaptive refinement tools for tetrahedral unstructured grids

    NASA Technical Reports Server (NTRS)

    Pao, S. Paul (Inventor); Abdol-Hamid, Khaled S. (Inventor)

    2011-01-01

    An exemplary embodiment providing one or more improvements includes software which is robust, efficient, and has a very fast run time for user directed grid enrichment and flow solution adaptive grid refinement. All user selectable options (e.g., the choice of functions, the choice of thresholds, etc.), other than a pre-marked cell list, can be entered on the command line. The ease of application is an asset for flow physics research and preliminary design CFD analysis where fast grid modification is often needed to deal with unanticipated development of flow details.

  7. Load Balancing Sequences of Unstructured Adaptive Grids

    NASA Technical Reports Server (NTRS)

    Biswas, Rupak; Oliker, Leonid

    1997-01-01

    Mesh adaption is a powerful tool for efficient unstructured grid computations but causes load imbalance on multiprocessor systems. To address this problem, we have developed PLUM, an automatic portable framework for performing adaptive large-scale numerical computations in a message-passing environment. This paper makes several important additions to our previous work. First, a new remapping cost model is presented and empirically validated on an SP2. Next, our load balancing strategy is applied to sequences of dynamically adapted unstructured grids. Results indicate that our framework is effective on many processors for both steady and unsteady problems with several levels of adaption. Additionally, we demonstrate that a coarse starting mesh produces high quality load balancing, at a fraction of the cost required for a fine initial mesh. Finally, we show that the data remapping overhead can be significantly reduced by applying our heuristic processor reassignment algorithm.

  8. Self-Avoiding Walks Over Adaptive Triangular Grids

    NASA Technical Reports Server (NTRS)

    Heber, Gerd; Biswas, Rupak; Gao, Guang R.; Saini, Subhash (Technical Monitor)

    1999-01-01

    Space-filling curves is a popular approach based on a geometric embedding for linearizing computational meshes. We present a new O(n log n) combinatorial algorithm for constructing a self avoiding walk through a two dimensional mesh containing n triangles. We show that for hierarchical adaptive meshes, the algorithm can be locally adapted and easily parallelized by taking advantage of the regularity of the refinement rules. The proposed approach should be very useful in the runtime partitioning and load balancing of adaptive unstructured grids.

  9. Elliptic Solvers for Adaptive Mesh Refinement Grids

    SciTech Connect

    Quinlan, D.J.; Dendy, J.E., Jr.; Shapira, Y.

    1999-06-03

    We are developing multigrid methods that will efficiently solve elliptic problems with anisotropic and discontinuous coefficients on adaptive grids. The final product will be a library that provides for the simplified solution of such problems. This library will directly benefit the efforts of other Laboratory groups. The focus of this work is research on serial and parallel elliptic algorithms and the inclusion of our black-box multigrid techniques into this new setting. The approach applies the Los Alamos object-oriented class libraries that greatly simplify the development of serial and parallel adaptive mesh refinement applications. In the final year of this LDRD, we focused on putting the software together; in particular we completed the final AMR++ library, we wrote tutorials and manuals, and we built example applications. We implemented the Fast Adaptive Composite Grid method as the principal elliptic solver. We presented results at the Overset Grid Conference and other more AMR specific conferences. We worked on optimization of serial and parallel performance and published several papers on the details of this work. Performance remains an important issue and is the subject of continuing research work.

  10. The emergence of grid cells: Intelligent design or just adaptation?

    PubMed

    Kropff, Emilio; Treves, Alessandro

    2008-01-01

    Individual medial entorhinal cortex (mEC) 'grid' cells provide a representation of space that appears to be essentially invariant across environments, modulo simple transformations, in contrast to multiple, rapidly acquired hippocampal maps; it may therefore be established gradually during rodent development. We explore with a simplified mathematical model the possibility that the self-organization of multiple grid fields into a triangular grid pattern may be a single-cell process, driven by firing rate adaptation and slowly varying spatial inputs. A simple analytical derivation indicates that triangular grids are favored asymptotic states of the self-organizing system, and computer simulations confirm that such states are indeed reached during a model learning process, provided it is sufficiently slow to effectively average out fluctuations. The interactions among local ensembles of grid units serve solely to stabilize a common grid orientation. Spatial information, in the real mEC network, may be provided by any combination of feedforward cortical afferents and feedback hippocampal projections from place cells, since either input alone is likely sufficient to yield grid fields. PMID:19021261

  11. Vortical Flow Prediction Using an Adaptive Unstructured Grid Method

    NASA Technical Reports Server (NTRS)

    Pirzadeh, Shahyar Z.

    2003-01-01

    A computational fluid dynamics (CFD) method has been employed to compute vortical flows around slender wing/body configurations. The emphasis of the paper is on the effectiveness of an adaptive grid procedure in "capturing" concentrated vortices generated at sharp edges or flow separation lines of lifting surfaces flying at high angles of attack. The method is based on a tetrahedral unstructured grid technology developed at the NASA Langley Research Center. Two steady-state, subsonic, inviscid and Navier-Stokes flow test cases are presented to demonstrate the applicability of the method for solving practical vortical flow problems. The first test case concerns vortex flow over a simple 65 delta wing with different values of leading-edge radius. Although the geometry is quite simple, it poses a challenging problem for computing vortices originating from blunt leading edges. The second case is that of a more complex fighter configuration. The superiority of the adapted solutions in capturing the vortex flow structure over the conventional unadapted results is demonstrated by comparisons with the wind-tunnel experimental data. The study shows that numerical prediction of vortical flows is highly sensitive to the local grid resolution and that the implementation of grid adaptation is essential when applying CFD methods to such complicated flow problems.

  12. Vortical Flow Prediction Using an Adaptive Unstructured Grid Method

    NASA Technical Reports Server (NTRS)

    Pirzadeh, Shahyar Z.

    2001-01-01

    A computational fluid dynamics (CFD) method has been employed to compute vortical flows around slender wing/body configurations. The emphasis of the paper is on the effectiveness of an adaptive grid procedure in "capturing" concentrated vortices generated at sharp edges or flow separation lines of lifting surfaces flying at high angles of attack. The method is based on a tetrahedral unstructured grid technology developed at the NASA Langley Research Center. Two steady-state, subsonic, inviscid and Navier-Stokes flow test cases are presented to demonstrate the applicability of the method for solving practical vortical flow problems. The first test case concerns vortex flow over a simple 65deg delta wing with different values of leading-edge bluntness, and the second case is that of a more complex fighter configuration. The superiority of the adapted solutions in capturing the vortex flow structure over the conventional unadapted results is demonstrated by comparisons with the windtunnel experimental data. The study shows that numerical prediction of vortical flows is highly sensitive to the local grid resolution and that the implementation of grid adaptation is essential when applying CFD methods to such complicated flow problems.

  13. Three-dimensional adaptive grid generation for body-fitted coordinate system

    NASA Astrophysics Data System (ADS)

    Chen, S. C.

    1988-08-01

    This report describes a numerical method for generating 3-D grids for general configurations. The basic method involves the solution of a set of quasi-linear elliptic partial differential equations via pointwise relaxation with a local relaxation factor. It allows specification of the grid spacing off the boundary surfaces and the grid orthogonality at the boundary surfaces. It includes adaptive mechanisms to improve smoothness, orthogonality, and flow resolution in the grid interior.

  14. Three-dimensional adaptive grid generation for body-fitted coordinate system

    NASA Astrophysics Data System (ADS)

    Chen, S. C.

    This report describes a numerical method for generating 3-D grids for general configurations. The basic method involves the solution of a set of quasi-linear elliptic partial differential equations via pointwise relaxation with a local relaxation factor. It allows specification of the grid spacing off the boundary surfaces and the grid orthogonality at the boundary surfaces. It includes adaptive mechanisms to improve smoothness, orthogonality, and flow resolution in the grid interior.

  15. A local coastal adaptation pathway

    NASA Astrophysics Data System (ADS)

    Barnett, J.; Graham, S.; Mortreux, C.; Fincher, R.; Waters, E.; Hurlimann, A.

    2014-12-01

    Local governments are not adapting to sea-level rise because it is difficult to build consensus on the need for change and the best way to implement it. In theory, adaptation pathways can resolve this impasse. Adaptation pathways are a sequence of linked strategies that are triggered by a change in environmental conditions, and in which initial decisions can have low regrets and preserve options for future generations. We report on a project that sought to empirically test the relevance and feasibility of a local pathway for adapting to sea-level rise. We find that triggers of change that have social impacts are salient to local people, and developing a local adaptation pathway helps build consensus among diverse constituencies. Our results show that adaptation pathways are feasible at the local scale, offering a low-risk, low-cost way to begin the long process of adaptation to sea-level rise.

  16. Shape optimization including finite element grid adaptation

    NASA Technical Reports Server (NTRS)

    Kikuchi, N.; Taylor, J. E.

    1984-01-01

    The prediction of optimal shape design for structures depends on having a sufficient level of precision in the computation of structural response. These requirements become critical in situations where the region to be designed includes stress concentrations or unilateral contact surfaces, for example. In the approach to shape optimization discussed here, a means to obtain grid adaptation is incorporated into the finite element procedures. This facility makes it possible to maintain a level of quality in the computational estimate of response that is surely adequate for the shape design problem.

  17. Conservative Smoothing on an Adaptive Quadrilateral Grid

    NASA Astrophysics Data System (ADS)

    Sun, M.; Takayama, K.

    1999-03-01

    The Lax-Wendroff scheme can be freed of spurious oscillations by introducing conservative smoothing. In this paper the approach is first tested in 1-D modeling equations and then extended to multidimensional flows by the finite volume method. The scheme is discretized by a space-splitting method on an adaptive quadrilateral grid. The artificial viscosity coefficients in the conservative smoothing step are specially designed to capture slipstreams and vortices. Algorithms are programmed using a vectorizable data structure, under which not only the flow solver but also the adaptation procedure is well vectorized. The good resolution and high efficiency of the approach are demonstrated in calculating both unsteady and steady compressible flows with either weak or strong shock waves.

  18. Adaptive grid methods for RLV environment assessment and nozzle analysis

    NASA Technical Reports Server (NTRS)

    Thornburg, Hugh J.

    1996-01-01

    Rapid access to highly accurate data about complex configurations is needed for multi-disciplinary optimization and design. In order to efficiently meet these requirements a closer coupling between the analysis algorithms and the discretization process is needed. In some cases, such as free surface, temporally varying geometries, and fluid structure interaction, the need is unavoidable. In other cases the need is to rapidly generate and modify high quality grids. Techniques such as unstructured and/or solution-adaptive methods can be used to speed the grid generation process and to automatically cluster mesh points in regions of interest. Global features of the flow can be significantly affected by isolated regions of inadequately resolved flow. These regions may not exhibit high gradients and can be difficult to detect. Thus excessive resolution in certain regions does not necessarily increase the accuracy of the overall solution. Several approaches have been employed for both structured and unstructured grid adaption. The most widely used involve grid point redistribution, local grid point enrichment/derefinement or local modification of the actual flow solver. However, the success of any one of these methods ultimately depends on the feature detection algorithm used to determine solution domain regions which require a fine mesh for their accurate representation. Typically, weight functions are constructed to mimic the local truncation error and may require substantial user input. Most problems of engineering interest involve multi-block grids and widely disparate length scales. Hence, it is desirable that the adaptive grid feature detection algorithm be developed to recognize flow structures of different type as well as differing intensity, and adequately address scaling and normalization across blocks. These weight functions can then be used to construct blending functions for algebraic redistribution, interpolation functions for unstructured grid generation

  19. A wavelet-optimized, very high order adaptive grid and order numerical method

    NASA Technical Reports Server (NTRS)

    Jameson, Leland

    1996-01-01

    Differencing operators of arbitrarily high order can be constructed by interpolating a polynomial through a set of data followed by differentiation of this polynomial and finally evaluation of the polynomial at the point where a derivative approximation is desired. Furthermore, the interpolating polynomial can be constructed from algebraic, trigonometric, or, perhaps exponential polynomials. This paper begins with a comparison of such differencing operator construction. Next, the issue of proper grids for high order polynomials is addressed. Finally, an adaptive numerical method is introduced which adapts the numerical grid and the order of the differencing operator depending on the data. The numerical grid adaptation is performed on a Chebyshev grid. That is, at each level of refinement the grid is a Chebvshev grid and this grid is refined locally based on wavelet analysis.

  20. Dynamic mesh adaption for triangular and tetrahedral grids

    NASA Technical Reports Server (NTRS)

    Biswas, Rupak; Strawn, Roger

    1993-01-01

    The following topics are discussed: requirements for dynamic mesh adaption; linked-list data structure; edge-based data structure; adaptive-grid data structure; three types of element subdivision; mesh refinement; mesh coarsening; additional constraints for coarsening; anisotropic error indicator for edges; unstructured-grid Euler solver; inviscid 3-D wing; and mesh quality for solution-adaptive grids. The discussion is presented in viewgraph form.

  1. JPEG 2000 coding of image data over adaptive refinement grids

    NASA Astrophysics Data System (ADS)

    Gamito, Manuel N.; Dias, Miguel S.

    2003-06-01

    An extension of the JPEG 2000 standard is presented for non-conventional images resulting from an adaptive subdivision process. Samples, generated through adaptive subdivision, can have different sizes, depending on the amount of subdivision that was locally introduced in each region of the image. The subdivision principle allows each individual sample to be recursively subdivided into sets of four progressively smaller samples. Image datasets generated through adaptive subdivision find application in Computational Physics where simulations of natural processes are often performed over adaptive grids. It is also found that compression gains can be achieved for non-natural imagery, like text or graphics, if they first undergo an adaptive subdivision process. The representation of adaptive subdivision images is performed by first coding the subdivision structure into the JPEG 2000 bitstream, ina lossless manner, followed by the entropy coded and quantized transform coefficients. Due to the irregular distribution of sample sizes across the image, the wavelet transform must be applied on irregular image subsets that are nested across all the resolution levels. Using the conventional JPEG 2000 coding standard, adaptive subdivision images would first have to be upsampled to the smallest sample size in order to attain a uniform resolution. The proposed method for coding adaptive subdivision images is shown to perform better than conventional JPEG 2000 for medium to high bitrates.

  2. Parallel architectures for iterative methods on adaptive, block structured grids

    NASA Technical Reports Server (NTRS)

    Gannon, D.; Vanrosendale, J.

    1983-01-01

    A parallel computer architecture well suited to the solution of partial differential equations in complicated geometries is proposed. Algorithms for partial differential equations contain a great deal of parallelism. But this parallelism can be difficult to exploit, particularly on complex problems. One approach to extraction of this parallelism is the use of special purpose architectures tuned to a given problem class. The architecture proposed here is tuned to boundary value problems on complex domains. An adaptive elliptic algorithm which maps effectively onto the proposed architecture is considered in detail. Two levels of parallelism are exploited by the proposed architecture. First, by making use of the freedom one has in grid generation, one can construct grids which are locally regular, permitting a one to one mapping of grids to systolic style processor arrays, at least over small regions. All local parallelism can be extracted by this approach. Second, though there may be a regular global structure to the grids constructed, there will be parallelism at this level. One approach to finding and exploiting this parallelism is to use an architecture having a number of processor clusters connected by a switching network. The use of such a network creates a highly flexible architecture which automatically configures to the problem being solved.

  3. Techniques for grid manipulation and adaptation. [computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Choo, Yung K.; Eisemann, Peter R.; Lee, Ki D.

    1992-01-01

    Two approaches have been taken to provide systematic grid manipulation for improved grid quality. One is the control point form (CPF) of algebraic grid generation. It provides explicit control of the physical grid shape and grid spacing through the movement of the control points. It works well in the interactive computer graphics environment and hence can be a good candidate for integration with other emerging technologies. The other approach is grid adaptation using a numerical mapping between the physical space and a parametric space. Grid adaptation is achieved by modifying the mapping functions through the effects of grid control sources. The adaptation process can be repeated in a cyclic manner if satisfactory results are not achieved after a single application.

  4. Comparing Anisotropic Output-Based Grid Adaptation Methods by Decomposition

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Loseille, Adrien; Krakos, Joshua A.; Michal, Todd

    2015-01-01

    Anisotropic grid adaptation is examined by decomposing the steps of flow solution, ad- joint solution, error estimation, metric construction, and simplex grid adaptation. Multiple implementations of each of these steps are evaluated by comparison to each other and expected analytic results when available. For example, grids are adapted to analytic metric fields and grid measures are computed to illustrate the properties of multiple independent implementations of grid adaptation mechanics. Different implementations of each step in the adaptation process can be evaluated in a system where the other components of the adaptive cycle are fixed. Detailed examination of these properties allows comparison of different methods to identify the current state of the art and where further development should be targeted.

  5. Adaptive-grid methods for time-dependent partial differential equations

    SciTech Connect

    Hedstrom, G.W.; Rodrique, G.H.

    1981-01-01

    This paper contains a survey of recent developments of adaptive-grid algorithms for time-dependent partial differential equations. Two lines of research are discussed. One involves the automatic selection of moving grids to follow propagating waves. The other is based on stationary grids but uses local mesh refinement in both space and time. Advantages and disadvantages of both approaches are discussed. The development of adaptive-grid schemes shows promise of greatly increasing our ability to solve problems in several spatial dimensions.

  6. A Solution Adaptive Technique Using Tetrahedral Unstructured Grids

    NASA Technical Reports Server (NTRS)

    Pirzadeh, Shahyar Z.

    2000-01-01

    An adaptive unstructured grid refinement technique has been developed and successfully applied to several three dimensional inviscid flow test cases. The method is based on a combination of surface mesh subdivision and local remeshing of the volume grid Simple functions of flow quantities are employed to detect dominant features of the flowfield The method is designed for modular coupling with various error/feature analyzers and flow solvers. Several steady-state, inviscid flow test cases are presented to demonstrate the applicability of the method for solving practical three-dimensional problems. In all cases, accurate solutions featuring complex, nonlinear flow phenomena such as shock waves and vortices have been generated automatically and efficiently.

  7. Moving and adaptive grid methods for compressible flows

    NASA Technical Reports Server (NTRS)

    Trepanier, Jean-Yves; Camarero, Ricardo

    1995-01-01

    This paper describes adaptive grid methods developed specifically for compressible flow computations. The basic flow solver is a finite-volume implementation of Roe's flux difference splitting scheme or arbitrarily moving unstructured triangular meshes. The grid adaptation is performed according to geometric and flow requirements. Some results are included to illustrate the potential of the methodology.

  8. Solving Fluid Flow Problems on Moving and Adaptive Overlapping Grids

    SciTech Connect

    Henshaw, W

    2005-07-28

    Solution of fluid dynamics problems on overlapping grids will be discussed. An overlapping grid consists of a set of structured component grids that cover a domain and overlap where they meet. Overlapping grids provide an effective approach for developing efficient and accurate approximations for complex, possibly moving geometry. Topics to be addressed include the reactive Euler equations, the incompressible Navier-Stokes equations and elliptic equations solved with a multigrid algorithm. Recent developments coupling moving grids and adaptive mesh refinement and preliminary parallel results will also be presented.

  9. Adaptive grid embedding for the two-dimensional Euler equations

    NASA Technical Reports Server (NTRS)

    Warren, Gary P.

    1990-01-01

    A numerical algorithm is presented for solving the two-dimensional flux-split Euler equations using a multigrid method with adaptive grid embedding. The method uses an unstructured data set along with a system of pointers for communication on the irregularly shaped grid topologies. An explicit two-stage time advancement scheme is implemented. A multigrid algorithm is used to provide grid level communication and to accelerate the convergence of the solution to steady state. Results are presented for an NACA 0012 airfoil in a freestream with Mach numbers of 0.95 and 1.054. Excellent resolution of the shock structures is obtained with the adaptive grid embedding method with significantly fewer grid points than the comparable structured grid.

  10. Development of a dynamically adaptive grid method for multidimensional problems

    NASA Astrophysics Data System (ADS)

    Holcomb, J. E.; Hindman, R. G.

    1984-06-01

    An approach to solution adaptive grid generation for use with finite difference techniques, previously demonstrated on model problems in one space dimension, has been extended to multidimensional problems. The method is based on the popular elliptic steady grid generators, but is 'dynamically' adaptive in the sense that a grid is maintained at all times satisfying the steady grid law driven by a solution-dependent source term. Testing has been carried out on Burgers' equation in one and two space dimensions. Results appear encouraging both for inviscid wave propagation cases and viscous boundary layer cases, suggesting that application to practical flow problems is now possible. In the course of the work, obstacles relating to grid correction, smoothing of the solution, and elliptic equation solvers have been largely overcome. Concern remains, however, about grid skewness, boundary layer resolution and the need for implicit integration methods. Also, the method in 3-D is expected to be very demanding of computer resources.

  11. A generic efficient adaptive grid scheme for rocket propulsion modeling

    NASA Technical Reports Server (NTRS)

    Mo, J. D.; Chow, Alan S.

    1993-01-01

    The objective of this research is to develop an efficient, time-accurate numerical algorithm to discretize the Navier-Stokes equations for the predictions of internal one-, two-dimensional and axisymmetric flows. A generic, efficient, elliptic adaptive grid generator is implicitly coupled with the Lower-Upper factorization scheme in the development of ALUNS computer code. The calculations of one-dimensional shock tube wave propagation and two-dimensional shock wave capture, wave-wave interactions, shock wave-boundary interactions show that the developed scheme is stable, accurate and extremely robust. The adaptive grid generator produced a very favorable grid network by a grid speed technique. This generic adaptive grid generator is also applied in the PARC and FDNS codes and the computational results for solid rocket nozzle flowfield and crystal growth modeling by those codes will be presented in the conference, too. This research work is being supported by NASA/MSFC.

  12. Conservative treatment of boundary interfaces for overlaid grids and multi-level grid adaptations

    NASA Technical Reports Server (NTRS)

    Moon, Young J.; Liou, Meng-Sing

    1989-01-01

    Conservative algorithms for boundaray interfaces of overlaid grids are presented. The basic method is zeroth order, and is extended to a higher order method using interpolation and subcell decomposition. The present method, strictly based on a conservative constraint, is tested with overlaid grids for various applications of unsteady and steady supersonic inviscid flows with strong shock waves. The algorithm is also applied to a multi-level grid adaptation in which the next level finer grid is overlaid on the coarse base grid with an arbitrary orientation.

  13. Conservative treatment of boundary interfaces for overlaid grids and multi-level grid adaptations

    NASA Technical Reports Server (NTRS)

    Moon, Young J.; Liou, Meng-Sing

    1989-01-01

    Conservative algorithms for boundary interfaces of overlaid grids are presented. The basic method is zeroth order, and is extended to a higher order method using interpolation and subcell decomposition. The present method, strictly based on a conservative constraint, is tested with overlaid grids for various applications of unsteady and steady supersonic inviscid flows with strong shock waves. The algorithm is also applied to a multi-level grid adaptation in which the next level finer grid is overlaid on the coarse base grid with an arbitrary orientation.

  14. Workshop on adaptive grid methods for fusion plasmas

    SciTech Connect

    Wiley, J.C.

    1995-07-01

    The author describes a general `hp` finite element method with adaptive grids. The code was based on the work of Oden, et al. The term `hp` refers to the method of spatial refinement (h), in conjunction with the order of polynomials used as a part of the finite element discretization (p). This finite element code seems to handle well the different mesh grid sizes occuring between abuted grids with different resolutions.

  15. Adaptive gridding strategies for Free-Lagrangian calculations of low speed flows

    NASA Astrophysics Data System (ADS)

    Fritts, Martin J.

    1988-01-01

    Free-Lagrangian methods have been employed in two-dimensional simulations of the long-term evolution of fluid instabilities for low speed flows. For example, calculations of the Rayleigh-Taylor instability have proceeded through the inversion and mixing of two fluid layers and simulations of droplet deformations have continued well beyond droplet shattering. The freedom to choose grid connections permits several important benefits for these calculations. 1. Mass conservation is enforced for all individual fluid elements. 2. Vertex movement is always Lagrangian. 3. Grid adjustments can be made automatically, with no user intervention. 4. Grid connections may be selected to ensure accuracy in the difference equations. 5. Adaptive gridding schemes are local, adding and deleting vertices as dictated by local accuracy estimators. 6. Any geometric configuration may be easily gridded, for any vertex distribution on the boundaries or in the interior of the fluids. This paper will review some two-dimensional results, with the emphasis on the adaptive gridding algorithms and the accuracy of the resultant difference templates for the mathematical operators. The relation of the triangular mesh to the Voronoi mesh will be explored, particularly for the case when they are dual meshes. Three-dimensional algorithms for adaptive gridding will be presented which are exact analogues to the two-dimensional case. Gridding efficiencies will be discussed for several schemes.

  16. Rapid Structured Volume Grid Smoothing and Adaption Technique

    NASA Technical Reports Server (NTRS)

    Alter, Stephen J.

    2006-01-01

    A rapid, structured volume grid smoothing and adaption technique, based on signal processing methods, was developed and applied to the Shuttle Orbiter at hypervelocity flight conditions in support of the Columbia Accident Investigation. Because of the fast pace of the investigation, computational aerothermodynamicists, applying hypersonic viscous flow solving computational fluid dynamic (CFD) codes, refined and enhanced a grid for an undamaged baseline vehicle to assess a variety of damage scenarios. Of the many methods available to modify a structured grid, most are time-consuming and require significant user interaction. By casting the grid data into different coordinate systems, specifically two computational coordinates with arclength as the third coordinate, signal processing methods are used for filtering the data [Taubin, CG v/29 1995]. Using a reverse transformation, the processed data are used to smooth the Cartesian coordinates of the structured grids. By coupling the signal processing method with existing grid operations within the Volume Grid Manipulator tool, problems related to grid smoothing are solved efficiently and with minimal user interaction. Examples of these smoothing operations are illustrated for reductions in grid stretching and volume grid adaptation. In each of these examples, other techniques existed at the time of the Columbia accident, but the incorporation of signal processing techniques reduced the time to perform the corrections by nearly 60%. This reduction in time to perform the corrections therefore enabled the assessment of approximately twice the number of damage scenarios than previously possible during the allocated investigation time.

  17. Rapid Structured Volume Grid Smoothing and Adaption Technique

    NASA Technical Reports Server (NTRS)

    Alter, Stephen J.

    2004-01-01

    A rapid, structured volume grid smoothing and adaption technique, based on signal processing methods, was developed and applied to the Shuttle Orbiter at hypervelocity flight conditions in support of the Columbia Accident Investigation. Because of the fast pace of the investigation, computational aerothermodynamicists, applying hypersonic viscous flow solving computational fluid dynamic (CFD) codes, refined and enhanced a grid for an undamaged baseline vehicle to assess a variety of damage scenarios. Of the many methods available to modify a structured grid, most are time-consuming and require significant user interaction. By casting the grid data into different coordinate systems, specifically two computational coordinates with arclength as the third coordinate, signal processing methods are used for filtering the data [Taubin, CG v/29 1995]. Using a reverse transformation, the processed data are used to smooth the Cartesian coordinates of the structured grids. By coupling the signal processing method with existing grid operations within the Volume Grid Manipulator tool, problems related to grid smoothing are solved efficiently and with minimal user interaction. Examples of these smoothing operations are illustrated for reduction in grid stretching and volume grid adaptation. In each of these examples, other techniques existed at the time of the Columbia accident, but the incorporation of signal processing techniques reduced the time to perform the corrections by nearly 60%. This reduction in time to perform the corrections therefore enabled the assessment of approximately twice the number of damage scenarios than previously possible during the allocated investigation time.

  18. Stability and error estimation for Component Adaptive Grid methods

    NASA Technical Reports Server (NTRS)

    Oliger, Joseph; Zhu, Xiaolei

    1994-01-01

    Component adaptive grid (CAG) methods for solving hyperbolic partial differential equations (PDE's) are discussed in this paper. Applying recent stability results for a class of numerical methods on uniform grids. The convergence of these methods for linear problems on component adaptive grids is established here. Furthermore, the computational error can be estimated on CAG's using the stability results. Using these estimates, the error can be controlled on CAG's. Thus, the solution can be computed efficiently on CAG's within a given error tolerance. Computational results for time dependent linear problems in one and two space dimensions are presented.

  19. Adaptive Mesh Refinement in Curvilinear Body-Fitted Grid Systems

    NASA Technical Reports Server (NTRS)

    Steinthorsson, Erlendur; Modiano, David; Colella, Phillip

    1995-01-01

    To be truly compatible with structured grids, an AMR algorithm should employ a block structure for the refined grids to allow flow solvers to take advantage of the strengths of unstructured grid systems, such as efficient solution algorithms for implicit discretizations and multigrid schemes. One such algorithm, the AMR algorithm of Berger and Colella, has been applied to and adapted for use with body-fitted structured grid systems. Results are presented for a transonic flow over a NACA0012 airfoil (AGARD-03 test case) and a reflection of a shock over a double wedge.

  20. Topology and grid adaption for high-speed flow computations

    NASA Technical Reports Server (NTRS)

    Abolhassani, Jamshid S.; Tiwari, Surendra N.

    1989-01-01

    This study investigates the effects of grid topology and grid adaptation on numerical solutions of the Navier-Stokes equations. In the first part of this study, a general procedure is presented for computation of high-speed flow over complex three-dimensional configurations. The flow field is simulated on the surface of a Butler wing in a uniform stream. Results are presented for Mach number 3.5 and a Reynolds number of 2,000,000. The O-type and H-type grids have been used for this study, and the results are compared together and with other theoretical and experimental results. The results demonstrate that while the H-type grid is suitable for the leading and trailing edges, a more accurate solution can be obtained for the middle part of the wing with an O-type grid. In the second part of this study, methods of grid adaption are reviewed and a method is developed with the capability of adapting to several variables. This method is based on a variational approach and is an algebraic method. Also, the method has been formulated in such a way that there is no need for any matrix inversion. This method is used in conjunction with the calculation of hypersonic flow over a blunt-nose body. A movie has been produced which shows simultaneously the transient behavior of the solution and the grid adaption.

  1. A local adaptive image descriptor

    NASA Astrophysics Data System (ADS)

    Zahid Ishraque, S. M.; Shoyaib, Mohammad; Abdullah-Al-Wadud, M.; Monirul Hoque, Md; Chae, Oksam

    2013-12-01

    The local binary pattern (LBP) is a robust but computationally simple approach in texture analysis. However, LBP performs poorly in the presence of noise and large illumination variation. Thus, a local adaptive image descriptor termed as LAID is introduced in this proposal. It is a ternary pattern and is able to generate persistent codes to represent microtextures in a given image, especially in noisy conditions. It can also generate stable texture codes if the pixel intensities change abruptly due to the illumination changes. Experimental results also show the superiority of the proposed method over other state-of-the-art methods.

  2. Higher-order schemes with CIP method and adaptive Soroban grid towards mesh-free scheme

    NASA Astrophysics Data System (ADS)

    Yabe, Takashi; Mizoe, Hiroki; Takizawa, Kenji; Moriki, Hiroshi; Im, Hyo-Nam; Ogata, Youichi

    2004-02-01

    A new class of body-fitted grid system that can keep the third-order accuracy in time and space is proposed with the help of the CIP (constrained interpolation profile/cubic interpolated propagation) method. The grid system consists of the straight lines and grid points moving along these lines like abacus - Soroban in Japanese. The length of each line and the number of grid points in each line can be different. The CIP scheme is suitable to this mesh system and the calculation of large CFL (>10) at locally refined mesh is easily performed. Mesh generation and searching of upstream departure point are very simple and almost mesh-free treatment is possible. Adaptive grid movement and local mesh refinement are demonstrated.

  3. Methods for prismatic/tetrahedral grid generation and adaptation

    NASA Astrophysics Data System (ADS)

    Kallinderis, Y.

    1995-10-01

    The present work involves generation of hybrid prismatic/tetrahedral grids for complex 3-D geometries including multi-body domains. The prisms cover the region close to each body's surface, while tetrahedra are created elsewhere. Two developments are presented for hybrid grid generation around complex 3-D geometries. The first is a new octree/advancing front type of method for generation of the tetrahedra of the hybrid mesh. The main feature of the present advancing front tetrahedra generator that is different from previous such methods is that it does not require the creation of a background mesh by the user for the determination of the grid-spacing and stretching parameters. These are determined via an automatically generated octree. The second development is a method for treating the narrow gaps in between different bodies in a multiply-connected domain. This method is applied to a two-element wing case. A High Speed Civil Transport (HSCT) type of aircraft geometry is considered. The generated hybrid grid required only 170 K tetrahedra instead of an estimated two million had a tetrahedral mesh been used in the prisms region as well. A solution adaptive scheme for viscous computations on hybrid grids is also presented. A hybrid grid adaptation scheme that employs both h-refinement and redistribution strategies is developed to provide optimum meshes for viscous flow computations. Grid refinement is a dual adaptation scheme that couples 3-D, isotropic division of tetrahedra and 2-D, directional division of prisms.

  4. Efficient Unstructured Grid Adaptation Methods for Sonic Boom Prediction

    NASA Technical Reports Server (NTRS)

    Campbell, Richard L.; Carter, Melissa B.; Deere, Karen A.; Waithe, Kenrick A.

    2008-01-01

    This paper examines the use of two grid adaptation methods to improve the accuracy of the near-to-mid field pressure signature prediction of supersonic aircraft computed using the USM3D unstructured grid flow solver. The first method (ADV) is an interactive adaptation process that uses grid movement rather than enrichment to more accurately resolve the expansion and compression waves. The second method (SSGRID) uses an a priori adaptation approach to stretch and shear the original unstructured grid to align the grid with the pressure waves and reduce the cell count required to achieve an accurate signature prediction at a given distance from the vehicle. Both methods initially create negative volume cells that are repaired in a module in the ADV code. While both approaches provide significant improvements in the near field signature (< 3 body lengths) relative to a baseline grid without increasing the number of grid points, only the SSGRID approach allows the details of the signature to be accurately computed at mid-field distances (3-10 body lengths) for direct use with mid-field-to-ground boom propagation codes.

  5. SAGE: The Self-Adaptive Grid Code. 3

    NASA Technical Reports Server (NTRS)

    Davies, Carol B.; Venkatapathy, Ethiraj

    1999-01-01

    The multi-dimensional self-adaptive grid code, SAGE, is an important tool in the field of computational fluid dynamics (CFD). It provides an efficient method to improve the accuracy of flow solutions while simultaneously reducing computer processing time. Briefly, SAGE enhances an initial computational grid by redistributing the mesh points into more appropriate locations. The movement of these points is driven by an equal-error-distribution algorithm that utilizes the relationship between high flow gradients and excessive solution errors. The method also provides a balance between clustering points in the high gradient regions and maintaining the smoothness and continuity of the adapted grid, The latest version, Version 3, includes the ability to change the boundaries of a given grid to more efficiently enclose flow structures and provides alternative redistribution algorithms.

  6. Variational method for adaptive grid generation

    SciTech Connect

    Brackbill, J.U.

    1983-01-01

    A variational method for generating adaptive meshes is described. Functionals measuring smoothness, skewness, orientation, and the Jacobian are minimized to generate a mapping from a rectilinear domain in natural coordinate to an arbitrary domain in physical coordinates. From the mapping, a mesh is easily constructed. In using the method to adaptively zone computational problems, as few as one third the number of mesh points are required in each coordinate direction compared with a uniformly zoned mesh.

  7. An adaptive grid algorithm for one-dimensional nonlinear equations

    NASA Technical Reports Server (NTRS)

    Gutierrez, William E.; Hills, Richard G.

    1990-01-01

    Richards' equation, which models the flow of liquid through unsaturated porous media, is highly nonlinear and difficult to solve. Step gradients in the field variables require the use of fine grids and small time step sizes. The numerical instabilities caused by the nonlinearities often require the use of iterative methods such as Picard or Newton interation. These difficulties result in large CPU requirements in solving Richards equation. With this in mind, adaptive and multigrid methods are investigated for use with nonlinear equations such as Richards' equation. Attention is focused on one-dimensional transient problems. To investigate the use of multigrid and adaptive grid methods, a series of problems are studied. First, a multigrid program is developed and used to solve an ordinary differential equation, demonstrating the efficiency with which low and high frequency errors are smoothed out. The multigrid algorithm and an adaptive grid algorithm is used to solve one-dimensional transient partial differential equations, such as the diffusive and convective-diffusion equations. The performance of these programs are compared to that of the Gauss-Seidel and tridiagonal methods. The adaptive and multigrid schemes outperformed the Gauss-Seidel algorithm, but were not as fast as the tridiagonal method. The adaptive grid scheme solved the problems slightly faster than the multigrid method. To solve nonlinear problems, Picard iterations are introduced into the adaptive grid and tridiagonal methods. Burgers' equation is used as a test problem for the two algorithms. Both methods obtain solutions of comparable accuracy for similar time increments. For the Burgers' equation, the adaptive grid method finds the solution approximately three times faster than the tridiagonal method. Finally, both schemes are used to solve the water content formulation of the Richards' equation. For this problem, the adaptive grid method obtains a more accurate solution in fewer work units and

  8. Adaptively-refined overlapping grids for the numerical solution of systems of hyperbolic conservation laws

    NASA Technical Reports Server (NTRS)

    Brislawn, Kristi D.; Brown, David L.; Chesshire, Geoffrey S.; Saltzman, Jeffrey S.

    1995-01-01

    Adaptive mesh refinement (AMR) in conjunction with higher-order upwind finite-difference methods have been used effectively on a variety of problems in two and three dimensions. In this paper we introduce an approach for resolving problems that involve complex geometries in which resolution of boundary geometry is important. The complex geometry is represented by using the method of overlapping grids, while local resolution is obtained by refining each component grid with the AMR algorithm, appropriately generalized for this situation. The CMPGRD algorithm introduced by Chesshire and Henshaw is used to automatically generate the overlapping grid structure for the underlying mesh.

  9. ICASE/LaRC Workshop on Adaptive Grid Methods

    NASA Technical Reports Server (NTRS)

    South, Jerry C., Jr. (Editor); Thomas, James L. (Editor); Vanrosendale, John (Editor)

    1995-01-01

    Solution-adaptive grid techniques are essential to the attainment of practical, user friendly, computational fluid dynamics (CFD) applications. In this three-day workshop, experts gathered together to describe state-of-the-art methods in solution-adaptive grid refinement, analysis, and implementation; to assess the current practice; and to discuss future needs and directions for research. This was accomplished through a series of invited and contributed papers. The workshop focused on a set of two-dimensional test cases designed by the organizers to aid in assessing the current state of development of adaptive grid technology. In addition, a panel of experts from universities, industry, and government research laboratories discussed their views of needs and future directions in this field.

  10. Parallel Implementation of an Adaptive Scheme for 3D Unstructured Grids on the SP2

    NASA Technical Reports Server (NTRS)

    Oliker, Leonid; Biswas, Rupak; Strawn, Roger C.

    1996-01-01

    Dynamic mesh adaption on unstructured grids is a powerful tool for computing unsteady flows that require local grid modifications to efficiently resolve solution features. For this work, we consider an edge-based adaption scheme that has shown good single-processor performance on the C90. We report on our experience parallelizing this code for the SP2. Results show a 47.OX speedup on 64 processors when 10% of the mesh is randomly refined. Performance deteriorates to 7.7X when the same number of edges are refined in a highly-localized region. This is because almost all mesh adaption is confined to a single processor. However, this problem can be remedied by repartitioning the mesh immediately after targeting edges for refinement but before the actual adaption takes place. With this change, the speedup improves dramatically to 43.6X.

  11. Parallel implementation of an adaptive scheme for 3D unstructured grids on the SP2

    NASA Technical Reports Server (NTRS)

    Strawn, Roger C.; Oliker, Leonid; Biswas, Rupak

    1996-01-01

    Dynamic mesh adaption on unstructured grids is a powerful tool for computing unsteady flows that require local grid modifications to efficiently resolve solution features. For this work, we consider an edge-based adaption scheme that has shown good single-processor performance on the C90. We report on our experience parallelizing this code for the SP2. Results show a 47.0X speedup on 64 processors when 10 percent of the mesh is randomly refined. Performance deteriorates to 7.7X when the same number of edges are refined in a highly-localized region. This is because almost all the mesh adaption is confined to a single processor. However, this problem can be remedied by repartitioning the mesh immediately after targeting edges for refinement but before the actual adaption takes place. With this change, the speedup improves dramatically to 43.6X.

  12. Grid generation strategies for turbomachinery configurations

    NASA Astrophysics Data System (ADS)

    Lee, K. D.; Henderson, T. L.

    1991-01-01

    Turbomachinery flow fields involve unique grid generation issues due to their geometrical and physical characteristics. Several strategic approaches are discussed to generate quality grids. The grid quality is further enhanced through blending and adapting. Grid blending smooths the grids locally through averaging and diffusion operators. Grid adaptation redistributes the grid points based on a grid quality assessment. These methods are demonstrated with several examples.

  13. Fast adaptive composite grid methods on distributed parallel architectures

    NASA Technical Reports Server (NTRS)

    Lemke, Max; Quinlan, Daniel

    1992-01-01

    The fast adaptive composite (FAC) grid method is compared with the adaptive composite method (AFAC) under variety of conditions including vectorization and parallelization. Results are given for distributed memory multiprocessor architectures (SUPRENUM, Intel iPSC/2 and iPSC/860). It is shown that the good performance of AFAC and its superiority over FAC in a parallel environment is a property of the algorithm and not dependent on peculiarities of any machine.

  14. Adaptive hybrid prismatic-tetrahedral grids for viscous flows

    NASA Astrophysics Data System (ADS)

    Kallinderis, Yannis; Khawaja, Aly; McMorris, Harlan

    1995-03-01

    The paper presents generation of adaptive hybrid prismatic/tetrahedral grids for complex 3-D geometries including multi-body domains. The prisms cover the region close to each body's surface, while tetrahedra are created elsewhere. Two developments are presented for hybrid grid generation around complex 3-D geometries. The first is a new octree/advancing front type of method for generation of the tetrahedra of the hybrid mesh. The main feature of the present advancing front tetrahedra generator that is different from previous such methods is that it does not require the creation of a background mesh by the user for the determination of the grid-spacing and stretching parameters. These are determined via an automatically generated octree. The second development is an Automatic Receding Method (ARM) for treating the narrow gaps in between different bodies in a multiply-connected domain. This method is applied to a two-element wing case. A hybrid grid adaptation scheme that employs both h-refinement and redistribution strategies is developed to provide optimum meshes for viscous flow computations. Grid refinement is a dual adaptation scheme that couples division of tetrahedra, as well as 2-D directional division of prisms.

  15. Adaptive hybrid prismatic-tetrahedral grids for viscous flows

    NASA Technical Reports Server (NTRS)

    Kallinderis, Yannis; Khawaja, Aly; Mcmorris, Harlan

    1995-01-01

    The paper presents generation of adaptive hybrid prismatic/tetrahedral grids for complex 3-D geometries including multi-body domains. The prisms cover the region close to each body's surface, while tetrahedra are created elsewhere. Two developments are presented for hybrid grid generation around complex 3-D geometries. The first is a new octree/advancing front type of method for generation of the tetrahedra of the hybrid mesh. The main feature of the present advancing front tetrahedra generator that is different from previous such methods is that it does not require the creation of a background mesh by the user for the determination of the grid-spacing and stretching parameters. These are determined via an automatically generated octree. The second development is an Automatic Receding Method (ARM) for treating the narrow gaps in between different bodies in a multiply-connected domain. This method is applied to a two-element wing case. A hybrid grid adaptation scheme that employs both h-refinement and redistribution strategies is developed to provide optimum meshes for viscous flow computations. Grid refinement is a dual adaptation scheme that couples division of tetrahedra, as well as 2-D directional division of prisms.

  16. A novel hyperbolic grid generation procedure with inherent adaptive dissipation

    SciTech Connect

    Tai, C.H.; Yin, S.L.; Soong, C.Y.

    1995-01-01

    This paper reports a novel hyperbolic grid-generation with an inherent adaptive dissipation (HGAD), which is capable of improving the oscillation and overlapping of grid lines. In the present work upwinding differencing is applied to discretize the hyperbolic system and, thereby, to develop the adaptive dissipation coefficient. Complex configurations with the features of geometric discontinuity, exceptional concavity and convexity are used as the test cases for comparison of the present HGAD procedure with the conventional hyerbolic and elliptic ones. The results reveal that the HGAD method is superior in orthogonality and smoothness of the grid system. In addition, the computational efficiency of the flow solver may be improved by using the present HGAD procedure. 15 refs., 8 figs.

  17. A Grid Sourcing and Adaptation Study Using Unstructured Grids for Supersonic Boom Prediction

    NASA Technical Reports Server (NTRS)

    Carter, Melissa B.; Deere, Karen A.

    2008-01-01

    NASA created the Supersonics Project as part of the NASA Fundamental Aeronautics Program to advance technology that will make a supersonic flight over land viable. Computational flow solvers have lacked the ability to accurately predict sonic boom from the near to far field. The focus of this investigation was to establish gridding and adaptation techniques to predict near-to-mid-field (<10 body lengths below the aircraft) boom signatures at supersonic speeds using the USM3D unstructured grid flow solver. The study began by examining sources along the body the aircraft, far field sourcing and far field boundaries. The study then examined several techniques for grid adaptation. During the course of the study, volume sourcing was introduced as a new way to source grids using the grid generation code VGRID. Two different methods of using the volume sources were examined. The first method, based on manual insertion of the numerous volume sources, made great improvements in the prediction capability of USM3D for boom signatures. The second method (SSGRID), which uses an a priori adaptation approach to stretch and shear the original unstructured grid to align the grid and pressure waves, showed similar results with a more automated approach. Due to SSGRID s results and ease of use, the rest of the study focused on developing a best practice using SSGRID. The best practice created by this study for boom predictions using the CFD code USM3D involved: 1) creating a small cylindrical outer boundary either 1 or 2 body lengths in diameter (depending on how far below the aircraft the boom prediction is required), 2) using a single volume source under the aircraft, and 3) using SSGRID to stretch and shear the grid to the desired length.

  18. The multidimensional Self-Adaptive Grid code, SAGE, version 2

    NASA Technical Reports Server (NTRS)

    Davies, Carol B.; Venkatapathy, Ethiraj

    1995-01-01

    This new report on Version 2 of the SAGE code includes all the information in the original publication plus all upgrades and changes to the SAGE code since that time. The two most significant upgrades are the inclusion of a finite-volume option and the ability to adapt and manipulate zonal-matching multiple-grid files. In addition, the original SAGE code has been upgraded to Version 1.1 and includes all options mentioned in this report, with the exception of the multiple grid option and its associated features. Since Version 2 is a larger and more complex code, it is suggested (but not required) that Version 1.1 be used for single-grid applications. This document contains all the information required to run both versions of SAGE. The formulation of the adaption method is described in the first section of this document. The second section is presented in the form of a user guide that explains the input and execution of the code. The third section provides many examples. Successful application of the SAGE code in both two and three dimensions for the solution of various flow problems has proven the code to be robust, portable, and simple to use. Although the basic formulation follows the method of Nakahashi and Deiwert, many modifications have been made to facilitate the use of the self-adaptive grid method for complex grid structures. Modifications to the method and the simple but extensive input options make this a flexible and user-friendly code. The SAGE code can accommodate two-dimensional and three-dimensional, finite-difference and finite-volume, single grid, and zonal-matching multiple grid flow problems.

  19. Local intensity adaptive image coding

    NASA Technical Reports Server (NTRS)

    Huck, Friedrich O.

    1989-01-01

    The objective of preprocessing for machine vision is to extract intrinsic target properties. The most important properties ordinarily are structure and reflectance. Illumination in space, however, is a significant problem as the extreme range of light intensity, stretching from deep shadow to highly reflective surfaces in direct sunlight, impairs the effectiveness of standard approaches to machine vision. To overcome this critical constraint, an image coding scheme is being investigated which combines local intensity adaptivity, image enhancement, and data compression. It is very effective under the highly variant illumination that can exist within a single frame or field of view, and it is very robust to noise at low illuminations. Some of the theory and salient features of the coding scheme are reviewed. Its performance is characterized in a simulated space application, the research and development activities are described.

  20. Efficient Load Balancing and Data Remapping for Adaptive Grid Calculations

    NASA Technical Reports Server (NTRS)

    Oliker, Leonid; Biswas, Rupak

    1997-01-01

    Mesh adaption is a powerful tool for efficient unstructured- grid computations but causes load imbalance among processors on a parallel machine. We present a novel method to dynamically balance the processor workloads with a global view. This paper presents, for the first time, the implementation and integration of all major components within our dynamic load balancing strategy for adaptive grid calculations. Mesh adaption, repartitioning, processor assignment, and remapping are critical components of the framework that must be accomplished rapidly and efficiently so as not to cause a significant overhead to the numerical simulation. Previous results indicated that mesh repartitioning and data remapping are potential bottlenecks for performing large-scale scientific calculations. We resolve these issues and demonstrate that our framework remains viable on a large number of processors.

  1. Digital breast tomosynthesis reconstruction with an adaptive voxel grid

    NASA Astrophysics Data System (ADS)

    Claus, Bernhard; Chan, Heang-Ping

    2014-03-01

    In digital breast tomosynthesis (DBT) volume datasets are typically reconstructed with an anisotropic voxel size, where the in-plane voxel size usually reflects the detector pixel size (e.g., 0.1 mm), and the slice separation is generally between 0.5-1.0 mm. Increasing the tomographic angle is expected to give better 3D image quality; however, the slice spacing in the reconstruction should be reduced, otherwise one may risk losing fine-scale image detail (e.g., small microcalcifications). An alternative strategy consists of reconstructing on an adaptive voxel grid, where the voxel height at each location is adapted based on the backprojected data at this location, with the goal to improve image quality for microcalcifications. In this paper we present an approach for generating such an adaptive voxel grid. This approach is based on an initial reconstruction step that is performed at a finer slice-spacing combined with a selection of an "optimal" height for each voxel. This initial step is followed by a (potentially iterative) reconstruction acting now on the adaptive grid only.

  2. Unstructured Adaptive Grid Computations on an Array of SMPs

    NASA Technical Reports Server (NTRS)

    Biswas, Rupak; Pramanick, Ira; Sohn, Andrew; Simon, Horst D.

    1996-01-01

    Dynamic load balancing is necessary for parallel adaptive methods to solve unsteady CFD problems on unstructured grids. We have presented such a dynamic load balancing framework called JOVE, in this paper. Results on a four-POWERnode POWER CHALLENGEarray demonstrated that load balancing gives significant performance improvements over no load balancing for such adaptive computations. The parallel speedup of JOVE, implemented using MPI on the POWER CHALLENCEarray, was significant, being as high as 31 for 32 processors. An implementation of JOVE that exploits 'an array of SMPS' architecture was also studied; this hybrid JOVE outperformed flat JOVE by up to 28% on the meshes and adaption models tested. With large, realistic meshes and actual flow-solver and adaption phases incorporated into JOVE, hybrid JOVE can be expected to yield significant advantage over flat JOVE, especially as the number of processors is increased, thus demonstrating the scalability of an array of SMPs architecture.

  3. Climate adaptation: Cultural knowledge and local risks

    NASA Astrophysics Data System (ADS)

    Strauss, Sarah

    2015-07-01

    A focus on African American communities on the Eastern Shore of Maryland highlights the ways that local cultural knowledge differs from place to place, developing understanding of local climate risks and resources for adaptation.

  4. Fast transport simulation with an adaptive grid refinement.

    PubMed

    Haefner, Frieder; Boy, Siegrun

    2003-01-01

    One of the main difficulties in transport modeling and calibration is the extraordinarily long computing times necessary for simulation runs. Improved execution time is a prerequisite for calibration in transport modeling. In this paper we investigate the problem of code acceleration using an adaptive grid refinement, neglecting subdomains, and devising a method by which the Courant condition can be ignored while maintaining accurate solutions. Grid refinement is based on dividing selected cells into regular subcells and including the balance equations of subcells in the equation system. The connection of coarse and refined cells satisfies the mass balance with an interpolation scheme that is implicitly included in the equation system. The refined subdomain can move with the average transport velocity of the subdomain. Very small time steps are required on a fine or a refined grid, because of the combined effect of the Courant and Peclet conditions. Therefore, we have developed a special upwind technique in small grid cells with high velocities (velocity suppression). We have neglected grid subdomains with very small concentration gradients (zero suppression). The resulting software, MODCALIF, is a three-dimensional, modularly constructed FORTRAN code. For convenience, the package names used by the well-known MODFLOW and MT3D computer programs are adopted, and the same input file structure and format is used, but the program presented here is separate and independent. Also, MODCALIF includes algorithms for variable density modeling and model calibration. The method is tested by comparison with an analytical solution, and illustrated by means of a two-dimensional theoretical example and three-dimensional simulations of the variable-density Cape Cod and SALTPOOL experiments. Crossing from fine to coarse grid produces numerical dispersion when the whole subdomain of interest is refined; however, we show that accurate solutions can be obtained using a fraction of the

  5. Large-Scale Liquid Simulation on Adaptive Hexahedral Grids.

    PubMed

    Ferstl, Florian; Westermann, Rudiger; Dick, Christian

    2014-10-01

    Regular grids are attractive for numerical fluid simulations because they give rise to efficient computational kernels. However, for simulating high resolution effects in complicated domains they are only of limited suitability due to memory constraints. In this paper we present a method for liquid simulation on an adaptive octree grid using a hexahedral finite element discretization, which reduces memory requirements by coarsening the elements in the interior of the liquid body. To impose free surface boundary conditions with second order accuracy, we incorporate a particular class of Nitsche methods enforcing the Dirichlet boundary conditions for the pressure in a variational sense. We then show how to construct a multigrid hierarchy from the adaptive octree grid, so that a time efficient geometric multigrid solver can be used. To improve solver convergence, we propose a special treatment of liquid boundaries via composite finite elements at coarser scales. We demonstrate the effectiveness of our method for liquid simulations that would require hundreds of millions of simulation elements in a non-adaptive regime. PMID:26357387

  6. A geometry-based adaptive unstructured grid generation algorithm for complex geological media

    NASA Astrophysics Data System (ADS)

    Bahrainian, Seyed Saied; Dezfuli, Alireza Daneh

    2014-07-01

    In this paper a novel unstructured grid generation algorithm is presented that considers the effect of geological features and well locations in grid resolution. The proposed grid generation algorithm presents a strategy for definition and construction of an initial grid based on the geological model, geometry adaptation of geological features, and grid resolution control. The algorithm is applied to seismotectonic map of the Masjed-i-Soleiman reservoir. Comparison of grid results with the “Triangle” program shows a more suitable permeability contrast. Immiscible two-phase flow solutions are presented for a fractured porous media test case using different grid resolutions. Adapted grid on the fracture geometry gave identical results with that of a fine grid. The adapted grid employed 88.2% less CPU time when compared to the solutions obtained by the fine grid.

  7. OMEGA: The operational multiscale environment model with grid adaptivity

    SciTech Connect

    Bacon, D.P.

    1995-07-01

    This review talk describes the OMEGA code, used for weather simulation and the modeling of aerosol transport through the atmosphere. Omega employs a 3D mesh of wedge shaped elements (triangles when viewed from above) that adapt with time. Because wedges are laid out in layers of triangular elements, the scheme can utilize structured storage and differencing techniques along the elevation coordinate, and is thus a hybrid of structured and unstructured methods. The utility of adaptive gridding in this moded, near geographic features such as coastlines, where material properties change discontinuously, is illustrated. Temporal adaptivity was used additionally to track moving internal fronts, such as clouds of aerosol contaminants. The author also discusses limitations specific to this problem, including manipulation of huge data bases and fixed turn-around times. In practice, the latter requires a carefully tuned optimization between accuracy and computation speed.

  8. Load Balancing Unstructured Adaptive Grids for CFD Problems

    NASA Technical Reports Server (NTRS)

    Biswas, Rupak; Oliker, Leonid

    1996-01-01

    Mesh adaption is a powerful tool for efficient unstructured-grid computations but causes load imbalance among processors on a parallel machine. A dynamic load balancing method is presented that balances the workload across all processors with a global view. After each parallel tetrahedral mesh adaption, the method first determines if the new mesh is sufficiently unbalanced to warrant a repartitioning. If so, the adapted mesh is repartitioned, with new partitions assigned to processors so that the redistribution cost is minimized. The new partitions are accepted only if the remapping cost is compensated by the improved load balance. Results indicate that this strategy is effective for large-scale scientific computations on distributed-memory multiprocessors.

  9. The multidimensional self-adaptive grid code, SAGE

    NASA Technical Reports Server (NTRS)

    Davies, Carol B.; Venkatapathy, Ethiraj

    1992-01-01

    This report describes the multidimensional self-adaptive grid code SAGE. A two-dimensional version of this code was described in an earlier report by the authors. The formulation of the multidimensional version is described in the first section of this document. The second section is presented in the form of a user guide that explains the input and execution of the code and provides many examples. Successful application of the SAGE code in both two and three dimensions for the solution of various flow problems has proven the code to be robust, portable, and simple to use. Although the basic formulation follows the method of Nakahashi and Deiwert, many modifications have been made to facilitate the use of the self-adaptive grid method for complex grid structures. Modifications to the method and the simplified input options make this a flexible and user-friendly code. The new SAGE code can accommodate both two-dimensional and three-dimensional flow problems.

  10. Optimal Design of Grid-Stiffened Composite Panels Using Global and Local Buckling Analysis

    SciTech Connect

    Ambur, D.R.; Jaunky, N.; Knight, N.F. Jr.

    1996-04-01

    A design strategy for optimal design of composite grid-stiffened panels subjected to global and local buckling constraints is developed using a discrete optimizer. An improved smeared stiffener theory is used for the global buckling analysis. Local buckling of skin segments is assessed using a Rayleigh-Ritz method that accounts for material anisotropy and transverse shear flexibility. The local buckling of stiffener segments is also assessed. Design variables are the axial and transverse stiffener spacing, stiffener height and thickness, skin laminate, and stiffening configuration. The design optimization process is adapted to identify the lightest-weight stiffening configuration and pattern for grid stiffened composite panels given the overall panel dimensions, design in-plane loads, material properties, and boundary conditions of the grid-stiffened panel.

  11. Optimal Design of Grid-Stiffened Composite Panels Using Global and Local Buckling Analysis

    NASA Technical Reports Server (NTRS)

    Ambur, Damodar R.; Jaunky, Navin; Knight, Norman F., Jr.

    1996-01-01

    A design strategy for optimal design of composite grid-stiffened panels subjected to global and local buckling constraints is developed using a discrete optimizer. An improved smeared stiffener theory is used for the global buckling analysis. Local buckling of skin segments is assessed using a Rayleigh-Ritz method that accounts for material anisotropy and transverse shear flexibility. The local buckling of stiffener segments is also assessed. Design variables are the axial and transverse stiffener spacing, stiffener height and thickness, skin laminate, and stiffening configuration. The design optimization process is adapted to identify the lightest-weight stiffening configuration and pattern for grid stiffened composite panels given the overall panel dimensions, design in-plane loads, material properties, and boundary conditions of the grid-stiffened panel.

  12. Vortical Flow Prediction using an Adaptive Unstructured Grid Method. Chapter 11

    NASA Technical Reports Server (NTRS)

    Pirzadeh, Shahyar Z.

    2009-01-01

    A computational fluid dynamics (CFD) method has been employed to compute vortical flows around slender wing/body configurations. The emphasis of the paper is on the effectiveness of an adaptive grid procedure in "capturing" concentrated vortices generated at sharp edges or flow separation lines of lifting surfaces flying at high angles of attack. The method is based on a tetrahedral unstructured grid technology developed at the NASA Langley Research Center. Two steady-state, subsonic, inviscid and Navier-Stokes flow test cases are presented to demonstrate the applicability of the method for solving vortical flow problems. The first test case concerns vortex flow over a simple 65 delta wing with different values of leading-edge radius. Although the geometry is quite simple, it poses a challenging problem for computing vortices originating from blunt leading edges. The second case is that of a more complex fighter configuration. The superiority of the adapted solutions in capturing the vortex flow structure over the conventional unadapted results is demonstrated by comparisons with the wind-tunnel experimental data. The study shows that numerical prediction of vortical flows is highly sensitive to the local grid resolution and that the implementation of grid adaptation is essential when applying CFD methods to such complicated flow problems.

  13. Automation of assertion testing - Grid and adaptive techniques

    NASA Technical Reports Server (NTRS)

    Andrews, D. M.

    1985-01-01

    Assertions can be used to automate the process of testing software. Two methods for automating the generation of input test data are described in this paper. One method selects the input values of variables at regular intervals in a 'grid'. The other, adaptive testing, uses assertion violations as a measure of errors detected and generates new test cases based on test results. The important features of assertion testing are that: it can be used throughout the entire testing cycle; it provides automatic notification of error conditions; and it can be used with automatic input generation techniques which eliminate the subjectivity in choosing test data.

  14. INITIAL APPL;ICATION OF THE ADAPTIVE GRID AIR POLLUTION MODEL

    EPA Science Inventory

    The paper discusses an adaptive-grid algorithm used in air pollution models. The algorithm reduces errors related to insufficient grid resolution by automatically refining the grid scales in regions of high interest. Meanwhile the grid scales are coarsened in other parts of the d...

  15. The development and application of the self-adaptive grid code, SAGE

    NASA Astrophysics Data System (ADS)

    Davies, Carol B.

    The multidimensional self-adaptive grid code, SAGE, has proven to be a flexible and useful tool in the solution of complex flow problems. Both 2- and 3-D examples given in this report show the code to be reliable and to substantially improve flowfield solutions. Since the adaptive procedure is a marching scheme the code is extremely fast and uses insignificant CPU time compared to the corresponding flow solver. The SAGE program is also machine and flow solver independent. Significant effort was made to simplify user interaction, though some parameters still need to be chosen with care. It is also difficult to tell when the adaption process has provided its best possible solution. This is particularly true if no experimental data are available or if there is a lack of theoretical understanding of the flow. Another difficulty occurs if local features are important but missing in the original grid; the adaption to this solution will not result in any improvement, and only grid refinement can result in an improved solution. These are complex issues that need to be explored within the context of each specific problem.

  16. The development and application of the self-adaptive grid code, SAGE

    NASA Technical Reports Server (NTRS)

    Davies, Carol B.

    1993-01-01

    The multidimensional self-adaptive grid code, SAGE, has proven to be a flexible and useful tool in the solution of complex flow problems. Both 2- and 3-D examples given in this report show the code to be reliable and to substantially improve flowfield solutions. Since the adaptive procedure is a marching scheme the code is extremely fast and uses insignificant CPU time compared to the corresponding flow solver. The SAGE program is also machine and flow solver independent. Significant effort was made to simplify user interaction, though some parameters still need to be chosen with care. It is also difficult to tell when the adaption process has provided its best possible solution. This is particularly true if no experimental data are available or if there is a lack of theoretical understanding of the flow. Another difficulty occurs if local features are important but missing in the original grid; the adaption to this solution will not result in any improvement, and only grid refinement can result in an improved solution. These are complex issues that need to be explored within the context of each specific problem.

  17. A new procedure for dynamic adaption of three-dimensional unstructured grids

    NASA Technical Reports Server (NTRS)

    Biswas, Rupak; Strawn, Roger

    1993-01-01

    A new procedure is presented for the simultaneous coarsening and refinement of three-dimensional unstructured tetrahedral meshes. This algorithm allows for localized grid adaption that is used to capture aerodynamic flow features such as vortices and shock waves in helicopter flowfield simulations. The mesh-adaption algorithm is implemented in the C programming language and uses a data structure consisting of a series of dynamically-allocated linked lists. These lists allow the mesh connectivity to be rapidly reconstructed when individual mesh points are added and/or deleted. The algorithm allows the mesh to change in an anisotropic manner in order to efficiently resolve directional flow features. The procedure has been successfully implemented on a single processor of a Cray Y-MP computer. Two sample cases are presented involving three-dimensional transonic flow. Computed results show good agreement with conventional structured-grid solutions for the Euler equations.

  18. Self-Avoiding Walks over Adaptive Triangular Grids

    NASA Technical Reports Server (NTRS)

    Heber, Gerd; Biswas, Rupak; Gao, Guang R.; Saini, Subhash (Technical Monitor)

    1998-01-01

    In this paper, we present a new approach to constructing a "self-avoiding" walk through a triangular mesh. Unlike the popular approach of visiting mesh elements using space-filling curves which is based on a geometric embedding, our approach is combinatorial in the sense that it uses the mesh connectivity only. We present an algorithm for constructing a self-avoiding walk which can be applied to any unstructured triangular mesh. The complexity of the algorithm is O(n x log(n)), where n is the number of triangles in the mesh. We show that for hierarchical adaptive meshes, the algorithm can be easily parallelized by taking advantage of the regularity of the refinement rules. The proposed approach should be very useful in the run-time partitioning and load balancing of adaptive unstructured grids.

  19. Modeling scramjet combustor flowfields with a grid adaptation scheme

    NASA Technical Reports Server (NTRS)

    Ramakrishnan, R.; Singh, D. J.

    1994-01-01

    The accurate description of flow features associated with the normal injection of fuel into supersonic primary flows is essential in the design of efficient engines for hypervelocity aerospace vehicles. The flow features in such injections are complex with multiple interactions between shocks and between shocks boundary layers. Numerical studies of perpendicular sonic N2 injection and mixing in a Mach 3.8 scramjet combustor environment are discussed. A dynamic grid adaptation procedure based on the equilibration of spring-mass system is employed to enhanced the description of the complicated flow features. Numerical results are compared with experimental measurements and indicate that the adaptation procedure enhances the capability of the modeling procedure to describe the flow features associated with scramjet combustor components.

  20. Complex Patterns of Local Adaptation in Teosinte

    PubMed Central

    Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

    2013-01-01

    Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

  1. Time-dependent grid adaptation for meshes of triangles and tetrahedra

    NASA Technical Reports Server (NTRS)

    Rausch, Russ D.

    1993-01-01

    This paper presents in viewgraph form a method of optimizing grid generation for unsteady CFD flow calculations that distributes the numerical error evenly throughout the mesh. Adaptive meshing is used to locally enrich in regions of relatively large errors and to locally coarsen in regions of relatively small errors. The enrichment/coarsening procedures are robust for isotropic cells; however, enrichment of high aspect ratio cells may fail near boundary surfaces with relatively large curvature. The enrichment indicator worked well for the cases shown, but in general requires user supervision for a more efficient solution.

  2. Parallel Computation of Three-Dimensional Flows using Overlapping Grids with Adaptive Mesh Refinement

    SciTech Connect

    Henshaw, W; Schwendeman, D

    2007-11-15

    This paper describes an approach for the numerical solution of time-dependent partial differential equations in complex three-dimensional domains. The domains are represented by overlapping structured grids, and block-structured adaptive mesh refinement (AMR) is employed to locally increase the grid resolution. In addition, the numerical method is implemented on parallel distributed-memory computers using a domain-decomposition approach. The implementation is flexible so that each base grid within the overlapping grid structure and its associated refinement grids can be independently partitioned over a chosen set of processors. A modified bin-packing algorithm is used to specify the partition for each grid so that the computational work is evenly distributed amongst the processors. All components of the AMR algorithm such as error estimation, regridding, and interpolation are performed in parallel. The parallel time-stepping algorithm is illustrated for initial-boundary-value problems involving a linear advection-diffusion equation and the (nonlinear) reactive Euler equations. Numerical results are presented for both equations to demonstrate the accuracy and correctness of the parallel approach. Exact solutions of the advection-diffusion equation are constructed, and these are used to check the corresponding numerical solutions for a variety of tests involving different overlapping grids, different numbers of refinement levels and refinement ratios, and different numbers of processors. The problem of planar shock diffraction by a sphere is considered as an illustration of the numerical approach for the Euler equations, and a problem involving the initiation of a detonation from a hot spot in a T-shaped pipe is considered to demonstrate the numerical approach for the reactive case. For both problems, the solutions are shown to be well resolved on the finest grid. The parallel performance of the approach is examined in detail for the shock diffraction problem.

  3. Local remeshing for large amplitude grid deformations

    NASA Astrophysics Data System (ADS)

    Moyle, Keri R.; Ventikos, Yiannis

    2008-02-01

    Fluid-structure interaction (FSI) modelling can involve large deformations in the fluid domain, which could lead to degenerating mesh quality and numerical inaccuracies or instabilities, if allowed to amplify unchecked. Complete remeshing of the entire domain during the solution process is computationally expensive, and can require interpolation of solution variables between meshes. As an alternative, we investigate a local remeshing algorithm, with two emphases: (a) the identification and remedy of flat, degenerate tetrahedra, and (b) the avoidance of node motion, and hence associated interpolation errors. Initially, possible topological changes are examined using a dynamic programming algorithm to maximise the minimum local element quality through edge reconnection. In the 3D situation it was found that reconnection improvements tend to be limited to long edges, and those with few (three or four) element neighbours. The remaining degenerate elements are classified into one of four types using three proposed metrics - the minimum edge-to-edge distance (EE), the minimum node-to-edge distance (NE), and the shortest edge length (SE) - and removed according to the best manner for their type. Optimised thresholds for identifying and classifying elements for removal were found to be EE < 0.18, NE < 0.21, SE < 0.2.

  4. Adaptive sparse grid expansions of the vibrational Hamiltonian

    NASA Astrophysics Data System (ADS)

    Strobusch, D.; Scheurer, Ch.

    2014-02-01

    The vibrational Hamiltonian involves two high dimensional operators, the kinetic energy operator (KEO), and the potential energy surface (PES). Both must be approximated for systems involving more than a few atoms. Adaptive approximation schemes are not only superior to truncated Taylor or many-body expansions (MBE), they also allow for error estimates, and thus operators of predefined precision. To this end, modified sparse grids (SG) are developed that can be combined with adaptive MBEs. This MBE/SG hybrid approach yields a unified, fully adaptive representation of the KEO and the PES. Refinement criteria, based on the vibrational self-consistent field (VSCF) and vibrational configuration interaction (VCI) methods, are presented. The combination of the adaptive MBE/SG approach and the VSCF plus VCI methods yields a black box like procedure to compute accurate vibrational spectra. This is demonstrated on a test set of molecules, comprising water, formaldehyde, methanimine, and ethylene. The test set is first employed to prove convergence for semi-empirical PM3-PESs and subsequently to compute accurate vibrational spectra from CCSD(T)-PESs that agree well with experimental values.

  5. Adaptive sparse grid expansions of the vibrational Hamiltonian

    SciTech Connect

    Strobusch, D.; Scheurer, Ch.

    2014-02-21

    The vibrational Hamiltonian involves two high dimensional operators, the kinetic energy operator (KEO), and the potential energy surface (PES). Both must be approximated for systems involving more than a few atoms. Adaptive approximation schemes are not only superior to truncated Taylor or many-body expansions (MBE), they also allow for error estimates, and thus operators of predefined precision. To this end, modified sparse grids (SG) are developed that can be combined with adaptive MBEs. This MBE/SG hybrid approach yields a unified, fully adaptive representation of the KEO and the PES. Refinement criteria, based on the vibrational self-consistent field (VSCF) and vibrational configuration interaction (VCI) methods, are presented. The combination of the adaptive MBE/SG approach and the VSCF plus VCI methods yields a black box like procedure to compute accurate vibrational spectra. This is demonstrated on a test set of molecules, comprising water, formaldehyde, methanimine, and ethylene. The test set is first employed to prove convergence for semi-empirical PM3-PESs and subsequently to compute accurate vibrational spectra from CCSD(T)-PESs that agree well with experimental values.

  6. The use of solution adaptive grids in solving partial differential equations

    NASA Technical Reports Server (NTRS)

    Anderson, D. A.; Rai, M. M.

    1982-01-01

    The grid point distribution used in solving a partial differential equation using a numerical method has a substantial influence on the quality of the solution. An adaptive grid which adjusts as the solution changes provides the best results when the number of grid points available for use during the calculation is fixed. Basic concepts used in generating and applying adaptive grids are reviewed in this paper, and examples illustrating applications of these concepts are presented.

  7. A parallel dynamic load balancing algorithm for 3-D adaptive unstructured grids

    NASA Technical Reports Server (NTRS)

    Vidwans, A.; Kallinderis, Y.; Venkatakrishnan, V.

    1993-01-01

    Adaptive local grid refinement and coarsening results in unequal distribution of workload among the processors of a parallel system. A novel method for balancing the load in cases of dynamically changing tetrahedral grids is developed. The approach employs local exchange of cells among processors in order to redistribute the load equally. An important part of the load balancing algorithm is the method employed by a processor to determine which cells within its subdomain are to be exchanged. Two such methods are presented and compared. The strategy for load balancing is based on the Divide-and-Conquer approach which leads to an efficient parallel algorithm. This method is implemented on a distributed-memory MIMD system.

  8. Local climatic adaptation in a widespread microorganism

    PubMed Central

    Leducq, Jean-Baptiste; Charron, Guillaume; Samani, Pedram; Dubé, Alexandre K.; Sylvester, Kayla; James, Brielle; Almeida, Pedro; Sampaio, José Paulo; Hittinger, Chris Todd; Bell, Graham; Landry, Christian R.

    2014-01-01

    Exploring the ability of organisms to locally adapt is critical for determining the outcome of rapid climate changes, yet few studies have addressed this question in microorganisms. We investigated the role of a heterogeneous climate on adaptation of North American populations of the wild yeast Saccharomyces paradoxus. We found abundant among-strain variation for fitness components across a range of temperatures, but this variation was only partially explained by climatic variation in the distribution area. Most of fitness variation was explained by the divergence of genetically distinct groups, distributed along a north–south cline, suggesting that these groups have adapted to distinct climatic conditions. Within-group fitness components were correlated with climatic conditions, illustrating that even ubiquitous microorganisms locally adapt and harbour standing genetic variation for climate-related traits. Our results suggest that global climatic changes could lead to adaptation to new conditions within groups, or changes in their geographical distributions. PMID:24403328

  9. Comparison of local grid refinement methods for MODFLOW

    USGS Publications Warehouse

    Mehl, S.; Hill, M.C.; Leake, S.A.

    2006-01-01

    Many ground water modeling efforts use a finite-difference method to solve the ground water flow equation, and many of these models require a relatively fine-grid discretization to accurately represent the selected process in limited areas of interest. Use of a fine grid over the entire domain can be computationally prohibitive; using a variably spaced grid can lead to cells with a large aspect ratio and refinement in areas where detail is not needed. One solution is to use local-grid refinement (LGR) whereby the grid is only refined in the area of interest. This work reviews some LGR methods and identifies advantages and drawbacks in test cases using MODFLOW-2000. The first test case is two dimensional and heterogeneous; the second is three dimensional and includes interaction with a meandering river. Results include simulations using a uniform fine grid, a variably spaced grid, a traditional method of LGR without feedback, and a new shared node method with feedback. Discrepancies from the solution obtained with the uniform fine grid are investigated. For the models tested, the traditional one-way coupled approaches produced discrepancies in head up to 6.8% and discrepancies in cell-to-cell fluxes up to 7.1%, while the new method has head and cell-to-cell flux discrepancies of 0.089% and 0.14%, respectively. Additional results highlight the accuracy, flexibility, and CPU time trade-off of these methods and demonstrate how the new method can be successfully implemented to model surface water-ground water interactions. Copyright ?? 2006 The Author(s).

  10. An a-posteriori finite element error estimator for adaptive grid computation of viscous incompressible flows

    NASA Astrophysics Data System (ADS)

    Wu, Heng

    2000-10-01

    In this thesis, an a-posteriori error estimator is presented and employed for solving viscous incompressible flow problems. In an effort to detect local flow features, such as vortices and separation, and to resolve flow details precisely, a velocity angle error estimator e theta which is based on the spatial derivative of velocity direction fields is designed and constructed. The a-posteriori error estimator corresponds to the antisymmetric part of the deformation-rate-tensor, and it is sensitive to the second derivative of the velocity angle field. Rationality discussions reveal that the velocity angle error estimator is a curvature error estimator, and its value reflects the accuracy of streamline curves. It is also found that the velocity angle error estimator contains the nonlinear convective term of the Navier-Stokes equations, and it identifies and computes the direction difference when the convective acceleration direction and the flow velocity direction have a disparity. Through benchmarking computed variables with the analytic solution of Kovasznay flow or the finest grid of cavity flow, it is demonstrated that the velocity angle error estimator has a better performance than the strain error estimator. The benchmarking work also shows that the computed profile obtained by using etheta can achieve the best matching outcome with the true theta field, and that it is asymptotic to the true theta variation field, with a promise of fewer unknowns. Unstructured grids are adapted by employing local cell division as well as unrefinement of transition cells. Using element class and node class can efficiently construct a hierarchical data structure which provides cell and node inter-reference at each adaptive level. Employing element pointers and node pointers can dynamically maintain the connection of adjacent elements and adjacent nodes, and thus avoids time-consuming search processes. The adaptive scheme is applied to viscous incompressible flow at different

  11. Anisotropic Solution Adaptive Unstructured Grid Generation Using AFLR

    NASA Technical Reports Server (NTRS)

    Marcum, David L.

    2007-01-01

    An existing volume grid generation procedure, AFLR3, was successfully modified to generate anisotropic tetrahedral elements using a directional metric transformation defined at source nodes. The procedure can be coupled with a solver and an error estimator as part of an overall anisotropic solution adaptation methodology. It is suitable for use with an error estimator based on an adjoint, optimization, sensitivity derivative, or related approach. This offers many advantages, including more efficient point placement along with robust and efficient error estimation. It also serves as a framework for true grid optimization wherein error estimation and computational resources can be used as cost functions to determine the optimal point distribution. Within AFLR3 the metric transformation is implemented using a set of transformation vectors and associated aspect ratios. The modified overall procedure is presented along with details of the anisotropic transformation implementation. Multiple two-and three-dimensional examples are also presented that demonstrate the capability of the modified AFLR procedure to generate anisotropic elements using a set of source nodes with anisotropic transformation metrics. The example cases presented use moderate levels of anisotropy and result in usable element quality. Future testing with various flow solvers and methods for obtaining transformation metric information is needed to determine practical limits and evaluate the efficacy of the overall approach.

  12. Volumetric Rendering of Geophysical Data on Adaptive Wavelet Grid

    NASA Astrophysics Data System (ADS)

    Vezolainen, A.; Erlebacher, G.; Vasilyev, O.; Yuen, D. A.

    2005-12-01

    Numerical modeling of geological phenomena frequently involves processes across a wide range of spatial and temporal scales. In the last several years, transport phenomena governed by the Navier-Stokes equations have been simulated in wavelet space using second generation wavelets [1], and most recently on fully adaptive meshes. Our objective is to visualize this time-dependent data using volume rendering while capitalizing on the available sparse data representation. We present a technique for volumetric ray casting of multi-scale datasets in wavelet space. Rather of working with the wavelets at the finest possible resolution, we perform a partial inverse wavelet transform as a preprocessing step to obtain scaling functions on a uniform grid at a user-prescribed resolution. As a result, a function in physical space is represented by a superposition of scaling functions on a coarse regular grid and wavelets on an adaptive mesh. An efficient and accurate ray casting algorithm is based just on these scaling functions. Additional detail is added during the ray tracing by taking an appropriate number of wavelets into account based on support overlap with the interpolation point, wavelet amplitude, and other characteristics, such as opacity accumulation (front to back ordering) and deviation from frontal viewing direction. Strategies for hardware implementation will be presented if available, inspired by the work in [2]. We will pressent error measures as a function of the number of scaling and wavelet functions used for interpolation. Data from mantle convection will be used to illustrate the method. [1] Vasilyev, O.V. and Bowman, C., Second Generation Wavelet Collocation Method for the Solution of Partial Differential Equations. J. Comp. Phys., 165, pp. 660-693, 2000. [2] Guthe, S., Wand, M., Gonser, J., and Straßer, W. Interactive rendering of large volume data sets. In Proceedings of the Conference on Visualization '02 (Boston, Massachusetts, October 27 - November

  13. Micro Benchmarking, Performance Assertions and Sensitivity Analysis: A Technique for Developing Adaptive Grid Applications

    SciTech Connect

    Corey, I R; Johnson, J R; Vetter, J S

    2002-02-25

    This study presents a technique that can significantly improve the performance of a distributed application by allowing the application to locally adapt to architectural characteristics of distinct resources in a distributed system. Application performance is sensitive to application parameter--system architecture pairings. In a distributed or Grid enabled applciation, a single parameter configuration for the whole application will not always be optimal for every participating resource. In particular, some configurations can significantly degrade performance. Furthermore, the behavior of a system may change during the course of the run. The technique described here provides an automated mechanism for run-time adaptation of application parameters to the local system architecture. Using a simulation of a Monte Carlo physics code, the authors demonstrate that this technique can achieve speedups of 18%-37% on individual resources in a distributed environment.

  14. Power Prediction in Smart Grids with Evolutionary Local Kernel Regression

    NASA Astrophysics Data System (ADS)

    Kramer, Oliver; Satzger, Benjamin; Lässig, Jörg

    Electric grids are moving from a centralized single supply chain towards a decentralized bidirectional grid of suppliers and consumers in an uncertain and dynamic scenario. Soon, the growing smart meter infrastructure will allow the collection of terabytes of detailed data about the grid condition, e.g., the state of renewable electric energy producers or the power consumption of millions of private customers, in very short time steps. For reliable prediction strong and fast regression methods are necessary that are able to cope with these challenges. In this paper we introduce a novel regression technique, i.e., evolutionary local kernel regression, a kernel regression variant based on local Nadaraya-Watson estimators with independent bandwidths distributed in data space. The model is regularized with the CMA-ES, a stochastic non-convex optimization method. We experimentally analyze the load forecast behavior on real power consumption data. The proposed method is easily parallelizable, and therefore well appropriate for large-scale scenarios in smart grids.

  15. FUN3D Grid Refinement and Adaptation Studies for the Ares Launch Vehicle

    NASA Technical Reports Server (NTRS)

    Bartels, Robert E.; Vasta, Veer; Carlson, Jan-Renee; Park, Mike; Mineck, Raymond E.

    2010-01-01

    This paper presents grid refinement and adaptation studies performed in conjunction with computational aeroelastic analyses of the Ares crew launch vehicle (CLV). The unstructured grids used in this analysis were created with GridTool and VGRID while the adaptation was performed using the Computational Fluid Dynamic (CFD) code FUN3D with a feature based adaptation software tool. GridTool was developed by ViGYAN, Inc. while the last three software suites were developed by NASA Langley Research Center. The feature based adaptation software used here operates by aligning control volumes with shock and Mach line structures and by refining/de-refining where necessary. It does not redistribute node points on the surface. This paper assesses the sensitivity of the complex flow field about a launch vehicle to grid refinement. It also assesses the potential of feature based grid adaptation to improve the accuracy of CFD analysis for a complex launch vehicle configuration. The feature based adaptation shows the potential to improve the resolution of shocks and shear layers. Further development of the capability to adapt the boundary layer and surface grids of a tetrahedral grid is required for significant improvements in modeling the flow field.

  16. A time-accurate adaptive grid method and the numerical simulation of a shock-vortex interaction

    NASA Technical Reports Server (NTRS)

    Bockelie, Michael J.; Eiseman, Peter R.

    1990-01-01

    A time accurate, general purpose, adaptive grid method is developed that is suitable for multidimensional steady and unsteady numerical simulations. The grid point movement is performed in a manner that generates smooth grids which resolve the severe solution gradients and the sharp transitions in the solution gradients. The temporal coupling of the adaptive grid and the PDE solver is performed with a grid prediction correction method that is simple to implement and ensures the time accuracy of the grid. Time accurate solutions of the 2-D Euler equations for an unsteady shock vortex interaction demonstrate the ability of the adaptive method to accurately adapt the grid to multiple solution features.

  17. Cartesian Off-Body Grid Adaption for Viscous Time- Accurate Flow Simulation

    NASA Technical Reports Server (NTRS)

    Buning, Pieter G.; Pulliam, Thomas H.

    2011-01-01

    An improved solution adaption capability has been implemented in the OVERFLOW overset grid CFD code. Building on the Cartesian off-body approach inherent in OVERFLOW and the original adaptive refinement method developed by Meakin, the new scheme provides for automated creation of multiple levels of finer Cartesian grids. Refinement can be based on the undivided second-difference of the flow solution variables, or on a specific flow quantity such as vorticity. Coupled with load-balancing and an inmemory solution interpolation procedure, the adaption process provides very good performance for time-accurate simulations on parallel compute platforms. A method of using refined, thin body-fitted grids combined with adaption in the off-body grids is presented, which maximizes the part of the domain subject to adaption. Two- and three-dimensional examples are used to illustrate the effectiveness and performance of the adaption scheme.

  18. Analysis of a Major Electric Grid -- Stability and Adaptive Protection

    NASA Astrophysics Data System (ADS)

    Alanzi, Sultan

    Protective systems of the electric grid are designed to detect and mitigate the effects of faults and other disturbances that may occur. Distance relays are used extensively for the detection of faults on transmission lines. Out-of-step relays are used for generator protection to detect loss of synchronism conditions that result from disturbances on the electric grid. Also, when a disturbance occurs and generators may tend to lose synchronism with each other, it is beneficial to separate the overall system into several independent systems that can remain stable. Unfortunately there have been cases, such as the 2003 Northeast blackout where the operation of protective relays, namely the zone 3 distance relay used for transmission line protection, contributed to the cascading effect of the blackout. It is the objective of this dissertation to propose adaptive relays for both distance protection of transmission lines and out-of-step protection of generators. By being adaptive, the relays are made aware of the system operating conditions and can adjust its settings accordingly. Inputs to the adaptive logic can come from system or environmental conditions. As a result of this effort, a new distance relay operating characteristic is proposed, referred to as a mushroom relay, which is a combination of a quadrilateral relay and a Mho relay. Also, a new criterion for determining if a power swing following a disturbance is stable or unstable is proposed. Distance protection of transmission lines is very important when discussing system responses to faults and disturbances. Distance relays are very common worldwide and although they offer great protection, there are limitations that need to be addressed. Parallel line operations (infeed effect) and the loadability limits are among the limitations that lead to improper response of relays. An Adaptive Distance Relays (ADR) offer great benefits to the protection scheme as their settings can be changed in accordance with prefault

  19. Analysis of a Major Electric Grid -- Stability and Adaptive Protection

    NASA Astrophysics Data System (ADS)

    Alanzi, Sultan

    Protective systems of the electric grid are designed to detect and mitigate the effects of faults and other disturbances that may occur. Distance relays are used extensively for the detection of faults on transmission lines. Out-of-step relays are used for generator protection to detect loss of synchronism conditions that result from disturbances on the electric grid. Also, when a disturbance occurs and generators may tend to lose synchronism with each other, it is beneficial to separate the overall system into several independent systems that can remain stable. Unfortunately there have been cases, such as the 2003 Northeast blackout where the operation of protective relays, namely the zone 3 distance relay used for transmission line protection, contributed to the cascading effect of the blackout. It is the objective of this dissertation to propose adaptive relays for both distance protection of transmission lines and out-of-step protection of generators. By being adaptive, the relays are made aware of the system operating conditions and can adjust its settings accordingly. Inputs to the adaptive logic can come from system or environmental conditions. As a result of this effort, a new distance relay operating characteristic is proposed, referred to as a mushroom relay, which is a combination of a quadrilateral relay and a Mho relay. Also, a new criterion for determining if a power swing following a disturbance is stable or unstable is proposed. Distance protection of transmission lines is very important when discussing system responses to faults and disturbances. Distance relays are very common worldwide and although they offer great protection, there are limitations that need to be addressed. Parallel line operations (infeed effect) and the loadability limits are among the limitations that lead to improper response of relays. An Adaptive Distance Relays (ADR) offer great benefits to the protection scheme as their settings can be changed in accordance with prefault

  20. The creation of local clusters in arbitrarily given grids

    NASA Technical Reports Server (NTRS)

    Eiseman, Peter R.

    1986-01-01

    A method is presented to smoothly insert pointwise clusters into any given grid regardless of its origin, its topology, or its dimensionality. The process amounts to a local movement of the given coordinate curves or surfaces to more highly resolve an object. The object about which clustering is created can be a point, a curve, a surface, or segments of a curve or surface. The basic clustering capability is established by forming a grid operator for a single cluster. With a view toward multiple clusters being created about various objects, the basic operator is seen as an elementary operator. An algorithm is presented to execute the general elementary operation in three dimensions. In FORTRAN, this assumes the form of a subroutine which is fully operational and is presented to serve as a basic model for any such elementary clustering operation.

  1. Adaptive data management in the ARC Grid middleware

    NASA Astrophysics Data System (ADS)

    Cameron, D.; Gholami, A.; Karpenko, D.; Konstantinov, A.

    2011-12-01

    The Advanced Resource Connector (ARC) Grid middleware was designed almost 10 years ago, and has proven to be an attractive distributed computing solution and successful in adapting to new data management and storage technologies. However, with an ever-increasing user base and scale of resources to manage, along with the introduction of more advanced data transfer protocols, some limitations in the current architecture have become apparent. The simple first-in first-out approach to data transfer leads to bottlenecks in the system, as does the built-in assumption that all data is immediately available from remote data storage. We present an entirely new data management architecture for ARC which aims to alleviate these problems, by introducing a three-layer structure. The top layer accepts incoming requests for data transfer and directs them to the middle layer, which schedules individual transfers and negotiates with various intermediate catalog and storage systems until the physical file is ready to be transferred. The lower layer performs all operations which use large amounts of bandwidth, i.e. the physical data transfer. Using such a layered structure allows more efficient use of the available bandwidth as well as enabling late-binding of jobs to data transfer slots based on a priority system. Here we describe in full detail the design and implementation of the new system.

  2. Emergent Adaptive Noise Reduction from Communal Cooperation of Sensor Grid

    NASA Technical Reports Server (NTRS)

    Jones, Kennie H.; Jones, Michael G.; Nark, Douglas M.; Lodding, Kenneth N.

    2010-01-01

    In the last decade, the realization of small, inexpensive, and powerful devices with sensors, computers, and wireless communication has promised the development of massive sized sensor networks with dense deployments over large areas capable of high fidelity situational assessments. However, most management models have been based on centralized control and research has concentrated on methods for passing data from sensor devices to the central controller. Most implementations have been small but, as it is not scalable, this methodology is insufficient for massive deployments. Here, a specific application of a large sensor network for adaptive noise reduction demonstrates a new paradigm where communities of sensor/computer devices assess local conditions and make local decisions from which emerges a global behaviour. This approach obviates many of the problems of centralized control as it is not prone to single point of failure and is more scalable, efficient, robust, and fault tolerant

  3. Adaptive finite-volume WENO schemes on dynamically redistributed grids for compressible Euler equations

    NASA Astrophysics Data System (ADS)

    Pathak, Harshavardhana S.; Shukla, Ratnesh K.

    2016-08-01

    A high-order adaptive finite-volume method is presented for simulating inviscid compressible flows on time-dependent redistributed grids. The method achieves dynamic adaptation through a combination of time-dependent mesh node clustering in regions characterized by strong solution gradients and an optimal selection of the order of accuracy and the associated reconstruction stencil in a conservative finite-volume framework. This combined approach maximizes spatial resolution in discontinuous regions that require low-order approximations for oscillation-free shock capturing. Over smooth regions, high-order discretization through finite-volume WENO schemes minimizes numerical dissipation and provides excellent resolution of intricate flow features. The method including the moving mesh equations and the compressible flow solver is formulated entirely on a transformed time-independent computational domain discretized using a simple uniform Cartesian mesh. Approximations for the metric terms that enforce discrete geometric conservation law while preserving the fourth-order accuracy of the two-point Gaussian quadrature rule are developed. Spurious Cartesian grid induced shock instabilities such as carbuncles that feature in a local one-dimensional contact capturing treatment along the cell face normals are effectively eliminated through upwind flux calculation using a rotated Hartex-Lax-van Leer contact resolving (HLLC) approximate Riemann solver for the Euler equations in generalized coordinates. Numerical experiments with the fifth and ninth-order WENO reconstructions at the two-point Gaussian quadrature nodes, over a range of challenging test cases, indicate that the redistributed mesh effectively adapts to the dynamic flow gradients thereby improving the solution accuracy substantially even when the initial starting mesh is non-adaptive. The high adaptivity combined with the fifth and especially the ninth-order WENO reconstruction allows remarkably sharp capture of

  4. Generation and adaptation of 3-D unstructured grids for transient problems

    NASA Technical Reports Server (NTRS)

    Loehner, Rainald

    1990-01-01

    Grid generation and adaptive refinement techniques suitable for the simulation of strongly unsteady flows past geometrically complex bodies in 3-D are described. The grids are generated using the advancing front technique. Emphasis is placed not to generate elements that are too small, as this would severely increase the cost of simulations with explicit flow solvers. The grids are adapted to an evolving flowfield using simple h-refinement. A grid change is performed every 5 to 10 timesteps, and only one level of refinement/coarsening is allowed per mesh change.

  5. Practical improvements of multi-grid iteration for adaptive mesh refinement method

    NASA Astrophysics Data System (ADS)

    Miyashita, Hisashi; Yamada, Yoshiyuki

    2005-03-01

    Adaptive mesh refinement(AMR) is a powerful tool to efficiently solve multi-scaled problems. However, the vanilla AMR method has a well-known critical demerit, i.e., it cannot be applied to non-local problems. Although multi-grid iteration (MGI) can be regarded as a good remedy for a non-local problem such as the Poisson equation, we observed fundamental difficulties in applying the MGI technique in AMR to realistic problems under complicated mesh layouts because it does not converge or it requires too many iterations even if it does converge. To cope with the problem, when updating the next approximation in the MGI process, we calculate the precise total corrections that are relatively accurate to the current residual by introducing a new iteration for such a total correction. This procedure greatly accelerates the MGI convergence speed especially under complicated mesh layouts.

  6. Automated Grid Disruption Response System: Robust Adaptive Topology Control (RATC)

    SciTech Connect

    2012-03-01

    GENI Project: The RATC research team is using topology control as a mechanism to improve system operations and manage disruptions within the electric grid. The grid is subject to interruption from cascading faults caused by extreme operating conditions, malicious external attacks, and intermittent electricity generation from renewable energy sources. The RATC system is capable of detecting, classifying, and responding to grid disturbances by reconfiguring the grid in order to maintain economically efficient operations while guaranteeing reliability. The RATC system would help prevent future power outages, which account for roughly $80 billion in losses for businesses and consumers each year. Minimizing the time it takes for the grid to respond to expensive interruptions will also make it easier to integrate intermittent renewable energy sources into the grid.

  7. A multigrid method for steady Euler equations on unstructured adaptive grids

    NASA Technical Reports Server (NTRS)

    Riemslagh, Kris; Dick, Erik

    1993-01-01

    A flux-difference splitting type algorithm is formulated for the steady Euler equations on unstructured grids. The polynomial flux-difference splitting technique is used. A vertex-centered finite volume method is employed on a triangular mesh. The multigrid method is in defect-correction form. A relaxation procedure with a first order accurate inner iteration and a second-order correction performed only on the finest grid, is used. A multi-stage Jacobi relaxation method is employed as a smoother. Since the grid is unstructured a Jacobi type is chosen. The multi-staging is necessary to provide sufficient smoothing properties. The domain is discretized using a Delaunay triangular mesh generator. Three grids with more or less uniform distribution of nodes but with different resolution are generated by successive refinement of the coarsest grid. Nodes of coarser grids appear in the finer grids. The multigrid method is started on these grids. As soon as the residual drops below a threshold value, an adaptive refinement is started. The solution on the adaptively refined grid is accelerated by a multigrid procedure. The coarser multigrid grids are generated by successive coarsening through point removement. The adaption cycle is repeated a few times. Results are given for the transonic flow over a NACA-0012 airfoil.

  8. Aeroacoustic Simulation of Nose Landing Gear on Adaptive Unstructured Grids With FUN3D

    NASA Technical Reports Server (NTRS)

    Vatsa, Veer N.; Khorrami, Mehdi R.; Park, Michael A.; Lockhard, David P.

    2013-01-01

    Numerical simulations have been performed for a partially-dressed, cavity-closed nose landing gear configuration that was tested in NASA Langley s closed-wall Basic Aerodynamic Research Tunnel (BART) and in the University of Florida's open-jet acoustic facility known as the UFAFF. The unstructured-grid flow solver FUN3D, developed at NASA Langley Research center, is used to compute the unsteady flow field for this configuration. Starting with a coarse grid, a series of successively finer grids were generated using the adaptive gridding methodology available in the FUN3D code. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence model is used for these computations. Time-averaged and instantaneous solutions obtained on these grids are compared with the measured data. In general, the correlation with the experimental data improves with grid refinement. A similar trend is observed for sound pressure levels obtained by using these CFD solutions as input to a FfowcsWilliams-Hawkings noise propagation code to compute the farfield noise levels. In general, the numerical solutions obtained on adapted grids compare well with the hand-tuned enriched fine grid solutions and experimental data. In addition, the grid adaption strategy discussed here simplifies the grid generation process, and results in improved computational efficiency of CFD simulations.

  9. Stable Collocated-grid Finite Difference Seismic Wave Modeling Using Discontinuous Grids with Locally Variable Time Steps

    NASA Astrophysics Data System (ADS)

    Li, H.; Zhang, Z.; Chen, X.

    2012-12-01

    It is widely accepted that they are oversampled in spatial grid spacing and temporal time step in the high speed medium if uniform grids are used for the numerical simulation. This oversampled grid spacing and time step will lower the efficiency of the calculation, especially high velocity contrast exists. Based on the collocated-grid finite-difference method (FDM), we present an algorithm of spatial discontinuous grid, with localized grid blocks and locally varying time steps, which will increase the efficiency of simulation of seismic wave propagation and earthquake strong ground motion. According to the velocity structure, we discretize the model into discontinuous grid blocks, and the time step of each block is determined according to the local stability. The key problem of the discontinuous grid method is the connection between grid blocks with different grid spacing. We use a transitional area overlapped by both of the finer and the coarser grids to deal with the problem. In the transitional area, the values of finer ghost points are obtained by interpolation from the coarser grid in space and time domain, while the values of coarser ghost points are obtained by downsampling from the finer grid. How to deal with coarser ghost points can influent the stability of long time simulation. After testing different downsampling methods and finally we choose the Gaussian filtering. Basically, 4th order Rung-Kutta scheme will be used for the time integral for our numerical method. For our discontinuous grid FDM, discontinuous time steps for the coarser and the finer grids will be used to increase the simulation efficiency. Numerical tests indicate that our method can provide a stable solution even for the long time simulation without any additional filtration for grid spacing ratio n=2. And for larger grid spacing ratio, Gaussian filtration could be used to preserve the stability. With the collocated-grid FDM, which is flexible and accurate in implementation of free

  10. Simulation of the dispersion of nuclear contamination using an adaptive Eulerian grid model.

    PubMed

    Lagzi, I; Kármán, D; Turányi, T; Tomlin, A S; Haszpra, L

    2004-01-01

    Application of an Eulerian model using layered adaptive unstructured grids coupled to a meso-scale meteorological model is presented for modelling the dispersion of nuclear contamination following the accidental release from a single but strong source to the atmosphere. The model automatically places a finer resolution grid, adaptively in time, in regions were high spatial numerical error is expected. The high-resolution grid region follows the movement of the contaminated air over time. Using this method, grid resolutions of the order of 6 km can be achieved in a computationally effective way. The concept is illustrated by the simulation of hypothetical nuclear accidents at the Paks NPP, in Central Hungary. The paper demonstrates that the adaptive model can achieve accuracy comparable to that of a high-resolution Eulerian model using significantly less grid points and computer simulation time. PMID:15149762

  11. Improving mobile robot localization: grid-based approach

    NASA Astrophysics Data System (ADS)

    Yan, Junchi

    2012-02-01

    Autonomous mobile robots have been widely studied not only as advanced facilities for industrial and daily life automation, but also as a testbed in robotics competitions for extending the frontier of current artificial intelligence. In many of such contests, the robot is supposed to navigate on the ground with a grid layout. Based on this observation, we present a localization error correction method by exploring the geometric feature of the tile patterns. On top of the classical inertia-based positioning, our approach employs three fiber-optic sensors that are assembled under the bottom of the robot, presenting an equilateral triangle layout. The sensor apparatus, together with the proposed supporting algorithm, are designed to detect a line's direction (vertical or horizontal) by monitoring the grid crossing events. As a result, the line coordinate information can be fused to rectify the cumulative localization deviation from inertia positioning. The proposed method is analyzed theoretically in terms of its error bound and also has been implemented and tested on a customary developed two-wheel autonomous mobile robot.

  12. Arbitrary Lagrangian-Eulerian Method with Local Structured Adaptive Mesh Refinement for Modeling Shock Hydrodynamics

    SciTech Connect

    Anderson, R W; Pember, R B; Elliott, N S

    2001-10-22

    A new method that combines staggered grid Arbitrary Lagrangian-Eulerian (ALE) techniques with structured local adaptive mesh refinement (AMR) has been developed for solution of the Euler equations. This method facilitates the solution of problems currently at and beyond the boundary of soluble problems by traditional ALE methods by focusing computational resources where they are required through dynamic adaption. Many of the core issues involved in the development of the combined ALEAMR method hinge upon the integration of AMR with a staggered grid Lagrangian integration method. The novel components of the method are mainly driven by the need to reconcile traditional AMR techniques, which are typically employed on stationary meshes with cell-centered quantities, with the staggered grids and grid motion employed by Lagrangian methods. Numerical examples are presented which demonstrate the accuracy and efficiency of the method.

  13. Grid generation and adaptation for the Direct Simulation Monte Carlo Method. [for complex flows past wedges and cones

    NASA Technical Reports Server (NTRS)

    Olynick, David P.; Hassan, H. A.; Moss, James N.

    1988-01-01

    A grid generation and adaptation procedure based on the method of transfinite interpolation is incorporated into the Direct Simulation Monte Carlo Method of Bird. In addition, time is advanced based on a local criterion. The resulting procedure is used to calculate steady flows past wedges and cones. Five chemical species are considered. In general, the modifications result in a reduced computational effort. Moreover, preliminary results suggest that the simulation method is time step dependent if requirements on cell sizes are not met.

  14. SIMULATION OF DISPERSION OF A POWER PLANT PLUME USING AN ADAPTIVE GRID ALGORITHM

    EPA Science Inventory

    A new dynamic adaptive grid algorithm has been developed for use in air quality modeling. This algorithm uses a higher order numerical scheme?the piecewise parabolic method (PPM)?for computing advective solution fields; a weight function capable of promoting grid node clustering ...

  15. Multi-Hop Localization Algorithm Based on Grid-Scanning for Wireless Sensor Networks*

    PubMed Central

    Wan, Jiangwen; Guo, Xiaolei; Yu, Ning; Wu, Yinfeng; Feng, Renjian

    2011-01-01

    For large-scale wireless sensor networks (WSNs) with a minority of anchor nodes, multi-hop localization is a popular scheme for determining the geographical positions of the normal nodes. However, in practice existing multi-hop localization methods suffer from various kinds of problems, such as poor adaptability to irregular topology, high computational complexity, low positioning accuracy, etc. To address these issues in this paper, we propose a novel Multi-hop Localization algorithm based on Grid-Scanning (MLGS). First, the factors that influence the multi-hop distance estimation are studied and a more realistic multi-hop localization model is constructed. Then, the feasible regions of the normal nodes are determined according to the intersection of bounding square rings. Finally, a verifiably good approximation scheme based on grid-scanning is developed to estimate the coordinates of the normal nodes. Additionally, the positioning accuracy of the normal nodes can be improved through neighbors’ collaboration. Extensive simulations are performed in isotropic and anisotropic networks. The comparisons with some typical algorithms of node localization confirm the effectiveness and efficiency of our algorithm. PMID:22163828

  16. Local adaptation in the ventral photoreceptors of Limulus

    PubMed Central

    1975-01-01

    Local adaptation was demonstrated in the ventral photoreceptors of Lumulus using either flashes or continuous illumination. Spots of light locally desensitized the region of the photoreceptor on which they were focused. In dark-adapted photoreceptors where "quantum bumps" were clearly discernible, local adaptation of the quantum bumps was observed. Local adaptation could induce differences of threshold of 1 decade over distances of 50-80 mum. With continuous local illumination these gradients could be maintained from 2 s to 30 min. In addition, the decrease in time scale associated with light adaptation was also found to be localized to the region of illumination. PMID:1194890

  17. Local adaptive tone mapping for video enhancement

    NASA Astrophysics Data System (ADS)

    Lachine, Vladimir; Dai, Min (.

    2015-03-01

    As new technologies like High Dynamic Range cameras, AMOLED and high resolution displays emerge on consumer electronics market, it becomes very important to deliver the best picture quality for mobile devices. Tone Mapping (TM) is a popular technique to enhance visual quality. However, the traditional implementation of Tone Mapping procedure is limited by pixel's value to value mapping, and the performance is restricted in terms of local sharpness and colorfulness. To overcome the drawbacks of traditional TM, we propose a spatial-frequency based framework in this paper. In the proposed solution, intensity component of an input video/image signal is split on low pass filtered (LPF) and high pass filtered (HPF) bands. Tone Mapping (TM) function is applied to LPF band to improve the global contrast/brightness, and HPF band is added back afterwards to keep the local contrast. The HPF band may be adjusted by a coring function to avoid noise boosting and signal overshooting. Colorfulness of an original image may be preserved or enhanced by chroma components correction by means of saturation function. Localized content adaptation is further improved by dividing an image to a set of non-overlapped regions and modifying each region individually. The suggested framework allows users to implement a wide range of tone mapping applications with perceptional local sharpness and colorfulness preserved or enhanced. Corresponding hardware circuit may be integrated in camera, video or display pipeline with minimal hardware budget

  18. An Efficient Means of Adaptive Refinement Within Systems of Overset Grids

    NASA Technical Reports Server (NTRS)

    Meakin, Robert L.

    1996-01-01

    An efficient means of adaptive refinement within systems of overset grids is presented. Problem domains are segregated into near-body and off-body fields. Near-body fields are discretized via overlapping body-fitted grids that extend only a short distance from body surfaces. Off-body fields are discretized via systems of overlapping uniform Cartesian grids of varying levels of refinement. a novel off-body grid generation and management scheme provides the mechanism for carrying out adaptive refinement of off-body flow dynamics and solid body motion. The scheme allows for very efficient use of memory resources, and flow solvers and domain connectivity routines that can exploit the structure inherent to uniform Cartesian grids.

  19. Two methods for the study of vortex patch evolution on locally refined grids

    SciTech Connect

    Minion, M.L.

    1994-05-01

    Two numerical methods for the solution of the two-dimensional Euler equations for incompressible flow on locally refined grids are presented. The first is a second order projection method adapted from the method of Bell, Colella, and Glaz. The second method is based on the vorticity-stream function form of the Euler equations and is designed to be free-stream preserving and conservative. Second order accuracy of both methods in time and space is established, and they are shown to agree on problems with a localized vorticity distribution. The filamentation of a perturbed patch of circular vorticity and the merger of two smooth vortex patches are studied. It is speculated that for nearly stable patches of vorticity, an arbitrarily small amount of viscosity is sufficient to effectively eliminate vortex filaments from the evolving patch and that the filamentation process affects the evolution of such patches very little. Solutions of the vortex merger problem show that filamentation is responsible for the creation of large gradients in the vorticity which, in the presence of an arbitrarily small viscosity, will lead to vortex merger. It is speculated that a small viscosity in this problem does not substantially affect the transition of the flow to a statistical equilibrium solution. The main contributions of this thesis concern the formulation and implementation of a projection for refined grids. A careful analysis of the adjointness relation between gradient and divergence operators for a refined grid MAC projection is presented, and a uniformly accurate, approximately stable projection is developed. An efficient multigrid method which exactly solves the projection is developed, and a method for casting certain approximate projections as MAC projections on refined grids is presented.

  20. An adaptive discretization of incompressible flow using a multitude of moving Cartesian grids

    NASA Astrophysics Data System (ADS)

    English, R. Elliot; Qiu, Linhai; Yu, Yue; Fedkiw, Ronald

    2013-12-01

    We present a novel method for discretizing the incompressible Navier-Stokes equations on a multitude of moving and overlapping Cartesian grids each with an independently chosen cell size to address adaptivity. Advection is handled with first and second order accurate semi-Lagrangian schemes in order to alleviate any time step restriction associated with small grid cell sizes. Likewise, an implicit temporal discretization is used for the parabolic terms including Navier-Stokes viscosity which we address separately through the development of a method for solving the heat diffusion equations. The most intricate aspect of any such discretization is the method used in order to solve the elliptic equation for the Navier-Stokes pressure or that resulting from the temporal discretization of parabolic terms. We address this by first removing any degrees of freedom which duplicately cover spatial regions due to overlapping grids, and then providing a discretization for the remaining degrees of freedom adjacent to these regions. We observe that a robust second order accurate symmetric positive definite readily preconditioned discretization can be obtained by constructing a local Voronoi region on the fly for each degree of freedom in question in order to obtain both its stencil (logically connected neighbors) and stencil weights. Internal curved boundaries such as at solid interfaces are handled using a simple immersed boundary approach which is directly applied to the Voronoi mesh in both the viscosity and pressure solves. We independently demonstrate each aspect of our approach on test problems in order to show efficacy and convergence before finally addressing a number of common test cases for incompressible flow with stationary and moving solid bodies.

  1. FLAG: A multi-dimensional adaptive free-Lagrange code for fully unstructured grids

    SciTech Connect

    Burton, D.E.; Miller, D.S.; Palmer, T.

    1995-07-01

    The authors describe FLAG, a 3D adaptive free-Lagrange method for unstructured grids. The grid elements were 3D polygons, which move with the flow, and are refined or reconnected as necessary to achieve uniform accuracy. The authors stressed that they were able to construct a 3D hydro version of this code in 3 months, using an object-oriented FORTRAN approach.

  2. A Lagrangian-Eulerian finite element method with adaptive gridding for advection-dispersion problems

    SciTech Connect

    Ijiri, Y.; Karasaki, K.

    1994-02-01

    In the present paper, a Lagrangian-Eulerian finite element method with adaptive gridding for solving advection-dispersion equations is described. The code creates new grid points in the vicinity of sharp fronts at every time step in order to reduce numerical dispersion. The code yields quite accurate solutions for a wide range of mesh Peclet numbers and for mesh Courant numbers well in excess of 1.

  3. Unstructured Grid Adaptation: Status, Potential Impacts, and Recommended Investments Toward CFD Vision 2030

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Krakos, Joshua A.; Michal, Todd; Loseille, Adrien; Alonso, Juan J.

    2016-01-01

    Unstructured grid adaptation is a powerful tool to control discretization error for Computational Fluid Dynamics (CFD). It has enabled key increases in the accuracy, automation, and capacity of some fluid simulation applications. Slotnick et al. provides a number of case studies in the CFD Vision 2030 Study: A Path to Revolutionary Computational Aerosciences to illustrate the current state of CFD capability and capacity. The authors forecast the potential impact of emerging High Performance Computing (HPC) environments forecast in the year 2030 and identify that mesh generation and adaptivity continue to be significant bottlenecks in the CFD work flow. These bottlenecks may persist because very little government investment has been targeted in these areas. To motivate investment, the impacts of improved grid adaptation technologies are identified. The CFD Vision 2030 Study roadmap and anticipated capabilities in complementary disciplines are quoted to provide context for the progress made in grid adaptation in the past fifteen years, current status, and a forecast for the next fifteen years with recommended investments. These investments are specific to mesh adaptation and impact other aspects of the CFD process. Finally, a strategy is identified to diffuse grid adaptation technology into production CFD work flows.

  4. Grid coupling mechanism in the semi-implicit adaptive Multi-Level Multi-Domain method

    NASA Astrophysics Data System (ADS)

    Innocenti, M. E.; Tronci, C.; Markidis, S.; Lapenta, G.

    2016-05-01

    The Multi-Level Multi-Domain (MLMD) method is a semi-implicit adaptive method for Particle-In-Cell plasma simulations. It has been demonstrated in the past in simulations of Maxwellian plasmas, electrostatic and electromagnetic instabilities, plasma expansion in vacuum, magnetic reconnection [1, 2, 3]. In multiple occasions, it has been commented on the coupling between the coarse and the refined grid solutions. The coupling mechanism itself, however, has never been explored in depth. Here, we investigate the theoretical bases of grid coupling in the MLMD system. We obtain an evolution law for the electric field solution in the overlap area of the MLMD system which highlights a dependance on the densities and currents from both the coarse and the refined grid, rather than from the coarse grid alone: grid coupling is obtained via densities and currents.

  5. Error-measure for anisotropic grid-adaptation in turbulence-resolving simulations

    NASA Astrophysics Data System (ADS)

    Toosi, Siavash; Larsson, Johan

    2015-11-01

    Grid-adaptation requires an error-measure that identifies where the grid should be refined. In the case of turbulence-resolving simulations (DES, LES, DNS), a simple error-measure is the small-scale resolved energy, which scales with both the modeled subgrid-stresses and the numerical truncation errors in many situations. Since this is a scalar measure, it does not carry any information on the anisotropy of the optimal grid-refinement. The purpose of this work is to introduce a new error-measure for turbulence-resolving simulations that is capable of predicting nearly-optimal anisotropic grids. Turbulent channel flow at Reτ ~ 300 is used to assess the performance of the proposed error-measure. The formulation is geometrically general, applicable to any type of unstructured grid.

  6. An object-oriented approach for parallel self adaptive mesh refinement on block structured grids

    NASA Technical Reports Server (NTRS)

    Lemke, Max; Witsch, Kristian; Quinlan, Daniel

    1993-01-01

    Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.

  7. A Domain-Decomposed Multilevel Method for Adaptively Refined Cartesian Grids with Embedded Boundaries

    NASA Technical Reports Server (NTRS)

    Aftosmis, M. J.; Berger, M. J.; Adomavicius, G.

    2000-01-01

    Preliminary verification and validation of an efficient Euler solver for adaptively refined Cartesian meshes with embedded boundaries is presented. The parallel, multilevel method makes use of a new on-the-fly parallel domain decomposition strategy based upon the use of space-filling curves, and automatically generates a sequence of coarse meshes for processing by the multigrid smoother. The coarse mesh generation algorithm produces grids which completely cover the computational domain at every level in the mesh hierarchy. A series of examples on realistically complex three-dimensional configurations demonstrate that this new coarsening algorithm reliably achieves mesh coarsening ratios in excess of 7 on adaptively refined meshes. Numerical investigations of the scheme's local truncation error demonstrate an achieved order of accuracy between 1.82 and 1.88. Convergence results for the multigrid scheme are presented for both subsonic and transonic test cases and demonstrate W-cycle multigrid convergence rates between 0.84 and 0.94. Preliminary parallel scalability tests on both simple wing and complex complete aircraft geometries shows a computational speedup of 52 on 64 processors using the run-time mesh partitioner.

  8. Impeller tandem blade study with grid embedding for local grid refinement

    NASA Technical Reports Server (NTRS)

    Bache, George

    1992-01-01

    Flow non-uniformity at the discharge of high power density impellers can result in significant unsteady interactions between impeller blades and downstream diffuser vanes. These interactions result in degradation of both performance and pump reliability. The MSFC Pump Technology Team has recognized the importance of resolving this problem and has thus initiated the development and testing of a high head coefficient impeller. One of the primary goals of this program is to improve impeller performance and discharge flow uniformity. The objective of the present work is complimentary. Flow uniformity and performance gains were sought through the application of a tandem blade arrangement. The approach adopted was to numerically establish flow characteristics at the impeller discharge for the baseline MSFC impeller and then parametrically evaluate tandem blade configurations. A tandem design was sought that improves both impeller performance and discharge uniformity. The Navier-Stokes solver AEROVISC was used to conduct the study. Grid embedding is used to resolve local gradients while attempting to minimize model size. Initial results indicate that significant gains in flow uniformity can be achieved through the tandem blade concept and that blade clocking rather than slot location is the primary driver for flow uniformity.

  9. Impeller tandem blade study with grid embedding for local grid refinement

    NASA Astrophysics Data System (ADS)

    Bache, George

    1992-07-01

    Flow non-uniformity at the discharge of high power density impellers can result in significant unsteady interactions between impeller blades and downstream diffuser vanes. These interactions result in degradation of both performance and pump reliability. The MSFC Pump Technology Team has recognized the importance of resolving this problem and has thus initiated the development and testing of a high head coefficient impeller. One of the primary goals of this program is to improve impeller performance and discharge flow uniformity. The objective of the present work is complimentary. Flow uniformity and performance gains were sought through the application of a tandem blade arrangement. The approach adopted was to numerically establish flow characteristics at the impeller discharge for the baseline MSFC impeller and then parametrically evaluate tandem blade configurations. A tandem design was sought that improves both impeller performance and discharge uniformity. The Navier-Stokes solver AEROVISC was used to conduct the study. Grid embedding is used to resolve local gradients while attempting to minimize model size. Initial results indicate that significant gains in flow uniformity can be achieved through the tandem blade concept and that blade clocking rather than slot location is the primary driver for flow uniformity.

  10. A self-adaptive-grid method with application to airfoil flow

    NASA Technical Reports Server (NTRS)

    Nakahashi, K.; Deiwert, G. S.

    1985-01-01

    A self-adaptive-grid method is described that is suitable for multidimensional steady and unsteady computations. Based on variational principles, a spring analogy is used to redistribute grid points in an optimal sense to reduce the overall solution error. User-specified parameters, denoting both maximum and minimum permissible grid spacings, are used to define the all-important constants, thereby minimizing the empiricism and making the method self-adaptive. Operator splitting and one-sided controls for orthogonality and smoothness are used to make the method practical, robust, and efficient. Examples are included for both steady and unsteady viscous flow computations about airfoils in two dimensions, as well as for a steady inviscid flow computation and a one-dimensional case. These examples illustrate the precise control the user has with the self-adaptive method and demonstrate a significant improvement in accuracy and quality of the solutions.

  11. A Solution Adaptive Structured/Unstructured Overset Grid Flow Solver with Applications to Helicopter Rotor Flows

    NASA Technical Reports Server (NTRS)

    Duque, Earl P. N.; Biswas, Rupak; Strawn, Roger C.

    1995-01-01

    This paper summarizes a method that solves both the three dimensional thin-layer Navier-Stokes equations and the Euler equations using overset structured and solution adaptive unstructured grids with applications to helicopter rotor flowfields. The overset structured grids use an implicit finite-difference method to solve the thin-layer Navier-Stokes/Euler equations while the unstructured grid uses an explicit finite-volume method to solve the Euler equations. Solutions on a helicopter rotor in hover show the ability to accurately convect the rotor wake. However, isotropic subdivision of the tetrahedral mesh rapidly increases the overall problem size.

  12. Adaptive grid finite element model of the tokamak scrapeoff layer

    SciTech Connect

    Kuprat, A.P.; Glasser, A.H.

    1995-07-01

    The authors discuss unstructured grids for application to transport in the tokamak edge SOL. They have developed a new metric with which to judge element elongation and resolution requirements. Using this method, the authors apply a standard moving finite element technique to advance the SOL equations while inserting/deleting dynamically nodes that violate an elongation criterion. In a tokamak plasma, this method achieves a more uniform accuracy, and results in highly stretched triangular finite elements, except near separatrix X-point where transport is more isotropic.

  13. An assessment of the adaptive unstructured tetrahedral grid, Euler Flow Solver Code FELISA

    NASA Technical Reports Server (NTRS)

    Djomehri, M. Jahed; Erickson, Larry L.

    1994-01-01

    A three-dimensional solution-adaptive Euler flow solver for unstructured tetrahedral meshes is assessed, and the accuracy and efficiency of the method for predicting sonic boom pressure signatures about simple generic models are demonstrated. Comparison of computational and wind tunnel data and enhancement of numerical solutions by means of grid adaptivity are discussed. The mesh generation is based on the advancing front technique. The FELISA code consists of two solvers, the Taylor-Galerkin and the Runge-Kutta-Galerkin schemes, both of which are spacially discretized by the usual Galerkin weighted residual finite-element methods but with different explicit time-marching schemes to steady state. The solution-adaptive grid procedure is based on either remeshing or mesh refinement techniques. An alternative geometry adaptive procedure is also incorporated.

  14. Grid-Adapted FUN3D Computations for the Second High Lift Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Lee-Rausch, E. M.; Rumsey, C. L.; Park, M. A.

    2014-01-01

    Contributions of the unstructured Reynolds-averaged Navier-Stokes code FUN3D to the 2nd AIAA CFD High Lift Prediction Workshop are described, and detailed comparisons are made with experimental data. Using workshop-supplied grids, results for the clean wing configuration are compared with results from the structured code CFL3D Using the same turbulence model, both codes compare reasonably well in terms of total forces and moments, and the maximum lift is similarly over-predicted for both codes compared to experiment. By including more representative geometry features such as slat and flap brackets and slat pressure tube bundles, FUN3D captures the general effects of the Reynolds number variation, but under-predicts maximum lift on workshop-supplied grids in comparison with the experimental data, due to excessive separation. However, when output-based, off-body grid adaptation in FUN3D is employed, results improve considerably. In particular, when the geometry includes both brackets and the pressure tube bundles, grid adaptation results in a more accurate prediction of lift near stall in comparison with the wind-tunnel data. Furthermore, a rotation-corrected turbulence model shows improved pressure predictions on the outboard span when using adapted grids.

  15. Application of a solution adaptive grid scheme, SAGE, to complex three-dimensional flows

    NASA Technical Reports Server (NTRS)

    Davies, Carol B.; Venkatapathy, Ethiraj

    1991-01-01

    A new three-dimensional (3D) adaptive grid code based on the algebraic, solution-adaptive scheme of Nakahashi and Deiwert is developed and applied to a variety of problems. The new computer code, SAGE, is an extension of the same-named two-dimensional (2D) solution-adaptive program that has already proven to be a powerful tool in computational fluid dynamics applications. The new code has been applied to a range of complex three-dimensional, supersonic and hypersonic flows. Examples discussed are a tandem-slot fuel injector, the hypersonic forebody of the Aeroassist Flight Experiment (AFE), the 3D base flow behind the AFE, the supersonic flow around a 3D swept ramp and a generic, hypersonic, 3D nozzle-plume flow. The associated adapted grids and the solution enhancements resulting from the grid adaption are presented for these cases. Three-dimensional adaption is more complex than its 2D counterpart, and the complexities unique to the 3D problems are discussed.

  16. Local tetrahedron modeling of microelectronics using the finite-volume hybrid-grid technique

    SciTech Connect

    Riley, D.J.; Turner, C.D.

    1995-12-01

    The finite-volume hybrid-grid (FVHG) technique uses both structured and unstructured grid regions in obtaining a solution to the time-domain Maxwell`s equations. The method is based on explicit time differencing and utilizes rectilinear finite-difference time-domain (FDTD) and nonorthogonal finite-volume time-domain (FVTD). The technique directly couples structured FDTD grids with unstructured FVTD grids without the need for spatial interpolation across grid interfaces. In this paper, the FVHG method is applied to simple planar microelectronic devices. Local tetrahedron grids are used to model portions of the device under study, with the remainder of the problem space being modeled with cubical hexahedral cells. The accuracy of propagating microstrip-guided waves from a low-density hexahedron region through a high-density tetrahedron grid is investigated.

  17. A Hyperspherical Adaptive Sparse-Grid Method for High-Dimensional Discontinuity Detection

    SciTech Connect

    Zhang, Guannan; Webster, Clayton G.; Gunzburger, Max D.; Burkardt, John V.

    2015-06-24

    This study proposes and analyzes a hyperspherical adaptive hierarchical sparse-grid method for detecting jump discontinuities of functions in high-dimensional spaces. The method is motivated by the theoretical and computational inefficiencies of well-known adaptive sparse-grid methods for discontinuity detection. Our novel approach constructs a function representation of the discontinuity hypersurface of an N-dimensional discontinuous quantity of interest, by virtue of a hyperspherical transformation. Then, a sparse-grid approximation of the transformed function is built in the hyperspherical coordinate system, whose value at each point is estimated by solving a one-dimensional discontinuity detection problem. Due to the smoothness of the hypersurface, the new technique can identify jump discontinuities with significantly reduced computational cost, compared to existing methods. In addition, hierarchical acceleration techniques are also incorporated to further reduce the overall complexity. Rigorous complexity analyses of the new method are provided as are several numerical examples that illustrate the effectiveness of the approach.

  18. Self-adaptive Fault-Tolerance of HLA-Based Simulations in the Grid Environment

    NASA Astrophysics Data System (ADS)

    Huang, Jijie; Chai, Xudong; Zhang, Lin; Li, Bo Hu

    The objects of a HLA-based simulation can access model services to update their attributes. However, the grid server may be overloaded and refuse the model service to handle objects accesses. Because these objects have been accessed this model service during last simulation loop and their medium state are stored in this server, this may terminate the simulation. A fault-tolerance mechanism must be introduced into simulations. But the traditional fault-tolerance methods cannot meet the above needs because the transmission latency between a federate and the RTI in grid environment varies from several hundred milliseconds to several seconds. By adding model service URLs to the OMT and expanding the HLA services and model services with some interfaces, this paper proposes a self-adaptive fault-tolerance mechanism of simulations according to the characteristics of federates accessing model services. Benchmark experiments indicate that the expanded HLA/RTI can make simulations self-adaptively run in the grid environment.

  19. Adaptive Grid Based Localized Learning for Multidimensional Data

    ERIC Educational Resources Information Center

    Saini, Sheetal

    2012-01-01

    Rapid advances in data-rich domains of science, technology, and business has amplified the computational challenges of "Big Data" synthesis necessary to slow the widening gap between the rate at which the data is being collected and analyzed for knowledge. This has led to the renewed need for efficient and accurate algorithms, framework,…

  20. White Light Schlieren Optics Using Bacteriorhodopsin as an Adaptive Image Grid

    NASA Technical Reports Server (NTRS)

    Peale, Robert; Ruffin, Boh; Donahue, Jeff; Barrett, Carolyn

    1996-01-01

    A Schlieren apparatus using a bacteriorhodopsin film as an adaptive image grid with white light illumination is demonstrated for the first time. The time dependent spectral properties of the film are characterized. Potential applications include a single-ended Schlieren system for leak detection.

  1. Algebraic grid adaptation method using non-uniform rational B-spline surface modeling

    NASA Technical Reports Server (NTRS)

    Yang, Jiann-Cherng; Soni, B. K.

    1992-01-01

    An algebraic adaptive grid system based on equidistribution law and utilized by the Non-Uniform Rational B-Spline (NURBS) surface for redistribution is presented. A weight function, utilizing a properly weighted boolean sum of various flow field characteristics is developed. Computational examples are presented to demonstrate the success of this technique.

  2. Generalized Monge-Kantorovich optimization for grid generation and adaptation in LP

    SciTech Connect

    Delzanno, G L; Finn, J M

    2009-01-01

    The Monge-Kantorovich grid generation and adaptation scheme of is generalized from a variational principle based on L{sub 2} to a variational principle based on L{sub p}. A generalized Monge-Ampere (MA) equation is derived and its properties are discussed. Results for p > 1 are obtained and compared in terms of the quality of the resulting grid. We conclude that for the grid generation application, the formulation based on L{sub p} for p close to unity leads to serious problems associated with the boundary. Results for 1.5 {approx}< p {approx}< 2.5 are quite good, but there is a fairly narrow range around p = 2 where the results are close to optimal with respect to grid distortion. Furthermore, the Newton-Krylov methods used to solve the generalized MA equation perform best for p = 2.

  3. A chimera grid scheme. [multiple overset body-conforming mesh system for finite difference adaptation to complex aircraft configurations

    NASA Technical Reports Server (NTRS)

    Steger, J. L.; Dougherty, F. C.; Benek, J. A.

    1983-01-01

    A mesh system composed of multiple overset body-conforming grids is described for adapting finite-difference procedures to complex aircraft configurations. In this so-called 'chimera mesh,' a major grid is generated about a main component of the configuration and overset minor grids are used to resolve all other features. Methods for connecting overset multiple grids and modifications of flow-simulation algorithms are discussed. Computational tests in two dimensions indicate that the use of multiple overset grids can simplify the task of grid generation without an adverse effect on flow-field algorithms and computer code complexity.

  4. Carving and adaptive drainage enforcement of grid digital elevation models

    NASA Astrophysics Data System (ADS)

    Soille, Pierre; Vogt, Jürgen; Colombo, Roberto

    2003-12-01

    An effective and widely used method for removing spurious pits in digital elevation models consists of filling them until they overflow. However, this method sometimes creates large flat regions which in turn pose a problem for the determination of accurate flow directions. In this study, we propose to suppress each pit by creating a descending path from it to the nearest point having a lower elevation value. This is achieved by carving, i.e., lowering, the terrain elevations along the detected path. Carving paths are identified through a flooding simulation starting from the river outlets. The proposed approach allows for adaptive drainage enforcement whereby river networks coming from other data sources are imposed to the digital elevation model only in places where the automatic river network extraction deviates substantially from the known networks. An improvement to methods for routing flow over flat regions is also introduced. Detailed results are presented over test areas of the Danube basin.

  5. A propagation method with adaptive mesh grid based on wave characteristics for wave optics simulation

    NASA Astrophysics Data System (ADS)

    Tang, Qiuyan; Wang, Jing; Lv, Pin; Sun, Quan

    2015-10-01

    Propagation simulation method and choosing mesh grid are both very important to get the correct propagation results in wave optics simulation. A new angular spectrum propagation method with alterable mesh grid based on the traditional angular spectrum method and the direct FFT method is introduced. With this method, the sampling space after propagation is not limited to propagation methods no more, but freely alterable. However, choosing mesh grid on target board influences the validity of simulation results directly. So an adaptive mesh choosing method based on wave characteristics is proposed with the introduced propagation method. We can calculate appropriate mesh grids on target board to get satisfying results. And for complex initial wave field or propagation through inhomogeneous media, we can also calculate and set the mesh grid rationally according to above method. Finally, though comparing with theoretical results, it's shown that the simulation result with the proposed method coinciding with theory. And by comparing with the traditional angular spectrum method and the direct FFT method, it's known that the proposed method is able to adapt to a wider range of Fresnel number conditions. That is to say, the method can simulate propagation results efficiently and correctly with propagation distance of almost zero to infinity. So it can provide better support for more wave propagation applications such as atmospheric optics, laser propagation and so on.

  6. Local adaptation at range edges: comparing elevation and latitudinal gradients.

    PubMed

    Halbritter, A H; Billeter, R; Edwards, P J; Alexander, J M

    2015-10-01

    Local adaptation at range edges influences species' distributions and how they respond to environmental change. However, the factors that affect adaptation, including gene flow and local selection pressures, are likely to vary across different types of range edge. We performed a reciprocal transplant experiment to investigate local adaptation in populations of Plantago lanceolata and P. major from central locations in their European range and from their latitudinal and elevation range edges (in northern Scandinavia and Swiss Alps, respectively). We also characterized patterns of genetic diversity and differentiation in populations using molecular markers. Range-centre plants of P. major were adapted to conditions at the range centre, but performed similarly to range-edge plants when grown at the range edges. There was no evidence for local adaptation when comparing central and edge populations of P. lanceolata. However, plants of both species from high elevation were locally adapted when compared with plants from high latitude, although the reverse was not true. This asymmetry was associated with greater genetic diversity and less genetic differentiation over the elevation gradient than over the latitudinal gradient. Our results suggest that adaptation in some range-edge populations could increase their performance following climate change. However, responses are likely to differ along elevation and latitudinal gradients, with adaptation more likely at high-elevation. Furthermore, based upon these results, we suggest that gene flow is unlikely to constrain adaptation in range-edge populations of these species. PMID:26201435

  7. An adaptive discretization of compressible flow using a multitude of moving Cartesian grids

    NASA Astrophysics Data System (ADS)

    Qiu, Linhai; Lu, Wenlong; Fedkiw, Ronald

    2016-01-01

    We present a novel method for simulating compressible flow on a multitude of Cartesian grids that can rotate and translate. Following previous work, we split the time integration into an explicit step for advection followed by an implicit solve for the pressure. A second order accurate flux based scheme is devised to handle advection on each moving Cartesian grid using an effective characteristic velocity that accounts for the grid motion. In order to avoid the stringent time step restriction imposed by very fine grids, we propose strategies that allow for a fluid velocity CFL number larger than 1. The stringent time step restriction related to the sound speed is alleviated by formulating an implicit linear system in order to find a pressure consistent with the equation of state. This implicit linear system crosses overlapping Cartesian grid boundaries by utilizing local Voronoi meshes to connect the various degrees of freedom obtaining a symmetric positive-definite system. Since a straightforward application of this technique contains an inherent central differencing which can result in spurious oscillations, we introduce a new high order diffusion term similar in spirit to ENO-LLF but solved for implicitly in order to avoid any associated time step restrictions. The method is conservative on each grid, as well as globally conservative on the background grid that contains all other grids. Moreover, a conservative interpolation operator is devised for conservatively remapping values in order to keep them consistent across different overlapping grids. Additionally, the method is extended to handle two-way solid fluid coupling in a monolithic fashion including cases (in the appendix) where solids in close proximity do not properly allow for grid based degrees of freedom in between them.

  8. Robust local search for spacecraft operations using adaptive noise

    NASA Technical Reports Server (NTRS)

    Fukunaga, Alex S.; Rabideau, Gregg; Chien, Steve

    2004-01-01

    Randomization is a standard technique for improving the performance of local search algorithms for constraint satisfaction. However, it is well-known that local search algorithms are constraints satisfaction. However, it is well-known that local search algorithms are to the noise values selected. We investigate the use of an adaptive noise mechanism in an iterative repair-based planner/scheduler for spacecraft operations. Preliminary results indicate that adaptive noise makes the use of randomized repair moves safe and robust; that is, using adaptive noise makes it possible to consistently achieve, performance comparable with the best tuned noise setting without the need for manually tuning the noise parameter.

  9. Dynamics of local grid manipulations for internal flow problems

    NASA Technical Reports Server (NTRS)

    Eiseman, Peter R.; Snyder, Aaron; Choo, Yung K.

    1991-01-01

    The control point method of algebraic grid generation is briefly reviewed. The review proceeds from the general statement of the method in 2-D unencumbered by detailed mathematical formulation. The method is supported by an introspective discussion which provides the basis for confidence in the approach. The more complex 3-D formulation is then presented as a natural generalization. Application of the method is carried out through 2-D examples which demonstrate the technique.

  10. A SUNTANS-based unstructured grid local exact particle tracking model

    NASA Astrophysics Data System (ADS)

    Liu, Guangliang; Chua, Vivien P.

    2016-07-01

    A parallel particle tracking model, which employs the local exact integration method to achieve high accuracy, has been developed and embedded in an unstructured-grid coastal ocean model, Stanford Unstructured Nonhydrostatic Terrain-following Adaptive Navier-Stokes Simulator (SUNTANS). The particle tracking model is verified and compared with traditional numerical integration methods, such as Runge-Kutta fourth-order methods using several test cases. In two-dimensional linear steady rotating flow, the local exact particle tracking model is able to track particles along the circular streamline accurately, while Runge-Kutta fourth-order methods produce trajectories that deviate from the streamlines. In periodically varying double-gyre flow, the trajectories produced by local exact particle tracking model with time step of 1.0 × 10- 2 s are similar to those trajectories obtained from the numerical integration methods with reduced time steps of 1.0 × 10- 4 s. In three-dimensional steady Arnold-Beltrami-Childress (ABC) flow, the trajectories integrated with the local exact particle tracking model compares well with the approximated true path. The trajectories spiral upward and their projection on the x- y plane is a periodic ellipse. The trajectories derived with the Runge-Kutta fourth-order method deviate from the approximated true path, and their projections on the x- y plane are unclosed ellipses with growing long and short axes. The spatial temporal resolution needs to be carefully chosen before particle tracking models are applied. Our results show that the developed local exact particle tracking model is accurate and suitable for marine Lagrangian (trajectory-based)-related research.

  11. A SUNTANS-based unstructured grid local exact particle tracking model

    NASA Astrophysics Data System (ADS)

    Liu, Guangliang; Chua, Vivien P.

    2016-04-01

    A parallel particle tracking model, which employs the local exact integration method to achieve high accuracy, has been developed and embedded in an unstructured-grid coastal ocean model, Stanford Unstructured Nonhydrostatic Terrain-following Adaptive Navier-Stokes Simulator (SUNTANS). The particle tracking model is verified and compared with traditional numerical integration methods, such as Runge-Kutta fourth-order methods using several test cases. In two-dimensional linear steady rotating flow, the local exact particle tracking model is able to track particles along the circular streamline accurately, while Runge-Kutta fourth-order methods produce trajectories that deviate from the streamlines. In periodically varying double-gyre flow, the trajectories produced by local exact particle tracking model with time step of 1.0 × 10- 2 s are similar to those trajectories obtained from the numerical integration methods with reduced time steps of 1.0 × 10- 4 s. In three-dimensional steady Arnold-Beltrami-Childress (ABC) flow, the trajectories integrated with the local exact particle tracking model compares well with the approximated true path. The trajectories spiral upward and their projection on the x-y plane is a periodic ellipse. The trajectories derived with the Runge-Kutta fourth-order method deviate from the approximated true path, and their projections on the x-y plane are unclosed ellipses with growing long and short axes. The spatial temporal resolution needs to be carefully chosen before particle tracking models are applied. Our results show that the developed local exact particle tracking model is accurate and suitable for marine Lagrangian (trajectory-based)-related research.

  12. Local adaptation and the evolution of chromosome fusions.

    PubMed

    Guerrero, Rafael F; Kirkpatrick, Mark

    2014-10-01

    We use forward and coalescent models of population genetics to study chromosome fusions that reduce the recombination between two locally adapted loci. Under a continent-island model, a fusion spreads and reaches a polymorphic equilibrium when it causes recombination between locally adapted alleles to be less than their selective advantage. In contrast, fusions in a two-deme model always spread; whether it reaches a polymorphic equilibrium or becomes fixed depends on the relative recombination rates of fused homozygotes and heterozygotes. Neutral divergence around fusion polymorphisms is markedly increased, showing peaks at the point of fusion and at the locally adapted loci. Local adaptation could explain the evolution of many of chromosome fusions, which are some of the most common chromosome rearrangements in nature. PMID:24964074

  13. GWM-2005 - A Groundwater-Management Process for MODFLOW-2005 with Local Grid Refinement (LGR) Capability

    USGS Publications Warehouse

    Ahlfeld, David P.; Baker, Kristine M.; Barlow, Paul M.

    2009-01-01

    This report describes the Groundwater-Management (GWM) Process for MODFLOW-2005, the 2005 version of the U.S. Geological Survey modular three-dimensional groundwater model. GWM can solve a broad range of groundwater-management problems by combined use of simulation- and optimization-modeling techniques. These problems include limiting groundwater-level declines or streamflow depletions, managing groundwater withdrawals, and conjunctively using groundwater and surface-water resources. GWM was initially released for the 2000 version of MODFLOW. Several modifications and enhancements have been made to GWM since its initial release to increase the scope of the program's capabilities and to improve its operation and reporting of results. The new code, which is called GWM-2005, also was designed to support the local grid refinement capability of MODFLOW-2005. Local grid refinement allows for the simulation of one or more higher resolution local grids (referred to as child models) within a coarser grid parent model. Local grid refinement is often needed to improve simulation accuracy in regions where hydraulic gradients change substantially over short distances or in areas requiring detailed representation of aquifer heterogeneity. GWM-2005 can be used to formulate and solve groundwater-management problems that include components in both parent and child models. Although local grid refinement increases simulation accuracy, it can also substantially increase simulation run times.

  14. Adaptive Harmonic Detection Control of Grid Interfaced Solar Photovoltaic Energy System with Power Quality Improvement

    NASA Astrophysics Data System (ADS)

    Singh, B.; Goel, S.

    2015-03-01

    This paper presents a grid interfaced solar photovoltaic (SPV) energy system with a novel adaptive harmonic detection control for power quality improvement at ac mains under balanced as well as unbalanced and distorted supply conditions. The SPV energy system is capable of compensation of linear and nonlinear loads with the objectives of load balancing, harmonics elimination, power factor correction and terminal voltage regulation. The proposed control increases the utilization of PV infrastructure and brings down its effective cost due to its other benefits. The adaptive harmonic detection control algorithm is used to detect the fundamental active power component of load currents which are subsequently used for reference source currents estimation. An instantaneous symmetrical component theory is used to obtain instantaneous positive sequence point of common coupling (PCC) voltages which are used to derive inphase and quadrature phase voltage templates. The proposed grid interfaced PV energy system is modelled and simulated in MATLAB Simulink and its performance is verified under various operating conditions.

  15. Efficient parallel seismic simulations including topography and 3-D material heterogeneities on locally refined composite grids

    NASA Astrophysics Data System (ADS)

    Petersson, Anders; Rodgers, Arthur

    2010-05-01

    The finite difference method on a uniform Cartesian grid is a highly efficient and easy to implement technique for solving the elastic wave equation in seismic applications. However, the spacing in a uniform Cartesian grid is fixed throughout the computational domain, whereas the resolution requirements in realistic seismic simulations usually are higher near the surface than at depth. This can be seen from the well-known formula h ≤ L-P which relates the grid spacing h to the wave length L, and the required number of grid points per wavelength P for obtaining an accurate solution. The compressional and shear wave lengths in the earth generally increase with depth and are often a factor of ten larger below the Moho discontinuity (at about 30 km depth), than in sedimentary basins near the surface. A uniform grid must have a grid spacing based on the small wave lengths near the surface, which results in over-resolving the solution at depth. As a result, the number of points in a uniform grid is unnecessarily large. In the wave propagation project (WPP) code, we address the over-resolution-at-depth issue by generalizing our previously developed single grid finite difference scheme to work on a composite grid consisting of a set of structured rectangular grids of different spacings, with hanging nodes on the grid refinement interfaces. The computational domain in a regional seismic simulation often extends to depth 40-50 km. Hence, using a refinement ratio of two, we need about three grid refinements from the bottom of the computational domain to the surface, to keep the local grid size in approximate parity with the local wave lengths. The challenge of the composite grid approach is to find a stable and accurate method for coupling the solution across the grid refinement interface. Of particular importance is the treatment of the solution at the hanging nodes, i.e., the fine grid points which are located in between coarse grid points. WPP implements a new, energy

  16. Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes.

    PubMed

    Forester, Brenna R; Jones, Matthew R; Joost, Stéphane; Landguth, Erin L; Lasky, Jesse R

    2016-01-01

    The spatial structure of the environment (e.g. the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multiscale habitat structure common in nature. Here, we use simulations to pursue two goals: (i) we explore how landscape heterogeneity, dispersal ability and selection affect the strength of local adaptation, and (ii) we evaluate the performance of several genotype-environment association (GEA) methods for detecting loci involved in local adaptation. We found that the strength of local adaptation increased in spatially aggregated selection regimes, but remained strong in patchy landscapes when selection was moderate to strong. Weak selection resulted in weak local adaptation that was relatively unaffected by landscape heterogeneity. In general, the power of detection methods closely reflected levels of local adaptation. False-positive rates (FPRs), however, showed distinct differences across GEA methods based on levels of population structure. The univariate GEA approach had high FPRs (up to 55%) under limited dispersal scenarios, due to strong isolation by distance. By contrast, multivariate, ordination-based methods had uniformly low FPRs (0-2%), suggesting these approaches can effectively control for population structure. Specifically, constrained ordinations had the best balance of high detection and low FPRs and will be a useful addition to the GEA toolkit. Our results provide both theoretical and practical insights into the conditions that shape local adaptation and how these conditions impact our ability to detect selection. PMID:26576498

  17. Iso-deviant 2D gridding with efficient adaptive gridder for littoral environments (EAGLE)

    NASA Astrophysics Data System (ADS)

    Rike, Erik R.; Delbalzo, Donald R.

    2005-09-01

    Transmission loss (TL) computations in littoral areas require a dense spatial and azimuthal grid to achieve acceptable accuracy and detail. The computational cost of accurate predictions led to a new concept, OGRES (Objective Grid/Radials using Environmentally-sensitive Selection), which produces sparse, irregular acoustic grids, with controlled accuracy. Recent work to further increase accuracy and efficiency with better metrics and interpolation led to EAGLE (Efficient Adaptive Gridder for Littoral Environments). On each iteration, EAGLE produces grids with approximately constant spatial uncertainty (hence, iso-deviance), yielding predictions with ever-increasing resolution and accuracy. The EAGLE point-selection mechanism is tested using the predictive error metric and 2D synthetic data sets created from combinations of simple signal functions (e.g., polynomials, sines, cosines, exponentials), along with white and chromatic noise. The speed, efficiency, fidelity, and iso-deviance of EAGLE are determined for each combination of signal, noise, and interpolator. The results show significant efficiency enhancements compared to uniform grids of the same accuracy. [Work sponsored by NAVAIR.

  18. The Urban Leaders Adaptation Initiative: Climate Resilient Local Governments

    NASA Astrophysics Data System (ADS)

    Foster, J. G.

    2008-12-01

    Local governments, the first responders to public health, safety and environmental hazards, must act now to lessen vulnerabilities to climate change. They must plan for and invest in "adapting" to inevitable impacts such as flood, fire, and draught that will occur notwithstanding best efforts to mitigate climate change. CCAP's Urban Leaders Adaptation Initiative is developing a framework for informed decision making on climate adaptation. Looking ahead to projected climate impacts and 'back casting' can identify what is needed now to both reduce greenhouse gas emissions and build local resiliency to climate change. CCAP's partnership with King County (WA), Chicago, Los Angeles, Miami-Dade County (FL), Milwaukee, Nassau County (NY), Phoenix, San Francisco, and Toronto is advancing policy discussions to ensure that state and local governments consider climate change when making decisions about infrastructure, transportation, land use, and resource management. Through the Initiative, local leaders will incorporate climate change into daily urban management and planning activities, proactively engage city and county managers and the public in developing solutions, and build community resilience. One goal is to change both institutional and public attitudes and behaviors. Determining appropriate adaptation strategies for each jurisdiction requires Asking the Climate Question: "How does what we are doing increase our resilience to climate change?" Over the next three years, the Initiative will design and implement specific adaptation plans, policies and 'catalytic' projects, collect and disseminate "best practices," and participate in framing national climate policy discussions. In the coming years, policy-makers will have to consider climate change in major infrastructure development decisions. If they are to be successful and have the resources they need, national climate change policy and emerging legislation will have to support these communities. The Urban Leaders

  19. Adjoint-Based, Three-Dimensional Error Prediction and Grid Adaptation

    NASA Technical Reports Server (NTRS)

    Park, Michael A.

    2002-01-01

    Engineering computational fluid dynamics (CFD) analysis and design applications focus on output functions (e.g., lift, drag). Errors in these output functions are generally unknown and conservatively accurate solutions may be computed. Computable error estimates can offer the possibility to minimize computational work for a prescribed error tolerance. Such an estimate can be computed by solving the flow equations and the linear adjoint problem for the functional of interest. The computational mesh can be modified to minimize the uncertainty of a computed error estimate. This robust mesh-adaptation procedure automatically terminates when the simulation is within a user specified error tolerance. This procedure for estimating and adapting to error in a functional is demonstrated for three-dimensional Euler problems. An adaptive mesh procedure that links to a Computer Aided Design (CAD) surface representation is demonstrated for wing, wing-body, and extruded high lift airfoil configurations. The error estimation and adaptation procedure yielded corrected functions that are as accurate as functions calculated on uniformly refined grids with ten times as many grid points.

  20. A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids.

    PubMed

    Boschitsch, Alexander H; Fenley, Marcia O

    2011-05-10

    An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical solution of the 3D Poisson-Boltzmann Equation (PBE) governing the electrostatic interactions of large-scale biomolecules and highly charged multi-biomolecular assemblies such as ribosomes and viruses. The ACG offers numerous advantages over competing grid topologies such as regular 3D lattices and unstructured grids. For very large biological molecules and multi-biomolecule assemblies, the total number of grid-points is several orders of magnitude less than that required in a conventional lattice grid used in the current PBE solvers thus allowing the end user to obtain accurate and stable nonlinear PBE solutions on a desktop computer. Compared to tetrahedral-based unstructured grids, ACG offers a simpler hierarchical grid structure, which is naturally suited to multigrid, relieves indirect addressing requirements and uses fewer neighboring nodes in the finite difference stencils. Construction of the ACG and determination of the dielectric/ionic maps are straightforward, fast and require minimal user intervention. Charge singularities are eliminated by reformulating the problem to produce the reaction field potential in the molecular interior and the total electrostatic potential in the exterior ionic solvent region. This approach minimizes grid-dependency and alleviates the need for fine grid spacing near atomic charge sites. The technical portion of this paper contains three parts. First, the ACG and its construction for general biomolecular geometries are described. Next, a discrete approximation to the PBE upon this mesh is derived. Finally, the overall solution procedure and multigrid implementation are summarized. Results obtained with the ACG-based PBE solver are presented for: (i) a low dielectric spherical cavity, containing interior point charges, embedded in a high dielectric ionic solvent - analytical solutions are available for this case, thus allowing rigorous

  1. Adaptive grid artifact reduction in the frequency domain with spatial properties for x-ray images

    NASA Astrophysics Data System (ADS)

    Kim, Dong Sik; Lee, Sanggyun

    2012-03-01

    By applying band-rejection filters (BRFs) in the frequency domain, we can efficiently reduce the grid artifacts, which are caused by using the antiscatter grid in obtaining x-ray digital images. However, if the frequency component of the grid artifact is relatively close to that of the object, then simply applying a BRF may seriously distort the object and cause the ringing artifacts. Since the ringing artifacts are quite dependent on the shape of the object to be recovered in the spatial domain, the spatial property of the x-ray image should be considered in applying BRFs. In this paper, we propose an adaptive filtering scheme, which can cooperate such different properties in the spatial domain. In the spatial domain, we compare several approaches, such as the mangnitude, edge, and frequency-modulation (FM) model-based algorithms, to detect the ringing artifact or the grid artifact component. In order to perform a robust detection whether the ringing artifact is strong or not, we employ the FM model for the extracted signal, which corresponds to a specific grid artifact. A detection of the position for the ringing artifact is then conducted based on the slope detection algorithm, which is commonly used as an FM discriminator in the communication area. However, the detected position of the ringing artifact is not accurate. Hence, in order to obtain an accurate detection result, we combine the edge-based approach with the FM model approach. Numerical result for real x-ray images shows that applying BRFs in the frequency domain in conjunction with the spatial property of the ringing artifact can successfully remove the grid artifact, distorting the object less.

  2. Introducing Enabling Computational Tools to the Climate Sciences: Multi-Resolution Climate Modeling with Adaptive Cubed-Sphere Grids

    SciTech Connect

    Jablonowski, Christiane

    2015-07-14

    The research investigates and advances strategies how to bridge the scale discrepancies between local, regional and global phenomena in climate models without the prohibitive computational costs of global cloud-resolving simulations. In particular, the research explores new frontiers in computational geoscience by introducing high-order Adaptive Mesh Refinement (AMR) techniques into climate research. AMR and statically-adapted variable-resolution approaches represent an emerging trend for atmospheric models and are likely to become the new norm in future-generation weather and climate models. The research advances the understanding of multi-scale interactions in the climate system and showcases a pathway how to model these interactions effectively with advanced computational tools, like the Chombo AMR library developed at the Lawrence Berkeley National Laboratory. The research is interdisciplinary and combines applied mathematics, scientific computing and the atmospheric sciences. In this research project, a hierarchy of high-order atmospheric models on cubed-sphere computational grids have been developed that serve as an algorithmic prototype for the finite-volume solution-adaptive Chombo-AMR approach. The foci of the investigations have lied on the characteristics of both static mesh adaptations and dynamically-adaptive grids that can capture flow fields of interest like tropical cyclones. Six research themes have been chosen. These are (1) the introduction of adaptive mesh refinement techniques into the climate sciences, (2) advanced algorithms for nonhydrostatic atmospheric dynamical cores, (3) an assessment of the interplay between resolved-scale dynamical motions and subgrid-scale physical parameterizations, (4) evaluation techniques for atmospheric model hierarchies, (5) the comparison of AMR refinement strategies and (6) tropical cyclone studies with a focus on multi-scale interactions and variable-resolution modeling. The results of this research project

  3. Convergent Evolution During Local Adaptation to Patchy Landscapes.

    PubMed

    Ralph, Peter L; Coop, Graham

    2015-11-01

    Species often encounter, and adapt to, many patches of similar environmental conditions across their range. Such adaptation can occur through convergent evolution if different alleles arise in different patches, or through the spread of shared alleles by migration acting to synchronize adaptation across the species. The tension between the two reflects the constraint imposed on evolution by the underlying genetic architecture versus how effectively selection and geographic isolation act to inhibit the geographic spread of locally adapted alleles. This paper studies the balance between these two routes to adaptation in a model of continuous environments with patchy selection pressures. We address the following questions: How long does it take for a novel allele to appear in a patch where it is locally adapted through mutation? Or, through migration from another, already adapted patch? Which is more likely to occur, as a function of distance between the patches? What population genetic signal is left by the spread of migrant alleles? To answer these questions we examine the family structure underlying migration-selection equilibrium surrounding an already adapted patch, treating those rare families that reach new patches as spatial branching processes. A main result is that patches further apart than a critical distance will likely evolve independent locally adapted alleles; this distance is proportional to the spatial scale of selection ([Formula: see text], where σ is the dispersal distance and sm is the selective disadvantage of these alleles between patches), and depends linearly on log(sm/μ), where μ is the mutation rate. This provides a way to understand the role of geographic separation between patches in promoting convergent adaptation and the genomic signals it leaves behind. We illustrate these ideas using the convergent evolution of cryptic coloration in the rock pocket mouse, Chaetodipus intermedius, as an empirical example. PMID:26571125

  4. Convergent Evolution During Local Adaptation to Patchy Landscapes

    PubMed Central

    2015-01-01

    Species often encounter, and adapt to, many patches of similar environmental conditions across their range. Such adaptation can occur through convergent evolution if different alleles arise in different patches, or through the spread of shared alleles by migration acting to synchronize adaptation across the species. The tension between the two reflects the constraint imposed on evolution by the underlying genetic architecture versus how effectively selection and geographic isolation act to inhibit the geographic spread of locally adapted alleles. This paper studies the balance between these two routes to adaptation in a model of continuous environments with patchy selection pressures. We address the following questions: How long does it take for a novel allele to appear in a patch where it is locally adapted through mutation? Or, through migration from another, already adapted patch? Which is more likely to occur, as a function of distance between the patches? What population genetic signal is left by the spread of migrant alleles? To answer these questions we examine the family structure underlying migration–selection equilibrium surrounding an already adapted patch, treating those rare families that reach new patches as spatial branching processes. A main result is that patches further apart than a critical distance will likely evolve independent locally adapted alleles; this distance is proportional to the spatial scale of selection (σ/sm, where σ is the dispersal distance and s m is the selective disadvantage of these alleles between patches), and depends linearly on log(s m/μ), where μ is the mutation rate. This provides a way to understand the role of geographic separation between patches in promoting convergent adaptation and the genomic signals it leaves behind. We illustrate these ideas using the convergent evolution of cryptic coloration in the rock pocket mouse, Chaetodipus intermedius, as an empirical example. PMID:26571125

  5. A Hyperspherical Adaptive Sparse-Grid Method for High-Dimensional Discontinuity Detection

    DOE PAGESBeta

    Zhang, Guannan; Webster, Clayton G.; Gunzburger, Max D.; Burkardt, John V.

    2015-06-24

    This study proposes and analyzes a hyperspherical adaptive hierarchical sparse-grid method for detecting jump discontinuities of functions in high-dimensional spaces. The method is motivated by the theoretical and computational inefficiencies of well-known adaptive sparse-grid methods for discontinuity detection. Our novel approach constructs a function representation of the discontinuity hypersurface of an N-dimensional discontinuous quantity of interest, by virtue of a hyperspherical transformation. Then, a sparse-grid approximation of the transformed function is built in the hyperspherical coordinate system, whose value at each point is estimated by solving a one-dimensional discontinuity detection problem. Due to the smoothness of the hypersurface, the newmore » technique can identify jump discontinuities with significantly reduced computational cost, compared to existing methods. In addition, hierarchical acceleration techniques are also incorporated to further reduce the overall complexity. Rigorous complexity analyses of the new method are provided as are several numerical examples that illustrate the effectiveness of the approach.« less

  6. A hyper-spherical adaptive sparse-grid method for high-dimensional discontinuity detection

    SciTech Connect

    Zhang, Guannan; Webster, Clayton G; Gunzburger, Max D; Burkardt, John V

    2014-03-01

    This work proposes and analyzes a hyper-spherical adaptive hi- erarchical sparse-grid method for detecting jump discontinuities of functions in high-dimensional spaces is proposed. The method is motivated by the the- oretical and computational inefficiencies of well-known adaptive sparse-grid methods for discontinuity detection. Our novel approach constructs a func- tion representation of the discontinuity hyper-surface of an N-dimensional dis- continuous quantity of interest, by virtue of a hyper-spherical transformation. Then, a sparse-grid approximation of the transformed function is built in the hyper-spherical coordinate system, whose value at each point is estimated by solving a one-dimensional discontinuity detection problem. Due to the smooth- ness of the hyper-surface, the new technique can identify jump discontinuities with significantly reduced computational cost, compared to existing methods. Moreover, hierarchical acceleration techniques are also incorporated to further reduce the overall complexity. Rigorous error estimates and complexity anal- yses of the new method are provided as are several numerical examples that illustrate the effectiveness of the approach.

  7. Three-dimensional unstructured grid generation via incremental insertion and local optimization

    NASA Technical Reports Server (NTRS)

    Barth, Timothy J.; Wiltberger, N. Lyn; Gandhi, Amar S.

    1992-01-01

    Algorithms for the generation of 3D unstructured surface and volume grids are discussed. These algorithms are based on incremental insertion and local optimization. The present algorithms are very general and permit local grid optimization based on various measures of grid quality. This is very important; unlike the 2D Delaunay triangulation, the 3D Delaunay triangulation appears not to have a lexicographic characterization of angularity. (The Delaunay triangulation is known to minimize that maximum containment sphere, but unfortunately this is not true lexicographically). Consequently, Delaunay triangulations in three-space can result in poorly shaped tetrahedral elements. Using the present algorithms, 3D meshes can be constructed which optimize a certain angle measure, albeit locally. We also discuss the combinatorial aspects of the algorithm as well as implementational details.

  8. Grid and basis adaptive polynomial chaos techniques for sensitivity and uncertainty analysis

    SciTech Connect

    Perkó, Zoltán Gilli, Luca Lathouwers, Danny Kloosterman, Jan Leen

    2014-03-01

    The demand for accurate and computationally affordable sensitivity and uncertainty techniques is constantly on the rise and has become especially pressing in the nuclear field with the shift to Best Estimate Plus Uncertainty methodologies in the licensing of nuclear installations. Besides traditional, already well developed methods – such as first order perturbation theory or Monte Carlo sampling – Polynomial Chaos Expansion (PCE) has been given a growing emphasis in recent years due to its simple application and good performance. This paper presents new developments of the research done at TU Delft on such Polynomial Chaos (PC) techniques. Our work is focused on the Non-Intrusive Spectral Projection (NISP) approach and adaptive methods for building the PCE of responses of interest. Recent efforts resulted in a new adaptive sparse grid algorithm designed for estimating the PC coefficients. The algorithm is based on Gerstner's procedure for calculating multi-dimensional integrals but proves to be computationally significantly cheaper, while at the same it retains a similar accuracy as the original method. More importantly the issue of basis adaptivity has been investigated and two techniques have been implemented for constructing the sparse PCE of quantities of interest. Not using the traditional full PC basis set leads to further reduction in computational time since the high order grids necessary for accurately estimating the near zero expansion coefficients of polynomial basis vectors not needed in the PCE can be excluded from the calculation. Moreover the sparse PC representation of the response is easier to handle when used for sensitivity analysis or uncertainty propagation due to the smaller number of basis vectors. The developed grid and basis adaptive methods have been implemented in Matlab as the Fully Adaptive Non-Intrusive Spectral Projection (FANISP) algorithm and were tested on four analytical problems. These show consistent good performance both

  9. Climate Change Adaptation Among Tibetan Pastoralists: Challenges in Enhancing Local Adaptation Through Policy Support

    NASA Astrophysics Data System (ADS)

    Fu, Yao; Grumbine, R. Edward; Wilkes, Andreas; Wang, Yun; Xu, Jian-Chu; Yang, Yong-Ping

    2012-10-01

    While researchers are aware that a mix of Local Ecological Knowledge (LEK), community-based resource management institutions, and higher-level institutions and policies can facilitate pastoralists' adaptation to climate change, policy makers have been slow to understand these linkages. Two critical issues are to what extent these factors play a role, and how to enhance local adaptation through government support. We investigated these issues through a case study of two pastoral communities on the Tibetan Plateau in China employing an analytical framework to understand local climate adaptation processes. We concluded that LEK and community-based institutions improve adaptation outcomes for Tibetan pastoralists through shaping and mobilizing resource availability to reduce risks. Higher-level institutions and policies contribute by providing resources from outside communities. There are dynamic interrelationships among these factors that can lead to support, conflict, and fragmentation. Government policy could enhance local adaptation through improvement of supportive relationships among these factors. While central government policies allow only limited room for overt integration of local knowledge/institutions, local governments often have some flexibility to buffer conflicts. In addition, government policies to support market-based economic development have greatly benefited adaptation outcomes for pastoralists. Overall, in China, there are still questions over how to create innovative institutions that blend LEK and community-based institutions with government policy making.

  10. Adaptation to abiotic conditions drives local adaptation in bacteria and viruses coevolving in heterogeneous environments

    PubMed Central

    Scanlan, Pauline D.; Buckling, Angus

    2016-01-01

    Parasite local adaptation, the greater performance of parasites on their local compared with foreign hosts, has important consequences for the maintenance of diversity and epidemiology. While the abiotic environment may significantly affect local adaptation, most studies to date have failed either to incorporate the effects of the abiotic environment, or to separate them from those of the biotic environment. Here, we tease apart biotic and abiotic components of local adaptation using the bacterium Pseudomonas fluorescens and its viral parasite bacteriophage Φ2. We coevolved replicate populations of bacteria and phages at three different temperatures, and determined their performance against coevolutionary partners from the same and different temperatures. Crucially, we measured performance at different assay temperatures, which allowed us to disentangle adaptation to biotic and abiotic habitat components. Our results show that bacteria and phages are more resistant and infectious, respectively, at the temperature at which they previously coevolved, confirming that local adaptation to abiotic conditions can play a crucial role in determining parasite infectivity and host resistance. Our work underlines the need to assess host–parasite interactions across multiple relevant abiotic environments, and suggests that microbial adaption to local temperatures can create ecological barriers to dispersal across temperature gradients. PMID:26888914

  11. Local adaptive filtering of images corrupted by nonstationary noise

    NASA Astrophysics Data System (ADS)

    Lukin, Vladimir V.; Fevralev, Dmitriy V.; Ponomarenko, Nikolay N.; Pogrebnyak, Oleksiy B.; Egiazarian, Karen O.; Astola, Jaakko T.

    2009-02-01

    In various practical situations of remote sensing image processing it is assumed that noise is nonstationary and no a priory information on noise dependence on local mean or about local properties of noise statistics is available. It is shown that in such situations it is difficult to find a proper filter for effective image processing, i.e., for noise removal with simultaneous edge/detail preservation. To deal with such images, a local adaptive filter based on discrete cosine transform in overlapping blocks is proposed. A threshold is set locally based on a noise standard deviation estimate obtained for each block. Several other operations to improve performance of the locally adaptive filter are proposed and studied. The designed filter effectiveness is demonstrated for simulated data as well as for real life radar remote sensing and marine polarimetric radar images.

  12. Locally-adaptive and memetic evolutionary pattern search algorithms.

    PubMed

    Hart, William E

    2003-01-01

    Recent convergence analyses of evolutionary pattern search algorithms (EPSAs) have shown that these methods have a weak stationary point convergence theory for a broad class of unconstrained and linearly constrained problems. This paper describes how the convergence theory for EPSAs can be adapted to allow each individual in a population to have its own mutation step length (similar to the design of evolutionary programing and evolution strategies algorithms). These are called locally-adaptive EPSAs (LA-EPSAs) since each individual's mutation step length is independently adapted in different local neighborhoods. The paper also describes a variety of standard formulations of evolutionary algorithms that can be used for LA-EPSAs. Further, it is shown how this convergence theory can be applied to memetic EPSAs, which use local search to refine points within each iteration. PMID:12804096

  13. Genetics of water use physiology in locally adapted Arabidopsis thaliana.

    PubMed

    Mojica, Julius P; Mullen, Jack; Lovell, John T; Monroe, J Grey; Paul, John R; Oakley, Christopher G; McKay, John K

    2016-10-01

    Identifying the genetic basis of adaptation to climate has long been a goal in evolutionary biology and has applications in agriculture. Adaptation to drought represents one important aspect of local adaptation, and drought is the major factor limiting agricultural yield. We examined local adaptation between Sweden and Italy Arabidopsis thaliana ecotypes, which show contrasting levels of water availability in their local environments. To identify quantitative trait loci (QTL) controlling water use physiology traits and adaptive trait QTL (genomic regions where trait QTL and fitness QTL colocalize), we performed QTL mapping on 374F9 recombinant inbred lines in well-watered and terminal drought conditions. We found 72 QTL (32 in well-watered, 31 in drought, 9 for plasticity) across five water use physiology traits: δ(13)C, rosette area, dry rosette weight, leaf water content and percent leaf nitrogen. Some of these genomic regions colocalize with fitness QTL and with other physiology QTL in defined hotspots. In addition, we found evidence of both constitutive and inducible water use physiology QTL. Finally, we identified highly divergent candidate genes, in silico. Our results suggest that many genes with minor effects may influence adaptation through water use physiology and that pleiotropic water use physiology QTL have fitness consequences. PMID:27593459

  14. An adaptive quadrature-free implementation of the high-order spectral volume method on unstructured grids

    NASA Astrophysics Data System (ADS)

    Harris, Robert Evan

    2008-10-01

    An efficient implementation of the high-order spectral volume (SV) method is presented for multi-dimensional conservation laws on unstructured grids. In the SV method, each simplex cell is called a spectral volume (SV), and the SV is further subdivided into polygonal (2D), or polyhedral (3D) control volumes (CVs) to support high-order data reconstructions. In the traditional implementation, Gauss quadrature formulas are used to approximate the flux integrals on all faces. In the new approach, a nodal set is selected and used to reconstruct a high-order polynomial approximation for the flux vector, and then the flux integrals on the internal faces are computed analytically, without the need for Gauss quadrature formulas. This gives a significant advantage over the traditional SV method in efficiency and ease of implementation. Fundamental properties of the new SV implementation are studied and high-order accuracy is demonstrated for linear and nonlinear advection equations, and the Euler equations. The new quadrature-free approach is then extended to handle local adaptive hp-refinement (grid and order refinement). Efficient edge-based adaptation utilizing a binary tree search algorithm is employed. Several different adaptation criteria which focus computational effort near high gradient regions are presented. Both h- and p-refinements are presented in a general framework where it is possible to perform either or both on any grid cell at any time. Several well-known inviscid flow test cases, subjected to various levels of adaptation, are utilized to demonstrate the effectiveness of the method. An analysis of the accuracy and stability properties of the spectral volume (SV) method is then presented. The current work seeks to address the issue of stability, as well as polynomial quality, in the design of SV partitions. A new approach is presented, which efficiently locates stable partitions by means of constrained minimization. Once stable partitions are located, a

  15. Enhancing adaptive sparse grid approximations and improving refinement strategies using adjoint-based a posteriori error estimates

    DOE PAGESBeta

    Jakeman, J. D.; Wildey, T.

    2015-01-01

    In this paper we present an algorithm for adaptive sparse grid approximations of quantities of interest computed from discretized partial differential equations. We use adjoint-based a posteriori error estimates of the interpolation error in the sparse grid to enhance the sparse grid approximation and to drive adaptivity. We show that utilizing these error estimates provides significantly more accurate functional values for random samples of the sparse grid approximation. We also demonstrate that alternative refinement strategies based upon a posteriori error estimates can lead to further increases in accuracy in the approximation over traditional hierarchical surplus based strategies. Throughout this papermore » we also provide and test a framework for balancing the physical discretization error with the stochastic interpolation error of the enhanced sparse grid approximation.« less

  16. Enhancing adaptive sparse grid approximations and improving refinement strategies using adjoint-based a posteriori error estimates

    SciTech Connect

    Jakeman, J. D.; Wildey, T.

    2015-01-01

    In this paper we present an algorithm for adaptive sparse grid approximations of quantities of interest computed from discretized partial differential equations. We use adjoint-based a posteriori error estimates of the interpolation error in the sparse grid to enhance the sparse grid approximation and to drive adaptivity. We show that utilizing these error estimates provides significantly more accurate functional values for random samples of the sparse grid approximation. We also demonstrate that alternative refinement strategies based upon a posteriori error estimates can lead to further increases in accuracy in the approximation over traditional hierarchical surplus based strategies. Throughout this paper we also provide and test a framework for balancing the physical discretization error with the stochastic interpolation error of the enhanced sparse grid approximation.

  17. Evaluating two sparse grid surrogates and two adaptation criteria for groundwater Bayesian uncertainty quantification

    NASA Astrophysics Data System (ADS)

    Zeng, Xiankui; Ye, Ming; Burkardt, John; Wu, Jichun; Wang, Dong; Zhu, Xiaobin

    2016-04-01

    Sparse grid (SG) stochastic collocation methods have been recently used to build accurate but cheap-to-run surrogates for groundwater models to reduce the computational burden of Bayesian uncertainty analysis. The surrogates can be built for either a log-likelihood function or state variables such as hydraulic head and solute concentration. Using a synthetic groundwater flow model, this study evaluates the log-likelihood and head surrogates in terms of the computational cost of building them, the accuracy of the surrogates, and the accuracy of the distributions of model parameters and predictions obtained using the surrogates. The head surrogates outperform the log-likelihood surrogates for the following four reasons: (1) the shape of the head response surface is smoother than that of the log-likelihood response surface in parameter space, (2) the head variation is smaller than the log-likelihood variation in parameter space, (3) the interpolation error of the head surrogates does not accumulate to be larger than the interpolation error of the log-likelihood surrogates, and (4) the model simulations needed for building one head surrogate can be recycled for building others. For both log-likelihood and head surrogates, adaptive sparse grids are built using two indicators: absolute error and relative error. The adaptive head surrogates are insensitive to the error indicators, because the ratio between the two indicators is hydraulic head, which has small variation in the parameter space. The adaptive log-likelihood surrogates based on the relative error indicators outperform those based on the absolute error indicators, because adaptation based on the relative error indicator puts more sparse-grid nodes in the areas in the parameter space where the log-likelihood is high. While our numerical study suggests building state-variable surrogates and using the relative error indicator for building log-likelihood surrogates, selecting appropriate type of surrogates and

  18. Winter wren populations show adaptation to local climate

    PubMed Central

    Morrison, Catriona A.; Robinson, Robert A.; Pearce-Higgins, James W.

    2016-01-01

    Most studies of evolutionary responses to climate change have focused on phenological responses to warming, and provide only weak evidence for evolutionary adaptation. This could be because phenological changes are more weakly linked to fitness than more direct mechanisms of climate change impacts, such as selective mortality during extreme weather events which have immediate fitness consequences for the individuals involved. Studies examining these other mechanisms may be more likely to show evidence for evolutionary adaptation. To test this, we quantify regional population responses of a small resident passerine (winter wren Troglodytes troglodytes) to a measure of winter severity (number of frost days). Annual population growth rate was consistently negatively correlated with this measure, but the point at which different populations achieved stability (λ = 1) varied across regions and was closely correlated with the historic average number of frost days, providing strong evidence for local adaptation. Despite this, regional variation in abundance remained negatively related to the regional mean number of winter frost days, potentially as a result of a time-lag in the rate of evolutionary response to climate change. As expected from Bergmann's rule, individual wrens were heavier in colder regions, suggesting that local adaptation may be mediated through body size. However, there was no evidence for selective mortality of small individuals in cold years, with annual variation in mean body size uncorrelated with the number of winter frost days, so the extent to which local adaptation occurs through changes in body size, or another mechanism remains uncertain. PMID:27429782

  19. Winter wren populations show adaptation to local climate.

    PubMed

    Morrison, Catriona A; Robinson, Robert A; Pearce-Higgins, James W

    2016-06-01

    Most studies of evolutionary responses to climate change have focused on phenological responses to warming, and provide only weak evidence for evolutionary adaptation. This could be because phenological changes are more weakly linked to fitness than more direct mechanisms of climate change impacts, such as selective mortality during extreme weather events which have immediate fitness consequences for the individuals involved. Studies examining these other mechanisms may be more likely to show evidence for evolutionary adaptation. To test this, we quantify regional population responses of a small resident passerine (winter wren Troglodytes troglodytes) to a measure of winter severity (number of frost days). Annual population growth rate was consistently negatively correlated with this measure, but the point at which different populations achieved stability (λ = 1) varied across regions and was closely correlated with the historic average number of frost days, providing strong evidence for local adaptation. Despite this, regional variation in abundance remained negatively related to the regional mean number of winter frost days, potentially as a result of a time-lag in the rate of evolutionary response to climate change. As expected from Bergmann's rule, individual wrens were heavier in colder regions, suggesting that local adaptation may be mediated through body size. However, there was no evidence for selective mortality of small individuals in cold years, with annual variation in mean body size uncorrelated with the number of winter frost days, so the extent to which local adaptation occurs through changes in body size, or another mechanism remains uncertain. PMID:27429782

  20. Adaptive windowed range-constrained Otsu method using local information

    NASA Astrophysics Data System (ADS)

    Zheng, Jia; Zhang, Dinghua; Huang, Kuidong; Sun, Yuanxi; Tang, Shaojie

    2016-01-01

    An adaptive windowed range-constrained Otsu method using local information is proposed for improving the performance of image segmentation. First, the reason why traditional thresholding methods do not perform well in the segmentation of complicated images is analyzed. Therein, the influences of global and local thresholdings on the image segmentation are compared. Second, two methods that can adaptively change the size of the local window according to local information are proposed by us. The characteristics of the proposed methods are analyzed. Thereby, the information on the number of edge pixels in the local window of the binarized variance image is employed to adaptively change the local window size. Finally, the superiority of the proposed method over other methods such as the range-constrained Otsu, the active contour model, the double Otsu, the Bradley's, and the distance-regularized level set evolution is demonstrated. It is validated by the experiments that the proposed method can keep more details and acquire much more satisfying area overlap measure as compared with the other conventional methods.

  1. A local adaptive discretization algorithm for Smoothed Particle Hydrodynamics

    NASA Astrophysics Data System (ADS)

    Spreng, Fabian; Schnabel, Dirk; Mueller, Alexandra; Eberhard, Peter

    2014-06-01

    In this paper, an extension to the Smoothed Particle Hydrodynamics (SPH) method is proposed that allows for an adaptation of the discretization level of a simulated continuum at runtime. By combining a local adaptive refinement technique with a newly developed coarsening algorithm, one is able to improve the accuracy of the simulation results while reducing the required computational cost at the same time. For this purpose, the number of particles is, on the one hand, adaptively increased in critical areas of a simulation model. Typically, these are areas that show a relatively low particle density and high gradients in stress or temperature. On the other hand, the number of SPH particles is decreased for domains with a high particle density and low gradients. Besides a brief introduction to the basic principle of the SPH discretization method, the extensions to the original formulation providing such a local adaptive refinement and coarsening of the modeled structure are presented in this paper. After having introduced its theoretical background, the applicability of the enhanced formulation, as well as the benefit gained from the adaptive model discretization, is demonstrated in the context of four different simulation scenarios focusing on solid continua. While presenting the results found for these examples, several properties of the proposed adaptive technique are discussed, e.g. the conservation of momentum as well as the existing correlation between the chosen refinement and coarsening patterns and the observed quality of the results.

  2. Fair Energy Scheduling for Vehicle-to-Grid Networks Using Adaptive Dynamic Programming.

    PubMed

    Xie, Shengli; Zhong, Weifeng; Xie, Kan; Yu, Rong; Zhang, Yan

    2016-08-01

    Research on the smart grid is being given enormous supports worldwide due to its great significance in solving environmental and energy crises. Electric vehicles (EVs), which are powered by clean energy, are adopted increasingly year by year. It is predictable that the huge charge load caused by high EV penetration will have a considerable impact on the reliability of the smart grid. Therefore, fair energy scheduling for EV charge and discharge is proposed in this paper. By using the vehicle-to-grid technology, the scheduler controls the electricity loads of EVs considering fairness in the residential distribution network. We propose contribution-based fairness, in which EVs with high contributions have high priorities to obtain charge energy. The contribution value is defined by both the charge/discharge energy and the timing of the action. EVs can achieve higher contribution values when discharging during the load peak hours. However, charging during this time will decrease the contribution values seriously. We formulate the fair energy scheduling problem as an infinite-horizon Markov decision process. The methodology of adaptive dynamic programming is employed to maximize the long-term fairness by processing online network training. The numerical results illustrate that the proposed EV energy scheduling is able to mitigate and flatten the peak load in the distribution network. Furthermore, contribution-based fairness achieves a fast recovery of EV batteries that have deeply discharged and guarantee fairness in the full charge time of all EVs. PMID:26930694

  3. Rapid local adaptation mediates zooplankton community assembly in experimental mesocosms.

    PubMed

    Pantel, Jelena H; Duvivier, Cathy; Meester, Luc De

    2015-10-01

    Adaptive evolution can occur over similar timescales as ecological processes such as community assembly, but its particular effects on community assembly and structure and their magnitude are poorly understood. In experimental evolution trials, Daphnia magna were exposed to varying environments (presence and absence of fish and artificial macrophytes) for 2 months. Then, in a common gardening experiment, we compared zooplankton community composition when either experimentally adapted or D. magna from the original population were present. Local adaptation of D. magna significantly altered zooplankton community composition, leading to a suppression of abundances for some zooplankton taxa and facilitation for others. The effect size of D. magna adaptation was similar to that of adding fish or macrophytes to mesocosms, two important drivers of zooplankton community structure. Our results suggest that substantial amounts of variation in community composition in natural systems may be unexplained if evolutionary dynamics are ignored. PMID:26251339

  4. Floral adaptation to local pollinator guilds in a terrestrial orchid

    PubMed Central

    Sun, Mimi; Gross, Karin; Schiestl, Florian P.

    2014-01-01

    Background and Aims Studies of local floral adaptation in response to geographically divergent pollinators are essential for understanding floral evolution. This study investigated local pollinator adaptation and variation in floral traits in the rewarding orchid Gymnadenia odoratissima, which spans a large altitudinal gradient and thus may depend on different pollinator guilds along this gradient. Methods Pollinator communities were assessed and reciprocal transfer experiments were performed between lowland and mountain populations. Differences in floral traits were characterized by measuring floral morphology traits, scent composition, colour and nectar sugar content in lowland and mountain populations. Key Results The composition of pollinator communities differed considerably between lowland and mountain populations; flies were only found as pollinators in mountain populations. The reciprocal transfer experiments showed that when lowland plants were transferred to mountain habitats, their reproductive success did not change significantly. However, when mountain plants were moved to the lowlands, their reproductive success decreased significantly. Transfers between populations of the same altitude did not lead to significant changes in reproductive success, disproving the potential for population-specific adaptations. Flower size of lowland plants was greater than for mountain flowers. Lowland plants also had significantly higher relative amounts of aromatic floral volatiles, while the mountain plants had higher relative amounts of other floral volatiles. The floral colour of mountain flowers was significantly lighter compared with the lowland flowers. Conclusions Local pollinator adaptation through pollinator attraction was shown in the mountain populations, possibly due to adaptation to pollinating flies. The mountain plants were also observed to receive pollination from a greater diversity of pollinators than the lowland plants. The different floral

  5. Adaptive phenotypic plasticity and local adaptation for temperature tolerance in freshwater zooplankton

    PubMed Central

    Yampolsky, Lev Y.; Schaer, Tobias M. M.; Ebert, Dieter

    2014-01-01

    Many organisms have geographical distributions extending from the tropics to near polar regions or can experience up to 30°C temperature variation within the lifespan of an individual. Two forms of evolutionary adaptation to such wide ranges in ambient temperatures are frequently discussed: local adaptation and phenotypic plasticity. The freshwater planktonic crustacean Daphnia magna, whose range extends from South Africa to near arctic sites, shows strong phenotypic and genotypic variation in response to temperature. In this study, we use D. magna clones from 22 populations (one clone per population) ranging from latitude 0° (Kenya) to 66° North (White Sea) to explore the contributions of phenotypic plasticity and local adaptation to high temperature tolerance. Temperature tolerance was studied as knockout time (time until immobilization, Timm) at 37°C in clones acclimatized to either 20°C or 28°C. Acclimatization to 28°C strongly increased Timm, testifying to adaptive phenotypic plasticity. At the same time, Timm significantly correlated with average high temperature at the clones’ sites of origin, suggesting local adaptation. As earlier studies have found that haemoglobin expression contributes to temperature tolerance, we also quantified haemoglobin concentration in experimental animals and found that both acclimatization temperature (AccT) and temperature at the site of origin are positively correlated with haemoglobin concentration. Furthermore, Daphnia from warmer climates upregulate haemoglobin much more strongly in response to AccT, suggesting local adaptation for plasticity in haemoglobin expression. Our results show that both local adaptation and phenotypic plasticity contribute to temperature tolerance, and elucidate a possible role of haemoglobin in mediating these effects that differs along a cold–warm gradient. PMID:24352948

  6. An adaptive sparse-grid high-order stochastic collocation method for Bayesian inference in groundwater reactive transport modeling

    SciTech Connect

    Zhang, Guannan; Webster, Clayton G; Gunzburger, Max D

    2012-09-01

    Although Bayesian analysis has become vital to the quantification of prediction uncertainty in groundwater modeling, its application has been hindered due to the computational cost associated with numerous model executions needed for exploring the posterior probability density function (PPDF) of model parameters. This is particularly the case when the PPDF is estimated using Markov Chain Monte Carlo (MCMC) sampling. In this study, we develop a new approach that improves computational efficiency of Bayesian inference by constructing a surrogate system based on an adaptive sparse-grid high-order stochastic collocation (aSG-hSC) method. Unlike previous works using first-order hierarchical basis, we utilize a compactly supported higher-order hierar- chical basis to construct the surrogate system, resulting in a significant reduction in the number of computational simulations required. In addition, we use hierarchical surplus as an error indi- cator to determine adaptive sparse grids. This allows local refinement in the uncertain domain and/or anisotropic detection with respect to the random model parameters, which further improves computational efficiency. Finally, we incorporate a global optimization technique and propose an iterative algorithm for building the surrogate system for the PPDF with multiple significant modes. Once the surrogate system is determined, the PPDF can be evaluated by sampling the surrogate system directly with very little computational cost. The developed method is evaluated first using a simple analytical density function with multiple modes and then using two synthetic groundwater reactive transport models. The groundwater models represent different levels of complexity; the first example involves coupled linear reactions and the second example simulates nonlinear ura- nium surface complexation. The results show that the aSG-hSC is an effective and efficient tool for Bayesian inference in groundwater modeling in comparison with conventional

  7. Vertical Scan (V-SCAN) for 3-D Grid Adaptive Mesh Refinement for an atmospheric Model Dynamical Core

    NASA Astrophysics Data System (ADS)

    Andronova, N. G.; Vandenberg, D.; Oehmke, R.; Stout, Q. F.; Penner, J. E.

    2009-12-01

    One of the major building blocks of a rigorous representation of cloud evolution in global atmospheric models is a parallel adaptive grid MPI-based communication library (an Adaptive Blocks for Locally Cartesian Topologies library -- ABLCarT), which manages the block-structured data layout, handles ghost cell updates among neighboring blocks and splits a block as refinements occur. The library has several modules that provide a layer of abstraction for adaptive refinement: blocks, which contain individual cells of user data; shells - the global geometry for the problem, including a sphere, reduced sphere, and now a 3D sphere; a load balancer for placement of blocks onto processors; and a communication support layer which encapsulates all data movement. A major performance concern with adaptive mesh refinement is how to represent calculations that have need to be sequenced in a particular order in a direction, such as calculating integrals along a specific path (e.g. atmospheric pressure or geopotential in the vertical dimension). This concern is compounded if the blocks have varying levels of refinement, or are scattered across different processors, as can be the case in parallel computing. In this paper we describe an implementation in ABLCarT of a vertical scan operation, which allows computing along vertical paths in the correct order across blocks transparent to their resolution and processor location. We test this functionality on a 2D and a 3D advection problem, which tests the performance of the model’s dynamics (transport) and physics (sources and sinks) for different model resolutions needed for inclusion of cloud formation.

  8. The response of local power grid at low-latitude to geomagnetic storm: An application of the Hilbert Huang transform

    NASA Astrophysics Data System (ADS)

    Liu, Jin; Wang, Chuan-Bing; Liu, Lu; Sun, Wei-Huai

    2016-04-01

    The Hilbert-Huang transform (HHT) is an adaptive data analysis method that can accommodate the variety of data generated by nonlinear and nonstationary processes in nature. In this paper, we focus on the small geomagnetically induced current (GIC) at the local substations in low-latitude power grid of China, responding to a moderate storm on 14-18 July 2012. The HHT is applied to analyze the neutral point currents (NPCs) of transformers measured at different substations, and the GIC indices converted from local geomagnetic field measurements. The original data are decomposed into intrinsic mode functions (IMFs) using the ensemble empirical mode decomposition. After removal of the quasi-diurnal components related with the solar quiet variation, the IMFs representing storm disturbances are transformed into Hilbert energy spectra. The results show that some transformers have more or less responses to the moderate storm in the form of Hilbert energy spectra with the frequency around 2-3 mHz. A comparison on the amplitude changes of the spectra total energy of NPCs' perturbation during storm time intervals at different sites suggests that a shell type of three-phase single transformer group seems to be more vulnerable in the storm. Although the low-latitude power grids usually show very small GIC, these can be used to investigate the potential risk of space weather to the system.

  9. Eigenanalysis-based adaptive interference suppression for source localization

    NASA Astrophysics Data System (ADS)

    Ren, Suiling; Ge, Fengxiang; Guo, Xin; Guo, Lianghao

    2012-11-01

    Passive sonar detection in shallow water environments is very difficult due to strong interference. In this paper, an eigenanalysis-based adaptive interference suppression method (EAAIS) is presented for source localization. First, using beamforming for each eigenvector of the cross-spectral density matrix (CSDM) and a priori knowledge of the target's bearing interval, the proposed method constructs an appropriate rule to adaptively and robustly identify which eigenvector does not contain dominant contributions from the target of interest (TOI). Then, the identified eigenvectors are subtracted from the CSDM for interference suppression and source location. Numerical simulation results show that the proposed method could effectively detect the TOI even in the presence of strong interference. In comparison with other adaptive interference suppression methods, the proposed method has better interference rejection capability and wider range of applications without a priori knowledge of the interference's position.

  10. The spatial scale of local adaptation in a stochastic environment.

    PubMed

    Hadfield, Jarrod D

    2016-07-01

    The distribution of phenotypes in space will be a compromise between adaptive plasticity and local adaptation increasing the fit of phenotypes to local conditions and gene flow reducing that fit. Theoretical models on the evolution of quantitative characters on spatially explicit landscapes have only considered scenarios where optimum trait values change as deterministic functions of space. Here, these models are extended to include stochastic spatially autocorrelated aspects to the environment, and consequently the optimal phenotype. Under these conditions, the regression of phenotype on the environmental variable becomes steeper as the spatial scale on which populations are sampled becomes larger. Under certain deterministic models - such as linear clines - the regression is constant. The way in which the regression changes with spatial scale is informative about the degree of phenotypic plasticity, the relative scale of effective gene flow and the environmental dependency of selection. Connections to temporal models are discussed. PMID:27188689

  11. A Freestream-Preserving High-Order Finite-Volume Method for Mapped Grids with Adaptive-Mesh Refinement

    SciTech Connect

    Guzik, S; McCorquodale, P; Colella, P

    2011-12-16

    A fourth-order accurate finite-volume method is presented for solving time-dependent hyperbolic systems of conservation laws on mapped grids that are adaptively refined in space and time. Novel considerations for formulating the semi-discrete system of equations in computational space combined with detailed mechanisms for accommodating the adapting grids ensure that conservation is maintained and that the divergence of a constant vector field is always zero (freestream-preservation property). Advancement in time is achieved with a fourth-order Runge-Kutta method.

  12. COLLABORATIVE RESEARCH: CONTINUOUS DYNAMIC GRID ADAPTATION IN A GLOBAL ATMOSPHERIC MODEL: APPLICATION AND REFINEMENT

    SciTech Connect

    Gutowski, William J.; Prusa, Joseph M.; Smolarkiewicz, Piotr K.

    2012-05-08

    This project had goals of advancing the performance capabilities of the numerical general circulation model EULAG and using it to produce a fully operational atmospheric global climate model (AGCM) that can employ either static or dynamic grid stretching for targeted phenomena. The resulting AGCM combined EULAG's advanced dynamics core with the "physics" of the NCAR Community Atmospheric Model (CAM). Effort discussed below shows how we improved model performance and tested both EULAG and the coupled CAM-EULAG in several ways to demonstrate the grid stretching and ability to simulate very well a wide range of scales, that is, multi-scale capability. We leveraged our effort through interaction with an international EULAG community that has collectively developed new features and applications of EULAG, which we exploited for our own work summarized here. Overall, the work contributed to over 40 peer-reviewed publications and over 70 conference/workshop/seminar presentations, many of them invited. 3a. EULAG Advances EULAG is a non-hydrostatic, parallel computational model for all-scale geophysical flows. EULAG's name derives from its two computational options: EULerian (flux form) or semi-LAGrangian (advective form). The model combines nonoscillatory forward-in-time (NFT) numerical algorithms with a robust elliptic Krylov solver. A signature feature of EULAG is that it is formulated in generalized time-dependent curvilinear coordinates. In particular, this enables grid adaptivity. In total, these features give EULAG novel advantages over many existing dynamical cores. For EULAG itself, numerical advances included refining boundary conditions and filters for optimizing model performance in polar regions. We also added flexibility to the model's underlying formulation, allowing it to work with the pseudo-compressible equation set of Durran in addition to EULAG's standard anelastic formulation. Work in collaboration with others also extended the demonstrated range of

  13. Asymmetrical local adaptation of maize landraces along an altitudinal gradient

    PubMed Central

    Mercer, Kristin; Martínez-Vásquez, Ángel; Perales, Hugo R

    2008-01-01

    Crop landraces are managed populations that evolve in response to gene flow and selection. Cross-pollination among fields, seed sharing by farmers, and selection by management and environmental conditions play roles in shaping crop characteristics. We used common gardens to explore the local adaptation of maize (Zea mays ssp. mays) landrace populations from Chiapas, Mexico to altitude. We sowed seeds of 21 populations from three altitudinal ranges in two common gardens and measured two characteristics that estimate fitness: likelihood of producing good quality seed and the total mass of good quality seed per plant. The probability of lowland plants producing good quality seed was invariably high regardless of garden, while highland landraces were especially sensitive to altitude. Their likelihood of producing good seed quadrupled in the highland site. The mass of good quality seed showed a different pattern, with lowland landraces producing 25% less seed mass than the other types at high elevations. Combining these two measures of fitness revealed that the highland landraces were clearly adapted to highland sites, while lowland and midland landraces appear more adapted to the midland site. We discuss this asymmetry in local adaptation in light of climate change and in situ conservation of crop genetic resources. PMID:25567730

  14. Asymmetrical local adaptation of maize landraces along an altitudinal gradient.

    PubMed

    Mercer, Kristin; Martínez-Vásquez, Ángel; Perales, Hugo R

    2008-08-01

    Crop landraces are managed populations that evolve in response to gene flow and selection. Cross-pollination among fields, seed sharing by farmers, and selection by management and environmental conditions play roles in shaping crop characteristics. We used common gardens to explore the local adaptation of maize (Zea mays ssp. mays) landrace populations from Chiapas, Mexico to altitude. We sowed seeds of 21 populations from three altitudinal ranges in two common gardens and measured two characteristics that estimate fitness: likelihood of producing good quality seed and the total mass of good quality seed per plant. The probability of lowland plants producing good quality seed was invariably high regardless of garden, while highland landraces were especially sensitive to altitude. Their likelihood of producing good seed quadrupled in the highland site. The mass of good quality seed showed a different pattern, with lowland landraces producing 25% less seed mass than the other types at high elevations. Combining these two measures of fitness revealed that the highland landraces were clearly adapted to highland sites, while lowland and midland landraces appear more adapted to the midland site. We discuss this asymmetry in local adaptation in light of climate change and in situ conservation of crop genetic resources. PMID:25567730

  15. Evidence of local adaptation in westslope cutthroat trout

    USGS Publications Warehouse

    Drinan, Daniel P.; Zale, Alexander V.; Webb, Molly A.H.; Taper, Mark L.; Shepard, Bradley B.; Kalinowski, Steven T.

    2012-01-01

    An understanding of the process of local adaptation would allow managers to better protect and conserve species. Many salmonids are in need of such efforts, and because they often persist in differing, isolated environments, they are useful organisms for studying local adaptation. In addition, the temperature sensitivity of salmonids provides a likely target for natural selection. We studied thermal adaptation in four wild populations and one hatchery stock of westslope cutthroat trout Oncorhynchus clarkii lewisi . The mean summer temperatures of source streams ranged from 6.7°C to 11.2°C. Embryos were collected from the wild, and embryonic development, embryonic survival, and juvenile growth were determined. A significant relationship between median embryonic survival and source stream temperature was detected. Based on a rank test, populations from colder streams had a greater decline in median embryonic survival at warm temperatures than populations from warmer streams. Embryonic development and juvenile growth did not appear to be influenced by source. These findings suggest that populations are thermally adapted to their source streams and this should be considered by managers. However, further study is necessary to sort out the potential confounding factors, whether genetic or epigenetic.

  16. Coral thermal tolerance shaped by local adaptation of photosymbionts

    NASA Astrophysics Data System (ADS)

    Howells, E. J.; Beltran, V. H.; Larsen, N. W.; Bay, L. K.; Willis, B. L.; van Oppen, M. J. H.

    2012-02-01

    Coral thermal tolerance is strongly influenced by the identity of obligate photosymbionts, which encompass numerous types belonging to the dinoflagellate genus Symbiodinium. Physiological advantages achieved by partnering with functionally diverse symbionts have been assumed to be available only to corals that can form associations with multiple Symbiodinium types. Functional variation among populations of the same type of Symbiodinium has been overlooked, despite local adaptation being feasible because of large population sizes, genetic isolation and short asexual generation times. Here we demonstrate divergent thermal tolerance in a generalist Symbiodinium type from two different thermal environments. Symbiodinium from the warmer reef maintained greater photo-chemical performance and survivorship when exposed to an elevated temperature of 32°C, both in symbiosis and in culture. Juvenile corals associated with Symbiodinium from the warmer reef grew rapidly when exposed to 32°C, yet underwent bleaching and tissue death when associated with Symbiodinium from the cooler reef. These results demonstrate that Symbiodinium types can adapt to local differences in thermal climate and that this adaptation shapes the fitness of coral hosts. If Symbiodinium populations are able to further adapt to increases in temperature at the pace at which ocean climates warm, they may assist corals to increase their thermal tolerance and persist into the future.

  17. Mediterranean blue tits as a case study of local adaptation.

    PubMed

    Charmantier, Anne; Doutrelant, Claire; Dubuc-Messier, Gabrielle; Fargevieille, Amélie; Szulkin, Marta

    2016-01-01

    While the study of the origins of biological diversity across species has provided numerous examples of adaptive divergence, the realization that it can occur at microgeographic scales despite gene flow is recent, and scarcely illustrated. We review here evidence suggesting that the striking phenotypic differentiation in ecologically relevant traits exhibited by blue tits Cyanistes caeruleus in their southern range-edge putatively reflects adaptation to the heterogeneity of the Mediterranean habitats. We first summarize the phenotypic divergence for a series of life history, morphological, behavioural, acoustic and colour ornament traits in blue tit populations of evergreen and deciduous forests. For each divergent trait, we review the evidence obtained from common garden experiments regarding a possible genetic origin of the observed phenotypic differentiation as well as evidence for heterogeneous selection. Second, we argue that most phenotypically differentiated traits display heritable variation, a fundamental requirement for evolution to occur. Third, we discuss nonrandom dispersal, selective barriers and assortative mating as processes that could reinforce local adaptation. Finally, we show how population genomics supports isolation - by - environment across landscapes. Overall, the combination of approaches converges to the conclusion that the strong phenotypic differentiation observed in Mediterranean blue tits is a fascinating case of local adaptation. PMID:27087844

  18. Adaptive-Grid Methods for Phase Field Models of Microstructure Development

    NASA Technical Reports Server (NTRS)

    Provatas, Nikolas; Goldenfeld, Nigel; Dantzig, Jonathan A.

    1999-01-01

    In this work the authors show how the phase field model can be solved in a computationally efficient manner that opens a new large-scale simulational window on solidification physics. Our method uses a finite element, adaptive-grid formulation, and exploits the fact that the phase and temperature fields vary significantly only near the interface. We illustrate how our method allows efficient simulation of phase-field models in very large systems, and verify the predictions of solvability theory at intermediate undercooling. We then present new results at low undercoolings that suggest that solvability theory may not give the correct tip speed in that regime. We model solidification using the phase-field model used by Karma and Rappel.

  19. CHARACTERIZATION OF DISCONTINUITIES IN HIGH-DIMENSIONAL STOCHASTIC PROBLEMS ON ADAPTIVE SPARSE GRIDS

    SciTech Connect

    Jakeman, John D; Archibald, Richard K; Xiu, Dongbin

    2011-01-01

    In this paper we present a set of efficient algorithms for detection and identification of discontinuities in high dimensional space. The method is based on extension of polynomial annihilation for edge detection in low dimensions. Compared to the earlier work, the present method poses significant improvements for high dimensional problems. The core of the algorithms relies on adaptive refinement of sparse grids. It is demonstrated that in the commonly encountered cases where a discontinuity resides on a small subset of the dimensions, the present method becomes optimal , in the sense that the total number of points required for function evaluations depends linearly on the dimensionality of the space. The details of the algorithms will be presented and various numerical examples are utilized to demonstrate the efficacy of the method.

  20. An efficient second-order accurate and continuous interpolation for block-adaptive grids

    NASA Astrophysics Data System (ADS)

    Borovikov, Dmitry; Sokolov, Igor V.; Tóth, Gábor

    2015-09-01

    In this paper we present a second-order and continuous interpolation algorithm for cell-centered adaptive-mesh-refinement (AMR) grids. Continuity requirement poses a non-trivial problem at resolution changes. We develop a classification of the resolution changes, which allows us to employ efficient and simple linear interpolation in the majority of the computational domain. The algorithm is well suited for massively parallel computations. Our interpolation algorithm allows extracting jump-free interpolated data distribution along lines and surfaces within the computational domain. This capability is important for various applications, including kinetic particles tracking in three dimensional vector fields, visualization (i.e. surface extraction) and extracting variables along one-dimensional curves such as field lines, streamlines and satellite trajectories, etc. Particular examples are models for acceleration of solar energetic particles (SEPs) along magnetic field-lines. As such models are sensitive to sharp gradients and discontinuities the capability to interpolate the data from the AMR grid to be passed to the SEP model without producing false gradients numerically becomes crucial. We provide a complete description of the algorithm and make the code publicly available as a Fortran 90 library.

  1. Adaptive multi-grid method for a periodic heterogeneous medium in 1-D

    SciTech Connect

    Fish, J.; Belsky, V.

    1995-12-31

    A multi-grid method for a periodic heterogeneous medium in 1-D is presented. Based on the homogenization theory special intergrid connection operators have been developed to imitate a low frequency response of the differential equations with oscillatory coefficients. The proposed multi-grid method has been proved to have a fast rate of convergence governed by the ratio q/(4-q), where oadaptive multiscale computational scheme is developed. By this technique a computational model entirely constructed on the scale of material heterogeneity is only used where it is necessary to do so, or as indicated by so called Microscale Reduction Error (MRE) indicators, while in the remaining portion of the problem domain, the medium is treated as homogeneous with effective properties. Such a posteriori MRE indicators and estimators are developed on the basis of assessing the validity of two-scale asymptotic expansion.

  2. An Adaptive Reputation-Based Algorithm for Grid Virtual Organization Formation

    NASA Astrophysics Data System (ADS)

    Cui, Yongrui; Li, Mingchu; Ren, Yizhi; Sakurai, Kouichi

    A novel adaptive reputation-based virtual organization formation is proposed. It restrains the bad performers effectively based on the consideration of the global experience of the evaluator and evaluates the direct trust relation between two grid nodes accurately by consulting the previous trust value rationally. It also consults and improves the reputation evaluation process in PathTrust model by taking account of the inter-organizational trust relationship and combines it with direct and recommended trust in a weighted way, which makes the algorithm more robust against collusion attacks. Additionally, the proposed algorithm considers the perspective of the VO creator and takes required VO services as one of the most important fine-grained evaluation criterion, which makes the algorithm more suitable for constructing VOs in grid environments that include autonomous organizations. Simulation results show that our algorithm restrains the bad performers and resists against fake transaction attacks and badmouth attacks effectively. It provides a clear advantage in the design of a VO infrastructure.

  3. Application of Open Loop H-Adaptation to an Unstructured Grid Tidal Flat Model

    NASA Astrophysics Data System (ADS)

    Cowles, G. W.

    2008-12-01

    The complex topology of tidal flats presents a challenge to coastal ocean models. Recently, several models have been developed employing unstructured grids, which can provide the flexibility in mesh resolution required to resolve the complex bathymetry and coastline. However, the distribution of element size in the initial mesh can be somewhat arbitrary, and is in general the product of the operator tailoring the resolution to the underlying bathymetry and regions of interest. In this work, the flow solution from an idealized tidal flat application is used to drive an open loop h-adaptation of the mesh. The model used for this work is the Finite Volume Coastal Ocean Model (FVCOM), an open source, terrain following model. A background length scale distribution derived from model output is used to generate a new initial mesh for the model run, thus defining an iteration of the procedure. Several metrics for computing the background length scale will be examined. These include direct estimation of spatial discretization error using Richardson's extrapolation from a sequence of meshes as well as heuristics derived from gradients in the primitive variables. Examination of grid independence, computational efficiency, and performance of the scheme for idealized tidal flats with inclusion of morphodynamics will be discussed.

  4. The use of the spectral method within the fast adaptive composite grid method

    SciTech Connect

    McKay, S.M.

    1994-12-31

    The use of efficient algorithms for the solution of partial differential equations has been sought for many years. The fast adaptive composite grid (FAC) method combines an efficient algorithm with high accuracy to obtain low cost solutions to partial differential equations. The FAC method achieves fast solution by combining solutions on different grids with varying discretizations and using multigrid like techniques to find fast solution. Recently, the continuous FAC (CFAC) method has been developed which utilizes an analytic solution within a subdomain to iterate to a solution of the problem. This has been shown to achieve excellent results when the analytic solution can be found. The CFAC method will be extended to allow solvers which construct a function for the solution, e.g., spectral and finite element methods. In this discussion, the spectral methods will be used to provide a fast, accurate solution to the partial differential equation. As spectral methods are more accurate than finite difference methods, the ensuing accuracy from this hybrid method outside of the subdomain will be investigated.

  5. Incorporating Adaptive Local Information Into Fuzzy Clustering for Image Segmentation.

    PubMed

    Liu, Guoying; Zhang, Yun; Wang, Aimin

    2015-11-01

    Fuzzy c-means (FCM) clustering with spatial constraints has attracted great attention in the field of image segmentation. However, most of the popular techniques fail to resolve misclassification problems due to the inaccuracy of their spatial models. This paper presents a new unsupervised FCM-based image segmentation method by paying closer attention to the selection of local information. In this method, region-level local information is incorporated into the fuzzy clustering procedure to adaptively control the range and strength of interactive pixels. First, a novel dissimilarity function is established by combining region-based and pixel-based distance functions together, in order to enhance the relationship between pixels which have similar local characteristics. Second, a novel prior probability function is developed by integrating the differences between neighboring regions into the mean template of the fuzzy membership function, which adaptively selects local spatial constraints by a tradeoff weight depending upon whether a pixel belongs to a homogeneous region or not. Through incorporating region-based information into the spatial constraints, the proposed method strengthens the interactions between pixels within the same region and prevents over smoothing across region boundaries. Experimental results over synthetic noise images, natural color images, and synthetic aperture radar images show that the proposed method achieves more accurate segmentation results, compared with five state-of-the-art image segmentation methods. PMID:26186787

  6. Numerical approximations to nonlinear conservation laws with locally varying time and space grids

    NASA Technical Reports Server (NTRS)

    Osher, S.; Sanders, R.

    1983-01-01

    Numerical approximations to the initial value problem for nonlinear systems of conservation laws are considered. The considered system is said to be hyperbolic when all eigenvalues of every real linear combination of the Jacobian matrices are real. Solutions may develop discontinuities in finite time, even when the initial data are smooth. In the investigation, explicit finite difference methods which use locally varying time grids are considered. The global CFL restriction is replaced by a local restriction. The numerical flux function is studied from a finite volume viewpoint, and a differencing technique is developed at interface points between regions of distinct time increments.

  7. Axisymmetric modeling of cometary mass loading on an adaptively refined grid: MHD results

    NASA Technical Reports Server (NTRS)

    Gombosi, Tamas I.; Powell, Kenneth G.; De Zeeuw, Darren L.

    1994-01-01

    The first results of an axisymmetric magnetohydrodynamic (MHD) model of the interaction of an expanding cometary atmosphere with the solar wind are presented. The model assumes that far upstream the plasma flow lines are parallel to the magnetic field vector. The effects of mass loading and ion-neutral friction are taken into account by the governing equations, whcih are solved on an adaptively refined unstructured grid using a Monotone Upstream Centered Schemes for Conservative Laws (MUSCL)-type numerical technique. The combination of the adaptive refinement with the MUSCL-scheme allows the entire cometary atmosphere to be modeled, while still resolving both the shock and the near nucleus of the comet. The main findingsare the following: (1) A shock is formed approximately = 0.45 Mkm upstream of the comet (its location is controlled by the sonic and Alfvenic Mach numbers of the ambient solar wind flow and by the cometary mass addition rate). (2) A contact surface is formed approximately = 5,600 km upstream of the nucleus separating an outward expanding cometary ionosphere from the nearly stagnating solar wind flow. The location of the contact surface is controlled by the upstream flow conditions, the mass loading rate and the ion-neutral drag. The contact surface is also the boundary of the diamagnetic cavity. (3) A closed inner shock terminates the supersonic expansion of the cometary ionosphere. This inner shock is closer to the nucleus on dayside than on the nightside.

  8. Moving Overlapping Grids with Adaptive Mesh Refinement for High-Speed Reactive and Non-reactive Flow

    SciTech Connect

    Henshaw, W D; Schwendeman, D W

    2005-08-30

    We consider the solution of the reactive and non-reactive Euler equations on two-dimensional domains that evolve in time. The domains are discretized using moving overlapping grids. In a typical grid construction, boundary-fitted grids are used to represent moving boundaries, and these grids overlap with stationary background Cartesian grids. Block-structured adaptive mesh refinement (AMR) is used to resolve fine-scale features in the flow such as shocks and detonations. Refinement grids are added to base-level grids according to an estimate of the error, and these refinement grids move with their corresponding base-level grids. The numerical approximation of the governing equations takes place in the parameter space of each component grid which is defined by a mapping from (fixed) parameter space to (moving) physical space. The mapped equations are solved numerically using a second-order extension of Godunov's method. The stiff source term in the reactive case is handled using a Runge-Kutta error-control scheme. We consider cases when the boundaries move according to a prescribed function of time and when the boundaries of embedded bodies move according to the surface stress exerted by the fluid. In the latter case, the Newton-Euler equations describe the motion of the center of mass of the each body and the rotation about it, and these equations are integrated numerically using a second-order predictor-corrector scheme. Numerical boundary conditions at slip walls are described, and numerical results are presented for both reactive and non-reactive flows in order to demonstrate the use and accuracy of the numerical approach.

  9. Locally adaptive vector quantization: Data compression with feature preservation

    NASA Technical Reports Server (NTRS)

    Cheung, K. M.; Sayano, M.

    1992-01-01

    A study of a locally adaptive vector quantization (LAVQ) algorithm for data compression is presented. This algorithm provides high-speed one-pass compression and is fully adaptable to any data source and does not require a priori knowledge of the source statistics. Therefore, LAVQ is a universal data compression algorithm. The basic algorithm and several modifications to improve performance are discussed. These modifications are nonlinear quantization, coarse quantization of the codebook, and lossless compression of the output. Performance of LAVQ on various images using irreversible (lossy) coding is comparable to that of the Linde-Buzo-Gray algorithm, but LAVQ has a much higher speed; thus this algorithm has potential for real-time video compression. Unlike most other image compression algorithms, LAVQ preserves fine detail in images. LAVQ's performance as a lossless data compression algorithm is comparable to that of Lempel-Ziv-based algorithms, but LAVQ uses far less memory during the coding process.

  10. Global/local interlaminar stress analysis of a grid-stiffened composite panel

    NASA Astrophysics Data System (ADS)

    Wiggenraad, J. F. M.; Bauld, N. R., Jr.

    1991-05-01

    A global/local procedure for the computation of the interlaminar stress components at the skin wrap, skin core, and wrap core interfaces for an advanced concept stiffened panel, is described. The procedure consists of a global model of two dimensional shell elements that is used to design a grid stiffened panel with blade type stiffeners, a local model of three dimensional solid elements that is used to compute interlaminar stress components, and a scheme devised to assign displacement boundary conditions for a local model that are based on displacement and rotation data of a few nodes of the global model. A global panel was designed according to strength, stiffness, and stability criteria associated with the design of traditional aircraft wing panels. Interlaminar normal and shearing stress components, computed via the local model, were found to be well below typical tensile normal and shearing strengths of a graphite epoxy material.

  11. Global/local interlaminar stress analysis of a grid-stiffened composite panel

    NASA Astrophysics Data System (ADS)

    Wiggenraad, J. F. M.; Bauld, N. R., Jr.

    1993-02-01

    A global/local procedure for the computation of the interlaminar stress components at the skin wrap, skin core, and wrap core interfaces for an advanced concept stiffened panel, is described. The procedure consists of a global model of two dimensional shell elements that is used to design a grid stiffened panel with blade type stiffeners, a local model of three dimensional solid elements that is used to compute interlaminar stress components, and a scheme devised to assign displacement boundary conditions for a local model that are based on displacement and rotation data of a few nodes of the global model. A global panel was designed according to strength, stiffness, and stability criteria associated with the design of traditional aircraft wing panels. Interlaminar normal and shearing stress components, computed via the local model, were found to be well below typical tensile normal and shearing strengths of a graphite epoxy material.

  12. Global/local interlaminar stress analysis of a grid-stiffened composite panel

    SciTech Connect

    Wiggenraad, J.F.M.; Bauld, N.R. Jr. Clemson Univ., SC )

    1993-02-01

    A global/local procedure for the computation of the interlaminar stress components at the skin wrap, skin core, and wrap core interfaces for an advanced concept stiffened panel, is described. The procedure consists of a global model of two dimensional shell elements that is used to design a grid stiffened panel with blade type stiffeners, a local model of three dimensional solid elements that is used to compute interlaminar stress components, and a scheme devised to assign displacement boundary conditions for a local model that are based on displacement and rotation data of a few nodes of the global model. A global panel was designed according to strength, stiffness, and stability criteria associated with the design of traditional aircraft wing panels. Interlaminar normal and shearing stress components, computed via the local model, were found to be well below typical tensile normal and shearing strengths of a graphite epoxy material. 8 refs.

  13. Global/local interlaminar stress analysis of a grid-stiffened composite panel

    NASA Technical Reports Server (NTRS)

    Wiggenraad, J. F. M.; Bauld, N. R., Jr.

    1993-01-01

    A global/local procedure for the computation of the interlaminar stress components at the skin wrap, skin core, and wrap core interfaces for an advanced concept stiffened panel, is described. The procedure consists of a global model of two dimensional shell elements that is used to design a grid stiffened panel with blade type stiffeners, a local model of three dimensional solid elements that is used to compute interlaminar stress components, and a scheme devised to assign displacement boundary conditions for a local model that are based on displacement and rotation data of a few nodes of the global model. A global panel was designed according to strength, stiffness, and stability criteria associated with the design of traditional aircraft wing panels. Interlaminar normal and shearing stress components, computed via the local model, were found to be well below typical tensile normal and shearing strengths of a graphite epoxy material.

  14. TranAir: A full-potential, solution-adaptive, rectangular grid code for predicting subsonic, transonic, and supersonic flows about arbitrary configurations. Theory document

    NASA Technical Reports Server (NTRS)

    Johnson, F. T.; Samant, S. S.; Bieterman, M. B.; Melvin, R. G.; Young, D. P.; Bussoletti, J. E.; Hilmes, C. L.

    1992-01-01

    A new computer program, called TranAir, for analyzing complex configurations in transonic flow (with subsonic or supersonic freestream) was developed. This program provides accurate and efficient simulations of nonlinear aerodynamic flows about arbitrary geometries with the ease and flexibility of a typical panel method program. The numerical method implemented in TranAir is described. The method solves the full potential equation subject to a set of general boundary conditions and can handle regions with differing total pressure and temperature. The boundary value problem is discretized using the finite element method on a locally refined rectangular grid. The grid is automatically constructed by the code and is superimposed on the boundary described by networks of panels; thus no surface fitted grid generation is required. The nonlinear discrete system arising from the finite element method is solved using a preconditioned Krylov subspace method embedded in an inexact Newton method. The solution is obtained on a sequence of successively refined grids which are either constructed adaptively based on estimated solution errors or are predetermined based on user inputs. Many results obtained by using TranAir to analyze aerodynamic configurations are presented.

  15. Preparing for Local Adaptation: Understanding Flood Risk Perceptions in Pittsburgh

    NASA Astrophysics Data System (ADS)

    Klima, K.; Wong-Parodi, G.

    2015-12-01

    The City of Pittsburgh experiences numerous floods every year. Aging and insufficient infrastructure contribute to flash floods and to over 20 billion gallons of combined sewer overflows annually, contaminating Pittsburgh's streets, basements, and waterways. Climate change is expected to further exacerbate this problem by causing more intense and more frequent extreme precipitation events in Western Pennsylvania. For a stormwater adaptation plan to be implemented effectively, the City will need informed public support. One way to achieve public understanding and support is through effective communication of the risks, benefits, and uncertainties of local flooding hazards and adaptation methods. In order to develop these communications effectively, the city and its partners will need to know what knowledge and attitudes the residents of Pittsburgh already hold about flood risks. Here we seek to (1) identify Pittsburgh residents' knowledge level, risk perception and attitudes towards flooding and storm water management, and (2) pre-test communications meant to inform and empower Pittsburghers about flood risks and adaptation strategies. We conduct a city-wide survey of 10,000 Pittsburgh renters and homeowners from four life situations: high risk, above poverty; high-risk, below poverty; low risk, above poverty; and low-risk, below poverty. Mixed media recruitment strategies (online and paper-based solicitations guided/organized by community organizations) assist in reaching all subpopulations. Preliminary results suggest participants know what stormwater runoff is, but have a weak understanding of how stormwater interacts with natural and built systems. Furthermore, although participants have a good understanding of the difference between green and gray infrastructure, this does not translate into a change in their willingness to pay for green infrastructure adaptation. This suggests additional communications about flood risks and adaptation strategies.

  16. Storage sizing for embedding of local gas production in a micro gas grid

    NASA Astrophysics Data System (ADS)

    Alkano, D.; Nefkens, W. J.; Scherpen, J. M. A.; Volkerts, M.

    2014-12-01

    In this paper we study the optimal control of a micro grid of biogas producers. The paper considers the possibility to have a local storage device for each producer, who partly consumes his own production, i.e. prosumer. In addition, connected prosumers can sell stored gas to create revenue from it. An optimization model is employed to derive the size of storage device and to provide a pricing mechanism in an effort to value the stored gas. Taking into account physical grid constraints, the model is constructed in a centralized scheme of model predictive control. Case studies show that there is a relation between the demand and price profiles in terms of peaks and lows. The price profiles generally follow each other. The case studies are employed as well to to study the impacts of model parameters on deriving the storage size.

  17. Adaptive Sound Localization with a Silicon Cochlea Pair

    PubMed Central

    Chan, Vincent Yue-Sek; Jin, Craig T.; van Schaik, André

    2010-01-01

    A neuromorphic sound localization system is presented. It employs two microphones and a pair of silicon cochleae with address event interface for front-end processing. The system is based the extraction of interaural time difference from a far-field source. At each frequency channel, a soft-winner-takes-all network is used to preserve timing information before it is processed by a simple neural network to estimate auditory activity at all bearing positions. The estimates are then combined across channels to produce the final estimate. The proposed algorithm is adaptive and supports online learning, enabling the system to compensate for circuit mismatch and environmental changes. Its localization capability was tested with white noise and pure tone stimuli, with an average error of around 3° in the −45° to 45° range. PMID:21152257

  18. Implementation of local grid refinement (LGR) for the Lake Michigan Basin regional groundwater-flow model

    USGS Publications Warehouse

    Hoard, C.J.

    2010-01-01

    The U.S. Geological Survey is evaluating water availability and use within the Great Lakes Basin. This is a pilot effort to develop new techniques and methods to aid in the assessment of water availability. As part of the pilot program, a regional groundwater-flow model for the Lake Michigan Basin was developed using SEAWAT-2000. The regional model was used as a framework for assessing local-scale water availability through grid-refinement techniques. Two grid-refinement techniques, telescopic mesh refinement and local grid refinement, were used to illustrate the capability of the regional model to evaluate local-scale problems. An intermediate model was developed in central Michigan spanning an area of 454 square miles (mi2) using telescopic mesh refinement. Within the intermediate model, a smaller local model covering an area of 21.7 mi2 was developed and simulated using local grid refinement. Recharge was distributed in space and time using a daily output from a modified Thornthwaite-Mather soil-water-balance method. The soil-water-balance method derived recharge estimates from temperature and precipitation data output from an atmosphere-ocean coupled general-circulation model. The particular atmosphere-ocean coupled general-circulation model used, simulated climate change caused by high global greenhouse-gas emissions to the atmosphere. The surface-water network simulated in the regional model was refined and simulated using a streamflow-routing package for MODFLOW. The refined models were used to demonstrate streamflow depletion and potential climate change using five scenarios. The streamflow-depletion scenarios include (1) natural conditions (no pumping), (2) a pumping well near a stream; the well is screened in surficial glacial deposits, (3) a pumping well near a stream; the well is screened in deeper glacial deposits, and (4) a pumping well near a stream; the well is open to a deep bedrock aquifer. Results indicated that a range of 59 to 50 percent of the

  19. Adaptive grid embedding for the two-dimensional flux-split Euler equations. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Warren, Gary Patrick

    1990-01-01

    A numerical algorithm is presented for solving the 2-D flux-split Euler equations using a multigrid method with adaptive grid embedding. The method uses an unstructured data set along with a system of pointers for communication on the irregularly shaped grid topologies. An explicit two-stage time advancement scheme is implemented. A multigrid algorithm is used to provide grid level communication and to accelerate the convergence of the solution to steady state. Results are presented for a subcritical airfoil and a transonic airfoil with 3 levels of adaptation. Comparisons are made with a structured upwind Euler code which uses the same flux integration techniques of the present algorithm. Good agreement is obtained with converged surface pressure coefficients. The lift coefficients of the adaptive code are within 2 1/2 percent of the structured code for the sub-critical case and within 4 1/2 percent of the structured code for the transonic case using approximately one-third the number of grid points.

  20. MODFLOW-LGR-Modifications to the streamflow-routing package (SFR2) to route streamflow through locally refined grids

    USGS Publications Warehouse

    Mehl, Steffen W.; Hill, Mary C.

    2011-01-01

    This report documents modifications to the Streamflow-Routing Package (SFR2) to route streamflow through grids constructed using the multiple-refined-areas capability of shared node Local Grid Refinement (LGR) of MODFLOW-2005. MODFLOW-2005 is the U.S. Geological Survey modular, three-dimensional, finite-difference groundwater-flow model. LGR provides the capability to simulate groundwater flow by using one or more block-shaped, higher resolution local grids (child model) within a coarser grid (parent model). LGR accomplishes this by iteratively coupling separate MODFLOW-2005 models such that heads and fluxes are balanced across the shared interfacing boundaries. Compatibility with SFR2 allows for streamflow routing across grids. LGR can be used in two- and three-dimensional, steady-state and transient simulations and for simulations of confined and unconfined groundwater systems.

  1. Building sustainable science curriculum: Acknowledging and accommodating local adaptation

    NASA Astrophysics Data System (ADS)

    Barab, Sasha Alexander; Luehmann, April Lynn

    2003-07-01

    A core challenge facing science educators is how to develop and support the implementation of project-based, technology-rich science curriculum that is consistent with international calls for a new approach to science education while at the same time meeting the everyday needs of classroom teachers. In this article, we discuss the challenges of scaling out university-developed, project-based curricula, providing a contextualizing frame for the articles that constitute this current issue of Science Education. Specifically, we overview (1) what constitutes and why implement inquiry-based, project-focused learning environments, (2) the role of integrating technology to support their implementation, (3) the value of engaging in design experiments for their development, (4) the importance of allowing for local adaptation, and (5) the process of curricular diffusion. In our thinking, the process of dissemination is not simply rubber-stamping the same program into multiple contexts; rather, the process of large-scale adoption involves additional, individual teacher-directed design, fitting, and adaptation for local circumstances.

  2. Computation of shock waves in media with an interphase boundary by the CIP-CUP method on an adaptive grid

    NASA Astrophysics Data System (ADS)

    Guseva, T. S.

    2016-01-01

    A numerical technique of computing shock waves in compressible media with movable deforming interphase boundaries including those of the gas-liquid type has been realized. The approach without explicit separation of the interphase boundary is applied. The CIP-CUP method is used for integrating the equations of gas dynamics. An adaptive grid of special kind (the soroban-grid) is utilized. Some results of testing the technique using one- and two-dimensional problems are given. Results of computation of impact of a jet on a thin liquid layer on a wall are presented.

  3. Strong Discrepancies between Local Temperature Mapping and Interpolated Climatic Grids in Tropical Mountainous Agricultural Landscapes

    PubMed Central

    Faye, Emile; Herrera, Mario; Bellomo, Lucio; Silvain, Jean-François; Dangles, Olivier

    2014-01-01

    Bridging the gap between the predictions of coarse-scale climate models and the fine-scale climatic reality of species is a key issue of climate change biology research. While it is now well known that most organisms do not experience the climatic conditions recorded at weather stations, there is little information on the discrepancies between microclimates and global interpolated temperatures used in species distribution models, and their consequences for organisms’ performance. To address this issue, we examined the fine-scale spatiotemporal heterogeneity in air, crop canopy and soil temperatures of agricultural landscapes in the Ecuadorian Andes and compared them to predictions of global interpolated climatic grids. Temperature time-series were measured in air, canopy and soil for 108 localities at three altitudes and analysed using Fourier transform. Discrepancies between local temperatures vs. global interpolated grids and their implications for pest performance were then mapped and analysed using GIS statistical toolbox. Our results showed that global interpolated predictions over-estimate by 77.5±10% and under-estimate by 82.1±12% local minimum and maximum air temperatures recorded in the studied grid. Additional modifications of local air temperatures were due to the thermal buffering of plant canopies (from −2.7°K during daytime to 1.3°K during night-time) and soils (from −4.9°K during daytime to 6.7°K during night-time) with a significant effect of crop phenology on the buffer effect. This discrepancies between interpolated and local temperatures strongly affected predictions of the performance of an ectothermic crop pest as interpolated temperatures predicted pest growth rates 2.3–4.3 times lower than those predicted by local temperatures. This study provides quantitative information on the limitation of coarse-scale climate data to capture the reality of the climatic environment experienced by living organisms. In highly heterogeneous

  4. A General Hybrid Radiation Transport Scheme for Star Formation Simulations on an Adaptive Grid

    NASA Astrophysics Data System (ADS)

    Klassen, Mikhail; Kuiper, Rolf; Pudritz, Ralph E.; Peters, Thomas; Banerjee, Robi; Buntemeyer, Lars

    2014-12-01

    Radiation feedback plays a crucial role in the process of star formation. In order to simulate the thermodynamic evolution of disks, filaments, and the molecular gas surrounding clusters of young stars, we require an efficient and accurate method for solving the radiation transfer problem. We describe the implementation of a hybrid radiation transport scheme in the adaptive grid-based FLASH general magnetohydrodyanmics code. The hybrid scheme splits the radiative transport problem into a raytracing step and a diffusion step. The raytracer captures the first absorption event, as stars irradiate their environments, while the evolution of the diffuse component of the radiation field is handled by a flux-limited diffusion solver. We demonstrate the accuracy of our method through a variety of benchmark tests including the irradiation of a static disk, subcritical and supercritical radiative shocks, and thermal energy equilibration. We also demonstrate the capability of our method for casting shadows and calculating gas and dust temperatures in the presence of multiple stellar sources. Our method enables radiation-hydrodynamic studies of young stellar objects, protostellar disks, and clustered star formation in magnetized, filamentary environments.

  5. A Domain-Decomposed Multi-Level Method for Adaptively Refined Cartesian Grids with Embedded Boundaries

    NASA Technical Reports Server (NTRS)

    Aftosmis, M. J.; Berger, M. J.; Adomavicius, G.; Nixon, David (Technical Monitor)

    1998-01-01

    The work presents a new method for on-the-fly domain decomposition technique for mapping grids and solution algorithms to parallel machines, and is applicable to both shared-memory and message-passing architectures. It will be demonstrated on the Cray T3E, HP Exemplar, and SGI Origin 2000. Computing time has been secured on all these platforms. The decomposition technique is an outgrowth of techniques used in computational physics for simulations of N-body problems and the event horizons of black holes, and has not been previously used by the CFD community. Since the technique offers on-the-fly partitioning, it offers a substantial increase in flexibility for computing in heterogeneous environments, where the number of available processors may not be known at the time of job submission. In addition, since it is dynamic it permits the job to be repartitioned without global communication in cases where additional processors become available after the simulation has begun, or in cases where dynamic mesh adaptation changes the mesh size during the course of a simulation. The platform for this partitioning strategy is a completely new Cartesian Euler solver tarcreted at parallel machines which may be used in conjunction with Ames' "Cart3D" arbitrary geometry simulation package.

  6. Features of CPB: A Poisson-Boltzmann Solver that Uses an Adaptive Cartesian Grid

    PubMed Central

    Harris, Robert C.; Mackoy, Travis

    2014-01-01

    The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction-field component (ϕrf) of the electrostatic potential (ϕ), eliminating the charge-induced singularities in ϕ. CPB can also use a least-squares reconstruction method to improve estimates of ϕ at the molecular surface. All surfaces, which include solvent excluded, Gaussians and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ϕ and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other PBE solvers. The reader is referred to http://www.continuum-dynamics.com/solution-mm.html for how to obtain the CPB software. PMID:25430617

  7. An efficient Bayesian inference approach to inverse problems based on an adaptive sparse grid collocation method

    NASA Astrophysics Data System (ADS)

    Ma, Xiang; Zabaras, Nicholas

    2009-03-01

    A new approach to modeling inverse problems using a Bayesian inference method is introduced. The Bayesian approach considers the unknown parameters as random variables and seeks the probabilistic distribution of the unknowns. By introducing the concept of the stochastic prior state space to the Bayesian formulation, we reformulate the deterministic forward problem as a stochastic one. The adaptive hierarchical sparse grid collocation (ASGC) method is used for constructing an interpolant to the solution of the forward model in this prior space which is large enough to capture all the variability/uncertainty in the posterior distribution of the unknown parameters. This solution can be considered as a function of the random unknowns and serves as a stochastic surrogate model for the likelihood calculation. Hierarchical Bayesian formulation is used to derive the posterior probability density function (PPDF). The spatial model is represented as a convolution of a smooth kernel and a Markov random field. The state space of the PPDF is explored using Markov chain Monte Carlo algorithms to obtain statistics of the unknowns. The likelihood calculation is performed by directly sampling the approximate stochastic solution obtained through the ASGC method. The technique is assessed on two nonlinear inverse problems: source inversion and permeability estimation in flow through porous media.

  8. A general hybrid radiation transport scheme for star formation simulations on an adaptive grid

    SciTech Connect

    Klassen, Mikhail; Pudritz, Ralph E.; Kuiper, Rolf; Peters, Thomas; Banerjee, Robi; Buntemeyer, Lars

    2014-12-10

    Radiation feedback plays a crucial role in the process of star formation. In order to simulate the thermodynamic evolution of disks, filaments, and the molecular gas surrounding clusters of young stars, we require an efficient and accurate method for solving the radiation transfer problem. We describe the implementation of a hybrid radiation transport scheme in the adaptive grid-based FLASH general magnetohydrodyanmics code. The hybrid scheme splits the radiative transport problem into a raytracing step and a diffusion step. The raytracer captures the first absorption event, as stars irradiate their environments, while the evolution of the diffuse component of the radiation field is handled by a flux-limited diffusion solver. We demonstrate the accuracy of our method through a variety of benchmark tests including the irradiation of a static disk, subcritical and supercritical radiative shocks, and thermal energy equilibration. We also demonstrate the capability of our method for casting shadows and calculating gas and dust temperatures in the presence of multiple stellar sources. Our method enables radiation-hydrodynamic studies of young stellar objects, protostellar disks, and clustered star formation in magnetized, filamentary environments.

  9. Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.

    PubMed

    Fenley, Marcia O; Harris, Robert C; Mackoy, Travis; Boschitsch, Alexander H

    2015-02-01

    The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction-field component (ϕrf ) of the electrostatic potential (ϕ), eliminating the charge-induced singularities in ϕ. CPB can also use a least-squares reconstruction method to improve estimates of ϕ at the molecular surface. All surfaces, which include solvent excluded, Gaussians, and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ϕ and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other Poisson-Boltzmann equation solvers. The reader is referred to http://www.continuum-dynamics.com/solution-mm.html for how to obtain the CPB software. PMID:25430617

  10. A locally refined rectangular grid finite element method - Application to computational fluid dynamics and computational physics

    NASA Technical Reports Server (NTRS)

    Young, David P.; Melvin, Robin G.; Bieterman, Michael B.; Johnson, Forrester T.; Samant, Satish S.

    1991-01-01

    The present FEM technique addresses both linear and nonlinear boundary value problems encountered in computational physics by handling general three-dimensional regions, boundary conditions, and material properties. The box finite elements used are defined by a Cartesian grid independent of the boundary definition, and local refinements proceed by dividing a given box element into eight subelements. Discretization employs trilinear approximations on the box elements; special element stiffness matrices are included for boxes cut by any boundary surface. Illustrative results are presented for representative aerodynamics problems involving up to 400,000 elements.

  11. Vasodilator factors in the systemic and local adaptations to pregnancy

    PubMed Central

    Valdes, Gloria; Kaufmann, Peter; Corthorn, Jenny; Erices, Rafaela; Brosnihan, K Bridget; Joyner-Grantham, JaNae

    2009-01-01

    We postulate that an orchestrated network composed of various vasodilatory systems participates in the systemic and local hemodynamic adaptations in pregnancy. The temporal patterns of increase in the circulating and urinary levels of five vasodilator factors/systems, prostacyclin, nitric oxide, kallikrein, angiotensin-(1–7) and VEGF, in normal pregnant women and animals, as well as the changes observed in preeclamptic pregnancies support their functional role in maintaining normotension by opposing the vasoconstrictor systems. In addition, the expression of these vasodilators in the different trophoblastic subtypes in various species supports their role in the transformation of the uterine arteries. Moreover, their expression in the fetal endothelium and in the syncytiotrophoblast in humans, rats and guinea-pigs, favour their participation in maintaining the uteroplacental circulation. The findings that sustain the functional associations of the various vasodilators, and their participation by endocrine, paracrine and autocrine regulation of the systemic and local vasoactive changes of pregnancy are abundant and compelling. However, further elucidation of the role of the various players is hampered by methodological problems. Among these difficulties is the complexity of the interactions between the different factors, the likelihood that experimental alterations induced in one system may be compensated by the other players of the network, and the possibility that data obtained by manipulating single factors in vitro or in animal studies may be difficult to translate to the human. In addition, the impossibility of sampling the uteroplacental interface along normal pregnancy precludes obtaining longitudinal profiles of the various players. Nevertheless, the possibility of improving maternal blood pressure regulation, trophoblast invasion and uteroplacental flow by enhancing vasodilation (e.g. L-arginine, NO donors, VEGF transfection) deserves unravelling the

  12. A first experiment on local combination of EGM2008 data and GOCE grids at satellite altitude

    NASA Astrophysics Data System (ADS)

    Gatti, A.; Pavlis, N. K.; Reguzzoni, M.; Sanso, F.

    2012-12-01

    The GOCE satellite of the European Space Agency (ESA), thanks to a low orbit and a very sophisticated gradiometer, is observing the Earth gravitational field with the highest level of accuracy and resolution ever reached by any geodetic missions. Although lower than other satellites, the GOCE orbit altitude of about 250 km inevitably limits the maximum achievable resolution of the estimated gravitational field; to overcome this limitations a combination with other sources of data is then necessary. One of the most informative and accurate spherical harmonic global models of the Earth gravitational field is EGM2008. It has been developed by a least squares combination between of the ITG-GRACE03S model (with its associated error covariance matrix) and a 5'x5' grid of free-air gravity anomalies. Therefore this model seems to be suitable for a combination with the newer GOCE data. The classical approach to merge these two types of information is a direct combination of the spherical harmonic coefficients coming from the satellite-only model and EGM2008. The possible drawbacks of this approach are the following: 1. Every GOCE-only spherical harmonic global model need a certain level of regularization (e.g. to deal with polar gaps) acting on a subset of coefficients but more or less affecting the estimated field all over the world. 2. The EGM2008 error description is based on publicly available coefficient variances or, at most, on a block diagonal covariance matrix when coefficients are sorted order by order; this implies that the corresponding geographical error is latitude dependent, which is an approximation far from reality. The main goal of this work is to try to overcome these limitations by computing local grids at ground level from GOCE data and EGM2008 grids. With this approach the GOCE information used is not yet regularized to produce a global model and EGM2008 could be weighted taking into account the actual geographic distribution of the error (e.g. the

  13. Subsurface characterization with localized ensemble Kalman filter employing adaptive thresholding

    NASA Astrophysics Data System (ADS)

    Delijani, Ebrahim Biniaz; Pishvaie, Mahmoud Reza; Boozarjomehry, Ramin Bozorgmehry

    2014-07-01

    Ensemble Kalman filter, EnKF, as a Monte Carlo sequential data assimilation method has emerged promisingly for subsurface media characterization during past decade. Due to high computational cost of large ensemble size, EnKF is limited to small ensemble set in practice. This results in appearance of spurious correlation in covariance structure leading to incorrect or probable divergence of updated realizations. In this paper, a universal/adaptive thresholding method is presented to remove and/or mitigate spurious correlation problem in the forecast covariance matrix. This method is, then, extended to regularize Kalman gain directly. Four different thresholding functions have been considered to threshold forecast covariance and gain matrices. These include hard, soft, lasso and Smoothly Clipped Absolute Deviation (SCAD) functions. Three benchmarks are used to evaluate the performances of these methods. These benchmarks include a small 1D linear model and two 2D water flooding (in petroleum reservoirs) cases whose levels of heterogeneity/nonlinearity are different. It should be noted that beside the adaptive thresholding, the standard distance dependant localization and bootstrap Kalman gain are also implemented for comparison purposes. We assessed each setup with different ensemble sets to investigate the sensitivity of each method on ensemble size. The results indicate that thresholding of forecast covariance yields more reliable performance than Kalman gain. Among thresholding function, SCAD is more robust for both covariance and gain estimation. Our analyses emphasize that not all assimilation cycles do require thresholding and it should be performed wisely during the early assimilation cycles. The proposed scheme of adaptive thresholding outperforms other methods for subsurface characterization of underlying benchmarks.

  14. A Selective Vision and Landmark based Approach to Improve the Efficiency of Position Probability Grid Localization

    NASA Astrophysics Data System (ADS)

    Loukianov, Andrey A.; Sugisaka, Masanori

    This paper presents a vision and landmark based approach to improve the efficiency of probability grid Markov localization for mobile robots. The proposed approach uses visual landmarks that can be detected by a rotating video camera on the robot. We assume that visual landmark positions in the map are known and that each landmark can be assigned to a certain landmark class. The method uses classes of observed landmarks and their relative arrangement to select regions in the robot posture space where the location probability density function is to be updated. Subsequent computations are performed only in these selected update regions thus the computational workload is significantly reduced. Probabilistic landmark-based localization method, details of the map and robot perception are discussed. A technique to compute the update regions and their parameters for selective computation is introduced. Simulation results are presented to show the effectiveness of the approach.

  15. Local adaptation for body color in Drosophila americana

    PubMed Central

    Wittkopp, P J; Smith-Winberry, G; Arnold, L L; Thompson, E M; Cooley, A M; Yuan, D C; Song, Q; McAllister, B F

    2011-01-01

    Pigmentation is one of the most variable traits within and between Drosophila species. Much of this diversity appears to be adaptive, with environmental factors often invoked as selective forces. Here, we describe the geographic structure of pigmentation in Drosophila americana and evaluate the hypothesis that it is a locally adapted trait. Body pigmentation was quantified using digital images and spectrometry in up to 10 flies from each of 93 isofemale lines collected from 17 locations across the United States and found to correlate most strongly with longitude. Sequence variation at putatively neutral loci showed no evidence of population structure and was inconsistent with an isolation-by-distance model, suggesting that the pigmentation cline exists despite extensive gene flow throughout the species range, and is most likely the product of natural selection. In all other Drosophila species examined to date, dark pigmentation is associated with arid habitats; however, in D. americana, the darkest flies were collected from the most humid regions. To investigate this relationship further, we examined desiccation resistance attributable to an allele that darkens pigmentation in D. americana. We found no significant effect of pigmentation on desiccation resistance in this experiment, suggesting that pigmentation and desiccation resistance are not unequivocally linked in all Drosophila species. PMID:20606690

  16. A low order flow/acoustics interaction method for the prediction of sound propagation using 3D adaptive hybrid grids

    SciTech Connect

    Kallinderis, Yannis; Vitsas, Panagiotis A.; Menounou, Penelope

    2012-07-15

    A low-order flow/acoustics interaction method for the prediction of sound propagation and diffraction in unsteady subsonic compressible flow using adaptive 3-D hybrid grids is investigated. The total field is decomposed into the flow field described by the Euler equations, and the acoustics part described by the Nonlinear Perturbation Equations. The method is shown capable of predicting monopole sound propagation, while employment of acoustics-guided adapted grid refinement improves the accuracy of capturing the acoustic field. Interaction of sound with solid boundaries is also examined in terms of reflection, and diffraction. Sound propagation through an unsteady flow field is examined using static and dynamic flow/acoustics coupling demonstrating the importance of the latter.

  17. Localized dynamic kinetic-energy-based models for stochastic coherent adaptive large eddy simulation

    NASA Astrophysics Data System (ADS)

    De Stefano, Giuliano; Vasilyev, Oleg V.; Goldstein, Daniel E.

    2008-04-01

    Stochastic coherent adaptive large eddy simulation (SCALES) is an extension of the large eddy simulation approach in which a wavelet filter-based dynamic grid adaptation strategy is employed to solve for the most "energetic" coherent structures in a turbulent field while modeling the effect of the less energetic background flow. In order to take full advantage of the ability of the method in simulating complex flows, the use of localized subgrid-scale models is required. In this paper, new local dynamic one-equation subgrid-scale models based on both eddy-viscosity and non-eddy-viscosity assumptions are proposed for SCALES. The models involve the definition of an additional field variable that represents the kinetic energy associated with the unresolved motions. This way, the energy transfer between resolved and residual flow structures is explicitly taken into account by the modeling procedure without an equilibrium assumption, as in the classical Smagorinsky approach. The wavelet-filtered incompressible Navier-Stokes equations for the velocity field, along with the additional evolution equation for the subgrid-scale kinetic energy variable, are numerically solved by means of the dynamically adaptive wavelet collocation solver. The proposed models are tested for freely decaying homogeneous turbulence at Reλ=72. It is shown that the SCALES results, obtained with less than 0.5% of the total nonadaptive computational nodes, closely match reference data from direct numerical simulation. In contrast to classical large eddy simulation, where the energetic small scales are poorly simulated, the agreement holds not only in terms of global statistical quantities but also in terms of spectral distribution of energy and, more importantly, enstrophy all the way down to the dissipative scales.

  18. Adaptively Reevaluated Bayesian Localization (ARBL): A novel technique for radiological source localization

    NASA Astrophysics Data System (ADS)

    Miller, Erin A.; Robinson, Sean M.; Anderson, Kevin K.; McCall, Jonathon D.; Prinke, Amanda M.; Webster, Jennifer B.; Seifert, Carolyn E.

    2015-06-01

    We present a novel technique for the localization of radiological sources in urban or rural environments from an aerial platform. The technique is based on a Bayesian approach to localization, in which measured count rates in a time series are compared with predicted count rates from a series of pre-calculated test sources to define likelihood. This technique is expanded by using a localized treatment with a limited field of view (FOV), coupled with a likelihood ratio reevaluation, allowing for real-time computation on commodity hardware for arbitrarily complex detector models and terrain. In particular, detectors with inherent asymmetry of response (such as those employing internal collimation or self-shielding for enhanced directional awareness) are leveraged by this approach to provide improved localization. Results from the localization technique are shown for simulated flight data using monolithic as well as directionally-aware detector models, and the capability of the methodology to locate radioisotopes is estimated for several test cases. This localization technique is shown to facilitate urban search by allowing quick and adaptive estimates of source location, in many cases from a single flyover near a source. In particular, this method represents a significant advancement from earlier methods like full-field Bayesian likelihood, which is not generally fast enough to allow for broad-field search in real time, and highest-net-counts estimation, which has a localization error that depends strongly on flight path and cannot generally operate without exhaustive search.

  19. Adaptively Reevaluated Bayesian Localization (ARBL). A Novel Technique for Radiological Source Localization

    SciTech Connect

    Miller, Erin A.; Robinson, Sean M.; Anderson, Kevin K.; McCall, Jonathon D.; Prinke, Amanda M.; Webster, Jennifer B.; Seifert, Carolyn E.

    2015-01-19

    Here we present a novel technique for the localization of radiological sources in urban or rural environments from an aerial platform. The technique is based on a Bayesian approach to localization, in which measured count rates in a time series are compared with predicted count rates from a series of pre-calculated test sources to define likelihood. Furthermore, this technique is expanded by using a localized treatment with a limited field of view (FOV), coupled with a likelihood ratio reevaluation, allowing for real-time computation on commodity hardware for arbitrarily complex detector models and terrain. In particular, detectors with inherent asymmetry of response (such as those employing internal collimation or self-shielding for enhanced directional awareness) are leveraged by this approach to provide improved localization. Our results from the localization technique are shown for simulated flight data using monolithic as well as directionally-aware detector models, and the capability of the methodology to locate radioisotopes is estimated for several test cases. This localization technique is shown to facilitate urban search by allowing quick and adaptive estimates of source location, in many cases from a single flyover near a source. In particular, this method represents a significant advancement from earlier methods like full-field Bayesian likelihood, which is not generally fast enough to allow for broad-field search in real time, and highest-net-counts estimation, which has a localization error that depends strongly on flight path and cannot generally operate without exhaustive search

  20. Adaptive non-local means filtering based on local noise level for CT denoising

    NASA Astrophysics Data System (ADS)

    Li, Zhoubo; Yu, Lifeng; Trzasko, Joshua D.; Fletcher, Joel G.; McCollough, Cynthia H.; Manduca, Armando

    2012-03-01

    Radiation dose from CT scans is an increasing health concern in the practice of radiology. Higher dose scans can produce clearer images with high diagnostic quality, but may increase the potential risk of radiation-induced cancer or other side effects. Lowering radiation dose alone generally produces a noisier image and may degrade diagnostic performance. Recently, CT dose reduction based on non-local means (NLM) filtering for noise reduction has yielded promising results. However, traditional NLM denoising operates under the assumption that image noise is spatially uniform noise, while in CT images the noise level varies significantly within and across slices. Therefore, applying NLM filtering to CT data using a global filtering strength cannot achieve optimal denoising performance. In this work, we have developed a technique for efficiently estimating the local noise level for CT images, and have modified the NLM algorithm to adapt to local variations in noise level. The local noise level estimation technique matches the true noise distribution determined from multiple repetitive scans of a phantom object very well. The modified NLM algorithm provides more effective denoising of CT data throughout a volume, and may allow significant lowering of radiation dose. Both the noise map calculation and the adaptive NLM filtering can be performed in times that allow integration with the clinical workflow.

  1. QoS Differential Scheduling in Cognitive-Radio-Based Smart Grid Networks: An Adaptive Dynamic Programming Approach.

    PubMed

    Yu, Rong; Zhong, Weifeng; Xie, Shengli; Zhang, Yan; Zhang, Yun

    2016-02-01

    As the next-generation power grid, smart grid will be integrated with a variety of novel communication technologies to support the explosive data traffic and the diverse requirements of quality of service (QoS). Cognitive radio (CR), which has the favorable ability to improve the spectrum utilization, provides an efficient and reliable solution for smart grid communications networks. In this paper, we study the QoS differential scheduling problem in the CR-based smart grid communications networks. The scheduler is responsible for managing the spectrum resources and arranging the data transmissions of smart grid users (SGUs). To guarantee the differential QoS, the SGUs are assigned to have different priorities according to their roles and their current situations in the smart grid. Based on the QoS-aware priority policy, the scheduler adjusts the channels allocation to minimize the transmission delay of SGUs. The entire transmission scheduling problem is formulated as a semi-Markov decision process and solved by the methodology of adaptive dynamic programming. A heuristic dynamic programming (HDP) architecture is established for the scheduling problem. By the online network training, the HDP can learn from the activities of primary users and SGUs, and adjust the scheduling decision to achieve the purpose of transmission delay minimization. Simulation results illustrate that the proposed priority policy ensures the low transmission delay of high priority SGUs. In addition, the emergency data transmission delay is also reduced to a significantly low level, guaranteeing the differential QoS in smart grid. PMID:25910254

  2. Adapting a commercial power system simulator for smart grid based system study and vulnerability assessment

    NASA Astrophysics Data System (ADS)

    Navaratne, Uditha Sudheera

    The smart grid is the future of the power grid. Smart meters and the associated network play a major role in the distributed system of the smart grid. Advance Metering Infrastructure (AMI) can enhance the reliability of the grid, generate efficient energy management opportunities and many innovations around the future smart grid. These innovations involve intense research not only on the AMI network itself but as also on the influence an AMI network can have upon the rest of the power grid. This research describes a smart meter testbed with hardware in loop that can facilitate future research in an AMI network. The smart meters in the testbed were developed such that their functionality can be customized to simulate any given scenario such as integrating new hardware components into a smart meter or developing new encryption algorithms in firmware. These smart meters were integrated into the power system simulator to simulate the power flow variation in the power grid on different AMI activities. Each smart meter in the network also provides a communication interface to the home area network. This research delivers a testbed for emulating the AMI activities and monitoring their effect on the smart grid.

  3. A locally adaptive kernel regression method for facies delineation

    NASA Astrophysics Data System (ADS)

    Fernàndez-Garcia, D.; Barahona-Palomo, M.; Henri, C. V.; Sanchez-Vila, X.

    2015-12-01

    Facies delineation is defined as the separation of geological units with distinct intrinsic characteristics (grain size, hydraulic conductivity, mineralogical composition). A major challenge in this area stems from the fact that only a few scattered pieces of hydrogeological information are available to delineate geological facies. Several methods to delineate facies are available in the literature, ranging from those based only on existing hard data, to those including secondary data or external knowledge about sedimentological patterns. This paper describes a methodology to use kernel regression methods as an effective tool for facies delineation. The method uses both the spatial and the actual sampled values to produce, for each individual hard data point, a locally adaptive steering kernel function, self-adjusting the principal directions of the local anisotropic kernels to the direction of highest local spatial correlation. The method is shown to outperform the nearest neighbor classification method in a number of synthetic aquifers whenever the available number of hard data is small and randomly distributed in space. In the case of exhaustive sampling, the steering kernel regression method converges to the true solution. Simulations ran in a suite of synthetic examples are used to explore the selection of kernel parameters in typical field settings. It is shown that, in practice, a rule of thumb can be used to obtain suboptimal results. The performance of the method is demonstrated to significantly improve when external information regarding facies proportions is incorporated. Remarkably, the method allows for a reasonable reconstruction of the facies connectivity patterns, shown in terms of breakthrough curves performance.

  4. Precipitation Variability and Projection Uncertainties in Climate Change Adaptation: Go Local!

    EPA Science Inventory

    Presentations agenda includes: Regional and local climate change effects: The relevance; Variability and uncertainty in decision- making and adaptation approaches; Adaptation attributes for the U.S. Southwest: Water availability, storage capacity, and related; EPA research...

  5. Advances and limits of using population genetics to understand local adaptation.

    PubMed

    Tiffin, Peter; Ross-Ibarra, Jeffrey

    2014-12-01

    Local adaptation shapes species diversity, can be a stepping stone to ecological speciation, and can facilitate species range expansion. Population genetic analyses, which complement organismal approaches in advancing our understanding of local adaptation, have become widespread in recent years. We focus here on using population genetics to address some key questions in local adaptation: what traits are involved? What environmental variables are the most important? Does local adaptation target the same genes in related species? Do loci responsible for local adaptation exhibit trade-offs across environments? After discussing these questions we highlight important limitations to population genetic analyses including challenges with obtaining high-quality data, deciding which loci are targets of selection, and limits to identifying the genetic basis of local adaptation. PMID:25454508

  6. Sound Source Localization for HRI Using FOC-Based Time Difference Feature and Spatial Grid Matching.

    PubMed

    Li, Xiaofei; Liu, Hong

    2013-08-01

    In human-robot interaction (HRI), speech sound source localization (SSL) is a convenient and efficient way to obtain the relative position between a speaker and a robot. However, implementing a SSL system based on TDOA method encounters many problems, such as noise of real environments, the solution of nonlinear equations, switch between far field and near field. In this paper, fourth-order cumulant spectrum is derived, based on which a time delay estimation (TDE) algorithm that is available for speech signal and immune to spatially correlated Gaussian noise is proposed. Furthermore, time difference feature of sound source and its spatial distribution are analyzed, and a spatial grid matching (SGM) algorithm is proposed for localization step, which handles some problems that geometric positioning method faces effectively. Valid feature detection algorithm and a decision tree method are also suggested to improve localization performance and reduce computational complexity. Experiments are carried out in real environments on a mobile robot platform, in which thousands of sets of speech data with noise collected by four microphones are tested in 3D space. The effectiveness of our TDE method and SGM algorithm is verified. PMID:26502430

  7. Site-specific group selection drives locally adapted group compositions.

    PubMed

    Pruitt, Jonathan N; Goodnight, Charles J

    2014-10-16

    Group selection may be defined as selection caused by the differential extinction or proliferation of groups. The socially polymorphic spider Anelosimus studiosus exhibits a behavioural polymorphism in which females exhibit either a 'docile' or 'aggressive' behavioural phenotype. Natural colonies are composed of a mixture of related docile and aggressive individuals, and populations differ in colonies' characteristic docile:aggressive ratios. Using experimentally constructed colonies of known composition, here we demonstrate that population-level divergence in docile:aggressive ratios is driven by site-specific selection at the group level--certain ratios yield high survivorship at some sites but not others. Our data also indicate that colonies responded to the risk of extinction: perturbed colonies tended to adjust their composition over two generations to match the ratio characteristic of their native site, thus promoting their long-term survival in their natal habitat. However, colonies of displaced individuals continued to shift their compositions towards mixtures that would have promoted their survival had they remained at their home sites, regardless of their contemporary environment. Thus, the regulatory mechanisms that colonies use to adjust their composition appear to be locally adapted. Our data provide experimental evidence of group selection driving collective traits in wild populations. PMID:25274310

  8. Local adaptation in Trinidadian guppies alters ecosystem processes.

    PubMed

    Bassar, Ronald D; Marshall, Michael C; López-Sepulcre, Andrés; Zandonà, Eugenia; Auer, Sonya K; Travis, Joseph; Pringle, Catherine M; Flecker, Alexander S; Thomas, Steven A; Fraser, Douglas F; Reznick, David N

    2010-02-23

    Theory suggests evolutionary change can significantly influence and act in tandem with ecological forces via ecological-evolutionary feedbacks. This theory assumes that significant evolutionary change occurs over ecologically relevant timescales and that phenotypes have differential effects on the environment. Here we test the hypothesis that local adaptation causes ecosystem structure and function to diverge. We demonstrate that populations of Trinidadian guppies (Poecilia reticulata), characterized by differences in phenotypic and population-level traits, differ in their impact on ecosystem properties. We report results from a replicated, common garden mesocosm experiment and show that differences between guppy phenotypes result in the divergence of ecosystem structure (algal, invertebrate, and detrital standing stocks) and function (gross primary productivity, leaf decomposition rates, and nutrient flux). These phenotypic effects are further modified by effects of guppy density. We evaluated the generality of these effects by replicating the experiment using guppies derived from two independent origins of the phenotype. Finally, we tested the ability of multiple guppy traits to explain observed differences in the mesocosms. Our findings demonstrate that evolution can significantly affect both ecosystem structure and function. The ecosystem differences reported here are consistent with patterns observed across natural streams and argue that guppies play a significant role in shaping these ecosystems. PMID:20133670

  9. Using Environmental Correlations to Identify Loci Underlying Local Adaptation

    PubMed Central

    Coop, Graham; Witonsky, David; Di Rienzo, Anna; Pritchard, Jonathan K.

    2010-01-01

    Loci involved in local adaptation can potentially be identified by an unusual correlation between allele frequencies and important ecological variables or by extreme allele frequency differences between geographic regions. However, such comparisons are complicated by differences in sample sizes and the neutral correlation of allele frequencies across populations due to shared history and gene flow. To overcome these difficulties, we have developed a Bayesian method that estimates the empirical pattern of covariance in allele frequencies between populations from a set of markers and then uses this as a null model for a test at individual SNPs. In our model the sample frequencies of an allele across populations are drawn from a set of underlying population frequencies; a transform of these population frequencies is assumed to follow a multivariate normal distribution. We first estimate the covariance matrix of this multivariate normal across loci using a Monte Carlo Markov chain. At each SNP, we then provide a measure of the support, a Bayes factor, for a model where an environmental variable has a linear effect on the transformed allele frequencies compared to a model given by the covariance matrix alone. This test is shown through power simulations to outperform existing correlation tests. We also demonstrate that our method can be used to identify SNPs with unusually large allele frequency differentiation and offers a powerful alternative to tests based on pairwise or global FST. Software is available at http://www.eve.ucdavis.edu/gmcoop/. PMID:20516501

  10. Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria)

    PubMed Central

    Muir, A P; Biek, R; Thomas, R; Mable, B K

    2014-01-01

    Both environmental and genetic influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. The aim of this study was to assess whether local adaptation occurs in the face of high gene flow and to identify potential environmental selection pressures that drive adaptation. Phenotypic variation in larval traits was quantified in R. temporaria from paired high- and low-altitude sites using three common temperature treatments. Local adaptation was assessed using QST–FST analyses, and quantitative phenotypic divergence was related to environmental parameters using Mantel tests. Although evidence of local adaptation was found for all traits measured, only variation in larval period and growth rate was consistent with adaptation to altitude. Moreover, this was only evident in the three mountains with the highest high-altitude sites. This variation was correlated with mean summer and winter temperatures, suggesting that temperature parameters are potentially strong selective pressures maintaining local adaptation, despite high gene flow. PMID:24330274

  11. Adaptive Generation of Multimaterial Grids from imaging data for Biomedical Lagrangian Fluid-Structure Simulations

    SciTech Connect

    Carson, James P.; Kuprat, Andrew P.; Jiao, Xiangmin; Dyedov, Volodymyr; del Pin, Facundo; Guccione, Julius M.; Ratcliffe, Mark B.; Einstein, Daniel R.

    2010-04-01

    Spatial discretization of complex imaging-derived fluid-solid geometries, such as the cardiac environment, is a critical but often overlooked challenge in biomechanical computations. This is particularly true in problems with Lagrangian interfaces, where, the fluid and solid phases must match geometrically. For simplicity and better accuracy, it is also highly desirable for the two phases to share the same surface mesh at the interface between them. We outline a method for solving this problem, and illustrate the approach with a 3D fluid-solid mesh of the mouse heart. An MRI perfusion-fixed dataset of a mouse heart with 50μm isotropic resolution was semi-automatically segmented using a customized multimaterial connected-threshold approach that divided the volume into non-overlapping regions of blood, tissue and background. Subsequently, a multimaterial marching cubes algorithm was applied to the segmented data to produce two detailed, compatible isosurfaces, one for blood and one for tissue. Both isosurfaces were simultaneously smoothed with a multimaterial smoothing algorithm that exactly conserves the volume for each phase. Using these two isosurfaces, we developed and applied novel automated meshing algorithms to generate anisotropic hybrid meshes on arbitrary biological geometries with the number of layers and the desired element anisotropy for each phase as the only input parameters. Since our meshes adapt to the local feature sizes and include boundary layer prisms, they are more efficient and accurate than non-adaptive, isotropic meshes, and the fluid-structure interaction computations will tend to have relative error equilibrated over the whole mesh.

  12. The geography of sex-specific selection, local adaptation, and sexual dimorphism.

    PubMed

    Connallon, Tim

    2015-09-01

    Local adaptation and sexual dimorphism are iconic evolutionary scenarios of intraspecific adaptive differentiation in the face of gene flow. Although theory has traditionally considered local adaptation and sexual dimorphism as conceptually distinct processes, emerging data suggest that they often act concurrently during evolutionary diversification. Here, I merge theories of local adaptation in space and sex-specific adaptation over time, and show that their confluence yields several new predictions about the roles of context-specific selection, migration, and genetic correlations, in adaptive diversification. I specifically revisit two influential predictions from classical studies of clinal adaptation and sexual dimorphism: (1) that local adaptation should decrease with distance from the species' range center and (2) that opposing directional selection between the sexes (sexual antagonism) should inevitably accompany the evolution of sexual dimorphism. I show that both predictions can break down under clinally varying selection. First, the geography of local adaptation can be sexually dimorphic, with locations of relatively high local adaptation differing profoundly between the sexes. Second, the intensity of sexual antagonism varies across the species' range, with subpopulations near the range center representing hotspots for antagonistic selection. The results highlight the context-dependent roles of migration versus sexual conflict as primary constraints to adaptive diversification. PMID:26194274

  13. Computations of Unsteady Viscous Compressible Flows Using Adaptive Mesh Refinement in Curvilinear Body-fitted Grid Systems

    NASA Technical Reports Server (NTRS)

    Steinthorsson, E.; Modiano, David; Colella, Phillip

    1994-01-01

    A methodology for accurate and efficient simulation of unsteady, compressible flows is presented. The cornerstones of the methodology are a special discretization of the Navier-Stokes equations on structured body-fitted grid systems and an efficient solution-adaptive mesh refinement technique for structured grids. The discretization employs an explicit multidimensional upwind scheme for the inviscid fluxes and an implicit treatment of the viscous terms. The mesh refinement technique is based on the AMR algorithm of Berger and Colella. In this approach, cells on each level of refinement are organized into a small number of topologically rectangular blocks, each containing several thousand cells. The small number of blocks leads to small overhead in managing data, while their size and regular topology means that a high degree of optimization can be achieved on computers with vector processors.

  14. MAGNETIC GRID

    DOEpatents

    Post, R.F.

    1960-08-01

    An electronic grid is designed employing magnetic forces for controlling the passage of charged particles. The grid is particularly applicable to use in gas-filled tubes such as ignitrons. thyratrons, etc., since the magnetic grid action is impartial to the polarity of the charged particles and, accordingly. the sheath effects encountered with electrostatic grids are not present. The grid comprises a conductor having sections spaced apart and extending in substantially opposite directions in the same plane, the ends of the conductor being adapted for connection to a current source.

  15. The morphing method as a flexible tool for adaptive local/non-local simulation of static fracture

    NASA Astrophysics Data System (ADS)

    Azdoud, Yan; Han, Fei; Lubineau, Gilles

    2014-09-01

    We introduce a framework that adapts local and non-local continuum models to simulate static fracture problems. Non-local models based on the peridynamic theory are promising for the simulation of fracture, as they allow discontinuities in the displacement field. However, they remain computationally expensive. As an alternative, we develop an adaptive coupling technique based on the morphing method to restrict the non-local model adaptively during the evolution of the fracture. The rest of the structure is described by local continuum mechanics. We conduct all simulations in three dimensions, using the relevant discretization scheme in each domain, i.e., the discontinuous Galerkin finite element method in the peridynamic domain and the continuous finite element method in the local continuum mechanics domain.

  16. On the equivalence of host local adaptation and parasite maladaptation: an experimental test.

    PubMed

    Lemoine, Mélissa; Doligez, Blandine; Richner, Heinz

    2012-02-01

    In spatiotemporally varying environments, host-parasite coevolution may lead to either host or parasite local adaptation. Using reciprocal infestations over 11 pairs of plots, we tested local adaptation in the hen flea and its main host, the great tit. Flea reproductive success (number of adults at host fledging) was lower on host individuals from the same plot compared with foreign hosts (from another plot), revealing flea local maladaptation. Host reproductive success (number of fledged young) for nests infested by foreign fleas was lower compared with the reproductive success of controls, with an intermediate success for nests infested by local fleas. This suggests host local adaptation although the absence of local adaptation could not be excluded. However, fledglings were heavier and larger when reared with foreign fleas than when reared with local fleas, which could also indicate host local maladaptation if the fitness gain in offspring size offsets the potential cost in offspring number. Our results therefore challenge the traditional view that parasite local maladaptation is equivalent to host local adaptation. The differences in fledgling morphology between nests infested with local fleas and those with foreign fleas suggest that flea origin affects host resource allocation strategy between nestling growth and defense against parasites. Therefore, determining the mechanisms that underlie these local adaptation patterns requires the identification of the relevant fitness measures and life-history trade-offs in both species. PMID:22218315

  17. Adaptive analog-SSOR iterative method for solving grid equations with nonselfadjoint operators

    NASA Astrophysics Data System (ADS)

    Alekseenko, Elena; Sukhinov, Alexander; Chistyakov, Alexander; Shishenya, Alexander; Roux, Bernard

    2013-04-01

    Motion models of wave processes in the coastal zone are highly demanded in the projection and construction of coastal surface structures and breakwaters, and also as a component of other models. The most common of the grid approaches is currently vof-method. A significant drawback of this method is in the necessity to solve the convection equation to find fullness of cells. The numerical solution of this equation leads to a strong grid viscosity and "smearing" of the interface. In this paper, we propose a method, which is based on the idea of using a fill, as in vof method, but its conversion is not required to solve the equation of convection. Thus in this work, a mathematical model for the wave hydrodynamics problem, describing wash ashore and taking into account such physical parameters as turbulent exchange, complexity of domain and coastal line geometry, and bottom friction is developed. For the given mathematical model a discrete model is constructed, taking into account dynamical changing of the calculation domain. Discretization of the model is performed on the structured rectangular grid with a new developed finite-volume technique that takes into account fullness of the grid cells that allows describing geometry more accurate. Proposed technique allows improving the real accuracy of a solution in case of complex domain geometry, by improving approximation of the boundary. A software implementation and numerical experiments of the posed problem of the wave hydrodynamics is performed. The results of numerical experiments show the feasibility of using discrete mathematical models of processes that take into account fullness of grid cells, for the simulation of systems with complex geometry of the border. Numerical experiments show that the use of this technique sufficiently smooth solutions are obtained even on coarse grids.

  18. Discrete cosine transform-based local adaptive filtering of images corrupted by nonstationary noise

    NASA Astrophysics Data System (ADS)

    Lukin, Vladimir V.; Fevralev, Dmitriy V.; Ponomarenko, Nikolay N.; Abramov, Sergey K.; Pogrebnyak, Oleksiy; Egiazarian, Karen O.; Astola, Jaakko T.

    2010-04-01

    In many image-processing applications, observed images are contaminated by a nonstationary noise and no a priori information on noise dependence on local mean or about local properties of noise statistics is available. In order to remove such a noise, a locally adaptive filter has to be applied. We study a locally adaptive filter based on evaluation of image local activity in a ``blind'' manner and on discrete cosine transform computed in overlapping blocks. Two mechanisms of local adaptation are proposed and applied. The first mechanism takes into account local estimates of noise standard deviation while the second one exploits discrimination of homogeneous and heterogeneous image regions by adaptive threshold setting. The designed filter performance is tested for simulated data as well as for real-life remote-sensing and maritime radar images. Recommendations concerning filter parameter setting are provided. An area of applicability of the proposed filter is defined.

  19. Adaptations to local environments in modern human populations.

    PubMed

    Jeong, Choongwon; Di Rienzo, Anna

    2014-12-01

    After leaving sub-Saharan Africa around 50000-100000 years ago, anatomically modern humans have quickly occupied extremely diverse environments. Human populations were exposed to further environmental changes resulting from cultural innovations, such as the spread of farming, which gave rise to new selective pressures related to pathogen exposures and dietary shifts. In addition to changing the frequency of individual adaptive alleles, natural selection may also shape the overall genetic architecture of adaptive traits. Here, we review recent advances in understanding the genetic architecture of adaptive human phenotypes based on insights from the studies of lactase persistence, skin pigmentation and high-altitude adaptation. These adaptations evolved in parallel in multiple human populations, providing a chance to investigate independent realizations of the evolutionary process. We suggest that the outcome of adaptive evolution is often highly variable even under similar selective pressures. Finally, we highlight a growing need for detecting adaptations that did not follow the classical sweep model and for incorporating new sources of genetic evidence such as information from ancient DNA. PMID:25129844

  20. Genetic structure and local adaptation of European wheat yellow rust populations: the role of temperature-specific adaptation

    PubMed Central

    Mboup, Mamadou; Bahri, Bochra; Leconte, Marc; De Vallavieille-Pope, Claude; Kaltz, Oliver; Enjalbert, Jérôme

    2012-01-01

    Environmental heterogeneity influences coevolution and local adaptation in host–parasite systems. This also concerns applied issues, because the geographic range of parasites may depend on their capacity to adapt to abiotic conditions. We studied temperature-specific adaptation in the wheat yellow/stripe rust pathogen, Puccinia striiformis f.sp. tritici (PST). Using laboratory experiments, PST isolates from northern and southern France were studied for their ability to germinate and to infect bread and durum wheat cultivars over a temperature gradient. Pathogen origin × temperature interactions for infectivity and germination rate suggest local adaptation to high- versus low-temperature regimes in south and north. Competition experiments in southern and northern field sites showed a general competitive advantage of southern over northern isolates. This advantage was particularly pronounced in the southern ‘home’ site, consistent with a model integrating laboratory infectivity and field temperature variation. The stable PST population structure in France likely reflects adaptation to ecological and genetic factors: persistence of southern PST may be due to adaptation to the warmer Mediterranean climate; and persistence of northern PST can be explained by adaptation to commonly used cultivars, for which southern isolates are lacking the relevant virulence genes. Thus, understanding the role of temperature-specific adaptations may help to improve forecast models or breeding programmes. PMID:25568055

  1. A Load Frequency Control in an Off-Grid Sustainable Power System Based on a Parameter Adaptive PID-Type Fuzzy Controller

    NASA Astrophysics Data System (ADS)

    Ronilaya, Ferdian; Miyauchi, Hajime

    2014-10-01

    This paper presents a new implementation of a parameter adaptive PID-type fuzzy controller (PAPIDfc) for a grid-supporting inverter of battery to alleviate frequency fluctuations in a wind-diesel power system. A variable speed wind turbine that drives a permanent magnet synchronous generator is assumed for demonstrations. The PAPIDfc controller is built from a set of control rules that adopts the droop method and uses only locally measurable frequency signal. The output control signal is determined from the knowledge base and the fuzzy inference. The input-derivative gain and the output-integral gain of the PAPIDfc are tuned online. To ensure safe battery operating limits, we also propose a protection scheme called intelligent battery protection (IBP). Several simulation experiments are performed by using MATLAB®/SimPowersystems™. Next, to verify the scheme's effectiveness, the simulation results are compared with the results of conventional controllers. The results demonstrate the effectiveness of the PAPIDfc scheme to control a grid-supporting inverter of the battery in the reduction of frequency fluctuations.

  2. Local adaptive mechanism and hierarchic social entropy in opinion formation on complex networks

    NASA Astrophysics Data System (ADS)

    Cheng, Jie; Hu, Yanqing; Di, Zengru; Fan, Ying

    2010-10-01

    In this paper we study the opinion formation using co-evolution model, in which network's structure interacts with the nodes' opinion. A local adaptive model is proposed to investigate the effects of local information on the opinion formation, including local rewiring and influencing mechanism. The results show that under the local adaptive mechanism, systems could reach steady state of consensus or fragmentation. Considering the local influencing factor only, we find that transition occurs under proper condition and local parameter affects the transition point. At last, the diversity of opinions is considered, and hierarchic social entropy is used as a macroscopic measurement which is proved to be well.

  3. Current Grid operation and future role of the Grid

    NASA Astrophysics Data System (ADS)

    Smirnova, O.

    2012-12-01

    Grid-like technologies and approaches became an integral part of HEP experiments. Some other scientific communities also use similar technologies for data-intensive computations. The distinct feature of Grid computing is the ability to federate heterogeneous resources of different ownership into a seamless infrastructure, accessible via a single log-on. Like other infrastructures of similar nature, Grid functioning requires not only technologically sound basis, but also reliable operation procedures, monitoring and accounting. The two aspects, technological and operational, are closely related: weaker is the technology, more burden is on operations, and other way around. As of today, Grid technologies are still evolving: at CERN alone, every LHC experiment uses an own Grid-like system. This inevitably creates a heavy load on operations. Infrastructure maintenance, monitoring and incident response are done on several levels, from local system administrators to large international organisations, involving massive human effort worldwide. The necessity to commit substantial resources is one of the obstacles faced by smaller research communities when moving computing to the Grid. Moreover, most current Grid solutions were developed under significant influence of HEP use cases, and thus need additional effort to adapt them to other applications. Reluctance of many non-HEP researchers to use Grid negatively affects the outlook for national Grid organisations, which strive to provide multi-science services. We started from the situation where Grid organisations were fused with HEP laboratories and national HEP research programmes; we hope to move towards the world where Grid will ultimately reach the status of generic public computing and storage service provider and permanent national and international Grid infrastructures will be established. How far will we be able to advance along this path, depends on us. If no standardisation and convergence efforts will take place

  4. The common cuckoo Cuculus canorus is not locally adapted to its reed warbler Acrocephalus scirpaceus host.

    PubMed

    Avilés, J M; Vikan, J R; Fossøy, F; Antonov, A; Moksnes, A; Røskaft, E; Shykoff, J A; Møller, A P; Jensen, H; Procházka, P; Stokke, B G

    2011-02-01

    The obligate avian brood parasitic common cuckoo Cuculus canorus comprises different strains of females that specialize on particular host species by laying eggs of a constant type that often mimics those of the host. Whether cuckoos are locally adapted for mimicking populations of the hosts on which they are specialized has never been investigated. In this study, we first explored the possibility of local adaptation in cuckoo egg mimicry over a geographical mosaic of selection exerted by one of its main European hosts, the reed warbler Acrocephalus scirpaceus. Secondly, we investigated whether cuckoos inhabiting reed warbler populations with a broad number of alternative suitable hosts at hand were less locally adapted. Cuckoo eggs showed different degrees of mimicry to different reed warbler populations. However, cuckoo eggs did not match the egg phenotypes of their local host population better than eggs of other host populations, indicating that cuckoos were not locally adapted for mimicry on reed warblers. Interestingly, cuckoos exploiting reed warblers in populations with a relatively larger number of co-occurring cuckoo gentes showed lower than average levels of local adaptation in egg volume. Our results suggest that cuckoo local adaptation might be prevented when different cuckoo populations exploit more or fewer different host species, with gene flow or frequent host switches breaking down local adaptation where many host races co-occur. PMID:21054625

  5. Grid-Search Location Methods for Ground-Truth Collection from Local and Regional Seismic Networks

    SciTech Connect

    Schultz, C A; Rodi, W; Myers, S C

    2003-07-24

    The objective of this project is to develop improved seismic event location techniques that can be used to generate more and better quality reference events using data from local and regional seismic networks. Their approach is to extend existing methods of multiple-event location with more general models of the errors affecting seismic arrival time data, including picking errors and errors in model-based travel-times (path corrections). Toward this end, they are integrating a grid-search based algorithm for multiple-event location (GMEL) with a new parameterization of travel-time corrections and new kriging method for estimating the correction parameters from observed travel-time residuals. Like several other multiple-event location algorithms, GMEL currently assumes event-independent path corrections and is thus restricted to small event clusters. The new parameterization assumes that travel-time corrections are a function of both the event and station location, and builds in source-receiver reciprocity and correlation between the corrections from proximate paths as constraints. The new kriging method simultaneously interpolates travel-time residuals from multiple stations and events to estimate the correction parameters as functions of position. They are currently developing the algorithmic extensions to GMEL needed to combine the new parameterization and kriging method with the simultaneous location of events. The result will be a multiple-event location method which is applicable to non-clustered, spatially well-distributed events. They are applying the existing components of the new multiple-event location method to a data set of regional and local arrival times from Nevada Test Site (NTS) explosions with known origin parameters. Preliminary results show the feasibility and potential benefits of combining the location and kriging techniques. They also show some preliminary work on generalizing of the error model used in GMEL with the use of mixture

  6. COLLABORATIVE RESEARCH: CONTINUOUS DYNAMIC GRID ADAPTATION IN A GLOBAL ATMOSPHERIC MODEL: APPLICATION AND REFINEMENT

    SciTech Connect

    Prusa, Joseph

    2012-05-08

    This project had goals of advancing the performance capabilities of the numerical general circulation model EULAG and using it to produce a fully operational atmospheric global climate model (AGCM) that can employ either static or dynamic grid stretching for targeted phenomena. The resulting AGCM combined EULAG's advanced dynamics core with the physics of the NCAR Community Atmospheric Model (CAM). Effort discussed below shows how we improved model performance and tested both EULAG and the coupled CAM-EULAG in several ways to demonstrate the grid stretching and ability to simulate very well a wide range of scales, that is, multi-scale capability. We leveraged our effort through interaction with an international EULAG community that has collectively developed new features and applications of EULAG, which we exploited for our own work summarized here. Overall, the work contributed to over 40 peer- reviewed publications and over 70 conference/workshop/seminar presentations, many of them invited.

  7. Salinity Is an Agent of Divergent Selection Driving Local Adaptation of Arabidopsis to Coastal Habitats.

    PubMed

    Busoms, Silvia; Teres, Joana; Huang, Xin-Yuan; Bomblies, Kirsten; Danku, John; Douglas, Alex; Weigel, Detlef; Poschenrieder, Charlotte; Salt, David E

    2015-07-01

    Understanding the molecular mechanism of adaptive evolution in plants provides insights into the selective forces driving adaptation and the genetic basis of adaptive traits with agricultural value. The genomic resources available for Arabidopsis (Arabidopsis thaliana) make it well suited to the rapid molecular dissection of adaptive processes. Although numerous potentially adaptive loci have been identified in Arabidopsis, the consequences of divergent selection and migration (both important aspects of the process of local adaptation) for Arabidopsis are not well understood. Here, we use a multiyear field-based reciprocal transplant experiment to detect local populations of Arabidopsis composed of multiple small stands of plants (demes) that are locally adapted to the coast and adjacent inland habitats in northeastern Spain. We identify fitness tradeoffs between plants from these different habitats when grown together in inland and coastal common gardens and also, under controlled conditions in soil excavated from coastal and inland sites. Plants from the coastal habitat also outperform those from inland when grown under high salinity, indicating local adaptation to soil salinity. Sodium can be toxic to plants, and we find its concentration to be elevated in soil and plants sampled at the coast. We conclude that the local adaptation that we observe between adjacent coastal and inland populations is caused by ongoing divergent selection driven by the differential salinity between coastal and inland soils. PMID:26034264

  8. Adaptive Environmental Source Localization and Tracking with Unknown Permittivity and Path Loss Coefficients †

    PubMed Central

    Fidan, Barış; Umay, Ilknur

    2015-01-01

    Accurate signal-source and signal-reflector target localization tasks via mobile sensory units and wireless sensor networks (WSNs), including those for environmental monitoring via sensory UAVs, require precise knowledge of specific signal propagation properties of the environment, which are permittivity and path loss coefficients for the electromagnetic signal case. Thus, accurate estimation of these coefficients has significant importance for the accuracy of location estimates. In this paper, we propose a geometric cooperative technique to instantaneously estimate such coefficients, with details provided for received signal strength (RSS) and time-of-flight (TOF)-based range sensors. The proposed technique is integrated to a recursive least squares (RLS)-based adaptive localization scheme and an adaptive motion control law, to construct adaptive target localization and adaptive target tracking algorithms, respectively, that are robust to uncertainties in aforementioned environmental signal propagation coefficients. The efficiency of the proposed adaptive localization and tracking techniques are both mathematically analysed and verified via simulation experiments. PMID:26690441

  9. Adaptive Environmental Source Localization and Tracking with Unknown Permittivity and Path Loss Coefficients.

    PubMed

    Fidan, Barış; Umay, Ilknur

    2015-01-01

    Accurate signal-source and signal-reflector target localization tasks via mobile sensory units and wireless sensor networks (WSNs), including those for environmental monitoring via sensory UAVs, require precise knowledge of specific signal propagation properties of the environment, which are permittivity and path loss coefficients for the electromagnetic signal case. Thus, accurate estimation of these coefficients has significant importance for the accuracy of location estimates. In this paper, we propose a geometric cooperative technique to instantaneously estimate such coefficients, with details provided for received signal strength (RSS) and time-of-flight (TOF)-based range sensors. The proposed technique is integrated to a recursive least squares (RLS)-based adaptive localization scheme and an adaptive motion control law, to construct adaptive target localization and adaptive target tracking algorithms, respectively, that are robust to uncertainties in aforementioned environmental signal propagation coefficients. The efficiency of the proposed adaptive localization and tracking techniques are both mathematically analysed and verified via simulation experiments. PMID:26690441

  10. Life history trait differentiation and local adaptation in invasive populations of Ambrosia artemisiifolia in China.

    PubMed

    Li, Xiao-Meng; She, Deng-Ying; Zhang, Da-Yong; Liao, Wan-Jin

    2015-03-01

    Local adaptation has been suggested to play an important role in range expansion, particularly among invasive species. However, the extent to which local adaptation affects the success of an invasive species and the factors that contribute to local adaptation are still unclear. This study aimed to investigate a case of population divergence that may have contributed to the local adaptation of invasive populations of Ambrosia artemisiifolia in China. Common garden experiments in seven populations indicated clinal variations along latitudinal gradients, with plants from higher latitudes exhibiting earlier flowering and smaller sizes at flowering. In reciprocal transplant experiments, plants of a northern Beijing origin produced more seeds at their home site than plants of a southern Wuhan origin, and the Wuhan-origin plants had grown taller at flowering than the Beijing-origin plants in Wuhan, which is believed to facilitate pollen dispersal. These results suggest that plants of Beijing origin may be locally adapted through female fitness and plants from Wuhan possibly locally adapted through male fitness. Selection and path analysis suggested that the phenological and growth traits of both populations have been influenced by natural selection and that flowering time has played an important role through its direct and indirect effects on the relative fitness of each individual. This study evidences the life history trait differentiation and local adaptation during range expansion of invasive A. artemisiifolia in China. PMID:25362583

  11. Early life stages contribute strongly to local adaptation in Arabidopsis thaliana.

    PubMed

    Postma, Froukje M; Ågren, Jon

    2016-07-01

    The magnitude and genetic basis of local adaptation is of fundamental interest in evolutionary biology. However, field experiments usually do not consider early life stages, and therefore may underestimate local adaptation and miss genetically based tradeoffs. We examined the contribution of differences in seedling establishment to adaptive differentiation and the genetic architecture of local adaptation using recombinant inbred lines (RIL) derived from a cross between two locally adapted populations (Italy and Sweden) of the annual plant Arabidopsis thaliana We planted freshly matured, dormant seeds (>180 000) representing >200 RILs at the native field sites of the parental genotypes, estimated the strength of selection during different life stages, mapped quantitative trait loci (QTL) for fitness and its components, and quantified selection on seed dormancy. We found that selection during the seedling establishment phase contributed strongly to the fitness advantage of the local genotype at both sites. With one exception, local alleles of the eight distinct establishment QTL were favored. The major QTL for establishment and total fitness showed evidence of a fitness tradeoff and was located in the same region as the major seed dormancy QTL and the dormancy gene DELAY OF GERMINATION 1 (DOG1). RIL seed dormancy could explain variation in seedling establishment and fitness across the life cycle. Our results demonstrate that genetically based differences in traits affecting performance during early life stages can contribute strongly to adaptive differentiation and genetic tradeoffs, and should be considered for a full understanding of the ecology and genetics of local adaptation. PMID:27330113

  12. A Low-Cost Solar LED Lighting System Designed for Local Assembly and Repair in Off-Grid Communities

    NASA Astrophysics Data System (ADS)

    Gazes, Michael

    This is about bringing sustainable lighting systems to the world's billion poorest people who live in off-grid, rural communities. The lack of infrastructure presents a distribution challenge that places this market beyond the reach of the companies that address the Base of the Economic Pyramid sector. Addressing this market requires enabling the end-user to set up a local infrastructure for system maintenance. This requires a shift from the traditional consumer electronics paradigm of high-volume automated assembly with no user-serviceable parts. A lighting system is presented for local assembly and repair using locally sourced materials.

  13. Prism adaptation changes the subjective proprioceptive localization of the hands.

    PubMed

    Scarpina, Federica; Van der Stigchel, Stefan; Nijboer, Tanja Cornelia Wilhelmina; Dijkerman, Hendrik Christiaan

    2015-03-01

    Prism adaptation involves a proprioceptive, a visual and a motor component. As the existing paradigms are not able to distinguish between these three components, the contribution of the proprioceptive component remains unclear. In the current study, a proprioceptive judgement task, in the absence of motor responses, was used to investigate how prism adaptation would specifically influences the felt position of the hands in healthy participants. The task was administered before and after adaptation to left and right displacing prisms using either the left or the right hand during the adaptation procedure. The results appeared to suggest that the prisms induced a drift in the felt position of the hands, although the after-effect depended on the combination of the pointing hand and the visual deviation induced by prisms. The results are interpreted as in line with the hypothesis of an asymmetrical neural architecture of somatosensory processing. Moreover, the passive proprioception of the hand position revealed different effects of proprioceptive re-alignment compared to active pointing straight ahead: different mechanisms about how visuo-proprioceptive discrepancy is resolved were hypothesized. PMID:24266883

  14. Detecting Local Item Dependence in Polytomous Adaptive Data

    ERIC Educational Resources Information Center

    Mislevy, Jessica L.; Rupp, Andre A.; Harring, Jeffrey R.

    2012-01-01

    A rapidly expanding arena for item response theory (IRT) is in attitudinal and health-outcomes survey applications, often with polytomous items. In particular, there is interest in computer adaptive testing (CAT). Meeting model assumptions is necessary to realize the benefits of IRT in this setting, however. Although initial investigations of…

  15. Grid-Search Location Methods for Ground-Truth Collection From Local and Regional Seismic Networks

    SciTech Connect

    William Rodi; Craig A. Schultz; Gardar Johannesson; Stephen C. Myers

    2005-05-13

    This project investigated new techniques for improving seismic event locations derived from regional and local networks. The technqiues include a new approach to empirical travel-time calibration that simultaneously fits data from multiple stations and events, using a generalization of the kriging method, and predicts travel-time corrections for arbitrary event-station paths. We combined this calibration approach with grid-search event location to produce a prototype new multiple-event location method that allows the use of spatially well-distributed events and takes into account correlations between the travel-time corrections from proximate event-station paths. Preliminary tests with a high quality data set from Nevada Test Site explosions indicated that our new calibration/location method offers improvement over the conventional multiple-event location methods now in common use, and is applicable to more general event-station geometries than the conventional methods. The tests were limited, however, and further research is needed to fully evaluate, and improve, the approach. Our project also demonstrated the importance of using a realistic model for observational errors in an event location procedure. We took the initial steps in developing a new error model based on mixture-of-Gaussians probability distributions, which possess the properties necessary to characterize the complex arrival time error processes that can occur when picking low signal-to-noise arrivals. We investigated various inference methods for fitting these distributions to observed travel-time residuals, including a Markov Chain Monte Carlo technique for computing Bayesian estimates of the distribution parameters.

  16. Impacts of local adaptation of forest trees on associations with herbivorous insects: implications for adaptive forest management.

    PubMed

    Sinclair, Frazer H; Stone, Graham N; Nicholls, James A; Cavers, Stephen; Gibbs, Melanie; Butterill, Philip; Wagner, Stefanie; Ducousso, Alexis; Gerber, Sophie; Petit, Rémy J; Kremer, Antoine; Schönrogge, Karsten

    2015-12-01

    Disruption of species interactions is a key issue in climate change biology. Interactions involving forest trees may be particularly vulnerable due to evolutionary rate limitations imposed by long generation times. One mitigation strategy for such impacts is Climate matching - the augmentation of local native tree populations by input from nonlocal populations currently experiencing predicted future climates. This strategy is controversial because of potential cascading impacts on locally adapted animal communities. We explored these impacts using abundance data for local native gallwasp herbivores sampled from 20 provenances of sessile oak (Quercus petraea) planted in a common garden trial. We hypothesized that non-native provenances would show (i) declining growth performance with increasing distance between provenance origin and trial site, and (ii) phenological differences to local oaks that increased with latitudinal differences between origin and trial site. Under a local adaptation hypothesis, we predicted declining gallwasp abundance with increasing phenological mismatch between native and climate-matched trees. Both hypotheses for oaks were supported. Provenance explained significant variation in gallwasp abundance, but no gall type showed the relationship between abundance and phenological mismatch predicted by a local adaptation hypothesis. Our results show that climate matching would have complex and variable impacts on oak gall communities. PMID:26640522

  17. Impacts of local adaptation of forest trees on associations with herbivorous insects: implications for adaptive forest management

    PubMed Central

    Sinclair, Frazer H; Stone, Graham N; Nicholls, James A; Cavers, Stephen; Gibbs, Melanie; Butterill, Philip; Wagner, Stefanie; Ducousso, Alexis; Gerber, Sophie; Petit, Rémy J; Kremer, Antoine; Schönrogge, Karsten

    2015-01-01

    Disruption of species interactions is a key issue in climate change biology. Interactions involving forest trees may be particularly vulnerable due to evolutionary rate limitations imposed by long generation times. One mitigation strategy for such impacts is Climate matching – the augmentation of local native tree populations by input from nonlocal populations currently experiencing predicted future climates. This strategy is controversial because of potential cascading impacts on locally adapted animal communities. We explored these impacts using abundance data for local native gallwasp herbivores sampled from 20 provenances of sessile oak (Quercus petraea) planted in a common garden trial. We hypothesized that non-native provenances would show (i) declining growth performance with increasing distance between provenance origin and trial site, and (ii) phenological differences to local oaks that increased with latitudinal differences between origin and trial site. Under a local adaptation hypothesis, we predicted declining gallwasp abundance with increasing phenological mismatch between native and climate-matched trees. Both hypotheses for oaks were supported. Provenance explained significant variation in gallwasp abundance, but no gall type showed the relationship between abundance and phenological mismatch predicted by a local adaptation hypothesis. Our results show that climate matching would have complex and variable impacts on oak gall communities. PMID:26640522

  18. Genomic rearrangements and the evolution of clusters of locally adaptive loci

    PubMed Central

    Yeaman, Sam

    2013-01-01

    Numerous studies of ecological genetics have found that alleles contributing to local adaptation sometimes cluster together, forming “genomic islands of divergence.” Divergence hitchhiking theory posits that these clusters evolve by the preferential establishment of tightly linked locally adapted mutations, because such linkage reduces the rate that recombination breaks up locally favorable combinations of alleles. Here, I use calculations based on previously developed analytical models of divergence hitchhiking to show that very few clustered mutations should be expected in a single bout of adaptation, relative to the number of unlinked mutations, suggesting that divergence hitchhiking theory alone may often be insufficient to explain empirical observations. Using individual-based simulations that allow for the transposition of a single genetic locus from one position on a chromosome to another, I then show that tight clustering of the loci involved in local adaptation tends to evolve on biologically realistic time scales. These results suggest that genomic rearrangements may often be an important component of local adaptation and the evolution of genomic islands of divergence. More generally, these results suggest that genomic architecture and functional neighborhoods of genes may be actively shaped by natural selection in heterogeneous environments. Because small-scale changes in gene order are relatively common in some taxa, comparative genomic studies could be coupled with studies of adaptation to explore how commonly such rearrangements are involved in local adaptation. PMID:23610436

  19. Impact of Load Balancing on Unstructured Adaptive Grid Computations for Distributed-Memory Multiprocessors

    NASA Technical Reports Server (NTRS)

    Sohn, Andrew; Biswas, Rupak; Simon, Horst D.

    1996-01-01

    The computational requirements for an adaptive solution of unsteady problems change as the simulation progresses. This causes workload imbalance among processors on a parallel machine which, in turn, requires significant data movement at runtime. We present a new dynamic load-balancing framework, called JOVE, that balances the workload across all processors with a global view. Whenever the computational mesh is adapted, JOVE is activated to eliminate the load imbalance. JOVE has been implemented on an IBM SP2 distributed-memory machine in MPI for portability. Experimental results for two model meshes demonstrate that mesh adaption with load balancing gives more than a sixfold improvement over one without load balancing. We also show that JOVE gives a 24-fold speedup on 64 processors compared to sequential execution.

  20. Mountain chickadees from different elevations sing different songs: acoustic adaptation, temporal drift or signal of local adaptation?

    PubMed

    Branch, Carrie L; Pravosudov, Vladimir V

    2015-04-01

    Song in songbirds is widely thought to function in mate choice and male-male competition. Song is also phenotypically plastic and typically learned from local adults; therefore, it varies across geographical space and can serve as a cue for an individual's location of origin, with females commonly preferring males from their respective location. Geographical variation in song dialect may reflect acoustic adaptation to different environments and/or serve as a signal of local adaptation. In montane environments, environmental differences can occur over an elevation gradient, favouring local adaptations across small spatial scales. We tested whether food caching mountain chickadees, known to exhibit elevation-related differences in food caching intensity, spatial memory and the hippocampus, also sing different dialects despite continuous distribution and close proximity. Male songs were collected from high and low elevations at two different mountains (separated by 35 km) to test whether song differs between elevations and/or between adjacent populations at each mountain. Song structure varied significantly between high and low elevation adjacent populations from the same mountain and between populations from different mountains at the same elevations, despite a continuous distribution across each mountain slope. These results suggest that elevation-related differences in song structure in chickadees might serve as a signal for local adaptation. PMID:26064641

  1. Mountain chickadees from different elevations sing different songs: acoustic adaptation, temporal drift or signal of local adaptation?

    PubMed Central

    Branch, Carrie L.; Pravosudov, Vladimir V.

    2015-01-01

    Song in songbirds is widely thought to function in mate choice and male–male competition. Song is also phenotypically plastic and typically learned from local adults; therefore, it varies across geographical space and can serve as a cue for an individual's location of origin, with females commonly preferring males from their respective location. Geographical variation in song dialect may reflect acoustic adaptation to different environments and/or serve as a signal of local adaptation. In montane environments, environmental differences can occur over an elevation gradient, favouring local adaptations across small spatial scales. We tested whether food caching mountain chickadees, known to exhibit elevation-related differences in food caching intensity, spatial memory and the hippocampus, also sing different dialects despite continuous distribution and close proximity. Male songs were collected from high and low elevations at two different mountains (separated by 35 km) to test whether song differs between elevations and/or between adjacent populations at each mountain. Song structure varied significantly between high and low elevation adjacent populations from the same mountain and between populations from different mountains at the same elevations, despite a continuous distribution across each mountain slope. These results suggest that elevation-related differences in song structure in chickadees might serve as a signal for local adaptation. PMID:26064641

  2. Locally adapted traits maintained in the face of high gene flow.

    PubMed

    Fitzpatrick, S W; Gerberich, J C; Kronenberger, J A; Angeloni, L M; Funk, W C

    2015-01-01

    Gene flow between phenotypically divergent populations can disrupt local adaptation or, alternatively, may stimulate adaptive evolution by increasing genetic variation. We capitalised on historical Trinidadian guppy transplant experiments to test the phenotypic effects of increased gene flow caused by replicated introductions of adaptively divergent guppies, which were translocated from high- to low-predation environments. We sampled two native populations prior to the onset of gene flow, six historic introduction sites, introduction sources and multiple downstream points in each basin. Extensive gene flow from introductions occurred in all streams, yet adaptive phenotypic divergence across a gradient in predation level was maintained. Descendants of guppies from a high-predation source site showed high phenotypic similarity with native low-predation guppies in as few as ~12 generations after gene flow, likely through a combination of adaptive evolution and phenotypic plasticity. Our results demonstrate that locally adapted phenotypes can be maintained despite extensive gene flow from divergent populations. PMID:25363522

  3. Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment?

    USGS Publications Warehouse

    Adkison, M.D.

    1995-01-01

    Morphological, behavioral, and life-history differences between Pacific salmon (Oncorhynchus spp.) populations are commonly thought to reflect local adaptation, and it is likewise common to assume that salmon populations separated by small distances are locally adapted. Two alternatives to local adaptation exist: random genetic differentiation owing to genetic drift and founder events, and genetic homogeneity among populations, in which differences reflect differential trait expression in differing environments. Population genetics theory and simulations suggest that both alternatives are possible. With selectively neutral alleles, genetic drift can result in random differentiation despite many strays per generation. Even weak selection can prevent genetic drift in stable populations; however, founder effects can result in random differentiation despite selective pressures. Overlapping generations reduce the potential for random differentiation. Genetic homogeneity can occur despite differences in selective regimes when straying rates are high. In sum, localized differences in selection should not always result in local adaptation. Local adaptation is favored when population sizes are large and stable, selection is consistent over large areas, selective diffeentials are large, and straying rates are neither too high nor too low. Consideration of alternatives to local adaptation would improve both biological research and salmon conservation efforts.

  4. ADAPTIVE-GRID SIMULATION OF GROUNDWATER FLOW IN HETEROGENEOUS AQUIFERS. (R825689C068)

    EPA Science Inventory

    Abstract

    The prediction of contaminant transport in porous media requires the computation of the flow velocity. This work presents a methodology for high-accuracy computation of flow in a heterogeneous isotropic formation, employing a dual-flow formulation and adaptive...

  5. An Extension Education Program to Help Local Governments with Flood Adaptation

    ERIC Educational Resources Information Center

    Gary, Gretchen; Allred, Shorna; LoGiudice, Elizabeth

    2014-01-01

    Education is an important tool to increase the capacity of local government officials for community flood adaptation. To address flood adaptation and post-flood stream management in municipalities, Cornell Cooperative Extension and collaborators developed an educational program to increase municipal officials' knowledge about how to work…

  6. The New England Climate Adaptation Project: Enhancing Local Readiness to Adapt to Climate Change through Role-Play Simulations

    NASA Astrophysics Data System (ADS)

    Rumore, D.; Kirshen, P. H.; Susskind, L.

    2014-12-01

    Despite scientific consensus that the climate is changing, local efforts to prepare for and manage climate change risks remain limited. How we can raise concern about climate change risks and enhance local readiness to adapt to climate change's effects? In this presentation, we will share the lessons learned from the New England Climate Adaptation Project (NECAP), a participatory action research project that tested science-based role-play simulations as a tool for educating the public about climate change risks and simulating collective risk management efforts. NECAP was a 2-year effort involving the Massachusetts Institute of Technology, the Consensus Building Institute, the National Estuarine Research Reserve System, and four coastal New England municipalities. During 2012-2013, the NECAP team produced downscaled climate change projections, a summary risk assessment, and a stakeholder assessment for each partner community. Working with local partners, we used these assessments to create a tailored, science-based role-play simulation for each site. Through a series of workshops in 2013, NECAP engaged between 115-170 diverse stakeholders and members of the public in each partner municipality in playing the simulation and a follow up conversation about local climate change risks and possible adaptation strategies. Data were collected through before-and-after surveys administered to all workshop participants, follow-up interviews with 25 percent of workshop participants, public opinion polls conducted before and after our intervention, and meetings with public officials. This presentation will report our research findings and explain how science-based role-play simulations can be used to help communicate local climate change risks and enhance local readiness to adapt.

  7. Prism adaptation reverses the local processing bias in patients with right temporo-parietal junction lesions

    PubMed Central

    Rafal, Robert D.; List, Alexandra

    2009-01-01

    Lesions to the right temporo-parietal cortex commonly result in hemispatial neglect. Lesions to the same area are also associated with hyperattention to local details of a scene and difficulty perceiving the global structure. This local processing bias is an important factor contributing to neglect and may contribute to the higher prevalence of the disorder following right compared with left hemisphere strokes. In recent years, visuomotor adaptation to rightward-shifting prisms has been introduced as a promising treatment for hemispatial neglect. Explanations for these improvements have generally described a leftward realignment of attention, however, the present investigation provides evidence that prism adaptation reduces the local processing bias. Five patients with right temporal-parietal junction lesions were asked to identify the global or local levels of hierarchical figures before and after visuomotor adaptation to rightward-shifting prisms. Prior to prism adaptation the patients had difficulty ignoring the local elements when identifying the global component. Following prism adaptation, however, this pattern was reversed, with greater global interference during local level identification. The results suggest that prism adaptation may improve non-spatially lateralized deficits that contribute to the neglect syndrome. PMID:19416951

  8. Rapid ecosystem change challenges the adaptive capacity of Local Environmental Knowledge

    PubMed Central

    Fernández-Llamazares, Álvaro; Díaz-Reviriego, Isabel; Luz, Ana C.; Cabeza, Mar; Pyhälä, Aili; Reyes-García, Victoria

    2015-01-01

    The use of Local Environmental Knowledge has been considered as an important strategy for adaptive management in the face of Global Environmental Change. However, the unprecedented rates at which global change occurs may pose a challenge to the adaptive capacity of local knowledge systems. In this paper, we use the concept of the shifting baseline syndrome to examine the limits in the adaptive capacity of the local knowledge of an indigenous society facing rapid ecosystem change. We conducted semi-structured interviews regarding perceptions of change in wildlife populations and in intergenerational transmission of knowledge amongst the Tsimane’, a group of hunter-gatherers of Bolivian Amazonia (n = 300 adults in 13 villages). We found that the natural baseline against which the Tsimane’ measure ecosystem changes might be shifting with every generation as a result of (a) age-related differences in the perception of change and (b) a decrease in the intergenerational sharing of environmental knowledge. Such findings suggest that local knowledge systems might not change at a rate quick enough to adapt to conditions of rapid ecosystem change, hence potentially compromising the adaptive success of the entire social-ecological system. With the current pace of Global Environmental Change, widening the gap between the temporal rates of on-going ecosystem change and the timescale needed for local knowledge systems to adjust to change, efforts to tackle the shifting baseline syndrome are urgent and critical for those who aim to use Local Environmental Knowledge as a tool for adaptive management. PMID:26097291

  9. Local adaptation of Gymnocypris przewalskii (Cyprinidae) on the Tibetan Plateau.

    PubMed

    Zhang, Renyi; Ludwig, Arne; Zhang, Cunfang; Tong, Chao; Li, Guogang; Tang, Yongtao; Peng, Zuogang; Zhao, Kai

    2015-01-01

    Divergent selection among environments affects species distributions and can lead to speciation. In this article, we investigated the transcriptomes of two ecotypes of scaleless carp (Gymnocypris przewalskii przewalskii and G. p. ganzihonensis) from the Tibetan Plateau. We used a transcriptome sequencing approach to screen approximately 250,000 expressed sequence tags (ESTs) from the gill and kidney tissues of twelve individuals from the Ganzi River and Lake Qinghai to understand how this freshwater fish has adapted to an ecological niche shift from saline to freshwater. We identified 9,429 loci in the gill transcriptome and 12,034 loci in the kidney transcriptome with significant differences in their expression, of which 242 protein-coding genes exhibited strong positive selection (Ka/Ks > 1). Many of the genes are involved in ion channel functions (e.g., Ca(2+)-binding proteins), immune responses (e.g., nephrosin) or cellular water absorption functions (e.g., aquaporins). These results have potentially broad importance in understanding shifts from saline to freshwater habitats. Furthermore, this study provides the first transcriptome of G. przewalskii, which will facilitate future ecological genomics studies and aid in the identification of genes underlying adaptation and incipient ecological speciation. PMID:25944748

  10. Local adaptation of Gymnocypris przewalskii (Cyprinidae) on the Tibetan Plateau

    PubMed Central

    Zhang, Renyi; Ludwig, Arne; Zhang, Cunfang; Tong, Chao; Li, Guogang; Tang, Yongtao; Peng, Zuogang; Zhao, Kai

    2015-01-01

    Divergent selection among environments affects species distributions and can lead to speciation. In this article, we investigated the transcriptomes of two ecotypes of scaleless carp (Gymnocypris przewalskii przewalskii and G. p. ganzihonensis) from the Tibetan Plateau. We used a transcriptome sequencing approach to screen approximately 250,000 expressed sequence tags (ESTs) from the gill and kidney tissues of twelve individuals from the Ganzi River and Lake Qinghai to understand how this freshwater fish has adapted to an ecological niche shift from saline to freshwater. We identified 9,429 loci in the gill transcriptome and 12,034 loci in the kidney transcriptome with significant differences in their expression, of which 242 protein-coding genes exhibited strong positive selection (Ka/Ks > 1). Many of the genes are involved in ion channel functions (e.g., Ca2+-binding proteins), immune responses (e.g., nephrosin) or cellular water absorption functions (e.g., aquaporins). These results have potentially broad importance in understanding shifts from saline to freshwater habitats. Furthermore, this study provides the first transcriptome of G. przewalskii, which will facilitate future ecological genomics studies and aid in the identification of genes underlying adaptation and incipient ecological speciation. PMID:25944748

  11. Adjoint-Based Algorithms for Adaptation and Design Optimizations on Unstructured Grids

    NASA Technical Reports Server (NTRS)

    Nielsen, Eric J.

    2006-01-01

    Schemes based on discrete adjoint algorithms present several exciting opportunities for significantly advancing the current state of the art in computational fluid dynamics. Such methods provide an extremely efficient means for obtaining discretely consistent sensitivity information for hundreds of design variables, opening the door to rigorous, automated design optimization of complex aerospace configuration using the Navier-Stokes equation. Moreover, the discrete adjoint formulation provides a mathematically rigorous foundation for mesh adaptation and systematic reduction of spatial discretization error. Error estimates are also an inherent by-product of an adjoint-based approach, valuable information that is virtually non-existent in today's large-scale CFD simulations. An overview of the adjoint-based algorithm work at NASA Langley Research Center is presented, with examples demonstrating the potential impact on complex computational problems related to design optimization as well as mesh adaptation.

  12. AMPHIBIAN DECLINE, ULTRAVIOLET RADIATION AND LOCAL POPULATION ADAPTATION

    EPA Science Inventory

    Amphibian population declines have been noted on both local and global scales. Causes for these declines are unknown although many hypotheses have been offered. In areas adjacent to human development, loss of habitat is a fairly well accepted cause. However in isolated, seemingl...

  13. Can Perceptions of Environmental and Climate Change in Island Communities Assist in Adaptation Planning Locally?

    NASA Astrophysics Data System (ADS)

    Aswani, Shankar; Vaccaro, Ismael; Abernethy, Kirsten; Albert, Simon; de Pablo, Javier Fernández-López

    2015-12-01

    Local perceptions of environmental and climate change, as well as associated adaptations made by local populations, are fundamental for designing comprehensive and inclusive mitigation and adaptation plans both locally and nationally. In this paper, we analyze people's perceptions of environmental and climate-related transformations in communities across the Western Solomon Islands through ethnographic and geospatial methods. Specifically, we documented people's observed changes over the past decades across various environmental domains, and for each change, we asked respondents to identify the causes, timing, and people's adaptive responses. We also incorporated this information into a geographical information system database to produce broad-scale base maps of local perceptions of environmental change. Results suggest that people detected changes that tended to be acute (e.g., water clarity, logging intensity, and agricultural diseases). We inferred from these results that most local observations of and adaptations to change were related to parts of environment/ecosystem that are most directly or indirectly related to harvesting strategies. On the other hand, people were less aware of slower insidious/chronic changes identified by scientific studies. For the Solomon Islands and similar contexts in the insular tropics, a broader anticipatory adaptation planning strategy to climate change should include a mix of local scientific studies and local observations of ongoing ecological changes.

  14. Can Perceptions of Environmental and Climate Change in Island Communities Assist in Adaptation Planning Locally?

    PubMed

    Aswani, Shankar; Vaccaro, Ismael; Abernethy, Kirsten; Albert, Simon; de Pablo, Javier Fernández-López

    2015-12-01

    Local perceptions of environmental and climate change, as well as associated adaptations made by local populations, are fundamental for designing comprehensive and inclusive mitigation and adaptation plans both locally and nationally. In this paper, we analyze people's perceptions of environmental and climate-related transformations in communities across the Western Solomon Islands through ethnographic and geospatial methods. Specifically, we documented people's observed changes over the past decades across various environmental domains, and for each change, we asked respondents to identify the causes, timing, and people's adaptive responses. We also incorporated this information into a geographical information system database to produce broad-scale base maps of local perceptions of environmental change. Results suggest that people detected changes that tended to be acute (e.g., water clarity, logging intensity, and agricultural diseases). We inferred from these results that most local observations of and adaptations to change were related to parts of environment/ecosystem that are most directly or indirectly related to harvesting strategies. On the other hand, people were less aware of slower insidious/chronic changes identified by scientific studies. For the Solomon Islands and similar contexts in the insular tropics, a broader anticipatory adaptation planning strategy to climate change should include a mix of local scientific studies and local observations of ongoing ecological changes. PMID:26142887

  15. Liking the good guys: amplifying local adaptation via the evolution of condition-dependent mate choice.

    PubMed

    Veen, T; Otto, S P

    2015-10-01

    Local adaptation can be strengthened through a diversity of mechanisms that reduce gene flow between contrasting environments. Recent work revealed that mate choice could enhance local adaptation when females preferentially mate with locally adapted males and that such female preferences readily evolve, but the opposing effects of recombination, migration and costs of female preferences remain relatively unexplored. To investigate these effects, we develop a two-patch model with two genes, one influencing an ecological trait and one influencing female preferences, where both male signals and female preferences are allowed to depend on the match between an individual's ecological trait and the local environment (condition). Because trait variation is limited when migration is rare and the benefits of preferential mating are short-lived when migration is frequent, we find that female preferences for males in high condition spread most rapidly with intermediate levels of migration. Surprisingly, we find that preferences for locally adapted males spread fastest with higher recombination rates, which contrasts with earlier studies. This is because a stronger preference allele for locally adapted males can only get uncoupled from maladapted ecological alleles following migration through recombination. The effects of migration and recombination depend strongly on the condition of the males being chosen by females, but only weakly on the condition of the females doing the choosing, except when it comes to the costs of preference. Although costs always impede the spread of female preferences for locally adapted males, the impact is substantially lessened if costs are borne primarily by females in poor condition. The abundance of empirical examples of condition-dependent mate choice combined with our theoretical results suggests that the evolution of mate choice could commonly facilitate local adaptation in nature. PMID:26189918

  16. Adapting to climate change through local municipal planning: barriers and challenges

    SciTech Connect

    Preston, Benjamin L

    2011-01-01

    Municipal planning represents a key avenue for local adaptation, but is subject to recognised constraints. To date, these constraints have focused on simplistic factors such as limited resources and lack of information. In this paper we argue that this focus has obscured a wider set of constraints which need to be acknowledged and addressed if adaptation is likely to advance through municipal planning. Although these recognised constraints are relevant, we argue that what underpins these issues are more fundamental challenges affecting local, placed-based planning by drawing on the related field of community-based environmental planning (CBEP). In considering a wider set of constraints to practical attempts towards adaptation, the paper considers planning based on a case study of three municipalities in Sydney, Australia in 2008. The results demonstrate that climate adaptation was widely accepted as an important issue for planning conducted by local governments. However, it was yet to be embedded in planning practice which retained a strong mitigation bias in relation to climate change. In considering the case study, we draw attention to factors thus far under-acknowledged in the climate adaptation literature. These include leadership, institutional context and competing planning agendas. These factors can serve as constraints or enabling mechanisms for achieving climate adaptation depending upon how they are exploited in any given situation. The paper concludes that, through addressing these issues, local, place-based planning can play a greater role in achieving climate adaptation.

  17. Stress avoidance in a common annual: reproductive timing is important for local adaptation and geographic distribution.

    PubMed

    Griffith, T M; Watson, M A

    2005-11-01

    Adaptation to local environments may be an important determinant of species' geographic range. However, little is known about which traits contribute to adaptation or whether their further evolution would facilitate range expansion. In this study, we assessed the adaptive value of stress avoidance traits in the common annual Cocklebur (Xanthium strumarium) by performing a reciprocal transplant across a broad latitudinal gradient extending to the species' northern border. Populations were locally adapted and stress avoidance traits accounted for most fitness differences between populations. At the northern border where growing seasons are cooler and shorter, native populations had evolved to reproduce earlier than native populations in the lower latitude gardens. This clinal pattern in reproductive timing corresponded to a shift in selection from favouring later to earlier reproduction. Thus, earlier reproduction is an important adaptation to northern latitudes and constraint on the further evolution of this trait in marginal populations could potentially limit distribution. PMID:16313471

  18. Effects of adaptation of vestibulo-ocular reflex function on manual target localization

    NASA Technical Reports Server (NTRS)

    Bloomberg, J. J.; Merkle, L. A.; Barry, S. R.; Huebner, W. P.; Cohen, H. S.; Mueller, S. A.; Fordice, J.

    2000-01-01

    The goal of the present study was to determine if adaptive modulation of vestibulo-ocular reflex (VOR) function is associated with commensurate alterations in manual target localization. To measure the effects of adapted VOR on manual responses we developed the Vestibular-Contingent Pointing Test (VCP). In the VCP test, subjects pointed to a remembered target following passive whole body rotation in the dark. In the first experiment, subjects performed VCP before and after wearing 0.5X minifying lenses that adaptively attenuate horizontal VOR gain. Results showed that adaptive reduction in horizontal VOR gain was accompanied by a commensurate change in VCP performance. In the second experiment, bilaterally labyrinthine deficient (LD) subjects were tested to confirm that vestibular cues were central to the spatial coding of both eye and hand movements during VCP. LD subjects performed significantly worse than normal subjects. These results demonstrate that adaptive change in VOR can lead to alterations in manual target localization.

  19. Numerous strategies but limited implementation guidance in US local adaptation plans

    NASA Astrophysics Data System (ADS)

    Woodruff, Sierra C.; Stults, Missy

    2016-08-01

    Adaptation planning offers a promising approach for identifying and devising solutions to address local climate change impacts. Yet there is little empirical understanding of the content and quality of these plans. We use content analysis to evaluate 44 local adaptation plans in the United States and multivariate regression to examine how plan quality varies across communities. We find that plans draw on multiple data sources to analyse future climate impacts and include a breadth of strategies. Most plans, however, fail to prioritize impacts and strategies or provide detailed implementation processes, raising concerns about whether adaptation plans will translate into on-the-ground reductions in vulnerability. Our analysis also finds that plans authored by the planning department and those that engaged elected officials in the planning process were of higher quality. The results provide important insights for practitioners, policymakers and scientists wanting to improve local climate adaptation planning and action.

  20. Experimental Evidence for an Eco-Evolutionary Coupling between Local Adaptation and Intraspecific Competition.

    PubMed

    Siepielski, Adam M; Nemirov, Alex; Cattivera, Matthew; Nickerson, Avery

    2016-04-01

    Determining how adaptive evolution can be coupled to ecological processes is key for developing a more integrative understanding of the demographic factors that regulate populations. Intraspecific competition is an especially important ecological process because it generates negative density dependence in demographic rates. Although ecological factors are most often investigated to determine the strength of density dependence, evolutionary processes such as local adaptation could also feed back to shape variation in the strength of density dependence among populations. Using an experimental approach with damselflies, a predaceous aquatic insect, we find evidence that both density-dependent intraspecific competition and local adaptation can reduce per capita growth rates. In some cases, the effects of local adaptation on reducing per capita growth rates exceeded the ecological competitive effects of a doubling of density. However, we also found that these ecological and evolutionary properties of populations are coupled, and we offer two interpretations of the causes underlying this pattern: (1) the strength of density-dependent competition depends on the extent of local adaptation, or (2) the extent of local adaptation is shaped by the strength of density-dependent competition. Regardless of the underlying causal pathway, these results show how eco-evolutionary dynamics can affect a key demographic process regulating populations. PMID:27028073

  1. The fluid dynamic approach to equidistribution methods for grid generation and adaptation

    SciTech Connect

    Delzanno, Gian Luca; Finn, John M

    2009-01-01

    The equidistribution methods based on L{sub p} Monge-Kantorovich optimization [Finn and Delzanno, submitted to SISC, 2009] and on the deformation [Moser, 1965; Dacorogna and Moser, 1990, Liao and Anderson, 1992] method are analyzed primarily in the context of grid generation. It is shown that the first class of methods can be obtained from a fluid dynamic formulation based on time-dependent equations for the mass density and the momentum density, arising from a variational principle. In this context, deformation methods arise from a fluid formulation by making a specific assumption on the time evolution of the density (but with some degree of freedom for the momentum density). In general, deformation methods do not arise from a variational principle. However, it is possible to prescribe an optimal deformation method, related to L{sub 1} Monge-Kantorovich optimization, by making a further assumption on the momentum density. Some applications of the L{sub p} fluid dynamic formulation to imaging are also explored.

  2. Large-Eddy Simulation of Flow Through an Array of Cubes with Local Grid Refinement

    NASA Astrophysics Data System (ADS)

    Goodfriend, Elijah; Katopodes Chow, Fotini; Vanella, Marcos; Balaras, Elias

    2016-05-01

    High resolution simulations of the transport of urban contaminants are important for disaster response and city planning. Large-eddy simulation (LES) and mesh refinement can each be used to decrease the computational cost of modelling, but combining these techniques can result in additional errors at grid-refinement interfaces. Here, we study the effect of the turbulence closure on the accuracy of LES results, for grids with mesh refinement, in a test case of flow through a periodic array of cubes. It is found that a mixed-model turbulence closure, using both an eddy viscosity and a scale similarity component, reduces energy accumulation at grid-refinement interfaces when used with explicit filtering of the advection term. The mixed model must be used with explicit filtering to control high wavenumber errors generated by the non-linear scale-similarity model. The results demonstrate that the turbulence closure mitigates errors associated with using LES on block-structured grids for urban-flow simulations.

  3. A comparison of locally adaptive multigrid methods: LDC, FAC and FIC

    NASA Technical Reports Server (NTRS)

    Khadra, Khodor; Angot, Philippe; Caltagirone, Jean-Paul

    1993-01-01

    This study is devoted to a comparative analysis of three 'Adaptive ZOOM' (ZOom Overlapping Multi-level) methods based on similar concepts of hierarchical multigrid local refinement: LDC (Local Defect Correction), FAC (Fast Adaptive Composite), and FIC (Flux Interface Correction)--which we proposed recently. These methods are tested on two examples of a bidimensional elliptic problem. We compare, for V-cycle procedures, the asymptotic evolution of the global error evaluated by discrete norms, the corresponding local errors, and the convergence rates of these algorithms.

  4. Sun/shade conditions affect recruitment and local adaptation of a columnar cactus in dry forests

    PubMed Central

    Miranda-Jácome, Antonio; Montaña, Carlos; Fornoni, Juan

    2013-01-01

    Background and Aims Facilitation among plants in water-limited environments (i.e. where evapotranspiration overcomes the availability of water during the growing season) has been considered a local adaptation to water and light conditions. Among cacti, early life-history stages can benefit from the facilitative effects of nurse plants that reduce solar radiation and water stress. However, whether light condition itself acts as an agent of selection through facilitation remains untested. The aim of this study was to determine (1) whether light conditions affect seedling recruitment, (2) whether the positive effect of shade on seedling recruitment is more intense under more stressful conditions and (3) whether shade condition (facilitation) reduces the magnitude of local adaptation on seedling recruitment relative to full sunlight conditions. Methods A reciprocal transplant experiment, coupled with the artificial manipulation of sun/shade conditions, was performed to test for the effects of local adaptation on germination, seedling survival and growth, using two demes of the columnar cactus Pilosocereus leucocephalus, representing different intensities of stressful conditions. Key Results Full sunlight conditions reduced recruitment success and supported the expectation of lower recruitment in more stressful environments. Significant local adaptation was mainly detected under full sunlight conditions, indicating that this environmental factor acts as an agent of selection at both sites. Conclusions The results supported the expectation that the magnitude of local adaptation, driven by the effects of facilitative nurse plants, is less intense under reduced stressful conditions. This study is the first to demonstrate that sun/shade conditions act as a selective agent accounting for local adaptation in water-limited environments, and that facilitation provided by nurse plants in these environments can attenuate the patterns of local adaptation among plants benefiting

  5. Hybridization can facilitate species invasions, even without enhancing local adaptation.

    PubMed

    Mesgaran, Mohsen B; Lewis, Mark A; Ades, Peter K; Donohue, Kathleen; Ohadi, Sara; Li, Chengjun; Cousens, Roger D

    2016-09-01

    The founding population in most new species introductions, or at the leading edge of an ongoing invasion, is likely to be small. Severe Allee effects-reductions in individual fitness at low population density-may then result in a failure of the species to colonize, even if the habitat could support a much larger population. Using a simulation model for plant populations that incorporates demography, mating systems, quantitative genetics, and pollinators, we show that Allee effects can potentially be overcome by transient hybridization with a resident species or an earlier colonizer. This mechanism does not require the invocation of adaptive changes usually attributed to invasions following hybridization. We verify our result in a case study of sequential invasions by two plant species where the outcrosser Cakile maritima has replaced an earlier, inbreeding, colonizer Cakile edentula (Brassicaceae). Observed historical rates of replacement are consistent with model predictions from hybrid-alleviated Allee effects in outcrossers, although other causes cannot be ruled out. PMID:27601582

  6. Adaptation of Mesoscale Weather Models to Local Forecasting

    NASA Technical Reports Server (NTRS)

    Manobianco, John T.; Taylor, Gregory E.; Case, Jonathan L.; Dianic, Allan V.; Wheeler, Mark W.; Zack, John W.; Nutter, Paul A.

    2003-01-01

    Methodologies have been developed for (1) configuring mesoscale numerical weather-prediction models for execution on high-performance computer workstations to make short-range weather forecasts for the vicinity of the Kennedy Space Center (KSC) and the Cape Canaveral Air Force Station (CCAFS) and (2) evaluating the performances of the models as configured. These methodologies have been implemented as part of a continuing effort to improve weather forecasting in support of operations of the U.S. space program. The models, methodologies, and results of the evaluations also have potential value for commercial users who could benefit from tailoring their operations and/or marketing strategies based on accurate predictions of local weather. More specifically, the purpose of developing the methodologies for configuring the models to run on computers at KSC and CCAFS is to provide accurate forecasts of winds, temperature, and such specific thunderstorm-related phenomena as lightning and precipitation. The purpose of developing the evaluation methodologies is to maximize the utility of the models by providing users with assessments of the capabilities and limitations of the models. The models used in this effort thus far include the Mesoscale Atmospheric Simulation System (MASS), the Regional Atmospheric Modeling System (RAMS), and the National Centers for Environmental Prediction Eta Model ( Eta for short). The configuration of the MASS and RAMS is designed to run the models at very high spatial resolution and incorporate local data to resolve fine-scale weather features. Model preprocessors were modified to incorporate surface, ship, buoy, and rawinsonde data as well as data from local wind towers, wind profilers, and conventional or Doppler radars. The overall evaluation of the MASS, Eta, and RAMS was designed to assess the utility of these mesoscale models for satisfying the weather-forecasting needs of the U.S. space program. The evaluation methodology includes

  7. Extensive variation, but not local adaptation in an Australian alpine daisy.

    PubMed

    Hirst, Megan J; Sexton, Jason P; Hoffmann, Ary A

    2016-08-01

    Alpine plants often occupy diverse habitats within a similar elevation range, but most research on local adaptation in these plants has focused on elevation gradients. In testing for habitat-related local adaptation, local effects on seed quality and initial plant growth should be considered in designs that encompass multiple populations and habitats. We tested for local adaptation across alpine habitats in a morphologically variable daisy species, Brachyscome decipiens, in the Bogong High Plains in Victoria, Australia. We collected seed from different habitats, controlled for maternal effects through initial seed size estimates, and characterized seedling survival and growth in a field transplant experiment. We found little evidence for local adaptation for survival or plant size, based on three adaptation measures: Home versus Away, Local versus Foreign, and Sympatric versus Allopatric (SA). The SA measure controlled for planting site and population (site-of-origin) effects. There were significant differences due to site-of-origin and planting site effects. An important confounding factor was the size of plants directly after transplantation of seedlings, which had a large impact on subsequent seedling survival and growth. Initial differences in plant width and height influenced subsequent survival across the growing season but in opposing directions: wide plants had higher survival, but tall plants had lower survival. In an additional controlled garden experiment at Cranbourne Royal Botanic Gardens, site-of-origin effects detected in the field experiments disappeared under more benign homogeneous conditions. Although B. decipiens from different source areas varied significantly when grown across a range of alpine habitats, these differences did not translate into a local or habitat-related fitness advantage. This lack of local advantage may signal weak past selection, and/or weak adaptive transgeneration (plasticity) effects. PMID:27551396

  8. Development and evaluation of a local grid refinement method for block-centered finite-difference groundwater models using shared nodes

    USGS Publications Warehouse

    Mehl, S.; Hill, M.C.

    2002-01-01

    A new method of local grid refinement for two-dimensional block-centered finite-difference meshes is presented in the context of steady-state groundwater-flow modeling. The method uses an iteration-based feedback with shared nodes to couple two separate grids. The new method is evaluated by comparison with results using a uniform fine mesh, a variably spaced mesh, and a traditional method of local grid refinement without a feedback. Results indicate: (1) The new method exhibits quadratic convergence for homogeneous systems and convergence equivalent to uniform-grid refinement for heterogeneous systems. (2) Coupling the coarse grid with the refined grid in a numerically rigorous way allowed for improvement in the coarse-grid results. (3) For heterogeneous systems, commonly used linear interpolation of heads from the large model onto the boundary of the refined model produced heads that are inconsistent with the physics of the flow field. (4) The traditional method works well in situations where the better resolution of the locally refined grid has little influence on the overall flow-system dynamics, but if this is not true, lack of a feedback mechanism produced errors in head up to 3.6% and errors in cell-to-cell flows up to 25%. ?? 2002 Elsevier Science Ltd. All rights reserved.

  9. Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.

    PubMed

    Hoban, Sean; Kelley, Joanna L; Lotterhos, Katie E; Antolin, Michael F; Bradburd, Gideon; Lowry, David B; Poss, Mary L; Reed, Laura K; Storfer, Andrew; Whitlock, Michael C

    2016-10-01

    Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change. PMID:27622873

  10. Ecological differentiation and local adaptation in two sister species of Neotropical Costus (Costaceae).

    PubMed

    Chen, Grace F; Schemske, Douglas W

    2015-02-01

    Reciprocal transplant experiments have often provided evidence of local adaptation in temperate plants, but few such studies have been conducted in the tropics. To enhance our knowledge of local adaptation in tropical plants, we studied natural populations of two recently diverged Neotropical plant species, Costus allenii and C. villosissimus, in central Panama. We found that these species display a parapatric distribution that reflects local environmental differences on a fine geographic scale: C. allenii is found along ravines in the understory of primary forest, while C. villosissimus is found along forest edges. Light availability was lower in C. allenii habitats, while precipitation and soil moisture were lower in C. villosissimus habitats. We carried out reciprocal transplant experiments with seeds and clones of mature plants to test the hypothesis that the parapatric distribution of these species is due to divergent adaptation to their local habitats. We found strong evidence of local adaptation, i.e., when grown in their "home" sites, each species outperformed the species from an "away" site. Our finding that C. allenii and C. villosissimus are mainly isolated by their microhabitats provides a first step toward understanding the mechanisms of adaptation and speciation in the tropics. PMID:26240865

  11. Differences in spawning date between populations of common frog reveal local adaptation

    PubMed Central

    Phillimore, Albert B.; Hadfield, Jarrod D.; Jones, Owen R.; Smithers, Richard J.

    2010-01-01

    Phenotypic differences between populations often correlate with climate variables, resulting from a combination of environment-induced plasticity and local adaptation. Species comprising populations that are genetically adapted to local climatic conditions should be more vulnerable to climate change than those comprising phenotypically plastic populations. Assessment of local adaptation generally requires logistically challenging experiments. Here, using a unique approach and a large dataset (>50,000 observations from across Britain), we compare the covariation in temperature and first spawning dates of the common frog (Rana temporaria) across space with that across time. We show that although all populations exhibit a plastic response to temperature, spawning earlier in warmer years, between-population differences in first spawning dates are dominated by local adaptation. Given climate change projections for Britain in 2050–2070, we project that for populations to remain as locally adapted as contemporary populations will require first spawning date to advance by ∼21–39 days but that plasticity alone will only enable an advance of ∼5–9 days. Populations may thus face a microevolutionary and gene flow challenge to advance first spawning date by a further ∼16–30 days over the next 50 years. PMID:20404185

  12. Using Local Stories as a Call to Action on Climate Change Adaptation and Mitigation in Minnesota

    NASA Astrophysics Data System (ADS)

    Phipps, M.

    2015-12-01

    Climate Generation: A Will Steger Legacy and the University of Minnesota's Regional Sustainability Development Partnerships (RSDP) have developed a novel approach to engaging rural Minnesotans on climate change issues. Through the use of personal, local stories about individuals' paths to action to mitigate and or adapt to climate change, Climate Generation and RSDP aim to spur others to action. Minnesota's Changing Climate project includes 12 Climate Convenings throughout rural Minnesota in a range of communities (tourism-based, agrarian, natural resources-based, university towns) to engage local populations in highly local conversations about climate change, its local impacts, and local solutions currently occurring. Climate Generation and RSDP have partnered with Molly Phipps Consulting to evaluate the efficacy of this approach in rural Minnesota. Data include pre and post convening surveys examining participants' current action around climate change, attitudes toward climate change (using questions from Maibach, Roser-Renouf, and Leiserowitz, 2009), and the strength of their social network to support their current and ongoing work toward mitigating and adapting to climate change. Although the Climate Convenings are tailored to each community, all include a resource fair of local organizations already engaging in climate change mitigation and adaptation activities which participants can participate in, a welcome from a trusted local official, a presentation on the science of climate change, sharing of local climate stories, and break-out groups where participants can learn how to get involved in a particular mitigation or adaptation strategy. Preliminary results have been positive: participants feel motivated to work toward mitigating and adapting to climate change, and more local stories have emerged that can be shared in follow-up webinars and on a project website to continue to inspire others to act.

  13. LoAd: a locally adaptive cortical segmentation algorithm.

    PubMed

    Cardoso, M Jorge; Clarkson, Matthew J; Ridgway, Gerard R; Modat, Marc; Fox, Nick C; Ourselin, Sebastien

    2011-06-01

    Thickness measurements of the cerebral cortex can aid diagnosis and provide valuable information about the temporal evolution of diseases such as Alzheimer's, Huntington's, and schizophrenia. Methods that measure the thickness of the cerebral cortex from in-vivo magnetic resonance (MR) images rely on an accurate segmentation of the MR data. However, segmenting the cortex in a robust and accurate way still poses a challenge due to the presence of noise, intensity non-uniformity, partial volume effects, the limited resolution of MRI and the highly convoluted shape of the cortical folds. Beginning with a well-established probabilistic segmentation model with anatomical tissue priors, we propose three post-processing refinements: a novel modification of the prior information to reduce segmentation bias; introduction of explicit partial volume classes; and a locally varying MRF-based model for enhancement of sulci and gyri. Experiments performed on a new digital phantom, on BrainWeb data and on data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) show statistically significant improvements in Dice scores and PV estimation (p<10(-3)) and also increased thickness estimation accuracy when compared to three well established techniques. PMID:21316470

  14. LoAd: A locally adaptive cortical segmentation algorithm

    PubMed Central

    Cardoso, M. Jorge; Clarkson, Matthew J.; Ridgway, Gerard R.; Modat, Marc; Fox, Nick C.; Ourselin, Sebastien

    2012-01-01

    Thickness measurements of the cerebral cortex can aid diagnosis and provide valuable information about the temporal evolution of diseases such as Alzheimer's, Huntington's, and schizophrenia. Methods that measure the thickness of the cerebral cortex from in-vivo magnetic resonance (MR) images rely on an accurate segmentation of the MR data. However, segmenting the cortex in a robust and accurate way still poses a challenge due to the presence of noise, intensity non-uniformity, partial volume effects, the limited resolution of MRI and the highly convoluted shape of the cortical folds. Beginning with a well-established probabilistic segmentation model with anatomical tissue priors, we propose three post-processing refinements: a novel modification of the prior information to reduce segmentation bias; introduction of explicit partial volume classes; and a locally varying MRF-based model for enhancement of sulci and gyri. Experiments performed on a new digital phantom, on BrainWeb data and on data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) show statistically significant improvements in Dice scores and PV estimation (p<10−3) and also increased thickness estimation accuracy when compared to three well established techniques. PMID:21316470

  15. Featured "Single Sign-In" interface enabling Grid, Cloud and local resources for HEP

    NASA Astrophysics Data System (ADS)

    Fischer, Max; Quast, Günter; Zvada, Marian

    2014-06-01

    The CMS collaboration is successfully using glideinWMS for managing grid resources within the WLCG project. The glidein mechanism with HTCondor underneath provides a clear separation of responsibilities between administrators operating the service and users utilizing computational resources. German CMS collaborators (dCMS) have explored modern capabilities of the glideinWMS aiming at merging national grid resources, institutional CPU power and cloud resources into the set of pools with common sign-in interface presented towards HEP analysis users. The key goals of service development include ease of use, uniform access, load balancing and automated selection among different resource technologies. The approach integrates experience of dCMS during the development and integration phases as well as production operations and highly encourages other countries to follow. First experience with the production system and an outlook towards ongoing development will be presented.

  16. Local adaptation to parasite selective pressure: comparing three congeneric co-occurring hosts.

    PubMed

    Keogh, Carolyn L; Sanderson, Martha E; Byers, James E

    2016-01-01

    Local adaptation may optimize an organism's investment in defenses in response to the risk of infection by spatially heterogeneous parasites and other natural enemies. However, local adaptation may be constrained if recruitment is decoupled from selective pressure experienced by the parent generation. We predicted that the ability of three intertidal littorinid snail species to defend against trematode parasites would depend on prior levels of population exposure to parasites and on larval dispersal mode, a proxy for population openness. In a common garden experiment, for two snail species with direct development and localized recruitment (Littorina obtusata and Littorina saxatilis), hosts from sites with high trematode infection risk were less susceptible to infection than hosts from low-risk sites. However, this relationship was not apparent for a third host species with broadcast larvae (Littorina littorea), suggesting that broad larval dispersal can impede local adaptation; alternatively, the lack of response in this species could owe to other factors that limited experimental infection in this host. Our findings support that locally recruiting hosts can adapt their defenses to scale with localized infection risk. PMID:26440801

  17. Local adaptation to temperature and the implications for vector-borne diseases.

    PubMed

    Sternberg, Eleanore D; Thomas, Matthew B

    2014-03-01

    Vector life-history traits and parasite development respond in strongly nonlinear ways to changes in temperature. These thermal sensitivities create the potential for climate change to have a marked impact on disease transmission. To date, most research considering impacts of climate change on vector-borne diseases assumes that all populations of a given parasite or vector species respond similarly to temperature, regardless of their source population. This may be an inappropriate assumption because spatial variation in selective pressures such as temperature can lead to local adaptation. We examine evidence for local adaptation in disease vectors and present conceptual models for understanding how local adaptation might modulate the effects of both short- and long-term changes in climate. PMID:24513566

  18. Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae).

    PubMed

    Picq, Sophie; McMillan, W Owen; Puebla, Oscar

    2016-04-01

    Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which (i) local adaptation and the early stages of speciation can be clearly identified and distinguished, (ii) the amount of genetic divergence driven by the two processes is similar, and (iii) comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the hamlets (Hypoplectrus spp), brightly colored reef fishes from the wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from three sympatric species sampled in three repeated populations provide genome-wide levels of divergence that are comparable among allopatric populations (F st estimate = 0.0042) and sympatric species (F st estimate = 0.0038). Population genetic, clustering, and phylogenetic analyses reveal very similar patterns for local adaptation and speciation, with a large fraction of the genome undifferentiated (F st estimate ≈ 0), a very small proportion of F st outlier loci (0.05-0.07%), and remarkably few repeated outliers (1-3). Nevertheless, different loci appear to be involved in the two processes in Hypoplectrus, with only 7% of the most differentiated SNPs and outliers shared between populations and species comparisons. In particular, a tropomyosin (Tpm4) and a previously identified hox (HoxCa) locus emerge as candidate loci (repeated outliers) for local adaptation and speciation, respectively. We conclude that marine populations may be locally adapted notwithstanding shallow levels of genetic divergence, and that from a population genomic perspective, this process does not appear to differ fundamentally from the early stages of speciation. PMID:27099711

  19. Demographic source-sink dynamics restrict local adaptation in Elliott's blueberry (Vaccinium elliottii).

    PubMed

    Anderson, Jill T; Geber, Monica A

    2010-02-01

    In heterogeneous landscapes, divergent selection can favor the evolution of locally adapted ecotypes, especially when interhabitat gene flow is minimal. However, if habitats differ in size or quality, source-sink dynamics can shape evolutionary trajectories. Upland and bottomland forests of the southeastern USA differ in water table depth, light availability, edaphic conditions, and plant community. We conducted a multiyear reciprocal transplant experiment to test whether Elliott's blueberry (Vaccinium elliottii) is locally adapted to these contrasting environments. Additionally, we exposed seedlings and cuttings to prolonged drought and flooding in the greenhouse to assess fitness responses to abiotic stress. Contrary to predictions of local adaptation, V. elliottii families exhibited significantly higher survivorship and growth in upland than in bottomland forests and under drought than flooded conditions, regardless of habitat of origin. Neutral population differentiation was minimal, suggesting widespread interhabitat migration. Population density, reproductive output, and genetic diversity were all significantly greater in uplands than in bottomlands. These disparities likely result in asymmetric gene flow from uplands to bottomlands. Thus, adaptation to a marginal habitat can be constrained by small populations, limited fitness, and immigration from a benign habitat. Our study highlights the importance of demography and genetic diversity in the evolution of local (mal)adaptation. PMID:19703223

  20. Scale-adaptive tensor algebra for local many-body methods of electronic structure theory

    SciTech Connect

    Liakh, Dmitry I

    2014-01-01

    While the formalism of multiresolution analysis (MRA), based on wavelets and adaptive integral representations of operators, is actively progressing in electronic structure theory (mostly on the independent-particle level and, recently, second-order perturbation theory), the concepts of multiresolution and adaptivity can also be utilized within the traditional formulation of correlated (many-particle) theory which is based on second quantization and the corresponding (generally nonorthogonal) tensor algebra. In this paper, we present a formalism called scale-adaptive tensor algebra (SATA) which exploits an adaptive representation of tensors of many-body operators via the local adjustment of the basis set quality. Given a series of locally supported fragment bases of a progressively lower quality, we formulate the explicit rules for tensor algebra operations dealing with adaptively resolved tensor operands. The formalism suggested is expected to enhance the applicability and reliability of local correlated many-body methods of electronic structure theory, especially those directly based on atomic orbitals (or any other localized basis functions).

  1. Two general methods for population pharmacokinetic modeling: non-parametric adaptive grid and non-parametric Bayesian

    PubMed Central

    Neely, Michael; Bartroff, Jay; van Guilder, Michael; Yamada, Walter; Bayard, David; Jelliffe, Roger; Leary, Robert; Chubatiuk, Alyona; Schumitzky, Alan

    2013-01-01

    Population pharmacokinetic (PK) modeling methods can be statistically classified as either parametric or nonparametric (NP). Each classification can be divided into maximum likelihood (ML) or Bayesian (B) approazches. In this paper we discuss the nonparametric case using both maximum likelihood and Bayesian approaches. We present two nonparametric methods for estimating the unknown joint population distribution of model parameter values in a pharmacokinetic/pharmacodynamic (PK/PD) dataset. The first method is the NP Adaptive Grid (NPAG). The second is the NP Bayesian (NPB) algorithm with a stick-breaking process to construct a Dirichlet prior. Our objective is to compare the performance of these two methods using a simulated PK/PD dataset. Our results showed excellent performance of NPAG and NPB in a realistically simulated PK study. This simulation allowed us to have benchmarks in the form of the true population parameters to compare with the estimates produced by the two methods, while incorporating challenges like unbalanced sample times and sample numbers as well as the ability to include the covariate of patient weight. We conclude that both NPML and NPB can be used in realistic PK/PD population analysis problems. The advantages of one versus the other are discussed in the paper. NPAG and NPB are implemented in R and freely available for download within the Pmetrics package from www.lapk.org. PMID:23404393

  2. Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe

    PubMed Central

    Postolache, Dragos; Lascoux, Martin; Drouzas, Andreas D.; Källman, Thomas; Leonarduzzi, Cristina; Liepelt, Sascha; Piotti, Andrea; Popescu, Flaviu; Roschanski, Anna M.; Zhelev, Peter; Fady, Bruno; Vendramin, Giovanni Giuseppe

    2016-01-01

    Background Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. Methods A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical ‘within-site’ approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). Results HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species’ southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. Conclusion Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales. PMID:27392065

  3. Local Laser Strengthening of Steel Sheets for Load Adapted Component Design in Car Body Structures

    NASA Astrophysics Data System (ADS)

    Jahn, Axel; Heitmanek, Marco; Standfuss, Jens; Brenner, Berndt; Wunderlich, Gerd; Donat, Bernd

    The current trend in car body construction concerning light weight design and car safety improvement increasingly requires an adaption of the local material properties on the component load. Martensitic hardenable steels, which are typically used in car body components, show a significant hardening effect, for instance in laser welded seams. This effect can be purposefully used as a local strengthening method. For several steel grades the local strengthening, resulting from a laser remelting process was investigated. The strength in the treated zone was determined at crash relevant strain rates. A load adapted design of complex reinforcement structures was developed for compression and bending loaded tube samples, using numerical simulation of the deformation behavior. Especially for bending loaded parts, the crash energy absorption can be increased significantly by local laser strengthening.

  4. Simulation of plasma based semiconductor processing using block structured locally refined grids

    SciTech Connect

    Wake, D.D.

    1998-01-01

    We have described a new numerical method for plasma simulation. Calculations have been presented which show that the method is accurate and suggest the regimes in which the method provides savings in CPU time and memory requirements. A steady state simulation of a four centimeter domain was modeled with sheath scale (150 microns) resolution using only 40 grid points. Simulations of semiconductor processing equipment have been performed which imply the usefulness of the method for engineering applications. It is the author`s opinion that these accomplishments represent a significant contribution to plasma simulation and the efficient numerical solution of certain systems of non-linear partial differential equations. More work needs to be done, however, for the algorithm to be of practical use in an engineering environment. Despite our success at avoiding the dielectric relaxation timestep restrictions the algorithm is still conditionally stable and requires timesteps which are relatively small. This represents a prohibitive runtime for steady state solutions on high resolution grids. Current research suggests that these limitations may be overcome and the use of much larger timesteps will be possible.

  5. Local adaptation in adult feeding preference and juvenile performance in the generalist herbivore Idotea balthica.

    PubMed

    Bell, Tina M; Sotka, Erik E

    2012-10-01

    Populations can respond to environmental heterogeneity by genetic adaptation to local conditions. Evidence for local adaptation in herbivores with relatively broad host breadth is scarce, either because generalists rarely locally adapt or because fewer studies have tested for local adaptation. The marine isopod Idotea balthica, a small (<3 cm) generalist herbivore common to estuaries of the northwestern Atlantic, is found on multiple macroalgae and sea grasses north of 42°N, while more southerly populations utilize sea grass-dominated and macroalgal-poor habitats. Feeding preference assays revealed a latitudinal shift in preference hierarchy that mirrors this geographic variation in host availability. Northern populations have higher feeding preference for fresh and freeze-dried tissue of the brown macroalga Fucus vesiculosus and consumed more of its water-soluble and lipophilic extracts relative to southern populations. In contrast, southern populations have a relatively higher preference for the green macroalga Ulva linza and sea grass Zostera marina. The rank of hosts in feeding assays exhibited by northern adults (Fucus = Ulva > Zostera) and southern adults (Ulva > Fucus > Zostera) closely mirrored ranking of juvenile growth rates, suggesting that preference and performance are strongly correlated across these macrophytes. Several of our assays included isopods that had parents reared under uniform laboratory conditions, indicating that geographic differences are genetically mediated and unlikely to reflect phenotypic plasticity or maternal effects. Local adaptation in host use traits may be common in broadly distributed, generalist herbivores in marine and terrestrial systems, and will manifest itself as local shifts in the preference ranking of hosts. PMID:22451011

  6. An h-adaptive local discontinuous Galerkin method for the Navier-Stokes-Korteweg equations

    NASA Astrophysics Data System (ADS)

    Tian, Lulu; Xu, Yan; Kuerten, J. G. M.; van der Vegt, J. J. W.

    2016-08-01

    In this article, we develop a mesh adaptation algorithm for a local discontinuous Galerkin (LDG) discretization of the (non)-isothermal Navier-Stokes-Korteweg (NSK) equations modeling liquid-vapor flows with phase change. This work is a continuation of our previous research, where we proposed LDG discretizations for the (non)-isothermal NSK equations with a time-implicit Runge-Kutta method. To save computing time and to capture the thin interfaces more accurately, we extend the LDG discretization with a mesh adaptation method. Given the current adapted mesh, a criterion for selecting candidate elements for refinement and coarsening is adopted based on the locally largest value of the density gradient. A strategy to refine and coarsen the candidate elements is then provided. We emphasize that the adaptive LDG discretization is relatively simple and does not require additional stabilization. The use of a locally refined mesh in combination with an implicit Runge-Kutta time method is, however, non-trivial, but results in an efficient time integration method for the NSK equations. Computations, including cases with solid wall boundaries, are provided to demonstrate the accuracy, efficiency and capabilities of the adaptive LDG discretizations.

  7. Health Aspects of Climate Change in Cities with Mediterranean Climate, and Local Adaptation Plans

    PubMed Central

    Paz, Shlomit; Negev, Maya; Clermont, Alexandra; Green, Manfred S.

    2016-01-01

    Cities with a Mediterranean-type climate (Med-cities) are particularly susceptible to health risks from climate change since they are located in biogeographical hot-spots that experience some of the strongest effects of the changing climate. The study aims to highlight health impacts of climate change in Med-cities, analyze local climate adaptation plans and make adaptation policy recommendations for the Med-city level. We identified five Med-cities with a climate change adaptation plan: Adelaide, Barcelona, Cape Town, Los Angeles and Santiago. Beyond their similar Med-climate features (although Santiago’s are slightly different), the cities have different socio-economic characteristics in various aspects. We analyzed each plan according to how it addresses climate change-related drivers of health impacts among city dwellers. For each driver, we identified the types of policy adaptation tools that address it in the urban climate adaptation plans. The surveyed cities address most of the fundamental climate change-related drivers of risks to human health, including rising temperatures, flooding and drought, but the policy measures to reduce negative impacts vary across cities. We suggest recommendations for Med-cities in various aspects, depending on their local needs and vulnerability challenges: assessment of health risks, extreme events management and long-term adaptation, among others. PMID:27110801

  8. Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops

    PubMed Central

    Allaby, Robin G.; Gutaker, Rafal; Clarke, Andrew C.; Pearson, Neil; Ware, Roselyn; Palmer, Sarah A.; Kitchen, James L.; Smith, Oliver

    2015-01-01

    Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity. PMID:25487329

  9. Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops.

    PubMed

    Allaby, Robin G; Gutaker, Rafal; Clarke, Andrew C; Pearson, Neil; Ware, Roselyn; Palmer, Sarah A; Kitchen, James L; Smith, Oliver

    2015-01-19

    Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity. PMID:25487329

  10. Health Aspects of Climate Change in Cities with Mediterranean Climate, and Local Adaptation Plans.

    PubMed

    Paz, Shlomit; Negev, Maya; Clermont, Alexandra; Green, Manfred S

    2016-04-01

    Cities with a Mediterranean-type climate (Med-cities) are particularly susceptible to health risks from climate change since they are located in biogeographical hot-spots that experience some of the strongest effects of the changing climate. The study aims to highlight health impacts of climate change in Med-cities, analyze local climate adaptation plans and make adaptation policy recommendations for the Med-city level. We identified five Med-cities with a climate change adaptation plan: Adelaide, Barcelona, Cape Town, Los Angeles and Santiago. Beyond their similar Med-climate features (although Santiago's are slightly different), the cities have different socio-economic characteristics in various aspects. We analyzed each plan according to how it addresses climate change-related drivers of health impacts among city dwellers. For each driver, we identified the types of policy adaptation tools that address it in the urban climate adaptation plans. The surveyed cities address most of the fundamental climate change-related drivers of risks to human health, including rising temperatures, flooding and drought, but the policy measures to reduce negative impacts vary across cities. We suggest recommendations for Med-cities in various aspects, depending on their local needs and vulnerability challenges: assessment of health risks, extreme events management and long-term adaptation, among others. PMID:27110801

  11. AFLPs and Mitochondrial Haplotypes Reveal Local Adaptation to Extreme Thermal Environments in a Freshwater Gastropod

    PubMed Central

    Quintela, María; Johansson, Magnus P.; Kristjánsson, Bjarni K.; Barreiro, Rodolfo; Laurila, Anssi

    2014-01-01

    The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher FST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence. PMID:25007329

  12. Local adaptation limits lifetime reproductive success of dispersers in a wild salmon metapopulation.

    PubMed

    Peterson, Daniel A; Hilborn, Ray; Hauser, Lorenz

    2014-01-01

    Demographic and evolutionary dynamics in wild metapopulations are critically affected by the balance between dispersal and local adaptation. Where populations are demographically interconnected by migration, gene flow is often assumed to prevent local adaptation. However, reduced fitness of immigrants may limit gene flow between populations adapted to distinct habitat types, although direct quantification of the lifetime reproductive success of immigrants in the wild is lacking. Here, we show that dispersers between stream-spawning populations of sockeye salmon (Oncorhynchus nerka) had similar reproductive success to those that spawned in their natal stream, whereas dispersers from a different habitat (nearby lake beaches) produced half as many offspring. The stream- and beach-spawning ecotypes exhibited striking morphological differences despite their close spatial proximity, yet dispersal from the beach to the streams was more common than dispersal between streams, presenting empirical evidence that variation in immigrant reproductive success is important for the maintenance of intraspecific biodiversity. PMID:24739514

  13. Gene expression clines reveal local adaptation and associated trade-offs at a continental scale

    PubMed Central

    Porcelli, Damiano; Westram, Anja M.; Pascual, Marta; Gaston, Kevin J.; Butlin, Roger K.; Snook, Rhonda R.

    2016-01-01

    Local adaptation, where fitness in one environment comes at a cost in another, should lead to spatial variation in trade-offs between life history traits and may be critical for population persistence. Recent studies have sought genomic signals of local adaptation, but often have been limited to laboratory populations representing two environmentally different locations of a species’ distribution. We measured gene expression, as a proxy for fitness, in males of Drosophila subobscura, occupying a 20° latitudinal and 11 °C thermal range. Uniquely, we sampled six populations and studied both common garden and semi-natural responses to identify signals of local adaptation. We found contrasting patterns of investment: transcripts with expression positively correlated to latitude were enriched for metabolic processes, expressed across all tissues whereas negatively correlated transcripts were enriched for reproductive processes, expressed primarily in testes. When using only the end populations, to compare our results to previous studies, we found that locally adaptive patterns were obscured. While phenotypic trade-offs between metabolic and reproductive functions across widespread species are well-known, our results identify underlying genetic and tissue responses at a continental scale that may be responsible for this. This may contribute to understanding population persistence under environmental change. PMID:27599812

  14. Addressing potential local adaptation in species distribution models: implications for conservation under climate change.

    PubMed

    Hällfors, Maria Helena; Liao, Jishan; Dzurisin, Jason; Grundel, Ralph; Hyvärinen, Marko; Towle, Kevin; Wu, Grace C; Hellmann, Jessica J

    2016-06-01

    Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate Max-Ent models, one considering the species as a single population and two of disjunct populations. Principal component analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species vs. population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered. PMID:27509755

  15. Addressing potential local adaptation in species distribution models: implications for conservation under climate change

    USGS Publications Warehouse

    Hällfors, Maria Helena; Liao, Jishan; Dzurisin, Jason D. K.; Grundel, Ralph; Hyvärinen, Marko; Towle, Kevin; Wu, Grace C.; Hellmann, Jessica J.

    2016-01-01

    Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account, may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted, however. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate MaxEnt models, one considering the species as a single population and two of disjunct populations. PCA analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species versus population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered.

  16. Gene expression clines reveal local adaptation and associated trade-offs at a continental scale.

    PubMed

    Porcelli, Damiano; Westram, Anja M; Pascual, Marta; Gaston, Kevin J; Butlin, Roger K; Snook, Rhonda R

    2016-01-01

    Local adaptation, where fitness in one environment comes at a cost in another, should lead to spatial variation in trade-offs between life history traits and may be critical for population persistence. Recent studies have sought genomic signals of local adaptation, but often have been limited to laboratory populations representing two environmentally different locations of a species' distribution. We measured gene expression, as a proxy for fitness, in males of Drosophila subobscura, occupying a 20° latitudinal and 11 °C thermal range. Uniquely, we sampled six populations and studied both common garden and semi-natural responses to identify signals of local adaptation. We found contrasting patterns of investment: transcripts with expression positively correlated to latitude were enriched for metabolic processes, expressed across all tissues whereas negatively correlated transcripts were enriched for reproductive processes, expressed primarily in testes. When using only the end populations, to compare our results to previous studies, we found that locally adaptive patterns were obscured. While phenotypic trade-offs between metabolic and reproductive functions across widespread species are well-known, our results identify underlying genetic and tissue responses at a continental scale that may be responsible for this. This may contribute to understanding population persistence under environmental change. PMID:27599812

  17. A new algorithm for high-dimensional uncertainty quantification based on dimension-adaptive sparse grid approximation and reduced basis methods

    NASA Astrophysics Data System (ADS)

    Chen, Peng; Quarteroni, Alfio

    2015-10-01

    In this work we develop an adaptive and reduced computational algorithm based on dimension-adaptive sparse grid approximation and reduced basis methods for solving high-dimensional uncertainty quantification (UQ) problems. In order to tackle the computational challenge of "curse of dimensionality" commonly faced by these problems, we employ a dimension-adaptive tensor-product algorithm [16] and propose a verified version to enable effective removal of the stagnation phenomenon besides automatically detecting the importance and interaction of different dimensions. To reduce the heavy computational cost of UQ problems modelled by partial differential equations (PDE), we adopt a weighted reduced basis method [7] and develop an adaptive greedy algorithm in combination with the previous verified algorithm for efficient construction of an accurate reduced basis approximation. The efficiency and accuracy of the proposed algorithm are demonstrated by several numerical experiments.

  18. Adaptive Decomposition of Highly Resolved Time Series into Local and Non‐local Components

    EPA Science Inventory

    Highly time-resolved air monitoring data are widely being collected over long time horizons in order to characterizeambient and near-source air quality trends. In many applications, it is desirable to split the time-resolved data into two ormore components (e.g., local and region...

  19. Invasion strategies in clonal aquatic plants: are phenotypic differences caused by phenotypic plasticity or local adaptation?

    PubMed Central

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit; Clayton, John S.; Brix, Hans; Sorrell, Brian K.

    2010-01-01

    Background and Aims The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important. Here the primary adaptive strategy in three non-native, clonally reproducing macrophytes (Egeria densa, Elodea canadensis and Lagarosiphon major) in New Zealand freshwaters were examined and an attempt was made to link observed differences in plant morphology to local variation in habitat conditions. Methods Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity of these same populations was also quantified. Key Results For all three species, greater variation in plant characteristics was found before they were grown in standardized conditions. Moreover, field populations displayed remarkably little genetic variation and there was little interaction between habitat conditions and plant morphological characteristics. Conclusions The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between populations may facilitate ecotypic differentiation in the future cannot be excluded. These results thus indicate that invasive clonal aquatic plants adapt to new introduced areas by phenotypic plasticity. Inorganic carbon, nitrogen and phosphorous were important in controlling plant size of E. canadensis and L. major, but no other relationships between plant characteristics and habitat conditions were apparent. This implies that within-species differences in plant size can be explained

  20. Evaluation of Spatially Fractionated Radiotherapy (GRID) and Definitive Chemoradiotherapy With Curative Intent for Locally Advanced Squamous Cell Carcinoma of the Head and Neck: Initial Response Rates and Toxicity

    SciTech Connect

    Penagaricano, Jose A.; Moros, Eduardo G.; Ratanatharathorn, Vaneerat; Yan Yulong; Corry, Peter

    2010-04-15

    Purpose: To present results and acute toxicity in 14 patients with bulky (>=6 cm) tumors from locally advanced squamous cell carcinoma of the head and neck who received spatially fractionated radiotherapy (GRID) therapy to the bulky mass followed by concomitant chemoradiotherapy using simultaneous integrated boost intensity-modulated radiotherapy (SIB-IMRT). Methods and Materials: GRID therapy to the GTV was delivered by creating one treatment field with a checkerboard pattern composed of open-closed areas using a multileaf collimator. The GRID prescription was 20 Gy in one fraction. Chemotherapy started the day of GRID therapy and continued throughout the course of SIB-IMRT. The SIB-IMRT prescription was 66, 60, and 54 Gy to the planning target volume (PTV), intermediate-risk PTV, and low-risk PTV, respectively, in 30 fractions. Results: With a median follow-up of 19.5 months (range, 2-38 months), the overall control rate of the GRID gross tumor volume was 79% (11 of 14). The most common acute skin and mucosal toxicities were Grade 3 and 2, respectively. Conclusion: For the treatment of locally advanced neck squamous cell carcinoma of the head and neck, GRID followed by chemotherapy and SIB-IMRT is well tolerated and yields encouraging clinical and pathologic responses, with similar acute toxicity profiles as in patients receiving chemoradiotherapy without GRID.

  1. Understanding the wide geographic range of a clonal perennial grass: plasticity versus local adaptation

    PubMed Central

    Liu, Yanjie; Zhang, Lirong; Xu, Xingliang; Niu, Haishan

    2016-01-01

    Both phenotypic plasticity and local adaptation may allow widely distributed plant species to either acclimate or adapt to environmental heterogeneity. Given the typically low genetic variation of clonal plants across their habitats, phenotypic plasticity may be the primary adaptive strategy allowing them to thrive across a wide range of habitats. In this study, the mechanism supporting the widespread distribution of the clonal plant Leymus chinensis was determined, i.e. phenotypic plasticity or local specialization in water use efficiency (WUE; reflected by foliar δ13C). To test whether plasticity is required for the species to thrive in different habitats, samples were collected across its distribution in the Mongolian steppe, and a controlled watering experiment was conducted with two populations at two different sites. Five populations were also transplanted from different sites into a control environment, and the foliar δ13C was compared between the control and original habitats, to test for local specialization in WUE. Results demonstrated decreased foliar δ13C with increasing precipitation during controlled watering experiments, with divergent responses between the two populations assessed. Change in foliar δ13C (−3.69 ‰) due to water addition was comparable to fluctuations of foliar δ13C observed in situ (−4.83 ‰). Foliar δ13C differed by −0.91 ‰ between two transplanted populations; however, this difference was not apparent between the two populations when growing in their original habitats. Findings provide evidence that local adaptation affects foliar δ13C much less than phenotypic plasticity. Thus, plasticity in WUE is more important than local adaptation in allowing the clonal plant L. chinensis to occupy a wide range of habitats in the Mongolian steppe. PMID:26644341

  2. Understanding the wide geographic range of a clonal perennial grass: plasticity versus local adaptation.

    PubMed

    Liu, Yanjie; Zhang, Lirong; Xu, Xingliang; Niu, Haishan

    2015-01-01

    Both phenotypic plasticity and local adaptation may allow widely distributed plant species to either acclimate or adapt to environmental heterogeneity. Given the typically low genetic variation of clonal plants across their habitats, phenotypic plasticity may be the primary adaptive strategy allowing them to thrive across a wide range of habitats. In this study, the mechanism supporting the widespread distribution of the clonal plant Leymus chinensis was determined, i.e. phenotypic plasticity or local specialization in water use efficiency (WUE; reflected by foliar δ(13)C). To test whether plasticity is required for the species to thrive in different habitats, samples were collected across its distribution in the Mongolian steppe, and a controlled watering experiment was conducted with two populations at two different sites. Five populations were also transplanted from different sites into a control environment, and the foliar δ(13)C was compared between the control and original habitats, to test for local specialization in WUE. Results demonstrated decreased foliar δ(13)C with increasing precipitation during controlled watering experiments, with divergent responses between the two populations assessed. Change in foliar δ(13)C (-3.69 ‰) due to water addition was comparable to fluctuations of foliar δ(13)C observed in situ (-4.83 ‰). Foliar δ(13)C differed by -0.91 ‰ between two transplanted populations; however, this difference was not apparent between the two populations when growing in their original habitats. Findings provide evidence that local adaptation affects foliar δ(13)C much less than phenotypic plasticity. Thus, plasticity in WUE is more important than local adaptation in allowing the clonal plant L. chinensis to occupy a wide range of habitats in the Mongolian steppe. PMID:26644341

  3. Road to evolution? Local adaptation to road adjacency in an amphibian (Ambystoma maculatum)

    PubMed Central

    Brady, Steven P.

    2012-01-01

    The network of roads on the landscape is vast, and contributes a suite of negative ecological effects on adjacent habitats, ranging from fragmentation to contamination by runoff. In addition to the immediate consequences faced by biota living in roaded landscapes, road effects may further function as novel agents of selection, setting the stage for contemporary evolutionary changes in local populations. Though the ecological consequences of roads are well described, evolutionary outcomes remain largely unevaluated. To address these potential responses in tandem, I conducted a reciprocal transplant experiment on early life history stages of a pool-breeding salamander. My data show that despite a strong, negative effect of roadside pools on salamander performance, populations adjacent to roads are locally adapted. This suggests that the response of species to human-altered environments varies across local populations, and that adaptive processes may mediate this response. PMID:22355748

  4. Local Adaptation and Vector-Mediated Population Structure in Plasmodium vivax Malaria

    PubMed Central

    Gonzalez-Ceron, Lilia; Carlton, Jane M.; Gueye, Amy; Fay, Michael; McCutchan, Thomas F.; Su, Xin-zhuan

    2008-01-01

    Plasmodium vivax in southern Mexico exhibits different infectivities to 2 local mosquito vectors, Anopheles pseudopunctipennis and Anopheles albimanus. Previous work has tied these differences in mosquito infectivity to variation in the central repeat motif of the malaria parasite's circumsporozoite (csp) gene, but subsequent studies have questioned this view. Here we present evidence that P. vivax in southern Mexico comprised 3 genetic populations whose distributions largely mirror those of the 2 mosquito vectors. Additionally, laboratory colony feeding experiments indicate that parasite populations are most compatible with sympatric mosquito species. Our results suggest that reciprocal selection between malaria parasites and mosquito vectors has led to local adaptation of the parasite. Adaptation to local vectors may play an important role in generating population structure in Plasmodium. A better understanding of coevolutionary dynamics between sympatric mosquitoes and parasites will facilitate the identification of molecular mechanisms relevant to disease transmission in nature and provide crucial information for malaria control. PMID:18385220

  5. Linking Federal, State, and Local Adaptation Strategies in New York (Invited)

    NASA Astrophysics Data System (ADS)

    Rosenzweig, C.

    2010-12-01

    New York City and New York State are leaders in adaptation in the U.S. In 2008 Mayor Bloomberg convened the NYC Climate Change Adaptation Task Force and the New York City Panel on Climate Change (NPCC). Also in 2008, the New York State Energy Research and Development Authority (NYSERDA) initiated the Integrated Assessment for Effective Climate Change Adaptation Strategies (ClimAID), to provide New York State decision-makers with cutting-edge information on its vulnerability to climate change and to facilitate the development of adaptation strategies informed by both local experience and scientific knowledge. The two efforts are working together to develop effective adaptation strategies across multiple jurisdictions. The New York Task Force consists of approximate 40 city, state, and federal agencies, regional public authorities, and private companies that operate, maintain, or regulate critical infrastructure in the region. The NPCC consisted of climate change and impacts scientists, and legal, insurance, and risk-management experts and served as the technical advisory body for the Mayor and the Task Force on issues related to climate change, impacts, and adaptation. In its 2010 report, the NPCC recommended adoption of a risk-based approach to climate change; creation of a monitoring program to track and analyze key climate change factors, impacts, and adaptation indicators; review of relevant standards and codes; inclusion of multiple layers of government and a wide range of public and private stakeholder experts to build buy-in; and formation of crucial partnerships for development of coordinated adaptation strategies. The task now is for these partnerships to create pilot programs that move adaptation from the planning phase to implementation; urban areas can provide critical ‘test-beds’ for such efforts.

  6. Local adaptation and the evolution of phenotypic plasticity in Trinidadian guppies (Poecilia reticulata).

    PubMed

    Torres-Dowdall, Julián; Handelsman, Corey A; Reznick, David N; Ghalambor, Cameron K

    2012-11-01

    Divergent selection pressures across environments can result in phenotypic differentiation that is due to local adaptation, phenotypic plasticity, or both. Trinidadian guppies exhibit local adaptation to the presence or absence of predators, but the degree to which predator-induced plasticity contributes to population differentiation is less clear. We conducted common garden experiments on guppies obtained from two drainages containing populations adapted to high- and low-predation environments. We reared full-siblings from all populations in treatments simulating the presumed ancestral (predator cues present) and derived (predator cues absent) conditions and measured water column use, head morphology, and size at maturity. When reared in presence of predator cues, all populations had phenotypes that were typical of a high-predation ecotype. However, when reared in the absence of predator cues, guppies from high- and low-predation regimes differed in head morphology and size at maturity; the qualitative nature of these differences corresponded to those that characterize adaptive phenotypes in high- versus low-predation environments. Thus, divergence in plasticity is due to phenotypic differences between high- and low-predation populations when reared in the absence of predator cues. These results suggest that plasticity might initially play an important role during colonization of novel environments, and then evolve as a by-product of adaptation to the derived environment. PMID:23106708

  7. On the evolutionary interplay between dispersal and local adaptation in heterogeneous environments.

    PubMed

    Berdahl, Andrew; Torney, Colin J; Schertzer, Emmanuel; Levin, Simon A

    2015-06-01

    Dispersal, whether in the form of a dandelion seed drifting on the breeze, or a salmon migrating upstream to breed in a nonnatal stream, transports genes between locations. At these locations, local adaptation modifies the gene frequencies so their carriers are better suited to particular conditions, be those of newly disturbed soil or a quiet river pool. Both dispersal and local adaptation are major drivers of population structure; however, in general, their respective roles are not independent and the two may often be at odds with one another evolutionarily, each one exhibiting negative feedback on the evolution of the other. Here, we investigate their joint evolution within a simple, discrete-time, metapopulation model. Depending on environmental conditions, their evolutionary interplay leads to either a monomorphic population of highly dispersing generalists or a collection of rarely dispersing, locally adapted, polymorphic sub-populations, each adapted to a particular habitat type. A critical value of environmental heterogeneity divides these two selection regimes and the nature of the transition between them is determined by the level of kin competition. When kin competition is low, at the transition we observe discontinuities, bistability, and hysteresis in the evolved strategies; however, when high, kin competition moderates the evolutionary feedback and the transition is smooth. PMID:25908012

  8. Complementary effect of natural and sexual selection against immigrants maintains differentiation between locally adapted fish

    NASA Astrophysics Data System (ADS)

    Plath, Martin; Riesch, Rüdiger; Oranth, Alexandra; Dzienko, Justina; Karau, Nora; Schießl, Angela; Stadler, Stefan; Wigh, Adriana; Zimmer, Claudia; Arias-Rodriguez, Lenin; Schlupp, Ingo; Tobler, Michael

    2010-08-01

    Adaptation to ecologically heterogeneous environments can drive speciation. But what mechanisms maintain reproductive isolation among locally adapted populations? Using poeciliid fishes in a system with naturally occurring toxic hydrogen sulfide, we show that (a) fish from non-sulfidic sites ( Poecilia mexicana) show high mortality (95 %) after 24 h when exposed to the toxicant, while locally adapted fish from sulfidic sites ( Poecilia sulphuraria) experience low mortality (13 %) when transferred to non-sulfidic water. (b) Mate choice tests revealed that P. mexicana females exhibit a preference for conspecific males in non-sulfidic water, but not in sulfidic water, whereas P. sulphuraria females never showed a preference. Increased costs of mate choice in sulfidic, hypoxic water, and the lack of selection for reinforcement due to the low survival of P. mexicana may explain the absence of a preference in P. sulphuraria females. Taken together, our study may be the first to demonstrate independent—but complementary—effects of natural and sexual selection against immigrants maintaining differentiation between locally adapted fish populations.

  9. Development of a protocol to quantify local bone adaptation over space and time: Quantification of reproducibility.

    PubMed

    Lu, Yongtao; Boudiffa, Maya; Dall'Ara, Enrico; Bellantuono, Ilaria; Viceconti, Marco

    2016-07-01

    In vivo micro-computed tomography (µCT) scanning of small rodents is a powerful method for longitudinal monitoring of bone adaptation. However, the life-time bone growth in small rodents makes it a challenge to quantify local bone adaptation. Therefore, the aim of this study was to develop a protocol, which can take into account large bone growth, to quantify local bone adaptations over space and time. The entire right tibiae of eight 14-week-old C57BL/6J female mice were consecutively scanned four times in an in vivo µCT scanner using a nominal isotropic image voxel size of 10.4µm. The repeated scan image datasets were aligned to the corresponding baseline (first) scan image dataset using rigid registration. 80% of tibia length (starting from the endpoint of the proximal growth plate) was selected as the volume of interest and partitioned into 40 regions along the tibial long axis (10 divisions) and in the cross-section (4 sectors). The bone mineral content (BMC) was used to quantify bone adaptation and was calculated in each region. All local BMCs have precision errors (PE%CV) of less than 3.5% (24 out of 40 regions have PE%CV of less than 2%), least significant changes (LSCs) of less than 3.8%, and 38 out of 40 regions have intraclass correlation coefficients (ICCs) of over 0.8. The proposed protocol allows to quantify local bone adaptations over an entire tibia in longitudinal studies, with a high reproducibility, an essential requirement to reduce the number of animals to achieve the necessary statistical power. PMID:27262181

  10. Three-dimensional local grid refinement for block-centered finite-difference groundwater models using iteratively coupled shared nodes: a new method of interpolation and analysis of errors

    NASA Astrophysics Data System (ADS)

    Mehl, Steffen; Hill, Mary C.

    2004-09-01

    This paper describes work that extends to three dimensions the two-dimensional local-grid refinement method for block-centered finite-difference groundwater models of Mehl and Hill [Development and evaluation of a local grid refinement method for block-centered finite-difference groundwater models using shared nodes. Adv Water Resour 2002;25(5):497-511]. In this approach, the (parent) finite-difference grid is discretized more finely within a (child) sub-region. The grid refinement method sequentially solves each grid and uses specified flux (parent) and specified head (child) boundary conditions to couple the grids. Iteration achieves convergence between heads and fluxes of both grids. Of most concern is how to interpolate heads onto the boundary of the child grid such that the physics of the parent-grid flow is retained in three dimensions. We develop a new two-step, "cage-shell" interpolation method based on the solution of the flow equation on the boundary of the child between nodes shared with the parent grid. Error analysis using a test case indicates that the shared-node local grid refinement method with cage-shell boundary head interpolation is accurate and robust, and the resulting code is used to investigate three-dimensional local grid refinement of stream-aquifer interactions. Results reveal that (1) the parent and child grids interact to shift the true head and flux solution to a different solution where the heads and fluxes of both grids are in equilibrium, (2) the locally refined model provided a solution for both heads and fluxes in the region of the refinement that was more accurate than a model without refinement only if iterations are performed so that both heads and fluxes are in equilibrium, and (3) the accuracy of the coupling is limited by the parent-grid size—a coarse parent grid limits correct representation of the hydraulics in the feedback from the child grid.

  11. Three-dimensional local grid refinement for block-centered finite-difference groundwater models using iteratively coupled shared nodes: A new method of interpolation and analysis of errors

    USGS Publications Warehouse

    Mehl, S.; Hill, M.C.

    2004-01-01

    This paper describes work that extends to three dimensions the two-dimensional local-grid refinement method for block-centered finite-difference groundwater models of Mehl and Hill [Development and evaluation of a local grid refinement method for block-centered finite-difference groundwater models using shared nodes. Adv Water Resour 2002;25(5):497-511]. In this approach, the (parent) finite-difference grid is discretized more finely within a (child) sub-region. The grid refinement method sequentially solves each grid and uses specified flux (parent) and specified head (child) boundary conditions to couple the grids. Iteration achieves convergence between heads and fluxes of both grids. Of most concern is how to interpolate heads onto the boundary of the child grid such that the physics of the parent-grid flow is retained in three dimensions. We develop a new two-step, "cage-shell" interpolation method based on the solution of the flow equation on the boundary of the child between nodes shared with the parent grid. Error analysis using a test case indicates that the shared-node local grid refinement method with cage-shell boundary head interpolation is accurate and robust, and the resulting code is used to investigate three-dimensional local grid refinement of stream-aquifer interactions. Results reveal that (1) the parent and child grids interact to shift the true head and flux solution to a different solution where the heads and fluxes of both grids are in equilibrium, (2) the locally refined model provided a solution for both heads and fluxes in the region of the refinement that was more accurate than a model without refinement only if iterations are performed so that both heads and fluxes are in equilibrium, and (3) the accuracy of the coupling is limited by the parent-grid size - A coarse parent grid limits correct representation of the hydraulics in the feedback from the child grid.

  12. On the importance of interpolation schemes for albedo data from local to global grid

    NASA Astrophysics Data System (ADS)

    Preuschmann, Swantje; Jacob, Daniela; Löw, Alexander

    2013-04-01

    Surface albedo has a key role in Earth's radiation balance. As vegetation cover is influencing the albedo of solid surfaces, it is clear that land cover changes are leading to changes in the radiation balance and further are influencing the whole Earth's energy budget. It is obvious, that a forested area reflects sunlight differently compared to a sparsely vegetated area of shrubs. Different studies have shown, that certain land cover types (even compounds) have a characteristic annual cycle of the albedo (Moody et al. 2005 and Preuschmann, 2012). An annual cycle for one land cover type might vary in a year about 2%. The difference of the surface albedo of a forested area in summer to an agricultural area at the same time is only about 0.5%. A major question in climate modelling under future conditions is to analyse the impact of land cover changes onto climate. Nevertheless for different reasons it is not easy to describe surface albedo changes due to land cover changes within a climate model. One reason is that differences in the albedo of different surfaces are comparatively small. Another reason is based in the spatial resolution of a climate model. Climate models are operating on grids with horizontal resolutions of 10x10 km² for regional models up to about 200x200 km² for global models with a spectral resolution of T63. This means, that spatial (and also temporal) mean values of surface albedo are taken into account. Therefore one grid box of a climate model is representing a composition of different surface albedos. For model validation, it is of interest to compare the modelled albedo data with observed albedo data, but a comparison is not as trivial as it looks in the first sight. One problematic is the necessity of comparing different data types in the same horizontal and temporal resolution. Commonly used satellite based albedo data are available in 0.05° horizontal resolution, which is about 5 km at the equator, for several-day means and monthly

  13. Unstructured grids on SIMD torus machines

    NASA Technical Reports Server (NTRS)

    Bjorstad, Petter E.; Schreiber, Robert

    1994-01-01

    Unstructured grids lead to unstructured communication on distributed memory parallel computers, a problem that has been considered difficult. Here, we consider adaptive, offline communication routing for a SIMD processor grid. Our approach is empirical. We use large data sets drawn from supercomputing applications instead of an analytic model of communication load. The chief contribution of this paper is an experimental demonstration of the effectiveness of certain routing heuristics. Our routing algorithm is adaptive, nonminimal, and is generally designed to exploit locality. We have a parallel implementation of the router, and we report on its performance.

  14. Adaptive triangular mesh generation

    NASA Technical Reports Server (NTRS)

    Erlebacher, G.; Eiseman, P. R.

    1984-01-01

    A general adaptive grid algorithm is developed on triangular grids. The adaptivity is provided by a combination of node addition, dynamic node connectivity and a simple node movement strategy. While the local restructuring process and the node addition mechanism take place in the physical plane, the nodes are displaced on a monitor surface, constructed from the salient features of the physical problem. An approximation to mean curvature detects changes in the direction of the monitor surface, and provides the pulling force on the nodes. Solutions to the axisymmetric Grad-Shafranov equation demonstrate the capturing, by triangles, of the plasma-vacuum interface in a free-boundary equilibrium configuration.

  15. Adaptive nonlocal means filtering based on local noise level for CT denoising

    SciTech Connect

    Li, Zhoubo; Trzasko, Joshua D.; Lake, David S.; Blezek, Daniel J.; Manduca, Armando; Yu, Lifeng; Fletcher, Joel G.; McCollough, Cynthia H.

    2014-01-15

    Purpose: To develop and evaluate an image-domain noise reduction method based on a modified nonlocal means (NLM) algorithm that is adaptive to local noise level of CT images and to implement this method in a time frame consistent with clinical workflow. Methods: A computationally efficient technique for local noise estimation directly from CT images was developed. A forward projection, based on a 2D fan-beam approximation, was used to generate the projection data, with a noise model incorporating the effects of the bowtie filter and automatic exposure control. The noise propagation from projection data to images was analytically derived. The analytical noise map was validated using repeated scans of a phantom. A 3D NLM denoising algorithm was modified to adapt its denoising strength locally based on this noise map. The performance of this adaptive NLM filter was evaluated in phantom studies in terms of in-plane and cross-plane high-contrast spatial resolution, noise power spectrum (NPS), subjective low-contrast spatial resolution using the American College of Radiology (ACR) accreditation phantom, and objective low-contrast spatial resolution using a channelized Hotelling model observer (CHO). Graphical processing units (GPU) implementation of this noise map calculation and the adaptive NLM filtering were developed to meet demands of clinical workflow. Adaptive NLM was piloted on lower dose scans in clinical practice. Results: The local noise level estimation matches the noise distribution determined from multiple repetitive scans of a phantom, demonstrated by small variations in the ratio map between the analytical noise map and the one calculated from repeated scans. The phantom studies demonstrated that the adaptive NLM filter can reduce noise substantially without degrading the high-contrast spatial resolution, as illustrated by modulation transfer function and slice sensitivity profile results. The NPS results show that adaptive NLM denoising preserves the

  16. Mycorrhizal symbiosis and local adaptation in Aster amellus: a field transplant experiment.

    PubMed

    Pánková, Hana; Raabová, Jana; Münzbergová, Zuzana

    2014-01-01

    Many plant populations have adapted to local soil conditions. However, the role of arbuscular mycorrhizal fungi is often overlooked in this context. Only a few studies have used reciprocal transplant experiments to study the relationships between soil conditions, mycorrhizal colonisation and plant growth. Furthermore, most of the studies were conducted under controlled greenhouse conditions. However, long-term field experiments can provide more realistic insights into this issue. We conducted a five-year field reciprocal transplant experiment to study the relationships between soil conditions, arbuscular mycorrhizal fungi and plant growth in the obligate mycotrophic herb Aster amellus. We conducted this study in two regions in the Czech Republic that differ significantly in their soil nutrient content, namely Czech Karst (region K) and Ceske Stredohori (region S). Plants that originated from region S had significantly higher mycorrhizal colonisation than plants from region K, indicating that the percentage of mycorrhizal colonisation has a genetic basis. We found no evidence of local adaptation in Aster amellus. Instead, plants from region S outperformed the plants from region K in both target regions. Similarly, plants from region S showed more mycorrhizal colonisation in all cases, which was likely driven by the lower nutrient content in the soil from that region. Thus, plant aboveground biomass and mycorrhizal colonisation exhibited corresponding differences between the two target regions and regions of origin. Higher mycorrhizal colonisation in the plants from region with lower soil nutrient content (region S) in both target regions indicates that mycorrhizal colonisation is an adaptive trait. However, lower aboveground biomass in the plants with lower mycorrhizal colonisation suggests that the plants from region K are in fact maladapted by their low inherent mycorrhizal colonization. We conclude that including mycorrhizal symbiosis in local adaptation studies

  17. Does selection by resistant hosts trigger local adaptation in plant-pathogen systems?

    PubMed

    Montarry, J; Corbiere, R; Lesueur, S; Glais, I; Andrivon, D

    2006-03-01

    Understanding the consequences of selection by host resistance on pathogen population structure provides useful insights into the dynamics of host-parasite co-evolution processes and is crucial for effective disease management through resistant cultivars. We tested general vs. local population adaptation to host cultivars, by characterizing a French collection of Phytophthora infestans (the causal organism of potato late blight) sampled during two consecutive years on cultivars exhibiting various levels of resistance. Local populations were structured by the host for virulence (qualitative pathogenicity) but also for aggressiveness (quantitative pathogenicity). All populations had a low genotypic diversity for amplified fragment length polymorphisms (AFLPs), and presumably consisted of a few closely related clonal lineages. No correlation was detected between pathogenicity traits and AFLP genotypes. The data support the hypothesis of general adaptation for aggressiveness, to which directional selection for virulence is superimposed when race-specific resistance is introduced. PMID:16599928

  18. Finite-difference modeling with variable grid-size and adaptive time-step in porous media

    NASA Astrophysics Data System (ADS)

    Liu, Xinxin; Yin, Xingyao; Wu, Guochen

    2014-04-01

    Forward modeling of elastic wave propagation in porous media has great importance for understanding and interpreting the influences of rock properties on characteristics of seismic wavefield. However, the finite-difference forward-modeling method is usually implemented with global spatial grid-size and time-step; it consumes large amounts of computational cost when small-scaled oil/gas-bearing structures or large velocity-contrast exist underground. To overcome this handicap, combined with variable grid-size and time-step, this paper developed a staggered-grid finite-difference scheme for elastic wave modeling in porous media. Variable finite-difference coefficients and wavefield interpolation were used to realize the transition of wave propagation between regions of different grid-size. The accuracy and efficiency of the algorithm were shown by numerical examples. The proposed method is advanced with low computational cost in elastic wave simulation for heterogeneous oil/gas reservoirs.

  19. FALCON: A method for flexible adaptation of local coordinates of nuclei.

    PubMed

    König, Carolin; Hansen, Mads Bøttger; Godtliebsen, Ian H; Christiansen, Ove

    2016-02-21

    We present a flexible scheme for calculating vibrational rectilinear coordinates with well-defined strict locality on a certain set of atoms. Introducing a method for Flexible Adaption of Local COordinates of Nuclei (FALCON) we show how vibrational subspaces can be "grown" in an adaptive manner. Subspace Hessian matrices are set up and used to calculate and analyze vibrational modes and frequencies. FALCON coordinates can more generally be used to construct vibrational coordinates for describing local and (semi-local) interacting modes with desired features. For instance, spatially local vibrations can be approximately described as internal motion within only a group of atoms and delocalized modes can be approximately expressed as relative motions of rigid groups of atoms. The FALCON method can support efficiency in the calculation and analysis of vibrational coordinates and energies in the context of harmonic and anharmonic calculations. The features of this method are demonstrated on a few small molecules, i.e., formylglycine, coumarin, and dimethylether as well as for the amide-I band and low-frequency modes of alanine oligomers and alpha conotoxin. PMID:26896977

  20. Similarities in butterfly emergence dates among populations suggest local adaptation to climate.

    PubMed

    Roy, David B; Oliver, Tom H; Botham, Marc S; Beckmann, Bjorn; Brereton, Tom; Dennis, Roger L H; Harrower, Colin; Phillimore, Albert B; Thomas, Jeremy A

    2015-09-01

    Phenology shifts are the most widely cited examples of the biological impact of climate change, yet there are few assessments of potential effects on the fitness of individual organisms or the persistence of populations. Despite extensive evidence of climate-driven advances in phenological events over recent decades, comparable patterns across species' geographic ranges have seldom been described. Even fewer studies have quantified concurrent spatial gradients and temporal trends between phenology and climate. Here we analyse a large data set (~129 000 phenology measures) over 37 years across the UK to provide the first phylogenetic comparative analysis of the relative roles of plasticity and local adaptation in generating spatial and temporal patterns in butterfly mean flight dates. Although populations of all species exhibit a plastic response to temperature, with adult emergence dates earlier in warmer years by an average of 6.4 days per °C, among-population differences are significantly lower on average, at 4.3 days per °C. Emergence dates of most species are more synchronised over their geographic range than is predicted by their relationship between mean flight date and temperature over time, suggesting local adaptation. Biological traits of species only weakly explained the variation in differences between space-temperature and time-temperature phenological responses, suggesting that multiple mechanisms may operate to maintain local adaptation. As niche models assume constant relationships between occurrence and environmental conditions across a species' entire range, an important implication of the temperature-mediated local adaptation detected here is that populations of insects are much more sensitive to future climate changes than current projections suggest. PMID:26390228

  1. Local genetic adaptation generates latitude-specific effects of warming on predator-prey interactions.

    PubMed

    De Block, Marjan; Pauwels, Kevin; Van Den Broeck, Maarten; De Meester, Luc; Stoks, Robby

    2013-03-01

    Temperature effects on predator-prey interactions are fundamental to better understand the effects of global warming. Previous studies never considered local adaptation of both predators and prey at different latitudes, and ignored the novel population combinations of the same predator-prey species system that may arise because of northward dispersal. We set up a common garden warming experiment to study predator-prey interactions between Ischnura elegans damselfly predators and Daphnia magna zooplankton prey from three source latitudes spanning >1500 km. Damselfly foraging rates showed thermal plasticity and strong latitudinal differences consistent with adaptation to local time constraints. Relative survival was higher at 24 °C than at 20 °C in southern Daphnia and higher at 20 °C than at 24 °C, in northern Daphnia indicating local thermal adaptation of the Daphnia prey. Yet, this thermal advantage disappeared when they were confronted with the damselfly predators of the same latitude, reflecting also a signal of local thermal adaptation in the damselfly predators. Our results further suggest the invasion success of northward moving predators as well as prey to be latitude-specific. We advocate the novel common garden experimental approach using predators and prey obtained from natural temperature gradients spanning the predicted temperature increase in the northern populations as a powerful approach to gain mechanistic insights into how community modules will be affected by global warming. It can be used as a space-for-time substitution to inform how predator-prey interaction may gradually evolve to long-term warming. PMID:23504827

  2. Demographic History, Population Structure, and Local Adaptation in Alpine Populations of Cardamine impatiens and Cardamine resedifolia

    PubMed Central

    Ometto, Lino; Li, Mingai; Bresadola, Luisa; Barbaro, Enrico; Neteler, Markus; Varotto, Claudio

    2015-01-01

    Species evolution depends on numerous and distinct forces, including demography and natural selection. For example, local adaptation and population structure affect the evolutionary history of species living along environmental clines. This is particularly relevant in plants, which are often characterized by limited dispersal ability and the need to respond to abiotic and biotic stress factors specific to the local environment. Here we study the demographic history and the possible existence of local adaptation in two related species of Brassicaceae, Cardamine impatiens and Cardamine resedifolia, which occupy separate habitats along the elevation gradient. Previous genome-wide analyses revealed the occurrence of distinct selective pressures in the two species, with genes involved in cold response evolving particularly fast in C. resedifolia. In this study we surveyed patterns of molecular evolution and genetic variability in a set of 19 genes, including neutral and candidate genes involved in cold response, across 10 populations each of C. resedifolia and C. impatiens from the Italian Alps (Trentino). We inferred the population structure and demographic history of the two species, and tested the occurrence of signatures of local adaptation in these genes. The results indicate that, despite a slightly higher population differentiation in C. resedifolia than in C. impatiens, both species are only weakly structured and that populations sampled at high altitude experience less gene flow than low-altitude ones. None of the genes showed signatures of positive selection, suggesting that they do not seem to play relevant roles in the current evolutionary processes of adaptation to alpine environments of these species. PMID:25933225

  3. Local adaptation despite high gene flow in the waterfall-climbing Hawaiian goby, Sicyopterus stimpsoni.

    PubMed

    Moody, K N; Hunter, S N; Childress, M J; Blob, R W; Schoenfuss, H L; Blum, M J; Ptacek, M B

    2015-02-01

    Environmental heterogeneity can promote the emergence of locally adapted phenotypes among subpopulations of a species, whereas gene flow can result in phenotypic and genotypic homogenization. For organisms like amphidromous fishes that change habitats during their life history, the balance between selection and migration can shift through ontogeny, making the likelihood of local adaptation difficult to predict. In Hawaiian waterfall-climbing gobies, it has been hypothesized that larval mixing during oceanic dispersal counters local adaptation to contrasting topographic features of streams, like slope gradient, that can select for predator avoidance or climbing ability in juvenile recruits. To test this hypothesis, we used morphological traits and neutral genetic markers to compare phenotypic and genotypic distributions in recruiting juveniles and adult subpopulations of the waterfall-climbing amphidromous goby, Sicyopterus stimpsoni, from the islands of Hawai'i and Kaua'i. We found that body shape is significantly different between adult subpopulations from streams with contrasting slopes and that trait divergence in recruiting juveniles tracked stream topography more so than morphological measures of adult subpopulation differentiation. Although no evidence of population genetic differentiation was observed among adult subpopulations, we observed low but significant levels of spatially and temporally variable genetic differentiation among juvenile cohorts, which correlated with morphological divergence. Such a pattern of genetic differentiation is consistent with chaotic genetic patchiness arising from variable sources of recruits to different streams. Thus, at least in S. stimpsoni, the combination of variation in settlement cohorts in space and time coupled with strong postsettlement selection on juveniles as they migrate upstream to adult habitats provides the opportunity for morphological adaptation to local stream environments despite high gene flow. PMID

  4. Ecological costs on local adaptation of an insect herbivore imposed by host plants and enemies.

    PubMed

    Zovi, Daniel; Stastny, Michael; Battisti, Andrea; Larsson, Stig

    2008-05-01

    Herbivore populations may become adapted to the defenses of their local hosts, but the traits that maximize host exploitation may also carry ecological costs. We investigated the patterns and costs of local adaptation in the pine processionary moth, Thaumetopoea pityocampa, to its host plants, Pinus nigra and P. sylvestris. The two hosts differ in needle toughness, a major feeding impediment for leaf-eating insects. We observed a west-to-east gradient of increasing progeny size in the Italian Alps, matching the pattern in toughness of their respective local host plant. Eastern populations that feed on the native P. nigra with tough needles had larger eggs, and neonate larvae with larger head capsules, than western populations that feed on the native P. sylvestris and the introduced P. nigra with softer foliage. In a reciprocal transfer experiment that involved the eastern-most and the western-most populations of T. pityocampa from this region, and excluded natural enemies, we found evidence for local adaptation to the host plant. Specifically, larvae from the western population only performed well when raised on their local hosts with soft needles, and they suffered near-complete mortality on the tough foliage at the eastern site. In contrast, larvae from the eastern population survived equally well at both sites. Local adaptation involved a trade-off between progeny size and the number of offspring. We hypothesized that an additional cost, imposed by natural enemies, may be associated with increased egg size: we also observed a west-to-east gradient of increased egg parasitism. We tested this hypothesis in a common garden by exposing eggs of both populations to parasitism by two native egg parasitoids, Ooencyrtus pityocampae and Baryscapus servadeii. The eastern population suffered a higher level of parasitoid attack by O. pityocampae than the western population, and performance of hatched adults of both parasitoids was enhanced in large eggs. Thus, increased

  5. Local adaptive approach toward segmentation of microscopic images of activated sludge flocs

    NASA Astrophysics Data System (ADS)

    Khan, Muhammad Burhan; Nisar, Humaira; Ng, Choon Aun; Lo, Po Kim; Yap, Vooi Voon

    2015-11-01

    Activated sludge process is a widely used method to treat domestic and industrial effluents. The conditions of activated sludge wastewater treatment plant (AS-WWTP) are related to the morphological properties of flocs (microbial aggregates) and filaments, and are required to be monitored for normal operation of the plant. Image processing and analysis is a potential time-efficient monitoring tool for AS-WWTPs. Local adaptive segmentation algorithms are proposed for bright-field microscopic images of activated sludge flocs. Two basic modules are suggested for Otsu thresholding-based local adaptive algorithms with irregular illumination compensation. The performance of the algorithms has been compared with state-of-the-art local adaptive algorithms of Sauvola, Bradley, Feng, and c-mean. The comparisons are done using a number of region- and nonregion-based metrics at different microscopic magnifications and quantification of flocs. The performance metrics show that the proposed algorithms performed better and, in some cases, were comparable to the state-of the-art algorithms. The performance metrics were also assessed subjectively for their suitability for segmentations of activated sludge images. The region-based metrics such as false negative ratio, sensitivity, and negative predictive value gave inconsistent results as compared to other segmentation assessment metrics.

  6. Testing Local Adaptation in a Natural Great Tit-Malaria System: An Experimental Approach

    PubMed Central

    Jenkins, Tania; Delhaye, Jessica; Christe, Philippe

    2015-01-01

    Finding out whether Plasmodium spp. are coevolving with their vertebrate hosts is of both theoretical and applied interest and can influence our understanding of the effects and dynamics of malaria infection. In this study, we tested for local adaptation as a signature of coevolution between malaria blood parasites, Plasmodium spp. and its host, the great tit, Parus major. We conducted a reciprocal transplant experiment of birds in the field, where we exposed birds from two populations to Plasmodium parasites. This experimental set-up also provided a unique opportunity to study the natural history of malaria infection in the wild and to assess the effects of primary malaria infection on juvenile birds. We present three main findings: i) there was no support for local adaptation; ii) there was a male-biased infection rate; iii) infection occurred towards the end of the summer and differed between sites. There were also site-specific effects of malaria infection on the hosts. Taken together, we present one of the few experimental studies of parasite-host local adaptation in a natural malaria system, and our results shed light on the effects of avian malaria infection in the wild. PMID:26555892

  7. Genome scans for detecting footprints of local adaptation using a Bayesian factor model.

    PubMed

    Duforet-Frebourg, Nicolas; Bazin, Eric; Blum, Michael G B

    2014-09-01

    There is a considerable impetus in population genomics to pinpoint loci involved in local adaptation. A powerful approach to find genomic regions subject to local adaptation is to genotype numerous molecular markers and look for outlier loci. One of the most common approaches for selection scans is based on statistics that measure population differentiation such as FST. However, there are important caveats with approaches related to FST because they require grouping individuals into populations and they additionally assume a particular model of population structure. Here, we implement a more flexible individual-based approach based on Bayesian factor models. Factor models capture population structure with latent variables called factors, which can describe clustering of individuals into populations or isolation-by-distance patterns. Using hierarchical Bayesian modeling, we both infer population structure and identify outlier loci that are candidates for local adaptation. In order to identify outlier loci, the hierarchical factor model searches for loci that are atypically related to population structure as measured by the latent factors. In a model of population divergence, we show that it can achieve a 2-fold or more reduction of false discovery rate compared with the software BayeScan or with an FST approach. We show that our software can handle large data sets by analyzing the single nucleotide polymorphisms of the Human Genome Diversity Project. The Bayesian factor model is implemented in the open-source PCAdapt software. PMID:24899666

  8. Adaptive non-local means method for speckle reduction in ultrasound images

    NASA Astrophysics Data System (ADS)

    Ai, Ling; Ding, Mingyue; Zhang, Xuming

    2016-03-01

    Noise removal is a crucial step to enhance the quality of ultrasound images. However, some existing despeckling methods cannot ensure satisfactory restoration performance. In this paper, an adaptive non-local means (ANLM) filter is proposed for speckle noise reduction in ultrasound images. The distinctive property of the proposed method lies in that the decay parameter will not take the fixed value for the whole image but adapt itself to the variation of the local features in the ultrasound images. In the proposed method, the pre-filtered image will be obtained using the traditional NLM method. Based on the pre-filtered result, the local gradient will be computed and it will be utilized to determine the decay parameter adaptively for each image pixel. The final restored image will be produced by the ANLM method using the obtained decay parameters. Simulations on the synthetic image show that the proposed method can deliver sufficient speckle reduction while preserving image details very well and it outperforms the state-of-the-art despeckling filters in terms of peak signal-to-noise ratio (PSNR) and structural similarity (SSIM). Experiments on the clinical ultrasound image further demonstrate the practicality and advantage of the proposed method over the compared filtering methods.

  9. A conservative finite volume scheme with time-accurate local time stepping for scalar transport on unstructured grids

    NASA Astrophysics Data System (ADS)

    Cavalcanti, José Rafael; Dumbser, Michael; Motta-Marques, David da; Fragoso Junior, Carlos Ruberto

    2015-12-01

    In this article we propose a new conservative high resolution TVD (total variation diminishing) finite volume scheme with time-accurate local time stepping (LTS) on unstructured grids for the solution of scalar transport problems, which are typical in the context of water quality simulations. To keep the presentation of the new method as simple as possible, the algorithm is only derived in two space dimensions and for purely convective transport problems, hence neglecting diffusion and reaction terms. The new numerical method for the solution of the scalar transport is directly coupled to the hydrodynamic model of Casulli and Walters (2000) that provides the dynamics of the free surface and the velocity vector field based on a semi-implicit discretization of the shallow water equations. Wetting and drying is handled rigorously by the nonlinear algorithm proposed by Casulli (2009). The new time-accurate LTS algorithm allows a different time step size for each element of the unstructured grid, based on an element-local Courant-Friedrichs-Lewy (CFL) stability condition. The proposed method does not need any synchronization between different time steps of different elements and is by construction locally and globally conservative. The LTS scheme is based on a piecewise linear polynomial reconstruction in space-time using the MUSCL-Hancock method, to obtain second order of accuracy in both space and time. The new algorithm is first validated on some classical test cases for pure advection problems, for which exact solutions are known. In all cases we obtain a very good level of accuracy, showing also numerical convergence results; we furthermore confirm mass conservation up to machine precision and observe an improved computational efficiency compared to a standard second order TVD scheme for scalar transport with global time stepping (GTS). Then, the new LTS method is applied to some more complex problems, where the new scalar transport scheme has also been coupled to

  10. Computational Aerothermodynamic Simulation Issues on Unstructured Grids

    NASA Technical Reports Server (NTRS)

    Gnoffo, Peter A.; White, Jeffery A.

    2004-01-01

    The synthesis of physical models for gas chemistry and turbulence from the structured grid codes LAURA and VULCAN into the unstructured grid code FUN3D is described. A directionally Symmetric, Total Variation Diminishing (STVD) algorithm and an entropy fix (eigenvalue limiter) keyed to local cell Reynolds number are introduced to improve solution quality for hypersonic aeroheating applications. A simple grid-adaptation procedure is incorporated within the flow solver. Simulations of flow over an ellipsoid (perfect gas, inviscid), Shuttle Orbiter (viscous, chemical nonequilibrium) and comparisons to the structured grid solvers LAURA (cylinder, Shuttle Orbiter) and VULCAN (flat plate) are presented to show current capabilities. The quality of heating in 3D stagnation regions is very sensitive to algorithm options in general, high aspect ratio tetrahedral elements complicate the simulation of high Reynolds number, viscous flow as compared to locally structured meshes aligned with the flow.

  11. A novel approach for SEMG signal classification with adaptive local binary patterns.

    PubMed

    Ertuğrul, Ömer Faruk; Kaya, Yılmaz; Tekin, Ramazan

    2016-07-01

    Feature extraction plays a major role in the pattern recognition process, and this paper presents a novel feature extraction approach, adaptive local binary pattern (aLBP). aLBP is built on the local binary pattern (LBP), which is an image processing method, and one-dimensional local binary pattern (1D-LBP). In LBP, each pixel is compared with its neighbors. Similarly, in 1D-LBP, each data in the raw is judged against its neighbors. 1D-LBP extracts feature based on local changes in the signal. Therefore, it has high a potential to be employed in medical purposes. Since, each action or abnormality, which is recorded in SEMG signals, has its own pattern, and via the 1D-LBP these (hidden) patterns may be detected. But, the positions of the neighbors in 1D-LBP are constant depending on the position of the data in the raw. Also, both LBP and 1D-LBP are very sensitive to noise. Therefore, its capacity in detecting hidden patterns is limited. To overcome these drawbacks, aLBP was proposed. In aLBP, the positions of the neighbors and their values can be assigned adaptively via the down-sampling and the smoothing coefficients. Therefore, the potential to detect (hidden) patterns, which may express an illness or an action, is really increased. To validate the proposed feature extraction approach, two different datasets were employed. Achieved accuracies by the proposed approach were higher than obtained results by employed popular feature extraction approaches and the reported results in the literature. Obtained accuracy results were brought out that the proposed method can be employed to investigate SEMG signals. In summary, this work attempts to develop an adaptive feature extraction scheme that can be utilized for extracting features from local changes in different categories of time-varying signals. PMID:26718556

  12. Salinity Is an Agent of Divergent Selection Driving Local Adaptation of Arabidopsis to Coastal Habitats1[OPEN

    PubMed Central

    Teres, Joana; Bomblies, Kirsten; Douglas, Alex; Salt, David E.

    2015-01-01

    Understanding the molecular mechanism of adaptive evolution in plants provides insights into the selective forces driving adaptation and the genetic basis of adaptive traits with agricultural value. The genomic resources available for Arabidopsis (Arabidopsis thaliana) make it well suited to the rapid molecular dissection of adaptive processes. Although numerous potentially adaptive loci have been identified in Arabidopsis, the consequences of divergent selection and migration (both important aspects of the process of local adaptation) for Arabidopsis are not well understood. Here, we use a multiyear field-based reciprocal transplant experiment to detect local populations of Arabidopsis composed of multiple small stands of plants (demes) that are locally adapted to the coast and adjacent inland habitats in northeastern Spain. We identify fitness tradeoffs between plants from these different habitats when grown together in inland and coastal common gardens and also, under controlled conditions in soil excavated from coastal and inland sites. Plants from the coastal habitat also outperform those from inland when grown under high salinity, indicating local adaptation to soil salinity. Sodium can be toxic to plants, and we find its concentration to be elevated in soil and plants sampled at the coast. We conclude that the local adaptation that we observe between adjacent coastal and inland populations is caused by ongoing divergent selection driven by the differential salinity between coastal and inland soils. PMID:26034264

  13. Medical image classification using spatial adjacent histogram based on adaptive local binary patterns.

    PubMed

    Liu, Dong; Wang, Shengsheng; Huang, Dezhi; Deng, Gang; Zeng, Fantao; Chen, Huiling

    2016-05-01

    Medical image recognition is an important task in both computer vision and computational biology. In the field of medical image classification, representing an image based on local binary patterns (LBP) descriptor has become popular. However, most existing LBP-based methods encode the binary patterns in a fixed neighborhood radius and ignore the spatial relationships among local patterns. The ignoring of the spatial relationships in the LBP will cause a poor performance in the process of capturing discriminative features for complex samples, such as medical images obtained by microscope. To address this problem, in this paper we propose a novel method to improve local binary patterns by assigning an adaptive neighborhood radius for each pixel. Based on these adaptive local binary patterns, we further propose a spatial adjacent histogram strategy to encode the micro-structures for image representation. An extensive set of evaluations are performed on four medical datasets which show that the proposed method significantly improves standard LBP and compares favorably with several other prevailing approaches. PMID:27058283

  14. Local stereo matching with adaptive shape support window based cost aggregation.

    PubMed

    Xu, Yafan; Zhao, Yan; Ji, Mengqi

    2014-10-10

    Cost aggregation is the most important step in a local stereo algorithm. In this work, a novel local stereo-matching algorithm with a cost-aggregation method based on adaptive shape support window (ASSW) is proposed. First, we compute the initial cost volume, which uses both absolute intensity difference and gradient similarity to measure dissimilarity. Second, we apply an ASSW-based cost-aggregation method to get the aggregated cost within the support window. There are two main parts: at first we construct a local support skeleton anchoring each pixel with four varying arm lengths decided on color similarity; as a result, the support window integral of multiple horizontal segments spanned by pixels in the neighboring vertical is established. Then we utilize extended implementation of guided filter to aggregate cost volume within the ASSW, which has better edge-preserving smoothing property than bilateral filter independent of the filtering kernel size. In this way, the number of bad pixels located in the incorrect depth regions can be effectively reduced through finding optimal support windows with an arbitrary shape and size adaptively. Finally, the initial disparity value of each pixel is selected using winner takes all optimization and post processing symmetrically, considering both the reference and the target image, is adopted. The experimental results demonstrate that the proposed algorithm achieves outstanding matching performance compared with other existing local algorithms on the Middlebury stereo benchmark, especially in depth discontinuities and piecewise smooth regions. PMID:25322396

  15. Using specific and adaptive arrangement of grid-type pilot in channel estimation for white-lightLED-based OFDM visible light communication system

    NASA Astrophysics Data System (ADS)

    Lin, Wan-Feng; Chow, Chi-Wai; Yeh, Chien-Hung

    2015-03-01

    Orthogonal frequency division multiplexing (OFDM) is a promising candidate for light emitting diode (LED)-based optical wireless communication (OWC); however, precise channel estimation is required for synchronization and equalization. In this work, we study and discover that the channel response of the white-lightLED-based OWC was smooth and stable. Hence we propose and demonstrate using a specific and adaptive arrangement of grid-type pilot scheme to estimate the LED OWC channel response. Experimental results show that our scheme can achieve better transmission performance and with some transmission capacity enhancement when compared with the method using training-symbol scheme (also called block-type pilot scheme).

  16. Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour.

    PubMed

    Frechin, Mathieu; Stoeger, Thomas; Daetwyler, Stephan; Gehin, Charlotte; Battich, Nico; Damm, Eva-Maria; Stergiou, Lilli; Riezman, Howard; Pelkmans, Lucas

    2015-07-01

    Cells sense the context in which they grow to adapt their phenotype and allow multicellular patterning by mechanisms of autocrine and paracrine signalling. However, patterns also form in cell populations exposed to the same signalling molecules and substratum, which often correlate with specific features of the population context of single cells, such as local cell crowding. Here we reveal a cell-intrinsic molecular mechanism that allows multicellular patterning without requiring specific communication between cells. It acts by sensing the local crowding of a single cell through its ability to spread and activate focal adhesion kinase (FAK, also known as PTK2), resulting in adaptation of genes controlling membrane homeostasis. In cells experiencing low crowding, FAK suppresses transcription of the ABC transporter A1 (ABCA1) by inhibiting FOXO3 and TAL1. Agent-based computational modelling and experimental confirmation identified membrane-based signalling and feedback control as crucial for the emergence of population patterns of ABCA1 expression, which adapts membrane lipid composition to cell crowding and affects multiple signalling activities, including the suppression of ABCA1 expression itself. The simple design of this cell-intrinsic system and its broad impact on the signalling state of mammalian single cells suggests a fundamental role for a tunable membrane lipid composition in collective cell behaviour. PMID:26009010

  17. Plant regeneration from seeds responds to phylogenetic relatedness and local adaptation in Mediterranean Romulea (Iridaceae) species.

    PubMed

    Carta, Angelino; Hanson, Sarah; Müller, Jonas V

    2016-06-01

    Seed germination is the most important transitional event between early stages in the life cycle of spermatophytes and understanding it is crucial to understand plant adaptation and evolution. However, so far seed germination of phylogenetically closely related species has been poorly investigated. To test the hypothises that phylogenetically related plant species have similar seed ecophysiological traits thereby reflecting certain habitat conditions as a result of local adaptation, we studied seed dormancy and germination in seven Mediterranean species in the genus Romulea (Iridaceae). Both the across-species model and the model accounting for shared evolutionary history showed that cool temperatures (≤ 15°C) were the main factor that promoted seed germination. The absence of embryo growth before radicle emergence is consistent with a prompt germination response at cool temperatures. The range of temperature conditions for germination became wider after a period of warm stratification, denoting a weak primary dormancy. Altogether these results indicate that the studied species exhibit a Mediterranean germination syndrome, but with species-specific germination requirements clustered in a way that follows the phylogenetic relatedness among those species. In addition, species with heavier seeds from humid habitats showed a wider range of conditions for germination at dispersal time than species from dry habitats possessing lighter seeds. We conclude that while phylogenetically related species showed very similar germination requirements, there are subtle ecologically meaningful differences, confirming the onset of adaptation to local ecological factors mediated by species relatedness. PMID:27516872

  18. No evidence for local adaptation of dengue viruses to mosquito vector populations in Thailand.

    PubMed

    Fansiri, Thanyalak; Pongsiri, Arissara; Klungthong, Chonticha; Ponlawat, Alongkot; Thaisomboonsuk, Butsaya; Jarman, Richard G; Scott, Thomas W; Lambrechts, Louis

    2016-04-01

    Despite their epidemiological importance, the evolutionary forces that shape the spatial structure of dengue virus genetic diversity are not fully understood. Fine-scale genetic structure of mosquito vector populations and evidence for genotype × genotype interactions between dengue viruses and their mosquito vectors are consistent with the hypothesis that the geographical distribution of dengue virus genetic diversity may reflect viral adaptation to local mosquito populations. To test this hypothesis, we measured vector competence in all sympatric and allopatric combinations of 14 low-passage dengue virus isolates and two wild-type populations of Aedes aegypti mosquitoes sampled in Bangkok and Kamphaeng Phet, two sites located about 300 km apart in Thailand. Despite significant genotype × genotype interactions, we found no evidence for superior vector competence in sympatric versus allopatric vector-virus combinations. Viral phylogenetic analysis revealed no geographical clustering of the 14 isolates, suggesting that high levels of viral migration (gene flow) in Thailand may counteract spatially heterogeneous natural selection. We conclude that it is unlikely that vector-mediated selection is a major driver of dengue virus adaptive evolution at the regional scale that we examined. Dengue virus local adaptation to mosquito vector populations could happen, however, in places or times that we did not test, or at a different geographical scale. PMID:27099625

  19. Genomic Analysis of Differentiation between Soil Types Reveals Candidate Genes for Local Adaptation in Arabidopsis lyrata

    PubMed Central

    Turner, Thomas L.; von Wettberg, Eric J.; Nuzhdin, Sergey V.

    2008-01-01

    Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low Ca∶Mg ratio in A. lyrata. PMID:18784841

  20. Multiple sites of adaptive plasticity in the owl's auditory localization pathway.

    PubMed

    DeBello, William M; Knudsen, Eric I

    2004-08-01

    In the midbrain auditory localization pathway of the barn owl, a map of auditory space is relayed from the external nucleus of the inferior colliculus (ICX) to the deep and intermediate layers of the optic tectum (OT) and from these layers to the superficial layers. Within the OT, the auditory space map aligns with a visual map of space. Raising young barn owls with a prismatic displacement of the visual field leads to progressive changes in auditory tuning in the OT that tend to realign the auditory space map with the prismatically displaced visual space map. The only known site of this adaptive plasticity is in the ICX, in which the auditory system first creates a map of space. In this study, we identified an additional site of plasticity in the OT. In owls that experienced prisms beginning late in the juvenile period, adaptive shifts in auditory tuning in the superficial layers of the OT exceeded the adaptive shifts that occurred in the deep layers of the OT or in the ICX. Anatomical results from these owls demonstrated that the topography of intrinsic OT connections was systematically altered in the adaptive direction. In juvenile owls, plasticity in the OT increased as plasticity in the ICX decreased. Because plasticity at both sites has been shown to decline substantially in adults, these results suggest that an age-dependent decrease in auditory map plasticity occurs first in the ICX and later at the higher level, in the OT. PMID:15295019

  1. The Effects of Climate Model Similarity on Local, Risk-Based Adaptation Planning

    NASA Astrophysics Data System (ADS)

    Steinschneider, S.; Brown, C. M.

    2014-12-01

    The climate science community has recently proposed techniques to develop probabilistic projections of climate change from ensemble climate model output. These methods provide a means to incorporate the formal concept of risk, i.e., the product of impact and probability, into long-term planning assessments for local systems under climate change. However, approaches for pdf development often assume that different climate models provide independent information for the estimation of probabilities, despite model similarities that stem from a common genealogy. Here we utilize an ensemble of projections from the Coupled Model Intercomparison Project Phase 5 (CMIP5) to develop probabilistic climate information, with and without an accounting of inter-model correlations, and use it to estimate climate-related risks to a local water utility in Colorado, U.S. We show that the tail risk of extreme climate changes in both mean precipitation and temperature is underestimated if model correlations are ignored. When coupled with impact models of the hydrology and infrastructure of the water utility, the underestimation of extreme climate changes substantially alters the quantification of risk for water supply shortages by mid-century. We argue that progress in climate change adaptation for local systems requires the recognition that there is less information in multi-model climate ensembles than previously thought. Importantly, adaptation decisions cannot be limited to the spread in one generation of climate models.

  2. Actin-Based Transport Adapts Polarity Domain Size to Local Cellular Curvature.

    PubMed

    Bonazzi, Daria; Haupt, Armin; Tanimoto, Hirokazu; Delacour, Delphine; Salort, Delphine; Minc, Nicolas

    2015-10-19

    Intracellular structures and organelles such as the nucleus, the centrosome, or the mitotic spindle typically scale their size to cell size [1]. Similarly, cortical polarity domains built around the active form of conserved Rho-GTPases, such as Cdc42p, exhibit widths that may range over two orders of magnitudes in cells with different sizes and shapes [2-6]. The establishment of such domains typically involves positive feedback loops based on reaction-diffusion and/or actin-mediated vesicle transport [3, 7, 8]. How these elements may adapt polarity domain size to cellular geometry is not known. Here, by tracking the width of successive oscillating Cdc42-GTP domains in fission yeast spores [9], we find that domain width scales with local cell-surface radii of curvature over an 8-fold range, independently of absolute cell volume, surface, or Cdc42-GTP concentration. This local scaling requires formin-nucleated cortical actin cables and the fusion of secretory vesicles transported along these cables with the membrane. These data suggest that reaction-diffusion may set a minimal domain size and that secretory vesicle transport along actin cables may dilute and extend polarity domains to adapt their size to local cell-surface curvature. This work reveals that actin networks may act as micrometric curvature sensors and uncovers a generic morphogenetic principle for how polarity domains define their size according to cell morphologies. PMID:26441355

  3. Local adaptation of stream communities to intraspecific variation in a terrestrial ecosystem subsidy.

    PubMed

    Jackrel, Sara L; Wootton, J Timothy

    2014-01-01

    Cross-ecosystem fluxes can intertwine otherwise disparate food webs, but the effects of biodiversity at the genotypic level on fluxes across ecosystems boundaries is not known. Fresh leaves, which vary in traits such as defensive compounds against terrestrial herbivores, drop off trees and enter streams, providing a vital resource for riverine organisms. We demonstrate substantial variation in decomposition rates among individual trees in four different rivers in the Olympic Peninsula of Washington State, USA. We show that locally derived red alder leaf litter decomposes on average 24% faster than red alder leaf litter introduced from other riparian zones. Within rivers, leaves downstream of their parent trees decompose nearly as quickly as leaves from local trees. Leaves upstream of the parent tree decomposed as slowly as leaves from trees growing alongside different rivers. Over time, aquatic decomposer communities have locally adapted to the specific trees supplying the riparian subsidies. In energy-limited environments, such as small shaded streams, consumers must be efficient foragers. Our results indicate that this pressure for efficiency has led to adaptation at a particularly fine scale. More broadly, these results illustrate how genetic diversity and the effects of selection in one ecosystem can indirectly shape the structure of other ecosystems through ecological fluxes across boundaries. PMID:24649644

  4. Gene-flow in a mosaic hybrid zone: is local introgression adaptive?

    PubMed

    Fraïsse, Christelle; Roux, Camille; Welch, John J; Bierne, Nicolas

    2014-07-01

    Genome-wide scans of genetic differentiation between hybridizing taxa can identify genome regions with unusual rates of introgression. Regions of high differentiation might represent barriers to gene flow, while regions of low differentiation might indicate adaptive introgression-the spread of selectively beneficial alleles between reproductively isolated genetic backgrounds. Here we conduct a scan for unusual patterns of differentiation in a mosaic hybrid zone between two mussel species, Mytilus edulis and M. galloprovincialis. One outlying locus, mac-1, showed a characteristic footprint of local introgression, with abnormally high frequency of edulis-derived alleles in a patch of M. galloprovincialis enclosed within the mosaic zone, but low frequencies outside of the zone. Further analysis of DNA sequences showed that almost all of the edulis allelic diversity had introgressed into the M. galloprovincialis background in this patch. We then used a variety of approaches to test the hypothesis that there had been adaptive introgression at mac-1. Simulations and model fitting with maximum-likelihood and approximate Bayesian computation approaches suggested that adaptive introgression could generate a "soft sweep," which was qualitatively consistent with our data. Although the migration rate required was high, it was compatible with the functioning of an effective barrier to gene flow as revealed by demographic inferences. As such, adaptive introgression could explain both the reduced intraspecific differentiation around mac-1 and the high diversity of introgressed alleles, although a localized change in barrier strength may also be invoked. Together, our results emphasize the need to account for the complex history of secondary contacts in interpreting outlier loci. PMID:24788603

  5. Parallel Adaptive Mesh Refinement

    SciTech Connect

    Diachin, L; Hornung, R; Plassmann, P; WIssink, A

    2005-03-04

    As large-scale, parallel computers have become more widely available and numerical models and algorithms have advanced, the range of physical phenomena that can be simulated has expanded dramatically. Many important science and engineering problems exhibit solutions with localized behavior where highly-detailed salient features or large gradients appear in certain regions which are separated by much larger regions where the solution is smooth. Examples include chemically-reacting flows with radiative heat transfer, high Reynolds number flows interacting with solid objects, and combustion problems where the flame front is essentially a two-dimensional sheet occupying a small part of a three-dimensional domain. Modeling such problems numerically requires approximating the governing partial differential equations on a discrete domain, or grid. Grid spacing is an important factor in determining the accuracy and cost of a computation. A fine grid may be needed to resolve key local features while a much coarser grid may suffice elsewhere. Employing a fine grid everywhere may be inefficient at best and, at worst, may make an adequately resolved simulation impractical. Moreover, the location and resolution of fine grid required for an accurate solution is a dynamic property of a problem's transient features and may not be known a priori. Adaptive mesh refinement (AMR) is a technique that can be used with both structured and unstructured meshes to adjust local grid spacing dynamically to capture solution features with an appropriate degree of resolution. Thus, computational resources can be focused where and when they are needed most to efficiently achieve an accurate solution without incurring the cost of a globally-fine grid. Figure 1.1 shows two example computations using AMR; on the left is a structured mesh calculation of a impulsively-sheared contact surface and on the right is the fuselage and volume discretization of an RAH-66 Comanche helicopter [35]. Note the

  6. Local stimulus disambiguation with global motion filters predicts adaptive surround modulation.

    PubMed

    Dellen, Babette; Torras, Carme

    2013-10-01

    Humans have no problem segmenting different motion stimuli despite the ambiguity of local motion signals. Adaptive surround modulation, i.e., the apparent switching between integrative and antagonistic modes, is assumed to play a crucial role in this process. However, so far motion processing models based on local integration have not been able to provide a unifying explanation for this phenomenon. This motivated us to investigate the problem of local stimulus disambiguation in an alternative and fundamentally distinct motion-processing model which uses global motion filters for velocity computation. Local information is reconstructed at the end of the processing stream through the constructive interference of global signals, i.e., inverse transformations. We show that in this model local stimulus disambiguation can be achieved by means of a novel filter embedded in this architecture. This gives rise to both integrative and antagonistic effects which are in agreement with those observed in psychophysical experiments with humans, providing a functional explanation for effects of motion repulsion. PMID:23685285

  7. The local enhancement conundrum: in search of the adaptive value of a social learning mechanism.

    PubMed

    Arbilly, Michal; Laland, Kevin N

    2014-02-01

    Social learning mechanisms are widely thought to vary in their degree of complexity as well as in their prevalence in the natural world. While learning the properties of a stimulus that generalize to similar stimuli at other locations (stimulus enhancement) prima facie appears more useful to an animal than learning about a specific stimulus at a specific location (local enhancement), empirical evidence suggests that the latter is much more widespread in nature. Simulating populations engaged in a producer-scrounger game, we sought to deploy mathematical models to identify the adaptive benefits of reliance on local enhancement and/or stimulus enhancement, and the alternative conditions favoring their evolution. Surprisingly, we found that while stimulus enhancement readily evolves, local enhancement is advantageous only under highly restricted conditions: when generalization of information was made unreliable or when error in social learning was high. Our results generate a conundrum over how seemingly conflicting empirical and theoretical findings can be reconciled. Perhaps the prevalence of local enhancement in nature is due to stimulus enhancement costs independent of the learning task itself (e.g. predation risk), perhaps natural habitats are often characterized by unreliable yet highly rewarding payoffs, or perhaps local enhancement occurs less frequently, and stimulus enhancement more frequently, than widely believed. PMID:24044984

  8. Decentralized Grid Scheduling with Evolutionary Fuzzy Systems

    NASA Astrophysics Data System (ADS)

    Fölling, Alexander; Grimme, Christian; Lepping, Joachim; Papaspyrou, Alexander

    In this paper, we address the problem of finding workload exchange policies for decentralized Computational Grids using an Evolutionary Fuzzy System. To this end, we establish a non-invasive collaboration model on the Grid layer which requires minimal information about the participating High Performance and High Throughput Computing (HPC/HTC) centers and which leaves the local resource managers completely untouched. In this environment of fully autonomous sites, independent users are assumed to submit their jobs to the Grid middleware layer of their local site, which in turn decides on the delegation and execution either on the local system or on remote sites in a situation-dependent, adaptive way. We find for different scenarios that the exchange policies show good performance characteristics not only with respect to traditional metrics such as average weighted response time and utilization, but also in terms of robustness and stability in changing environments.

  9. Local adaptation and effects of grazing among seedlings of two native California bunchgrass species: implications for restoration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Adaptation to environmental factors may influence the germination and establishment of focal species in ecological restoration. Reciprocal transplants remain one of the best methods to detect local adaptation, but long-term studies are often not feasible. We conducted reciprocal transplants of the...

  10. The simulation of localized surface plasmon and surface plasmon polariton in wire grid polarizer integrated on InP substrate for InGaAs sensor

    NASA Astrophysics Data System (ADS)

    Wang, Rui; Li, Tao; Shao, Xiumei; Li, Xue; Gong, Haimei

    2015-07-01

    We numerically demonstrate the integration of gold wire grid polarizer on InP substrate for InGaAs polarimetric imaging. The effective spectral range of wire grid polarizer has been designed in 0.8-3 μm according to InGaAs response waveband. The dips in TM transmission are observed due to surface plasmon (SPs) significantly damaging polarization performance. To further understand the coupling mechanism between gold wire grid grating and InP, the different contributions of surface plasmon polariton (SPP) and localized surface plasmon (LSP) to the dips are analyzed. Both transmission and reflectance spectra are simulated at different grating periods and duty cycles by finite-different time-domain (FDTD) method. LSP wavelength is located at around 1 μm and sensitive to the specific shape of metal wire. SPP presents higher resonance wavelength closely related to grating period. The simulations of electric field distribution show the same results.

  11. Coastal Adaptation Planning for Sea Level Rise and Extremes: A Global Model for Adaptation Decision-making at the Local Level Given Uncertain Climate Projections

    NASA Astrophysics Data System (ADS)

    Turner, D.

    2014-12-01

    Understanding the potential economic and physical impacts of climate change on coastal resources involves evaluating a number of distinct adaptive responses. This paper presents a tool for such analysis, a spatially-disaggregated optimization model for adaptation to sea level rise (SLR) and storm surge, the Coastal Impact and Adaptation Model (CIAM). This decision-making framework fills a gap between very detailed studies of specific locations and overly aggregate global analyses. While CIAM is global in scope, the optimal adaptation strategy is determined at the local level, evaluating over 12,000 coastal segments as described in the DIVA database (Vafeidis et al. 2006). The decision to pursue a given adaptation measure depends on local socioeconomic factors like income, population, and land values and how they develop over time, relative to the magnitude of potential coastal impacts, based on geophysical attributes like inundation zones and storm surge. For example, the model's decision to protect or retreat considers the costs of constructing and maintaining coastal defenses versus those of relocating people and capital to minimize damages from land inundation and coastal storms. Uncertain storm surge events are modeled with a generalized extreme value distribution calibrated to data on local surge extremes. Adaptation is optimized for the near-term outlook, in an "act then learn then act" framework that is repeated over the model time horizon. This framework allows the adaptation strategy to be flexibly updated, reflecting the process of iterative risk management. CIAM provides new estimates of the economic costs of SLR; moreover, these detailed results can be compactly represented in a set of adaptation and damage functions for use in integrated assessment models. Alongside the optimal result, CIAM evaluates suboptimal cases and finds that global costs could increase by an order of magnitude, illustrating the importance of adaptive capacity and coastal policy.

  12. Sex-specific local life-history adaptation in surface- and cave-dwelling Atlantic mollies (Poecilia mexicana).

    PubMed

    Riesch, Rüdiger; Reznick, David N; Plath, Martin; Schlupp, Ingo

    2016-01-01

    Cavefishes have long been used as model organisms showcasing adaptive diversification, but does adaptation to caves also facilitate the evolution of reproductive isolation from surface ancestors? We raised offspring of wild-caught surface- and cave-dwelling ecotypes of the neotropical fish Poecilia mexicana to sexual maturity in a 12-month common garden experiment. Fish were raised under one of two food regimes (high vs. low), and this was crossed with differences in lighting conditions (permanent darkness vs. 12:12 h light:dark cycle) in a 2 × 2 factorial design, allowing us to elucidate potential patterns of local adaptation in life histories. Our results reveal a pattern of sex-specific local life-history adaptation: Surface molly females had the highest fitness in the treatment best resembling their habitat of origin (high food and a light:dark cycle), and suffered from almost complete reproductive failure in darkness, while cave molly females were not similarly affected in any treatment. Males of both ecotypes, on the other hand, showed only weak evidence for local adaptation. Nonetheless, local life-history adaptation in females likely contributes to ecological diversification in this system and other cave animals, further supporting the role of local adaptation due to strong divergent selection as a major force in ecological speciation. PMID:26960566

  13. Sex-specific local life-history adaptation in surface- and cave-dwelling Atlantic mollies (Poecilia mexicana)

    PubMed Central

    Riesch, Rüdiger; Reznick, David N.; Plath, Martin; Schlupp, Ingo

    2016-01-01

    Cavefishes have long been used as model organisms showcasing adaptive diversification, but does adaptation to caves also facilitate the evolution of reproductive isolation from surface ancestors? We raised offspring of wild-caught surface- and cave-dwelling ecotypes of the neotropical fish Poecilia mexicana to sexual maturity in a 12-month common garden experiment. Fish were raised under one of two food regimes (high vs. low), and this was crossed with differences in lighting conditions (permanent darkness vs. 12:12 h light:dark cycle) in a 2 × 2 factorial design, allowing us to elucidate potential patterns of local adaptation in life histories. Our results reveal a pattern of sex-specific local life-history adaptation: Surface molly females had the highest fitness in the treatment best resembling their habitat of origin (high food and a light:dark cycle), and suffered from almost complete reproductive failure in darkness, while cave molly females were not similarly affected in any treatment. Males of both ecotypes, on the other hand, showed only weak evidence for local adaptation. Nonetheless, local life-history adaptation in females likely contributes to ecological diversification in this system and other cave animals, further supporting the role of local adaptation due to strong divergent selection as a major force in ecological speciation. PMID:26960566

  14. On Building Immersive Audio Applications Using Robust Adaptive Beamforming and Joint Audio-Video Source Localization

    NASA Astrophysics Data System (ADS)

    Beracoechea, J. A.; Torres-Guijarro, S.; García, L.; Casajús-Quirós, F. J.

    2006-12-01

    This paper deals with some of the different problems, strategies, and solutions of building true immersive audio systems oriented to future communication applications. The aim is to build a system where the acoustic field of a chamber is recorded using a microphone array and then is reconstructed or rendered again, in a different chamber using loudspeaker array-based techniques. Our proposal explores the possibility of using recent robust adaptive beamforming techniques for effectively estimating the original sources of the emitting room. A joint audio-video localization method needed in the estimation process as well as in the rendering engine is also presented. The estimated source signal and the source localization information drive a wave field synthesis engine that renders the acoustic field again at the receiving chamber. The system performance is tested using MUSHRA-based subjective tests.

  15. Adaptive Kalman filter for indoor localization using Bluetooth Low Energy and inertial measurement unit.

    PubMed

    Yoon, Paul K; Zihajehzadeh, Shaghayegh; Bong-Soo Kang; Park, Edward J

    2015-08-01

    This paper proposes a novel indoor localization method using the Bluetooth Low Energy (BLE) and an inertial measurement unit (IMU). The multipath and non-line-of-sight errors from low-power wireless localization systems commonly result in outliers, affecting the positioning accuracy. We address this problem by adaptively weighting the estimates from the IMU and BLE in our proposed cascaded Kalman filter (KF). The positioning accuracy is further improved with the Rauch-Tung-Striebel smoother. The performance of the proposed algorithm is compared against that of the standard KF experimentally. The results show that the proposed algorithm can maintain high accuracy for position tracking the sensor in the presence of the outliers. PMID:26736389

  16. Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

    PubMed Central

    Montano, Valeria; Didelot, Xavier; Foll, Matthieu; Linz, Bodo; Reinhardt, Richard; Suerbaum, Sebastian; Moodley, Yoshan; Jensen, Jeffrey D.

    2015-01-01

    Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipα) and hitherto unknown functional genes. PMID:25995212

  17. Fast adaptive schemes for tracking voltage phasor and local frequency in power transmission and distribution systems

    SciTech Connect

    Kamwa, I.; Grondin, R. )

    1992-04-01

    Real-time measurements of voltage phasor and local frequency deviation find applications in computer-based relaying, static state estimation, disturbance monitoring and control. This paper proposes two learning schemes for fast estimation of these basic quantities. We attacked the problem from a system identification perspective, in opposition to the well-established Extended Kalman Filtering (EKF) technique. It is shown that, from a simple non-linear model of the system voltage which involves only two parameters, the Recursive Least Squares (RLS) and the Least Means Squares (LMS) algorithms can each provide dynamic estimates of the voltage phasor. The finite derivative of the phase deviation, followed by a moving-average filter, then leads to the local frequency deviation. A constant forgetting factor included in these algorithms provides both fast adaptation in time-varying situations and good smoothing of the estimates when necessary.

  18. Hybrid Grid Generation Using NW Grid

    SciTech Connect

    Jones-Oliveira, Janet B.; Oliveira, Joseph S.; Trease, Lynn L.; Trease, Harold E.; B.K. Soni, J. Hauser, J.F. Thompson, P.R. Eiseman

    2000-09-01

    We describe the development and use of a hybrid n-dimensional grid generation system called NWGRID. The Applied Mathematics Group at Pacific Northwest National Laboratory (PNNL) is developing this tool to support the Laboratory's computational science efforts in chemistry, biology, engineering and environmental (subsurface and atmospheric) modeling. NWGRID is the grid generation system, which is designed for multi-scale, multi-material, multi-physics, time-dependent, 3-D, hybrid grids that are either statically adapted or evolved in time. NWGRID'S capabilities include static and dynamic grids, hybrid grids, managing colliding surfaces, and grid optimization[using reconnections, smoothing, and adaptive mesh refinement (AMR) algorithms]. NWGRID'S data structure can manage an arbitrary number of grid objects, each with an arbitrary number of grid attributes. NWGRID uses surface geometry to build volumes by using combinations of Boolean operators and order relations. Point distributions can be input, generated using either ray shooting techniques or defined point-by-point. Connectivity matrices are then generated automatically for all variations of hybrid grids.

  19. MODFLOW–LGR—Documentation of ghost node local grid refinement (LGR2) for multiple areas and the boundary flow and head (BFH2) package

    USGS Publications Warehouse

    Mehl, Steffen W.; Hill, Mary C.

    2013-01-01

    This report documents the addition of ghost node Local Grid Refinement (LGR2) to MODFLOW-2005, the U.S. Geological Survey modular, transient, three-dimensional, finite-difference groundwater flow model. LGR2 provides the capability to simulate groundwater flow using multiple block-shaped higher-resolution local grids (a child model) within a coarser-grid parent model. LGR2 accomplishes this by iteratively coupling separate MODFLOW-2005 models such that heads and fluxes are balanced across the grid-refinement interface boundary. LGR2 can be used in two-and three-dimensional, steady-state and transient simulations and for simulations of confined and unconfined groundwater systems. Traditional one-way coupled telescopic mesh refinement methods can have large, often undetected, inconsistencies in heads and fluxes across the interface between two model grids. The iteratively coupled ghost-node method of LGR2 provides a more rigorous coupling in which the solution accuracy is controlled by convergence criteria defined by the user. In realistic problems, this can result in substantially more accurate solutions and require an increase in computer processing time. The rigorous coupling enables sensitivity analysis, parameter estimation, and uncertainty analysis that reflects conditions in both model grids. This report describes the method used by LGR2, evaluates accuracy and performance for two-and three-dimensional test cases, provides input instructions, and lists selected input and output files for an example problem. It also presents the Boundary Flow and Head (BFH2) Package, which allows the child and parent models to be simulated independently using the boundary conditions obtained through the iterative process of LGR2.

  20. Scientific Final Report: COLLABORATIVE RESEARCH: CONTINUOUS DYNAMIC GRID ADAPTATION IN A GLOBAL ATMOSPHERIC MODEL: APPLICATION AND REFINEMENT

    SciTech Connect

    William J. Gutowski; Joseph M. Prusa, Piotr K. Smolarkiewicz

    2012-04-09

    This project had goals of advancing the performance capabilities of the numerical general circulation model EULAG and using it to produce a fully operational atmospheric global climate model (AGCM) that can employ either static or dynamic grid stretching for targeted phenomena. The resulting AGCM combined EULAG's advanced dynamics core with the 'physics' of the NCAR Community Atmospheric Model (CAM). Effort discussed below shows how we improved model performance and tested both EULAG and the coupled CAM-EULAG in several ways to demonstrate the grid stretching and ability to simulate very well a wide range of scales, that is, multi-scale capability. We leveraged our effort through interaction with an international EULAG community that has collectively developed new features and applications of EULAG, which we exploited for our own work summarized here. Overall, the work contributed to over 40 peer-reviewed publications and over 70 conference/workshop/seminar presentations, many of them invited.

  1. Fast and persistent adaptation to new spectral cues for sound localization suggests a many-to-one mapping mechanism.

    PubMed

    Trapeau, Régis; Aubrais, Valérie; Schönwiesner, Marc

    2016-08-01

    The adult human auditory system can adapt to changes in spectral cues for sound localization. This plasticity was demonstrated by changing the shape of the pinna with earmolds. Previous results indicate that participants regain localization accuracy after several weeks of adaptation and that the adapted state is retained for at least one week without earmolds. No aftereffect was observed after mold removal, but any aftereffect may be too short to be observed when responses are averaged over many trials. This work investigated the lack of aftereffect by analyzing single-trial responses and modifying visual, auditory, and tactile information during the localization task. Results showed that participants localized accurately immediately after mold removal, even at the first stimulus presentation. Knowledge of the stimulus spectrum, tactile information about the absence of the earmolds, and visual feedback were not necessary to localize accurately after adaptation. Part of the adaptation persisted for one month without molds. The results are consistent with the hypothesis of a many-to-one mapping of the spectral cues, in which several spectral profiles are simultaneously associated with one sound location. Additionally, participants with acoustically more informative spectral cues localized sounds more accurately, and larger acoustical disturbances by the molds reduced adaptation success. PMID:27586720

  2. Local error estimates for adaptive simulation of the Reaction–Diffusion Master Equation via operator splitting

    PubMed Central

    Hellander, Andreas; Lawson, Michael J; Drawert, Brian; Petzold, Linda

    2015-01-01

    The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity. PMID:26865735

  3. Local error estimates for adaptive simulation of the reaction-diffusion master equation via operator splitting

    NASA Astrophysics Data System (ADS)

    Hellander, Andreas; Lawson, Michael J.; Drawert, Brian; Petzold, Linda

    2014-06-01

    The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps were adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the diffusive finite-state projection (DFSP) method, to incorporate temporal adaptivity.

  4. Locally adaptive MR intensity models and MRF-based segmentation of multiple sclerosis lesions

    NASA Astrophysics Data System (ADS)

    Galimzianova, Alfiia; Lesjak, Žiga; Likar, Boštjan; Pernuš, Franjo; Špiclin, Žiga

    2015-03-01

    Neuroimaging biomarkers are an important paraclinical tool used to characterize a number of neurological diseases, however, their extraction requires accurate and reliable segmentation of normal and pathological brain structures. For MR images of healthy brains the intensity models of normal-appearing brain tissue (NABT) in combination with Markov random field (MRF) models are known to give reliable and smooth NABT segmentation. However, the presence of pathology, MR intensity bias and natural tissue-dependent intensity variability altogether represent difficult challenges for a reliable estimation of NABT intensity model based on MR images. In this paper, we propose a novel method for segmentation of normal and pathological structures in brain MR images of multiple sclerosis (MS) patients that is based on locally-adaptive NABT model, a robust method for the estimation of model parameters and a MRF-based segmentation framework. Experiments on multi-sequence brain MR images of 27 MS patients show that, compared to whole-brain model and compared to the widely used Expectation-Maximization Segmentation (EMS) method, the locally-adaptive NABT model increases the accuracy of MS lesion segmentation.

  5. Plant quality and local adaptation undermine relocation in a bog specialist butterfly

    PubMed Central

    Turlure, Camille; Radchuk, Viktoriia; Baguette, Michel; Meijrink, Mark; den Burg, Arnold; Vries, Michiel Wallis; Duinen, Gert-Jan

    2013-01-01

    The butterfly Boloria aquilonaris is a specialist of oligotrophic ecosystems. Population viability analysis predicted the species to be stable in Belgium and to collapse in the Netherlands with reduced host plant quality expected to drive species decline in the latter. We tested this hypothesis by rearing B. aquilonaris caterpillars from Belgian and Dutch sites on host plants (the cranberry, Vaccinium oxycoccos). Dutch plant quality was lower than Belgian one conferring lower caterpillar growth rate and survival. Reintroduction and/or supplementation may be necessary to ensure the viability of the species in the Netherlands, but some traits may have been selected solely in Dutch caterpillars to cope with gradual changes in host plant quality. To test this hypothesis, the performance of Belgian and Dutch caterpillars fed with plants from both countries were compared. Dutch caterpillars performed well on both plant qualities, whereas Belgian caterpillars could not switch to lower quality plants. This can be considered as an environmentally induced plastic response of caterpillars and/or a local adaptation to plant quality, which precludes the use of Belgian individuals as a unique solution for strengthening Dutch populations. More generally, these results stress that the relevance of local adaptation in selecting source populations for relocation may be as important as restoring habitat quality. PMID:23467336

  6. Life History Variation in an Alpine Caddisfly: Local Adaptation or Phenotypic Plasticity?

    NASA Astrophysics Data System (ADS)

    Shama, L. N.; Robinson, C. T.

    2005-05-01

    Facultative species that inhabit permanent and temporary streams can be locally adapted to their stream of origin or exhibit life history plasticity. Temporary stream populations should respond to environmental cues signalling stream drying, whereas permanent stream populations may not. We used a common garden experiment to test whether males and females of an alpine caddisfly from six populations (3 permanent/3 temporary streams) differed in their life history responses to combined changes in photoperiod (ambient/late) and hydroperiod (constant/drying). Responses varied by sex, time-constraint cue and population. Both sexes shortened development time in the late photoperiod, and males emerged before females in all treatments. Growth rates were higher in the late photoperiod for both sexes, and females had higher growth rates and mass at emergence than males. Growth rate compensation in the late photoperiod resulted in similar masses at emergence for both photoperiods. Population-level differences in responses varied according to microgeographic co-gradient variation. Our results suggest that while stream drying cues may not exert sufficient selection pressure to promote faster development in temporary streams, populations may be locally adapted to differences in growing season length associated with stream-specific environmental characteristics.

  7. Local adaptation: Mechanical fit between floral ecotypes of Nerine humilis (Amaryllidaceae) and pollinator communities.

    PubMed

    Newman, Ethan; Manning, John; Anderson, Bruce

    2015-09-01

    Geographic variation in floral morphology is often assumed to reflect geographic variation in pollinator communities and associated divergence in selective pressures. We studied populations of Nerine humilis (Amaryllidaceae) to assess whether geographic variation in floral form is the result of local adaptation to different pollinator communities. We first tested for associations between floral traits and visitor communities, and found that populations with similar floral morphologies were visited by similar insect communities. Mean style length in each population was also closely associated with the mean body length of the local visitor community. A reciprocal translocation experiment demonstrated that native phenotypes set more seed than translocated phenotypes. Single visitation experiments showed that native flowers received more pollen, and set more seed per visit, than introduced phenotypes in both populations. This suggests that the effectiveness of pollinator visits is determined by the degree of mechanical fit between flowers and visitors. We provide strong evidence that the observed among-population variation in floral traits is an adaptive response to geographic variation in the pollinator community. PMID:26194119

  8. Adaptation in sound localization: from GABA(B) receptor-mediated synaptic modulation to perception.

    PubMed

    Stange, Annette; Myoga, Michael H; Lingner, Andrea; Ford, Marc C; Alexandrova, Olga; Felmy, Felix; Pecka, Michael; Siveke, Ida; Grothe, Benedikt

    2013-12-01

    Across all sensory modalities, the effect of context-dependent neural adaptation can be observed at every level, from receptors to perception. Nonetheless, it has long been assumed that the processing of interaural time differences, which is the primary cue for sound localization, is nonadaptive, as its outputs are mapped directly onto a hard-wired representation of space. Here we present evidence derived from in vitro and in vivo experiments in gerbils indicating that the coincidence-detector neurons in the medial superior olive modulate their sensitivity to interaural time differences through a rapid, GABA(B) receptor-mediated feedback mechanism. We show that this mechanism provides a gain control in the form of output normalization, which influences the neuronal population code of auditory space. Furthermore, psychophysical tests showed that the paradigm used to evoke neuronal GABA(B) receptor-mediated adaptation causes the perceptual shift in sound localization in humans that was expected on the basis of our physiological results in gerbils. PMID:24141311

  9. Plant quality and local adaptation undermine relocation in a bog specialist butterfly.

    PubMed

    Turlure, Camille; Radchuk, Viktoriia; Baguette, Michel; Meijrink, Mark; den Burg, Arnold; Vries, Michiel Wallis; Duinen, Gert-Jan

    2013-02-01

    The butterfly Boloria aquilonaris is a specialist of oligotrophic ecosystems. Population viability analysis predicted the species to be stable in Belgium and to collapse in the Netherlands with reduced host plant quality expected to drive species decline in the latter. We tested this hypothesis by rearing B. aquilonaris caterpillars from Belgian and Dutch sites on host plants (the cranberry, Vaccinium oxycoccos). Dutch plant quality was lower than Belgian one conferring lower caterpillar growth rate and survival. Reintroduction and/or supplementation may be necessary to ensure the viability of the species in the Netherlands, but some traits may have been selected solely in Dutch caterpillars to cope with gradual changes in host plant quality. To test this hypothesis, the performance of Belgian and Dutch caterpillars fed with plants from both countries were compared. Dutch caterpillars performed well on both plant qualities, whereas Belgian caterpillars could not switch to lower quality plants. This can be considered as an environmentally induced plastic response of caterpillars and/or a local adaptation to plant quality, which precludes the use of Belgian individuals as a unique solution for strengthening Dutch populations. More generally, these results stress that the relevance of local adaptation in selecting source populations for relocation may be as important as restoring habitat quality. PMID:23467336

  10. Adaptation to enemy shifts: rapid resistance evolution to local Vibrio spp. in invasive Pacific oysters

    PubMed Central

    Wendling, Carolin C.; Wegner, K. Mathias

    2015-01-01

    One hypothesis for the success of invasive species is reduced pathogen burden, resulting from a release from infections or high immunological fitness of invaders. Despite strong selection exerted on the host, the evolutionary response of invaders to newly acquired pathogens has rarely been considered. The two independent and genetically distinct invasions of the Pacific oyster Crassostrea gigas into the North Sea represent an ideal model system to study fast evolutionary responses of invasive populations. By exposing both invasion sources to ubiquitous and phylogenetically diverse pathogens (Vibrio spp.), we demonstrate that within a few generations hosts adapted to newly encountered pathogen communities. However, local adaptation only became apparent in selective environments, i.e. at elevated temperatures reflecting patterns of disease outbreaks in natural populations. Resistance against sympatric and allopatric Vibrio spp. strains was dominantly inherited in crosses between both invasion sources, resulting in an overall higher resistance of admixed individuals than pure lines. Therefore, we suggest that a simple genetic resistance mechanism of the host is matched to a common virulence mechanism shared by local Vibrio strains. This combination might have facilitated a fast evolutionary response that can explain another dimension of why invasive species can be so successful in newly invaded ranges. PMID:25716784

  11. Tailoring the visual communication of climate projections for local adaptation practitioners in Germany and the UK

    PubMed Central

    Lorenz, Susanne; Dessai, Suraje; Forster, Piers M.; Paavola, Jouni

    2015-01-01

    Visualizations are widely used in the communication of climate projections. However, their effectiveness has rarely been assessed among their target audience. Given recent calls to increase the usability of climate information through the tailoring of climate projections, it is imperative to assess the effectiveness of different visualizations. This paper explores the complexities of tailoring through an online survey conducted with 162 local adaptation practitioners in Germany and the UK. The survey examined respondents’ assessed and perceived comprehension (PC) of visual representations of climate projections as well as preferences for using different visualizations in communicating and planning for a changing climate. Comprehension and use are tested using four different graph formats, which are split into two pairs. Within each pair the information content is the same but is visualized differently. We show that even within a fairly homogeneous user group, such as local adaptation practitioners, there are clear differences in respondents’ comprehension of and preference for visualizations. We do not find a consistent association between assessed comprehension and PC or use within the two pairs of visualizations that we analysed. There is, however, a clear link between PC and use of graph format. This suggests that respondents use what they think they understand the best, rather than what they actually understand the best. These findings highlight that audience-specific targeted communication may be more complex and challenging than previously recognized. PMID:26460109

  12. Toward fast feature adaptation and localization for real-time face recognition systems

    NASA Astrophysics Data System (ADS)

    Zuo, Fei; de With, Peter H.

    2003-06-01

    In a home environment, video surveillance employing face detection and recognition is attractive for new applications. Facial feature (e.g. eyes and mouth) localization in the face is an essential task for face recognition because it constitutes an indispensable step for face geometry normalization. This paper presents a new and efficient feature localization approach for real-time personal surveillance applications with low-quality images. The proposed approach consists of three major steps: (1) self-adaptive iris tracing, which is preceded by a trace-point selection process with multiple initializations to overcome the local convergence problem, (2) eye structure verification using an eye template with limited deformation freedom, and (3) eye-pair selection based on a combination of metrics. We have tested our facial feature localization method on about 100 randomly selected face images from the AR database and 30 face images downloaded from the Internet. The results show that our approach achieves a correct detection rate of 96%. Since our eye-selection technique does not involve time-consuming deformation processes, it yields relatively fast processing. The proposed algorithm has been successfully applied to a real-time home video surveillance system and proven to be an effective and computationally efficient face normalization method preceding the face recognition.

  13. Automatic adaptive parameterization in local phase feature-based bone segmentation in ultrasound.

    PubMed

    Hacihaliloglu, Ilker; Abugharbieh, Rafeef; Hodgson, Antony J; Rohling, Robert N

    2011-10-01

    Intensity-invariant local phase features based on Log-Gabor filters have been recently shown to produce highly accurate localizations of bone surfaces from three-dimensional (3-D) ultrasound. A key challenge, however, remains in the proper selection of filter parameters, whose values have so far been chosen empirically and kept fixed for a given image. Since Log-Gabor filter responses widely change when varying the filter parameters, actual parameter selection can significantly affect the quality of extracted features. This article presents a novel method for contextual parameter selection that autonomously adapts to image content. Our technique automatically selects the scale, bandwidth and orientation parameters of Log-Gabor filters for optimizing local phase symmetry. The proposed approach incorporates principle curvature computed from the Hessian matrix and directional filter banks in a phase scale-space framework. Evaluations performed on carefully designed in vitro experiments demonstrate 35% improvement in accuracy of bone surface localization compared with empirically-set parameterization results. Results from a pilot in vivo study on human subjects, scanned in the operating room, show similar improvements. PMID:21821346

  14. Local adaptations and climate change: converging sensitivity of bud break in black spruce provenances.

    PubMed

    Rossi, Sergio

    2015-07-01

    Species with transcontinental distribution or spread over wide geographical regions develop populations with growth traits genetically adapted to the local climate. The aim of this study was to investigate the ecotypic sensitivity of bud break, a strong adaptive trait, to a changing environment. Six phenological phases of bud break were monitored daily on black spruce [Picea mariana (Mill.) BSP] seedlings submitted to different temperatures (12, 16 and 20 °C) and photoperiods (14, 18 and 22 h). Six provenances were tested in growth chambers, produced from seeds collected along the whole latitudinal range of the closed boreal forest in Quebec, Canada. Bud break lasted 13.3 days on average and occurred earlier in seedlings from colder sites. The annual temperature of the sites suitably tracked the clinal variation among ecotypes, providing a clear biological explanation for the environmental signal driving the adaptive divergence of populations to the local climate. Increasing temperature induced an earlier bud break according to a non-linear pattern with greater advancements observed between 12 and 16 °C. Photoperiod was significant, but sensitivity analysis indicated that its effect on bud break was marginal with respect to temperature. No interaction of provenance × treatment was observed, demonstrating an ecotypic convergence of the responses to both factors. Changes in the growing conditions could substantially modify the synchronization between bud phenology and climate, thus exposing the developing meristems of black spruce to frost damage. However, similar advancements of bud break could be expected in the different ecotypes subjected to warmer temperatures or longer day lengths. PMID:25225116

  15. Local adaptations and climate change: converging sensitivity of bud break in black spruce provenances

    NASA Astrophysics Data System (ADS)

    Rossi, Sergio

    2015-07-01

    Species with transcontinental distribution or spread over wide geographical regions develop populations with growth traits genetically adapted to the local climate. The aim of this study was to investigate the ecotypic sensitivity of bud break, a strong adaptive trait, to a changing environment. Six phenological phases of bud break were monitored daily on black spruce [ Picea mariana (Mill.) BSP] seedlings submitted to different temperatures (12, 16 and 20 °C) and photoperiods (14, 18 and 22 h). Six provenances were tested in growth chambers, produced from seeds collected along the whole latitudinal range of the closed boreal forest in Quebec, Canada. Bud break lasted 13.3 days on average and occurred earlier in seedlings from colder sites. The annual temperature of the sites suitably tracked the clinal variation among ecotypes, providing a clear biological explanation for the environmental signal driving the adaptive divergence of populations to the local climate. Increasing temperature induced an earlier bud break according to a non-linear pattern with greater advancements observed between 12 and 16 °C. Photoperiod was significant, but sensitivity analysis indicated that its effect on bud break was marginal with respect to temperature. No interaction of provenance × treatment was observed, demonstrating an ecotypic convergence of the responses to both factors. Changes in the growing conditions could substantially modify the synchronization between bud phenology and climate, thus exposing the developing meristems of black spruce to frost damage. However, similar advancements of bud break could be expected in the different ecotypes subjected to warmer temperatures or longer day lengths.

  16. Application of Parallel Adjoint-Based Error Estimation and Anisotropic Grid Adaptation for Three-Dimensional Aerospace Configurations

    NASA Technical Reports Server (NTRS)

    Lee-Rausch, E. M.; Park, M. A.; Jones, W. T.; Hammond, D. P.; Nielsen, E. J.

    2005-01-01

    This paper demonstrates the extension of error estimation and adaptation methods to parallel computations enabling larger, more realistic aerospace applications and the quantification of discretization errors for complex 3-D solutions. Results were shown for an inviscid sonic-boom prediction about a double-cone configuration and a wing/body segmented leading edge (SLE) configuration where the output function of the adjoint was pressure integrated over a part of the cylinder in the near field. After multiple cycles of error estimation and surface/field adaptation, a significant improvement in the inviscid solution for the sonic boom signature of the double cone was observed. Although the double-cone adaptation was initiated from a very coarse mesh, the near-field pressure signature from the final adapted mesh compared very well with the wind-tunnel data which illustrates that the adjoint-based error estimation and adaptation process requires no a priori refinement of the mesh. Similarly, the near-field pressure signature for the SLE wing/body sonic boom configuration showed a significant improvement from the initial coarse mesh to the final adapted mesh in comparison with the wind tunnel results. Error estimation and field adaptation results were also presented for the viscous transonic drag prediction of the DLR-F6 wing/body configuration, and results were compared to a series of globally refined meshes. Two of these globally refined meshes were used as a starting point for the error estimation and field-adaptation process where the output function for the adjoint was the total drag. The field-adapted results showed an improvement in the prediction of the drag in comparison with the finest globally refined mesh and a reduction in the estimate of the remaining drag error. The adjoint-based adaptation parameter showed a need for increased resolution in the surface of the wing/body as well as a need for wake resolution downstream of the fuselage and wing trailing edge

  17. Generating relevant climate adaptation science tools in concert with local natural resource agencies

    NASA Astrophysics Data System (ADS)

    Micheli, L.; Flint, L. E.; Veloz, S.; Heller, N. E.

    2015-12-01

    To create a framework for adapting to climate change, decision makers operating at the urban-wildland interface need to define climate vulnerabilities in the context of site-specific opportunities and constraints relative to water supply, land use suitability, wildfire risks, ecosystem services and quality of life. Pepperwood's TBC3.org is crafting customized climate vulnerability assessments with selected water and natural resource agencies of California's Sonoma, Marin, Napa and Mendocino counties under the auspices of Climate Ready North Bay, a public-private partnership funded by the California Coastal Conservancy. Working directly with managers from the very start of the process to define resource-specific information needs, we are developing high-resolution, spatially-explicit data products to help local governments and agency staff implement informed and effective climate adaptation strategies. Key preliminary findings for the region using the USGS' Basin Characterization Model (at a 270 m spatial resolution) include a unidirectional trend, independent of greater or lesser precipitation, towards increasing climatic water deficits across model scenarios. Therefore a key message is that managers will be facing an increasingly arid environment. Companion models translate the impacts of shifting climate and hydrology on vegetation composition and fire risks. The combination of drought stress on water supplies and native vegetation with an approximate doubling of fire risks may demand new approaches to watershed planning. Working with agencies we are exploring how to build capacity for protection and enhancement of key watershed functions with a focus on groundwater recharge, facilitating greater drought tolerance in forest and rangeland systems, and considering more aggressive approaches to management of fuel loads. Lessons learned about effective engagement include the need for extended in-depth dialog, translation of key climate adaptation questions into

  18. Adaptation.

    PubMed

    Broom, Donald M

    2006-01-01

    The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and

  19. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

    PubMed Central

    Gómez, Pedro; Paterson, Steve; De Meester, Luc; Liu, Xuan; Lenzi, Luca; Sharma, M. D.; McElroy, Kerensa; Buckling, Angus

    2016-01-01

    Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting. PMID:27501868

  20. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community.

    PubMed

    Gómez, Pedro; Paterson, Steve; De Meester, Luc; Liu, Xuan; Lenzi, Luca; Sharma, M D; McElroy, Kerensa; Buckling, Angus

    2016-01-01

    Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting. PMID:27501868

  1. High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation?

    PubMed

    Roulin, Anne C; Mariadassou, Mahendra; Hall, Matthew D; Walser, Jean-Claude; Haag, Christoph; Ebert, Dieter

    2015-10-01

    Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy, as resting stages can only be produced sexually. In this species, on a continental scale, resting-stage production is locally adapted--that is, it is induced when the photoperiod indicates the imminence of habitat deterioration. Here, we aimed to explore whether selection is strong enough to maintain local adaptation at a scale of a few kilometers. We assessed life-history traits of 64 D. magna clones originating from 11 populations of a metapopulation with permanent and intermittent pool habitats. We found large within- and between-population variation for all dormancy-related traits, but no evidence for the hypothesized higher resting-stage production in animals from intermittent habitats. We discuss how gene flow, founder events, or other forms of selection might interfere with the process of local adaptation. PMID:26418426

  2. Solution of free-boundary problems using finite-element/Newton methods and locally refined grids - Application to analysis of solidification microstructure

    NASA Technical Reports Server (NTRS)

    Tsiveriotis, K.; Brown, R. A.

    1993-01-01

    A new method is presented for the solution of free-boundary problems using Lagrangian finite element approximations defined on locally refined grids. The formulation allows for direct transition from coarse to fine grids without introducing non-conforming basis functions. The calculation of elemental stiffness matrices and residual vectors are unaffected by changes in the refinement level, which are accounted for in the loading of elemental data to the global stiffness matrix and residual vector. This technique for local mesh refinement is combined with recently developed mapping methods and Newton's method to form an efficient algorithm for the solution of free-boundary problems, as demonstrated here by sample calculations of cellular interfacial microstructure during directional solidification of a binary alloy.

  3. Local Adaptation of Central Policies: The Policymaking and Implementation of Compulsory Education for Migrant Children in China

    ERIC Educational Resources Information Center

    Wang, Lihua

    2016-01-01

    This article looks at the central and local governments' policymaking and implementation of compulsory education for migrant children in China. Three distinct models of policy implementation were identified through a case study approach. They indicated a selective adaptation of central policy objective and principles by the local governments and…

  4. On Bi-Grid Local Mode Analysis of Solution Techniques for 3-D Euler and Navier-Stokes Equations

    NASA Technical Reports Server (NTRS)

    Ibraheem, S. O.; Demuren, A. O.

    1994-01-01

    A procedure is presented for utilizing a bi-grid stability analysis as a practical tool for predicting multigrid performance in a range of numerical methods for solving Euler and Navier-Stokes equations. Model problems based on the convection, diffusion and Burger's equation are used to illustrate the superiority of the bi-grid analysis as a predictive tool for multigrid performance in comparison to the smoothing factor derived from conventional von Neumann analysis. For the Euler equations, bi-grid analysis is presented for three upwind difference based factorizations, namely Spatial, Eigenvalue and Combination splits, and two central difference based factorizations, namely LU and ADI methods. In the former, both the Steger-Warming and van Leer flux-vector splitting methods are considered. For the Navier-Stokes equations, only the Beam-Warming (ADI) central difference scheme is considered. In each case, estimates of multigrid convergence rates from the bi-grid analysis are compared to smoothing factors obtained from single-grid stability analysis. Effects of grid aspect ratio and flow skewness are examined. Both predictions are compared with practical multigrid convergence rates for 2-D Euler and Navier-Stokes solutions based on the Beam-Warming central scheme.

  5. 3-D inversion of airborne electromagnetic data parallelized and accelerated by local mesh and adaptive soundings

    NASA Astrophysics Data System (ADS)

    Yang, Dikun; Oldenburg, Douglas W.; Haber, Eldad

    2014-03-01

    Airborne electromagnetic (AEM) methods are highly efficient tools for assessing the Earth's conductivity structures in a large area at low cost. However, the configuration of AEM measurements, which typically have widely distributed transmitter-receiver pairs, makes the rigorous modelling and interpretation extremely time-consuming in 3-D. Excessive overcomputing can occur when working on a large mesh covering the entire survey area and inverting all soundings in the data set. We propose two improvements. The first is to use a locally optimized mesh for each AEM sounding for the forward modelling and calculation of sensitivity. This dedicated local mesh is small with fine cells near the sounding location and coarse cells far away in accordance with EM diffusion and the geometric decay of the signals. Once the forward problem is solved on the local meshes, the sensitivity for the inversion on the global mesh is available through quick interpolation. Using local meshes for AEM forward modelling avoids unnecessary computing on fine cells on a global mesh that are far away from the sounding location. Since local meshes are highly independent, the forward modelling can be efficiently parallelized over an array of processors. The second improvement is random and dynamic down-sampling of the soundings. Each inversion iteration only uses a random subset of the soundings, and the subset is reselected for every iteration. The number of soundings in the random subset, determined by an adaptive algorithm, is tied to the degree of model regularization. This minimizes the overcomputing caused by working with redundant soundings. Our methods are compared against conventional methods and tested with a synthetic example. We also invert a field data set that was previously considered to be too large to be practically inverted in 3-D. These examples show that our methodology can dramatically reduce the processing time of 3-D inversion to a practical level without losing resolution

  6. No evidence for local adaptation in an invasive alien plant: field and greenhouse experiments tracing a colonization sequence

    PubMed Central

    Pahl, Anna T.; Kollmann, Johannes; Mayer, Andreas; Haider, Sylvia

    2013-01-01

    Background and Aims Local adaptation enables plant species to persist under different environmental conditions. Evolutionary change can occur rapidly in invasive annual species and has been shown to lead to local adaptation. However, the patterns and mechanisms of local adaptation in invasive species along colonization sequences are not yet understood. Thus, in this study the alien annual Impatiens glandulifera was used to investigate local adaptation to distinct habitats that have been consecutively invaded in central Europe. Methods A reciprocal transplant experiment was performed using 15 populations from alluvial deciduous forests, fallow meadows and coniferous upland forests, and a greenhouse experiment was performed in which plants from these habitats were grown under treatments reflecting the main habitat differentiators (shade, soil acidity, competition). Key Results Biomass production, specific leaf area, plant height and relative growth rate differed between habitats in the field experiment and between treatments in the greenhouse, but not between seed origins. Overall, there was no indication of local adaptation in either experiment. Conclusions Since I. glandulifera is a successful invader in many habitats without showing local adaptation, it is suggested that the species is coping with environmental variation by means of high phenotypic plasticity. The species seems to follow a ‘jack-and-master’ strategy, i.e. it is able to maintain high fitness under a wide range of environmental conditions, but performs particularly well in favourable habitats. Therefore, the proposed colonization sequence is likely to be based primarily on changes in propagule pressure. It is concluded that invasive alien plants can become dominant in distinct habitats without local adaptation. PMID:24214934

  7. Integrated soil fertility management in sub-Saharan Africa: unravelling local adaptation

    NASA Astrophysics Data System (ADS)

    Vanlauwe, B.; Descheemaeker, K.; Giller, K. E.; Huising, J.; Merckx, R.; Nziguheba, G.; Wendt, J.; Zingore, S.

    2015-06-01

    Intensification of smallholder agriculture in sub-Saharan Africa is necessary to address rural poverty and natural resource degradation. Integrated soil fertility management (ISFM) is a means to enhance crop productivity while maximizing the agronomic efficiency (AE) of applied inputs, and can thus contribute to sustainable intensification. ISFM consists of a set of best practices, preferably used in combination, including the use of appropriate germplasm, the appropriate use of fertilizer and of organic resources, and good agronomic practices. The large variability in soil fertility conditions within smallholder farms is also recognized within ISFM, including soils with constraints beyond those addressed by fertilizer and organic inputs. The variable biophysical environments that characterize smallholder farming systems have profound effects on crop productivity and AE, and targeted application of agro-inputs and management practices is necessary to enhance AE. Further, management decisions depend on the farmer's resource endowments and production objectives. In this paper we discuss the "local adaptation" component of ISFM and how this can be conceptualized within an ISFM framework, backstopped by analysis of AE at plot and farm level. At plot level, a set of four constraints to maximum AE is discussed in relation to "local adaptation": soil acidity, secondary nutrient and micronutrient (SMN) deficiencies, physical constraints, and drought stress. In each of these cases, examples are presented whereby amendments and/or practices addressing these have a significantly positive impact on fertilizer AE, including mechanistic principles underlying these effects. While the impact of such amendments and/or practices is easily understood for some practices (e.g. the application of SMNs where these are limiting), for others, more complex processes influence AE (e.g. water harvesting under varying rainfall conditions). At farm scale, adjusting fertilizer applications to

  8. Integrated soil fertility management in sub-Saharan Africa: unravelling local adaptation

    NASA Astrophysics Data System (ADS)

    Vanlauwe, B.; Descheemaeker, K.; Giller, K. E.; Huising, J.; Merckx, R.; Nziguheba, G.; Wendt, J.; Zingore, S.

    2014-12-01

    Intensification of smallholder agriculture in sub-Saharan Africa is necessary to address rural poverty and natural resource degradation. Integrated Soil Fertility Management (ISFM) is a means to enhance crop productivity while maximizing the agronomic efficiency (AE) of applied inputs, and can thus contribute to sustainable intensification. ISFM consists of a set of best practices, preferably used in combination, including the use of appropriate germplasm, the appropriate use of fertilizer and of organic resources, and good agronomic practices. The large variability in soil fertility conditions within smallholder farms is also recognised within ISFM, including soils with constraints beyond those addressed by fertilizer and organic inputs. The variable biophysical environments that characterize smallholder farming systems have profound effects on crop productivity and AE and targeted application of limited agro-inputs and management practices is necessary to enhance AE. Further, management decisions depend on the farmer's resource endowments and production objectives. In this paper we discuss the "local adaptation" component of ISFM and how this can be conceptualized within an ISFM framework, backstopped by analysis of AE at plot and farm level. At plot level, a set of four constraints to maximum AE is discussed in relation to "local adaptation": soil acidity, secondary nutrient and micro-nutrient (SMN) deficiencies, physical constraints, and drought stress. In each of these cases, examples are presented whereby amendments and/or practices addressing these have a significantly positive impact on fertilizer AE, including mechanistic principles underlying these effects. While the impact of such amendments and/or practices is easily understood for some practices (e.g., the application of SMNs where these are limiting), for others, more complex interactions with fertilizer AE can be identified (e.g., water harvesting under varying rainfall conditions). At farm scale

  9. Elliptic Solvers with Adaptive Mesh Refinement on Complex Geometries

    SciTech Connect

    Phillip, B.

    2000-07-24

    Adaptive Mesh Refinement (AMR) is a numerical technique for locally tailoring the resolution computational grids. Multilevel algorithms for solving elliptic problems on adaptive grids include the Fast Adaptive Composite grid method (FAC) and its parallel variants (AFAC and AFACx). Theory that confirms the independence of the convergence rates of FAC and AFAC on the number of refinement levels exists under certain ellipticity and approximation property conditions. Similar theory needs to be developed for AFACx. The effectiveness of multigrid-based elliptic solvers such as FAC, AFAC, and AFACx on adaptively refined overlapping grids is not clearly understood. Finally, a non-trivial eye model problem will be solved by combining the power of using overlapping grids for complex moving geometries, AMR, and multilevel elliptic solvers.

  10. Prediction and Control of Network Cascade: Example of Power Grid or Networking Adaptability from WMD Disruption and Cascading Failures

    SciTech Connect

    Chertkov, Michael

    2012-07-24

    The goal of the DTRA project is to develop a mathematical framework that will provide the fundamental understanding of network survivability, algorithms for detecting/inferring pre-cursors of abnormal network behaviors, and methods for network adaptability and self-healing from cascading failures.

  11. Local adaptation of an introduced transgenic insect fungal pathogen due to new beneficial mutations.

    PubMed

    Wang, Sibao; O'Brien, Tammatha R; Pava-Ripoll, Monica; St Leger, Raymond J

    2011-12-20

    Genetically modified Metarhizium spp represent a major new arsenal for combating insect pests and insect-borne diseases. However, for these tools to be used safely and effectively, we need a much better understanding of their evolutionary potential and invasion ecology. In order to model natural as well as anthropogenic dispersal scenarios, we investigated evolutionary processes in a green fluorescent protein tagged strain of Metarhizium robertsii following transfer from a semitropical to a temperate soil community. Adaptive changes occurred over four years despite recurrent genetic bottlenecks and lack of recombination with locally well adapted strains. By coupling microarray-based functional analysis with DNA hybridizations we determined that expression of cell wall and stress response genes evolved at an accelerated rate in multiple replicates, whereas virulence determinants, transposons, and chromosome structure were unaltered. The mutable genes were enriched for TATA boxes possibly because they are larger mutational targets. In further field trials, we showed that the new mutations increased the fitness of M. robertsii in the new range by enhancing saprophytic associations, and these benefits were maintained in subsequent years. Consistent with selection being habitat rather than host specific, populations of an avirulent mutant cycled with seasons similarly to the wild type, whereas a mutant unable to adhere to plant roots showed a linear decrease in population. Our results provide a mechanistic basis for understanding postrelease adaptations, show that agents can be selected that lack gene flow and virulence evolution, and describe a means of genetically containing transgenic strains by disrupting the Mad2 gene. PMID:22143757

  12. Localization of Tubular Adaptation to Renal Sodium Loss in Gitelman Syndrome

    PubMed Central

    Nau, Valérie; Kolb, Isabelle; Vargas-Poussou, Rosa; Hannedouche, Thierry; Moulin, Bruno

    2012-01-01

    Summary Background and objectives Gitelman syndrome (GS) is a salt-wasting tubulopathy that results from the inactivation of the human thiazide–sensitive sodium chloride cotransporter located in the distal convoluted tubule. Tubular adaptation to renal sodium loss has been described and localized in the distal tubule in experimental models of GS but not in humans with GS. Design, setting, participants, & measurements The tubular adaptation to renal sodium loss is described. Osmole-free water clearance and endogenous lithium clearance with furosemide infusion are used to compare 7 patients with genetically confirmed GS and 13 control participants. Results Neither endogenous lithium clearance nor osmole-free water clearance disclosed enhanced proximal fluid reabsorption in patients with GS. These patients displayed significantly lower osmole-free water clearance factored by inulin clearance (7.1±1.9 versus 10.1±2.2; P<0.01) and significantly lower fractional sodium reabsorption in the diluting nephron (73.2%±7.1% versus 86.1%±4.7%; P<0.005), consistent with the inactivation of the thiazide-sensitive sodium chloride cotransporter. The furosemide-induced reduction rate of fractional sodium reabsorption in the diluting segment was higher in patients with GS (75.6%±6.1% versus 69.9%±3.2%; P<0.039), suggesting that sodium reabsorption would be enhanced in the cortical part of the thick ascending limb of the loop of Henle in patients with GS. Conclusions These findings suggest that tubular adaptation to renal sodium loss in GS would be devoted to the cortical part of the thick ascending limb of the loop of Henle in humans. PMID:22241817

  13. Multifluid adaptive-mesh simulation of the solar wind interaction with the local interstellar medium

    SciTech Connect

    Kryukov, I. A.; Borovikov, S. N.; Pogorelov, N. V.; Zank, G. P.

    2006-09-26

    DOE's SciDAC adaptive mesh refinement code Chombo has been modified for solution of compressible MHD flows with the application of high resolution, shock-capturing numerical schemes. The code developed is further extended to involve multiple fluids and applied to the problem of the solar wind interaction with the local interstellar medium. For this purpose, a set of MHD equations is solved together with a few sets of the Euler gas dynamics equations, depending on the number of neutral fluids included in the model. Our first results are presented that were obtained in the framework of an axially symmetric multifluid model which is applicable to magnetic-field-aligned flows. Details are shown of the generation and development of Rayleigh-Taylor and Kelvin-Helmholtz instabilities of the heliopause. A comparison is given of the results obtained with a two- and four-fluid models.

  14. Adaptation to Supernormal Auditory Localization Cues in AN Auditory Virtual Enrivonment.

    NASA Astrophysics Data System (ADS)

    Shinn-Cunningham, Barbara Gail

    An auditory virtual environment was used to investigate adaptation to transformed auditory localization cues which were "supernormal" in that physical cues were emphasized. A nonlinear transformation of the mapping from auditory localization cues to source position was used to create an artificial acoustic "fovea" in which cue resolution was enhanced directly in front of the subject and was decreased at the edges of the range. The experiments were driven in part by the fact that sensorimotor alterations will occur in all types of virtual environments, making it important to learn how such changes affect users of these systems. In addition, these experiments were designed to see whether better-than -normal performance could be achieved when supernormal localization cues were used. Bias and resolution were measured over time to see how changes in performance evolved with exposure to the altered cues. In all the experiments, mean response changed over time as expected, reducing the size of the average errors. Changes in bias were consistent with the changes in mean response, showing a reduction of about 50% at the end of the altered-cue exposure period. Resolution in the initial altered-cue run showed better-than-normal resolution in the fovea; however, resolution in the final altered -cue run tended to be smaller than the initial altered-cue test. Additional analysis showed that the mean responses during each run were always linearly related to the position that corresponded to the normal position of the cues before they were transformed. It was concluded that subjects did not adapt to the nonlinear transformation employed but rather to a linear approximation of the transformation. This mean slope (between perceived position and corresponding normal-cue position) changed exponentially over time, approaching an asymptote by the final altered -cue test. This asymptote was, on average, only 5% away from the slope of the line which minimized the mean-square error from

  15. An adaptive way for improving noise reduction using local geometric projection

    NASA Astrophysics Data System (ADS)

    Leontitsis, Alexandros; Bountis, Tassos; Pagge, Jenny

    2004-03-01

    We propose an adaptive way to improve noise reduction by local geometric projection. From the neighborhood of each candidate point in phase space, we identify the best subspace that the point will be orthogonally projected to. The signal subspace is formed by the most significant eigendirections of the neighborhood, while the less significant ones define the noise subspace. We provide a simple criterion to separate the most significant eigendirections from the less significant ones. This criterion is based on the maximum logarithmic difference between the neighborhood eigendirection lengths, and the assumption that there is at least one eigendirection that corresponds to the noise subspace. In this way, we take into account the special characteristics of each neighborhood and introduce a more successful noise reduction technique. Results are presented for a chaotic time series of the Hénon map and Ikeda map, as well as on the Nasdaq Composite index.

  16. PSO-based multiobjective optimization with dynamic population size and adaptive local archives.

    PubMed

    Leong, Wen-Fung; Yen, Gary G

    2008-10-01

    Recently, various multiobjective particle swarm optimization (MOPSO) algorithms have been developed to efficiently and effectively solve multiobjective optimization problems. However, the existing MOPSO designs generally adopt a notion to "estimate" a fixed population size sufficiently to explore the search space without incurring excessive computational complexity. To address the issue, this paper proposes the integration of a dynamic population strategy within the multiple-swarm MOPSO. The proposed algorithm is named dynamic population multiple-swarm MOPSO. An additional feature, adaptive local archives, is designed to improve the diversity within each swarm. Performance metrics and benchmark test functions are used to examine the performance of the proposed algorithm compared with that of five selected MOPSOs and two selected multiobjective evolutionary algorithms. In addition, the computational cost of the proposed algorithm is quantified and compared with that of the selected MOPSOs. The proposed algorithm shows competitive results with improved diversity and convergence and demands less computational cost. PMID:18784011

  17. Localized adaptive inflation in ensemble data assimilation for a radiation belt model

    NASA Astrophysics Data System (ADS)

    Godinez, H. C.; Koller, J.

    2012-08-01

    In this work a one-dimensional radial diffusion model for phase space density, together with observational satellite data, is used in an ensemble data assimilation with the purpose of accurately estimating Earth's radiation belt particle distribution. A particular concern in data assimilation for radiation belt models are model deficiencies, which can adversely impact the solution of the assimilation. To adequately address these deficiencies, a localized adaptive covariance inflation technique is implemented in the data assimilation to account for model uncertainty. Numerical results from identical-twin experiments, where data is generated from the same model, as well as the assimilation of real observational data, are presented. The results show improvement in the predictive skill of the model solution due to the proper inclusion of model errors in the data assimilation.

  18. A scale- and orientation-adaptive extension of Local Binary Patterns for texture classification

    PubMed Central

    Hegenbart, Sebastian; Uhl, Andreas

    2015-01-01

    Local Binary Patterns (LBPs) have been used in a wide range of texture classification scenarios and have proven to provide a highly discriminative feature representation. A major limitation of LBP is its sensitivity to affine transformations. In this work, we present a scale- and rotation-invariant computation of LBP. Rotation-invariance is achieved by explicit alignment of features at the extraction level, using a robust estimate of global orientation. Scale-adapted features are computed in reference to the estimated scale of an image, based on the distribution of scale normalized Laplacian responses in a scale-space representation. Intrinsic-scale-adaption is performed to compute features, independent of the intrinsic texture scale, leading to a significantly increased discriminative power for a large amount of texture classes. In a final step, the rotation- and scale-invariant features are combined in a multi-resolution representation, which improves the classification accuracy in texture classification scenarios with scaling and rotation significantly. PMID:26240440

  19. An automatic locally-adaptive method to estimate heavily-tailed breakthrough curves from particle distributions

    NASA Astrophysics Data System (ADS)

    Pedretti, Daniele; Fernàndez-Garcia, Daniel

    2013-09-01

    Particle tracking methods to simulate solute transport deal with the issue of having to reconstruct smooth concentrations from a limited number of particles. This is an error-prone process that typically leads to large fluctuations in the determined late-time behavior of breakthrough curves (BTCs). Kernel density estimators (KDE) can be used to automatically reconstruct smooth BTCs from a small number of particles. The kernel approach incorporates the uncertainty associated with subsampling a large population by equipping each particle with a probability density function. Two broad classes of KDE methods can be distinguished depending on the parametrization of this function: global and adaptive methods. This paper shows that each method is likely to estimate a specific portion of the BTCs. Although global methods offer a valid approach to estimate early-time behavior and peak of BTCs, they exhibit important fluctuations at the tails where fewer particles exist. In contrast, locally adaptive methods improve tail estimation while oversmoothing both early-time and peak concentrations. Therefore a new method is proposed combining the strength of both KDE approaches. The proposed approach is universal and only needs one parameter (α) which slightly depends on the shape of the BTCs. Results show that, for the tested cases, heavily-tailed BTCs are properly reconstructed with α ≈ 0.5 .

  20. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

    PubMed Central

    Dubin, Manu J; Zhang, Pei; Meng, Dazhe; Remigereau, Marie-Stanislas; Osborne, Edward J; Paolo Casale, Francesco; Drewe, Philipp; Kahles, André; Jean, Geraldine; Vilhjálmsson, Bjarni; Jagoda, Joanna; Irez, Selen; Voronin, Viktor; Song, Qiang; Long, Quan; Rätsch, Gunnar; Stegle, Oliver; Clark, Richard M; Nordborg, Magnus

    2015-01-01

    Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation. DOI: http://dx.doi.org/10.7554/eLife.05255.001 PMID:25939354

  1. Local adaptation and evolutionary potential along a temperature gradient in the fungal pathogen Rhynchosporium commune

    PubMed Central

    Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

    2013-01-01

    To predict the response of plant pathogens to climate warming, data are needed on current thermal adaptation, the pathogen's evolutionary potential, and the link between them. We conducted a common garden experiment using isolates of the fungal pathogen Rhynchosporium commune from nine barley populations representing climatically diverse locations. Clonal replicates of 126 genetically distinct isolates were assessed for their growth rate at 12°C, 18°C, and 22°C. Populations originating from climates with higher monthly temperature variation had higher growth rate at all three temperatures compared with populations from climates with less temperature fluctuation. Population differentiation in growth rate (QST) was significantly higher at 22°C than population differentiation for neutral microsatellite loci (GST), consistent with local adaptation for growth at higher temperatures. At 18°C, we found evidence for stabilizing selection for growth rate as QST was significantly lower than GST. Heritability of growth rate under the three temperatures was substantial in all populations (0.58–0.76). Genetic variation was lower in populations with higher growth rate at the three temperatures and evolvability increased under heat stress in seven of nine populations. Our findings imply that the distribution of this pathogen is unlikely to be genetically limited under climate warming, due to its high genetic variation and plasticity for thermal tolerance. PMID:23745143

  2. Cooperation, social networks, and the emergence of leadership in a prisoner's dilemma with adaptive local interactions.

    PubMed

    Zimmermann, Martín G; Eguíluz, Víctor M

    2005-11-01

    Cooperative behavior among a group of agents is studied assuming adaptive interactions. Each agent plays a Prisoner's Dilemma game with its local neighbors, collects an aggregate payoff, and imitates the strategy of its best neighbor. Agents may punish or reward their neighbors by removing or sustaining the interactions, according to their satisfaction level and strategy played. An agent may dismiss an interaction, and the corresponding neighbor is replaced by another randomly chosen agent, introducing diversity and evolution to the network structure. We perform an extensive numerical and analytical study, extending results in M. G. Zimmermann, V. M. Eguíluz, and M. San Miguel, Phys. Rev. E 69, 065102(R) (2004). We show that the system typically reaches either a full-defective state or a highly cooperative steady state. The latter equilibrium solution is composed mostly by cooperative agents, with a minor population of defectors that exploit the cooperators. It is shown how the network adaptation dynamics favors the emergence of cooperators with the highest payoff. These "leaders" are shown to sustain the global cooperative steady state. Also we find that the average payoff of defectors is larger than the average payoff of cooperators. Whenever "leaders" are perturbed (e.g., by addition of noise), an unstable situation arises and global cascades with oscillations between the nearly full defection network and the fully cooperative outcome are observed. PMID:16383699

  3. The placenta in toxicology. Part II: Systemic and local immune adaptations in pregnancy.

    PubMed

    Svensson-Arvelund, Judit; Ernerudh, Jan; Buse, Eberhard; Cline, J Mark; Haeger, Jan-Dirk; Dixon, Darlene; Markert, Udo R; Pfarrer, Christiane; De Vos, Paul; Faas, Marijke M

    2014-01-01

    During pregnancy, the maternal immune system is challenged by the semiallogeneic fetus, which must be tolerated without compromising fetal or maternal health. This review updates the systemic and local immune changes taking place during human pregnancy, including some examples in rodents. Systemic changes are induced by contact of maternal blood with placental factors and include enhanced innate immunity with increased activation of granulocytes and nonclassical monocytes. Although a bias toward T helper (Th2) and regulatory T cell (Treg) immunity has been associated with healthy pregnancy, the relationship between different circulating Th cell subsets is not straightforward. Instead, these adaptations appear most evidently at the fetal-maternal interface, where for instance Tregs are enriched and promote fetal tolerance. Also innate immune cells, that is, natural killer cells and macrophages, are enriched, constituting the majority of decidual leukocytes. These cells not only contribute to immune regulation but also aid in establishing the placenta by promoting trophoblast recruitment and angiogenesis. Thus, proper interaction between leukocytes and placental trophoblasts is necessary for normal placentation and immune adaptation. Consequently, spontaneous maladaptation or interference of the immune system with toxic substances may be important contributing factors for the development of pregnancy complications such as preeclampsia, preterm labor, and recurrent miscarriages. PMID:23531796

  4. Stent enhancement using a locally adaptive unsharp masking filter in digital x-ray fluoroscopy

    NASA Astrophysics Data System (ADS)

    Jiang, Yuhao; Ekanayake, Eranda

    2014-03-01

    Low exposure X-ray fluoroscopy is used to guide some complicate interventional procedures. Due to the inherent high levels of noise, improving the visibility of some interventional devices such as stent will greatly benefit those interventional procedures. Stent, which is made up of tiny steel wires, is also suffered from contrast dilutions of large flat panel detector pixels. A novel adaptive unsharp masking filter has been developed to improve stent contrast in real-time applications. In unsharp masking processing, the background is estimated and subtracted from the original input image to create a foreground image containing objects of interest. A background estimator is therefore critical in the unsharp masking processing. In this specific study, orientation filter kernels are used as the background estimator. To make the process simple and fast, the kernels average along a line of pixels. A high orientation resolution of 18° is used. A nonlinear operator is then used to combine the information from the images generated from convolving the original background and noise only images with orientation filters. A computerized Monte Carlo simulation followed by ROC study is used to identify the best nonlinear operator. We then apply the unsharp masking filter to the images with stents present. It is shown that the locally adaptive unsharp making filter is an effective filter for improving stent visibility in the interventional fluoroscopy. We also apply a spatio-temporal channelized human observer model to quantitatively optimize and evaluate the filter.

  5. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

    PubMed

    Dubin, Manu J; Zhang, Pei; Meng, Dazhe; Remigereau, Marie-Stanislas; Osborne, Edward J; Paolo Casale, Francesco; Drewe, Philipp; Kahles, André; Jean, Geraldine; Vilhjálmsson, Bjarni; Jagoda, Joanna; Irez, Selen; Voronin, Viktor; Song, Qiang; Long, Quan; Rätsch, Gunnar; Stegle, Oliver; Clark, Richard M; Nordborg, Magnus

    2015-01-01

    Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation. PMID:25939354

  6. Colwellia psychrerythraea strains from distant deep sea basins show adaptation to local conditions

    DOE PAGESBeta

    Techtmann, Stephen M.; Fitzgerald, Kathleen S.; Stelling, Savannah C.; Joyner, Dominique C.; Utturkar, Sagar M.; Harris, Austin P.; Alshibli, Noor K.; Brown, Steven D.; Hazen, Terry C.

    2016-05-09

    Many studies have shown that microbes, which share nearly identical 16S rRNA genes, can have highly divergent genomes. Microbes from distinct parts of the ocean also exhibit biogeographic patterning. Here in this study we seek to better understand how certain microbes from the same species have adapted for growth under local conditions. The phenotypic and genomic heterogeneity of three strains of Colwellia psychrerythraea was investigated in order to understand adaptions to local environments. Colwellia are psychrophilic heterotrophic marine bacteria ubiquitous in cold marine ecosystems. We have recently isolated two Colwellia strains: ND2E from the Eastern Mediterranean and GAB14E from themore » Great Australian Bight. The 16S rRNA sequence of these two strains were greater than 98.2% identical to the well-characterized C. psychrerythraea 34H, which was isolated from arctic sediments. Salt tolerance, and carbon source utilization profiles for these strains were determined using Biolog Phenotype MicoArrays. These strains exhibited distinct salt tolerance, which was not associated with the salinity of sites of isolation. The carbon source utilization profiles were distinct with less than half of the tested carbon sources being metabolized by all three strains. Whole genome sequencing revealed that the genomes of these three strains were quite diverse with some genomes having up to 1600 strain-specific genes. Many genes involved in degrading strain-specific carbon sources were identified. Finally, there appears to be a link between carbon source utilization and location of isolation with distinctions observed between the Colwellia isolate recovered from sediment compared to water column isolates.« less

  7. A local anisotropic adaptive algorithm for the solution of low-Mach transient combustion problems

    NASA Astrophysics Data System (ADS)

    Carpio, Jaime; Prieto, Juan Luis; Vera, Marcos

    2016-02-01

    A novel numerical algorithm for the simulation of transient combustion problems at low Mach and moderately high Reynolds numbers is presented. These problems are often characterized by the existence of a large disparity of length and time scales, resulting in the development of directional flow features, such as slender jets, boundary layers, mixing layers, or flame fronts. This makes local anisotropic adaptive techniques quite advantageous computationally. In this work we propose a local anisotropic refinement algorithm using, for the spatial discretization, unstructured triangular elements in a finite element framework. For the time integration, the problem is formulated in the context of semi-Lagrangian schemes, introducing the semi-Lagrange-Galerkin (SLG) technique as a better alternative to the classical semi-Lagrangian (SL) interpolation. The good performance of the numerical algorithm is illustrated by solving a canonical laminar combustion problem: the flame/vortex interaction. First, a premixed methane-air flame/vortex interaction with simplified transport and chemistry description (Test I) is considered. Results are found to be in excellent agreement with those in the literature, proving the superior performance of the SLG scheme when compared with the classical SL technique, and the advantage of using anisotropic adaptation instead of uniform meshes or isotropic mesh refinement. As a more realistic example, we then conduct simulations of non-premixed hydrogen-air flame/vortex interactions (Test II) using a more complex combustion model which involves state-of-the-art transport and chemical kinetics. In addition to the analysis of the numerical features, this second example allows us to perform a satisfactory comparison with experimental visualizations taken from the literature.

  8. Environmental associations with gene transcription in Babine Lake rainbow trout: evidence for local adaptation

    PubMed Central

    Wellband, Kyle W; Heath, Daniel D

    2013-01-01

    The molecular genetic mechanisms facilitating local adaptation in salmonids continue to be poorly characterized. Gene transcription is a highly regulated step in the expression of a phenotype and it has been shown to respond to selection and thus may be one mechanism that facilitates the development of local adaptation. Advances in molecular genetic tools and an increased understanding of the functional roles of specific genes allow us to test hypotheses concerning the role of variable environments in shaping transcription at known-function candidate loci. To address these hypotheses, wild rainbow trout were collected in their first summer and subjected to metabolic and immune challenges. We assayed gene transcription at candidate loci that play a role in the molecular genetic response to these stresses, and correlated transcription with temperature data from the streams and the abundance and diversity of bacteria as characterized by massively parallel pyrosequencing. Patterns of transcriptional regulation from resting to induced levels varied among populations for both treatments. Co-inertia analysis demonstrated significant associations between resting levels of metabolic gene transcription and thermal regime (R2 = 0.19, P = 0.013) as well as in response to challenge (R2 = 0.39, P = 0.001) and resting state and challenged levels of cytokine gene transcription with relative abundances of bacteria (resting: R2 = 0.25, P = 0.009, challenged: R2 = 0.65, P = 0.001). These results show that variable environments, even within a small geographic range (<250 km), can drive divergent selection among populations for transcription of genes related to surviving stress. PMID:23762507

  9. Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae).

    PubMed

    Rajora, Om P; Eckert, Andrew J; Zinck, John W R

    2016-01-01

    Natural plant populations are often adapted to their local climate and environmental conditions, and populations of forest trees offer some of the best examples of this pattern. However, little empirical work has focused on the relative contribution of single-locus versus multilocus effects to the genetic architecture of local adaptation in plants/forest trees. Here, we employ eastern white pine (Pinus strobus) to test the hypothesis that it is the inter-genic effects that primarily drive climate-induced local adaptation. The genetic structure of 29 range-wide natural populations of eastern white pine was determined in relation to local climatic factors using both a reference set of SSR markers, and SNPs located in candidate genes putatively involved in adaptive response to climate. Comparisons were made between marker sets using standard single-locus outlier analysis, single-locus and multilocus environment association analyses and a novel implementation of Population Graphs. Magnitudes of population structure were similar between the two marker sets. Outlier loci consistent with diversifying selection were rare for both SNPs and SSRs. However, genetic distances based on the multilocus among population covariances (cGD) were significantly more correlated to climate, even after correcting for spatial effects, for SNPs as compared to SSRs. Coalescent simulations confirmed that the differences in mutation rates between SSRs and SNPs did not affect the topologies of the Population Graphs, and hence values of cGD and their correlations with associated climate variables. We conclude that the multilocus covariances among populations primarily reflect adaptation to local climate and environment in eastern white pine. This result highlights the complexity of the genetic architecture of adaptive traits, as well as the need to consider multilocus effects in studies of local adaptation. PMID:27387485

  10. Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae)

    PubMed Central

    Zinck, John W. R.

    2016-01-01

    Natural plant populations are often adapted to their local climate and environmental conditions, and populations of forest trees offer some of the best examples of this pattern. However, little empirical work has focused on the relative contribution of single-locus versus multilocus effects to the genetic architecture of local adaptation in plants/forest trees. Here, we employ eastern white pine (Pinus strobus) to test the hypothesis that it is the inter-genic effects that primarily drive climate-induced local adaptation. The genetic structure of 29 range-wide natural populations of eastern white pine was determined in relation to local climatic factors using both a reference set of SSR markers, and SNPs located in candidate genes putatively involved in adaptive response to climate. Comparisons were made between marker sets using standard single-locus outlier analysis, single-locus and multilocus environment association analyses and a novel implementation of Population Graphs. Magnitudes of population structure were similar between the two marker sets. Outlier loci consistent with diversifying selection were rare for both SNPs and SSRs. However, genetic distances based on the multilocus among population covariances (cGD) were significantly more correlated to climate, even after correcting for spatial effects, for SNPs as compared to SSRs. Coalescent simulations confirmed that the differences in mutation rates between SSRs and SNPs did not affect the topologies of the Population Graphs, and hence values of cGD and their correlations with associated climate variables. We conclude that the multilocus covariances among populations primarily reflect adaptation to local climate and environment in eastern white pine. This result highlights the complexity of the genetic architecture of adaptive traits, as well as the need to consider multilocus effects in studies of local adaptation. PMID:27387485

  11. Adaptive meshless local maximum-entropy finite element method for convection-diffusion problems

    NASA Astrophysics Data System (ADS)

    Wu, C. T.; Young, D. L.; Hong, H. K.

    2014-01-01

    In this paper, a meshless local maximum-entropy finite element method (LME-FEM) is proposed to solve 1D Poisson equation and steady state convection-diffusion problems at various Peclet numbers in both 1D and 2D. By using local maximum-entropy (LME) approximation scheme to construct the element shape functions in the formulation of finite element method (FEM), additional nodes can be introduced within element without any mesh refinement to increase the accuracy of numerical approximation of unknown function, which procedure is similar to conventional p-refinement but without increasing the element connectivity to avoid the high conditioning matrix. The resulted LME-FEM preserves several significant characteristics of conventional FEM such as Kronecker-delta property on element vertices, partition of unity of shape function and exact reproduction of constant and linear functions. Furthermore, according to the essential properties of LME approximation scheme, nodes can be introduced in an arbitrary way and the continuity of the shape function along element edge is kept at the same time. No transition element is needed to connect elements of different orders. The property of arbitrary local refinement makes LME-FEM be a numerical method that can adaptively solve the numerical solutions of various problems where troublesome local mesh refinement is in general necessary to obtain reasonable solutions. Several numerical examples with dramatically varying solutions are presented to test the capability of the current method. The numerical results show that LME-FEM can obtain much better and stable solutions than conventional FEM with linear element.

  12. Global and local concerns: what attitudes and beliefs motivate farmers to mitigate and adapt to climate change?

    PubMed

    Haden, Van R; Niles, Meredith T; Lubell, Mark; Perlman, Joshua; Jackson, Louise E

    2012-01-01

    In response to agriculture's vulnerability and contribution to climate change, many governments are developing initiatives that promote the adoption of mitigation and adaptation practices among farmers. Since most climate policies affecting agriculture rely on voluntary efforts by individual farmers, success requires a sound understanding of the factors that motivate farmers to change practices. Recent evidence suggests that past experience with the effects of climate change and the psychological distance associated with people's concern for global and local impacts can influence environmental behavior. Here we surveyed farmers in a representative rural county in California's Central Valley to examine how their intention to adopt mitigation and adaptation practices is influenced by previous climate experiences and their global and local concerns about climate change. Perceived changes in water availability had significant effects on farmers' intention to adopt mitigation and adaptation strategies, which were mediated through global and local concerns respectively. This suggests that mitigation is largely motivated by psychologically distant concerns and beliefs about climate change, while adaptation is driven by psychologically proximate concerns for local impacts. This match between attitudes and behaviors according to the psychological distance at which they are cognitively construed indicates that policy and outreach initiatives may benefit by framing climate impacts and behavioral goals concordantly; either in a global context for mitigation or a local context for adaptation. PMID:23300805

  13. Global and Local Concerns: What Attitudes and Beliefs Motivate Farmers to Mitigate and Adapt to Climate Change?

    PubMed Central

    Haden, Van R.; Niles, Meredith T.; Lubell, Mark; Perlman, Joshua; Jackson, Louise E.

    2012-01-01

    In response to agriculture's vulnerability and contribution to climate change, many governments are developing initiatives that promote the adoption of mitigation and adaptation practices among farmers. Since most climate policies affecting agriculture rely on voluntary efforts by individual farmers, success requires a sound understanding of the factors that motivate farmers to change practices. Recent evidence suggests that past experience with the effects of climate change and the psychological distance associated with people's concern for global and local impacts can influence environmental behavior. Here we surveyed farmers in a representative rural county in California's Central Valley to examine how their intention to adopt mitigation and adaptation practices is influenced by previous climate experiences and their global and local concerns about climate change. Perceived changes in water availability had significant effects on farmers' intention to adopt mitigation and adaptation strategies, which were mediated through global and local concerns respectively. This suggests that mitigation is largely motivated by psychologically distant concerns and beliefs about climate change, while adaptation is driven by psychologically proximate concerns for local impacts. This match between attitudes and behaviors according to the psychological distance at which they are cognitively construed indicates that policy and outreach initiatives may benefit by framing climate impacts and behavioral goals concordantly; either in a global context for mitigation or a local context for adaptation. PMID:23300805

  14. Decision Support from Local Data: Creating Adaptive Order Menus from Past Clinician Behavior

    PubMed Central

    Klann, Jeffrey G.; Szolovits, Peter; Downs, Stephen; Schadow, Gunther

    2014-01-01

    Objective Reducing care variability through guidelines has significantly benefited patients. Nonetheless, guideline-based clinical decision support (CDS) systems are not widely implemented or used, are frequently out-of-date, and cannot address complex care for which guidelines do not exist. Here, we develop and evaluate a complementary approach - using Bayesian network (BN) learning to generate adaptive, context-specific treatment menus based on local order-entry data. These menus can be used as a draft for expert review, in order to minimize development time for local decision support content. This is in keeping with the vision outlined in the US Health Information Technology Strategic Plan, which describes a healthcare system that learns from itself. Materials and Methods We used the Greedy Equivalence Search algorithm to learn four 50-node domain-specific BNs from 11,344 encounters: abdominal pain in the emergency department, inpatient pregnancy, hypertension in the urgent visit clinic, and altered mental state in the intensive care unit. We developed a system to produce situation-specific, rank-ordered treatment menus from these networks. We evaluated this system with a hospital-simulation methodology and computed Area Under the Receiver-Operator Curve (AUC) and average menu position at time of selection. We also compared this system with a similar association-rule-mining approach. Results A short order menu on average contained the next order (weighted average length 3.91–5.83 items). Overall predictive ability was good: average AUC above 0.9 for 25% of order types and overall average AUC .714–.844 (depending on domain). However, AUC had high variance (.50–.99). Higher AUC correlated with tighter clusters and more connections in the graphs, indicating importance of appropriate contextual data. Comparison with an association rule mining approach showed similar performance for only the most common orders with dramatic divergence as orders are less

  15. Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations.

    PubMed

    Platt, Alexander; Gugger, Paul F; Pellegrini, Matteo; Sork, Victoria L

    2015-08-01

    It has long been known that adaptive evolution can occur through genetic mutations in DNA sequence, but it is unclear whether adaptive evolution can occur through analogous epigenetic mechanisms, such as through DNA methylation. If epigenetic variation contributes directly to evolution, species under threat of disease, invasive competition, climate change or other stresses would have greater stores of variation from which to draw. We looked for evidence of natural selection acting on variably methylated DNA sites using population genomic analysis across three climatologically distinct populations of valley oaks. We found patterns of genetic and epigenetic differentiations that indicate local adaptation is operating on large portions of the oak genome. While CHG methyl polymorphisms are not playing a significant role and would make poor targets for natural selection, our findings suggest that CpG methyl polymorphisms as a whole are involved in local adaptation, either directly or through linkage to regions under selection. PMID:25951436

  16. Locally-Adaptive, Spatially-Explicit Projection of U.S. Population for 2030 and 2050

    DOE PAGESBeta

    McKee, Jacob J.; Rose, Amy N.; Bright, Eddie A.; Huynh, Timmy N.; Bhaduri, Budhendra L.

    2015-02-03

    Localized adverse events, including natural hazards, epidemiological events, and human conflict, underscore the criticality of quantifying and mapping current population. Moreover, knowing the spatial distribution of future population allows for increased preparation in the event of an emergency. Building on the spatial interpolation technique previously developed for high resolution population distribution data (LandScan Global and LandScan USA), we have constructed an empirically-informed spatial distribution of the projected population of the contiguous U.S. for 2030 and 2050. Whereas most current large-scale, spatially explicit population projections typically rely on a population gravity model to determine areas of future growth, our projection modelmore » departs from these by accounting for multiple components that affect population distribution. Modelled variables, which included land cover, slope, distances to larger cities, and a moving average of current population, were locally adaptive and geographically varying. The resulting weighted surface was used to determine which areas had the greatest likelihood for future population change. Population projections of county level numbers were developed using a modified version of the U.S. Census s projection methodology with the U.S. Census s official projection as the benchmark. Applications of our model include, but are not limited to, suitability modelling, service area planning for governmental agencies, consequence assessment, mitigation planning and implementation, and assessment of spatially vulnerable populations.« less

  17. Locally-Adaptive, Spatially-Explicit Projection of U.S. Population for 2030 and 2050

    SciTech Connect

    McKee, Jacob J.; Rose, Amy N.; Bright, Eddie A.; Huynh, Timmy N.; Bhaduri, Budhendra L.

    2015-02-03

    Localized adverse events, including natural hazards, epidemiological events, and human conflict, underscore the criticality of quantifying and mapping current population. Moreover, knowing the spatial distribution of future population allows for increased preparation in the event of an emergency. Building on the spatial interpolation technique previously developed for high resolution population distribution data (LandScan Global and LandScan USA), we have constructed an empirically-informed spatial distribution of the projected population of the contiguous U.S. for 2030 and 2050. Whereas most current large-scale, spatially explicit population projections typically rely on a population gravity model to determine areas of future growth, our projection model departs from these by accounting for multiple components that affect population distribution. Modelled variables, which included land cover, slope, distances to larger cities, and a moving average of current population, were locally adaptive and geographically varying. The resulting weighted surface was used to determine which areas had the greatest likelihood for future population change. Population projections of county level numbers were developed using a modified version of the U.S. Census s projection methodology with the U.S. Census s official projection as the benchmark. Applications of our model include, but are not limited to, suitability modelling, service area planning for governmental agencies, consequence assessment, mitigation planning and implementation, and assessment of spatially vulnerable populations.

  18. An adaptive localization system for outdoor/indoor navigation for autonomous robots

    NASA Astrophysics Data System (ADS)

    Pacis, E. B.; Sights, B.; Ahuja, G.; Kogut, G.; Everett, H. R.

    2006-05-01

    Many envisioned applications of mobile robotic systems require the robot to navigate in complex urban environments. This need is particularly critical if the robot is to perform as part of a synergistic team with human forces in military operations. Historically, the development of autonomous navigation for mobile robots has targeted either outdoor or indoor scenarios, but not both, which is not how humans operate. This paper describes efforts to fuse component technologies into a complete navigation system, allowing a robot to seamlessly transition between outdoor and indoor environments. Under the Joint Robotics Program's Technology Transfer project, empirical evaluations of various localization approaches were conducted to assess their maturity levels and performance metrics in different exterior/interior settings. The methodologies compared include Markov localization, global positioning system, Kalman filtering, and fuzzy-logic. Characterization of these technologies highlighted their best features, which were then fused into an adaptive solution. A description of the final integrated system is discussed, including a presentation of the design, experimental results, and a formal demonstration to attendees of the Unmanned Systems Capabilities Conference II in San Diego in December 2005.

  19. Parallel evolution of local adaptation and reproductive isolation in the face of gene flow.

    PubMed

    Butlin, Roger K; Saura, Maria; Charrier, Grégory; Jackson, Benjamin; André, Carl; Caballero, Armando; Coyne, Jerry A; Galindo, Juan; Grahame, John W; Hollander, Johan; Kemppainen, Petri; Martínez-Fernández, Mónica; Panova, Marina; Quesada, Humberto; Johannesson, Kerstin; Rolán-Alvarez, Emilio

    2014-04-01

    Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to either wave action or crab predation. This divergence is associated with barriers to gene exchange but, nevertheless, genetic variation is more strongly structured by geography than by ecotype. Using approximate Bayesian analysis of sequence data and amplified fragment length polymorphism markers, we show that the ecotypes are likely to have arisen in the face of continuous gene flow and that the demographic separation of ecotypes has occurred in parallel at both regional and local scales. Parameter estimates suggest a long delay between colonization of a locality and ecotype formation, perhaps because the postglacial spread of crab populations was slower than the spread of snails. Adaptive differentiation may not be fully genetically independent despite being demographically parallel. These results provide new insight into a major model of ecologically driven speciation. PMID:24299519

  20. PARALLEL EVOLUTION OF LOCAL ADAPTATION AND REPRODUCTIVE ISOLATION IN THE FACE OF GENE FLOW

    PubMed Central

    Butlin, Roger K; Saura, Maria; Charrier, Grégory; Jackson, Benjamin; André, Carl; Caballero, Armando; Coyne, Jerry A; Galindo, Juan; Grahame, John W; Hollander, Johan; Kemppainen, Petri; Martínez-Fernández, Mónica; Panova, Marina; Quesada, Humberto; Johannesson, Kerstin; Rolán-Alvarez, Emilio

    2014-01-01

    Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to either wave action or crab predation. This divergence is associated with barriers to gene exchange but, nevertheless, genetic variation is more strongly structured by geography than by ecotype. Using approximate Bayesian analysis of sequence data and amplified fragment length polymorphism markers, we show that the ecotypes are likely to have arisen in the face of continuous gene flow and that the demographic separation of ecotypes has occurred in parallel at both regional and local scales. Parameter estimates suggest a long delay between colonization of a locality and ecotype formation, perhaps because the postglacial spread of crab populations was slower than the spread of snails. Adaptive differentiation may not be fully genetically independent despite being demographically parallel. These results provide new insight into a major model of ecologically driven speciation. PMID:24299519

  1. SuBSENSE: a universal change detection method with local adaptive sensitivity.

    PubMed

    St-Charles, Pierre-Luc; Bilodeau, Guillaume-Alexandre; Bergevin, Robert

    2015-01-01

    Foreground/background segmentation via change detection in video sequences is often used as a stepping stone in high-level analytics and applications. Despite the wide variety of methods that have been proposed for this problem, none has been able to fully address the complex nature of dynamic scenes in real surveillance tasks. In this paper, we present a universal pixel-level segmentation method that relies on spatiotemporal binary features as well as color information to detect changes. This allows camouflaged foreground objects to be detected more easily while most illumination variations are ignored. Besides, instead of using manually set, frame-wide constants to dictate model sensitivity and adaptati