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. Staggered grid lagrangian method with local structured adaptive mesh refinement for modeling shock hydrodynamics

    SciTech Connect

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

    2000-09-26

    A new method for the solution of the unsteady Euler equations has been developed. The method combines staggered grid Lagrangian techniques with structured local adaptive mesh refinement (AMR). This method is a precursor to a more general adaptive arbitrary Lagrangian Eulerian (ALE-AMR) algorithm under development, which will facilitate 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. Many of the core issues involved in the development of the ALE-AMR method hinge upon the integration of AMR with a Lagrange step, which is the focus of the work described here. 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. These new algorithmic components are first developed in one dimension and are then generalized to two dimensions. Solutions of several model problems involving shock hydrodynamics are presented and discussed.

  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. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. A comparison of the structures of lean and rich axisymmetric laminar Bunsen flames: application of local rectangular refinement solution-adaptive gridding

    NASA Astrophysics Data System (ADS)

    Bennett, Beth Anne V.; Fielding, Joseph; Mauro, Richard J.; Long, Marshall B.; Smooke, Mitchell D.

    1999-12-01

    Axisymmetric laminar methane-air Bunsen flames are computed for two equivalence ratios: lean (icons/Journals/Common/Phi" ALT="Phi" ALIGN="TOP"/> = 0.776), in which the traditional Bunsen cone forms above the burner; and rich (icons/Journals/Common/Phi" ALT="Phi" ALIGN="TOP"/> = 1.243), in which the premixed Bunsen cone is accompanied by a diffusion flame halo located further downstream. Because the extremely large gradients at premixed flame fronts greatly exceed those in diffusion flames, their resolution requires a more sophisticated adaptive numerical method than those ordinarily applied to diffusion flames. The local rectangular refinement (LRR) solution-adaptive gridding method produces robust unstructured rectangular grids, utilizes multiple-scale finite-difference discretizations, and incorporates Newton's method to solve elliptic partial differential equation systems simultaneously. The LRR method is applied to the vorticity-velocity formulation of the fully elliptic governing equations, in conjunction with detailed chemistry, multicomponent transport and an optically-thin radiation model. The computed lean flame is lifted above the burner, and this liftoff is verified experimentally. For both lean and rich flames, grid spacing greatly influences the Bunsen cone's position, which only stabilizes with adequate refinement. In the rich configuration, the oxygen-free region above the Bunsen cone inhibits the complete decay of CH4, thus indirectly initiating the diffusion flame halo where CO oxidizes to CO2. In general, the results computed by the LRR method agree quite well with those obtained on equivalently refined conventional grids, yet the former require less than half the computational resources.

  16. 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.

  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. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. Visualizing 3D Turbulence On Temporally Adaptive Wavelet Collocation Grids

    NASA Astrophysics Data System (ADS)

    Goldstein, D. E.; Kadlec, B. J.; Yuen, D. A.; Erlebacher, G.

    2005-12-01

    Today there is an explosion in data from high-resolution computations of nonlinear phenomena in many fields, including the geo- and environmental sciences. The efficient storage and subsequent visualization of these large data sets is a trade off in storage costs versus data quality. New dynamically adaptive simulation methodologies promise significant computational cost savings and have the added benefit of producing results on adapted grids that significantly reduce storage and data manipulation costs. Yet, with these adaptive simulation methodologies come new challenges in the visualization of temporally adaptive data sets. In this work turbulence data sets from Stochastic Coherent Adaptive Large Eddy Simulations (SCALES) are visualized with the open source tool ParaView, as a challenging case study. SCALES simulations use a temporally adaptive collocation grid defined by wavelet threshold filtering to resolve the most energetic coherent structures in a turbulence field. A subgrid scale model is used to account for the effect of unresolved subgrid scale modes. The results from the SCALES simulations are saved on a thresholded dyadic wavelet collocation grid, which by its nature does not include cell information. Paraview is an open source visualization package developed by KitWare(tm) that is based on the widely used VTK graphics toolkit. The efficient generation of cell information, required with current ParaView data formats, is explored using custom algorithms and VTK toolkit routines. Adaptive 3d visualizations using isosurfaces and volume visualizations are compared with non-adaptive visualizations. To explore the localized multiscale structures in the turbulent data sets the wavelet coefficients are also visualized allowing visualization of energy contained in local physical regions as well as in local wave number space.

  7. 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.

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

    NASA Technical Reports Server (NTRS)

    Chen, S. C.

    1988-01-01

    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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. An adaptive grid method for computing time accurate solutions on structured grids

    NASA Technical Reports Server (NTRS)

    Bockelie, Michael J.; Smith, Robert E.; Eiseman, Peter R.

    1991-01-01

    The solution method consists of three parts: a grid movement scheme; an unsteady Euler equation solver; and a temporal coupling routine that links the dynamic grid to the Euler solver. The grid movement scheme is an algebraic method containing grid controls that generate a smooth grid that resolves the severe solution gradients and the sharp transitions in the solution gradients. The temporal coupling is performed with a grid prediction correction procedure that is simple to implement and provides a grid that does not lag the solution in time. The adaptive solution method is tested by computing the unsteady inviscid solutions for a one dimensional shock tube and a two dimensional shock vortex iteraction.

  15. 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.

  16. Adapting Grids For Computing Two-Dimensional Flows

    NASA Technical Reports Server (NTRS)

    Davies, Carol B.; Venkatapathy, Ethiraj

    1992-01-01

    SAGE2D is two-dimensional implementation of Self Adaptive Grid Evolution computer program that intelligently redistributes initial grid points on basis of initial flow-field solution. Grids modified according to initial computed flows enabling recomputation at greater accuracy. Written in FORTRAN 77.

  17. 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.

  18. 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.

  19. Local Adaptation in Marine Invertebrates

    NASA Astrophysics Data System (ADS)

    Sanford, Eric; Kelly, Morgan W.

    2011-01-01

    Local adaptation in the sea was regarded historically as a rare phenomenon that was limited to a handful of species with exceptionally low dispersal potential. However, a growing body of experimental studies indicates that adaptive differentiation occurs in numerous marine invertebrates in response to selection imposed by strong gradients (and more complex mosaics) of abiotic and biotic conditions. Moreover, a surprisingly high proportion of the marine invertebrates known or suspected of exhibiting local adaptation are species with planktonic dispersal. Adaptive divergence among populations can occur over a range of spatial scales, including those that are fine-grained (i.e., meters to kilometers), reflecting a balance between scales of gene flow and selection. Addressing the causes and consequences of adaptive genetic differentiation among invertebrate populations promises to advance community ecology, climate change research, and the effective management of marine ecosystems.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Adaptive mesh refinement in curvilinear body-fitted grid systems

    NASA Astrophysics Data System (ADS)

    Steinthorsson, Erlendur; Modiano, David; Colella, Phillip

    1995-10-01

    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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  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. Three-dimensional Navier-Stokes calculations using solution-adapted grids

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

    A three-dimensional solution-adaptive grid generation technique is presented. The adaptation technique redistributes grid points to improve the accuracy of a flow solution without increasing the number of grid points. It is applicable to structured grids with a multiblock topology. The method uses a numerical mapping and potential theory to modify the initial grid distribution based on the properties of the flow solution on the initial grid. The technique is demonstrated with two examples - a transonic finite wing and a supersonic blunt fin. The advantages are shown by comparing flow solutions on the adapted grids with those on the initial grids.

  2. Genomics of local adaptation with gene flow.

    PubMed

    Tigano, Anna; Friesen, Vicki L

    2016-05-01

    Gene flow is a fundamental evolutionary force in adaptation that is especially important to understand as humans are rapidly changing both the natural environment and natural levels of gene flow. Theory proposes a multifaceted role for gene flow in adaptation, but it focuses mainly on the disruptive effect that gene flow has on adaptation when selection is not strong enough to prevent the loss of locally adapted alleles. The role of gene flow in adaptation is now better understood due to the recent development of both genomic models of adaptive evolution and genomic techniques, which both point to the importance of genetic architecture in the origin and maintenance of adaptation with gene flow. In this review, we discuss three main topics on the genomics of adaptation with gene flow. First, we investigate selection on migration and gene flow. Second, we discuss the three potential sources of adaptive variation in relation to the role of gene flow in the origin of adaptation. Third, we explain how local adaptation is maintained despite gene flow: we provide a synthesis of recent genomic models of adaptation, discuss the genomic mechanisms and review empirical studies on the genomics of adaptation with gene flow. Despite predictions on the disruptive effect of gene flow in adaptation, an increasing number of studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow.

  3. Evaluation of truncation error and adaptive grid generation for the transonic full potential flow calculations

    NASA Technical Reports Server (NTRS)

    Nakamura, S.

    1983-01-01

    The effects of truncation error on the numerical solution of transonic flows using the full potential equation are studied. The effects of adapting grid point distributions to various solution aspects including shock waves is also discussed. A conclusion is that a rapid change of grid spacing is damaging to the accuracy of the flow solution. Therefore, in a solution adaptive grid application an optimal grid is obtained as a tradeoff between the amount of grid refinement and the rate of grid stretching.

  4. Multigrid-based grid-adaptive solution of the Navier-Stokes equations

    NASA Astrophysics Data System (ADS)

    Michelsen, Jess

    A finite volume scheme for solution of the incompressible Navier-Stokes equations in two dimensions and axisymmetry is described. Solutions are obtained on nonorthogonal, solution adaptive BFC grids, based on the Brackbill-Saltzman generator. Adaptivity is achieved by the use of a single control function based on the local kinetic energy production. Nonstaggered allocation of pressure and Cartesian velocity components avoids the introduction of curvature terms associated with the use of a grid-direction vector-base. A special interpolation of the pressure correction equation in the SIMPLE algorithm ensures firm coupling between velocity and pressure field. Steady-state solutions are accelerated by a full approximation multigrid scheme working on the decoupled grid-flow problem, while an algebraic multigrid scheme is employed for the pressure correction equation.

  5. 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.

  6. Unstructured viscous flow solution using adaptive hybrid grids

    NASA Technical Reports Server (NTRS)

    Galle, Martin

    1995-01-01

    A three dimensional finite volume scheme based on hybrid grids containing both tetrahedral and hexahedral cells is presented. The application to hybrid grids offers the possibility to combine the flexibility of tetrahedral meshes with the accuracy of hexahedral grids. An algorithm to compute a dual mesh for the entire computational domain was developed. The dual mesh technique guarantees conservation in the whole flow field even at interfaces between hexahedral and tetrahedral domains and enables the employment of an accurate upwind flow solver. The hybrid mesh can be adapted to the solution by dividing cells in areas of insufficient resolution. The method is tested on different viscous and inviscid cases for hypersonic, transonic and subsonic flows.

  7. Solution adaptive grids applied to low Reynolds number flow

    NASA Astrophysics Data System (ADS)

    de With, G.; Holdø, A. E.; Huld, T. A.

    2003-08-01

    A numerical study has been undertaken to investigate the use of a solution adaptive grid for flow around a cylinder in the laminar flow regime. The main purpose of this work is twofold. The first aim is to investigate the suitability of a grid adaptation algorithm and the reduction in mesh size that can be obtained. Secondly, the uniform asymmetric flow structures are ideal to validate the mesh structures due to mesh refinement and consequently the selected refinement criteria. The refinement variable used in this work is a product of the rate of strain and the mesh cell size, and contains two variables Cm and Cstr which determine the order of each term. By altering the order of either one of these terms the refinement behaviour can be modified.

  8. On the dynamics of some grid adaption schemes

    NASA Technical Reports Server (NTRS)

    Sweby, Peter K.; Yee, Helen C.

    1994-01-01

    The dynamics of a one-parameter family of mesh equidistribution schemes coupled with finite difference discretisations of linear and nonlinear convection-diffusion model equations is studied numerically. It is shown that, when time marched to steady state, the grid adaption not only influences the stability and convergence rate of the overall scheme, but can also introduce spurious dynamics to the numerical solution procedure.

  9. 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.

  10. Some aspects of adaptive grid technology related to boundary and interior layers

    NASA Astrophysics Data System (ADS)

    Carey, Graham F.; Anderson, M.; Carnes, B.; Kirk, B.

    2004-04-01

    We consider the use of adaptive mesh strategies for solution of problems exhibiting boundary and interior layer solutions. As the presence of these layer structures suggests, reliable and accurate solution of this class of problems using finite difference, finite volume or finite element schemes requires grading the mesh into the layers and due attention to the associated algorithms. When the nature and structure of the layer is known, mesh grading can be achieved during the grid generation by specifying an appropriate grading function. However, in many applications the location and nature of the layer behavior is not known in advance. Consequently, adaptive mesh techniques that employ feedback from intermediate grid solutions are an appealing approach. In this paper, we provide a brief overview of the main adaptive grid strategies in the context of problems with layers. Associated error indicators that guide the refinement feedback control/grid optimization process are also covered and there is a brief commentary on the supporting data structure requirements. Some current issues concerning the use of stabilization in conjunction with adaptive mesh refinement (AMR), the question of "pollution effects" in computation of local error indicators, the influence of nonlinearities and the design of meshes for targeted optimization of specific quantities are considered. The application of AMR for layer problems is illustrated by means of case studies from semiconductor device transport (drift diffusion), nonlinear reaction-diffusion, layers due to surface capillary effects, and shockwaves in compressible gas dynamics.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. An adaptive grid refinement strategy for the simulation of negative streamers

    SciTech Connect

    Montijn, C. . E-mail: carolynne.montijn@cwi.nl; Hundsdorfer, W. . E-mail: willem.hundsdorfer@cwi.nl; Ebert, U. . E-mail: ute.ebert@cwi.nl

    2006-12-10

    The evolution of negative streamers during electric breakdown of a non-attaching gas can be described by a two-fluid model for electrons and positive ions. It consists of continuity equations for the charged particles including drift, diffusion and reaction in the local electric field, coupled to the Poisson equation for the electric potential. The model generates field enhancement and steep propagating ionization fronts at the tip of growing ionized filaments. An adaptive grid refinement method for the simulation of these structures is presented. It uses finite volume spatial discretizations and explicit time stepping, which allows the decoupling of the grids for the continuity equations from those for the Poisson equation. Standard refinement methods in which the refinement criterion is based on local error monitors fail due to the pulled character of the streamer front that propagates into a linearly unstable state. We present a refinement method which deals with all these features. Tests on one-dimensional streamer fronts as well as on three-dimensional streamers with cylindrical symmetry (hence effectively 2D for numerical purposes) are carried out successfully. Results on fine grids are presented, they show that such an adaptive grid method is needed to capture the streamer characteristics well. This refinement strategy enables us to adequately compute negative streamers in pure gases in the parameter regime where a physical instability appears: branching streamers.

  19. 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...

  20. 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.

  1. 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.

  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. 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.

  4. 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).

  5. 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.

  6. 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

  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. Adaptive sparse grid expansions of the vibrational Hamiltonian.

    PubMed

    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.

  9. 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.

  10. Local climatic adaptation in a widespread microorganism.

    PubMed

    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

    2014-02-22

    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.

  11. 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

  12. Parallel, grid-adaptive approaches for relativistic hydro and magnetohydrodynamics

    NASA Astrophysics Data System (ADS)

    Keppens, R.; Meliani, Z.; van Marle, A. J.; Delmont, P.; Vlasis, A.; van der Holst, B.

    2012-02-01

    Relativistic hydro and magnetohydrodynamics provide continuum fluid descriptions for gas and plasma dynamics throughout the visible universe. We present an overview of state-of-the-art modeling in special relativistic regimes, targeting strong shock-dominated flows with speeds approaching the speed of light. Significant progress in its numerical modeling emerged in the last two decades, and we highlight specifically the need for grid-adaptive, shock-capturing treatments found in several contemporary codes in active use and development. Our discussion highlights one such code, MPI-AMRVAC (Message-Passing Interface-Adaptive Mesh Refinement Versatile Advection Code), but includes generic strategies for allowing massively parallel, block-tree adaptive simulations in any dimensionality. We provide implementation details reflecting the underlying data structures as used in MPI-AMRVAC. Parallelization strategies and scaling efficiencies are discussed for representative applications, along with guidelines for data formats suitable for parallel I/O. Refinement strategies available in MPI-AMRVAC are presented, which cover error estimators in use in many modern AMR frameworks. A test suite for relativistic hydro and magnetohydrodynamics is provided, chosen to cover all aspects encountered in high-resolution, shock-governed astrophysical applications. This test suite provides ample examples highlighting the advantages of AMR in relativistic flow problems.

  13. 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.

  14. 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.

  15. Adaptive predictive image coding using local characteristics

    NASA Astrophysics Data System (ADS)

    Hsieh, C. H.; Lu, P. C.; Liou, W. G.

    1989-12-01

    The paper presents an efficient adaptive predictive coding method using the local characteristics of images. In this method, three coding schemes, namely, mean, subsampling combined with fixed DPCM, and ADPCM/PCM, are used and one of these is chosen adaptively based on the local characteristics of images. The prediction parameters of the two-dimensional linear predictor in the ADPCM/PCM are extracted on a block by block basis. Simulation results show that the proposed method is effective in reducing the slope overload distortion and the granular noise at low bit rates, and thus it can improve the visual quality of reconstructed images.

  16. Adaptive 3D single-block grids for the computation of viscous flows around wings

    SciTech Connect

    Hagmeijer, R.; Kok, J.C.

    1996-12-31

    A robust algorithm for the adaption of a 3D single-block structured grid suitable for the computation of viscous flows around a wing is presented and demonstrated by application to the ONERA M6 wing. The effects of grid adaption on the flow solution and accuracy improvements is analyzed. Reynolds number variations are studied.

  17. An Arbitrary Lagrangian-Eulerian Method with Local Adaptive Mesh Refinement for Modeling Compressible Flow

    NASA Astrophysics Data System (ADS)

    Anderson, Robert; Pember, Richard; Elliott, Noah

    2001-11-01

    We present a method, ALE-AMR, for modeling unsteady compressible flow that combines a staggered grid arbitrary Lagrangian-Eulerian (ALE) scheme with structured local adaptive mesh refinement (AMR). The ALE method is a three step scheme on a staggered grid of quadrilateral cells: Lagrangian advance, mesh relaxation, and remap. The AMR scheme uses a mesh hierarchy that is dynamic in time and is composed of nested structured grids of varying resolution. The integration algorithm on the hierarchy is a recursive procedure in which the coarse grids are advanced a single time step, the fine grids are advanced to the same time, and the coarse and fine grid solutions are synchronized. The novel details of ALE-AMR are primarily motivated by the need to reconcile and extend AMR techniques typically employed for stationary rectangular meshes with cell-centered quantities to the moving quadrilateral meshes with staggered quantities used in the ALE scheme. Solutions of several test problems are discussed.

  18. 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.

  19. 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.

  20. An adaptive grid method for computing the high speed 3D viscous flow about a re-entry vehicle

    NASA Technical Reports Server (NTRS)

    Bockelie, Michael J.; Smith, Robert E.

    1992-01-01

    An algebraic solution adaptive grid generation method that allows adapting the grid in all three coordinate directions is presented. Techniques are described that maintain the integrity of the original vehicle definition for grid point movement on the vehicle surface and that avoid grid cross over in the boundary layer portion of the grid lying next to the vehicle surface. The adaptive method is tested by computing the Mach 6 hypersonic three dimensional viscous flow about a proposed Martian entry vehicle.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Three-dimensional solution-adaptive grid generation of composite configurations

    NASA Astrophysics Data System (ADS)

    Tu, Yen

    A solution adaptive grid generation procedure is developed and applied to 3-D inviscid transonic fluid flow around complex geometries using a composite block grid structure. The adaptation is based upon control functions in an elliptic grid generation system. The control function is constructed in a manner such that a proper grid network can be generated as a fluid flow solution is evolving. The grid network is boundary conforming for accurate representation of boundary conditions. The procedure implemented allows orthodonality at boundaries for more accurate computations, while smoothness is implicit in the elliptic equations. The approach allows multiple block grid systems to be constructed to treat complex configurations as well. The solution adaptive computational procedure was accomplished by coupling the elliptic grid generation technique with an implicit, finite volume, upwind Euler flow solver. In simulating trasonic fluid flow around finned body of revolution and a multiple store configuration, the grid systems adapt to pressure gradients in the flow field. Results obtained show that the technique is capable of generating grid networks proper for the simulations of complex aerodynamic configurations.

  11. 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.

  12. Block-structured adaptive meshes and reduced grids for atmospheric general circulation models.

    PubMed

    Jablonowski, Christiane; Oehmke, Robert C; Stout, Quentin F

    2009-11-28

    Adaptive mesh refinement techniques offer a flexible framework for future variable-resolution climate and weather models since they can focus their computational mesh on certain geographical areas or atmospheric events. Adaptive meshes can also be used to coarsen a latitude-longitude grid in polar regions. This allows for the so-called reduced grid setups. A spherical, block-structured adaptive grid technique is applied to the Lin-Rood finite-volume dynamical core for weather and climate research. This hydrostatic dynamics package is based on a conservative and monotonic finite-volume discretization in flux form with vertically floating Lagrangian layers. The adaptive dynamical core is built upon a flexible latitude-longitude computational grid and tested in two- and three-dimensional model configurations. The discussion is focused on static mesh adaptations and reduced grids. The two-dimensional shallow water setup serves as an ideal testbed and allows the use of shallow water test cases like the advection of a cosine bell, moving vortices, a steady-state flow, the Rossby-Haurwitz wave or cross-polar flows. It is shown that reduced grid configurations are viable candidates for pure advection applications but should be used moderately in nonlinear simulations. In addition, static grid adaptations can be successfully used to resolve three-dimensional baroclinic waves in the storm-track region.

  13. 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

  14. 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.

  15. 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 ...

  16. Grid adaption based on modified anisotropic diffusion equations formulated in the parametic domain

    SciTech Connect

    Hagmeijer, R.

    1994-11-01

    A new grid-adaption algorithm for problems in computational fluid dynamics is presented. The basic equations are derived from a variational problem formulated in the parametric domain of the mapping that defines the existing grid. Modification of the basic equations provides desirable properties in boundary layers. The resulting modified anisotropic diffusion equations are solved for the computational coordinates as functions of the parametric coordinates and these functions are numerically inverted. Numerical examples show that the algorithm is robust, that shocks and boundary layers are well-resolved on the adapted grid, and that the flow solution becomes a globally smooth function of the computational coordinates.

  17. A fifth-order finite difference scheme for hyperbolic equations on block-adaptive curvilinear grids

    NASA Astrophysics Data System (ADS)

    Chen, Yuxi; Tóth, Gábor; Gombosi, Tamas I.

    2016-01-01

    We present a new fifth-order accurate finite difference method for hyperbolic equations on block-adaptive curvilinear grids. The scheme employs the 5th order accurate monotonicity preserving limiter MP5 to construct high order accurate face fluxes. The fifth-order accuracy of the spatial derivatives is ensured by a flux correction step. The method is generalized to curvilinear grids with a free-stream preserving discretization. It is also extended to block-adaptive grids using carefully designed ghost cell interpolation algorithms. Only three layers of ghost cells are required, and the grid blocks can be as small as 6 × 6 × 6 cells. Dynamic grid refinement and coarsening are also fifth-order accurate. All interpolation algorithms employ a general limiter based on the principles of the MP5 limiter. The finite difference scheme is fully conservative on static uniform grids. Conservation is only maintained at the truncation error level at grid resolution changes and during grid adaptation, but our numerical tests indicate that the results are still very accurate. We demonstrate the capabilities of the new method on a number of numerical tests, including smooth but non-linear problems as well as simulations involving discontinuities.

  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. 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

  20. 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.

  1. Spatial grid services for adaptive spatial query optimization

    NASA Astrophysics Data System (ADS)

    Gao, Bingbo; Xie, Chuanjie; Sheng, Wentao

    2008-10-01

    Spatial information sharing and integration has now become an important issue of Geographical Information Science (GIS). Web Service technologies provide a easy and standard way to share spatial resources over network, and grid technologies which aim at sharing resources such as data, storage, and computational powers can help the sharing go deeper. However, the dynamic characteristic of grid brings complexity to spatial query optimization which is more stressed in GIS domain because spatial operations are both CPU intensive and data intensive. To address this problem, a new grid framework is employed to provide standard spatial services which can also manage and report their state information to the coordinator which is responsible for distributed spatial query optimization.

  2. Local adaptation in transgenerational responses to predators.

    PubMed

    Walsh, Matthew R; Castoe, Todd; Holmes, Julian; Packer, Michelle; Biles, Kelsey; Walsh, Melissa; Munch, Stephan B; Post, David M

    2016-01-27

    Environmental signals can induce phenotypic changes that span multiple generations. Along with phenotypic responses that occur during development (i.e. 'within-generation' plasticity), such 'transgenerational plasticity' (TGP) has been documented in a diverse array of taxa spanning many environmental perturbations. New theory predicts that temporal stability is a key driver of the evolution of TGP. We tested this prediction using natural populations of zooplankton from lakes in Connecticut that span a large gradient in the temporal dynamics of predator-induced mortality. We reared more than 120 clones of Daphnia ambigua from nine lakes for multiple generations in the presence/absence of predator cues. We found that temporal variation in mortality selects for within-generation plasticity while consistently strong (or weak) mortality selects for increased TGP. Such results provide us the first evidence for local adaptation in TGP and argue that divergent ecological conditions select for phenotypic responses within and across generations. PMID:26817775

  3. Line orientation adaptation: local or global?

    PubMed

    Gheorghiu, Elena; Bell, Jason; Kingdom, Frederick A A

    2013-01-01

    Prolonged exposure to an oriented line shifts the perceived orientation of a subsequently observed line in the opposite direction, a phenomenon known as the tilt aftereffect (TAE). Here we consider whether the TAE for line stimuli is mediated by a mechanism that integrates the local parts of the line into a single global entity prior to the site of adaptation, or the result of the sum of local TAEs acting separately on the parts of the line. To test between these two alternatives we used the fact the TAE transfers almost completely across luminance contrast polarity [1]. We measured the TAE using adaptor and test lines that (1) either alternated in luminance polarity or were of a single polarity, and (2) either alternated in local orientation or were of a single orientation. We reasoned that if the TAE was agnostic to luminance polarity and was parts-based, we should obtain large TAEs using alternating-polarity adaptors with single-polarity tests. However we found that (i) TAEs using one-alternating-polarity adaptors with all-white tests were relatively small, increased slightly for two-alternating-polarity adaptors, and were largest with all-white or all-black adaptors. (ii) however TAEs were relatively large when the test was one-alternating polarity, irrespective of the adaptor type. (iii) The results with orientation closely mirrored those obtained with polarity with the difference that the TAE transfer across orthogonal orientations was weak. Taken together, our results demonstrate that the TAE for lines is mediated by a global shape mechanism that integrates the parts of lines into whole prior to the site of orientation adaptation. The asymmetry in the magnitude of TAE depending on whether the alternating-polarity lines was the adaptor or test can be explained by an imbalance in the population of neurons sensitive to 1(st)-and 2(nd)-order lines, with the 2(nd)-order lines being encoded by a subset of the mechanisms sensitive to 1(st)-order lines.

  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. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. A fast, robust, and simple implicit method for adaptive time-stepping on adaptive mesh-refinement grids

    NASA Astrophysics Data System (ADS)

    Commerçon, B.; Debout, V.; Teyssier, R.

    2014-03-01

    Context. Implicit solvers present strong limitations when used on supercomputing facilities and in particular for adaptive mesh-refinement codes. Aims: We present a new method for implicit adaptive time-stepping on adaptive mesh-refinement grids. We implement it in the radiation-hydrodynamics solver we designed for the RAMSES code for astrophysical purposes and, more particularly, for protostellar collapse. Methods: We briefly recall the radiation-hydrodynamics equations and the adaptive time-stepping methodology used for hydrodynamical solvers. We then introduce the different types of boundary conditions (Dirichlet, Neumann, and Robin) that are used at the interface between levels and present our implementation of the new method in the RAMSES code. The method is tested against classical diffusion and radiation-hydrodynamics tests, after which we present an application for protostellar collapse. Results: We show that using Dirichlet boundary conditions at level interfaces is a good compromise between robustness and accuracy and that it can be used in structure formation calculations. The gain in computational time over our former unique time step method ranges from factors of 5 to 50 depending on the level of adaptive time-stepping and on the problem. We successfully compare the old and new methods for protostellar collapse calculations that involve highly non linear physics. Conclusions: We have developed a simple but robust method for adaptive time-stepping of implicit scheme on adaptive mesh-refinement grids. It can be applied to a wide variety of physical problems that involve diffusion processes.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Stability of a modified Peaceman-Rachford method for the paraxial Helmholtz equation on adaptive grids

    NASA Astrophysics Data System (ADS)

    Sheng, Qin; Sun, Hai-wei

    2016-11-01

    This study concerns the asymptotic stability of an eikonal, or ray, transformation based Peaceman-Rachford splitting method for solving the paraxial Helmholtz equation with high wave numbers. Arbitrary nonuniform grids are considered in transverse and beam propagation directions. The differential equation targeted has been used for modeling propagations of high intensity laser pulses over a long distance without diffractions. Self-focusing of high intensity beams may be balanced with the de-focusing effect of created ionized plasma channel in the situation, and applications of grid adaptations are frequently essential. It is shown rigorously that the fully discretized oscillation-free decomposition method on arbitrary adaptive grids is asymptotically stable with a stability index one. Simulation experiments are carried out to illustrate our concern and conclusions.

  20. 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,…

  1. An adaptive grid-based all hexahedral meshing algorithm based on 2-refinement.

    SciTech Connect

    Edgel, Jared; Benzley, Steven E.; Owen, Steven James

    2010-08-01

    Most adaptive mesh generation algorithms employ a 3-refinement method. This method, although easy to employ, provides a mesh that is often too coarse in some areas and over refined in other areas. Because this method generates 27 new hexes in place of a single hex, there is little control on mesh density. This paper presents an adaptive all-hexahedral grid-based meshing algorithm that employs a 2-refinement method. 2-refinement is based on dividing the hex to be refined into eight new hexes. This method allows a greater control on mesh density when compared to a 3-refinement procedure. This adaptive all-hexahedral meshing algorithm provides a mesh that is efficient for analysis by providing a high element density in specific locations and a reduced mesh density in other areas. In addition, this tool can be effectively used for inside-out hexahedral grid based schemes, using Cartesian structured grids for the base mesh, which have shown great promise in accommodating automatic all-hexahedral algorithms. This adaptive all-hexahedral grid-based meshing algorithm employs a 2-refinement insertion method. This allows greater control on mesh density when compared to 3-refinement methods. This algorithm uses a two layer transition zone to increase element quality and keeps transitions from lower to higher mesh densities smooth. Templates were introduced to allow both convex and concave refinement.

  2. SIMULATION OF DISPERSION OF A POWER PLANT PLUME USING AN ADAPTIVE GRID ALGORITHM. (R827028)

    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 o...

  3. 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.

  4. SIMULATION OF A REACTING POLLUTANT PUFF USING AN ADAPTIVE GRID ALGORITHM

    EPA Science Inventory

    A new dynamic solution adaptive grid algorithm DSAGA-PPM, has been developed for use in air quality modeling. In this paper, this algorithm is described and evaluated with a test problem. Cone-shaped distributions of various chemical species undergoing chemical reactions are rota...

  5. 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.

  6. 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.

  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. 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.

  9. A three-dimensional adaptive grid method. [for computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Nakahashi, K.; Deiwert, G. S.

    1985-01-01

    A three-dimensional solution-adaptive-grid scheme is described which is suitable for complex fluid flows. This method, using tension and torsion spring analogies, was previously developed and successfully applied for two-dimensional flows. In the present work, a collection of three-dimensional flow fields are used to demonstrate the feasibility and versatility of this concept to include an added dimension. Flow fields considered include: (1) supersonic flow past an aerodynamic afterbody with a propulsive jet at incidence to the free stream, (2) supersonic flow past a blunt fin mounted on a solid wall, and (3) supersonic flow over a bump. In addition to generating three-dimensional solution-adapted grids, the method can also be used effectively as an initial grid generator. The utility of the method lies in: (1) optimum distribution of discrete grid points, (2) improvement of accuracy, (3) improved computational efficiency, (4) minimization of data base sizes, and (5) simplified three-dimensional grid generation.

  10. 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.

  11. Adaptive integral method with fast Gaussian gridding for solving combined field integral equations

    NASA Astrophysics Data System (ADS)

    Bakır, O.; Baǧ; Cı, H.; Michielssen, E.

    Fast Gaussian gridding (FGG), a recently proposed nonuniform fast Fourier transform algorithm, is used to reduce the memory requirements of the adaptive integral method (AIM) for accelerating the method of moments-based solution of combined field integral equations pertinent to the analysis of scattering from three-dimensional perfect electrically conducting surfaces. Numerical results that demonstrate the efficiency and accuracy of the AIM-FGG hybrid in comparison to an AIM-accelerated solver, which uses moment matching to project surface sources onto an auxiliary grid, are presented.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. An adaptive grid for graph-based segmentation in retinal OCT

    PubMed Central

    Lang, Andrew; Carass, Aaron; Calabresi, Peter A.; Ying, Howard S.; Prince, Jerry L.

    2016-01-01

    Graph-based methods for retinal layer segmentation have proven to be popular due to their efficiency and accuracy. These methods build a graph with nodes at each voxel location and use edges connecting nodes to encode the hard constraints of each layer’s thickness and smoothness. In this work, we explore deforming the regular voxel grid to allow adjacent vertices in the graph to more closely follow the natural curvature of the retina. This deformed grid is constructed by fixing node locations based on a regression model of each layer’s thickness relative to the overall retina thickness, thus we generate a subject specific grid. Graph vertices are not at voxel locations, which allows for control over the resolution that the graph represents. By incorporating soft constraints between adjacent nodes, segmentation on this grid will favor smoothly varying surfaces consistent with the shape of the retina. Our final segmentation method then follows our previous work. Boundary probabilities are estimated using a random forest classifier followed by an optimal graph search algorithm on the new adaptive grid to produce a final segmentation. Our method is shown to produce a more consistent segmentation with an overall accuracy of 3.38 μm across all boundaries.

  19. 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.

  20. 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 physical discretization error and the interpolation error in the sparse grid to enhance the sparse grid approximation and to drive adaptivity of the sparse grid. 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.

  1. 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

  2. Brain source localization based on fast fully adaptive approach.

    PubMed

    Ravan, Maryam; Reilly, James P

    2012-01-01

    In the electroencephalogram (EEG) or magnetoencephalogram (MEG) context, brain source localization (beamforming) methods often fail when the number of observations is small. This is particularly true when measuring evoked potentials, especially when the number of electrodes is large. Due to the nonstationarity of the EEG/MEG, an adaptive capability is desirable. Previous work has addressed these issues by reducing the adaptive degrees of freedom (DoFs). This paper develops and tests a new multistage adaptive processing for brain source localization that has been previously used for radar statistical signal processing application with uniform linear antenna array. This processing, referred to as the fast fully adaptive (FFA) approach, could significantly reduce the required sample support and computational complexity, while still processing all available DoFs. The performance improvement offered by the FFA approach in comparison to the fully adaptive minimum variance beamforming (MVB) with limited data is demonstrated by bootstrapping simulated data to evaluate the variability of the source location.

  3. 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.

  4. 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

  5. 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.

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

    DOE PAGES

    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

  7. Are adaptation costs necessary to build up a local adaptation pattern?

    PubMed Central

    Magalhães, Sara; Blanchet, Elodie; Egas, Martijn; Olivieri, Isabelle

    2009-01-01

    Background Ecological specialization is pervasive in phytophagous arthropods. In such specialization mode, limits to host range are imposed by trade-offs preventing adaptation to several hosts. The occurrence of such trade-offs is inferred by a pattern of local adaptation, i.e., a negative correlation between relative performance on different hosts. Results To establish a causal link between local adaptation and trade-offs, we performed experimental evolution of spider mites on cucumber, tomato and pepper, starting from a population adapted to cucumber. Spider mites adapted to each novel host within 15 generations and no further evolution was observed at generation 25. A pattern of local adaptation was found, as lines evolving on a novel host performed better on that host than lines evolving on other hosts. However, costs of adaptation were absent. Indeed, lines adapted to tomato had similar or higher performance on pepper than lines evolving on the ancestral host (which represent the initial performance of all lines) and the converse was also true, e.g. negatively correlated responses were not observed on the alternative novel host. Moreover, adapting to novel hosts did not result in decreased performance on the ancestral host. Adaptation did not modify host ranking, as all lines performed best on the ancestral host. Furthermore, mites from all lines preferred the ancestral to novel hosts. Mate choice experiments indicated that crosses between individuals from the same or from a different selection regime were equally likely, hence development of reproductive isolation among lines adapted to different hosts is unlikely. Conclusion Therefore, performance and preference are not expected to impose limits to host range in our study species. Our results show that the evolution of a local adaptation pattern is not necessarily associated with the evolution of an adaptation cost. PMID:19650899

  8. 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

  9. Private haplotypes can reveal local adaptation

    PubMed Central

    2014-01-01

    Background Genome-wide scans for regions that demonstrate deviating patterns of genetic variation have become common approaches for finding genes targeted by selection. Several genomic patterns have been utilized for this purpose, including deviations in haplotype homozygosity, frequency spectra and genetic differentiation between populations. Results We describe a novel approach based on the Maximum Frequency of Private Haplotypes – MFPH – to search for signals of recent population-specific selection. The MFPH statistic is straightforward to compute for phased SNP- and sequence-data. Using both simulated and empirical data, we show that MFPH can be a powerful statistic to detect recent population-specific selection, that it performs at the same level as other commonly used summary statistics (e.g. FST, iHS and XP-EHH), and that MFPH in some cases capture signals of selection that are missed by other statistics. For instance, in the Maasai, MFPH reveals a strong signal of selection in a region where other investigated statistics fail to pick up a clear signal that contains the genes DOCK3, MAPKAPK3 and CISH. This region has been suggested to affect height in many populations based on phenotype-genotype association studies. It has specifically been suggested to be targeted by selection in Pygmy groups, which are on the opposite end of the human height spectrum compared to the Maasai. Conclusions From the analysis of both simulated and publicly available empirical data, we show that MFPH represents a summary statistic that can provide further insight concerning population-specific adaptation. PMID:24885734

  10. Local plant adaptation across a subarctic elevational gradient.

    PubMed

    Kardol, Paul; De Long, Jonathan R; Wardle, David A

    2014-11-01

    Predicting how plants will respond to global warming necessitates understanding of local plant adaptation to temperature. Temperature may exert selective effects on plants directly, and also indirectly through environmental factors that covary with temperature, notably soil properties. However, studies on the interactive effects of temperature and soil properties on plant adaptation are rare, and the role of abiotic versus biotic soil properties in plant adaptation to temperature remains untested. We performed two growth chamber experiments using soils and Bistorta vivipara bulbil ecotypes from a subarctic elevational gradient (temperature range: ±3(°)C) in northern Sweden to disentangle effects of local ecotype, temperature, and biotic and abiotic properties of soil origin on plant growth. We found partial evidence for local adaption to temperature. Although soil origin affected plant growth, we did not find support for local adaptation to either abiotic or biotic soil properties, and there were no interactive effects of soil origin with ecotype or temperature. Our results indicate that ecotypic variation can be an important driver of plant responses to the direct effects of increasing temperature, while responses to covariation in soil properties are of a phenotypic, rather than adaptive, nature. PMID:26064553

  11. Three-dimensional compressible jet-in-crossflow calculations using improved viscosity models and adapted grid

    NASA Technical Reports Server (NTRS)

    Lytle, John K.; Harloff, Gary J.; Hsu, Andrew T.

    1990-01-01

    Previous calculations of jet-in-crossflow problems have been sensitive to the turbulence and artificial viscosity models and to the grid. Consequently, the eddy viscosity model in the PARC3D code was modified to consider the turbulent jet by switching from the Baldwin-Lomax (1978) model to an axisymmetric jet model. A modified artificial viscosity model has been utilized and evaluated in this study as well. The new model includes cell size scaling and a directional dependence in the coefficients. Computational results from PARC3D demonstrate the effects of the viscosity models on the pressure distribution fore and aft of the jet and the ability of the adaptive grid scheme to adjust to the three-dimensional gradients around the jet.

  12. 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

  13. 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

  14. 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

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

    DOE PAGES

    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. A Numerical Analysis on the Local Deformation of a Spacer Grid Structure for Nuclear Fuel Cells

    NASA Astrophysics Data System (ADS)

    Jang, Myung-Geun; Na, Geum Ju; Shin, Hyunho; Kim, Jong-Bong

    2016-08-01

    The result of a preliminary numerical investigation on local deformation characteristics of a multi-layered spacer-grid structure with five guide tubes is reported based on implicit finite element analysis. For the numerical analysis, displacements of top and bottom cross sections of each guide tube in a single-layer model were constrained while a lateral displacement was imposed on the single layer. Unlike the impact hammer test that is generally employed to characterize the deformation characteristics of the space-grid structure, the buckling phenomenon occurs locally in this study; it takes place at the inner grids around each tube and the degree of bucking is more apparent for tubes near the lateral surface where the lateral displacement was imposed.

  18. Local adaptation in brown trout early life-history traits: implications for climate change adaptability.

    PubMed

    Jensen, Lasse Fast; Hansen, Michael M; Pertoldi, Cino; Holdensgaard, Gert; Mensberg, Karen-Lise Dons; Loeschcke, Volker

    2008-12-22

    Knowledge of local adaptation and adaptive potential of natural populations is becoming increasingly relevant due to anthropogenic changes in the environment, such as climate change. The concern is that populations will be negatively affected by increasing temperatures without the capacity to adapt. Temperature-related adaptability in traits related to phenology and early life history are expected to be particularly important in salmonid fishes. We focused on the latter and investigated whether four populations of brown trout (Salmo trutta) are locally adapted in early life-history traits. These populations spawn in rivers that experience different temperature conditions during the time of incubation of eggs and embryos. They were reared in a common-garden experiment at three different temperatures. Quantitative genetic differentiation (QST) exceeded neutral molecular differentiation (FST) for two traits, indicating local adaptation. A temperature effect was observed for three traits. However, this effect varied among populations due to locally adapted reaction norms, corresponding to the temperature regimes experienced by the populations in their native environments. Additive genetic variance and heritable variation in phenotypic plasticity suggest that although increasing temperatures are likely to affect some populations negatively, they may have the potential to adapt to changing temperature regimes.

  19. Parallel level-set methods on adaptive tree-based grids

    NASA Astrophysics Data System (ADS)

    Mirzadeh, Mohammad; Guittet, Arthur; Burstedde, Carsten; Gibou, Frederic

    2016-10-01

    We present scalable algorithms for the level-set method on dynamic, adaptive Quadtree and Octree Cartesian grids. The algorithms are fully parallelized and implemented using the MPI standard and the open-source p4est library. We solve the level set equation with a semi-Lagrangian method which, similar to its serial implementation, is free of any time-step restrictions. This is achieved by introducing a scalable global interpolation scheme on adaptive tree-based grids. Moreover, we present a simple parallel reinitialization scheme using the pseudo-time transient formulation. Both parallel algorithms scale on the Stampede supercomputer, where we are currently using up to 4096 CPU cores, the limit of our current account. Finally, a relevant application of the algorithms is presented in modeling a crystallization phenomenon by solving a Stefan problem, illustrating a level of detail that would be impossible to achieve without a parallel adaptive strategy. We believe that the algorithms presented in this article will be of interest and useful to researchers working with the level-set framework and modeling multi-scale physics in general.

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

    PubMed

    Gorter, Florien A; Scanlan, Pauline D; Buckling, Angus

    2016-02-01

    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.

  1. Climate change adaptation among Tibetan pastoralists: challenges in enhancing local adaptation through policy support.

    PubMed

    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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. Functional Genomics of Physiological Plasticity and Local Adaptation in Killifish

    PubMed Central

    Galvez, Fernando; Zhang, Shujun; Williams, Larissa M.; Oleksiak, Marjorie F.

    2011-01-01

    Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted phenotypes within different selective contexts, providing a comparative system in which to explore the genomic underpinnings of physiological plasticity and adaptive variation. Importantly, extensive variation exists among populations and species for tolerance to a variety of stressors, and we exploit this variation in comparative studies to yield insights into the genomic basis of evolved phenotypic variation. Notably, species of Fundulus occupy the continuum of osmotic habitats from freshwater to marine and populations within Fundulus heteroclitus span far greater variation in pollution tolerance than across all species of fish. Here, we explore how transcriptome regulation underpins extreme physiological plasticity on osmotic shock and how genomic and transcriptomic variation is associated with locally evolved pollution tolerance. We show that F. heteroclitus quickly acclimate to extreme osmotic shock by mounting a dramatic rapid transcriptomic response including an early crisis control phase followed by a tissue remodeling phase involving many regulatory pathways. We also show that convergent evolution of locally adapted pollution tolerance involves complex patterns of gene expression and genome sequence variation, which is confounded with body-weight dependence for some genes. Similarly, exploiting the natural phenotypic variation associated with other established and emerging model organisms is likely to greatly accelerate the pace of discovery of the genomic basis of phenotypic variation. PMID:20581107

  13. 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.

  14. 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

  15. 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

  16. 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

  17. Locally adaptive bilateral clustering for universal image denoising

    NASA Astrophysics Data System (ADS)

    Toh, K. K. V.; Mat Isa, N. A.

    2012-12-01

    This paper presents a novel and efficient locally adaptive denoising method based on clustering of pixels into regions of similar geometric and radiometric structures. Clustering is performed by adaptively segmenting pixels in the local kernel based on their augmented variational series. Then, noise pixels are restored by selectively considering the radiometric and spatial properties of every pixel in the formed clusters. The proposed method is exceedingly robust in conveying reliable local structural information even in the presence of noise. As a result, the proposed method substantially outperforms other state-of-the-art methods in terms of image restoration and computational cost. We support our claims with ample simulated and real data experiments. The relatively fast runtime from extensive simulations also suggests that the proposed method is suitable for a variety of image-based products — either embedded in image capturing devices or applied as image enhancement software.

  18. 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.

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

    PubMed

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

    2014-02-01

    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, T(imm)) at 37°C in clones acclimatized to either 20°C or 28°C. Acclimatization to 28°C strongly increased T(imm), 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.

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

    PubMed

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

    2014-02-01

    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, T(imm)) at 37°C in clones acclimatized to either 20°C or 28°C. Acclimatization to 28°C strongly increased T(imm), 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

  1. Adaptive local routing strategy on a scale-free network

    NASA Astrophysics Data System (ADS)

    Liu, Feng; Zhao, Han; Li, Ming; Ren, Feng-Yuan; Zhu, Yan-Bo

    2010-04-01

    Due to the heterogeneity of the structure on a scale-free network, making the betweennesses of all nodes become homogeneous by reassigning the weights of nodes or edges is very difficult. In order to take advantage of the important effect of high degree nodes on the shortest path communication and preferentially deliver packets by them to increase the probability to destination, an adaptive local routing strategy on a scale-free network is proposed, in which the node adjusts the forwarding probability with the dynamical traffic load (packet queue length) and the degree distribution of neighbouring nodes. The critical queue length of a node is set to be proportional to its degree, and the node with high degree has a larger critical queue length to store and forward more packets. When the queue length of a high degree node is shorter than its critical queue length, it has a higher probability to forward packets. After higher degree nodes are saturated (whose queue lengths are longer than their critical queue lengths), more packets will be delivered by the lower degree nodes around them. The adaptive local routing strategy increases the probability of a packet finding its destination quickly, and improves the transmission capacity on the scale-free network by reducing routing hops. The simulation results show that the transmission capacity of the adaptive local routing strategy is larger than that of three previous local routing strategies.

  2. 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.

  3. 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.

  4. GPU accelerated cell-based adaptive mesh refinement on unstructured quadrilateral grid

    NASA Astrophysics Data System (ADS)

    Luo, Xisheng; Wang, Luying; Ran, Wei; Qin, Fenghua

    2016-10-01

    A GPU accelerated inviscid flow solver is developed on an unstructured quadrilateral grid in the present work. For the first time, the cell-based adaptive mesh refinement (AMR) is fully implemented on GPU for the unstructured quadrilateral grid, which greatly reduces the frequency of data exchange between GPU and CPU. Specifically, the AMR is processed with atomic operations to parallelize list operations, and null memory recycling is realized to improve the efficiency of memory utilization. It is found that results obtained by GPUs agree very well with the exact or experimental results in literature. An acceleration ratio of 4 is obtained between the parallel code running on the old GPU GT9800 and the serial code running on E3-1230 V2. With the optimization of configuring a larger L1 cache and adopting Shared Memory based atomic operations on the newer GPU C2050, an acceleration ratio of 20 is achieved. The parallelized cell-based AMR processes have achieved 2x speedup on GT9800 and 18x on Tesla C2050, which demonstrates that parallel running of the cell-based AMR method on GPU is feasible and efficient. Our results also indicate that the new development of GPU architecture benefits the fluid dynamics computing significantly.

  5. 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.

  6. 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.

  7. 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.

  8. 3D Continuum Radiative Transfer. An adaptive grid construction algorithm based on the Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Niccolini, G.; Alcolea, J.

    Solving the radiative transfer problem is a common problematic to may fields in astrophysics. With the increasing angular resolution of spatial or ground-based telescopes (VLTI, HST) but also with the next decade instruments (NGST, ALMA, ...), astrophysical objects reveal and will certainly reveal complex spatial structures. Consequently, it is necessary to develop numerical tools being able to solve the radiative transfer equation in three dimensions in order to model and interpret these observations. I present a 3D radiative transfer program, using a new method for the construction of an adaptive spatial grid, based on the Monte Claro method. With the help of this tools, one can solve the continuum radiative transfer problem (e.g. a dusty medium), computes the temperature structure of the considered medium and obtain the flux of the object (SED and images).

  9. An adaptive locally optimal method detecting weak deterministic signals

    NASA Astrophysics Data System (ADS)

    Wang, C. H.

    1983-10-01

    A new method for detecting weak signals in interference and clutter in radar systems is presented. The detector which uses this method is adaptive for an environment varying with time and locally optimal for detecting targets and constant false-alarm ratio (CFAR) for the statistics of interference and clutter varying with time. The loss of CFAR is small, and the detector is also simple in structure. The statistical equivalent transfer characteristic of a rank quantizer which can be used as part of an adaptive locally most powerful detector (ALMP) is obtained. It is shown that the distribution-free Doppler processor of Dillard (1974) is not only a nonparameter detector, but also an ALMP detector under certain conditions.

  10. 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.

  11. Adapting mobile beacon-assisted localization in wireless sensor networks.

    PubMed

    Teng, Guodong; Zheng, Kougen; Dong, Wei

    2009-01-01

    The ability to automatically locate sensor nodes is essential in many Wireless Sensor Network (WSN) applications. To reduce the number of beacons, many mobile-assisted approaches have been proposed. Current mobile-assisted approaches for localization require special hardware or belong to centralized localization algorithms involving some deterministic approaches due to the fact that they explicitly consider the impreciseness of location estimates. In this paper, we first propose a range-free, distributed and probabilistic Mobile Beacon-assisted Localization (MBL) approach for static WSNs. Then, we propose another approach based on MBL, called Adapting MBL (A-MBL), to increase the efficiency and accuracy of MBL by adapting the size of sample sets and the parameter of the dynamic model during the estimation process. Evaluation results show that the accuracy of MBL and A-MBL outperform both Mobile and Static sensor network Localization (MSL) and Arrival and Departure Overlap (ADO) when both of them use only a single mobile beacon for localization in static WSNs.

  12. Preliminary Benchmarking of Plinian Eruption Simulations Using an Adaptive Grid Eulerian Technique

    NASA Astrophysics Data System (ADS)

    Peterson, A. H.; Ogden, D. E.; Wohletz, K. H.; Gisler, G.; Glatzmaier, G. A.

    2005-12-01

    The SAGE (SAIC Adaptive Grid Eulerian) code is an Eulerian hydrodynamics numerical technique employing adaptive mesh refinement at each cycle for every cell in 1-, 2-, and 3-D grids. It is primarily designed to solve high deformation flow of multiple materials and thus provides important capabilities for simulating volcanic eruption phenomena. Its multimaterial equation of state libraries includes a comprehensive coverage of water from solid ice through two-phase liquid and vapor to supercritical states approaching the Hugoniot, and extremely important aspect for simulating volcanic gases in general. In development are strength and failure rules that model non-Newtonian fluid/solid deformation. Because of the low effective sound speeds of eruptive mixtures, the facts that SAGE uses a piecewise, linear, multi-material, Gudonov numerical method to resolve shocks with second-order precision and exactly conserves mass, momentum, and energy, are a highly desirable attributes. Although this code has been previously used to simulate a volcanic eruption (i.e., eruption through a crater lake at Ruapehu volcano by Morrissey and Gisler), we are embarking in an effort to benchmark the code with CFDLib, a well-validated arbitrary Lagrangian-Eulerian code developed at Los Alamos National Laboratory. Through this effort we expect to better understand the strengths and weaknesses, the limitations, and provide direction for important enhancement of SAGE, and potentially provide the volcanological community with a powerful alternative to numerical codes currently available. At this point in our benchmarking, we demonstrate some results for fluid convection within a chamber and fluid jetting through a conduit.

  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. 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.

  16. 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.

  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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations. PMID:15446426

  6. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations.

  7. 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.

  8. Controlling the local false discovery rate in the adaptive Lasso.

    PubMed

    Sampson, Joshua N; Chatterjee, Nilanjan; Carroll, Raymond J; Müller, Samuel

    2013-09-01

    The Lasso shrinkage procedure achieved its popularity, in part, by its tendency to shrink estimated coefficients to zero, and its ability to serve as a variable selection procedure. Using data-adaptive weights, the adaptive Lasso modified the original procedure to increase the penalty terms for those variables estimated to be less important by ordinary least squares. Although this modified procedure attained the oracle properties, the resulting models tend to include a large number of "false positives" in practice. Here, we adapt the concept of local false discovery rates (lFDRs) so that it applies to the sequence, λn, of smoothing parameters for the adaptive Lasso. We define the lFDR for a given λn to be the probability that the variable added to the model by decreasing λn to λn-δ is not associated with the outcome, where δ is a small value. We derive the relationship between the lFDR and λn, show lFDR =1 for traditional smoothing parameters, and show how to select λn so as to achieve a desired lFDR. We compare the smoothing parameters chosen to achieve a specified lFDR and those chosen to achieve the oracle properties, as well as their resulting estimates for model coefficients, with both simulation and an example from a genetic study of prostate specific antigen.

  9. 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

  10. 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

  11. Adaptation to sea level rise: does local adaptation influence the demography of coastal fish populations?

    PubMed

    Purcell, K M; Klerks, P L; Leberg, P L

    2010-10-01

    This study compared the growth of two western mosquitofish Gambusia affinis populations that were previously demonstrated to have genetic adaptations that increased survival under lethal salinity exposures. The objective was to evaluate how genetic adaptations to lethal salinity stress affect population demography when exposed to sublethal salinity stress. Results indicate that chronic salinity exposure had a generally negative impact on population size, but fish originating from one of the two populations established with fish from a brackish site exhibited an increase in population size. Saltwater intrusion seems to result in reduced population size for most populations. Some populations inhabiting more saline sites, however, may develop localized adaptations, mitigating the consequences of increased salinity on population productivity. PMID:21039500

  12. 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.

  13. 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.

  14. 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

  15. Invasion and adaptation of a warm-adapted species to montane localities: effect of acclimation potential.

    PubMed

    Chahal, Jyoti; Kataria, Sudhir Kumar; Parkash, Ravi

    2013-05-01

    Drosophila ananassae has successfully invaded the cold and dry montane localities of the Western Himalayas in recent years. The ability of this desiccation- and cold-sensitive tropical species to evolve in response to seasonal changes in montane localities is largely unknown. Here, we investigated how this sensitive species adapt to seasonally varying environmental conditions that are lethal to its survival. We observed change in the frequency of dark and light morphs of D. ananassae in five mid-altitude localities during the last decade (2000-2010). We document invasion of D. ananassae to montane localities and increase in frequency of the dark morph. The stress tolerance of morphs (dark and light) remained unaffected of developmental acclimation. However, adult acclimation has shown significant effects on tolerance to various environmental stresses in morphs and effect of this acclimation persist for long durations. Desiccation and cold stress tolerance was increased after adult acclimation for respective stress in the dark morph; while tolerance of the light morph was not affected. Further, heat tolerance of the light morph was increased after adult heat acclimation with no influence on heat tolerance of the dark morph. Our results suggest a possible role of adult acclimation in successful invasion and adaptation of D. ananassae to montane localities. Future experiments should be carried out to determine whether the survival in adverse conditions of low versus high temperature and humidity during seasonal changes is assisted by different acclimation abilities of the two morphs of D. ananassae.

  16. 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.

  17. A Controls-CFD Approach for Estimation of Concentration from a Moving Aerial Source: Advantages of a Finite Volume-TVD implementation with Guidance-Based Grid Adaptation

    NASA Astrophysics Data System (ADS)

    Egorova, Tatiana; Gatsonis, Nikolaos A.; Demetriou, Michael A.

    2013-11-01

    In this work the process of gas release into the atmosphere by a moving aerial source is simulated and estimated using a sensing aerial vehicle (SAV). The process is modeled with atmospheric advection diffusion equation, which is solved by the finite volume method (FVM). Advective fluxes are constrained using total variation diminishing (TVD) approach. The estimator provides on-line estimates of concentration field and proximity of the source. The guidance of the SAV is dictated by the performance of the estimator. To further improve the estimation algorithm from the computational prospective, the grid is adapted dynamically through local refinement and coarsening. The adaptation algorithm uses the current sensor position as a center of refinement, with the areas further away from the SAV being covered by a coarse grid. This leads to the time varying state matrix of the estimator and the variation depends on the SAV motion. Advantages of the adaptive FVM-TVD implementation are illustrated on the examples of estimator performance for different source trajectories.

  18. 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

  19. Learning without labeling: domain adaptation for ultrasound transducer localization.

    PubMed

    Heimann, Tobias; Mountney, Peter; John, Matthias; Ionasec, Razvan

    2013-01-01

    The fusion of image data from trans-esophageal echography (TEE) and X-ray fluoroscopy is attracting increasing interest in minimally-invasive treatment of structural heart disease. In order to calculate the needed transform between both imaging systems, we employ a discriminative learning based approach to localize the TEE transducer in X-ray images. Instead of time-consuming manual labeling, we generate the required training data automatically from a single volumetric image of the transducer. In order to adapt this system to real X-ray data, we use unlabeled fluoroscopy images to estimate differences in feature space density and correct covariate shift by instance weighting. An evaluation on more than 1900 images reveals that our approach reduces detection failures by 95% compared to cross validation on the test set and improves the localization error from 1.5 to 0.8 mm. Due to the automatic generation of training data, the proposed system is highly flexible and can be adapted to any medical device with minimal efforts.

  20. Learning without labeling: domain adaptation for ultrasound transducer localization.

    PubMed

    Heimann, Tobias; Mountney, Peter; John, Matthias; Ionasec, Razvan

    2013-01-01

    The fusion of image data from trans-esophageal echography (TEE) and X-ray fluoroscopy is attracting increasing interest in minimally-invasive treatment of structural heart disease. In order to calculate the needed transform between both imaging systems, we employ a discriminative learning based approach to localize the TEE transducer in X-ray images. Instead of time-consuming manual labeling, we generate the required training data automatically from a single volumetric image of the transducer. In order to adapt this system to real X-ray data, we use unlabeled fluoroscopy images to estimate differences in feature space density and correct covariate shift by instance weighting. An evaluation on more than 1900 images reveals that our approach reduces detection failures by 95% compared to cross validation on the test set and improves the localization error from 1.5 to 0.8 mm. Due to the automatic generation of training data, the proposed system is highly flexible and can be adapted to any medical device with minimal efforts. PMID:24505743

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. Symmetry-adapted Wannier functions in the maximal localization procedure

    NASA Astrophysics Data System (ADS)

    Sakuma, R.

    2013-06-01

    A procedure to construct symmetry-adapted Wannier functions in the framework of the maximally localized Wannier function approach [Marzari and Vanderbilt, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.56.12847 56, 12847 (1997); Souza, Marzari, and Vanderbilt, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.65.035109 65, 035109 (2001)] is presented. In this scheme, the minimization of the spread functional of the Wannier functions is performed with constraints that are derived from symmetry properties of the specified set of the Wannier functions and the Bloch functions used to construct them, therefore one can obtain a solution that does not necessarily yield the global minimum of the spread functional. As a test of this approach, results of atom-centered Wannier functions for GaAs and Cu are presented.

  10. 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

  11. Glacial survival and local adaptation in an alpine leaf beetle.

    PubMed

    Margraf, Nicolas; Verdon, Aline; Rahier, Martine; Naisbit, Russell E

    2007-06-01

    The challenge in defining conservation units so that they represent evolutionary entities has been to combine both genetic properties and ecological significance. Here we make use of the complexity of the European Alps, with their genetic landscape shaped by geographical barriers and postglacial colonization, to examine the correlation between ecological and genetic divergence. Montane species, because of the fragmentation of their present habitat, constitute extreme cases in which to test if genetically distinct subgroups based on neutral markers are also ecologically differentiated and show local adaptation. In the leaf beetle Oreina elongata, populations show variation in host plant use and a patchy distribution throughout the Alps and Apennines. We demonstrate that despite very strong genetic isolation (F(ST) = 0.381), variation in host plant use has led to differences in larval life-history traits between populations only as a secondary effect of host defence chemistry, and not through physiological adaptation to plant nutritional value. We also establish that populations that are more ecologically different in terms of larval performance are also more genetically divergent. In addition, morphological variation used to define subspecies appears to be mirrored in the population genetics of this species, resulting in almost perfect clustering based on microsatellite data. Finally, we argue from their strong genetic structure and congruent distribution that the subspecies of O. elongata were divided among the same glacial refugia within the Alps that have been proposed for alpine plants.

  12. 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.

  13. 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.

  14. How does spatial dispersal network affect the evolution of parasite local adaptation?

    PubMed

    Vogwill, Tom; Fenton, Andy; Brockhurst, Michael A

    2010-06-01

    Studying patterns of parasite local adaptation can provide insights into the spatiotemporal dynamics of host-parasite coevolution. Many factors, both biotic and abiotic, have been identified that influence parasite local adaptation. In particular, dispersal and population structuring are considered important determinants of local adaptation. We investigated how the shape of the spatial dispersal network within experimental landscapes affected local adaptation of a bacteriophage parasite to its bacterial host. Regardless of landscape topology, dispersal always led to the evolution of phages with broader infectivity range. However, when the spatial dispersal network resulted in spatial variation in the breadth of phage infectivity range, significant levels of parasite local adaptation and local maladaptation were detected within the same landscape using the local versus foreign definition of local adaptation. By contrast, local adaptation was not detected using the home versus away or local versus global definitions of local adaptation. This suggests that spatial dispersal networks may play an important role in driving parasite local adaptation, particularly when the shape of the dispersal network generates nonuniform levels of host resistance or parasite infectivity throughout a species' range. PMID:20050909

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Adaptive Generation of Multimaterial Grids from Imaging Data for Biomedical Lagrangian Fluid-Structure Simulations

    PubMed Central

    Carson, J.P.; Kuprat, A.P; Jiao, X.; Dyedov, V.; del Pin, F.; Johnson, G.A.; Guccione, J.M.; Ratcliffe, M.B.; Einstein, D.R.

    2009-01-01

    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 share a common interface geometrically. For simplicity and better accuracy, it is also highly desirable for the two phases to have a matching 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. PMID:19727874

  1. 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.

  2. Divergent selection on locally adapted major histocompatibility complex immune genes experimentally proven in the field

    PubMed Central

    Eizaguirre, Christophe; Lenz, Tobias L; Kalbe, Martin; Milinski, Manfred

    2012-01-01

    Although crucial for the understanding of adaptive evolution, genetically resolved examples of local adaptation are rare. To maximize survival and reproduction in their local environment, hosts should resist their local parasites and pathogens. The major histocompatibility complex (MHC) with its key function in parasite resistance represents an ideal candidate to investigate parasite-mediated local adaptation. Using replicated field mesocosms, stocked with second-generation lab-bred three-spined stickleback hybrids of a lake and a river population, we show local adaptation of MHC genotypes to population-specific parasites, independently of the genetic background. Increased allele divergence of lake MHC genotypes allows lake fish to fight the broad range of lake parasites, whereas more specific river genotypes confer selective advantages against the less diverse river parasites. Hybrids with local MHC genotype gained more body weight and thus higher fitness than those with foreign MHC in either habitat, suggesting the evolutionary significance of locally adapted MHC genotypes. PMID:22583762

  3. 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.

  4. 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

  5. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of "standardized allele frequencies" that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools-a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

  6. Robust Identification of Local Adaptation from Allele Frequencies

    PubMed Central

    Günther, Torsten; Coop, Graham

    2013-01-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of “standardized allele frequencies” that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools—a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

  7. Adaptive local backlight dimming algorithm based on local histogram and image characteristics

    NASA Astrophysics Data System (ADS)

    Nadernejad, Ehsan; Burini, Nino; Korhonen, Jari; Forchhammer, Søren; Mantel, Claire

    2013-02-01

    Liquid Crystal Display (LCDs) with Light Emitting Diode (LED) backlight is a very popular display technology, used for instance in television sets, monitors and mobile phones. This paper presents a new backlight dimming algorithm that exploits the characteristics of the target image, such as the local histograms and the average pixel intensity of each backlight segment, to reduce the power consumption of the backlight and enhance image quality. The local histogram of the pixels within each backlight segment is calculated and, based on this average, an adaptive quantile value is extracted. A classification into three classes based on the average luminance value is performed and, depending on the image luminance class, the extracted information on the local histogram determines the corresponding backlight value. The proposed method has been applied on two modeled screens: one with a high resolution direct-lit backlight, and the other screen with 16 edge-lit backlight segments placed in two columns and eight rows. We have compared the proposed algorithm against several known backlight dimming algorithms by simulations; and the results show that the proposed algorithm provides better trade-off between power consumption and image quality preservation than the other algorithms representing the state of the art among feature based backlight algorithms.

  8. 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

  9. 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

  10. Adaptations to local environments in modern human populations

    PubMed Central

    Jeong, Choongwon; Di Rienzo, Anna

    2014-01-01

    After leaving sub-Saharan Africa around 50,000–100,000 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  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. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils.

    PubMed

    Turner, Thomas L; Bourne, Elizabeth C; Von Wettberg, Eric J; Hu, Tina T; Nuzhdin, Sergey V

    2010-03-01

    A powerful way to map functional genomic variation and reveal the genetic basis of local adaptation is to associate allele frequency across the genome with environmental conditions. Serpentine soils, characterized by high heavy-metal content and low calcium-to-magnesium ratios, are a classic context for studying adaptation of plants to local soil conditions. To investigate whether Arabidopsis lyrata is locally adapted to serpentine soil, and to map the polymorphisms responsible for such adaptation, we pooled DNA from individuals from serpentine and nonserpentine soils and sequenced each 'gene pool' with the Illumina Genome Analyzer. The polymorphisms that are most strongly associated with soil type are enriched at heavy-metal detoxification and calcium and magnesium transport loci, providing numerous candidate mutations for serpentine adaptation. Sequencing of three candidate loci in the European subspecies of A. lyrata indicates parallel differentiation of the same polymorphism at one locus, confirming ecological adaptation, and different polymorphisms at two other loci, which may indicate convergent evolution.

  17. 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.

  18. 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

  19. Local adaptation and maladaptation to pollinators in a generalist geographic mosaic.

    PubMed

    Gómez, José M; Abdelaziz, M; Camacho, J P M; Muñoz-Pajares, A J; Perfectti, F

    2009-07-01

    The Geographic Mosaic Theory of Coevolution predicts the occurrence of mosaics of interaction-mediated local adaptations and maladaptations. Empirical support to this prediction has come mostly from specialist interactions. In contrast, local adaptation is considered highly unlikely in generalist interactions. In this study, we experimentally test local adaptation in a generalist plant-pollinator geographic mosaic, by means of a transplant experiment in which plants coming from two evolutionary hotspots and two coldspots were offered to pollinators at the same four localities. Plants produced in the hotspots attracted more pollinators in all populations, whereas coldspot plants attracted fewer pollinators in all populations. Differences in adaptation were not related to genetic similarity between populations, suggesting that it was mainly due to spatial variation in previous selective regimes. Our experiment provides the first strong support for a spatially structured pattern of adaptation and maladaptation generated by a generalist free-living mutualism.

  20. On the use of adaptive moving grid methods in combustion problems

    SciTech Connect

    Hyman, J.M.; Larrouturou, B.

    1986-01-01

    The investigators have presented the reasons and advantages of adaptively moving the mesh points for the solution of time-dependent PDEs (partial differential equations) systems developing sharp gradients, and more specifically for combustion problems. Several available adaptive dynamic rezone methods have been briefly reviewed, and the effectiveness of these algorithms for combustion problems has been illustrated by the numerical solution of a simple flame propagation problem. 29 refs., 7 figs.

  1. 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.

  2. On Multigrid for Overlapping Grids

    SciTech Connect

    Henshaw, W

    2004-01-13

    The solution of elliptic partial differential equations on composite overlapping grids using multigrid is discussed. An approach is described that provides a fast and memory efficient scheme for the solution of boundary value problems in complex geometries. The key aspects of the new scheme are an automatic coarse grid generation algorithm, an adaptive smoothing technique for adjusting residuals on different component grids, and the use of local smoothing near interpolation boundaries. Other important features include optimizations for Cartesian component grids, the use of over-relaxed Red-Black smoothers and the generation of coarse grid operators through Galerkin averaging. Numerical results in two and three dimensions show that very good multigrid convergence rates can be obtained for both Dirichlet and Neumann/mixed boundary conditions. A comparison to Krylov based solvers shows that the multigrid solver can be much faster and require significantly less memory.

  3. Adaptation to Leftward-shifting Prisms Enhances Local Processing in Healthy Individuals

    PubMed Central

    Reed, Scott A.; Dassonville, Paul

    2014-01-01

    In healthy individuals, adaptation to left-shifting prisms has been shown to simulate the symptoms of hemispatial neglect, including a reduction in global processing that approximates the local bias observed in neglect patients. The current study tested whether leftward prism adaptation can more specifically enhance local processing abilities. In three experiments, the impact of local and global processing was assessed through tasks that measure susceptibility to illusions that are known to be driven by local or global contextual effects. Susceptibility to the rod-and-frame illusion – an illusion disproportionately driven by both local and global effects depending on frame size – was measured before and after adaptation to left- and right-shifting prisms. A significant increase in rod-and-frame susceptibility was found for the left-shifting prism group, suggesting that adaptation caused an increase in local processing effects. The results of a second experiment confirmed that leftward prism adaptation enhances local processing, as assessed with susceptibility to the simultaneous-tilt illusion. A final experiment employed a more specific measure of the global effect typically associated with the rod-andframe illusion, and found that although the global effect was somewhat diminished after leftward prism adaptation, the trend failed to reach significance (p = .078). Rightward prism adaptation had no significant effects on performance in any of the experiments. Combined, these findings indicate that leftward prism adaptation in healthy individuals can simulate the local processing bias of neglect patients primarily through an increased sensitivity to local visual cues, and confirm that prism adaptation not only modulates lateral shifts of attention, but also prompts shifts from one level of processing to another. PMID:24560913

  4. Adaptation to leftward-shifting prisms enhances local processing in healthy individuals.

    PubMed

    Reed, Scott A; Dassonville, Paul

    2014-04-01

    In healthy individuals, adaptation to left-shifting prisms has been shown to simulate the symptoms of hemispatial neglect, including a reduction in global processing that approximates the local bias observed in neglect patients. The current study tested whether leftward prism adaptation can more specifically enhance local processing abilities. In three experiments, the impact of local and global processing was assessed through tasks that measure susceptibility to illusions that are known to be driven by local or global contextual effects. Susceptibility to the rod-and-frame illusion - an illusion disproportionately driven by both local and global effects depending on frame size - was measured before and after adaptation to left- and right-shifting prisms. A significant increase in rod-and-frame susceptibility was found for the left-shifting prism group, suggesting that adaptation caused an increase in local processing effects. The results of a second experiment confirmed that leftward prism adaptation enhances local processing, as assessed with susceptibility to the simultaneous-tilt illusion. A final experiment employed a more specific measure of the global effect typically associated with the rod-and-frame illusion, and found that although the global effect was somewhat diminished after leftward prism adaptation, the trend failed to reach significance (p=.078). Rightward prism adaptation had no significant effects on performance in any of the experiments. Combined, these findings indicate that leftward prism adaptation in healthy individuals can simulate the local processing bias of neglect patients primarily through an increased sensitivity to local visual cues, and confirm that prism adaptation not only modulates lateral shifts of attention, but also prompts shifts from one level of processing to another.

  5. 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…

  6. 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.

  7. Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations.

    PubMed

    Miner, Brooks E; Kerr, Benjamin

    2011-05-01

    Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system.

  8. Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations

    PubMed Central

    Miner, Brooks E.; Kerr, Benjamin

    2011-01-01

    Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system. PMID:20943691

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

    NASA Technical Reports Server (NTRS)

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

    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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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...

  16. 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

  17. Accuracy enhancements for overset grids using a defect correction approach

    NASA Technical Reports Server (NTRS)

    Rogers, Stuart E.; Pulliam, Thomas H.

    1994-01-01

    A defect-correction approach is investigated as a means of enhancing the accuracy of flow computations on overset grids. Typically, overset-grid techniques process and pass information only at grid boundaries. In the current approach, error corrections at all overlapped interior points are injected between grids by using a defect-correction scheme. In some cases this is found to enhance the overall accuracy of the overset-grid method. Locally refined overset grids can be used to provide an efficient solution-adaptation method. The defect correction can also be ultilized as an error-correction technique for a coarse grid by evaluating the residual using a fine base grid, but solving the implicit equations only on the coarse grid. Numerical examples include an accuracy and dissipation study of an unsteady decaying vortex flow, the flow over a NACA 0012 airfoil, and the flow over a mulit-element high-lift airfoil.

  18. Effects of local adaptation and interspecific competition on species' responses to climate change.

    PubMed

    Bocedi, Greta; Atkins, Katherine E; Liao, Jishan; Henry, Roslyn C; Travis, Justin M J; Hellmann, Jessica J

    2013-09-01

    Local adaptation and species interactions have been shown to affect geographic ranges; therefore, we need models of climate impact that include both factors. To identify possible dynamics of species when including these factors, we ran simulations of two competing species using an individual-based, coupled map-lattice model using a linear climatic gradient that varies across latitude and is warmed over time. Reproductive success is governed by an individual's adaptation to local climate as well as its location relative to global constraints. In exploratory experiments varying the strength of adaptation and competition, competition reduces genetic diversity and slows range change, although the two species can coexist in the absence of climate change and shift in the absence of competitors. We also found that one species can drive the other to extinction, sometimes long after climate change ends. Weak selection on local adaptation and poor dispersal ability also caused surfing of cooler-adapted phenotypes from the expanding margin backwards, causing loss of warmer-adapted phenotypes. Finally, geographic ranges can become disjointed, losing centrally-adapted genotypes. These initial results suggest that the interplay between local adaptation and interspecific competition can significantly influence species' responses to climate change, in a way that demands future research.

  19. 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…

  20. A Framework for Spatial Assessment of Local Level Vulnerability and Adaptive Capacity to Extreme Heat

    NASA Astrophysics Data System (ADS)

    Wilhelmi, O.; Hayden, M.; Harlan, S.; Ruddell, D.; Komatsu, K.; England, B.; Uejio, C.

    2008-12-01

    Changing climate is predicted to increase the intensity and impacts of heat waves prompting the need to develop preparedness and adaptation strategies that reduce societal vulnerability. Central to understanding societal vulnerability, is adaptive capacity, the potential of a system or population to modify its features/behaviors so as to better cope with existing and anticipated stresses and fluctuations. Adaptive capacity influences adaptation, the actual adjustments made to cope with the impacts from current and future hazardous heat events. Understanding societal risks, vulnerabilities and adaptive capacity to extreme heat events and climate change requires an interdisciplinary approach that includes information about weather and climate, the natural and built environment, social processes and characteristics, interactions with the stakeholders, and an assessment of community vulnerability. This project presents a framework for an interdisciplinary approach and a case study that explore linkages between quantitative and qualitative data for a more comprehensive understanding of local level vulnerability and adaptive capacity to extreme heat events in Phoenix, Arizona. In this talk, we will present a methodological framework for conducting collaborative research on societal vulnerability and adaptive capacity on a local level that includes integration of household surveys into a quantitative spatial assessment of societal vulnerability. We highlight a collaborative partnership among researchers, community leaders and public health officials. Linkages between assessment of local adaptive capacity and development of regional climate change adaptation strategies will be discussed.

  1. 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.

  2. 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.

  3. Going Glocal: Adaptive Education for Local and Global Citizenship

    ERIC Educational Resources Information Center

    Harth, Chris

    2010-01-01

    Technological advances in communications, transportation, and information processing have deepened and broadened connections on multiple levels, local through global, thickening the webs of interactivity that bind us to each other economically, politically, militarily, socially, culturally, environmentally, and ethically. As with most complex…

  4. 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...

  5. 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

    2015-05-06

    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.

  6. 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

  7. Interactions between genetic drift, gene flow, and selection mosaics drive parasite local adaptation.

    PubMed

    Gandon, Sylvain; Nuismer, Scott L

    2009-02-01

    Interactions between gene flow, spatially variable selection, and genetic drift have long been a central focus of evolutionary research. In contrast, only recently has the potential importance of interactions between these factors for coevolutionary dynamics and the emergence of parasite local adaptation been realized. Here we study host-parasite coevolution in a metapopulation model when both the biotic and the abiotic components of the environment vary in space. We provide a general expression for parasite local adaptation that allows local adaptation to be partitioned into the contributions of spatial covariances between host and parasite genotype frequencies within and between habitats. This partitioning clarifies how relative rates of gene flow, spatially variable patterns of selection, and genetic drift interact to shape parasite local adaptation. Specifically, by using this expression in conjunction with coevolutionary models, we show that genetic drift can dramatically increase the level of parasite local adaptation under some models of specificity. We also show that the effect of migration on parasite local adaptation depends on the geographic mosaic of selection. We discuss how these predictions could be tested empirically or experimentally using microbial systems.

  8. Does local adaptation to resources explain genetic differentiation among Daphnia populations?

    PubMed

    Allen, Michael R; Thum, Ryan A; Cáceres, Carla E

    2010-08-01

    Substantial genetic differentiation is frequently observed among populations of cyclically parthenogenetic zooplankton despite their high dispersal capabilities and potential for gene flow. Local adaptation has been invoked to explain population genetic differentiation despite high dispersal, but several neutral models that account for basic life history features also predict high genetic differentiation. Here, we study genetic differentiation among four populations of Daphnia pulex in east central Illinois. As with other studies of Daphnia, we demonstrate substantial population genetic differentiation despite close geographic proximity (<50 km; mean theta = 0.22). However, we explicitly tested and failed to find evidence for, the hypothesis that local adaptation to food resources occurs in these populations. Recognizing that local adaptation can occur in traits unrelated to resources, we estimated contemporary migration rates (m) and tested for admixture to evaluate the hypothesis that observed genetic differentiation is consistent with local adaptation to other untested ecological factors. Using Bayesian assignment methods, we detected migrants in three of the four study populations including substantial evidence for successful reproduction by immigrants in one pond, allowing us to reject the hypothesis that local adaptation limits gene flow for at least this population. Thus, we suggest that local adaptation does not explain genetic differentiation among these Daphnia populations and that other factors related to extinction/colonization dynamics, a long approach to equilibrium F(ST) or substantial genetic drift due to a low number of individuals hatching from the egg bank each season may explain genetic differentiation.

  9. 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.

  10. 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.

  11. 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.

  12. Ensemble covariances adaptively localized with ECO-RAP. Part 1: tests on simple error models

    NASA Astrophysics Data System (ADS)

    Bishop, Craig H.; Hodyss, Daniel

    2009-01-01

    In atmospheric data assimilation (DA), observations over a 6-12-h time window are used to estimate the state. Non-adaptive moderation or localization functions are widely used in ensemble DA to reduce the amplitude of spurious ensemble correlations. These functions are inappropriate (1) if true error correlation functions move a comparable distance to the localization length scale over the time window and/or (2) if the widths of true error correlation functions are highly flow dependent. A method for generating localization functions that move with the true error correlation functions and that also adapt to the width of the true error correlation function is given. The method uses ensemble correlations raised to a power (ECO-RAP). A gallery of periodic one-dimensional error models is used to show how the method uses error propagation information and error correlation width information retained by powers of raw ensemble correlations to propagate and adaptively adjust the width of the localization function. It is found that ECO-RAP localization outperforms non-adaptive localization when the true errors are propagating or the error correlation length scale is varying and is as good as non-adaptive localization when such variations in error covariance structure are absent.

  13. 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.

  14. 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.

  15. 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.

  16. The relative contributions of global and local acceleration components on speed perception and discriminability following adaptation.

    PubMed

    Hietanen, Markus A

    2015-10-01

    The perception of speed is dependent on the history of previously presented speeds. Adaptation to a given speed regularly results in a reduction of perceived speed and an increase in speed discriminability and in certain circumstances can result in an increase in perceived speed. In order to determine the relative contributions of the local and global speed components on perceived speed, this experiment used expanding dot flow fields with accelerating (global), decelerating (global) and mixed accelerating/decelerating (local) speed patterns. Profound decreases in perceived speed are found when viewing low test speeds after adaptation to high speeds. Small increases in the perceived speed of high test speeds occur following adaptation to low speeds. There were small but significant differences in perceived stimulus speed after adaptation due to different acceleration profiles. No evidence for global modulation of speed discriminability following adaptation was found.

  17. 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.

  18. 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.

  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. 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

  1. 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.

  2. 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

  3. Population admixture, biological invasions and the balance between local adaptation and inbreeding depression.

    PubMed

    Verhoeven, Koen J F; Macel, Mirka; Wolfe, Lorne M; Biere, Arjen

    2011-01-01

    When previously isolated populations meet and mix, the resulting admixed population can benefit from several genetic advantages, including increased genetic variation, the creation of novel genotypes and the masking of deleterious mutations. These admixture benefits are thought to play an important role in biological invasions. In contrast, populations in their native range often remain differentiated and frequently suffer from inbreeding depression owing to isolation. While the advantages of admixture are evident for introduced populations that experienced recent bottlenecks or that face novel selection pressures, it is less obvious why native range populations do not similarly benefit from admixture. Here we argue that a temporary loss of local adaptation in recent invaders fundamentally alters the fitness consequences of admixture. In native populations, selection against dilution of the locally adapted gene pool inhibits unconstrained admixture and reinforces population isolation, with some level of inbreeding depression as an expected consequence. We show that admixture is selected against despite significant inbreeding depression because the benefits of local adaptation are greater than the cost of inbreeding. In contrast, introduced populations that have not yet established a pattern of local adaptation can freely reap the benefits of admixture. There can be strong selection for admixture because it instantly lifts the inbreeding depression that had built up in isolated parental populations. Recent work in Silene suggests that reduced inbreeding depression associated with post-introduction admixture may contribute to enhanced fitness of invasive populations. We hypothesize that in locally adapted populations, the benefits of local adaptation are balanced against an inbreeding cost that could develop in part owing to the isolating effect of local adaptation itself. The inbreeding cost can be revealed in admixing populations during recent invasions.

  4. 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

  5. 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

  6. Local adaptation and the evolution of species' ranges under climate change.

    PubMed

    Atkins, K E; Travis, J M J

    2010-10-01

    The potential impact of climate change on biodiversity is well documented. A well developed range of statistical methods currently exists that projects the possible future habitat of a species directly from the current climate and a species distribution. However, studies incorporating ecological and evolutionary processes remain limited. Here, we focus on the potential role that local adaptation to climate may play in driving the range dynamics of sessile organisms. Incorporating environmental adaptation into a stochastic simulation yields several new insights. Counter-intuitively, our simulation results suggest that species with broader ranges are not necessarily more robust to climate change. Instead, species with broader ranges can be more susceptible to extinction as locally adapted genotypes are often blocked from range shifting by the presence of cooler adapted genotypes that persist even when their optimum climate has left them behind. Interestingly, our results also suggest that it will not always be the cold-adapted phenotypes that drive polewards range expansion. Instead, range shifts may be driven by phenotypes conferring adaptation to conditions prevalent towards the centre of a species' equilibrium distribution. This may have important consequences for the conservation method termed predictive provenancing. These initial results highlight the potential importance of local adaptation in determining how species will respond to climate change and we argue that this is an area requiring urgent theoretical and empirical attention.

  7. Aortic pulse pressure homeostasis emerges from physiological adaptation of systemic arteries to local mechanical stresses.

    PubMed

    Nguyen, Phuc H; Tuzun, Egemen; Quick, Christopher M

    2016-09-01

    Aortic pulse pressure arises from the interaction of the heart, the systemic arterial system, and peripheral microcirculations. The complex interaction between hemodynamics and arterial remodeling precludes the ability to experimentally ascribe changes in aortic pulse pressure to particular adaptive responses. Therefore, the purpose of the present work was to use a human systemic arterial system model to test the hypothesis that pulse pressure homeostasis can emerge from physiological adaptation of systemic arteries to local mechanical stresses. First, we assumed a systemic arterial system that had a realistic topology consisting of 121 arterial segments. Then the relationships of pulsatile blood pressures and flows in arterial segments were characterized by standard pulse transmission equations. Finally, each arterial segment was assumed to remodel to local stresses following three simple rules: 1) increases in endothelial shear stress increases radius, 2) increases in wall circumferential stress increases wall thickness, and 3) increases in wall circumferential stress decreases wall stiffness. Simulation of adaptation by iteratively calculating pulsatile hemodynamics, mechanical stresses, and vascular remodeling led to a general behavior in response to mechanical perturbations: initial increases in pulse pressure led to increased arterial compliances, and decreases in pulse pressure led to decreased compliances. Consequently, vascular adaptation returned pulse pressures back toward baseline conditions. This behavior manifested when modeling physiological adaptive responses to changes in cardiac output, changes in peripheral resistances, and changes in local arterial radii. The present work, thus, revealed that pulse pressure homeostasis emerges from physiological adaptation of systemic arteries to local mechanical stresses.

  8. Adaptive local thresholding for robust nucleus segmentation utilizing shape priors

    NASA Astrophysics Data System (ADS)

    Wang, Xiuzhong; Srinivas, Chukka

    2016-03-01

    This paper describes a novel local thresholding method for foreground detection. First, a Canny edge detection method is used for initial edge detection. Then, tensor voting is applied on the initial edge pixels, using a nonsymmetric tensor field tailored to encode prior information about nucleus size, shape, and intensity spatial distribution. Tensor analysis is then performed to generate the saliency image and, based on that, the refined edge. Next, the image domain is divided into blocks. In each block, at least one foreground and one background pixel are sampled for each refined edge pixel. The saliency weighted foreground histogram and background histogram are then created. These two histograms are used to calculate a threshold by minimizing the background and foreground pixel classification error. The block-wise thresholds are then used to generate the threshold for each pixel via interpolation. Finally, the foreground is obtained by comparing the original image with the threshold image. The effective use of prior information, combined with robust techniques, results in far more reliable foreground detection, which leads to robust nucleus segmentation.

  9. Influence of adaptation state and stimulus luminance on peri-saccadic localization.

    PubMed

    Georg, Katharina; Hamker, Fred H; Lappe, Markus

    2008-01-01

    Spatial localization of flashed stimuli across saccades shows transient distortions of perceived position: Stimuli appear shifted in saccade direction and compressed towards the saccade target. The strength and spatial pattern of this mislocalization is influenced by contrast, duration, and spatial and temporal arrangement of stimuli and background. Because mislocalization of stimuli on a background depends on contrast, we asked whether mislocalization of stimuli in darkness depends on luminance. Since dark adaptation changes luminance thresholds, we compared mislocalization in dark-adapted and light-adapted states. Peri-saccadic mislocalization was measured with near-threshold stimuli and above-threshold stimuli in dark-adapted and light-adapted subjects. In both adaptation states, near-threshold stimuli gave much larger mislocalization than above-threshold stimuli. Furthermore, when the stimulus was presented near-threshold, the perceived positions of the stimuli clustered closer together. Stimulus luminance that produced strong mislocalization in the light-adapted state produced very little mislocalization in the dark-adapted state because it was now well above threshold. We conclude that the strength of peri-saccadic mislocalization depends on the strength of the stimulus: stimuli with near-threshold luminance, and hence low visibility, are more mis-localized than clearly visible stimuli with high luminance.

  10. 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

  11. 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.

  12. Myocardial Strain Imaging with High-Performance Adaptive Dynamic Grid Interpolation Method

    NASA Astrophysics Data System (ADS)

    Shuhui Bu,; Makoto Yamakawa,; Tsuyoshi Shiina,

    2010-07-01

    The accurate assessment of local myocardial strain is important for diagnosing ischemic heart diseases because decreased myocardial motion often appears in the early stage. Calculating the spatial derivation of displacement is a necessary step in the strain calculation, but the numerical calculation is extremely sensitive to noise. Commonly used smoothing methods are the moving-average and median filters; however, these methods have a trade-off between spatial resolution and accuracy. A novel smoothing/fitting method is proposed for overcoming this problem. In this method, the detected displacement vectors are discretized at mesh nodes, and virtual springs are connected between adjacent nodes. By controlling the elasticity of the virtual springs, misdetected displacements are fitted without the above problem. Further improvements can be achieved by applying a Kalman filter for position tracking, and then calculating the strain from the accumulated displacement vectors. From the simulation results, we conclude that the proposed method improves the accuracy and spatial resolution of the strain images.

  13. 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.

  14. 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.

  15. 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

  16. A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species.

    PubMed

    Kubota, Shosei; Iwasaki, Takaya; Hanada, Kousuke; Nagano, Atsushi J; Fujiyama, Asao; Toyoda, Atsushi; Sugano, Sumio; Suzuki, Yutaka; Hikosaka, Kouki; Ito, Motomi; Morinaga, Shin-Ichi

    2015-07-01

    Adaptive divergence at the microgeographic scale has been generally disregarded because high gene flow is expected to disrupt local adaptation. Yet, growing number of studies reporting adaptive divergence at a small spatial scale highlight the importance of this process in evolutionary biology. To investigate the genetic basis of microgeographic local adaptation, we conducted a genome-wide scan among sets of continuously distributed populations of Arabidopsis halleri subsp. gemmifera that show altitudinal phenotypic divergence despite gene flow. Genomic comparisons were independently conducted in two distinct mountains where similar highland ecotypes are observed, presumably as a result of convergent evolution. Here, we established a de novo reference genome and employed an individual-based resequencing for a total of 56 individuals. Among 527,225 reliable SNP loci, we focused on those showing a unidirectional allele frequency shift across altitudes. Statistical tests on the screened genes showed that our microgeographic population genomic approach successfully retrieve genes with functional annotations that are in line with the known phenotypic and environmental differences between altitudes. Furthermore, comparison between the two distinct mountains enabled us to screen out those genes that are neutral or adaptive only in either mountain, and identify the genes involved in the convergent evolution. Our study demonstrates that the genomic comparison among a set of genetically connected populations, instead of the commonly-performed comparison between two isolated populations, can also offer an effective screening for the genetic basis of local adaptation.

  17. North-South Colonization Associated with Local Adaptation of the Wild Tomato Species Solanum chilense.

    PubMed

    Böndel, Katharina B; Lainer, Hilde; Nosenko, Tetyana; Mboup, Mamadou; Tellier, Aurélien; Stephan, Wolfgang

    2015-11-01

    After colonization population sizes may vary across the species range depending on environmental conditions and following colonizations. An interesting question is whether local adaptation occurs more frequently in large ancestral populations or in small derived populations. A higher number of new mutations and a lower effect of genetic drift should favor selection in large populations, whereas small derived populations may require an initial local adaptation event to facilitate the colonization of new habitats. Wild tomatoes are native to a broad range of different habitats characterized by variable abiotic conditions in South America, and represent an ideal system to study this interplay between demography and natural selection. Population genetic analyses and statistical inference of past demography were conducted on pooled-sequencing data from 30 genes (8,080 single nucleotide polymorphisms) from an extensive sampling of 23 Solanum chilense populations over Chile and Peru. We reveal first a north-south colonization associated with relaxed purifying selection in the south as shown by a decrease of genetic variation and an increasing proportion of nonsynonymous polymorphism from north to south, and population substructure with at least four genetic groups. Second, we uncover a dual picture of adaptation consisting of 1) a decreasing proportion of adaptive amino acid substitutions from north to south suggesting that adaptation is favored in large populations, whereas 2) signatures of local adaptation predominantly occur in the smaller populations from the marginal ranges in the south.

  18. Local adaptation in the flowering-time gene network of balsam poplar, Populus balsamifera L.

    PubMed

    Keller, Stephen R; Levsen, Nicholas; Olson, Matthew S; Tiffin, Peter

    2012-10-01

    Identifying the signature and targets of local adaptation is an increasingly important goal in empirical population genetics. Using data from 443 balsam poplar Populus balsamifera trees sampled from 31 populations, we tested for evidence of geographically variable selection shaping diversity at 27 homologues of the Arabidopsis flowering-time network. These genes are implicated in the control of seasonal phenology, an important determinant of fitness. Using 335 candidate and 412 reference single nucleotide polymorphisms (SNPs), we tested for evidence of local adaptation by searching for elevated population differentiation using F(ST)-based outlier analyses implemented in BayeScan or a Hierarchical Model in Arelquin and by testing for significant associations between allele frequency and environmental variables using BAYENV. A total of 46 SNPs from 14 candidate genes had signatures of local adaptation-either significantly greater population differentiation or significant covariance with one or more environmental variable relative to reference SNP distributions. Only 11 SNPs from two genes exhibited both elevated population differentiation and covariance with one or more environmental variables. Several genes including the abscisic acid gene ABI1B and the circadian clock genes ELF3 and GI5 harbored a large number of SNPs with signatures of local adaptation-with SNPs in GI5 strongly covarying with both latitude and precipitation and SNPs in ABI1B strongly covarying with temperature. In contrast to several other systems, we find little evidence that photoreceptors, including phytochromes, play an important role in local adaptation. Our results additionally show that detecting local adaptation is sensitive to the analytical approaches used and that model-based significance thresholds should be viewed with caution.

  19. 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).

  20. Performance and scaling of locally-structured grid methods forpartial differential equations

    SciTech Connect

    Colella, Phillip; Bell, John; Keen, Noel; Ligocki, Terry; Lijewski, Michael; Van Straalen, Brian

    2007-07-19

    In this paper, we discuss some of the issues in obtaining high performance for block-structured adaptive mesh refinement software for partial differential equations. We show examples in which AMR scales to thousands of processors. We also discuss a number of metrics for performance and scalability that can provide a basis for understanding the advantages and disadvantages of this approach.

  1. Evidence of concurrent local adaptation and high phenotypic plasticity in a polar microeukaryote.

    PubMed

    Rengefors, Karin; Logares, Ramiro; Laybourn-Parry, Johanna; Gast, Rebecca J

    2015-05-01

    Here we investigated whether there is evidence of local adaptation in strains of an ancestrally marine dinoflagellate to the lacustrine environment they now inhabit (optimal genotypes) and/or if they have evolved phenotypic plasticity (a range of phenotypes). Eleven strains of Polarella glacialis were isolated and cultured from three different environments: the polar seas, a hyposaline and a hypersaline Antarctic lake. Local adaptation was tested by comparing growth rates of lacustrine and marine strains at their own and reciprocal site conditions. To determine phenotypic plasticity, we measured the reaction norm for salinity. We found evidence of both, limited local adaptation and higher phenotypic plasticity in lacustrine strains when compared with marine ancestors. At extreme high salinities, local lake strains outperformed other strains, and at extreme low salinities, strains from the hyposaline lake outperformed all other strains. The data suggest that lake populations may have evolved higher phenotypic plasticity in the lake habitats compared with the sea, presumably due to the high temporal variability in salinity in the lacustrine systems. Moreover, the interval of salinity tolerance differed between strains from the hyposaline and hypersaline lakes, indicating local adaptation promoted by different salinity.

  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. Spatiotemporal variation in local adaptation of a specialist insect herbivore to its long-lived host plant.

    PubMed

    Kalske, Aino; Leimu, Roosa; Scheepens, J F; Mutikainen, Pia

    2016-09-01

    Local adaptation of interacting species to one another indicates geographically variable reciprocal selection. This process of adaptation is central in the organization and maintenance of genetic variation across populations. Given that the strength of selection and responses to it often vary in time and space, the strength of local adaptation should in theory vary between generations and among populations. However, such spatiotemporal variation has rarely been explicitly demonstrated in nature and local adaptation is commonly considered to be relatively static. We report persistent local adaptation of the short-lived herbivore Abrostola asclepiadis to its long-lived host plant Vincetoxicum hirundinaria over three successive generations in two studied populations and considerable temporal variation in local adaptation in six populations supporting the geographic mosaic theory. The observed variation in local adaptation among populations was best explained by geographic distance and population isolation, suggesting that gene flow reduces local adaptation. Changes in herbivore population size did not conclusively explain temporal variation in local adaptation. Our results also imply that short-term studies are likely to capture only a part of the existing variation in local adaptation.

  4. Spatiotemporal variation in local adaptation of a specialist insect herbivore to its long-lived host plant.

    PubMed

    Kalske, Aino; Leimu, Roosa; Scheepens, J F; Mutikainen, Pia

    2016-09-01

    Local adaptation of interacting species to one another indicates geographically variable reciprocal selection. This process of adaptation is central in the organization and maintenance of genetic variation across populations. Given that the strength of selection and responses to it often vary in time and space, the strength of local adaptation should in theory vary between generations and among populations. However, such spatiotemporal variation has rarely been explicitly demonstrated in nature and local adaptation is commonly considered to be relatively static. We report persistent local adaptation of the short-lived herbivore Abrostola asclepiadis to its long-lived host plant Vincetoxicum hirundinaria over three successive generations in two studied populations and considerable temporal variation in local adaptation in six populations supporting the geographic mosaic theory. The observed variation in local adaptation among populations was best explained by geographic distance and population isolation, suggesting that gene flow reduces local adaptation. Changes in herbivore population size did not conclusively explain temporal variation in local adaptation. Our results also imply that short-term studies are likely to capture only a part of the existing variation in local adaptation. PMID:27436540

  5. 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.

  6. Global Optimization, Local Adaptation, and the Role of Growth in Distribution Networks

    NASA Astrophysics Data System (ADS)

    Ronellenfitsch, Henrik; Katifori, Eleni

    2016-09-01

    Highly optimized complex transport networks serve crucial functions in many man-made and natural systems such as power grids and plant or animal vasculature. Often, the relevant optimization functional is nonconvex and characterized by many local extrema. In general, finding the global, or nearly global optimum is difficult. In biological systems, it is believed that such an optimal state is slowly achieved through natural selection. However, general coarse grained models for flow networks with local positive feedback rules for the vessel conductivity typically get trapped in low efficiency, local minima. In this work we show how the growth of the underlying tissue, coupled to the dynamical equations for network development, can drive the system to a dramatically improved optimal state. This general model provides a surprisingly simple explanation for the appearance of highly optimized transport networks in biology such as leaf and animal vasculature.

  7. Dose Escalation for Locally Advanced Lung Cancer Using Adaptive Radiation Therapy With Simultaneous Integrated Volume-Adapted Boost

    SciTech Connect

    Weiss, Elisabeth; Fatyga, Mirek; Wu, Yan; Dogan, Nesrin; Balik, Salim; Sleeman, William; Hugo, Geoffrey

    2013-07-01

    Purpose: To test the feasibility of a planned phase 1 study of image-guided adaptive radiation therapy in locally advanced lung cancer. Methods and Materials: Weekly 4-dimensional fan beam computed tomographs (4D FBCT) of 10 lung cancer patients undergoing concurrent chemoradiation therapy were used to simulate adaptive radiation therapy: After an initial intensity modulated radiation therapy plan (0-30 Gy/2 Gy), adaptive replanning was performed on week 2 (30-50 Gy/2 Gy) and week 4 scans (50-66 Gy/2 Gy) to adjust for volume and shape changes of primary tumors and lymph nodes. Week 2 and 4 clinical target volumes (CTV) were deformably warped from the initial planning scan to adjust for anatomical changes. On the week 4 scan, a simultaneous integrated volume-adapted boost was created to the shrunken primary tumor with dose increases in 5 0.4-Gy steps from 66 Gy to 82 Gy in 2 scenarios: plan A, lung isotoxicity; plan B, normal tissue tolerance. Cumulative dose was assessed by deformably mapping and accumulating biologically equivalent dose normalized to 2 Gy-fractions (EQD2). Results: The 82-Gy level was achieved in 1 in 10 patients in scenario A, resulting in a 13.4-Gy EQD2 increase and a 22.1% increase in tumor control probability (TCP) compared to the 66-Gy plan. In scenario B, 2 patients reached the 82-Gy level with a 13.9 Gy EQD2 and 23.4% TCP increase. Conclusions: The tested image-guided adaptive radiation therapy strategy enabled relevant increases in EQD2 and TCP. Normal tissue was often dose limiting, indicating a need to modify the present study design before clinical implementation.

  8. 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...

  9. 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.

  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

    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.

  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. 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

  13. 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

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

    PubMed

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

    2016-04-21

    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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. An efficient and self-adapting localization in static wireless sensor networks.

    PubMed

    Teng, Guodong; Zheng, Kougen; Dong, Wei

    2009-01-01

    Localization is one of the most important subjects in Wireless Sensor Networks (WSNs). To reduce the number of beacons and adopt probabilistic methods, some particle filter-based mobile beacon-assisted localization approaches have been proposed, such as Mobile Beacon-assisted Localization (MBL), Adapting MBL (A-MBL), and the method proposed by Hang et al. Some new significant problems arise in these approaches, however. The first question is which probability distribution should be selected as the dynamic model in the prediction stage. The second is whether the unknown node adopts neighbors' observation in the update stage. The third is how to find a self-adapting mechanism to achieve more flexibility in the adapting stage. In this paper, we give the theoretical analysis and experimental evaluations to suggest which probability distribution in the dynamic model should be adopted to improve the efficiency in the prediction stage. We also give the condition for whether the unknown node should use the observations from its neighbors to improve the accuracy. Finally, we propose a Self-Adapting Mobile Beacon-assisted Localization (SA-MBL) approach to achieve more flexibility and achieve almost the same performance with A-MBL.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. Local Host Adaptation and Use of a Novel Host in the Seed Beetle Megacerus eulophus

    PubMed Central

    Stotz, Gisela C.; Suárez, Lorena H.; Gonzáles, Wilfredo L.; Gianoli, Ernesto

    2013-01-01

    Spatial variation in host plant availability may lead to specialization in host use and local host adaptation in herbivorous insects, which may involve a cost in performance on other hosts. We studied two geographically separated populations of the seed beetle Megacerus eulophus (Coleoptera: Bruchidae) in central Chile: a population from the host Convolvulus chilensis (in Aucó) and a population from C. bonariensis (in Algarrobo). In Aucó C. chilensis is the only host plant, while in Algarrobo both C. bonariensis and C. chilensis are available. We tested local adaptation to these native host plants and its influence on the use of another, exotic host plant. We hypothesized that local adaptation would be verified, particularly for the one-host population (Aucó), and that the Aucó population would be less able to use an alternative, high-quality host. We found evidence of local adaptation in the population from C. chilensis. Thus, when reared on C. chilensis, adults from the C. chilensis population were larger and lived longer than individuals from the C. bonariensis population, while bruchids from the two populations had the same body size and longevity when reared on C. bonariensis. Overall, bruchids from the C. chilensis population showed greater performance traits than those from the C. bonariensis population. There were no differences between the bruchid populations in their ability to use the alternative, exotic host Calystegia sepium, as shown by body size and longevity patterns. Results suggest that differences in local adaptation might be explained by differential host availability in the study populations. PMID:23326528

  6. 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

  7. Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world.

    PubMed

    O'Neil, Shawn T; Dzurisin, Jason D K; Williams, Caroline M; Lobo, Neil F; Higgins, Jessica K; Deines, Jillian M; Carmichael, Rory D; Zeng, Erliang; Tan, John C; Wu, Grace C; Emrich, Scott J; Hellmann, Jessica J

    2014-06-01

    Local adaptation of populations could preclude or slow range expansions in response to changing climate, particularly when dispersal is limited. To investigate the differential responses of populations to changing climatic conditions, we exposed poleward peripheral and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared their whole-transcriptome expression. We found evidence of simple population differentiation in both species, and in the species with previously identified population structure and phenotypic local adaptation, we found several hundred genes that responded in a synchronized and localized fashion. These genes were primarily involved in energy metabolism and oxidative stress, and expression levels were most divergent between populations in the same environment in which we previously detected divergence for metabolism. We found no localized genes in the species with less population structure and for which no local adaptation was previously detected. These results challenge the assumption that species are functionally similar across their ranges and poleward peripheral populations are preadapted to warmer conditions. Rather, some taxa deserve population-level consideration when predicting the effects of climate change because they respond in genetically based, distinctive ways to changing conditions.

  8. 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

  9. Dose Escalation for Locally Advanced Lung Cancer using Adaptive Radiotherapy with Simultaneous Integrated Volume-Adapted Boost

    PubMed Central

    Weiss, Elisabeth; Fatyga, Mirek; Wu, Yan; Dogan, Nesrin; Balik, Salim; Sleeman, William; Hugo, Geoffrey

    2013-01-01

    Purpose Test the feasibility of a planned phase I study of image-guided adaptive radiotherapy in locally advanced lung cancer. Methods and Materials Weekly 4D FBCTs of ten lung cancer patients undergoing concurrent radiochemotherapy were used to simulate adaptive radiotherapy: After an initial IMRT plan (0–30 Gy/2 Gy), adaptive replanning was performed on week 2 (30 to 50 Gy/2 Gy) and week 4 scans (50 to 66 Gy/2 Gy) to adjust for volume and shape changes of primary tumors and lymph nodes. Week 2 and 4 clinical target volumes (CTV) were deformably warped from the initial planning scan to adjust for anatomical changes. On week 4 scan a simultaneous integrated volume-adapted boost was created to the shrunken PT with dose increases in five 0.4 Gy steps from 66 Gy to 82 Gy in two scenarios: Plan A. lung isotoxicity and B. normal tissue tolerance. Cumulative dose was assessed by deformably mapping and accumulating biologically equivalent dose normalized to 2 Gy-fractions (EQD2). Results The 82 Gy level was achieved in 1/10 patients in scenario A resulting in a 13.4 Gy EQD2 increase and a 22.1% increase in tumor control probability (TCP) compared to the 66 Gy plan. In scenario B, 2 patients reached the 82 Gy level with a 13.9 Gy EQD2 and 23.4% TCP increase. Conclusions The tested IGART strategy enabled relevant increases in EQD2 and TCP. Normal tissue was often dose limiting, indicating a need to modify the present study design prior to clinical implementation. PMID:23523321

  10. Design of an Internal Model Control strategy for single-phase grid-connected PWM inverters and its performance analysis with a non-linear local load and weak grid.

    PubMed

    Chaves, Eric N; Coelho, Ernane A A; Carvalho, Henrique T M; Freitas, Luiz C G; Júnior, João B V; Freitas, Luiz C

    2016-09-01

    This paper presents the design of a controller based on Internal Model Control (IMC) applied to a grid-connected single-phase PWM inverter. The mathematical modeling of the inverter and the LCL output filter, used to project the 1-DOF IMC controller, is presented and the decoupling of grid voltage by a Feedforward strategy is analyzed. A Proportional - Resonant Controller (P+Res) was used for the control of the same plant in the running of experimental results, thus moving towards the discussion of differences regarding IMC and P+Res performances, which arrived at the evaluation of the proposed control strategy. The results are presented for typical conditions, for weak-grid and for non-linear local load, in order to verify the behavior of the controller against such situations. PMID:27236535

  11. Design of an Internal Model Control strategy for single-phase grid-connected PWM inverters and its performance analysis with a non-linear local load and weak grid.

    PubMed

    Chaves, Eric N; Coelho, Ernane A A; Carvalho, Henrique T M; Freitas, Luiz C G; Júnior, João B V; Freitas, Luiz C

    2016-09-01

    This paper presents the design of a controller based on Internal Model Control (IMC) applied to a grid-connected single-phase PWM inverter. The mathematical modeling of the inverter and the LCL output filter, used to project the 1-DOF IMC controller, is presented and the decoupling of grid voltage by a Feedforward strategy is analyzed. A Proportional - Resonant Controller (P+Res) was used for the control of the same plant in the running of experimental results, thus moving towards the discussion of differences regarding IMC and P+Res performances, which arrived at the evaluation of the proposed control strategy. The results are presented for typical conditions, for weak-grid and for non-linear local load, in order to verify the behavior of the controller against such situations.

  12. 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.

  13. 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.

  14. Community-based disaster preparedness and climate adaptation: local capacity-building in the Philippines.

    PubMed

    Allen, Katrina M

    2006-03-01

    Community-based disaster preparedness (CBDP) approaches are increasingly important elements of vulnerability reduction and disaster management strategies. They are associated with a policy trend that values the knowledge and capacities of local people and builds on local resources, including social capital. CBDP may be instrumental not only in formulating local coping and adaptation strategies, but also in situating them within wider development planning and debates. In theory, local people can be mobilised to resist unsustainable (vulnerability increasing) forms of development or livelihood practices and to raise local concerns more effectively with political representatives. This paper focuses on the potential of CBDP initiatives to alleviate vulnerability in the context of climate change, and their limitations. It presents evidence from the Philippines that, in the limited forms in which they are currently employed, CBDP initiatives have the potential both to empower and disempower, and warns against treating CBDP as a panacea to disaster management problems.

  15. 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.

  16. 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

  17. 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.

  18. Local adaptation and matching habitat choice in female barn owls with respect to melanic coloration.

    PubMed

    Dreiss, A N; Antoniazza, S; Burri, R; Fumagalli, L; Sonnay, C; Frey, C; Goudet, J; Roulin, Alexandre

    2012-01-01

    Local adaptation is a major mechanism underlying the maintenance of phenotypic variation in spatially heterogeneous environments. In the barn owl (Tyto alba), dark and pale reddish-pheomelanic individuals are adapted to conditions prevailing in northern and southern Europe, respectively. Using a long-term dataset from Central Europe, we report results consistent with the hypothesis that the different pheomelanic phenotypes are adapted to specific local conditions in females, but not in males. Compared to whitish females, reddish females bred in sites surrounded by more arable fields and less forests. Colour-dependent habitat choice was apparently beneficial. First, whitish females produced more fledglings when breeding in wooded areas, whereas reddish females when breeding in sites with more arable fields. Second, cross-fostering experiments showed that female nestlings grew wings more rapidly when both their foster and biological mothers were of similar colour. The latter result suggests that mothers should particularly produce daughters in environments that best match their own coloration. Accordingly, whiter females produced fewer daughters in territories with more arable fields. In conclusion, females displaying alternative melanic phenotypes bred in habitats providing them with the highest fitness benefits. Although small in magnitude, matching habitat selection and local adaptation may help maintain variation in pheomelanin coloration in the barn owl. PMID:22070193

  19. 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.

  20. Evidence of local adaptation in the demographic response of American ginseng to interannual temperature variation.

    PubMed

    Souther, Sara; McGraw, James B

    2011-10-01

    Bioclimatic envelope models of species' responses to climate change are used to predict how species will respond to increasing temperatures. These models are frequently based on the assumption that the northern and southern boundaries of a species' range define its thermal niche. However, this assumption may be violated if populations are adapted to local temperature regimes and have evolved population-specific thermal optima. Considering the prevalence of local adaptation, the assumption of a species-wide thermal optimum may be violated for many species. We used spatially and temporally extensive demographic data for American ginseng (Panax quinquefolius L.) to examine range-wide variation in response of population growth rate (λ) to climatic factors. Our results suggest adaptation to local temperature, but not precipitation. For each population, λ was maximized when annual temperatures were similar to site-specific, long-term mean temperatures. Populations from disparate climatic zones responded differently to temperature variation, and there was a linear relation between population-level thermal optima and the 30-year mean temperature at each site. For species that are locally adapted to temperature, bioclimatic envelope models may underestimate the extent to which increasing temperatures will decrease population growth rate. Because any directional change from long-term mean temperatures will decrease population growth rates, all populations throughout a species' range will be adversely affected by temperature increase, not just populations at southern and low-elevation boundaries. Additionally, when a species' local thermal niche is narrower than its range-wide thermal niche, a smaller temperature increase than would be predicted by bioclimatic envelope approaches may be sufficient to decrease population growth.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies.

    PubMed

    Pratlong, M; Haguenauer, A; Chabrol, O; Klopp, C; Pontarotti, P; Aurelle, D

    2015-09-01

    The question of species survival and evolution in heterogeneous environments has long been a subject for study. Indeed, it is often difficult to identify the molecular basis of adaptation to contrasted environments, and nongenetic effects increase the difficulty to disentangle fixed effects, such as genetic adaptation, from variable effects, such as individual phenotypic plasticity, in adaptation. Nevertheless, this question is also of great importance for understanding the evolution of species in a context of climate change. The red coral (Corallium rubrum) lives in the Mediterranean Sea, where at depths ranging from 5 to 600 m, it meets very contrasted thermal conditions. The shallowest populations of this species suffered from mortality events linked with thermal anomalies that have highlighted thermotolerance differences between individuals. We provide here a new transcriptomic resource, as well as candidate markers for the study of local adaptation. We sequenced the transcriptome of six individuals from 5 m and six individuals from 40 m depth at the same site of the Marseilles bay, after a period of common garden acclimatization. We found differential expression maintained between the two depths even after common garden acclimatization, and we analysed the polymorphism pattern of these samples. We highlighted contigs potentially implicated in the response to thermal stress, which could be good candidates for the study of thermal adaptation for the red coral. Some of these genes are also involved in the response to thermal stress in other corals. Our method enables the identification of candidate loci of local adaptation useful for other nonmodel organisms.

  7. 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.

  8. FALCON: A method for flexible adaptation of local coordinates of nuclei

    NASA Astrophysics Data System (ADS)

    König, Carolin; Hansen, Mads Bøttger; Godtliebsen, Ian H.; Christiansen, Ove

    2016-02-01

    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.

  9. Ensemble covariances adaptively localized with ECO-RAP. Part 2: a strategy for the atmosphere

    NASA Astrophysics Data System (ADS)

    Bishop, Craig H.; Hodyss, Daniel

    2009-01-01

    Part 1's localization method, Ensemble COrrelations Raised to A Power (ECO-RAP), is incorporated into a Local Ensemble Transform Kalman Filter (LETKF). Because brute force incorporation would be too expensive, we demonstrate a factorization property for Part 1's Covariances Adaptively Localized with ECO-rap (CALECO) forecast error covariance matrix that, together with other simplifications, reduces the cost. The property inexpensively provides a large CALECO ensemble whose covariance is the CALECO matrix. Each member of the CALECO ensemble is an element-wise product between one raw ensemble member and one column of the square root of the ECO-RAP matrix. The LETKF is applied to the CALECO ensemble rather than the raw ensemble. The approach enables the update of large numbers of variables within each observation volume at little additional computational cost. Under plausible assumptions, this makes the CALECO and standard LETKF costs similar. The CALECO LETKF does not require artificial observation error inflation or vertically confined observation volumes both of which confound the assimilation of non-local observations such as satellite observations. Using a 27 member ensemble from a global Numerical Weather Prediction (NWP) system, we depict four-dimensional (4-D) flow-adaptive error covariance localization and test the ability of the CALECO LETKF to reduce analysis error.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. The consequences of dominance and gene flow for local adaptation and differentiation at two linked loci

    PubMed Central

    Akerman, Ada; Bürger, Reinhard

    2014-01-01

    For a subdivided population the consequences of dominance and gene flow for the maintenance of multilocus polymorphism, local adaptation, and differentiation are investigated. The dispersing population inhabits two demes in which selection acts in opposite direction. Fitness is determined additively by two linked diallelic loci with arbitrary intermediate dominance (no over- or underdominance). For weak as well as strong migration, the equilibrium structure is derived. As a special case, a continuous-time continent–island model (CI model) is analyzed, with one-way migration from the continent to the island. For this CI model, the equilibrium and stability configuration is obtained explicitly for weak migration, for strong migration, for independent loci, and for complete linkage. For independent loci, the possible bifurcation patterns are derived as functions of the migration rate. These patterns depend strongly on the degree of dominance. The effects of dominance, linkage, and migration on the amount of linkage disequilibrium (LD) and the degree of local adaptation are explored. Explicit formulas are obtained for D   (=x1x4−x2x3) and r2 (the squared correlation in allelic state). They demonstrate that dominant island alleles increase D and decrease r2. Local adaptation is elevated by dominance of the locally adaptive alleles. The effective migration rate at a linked neutral locus is calculated. If advantageous alleles are dominant, it is decreased only slightly below the actual migration rate. For a quantitative trait that is determined by two additive loci, the influence of dominance on measures of differentiation is studied. Explicit expressions for QST and two types of FST at equilibrium are deduced and their relation is discussed. PMID:24793653

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. Patterns of local adaptation in space and time among soil bacteria.

    PubMed

    Kraemer, Susanne A; Kassen, Rees

    2015-03-01

    Our understanding of microbial biogeography has been governed by the dictum "Everything is everywhere, but the environment selects." In other words, the distribution of microbes is thought to occur in a regime of extensive dispersal and strong selection, generating local adaptation. However, direct tests of these assumptions are rare. Here, we investigate the extent of local adaptation in space and time of a collection of soil-derived microbial isolates, most belonging to the genus Pseudomonas, across a growing season from a deciduous forest in western Quebec, Canada, using a reciprocal transplant design. Average performance of all clones varied substantially in both space and time, in line with the expectation of strong selection in both dimensions. The behavior of genotype-by-environment variance in fitness and its components, responsiveness and inconsistency, in space and through time suggests that the strength of divergent selection increases as sites become more distant from each other in both dimensions. However, divergent selection was not strong enough to maintain different specialized types across the environments studied, which suggests that Pseudomonas and their close relatives are not locally adapted to the prevailing conditions of growth.

  1. 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

  2. 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.

  3. Diffuse and local effects of light adaptation in photoreceptors of the honey bee drone.

    PubMed

    Bader, C R; Baumann, F; Bertrand, D; Carreras, J; Fuortes, G

    1982-01-01

    Intracellular recordings from drone photoreceptors were made by means of glass microelectrodes in superfused retinae. Exposure of a small portion of a cell to white light decreased the amplitude of responses to a small stimulus subsequently applied at different sites of the photoreceptor cell, i.e. light adaptation occurred throughout the cell. After 7 min of darkness, the responses had completely recovered. When a violet light (404 nm) was used to adapt a small portion of the cell, the responses at the site of exposure to the adapting stimulus remained depressed for at least 30 min. Illumination at the site of the violet adapting stimulus with green light (585 nm) caused an immediate recovery of the amplitude of the response. These results can be explained by the existence of two processes responsible for light adaptation: one is localized and persistent and appears to be due to changes in concentration of rhodopsin. The other affects the whole cell, is spontaneously reversible and depends upon the ability of the light to produce a receptor potential but not on any lasting change in rhodopsin concentration.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. Locally adapted social parasite affects density, social structure, and life history of its ant hosts.

    PubMed

    Foitzik, Susanne; Achenbach, Alexandra; Brandt, Miriam

    2009-05-01

    Selection and adaptation are important processes in the coevolution between parasites and their hosts. The slave-making ant Protomognathus americanus, an obligate ant social parasite, has previously been shown to evolve morphological, behavioral, and chemical adaptations in the coevolutionary arms race with its Temnothorax hosts. Yet empirical studies have given variable results on the strength of the selection pressure this parasite exerts on its host populations. In this study, we directly investigated the pressure exerted by P. americanus and the reactions of the main host species, T. longispinosus, in two ant communities by manipulating parasite density in the field over several years. In addition, a cross-fostering design with the exchange of parasites between host populations allowed us to investigate local adaptation of parasite or host. We demonstrate a severe impact of the social parasite on the two host populations in West Virginia and New York, but also variation in host reactions between sites, as expected by the geographic mosaic theory of coevolution. Host density decreased at the West Virginia site with the presence of local slave-makers, whereas at the ecologically favorable New York site, density was unaffected. Nevertheless, social organization, colony size, and investment patterns of these host colonies at this site changed in response to our parasite manipulation. The release of P. americanus colonies led to a reduction in the number of resident queens and workers, an increase in intranest relatedness, and lower productivity, but also a higher investment in reproductives. In West Virginia, colony demography did not change, but raiding activity by New York slave-makers caused different investment patterns of host colonies. In addition, the cross-fostering element revealed local adaptation of the parasite P. americanus: slave-making colonies fared better in their sympatric host population, as they contained more slave-making ant workers and slaves

  9. Local adaptation to altitude underlies divergent thermal physiology in tropical killifishes of the genus Aphyosemion.

    PubMed

    McKenzie, David J; Estivales, Guillan; Svendsen, Jon C; Steffensen, John F; Agnèse, Jean-François

    2013-01-01

    In watersheds of equatorial West Africa, monophyletic groups of killifish species (genus Aphyosemion) occur in discrete altitudinal ranges, low altitude species (LA, sea level to ∼350 m) or high altitude species (HA, 350 to 900 m). We investigated the hypothesis that local adaptation to altitude by the LA and HA species would be revealed as divergent effects of temperature on their physiological energetics. Two species from each group (mass ∼350 mg) were acclimated to 19, 25 and 28°C, with 19 and 28°C estimated to be outside the thermal envelope for LA or HA, respectively, in the wild. Wild-caught animals (F0 generation) were compared with animals raised in captivity at 25°C (F1 generation) to investigate the contribution of adaptation versus plasticity. Temperature significantly increased routine metabolic rate in all groups and generations. However, LA and HA species differed in the effects of temperature on their ability to process a meal. At 25°C, the specific dynamic action (SDA) response was completed within 8 h in all groups, but acclimation to temperatures beyond the thermal envelope caused profound declines in SDA performance. At 19°C, the LA required ∼14 h to complete the SDA, whereas the HA required only ∼7 h. The opposite effect was observed at 28°C. This effect was evident in both F0 and F1. Reaction norms for effects of temperature on SDA therefore revealed a trade-off, with superior performance at warmer temperatures by LA being associated with inferior performance at cooler temperatures, and vice-versa in HA. The data indicate that divergent physiological responses to temperature in the LA and HA species reflect local adaptation to the thermal regime in their habitat, and that local adaptation to one thermal environment trades off against performance in another.

  10. Adaptive/non-adaptive proton radiation planning and outcome in a phase II trial for locally advanced non-small cell lung cancer

    PubMed Central

    Koay, Eugene J.; Lege, David; Mohan, Radhe; Komaki, Ritsuko; Cox, James D.; Chang, Joe Y.

    2012-01-01

    Purpose To analyze dosimetric variables and outcomes after adaptive replanning of radiotherapy during concurrent high-dose protons and chemotherapy for locally advanced non-small cell lung cancer (NSCLC). Methods and Materials Nine of 44 patients with stage III NSCLC in a prospective phase II trial of concurrent paclitaxel/carboplatin with proton radiation [74 Gy(RBE) in 37 fractions] had modifications to their original treatment plans after re-evaluation revealed changes that would compromise coverage of the target volume or violate dose constraints; plans for the other 35 patients were not changed. We compared patients with adaptive plans with those with nonadaptive plans in terms of dosimetry and outcomes. Results At a median follow-up of 21.2 months (median overall survival, 29.6 months), no differences were found in local, regional, or distant failure or overall survival between groups. Adaptive planning was used more often for large tumors that shrank to a greater extent (median, 107.1 cm3 adaptive and 86.4 cm3 non-adaptive; median changes in volume, 25.3% adaptive and 1.2% non-adaptive; p<0.01). The median number of fractions delivered using adaptive planning was 13 (range, 4–22). Adaptive planning generally improved sparing of the esophagus (median absolute decrease in V70, 1.8%; range, 0–22.9%) and spinal cord (median absolute change in maximum dose, 3.7 Gy; range, 0–13.8 Gy). Without adaptive replanning, target coverage would have been compromised in 2 cases (57% and 82% coverage without adaptation vs. 100% for both with adaptation); neither patient experienced local failure. Radiation-related grade 3 toxicity rates were similar between groups. Conclusions Adaptive planning can reduce normal tissue doses and prevent target misses, particularly for patients with large tumors that shrink substantially during therapy. Adaptive plans seem to have acceptable toxicity and achieve similar local, regional, and distant control and overall survival, even in

  11. Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana.

    PubMed

    Lasky, Jesse R; Des Marais, David L; Lowry, David B; Povolotskaya, Inna; McKay, John K; Richards, James H; Keitt, Timothy H; Juenger, Thomas E

    2014-09-01

    Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients.

  12. Natural Variation in Abiotic Stress Responsive Gene Expression and Local Adaptation to Climate in Arabidopsis thaliana

    PubMed Central

    Lasky, Jesse R.; Des Marais, David L.; Lowry, David B.; Povolotskaya, Inna; McKay, John K.; Richards, James H.; Keitt, Timothy H.; Juenger, Thomas E.

    2014-01-01

    Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, “eSR”) to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, “eGEI”). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients. PMID:24850899

  13. 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.

  14. 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

  15. 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.

  16. Local adaptation and cogradient selection in the alpine plant, Poa hiemata, along a narrow altitudinal gradient.

    PubMed

    Byars, Sean G; Papst, Warwick; Hoffmann, Ary A

    2007-12-01

    Alpine environments are particularly susceptible to environmental changes associated with global warming but there is potential for alpine plants to adapt to warming if local adaptation occurs and gene flow allows genotypes adapted to low altitudes to colonize higher altitude sites. Here we examine the adaptive potential of a common alpine grass, Poa hiemata, within the restricted alpine habitat of Australian mountains, across a narrow altitudinal gradient replicated in three areas. Grasses at high altitude sites had shorter leaf lengths and larger circumferences than those at lower sites. Transplant experiments with clonal material and plants grown from seed indicated that these differences were partly genetic, with environmental and genetic factors both contributing to the differences between altitudes. Differences in altitudinal forms were also evident in a common garden experiment. Plants showed a home-site advantage in terms of survival. A fitness analysis indicated that at high altitude sites, selection favored plants with short leaves and larger circumferences, whereas these traits were selected in the opposite direction at the low altitude sites. These findings indicate cogradient selection and potential for both plastic and genotypic shifts in response to climate change in P. hiemata.

  17. 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

  18. Adaptation of diploid and tetraploid chamerion angustifolium to elevation but not local environment.

    PubMed

    Martin, Sara L; Husband, Brian C

    2013-06-01

    Polyploid organisms often have different geographic ranges than their diploid relatives. However, it is unclear whether this divergence is maintained by adaptation or results from historical differences in colonization. Here, we conducted a reciprocal transplant experiment with diploid and autotetraploid Chamerion angustifolium to test for adaptation at the ploidy and population level. In the Rocky Mountains, pure diploid populations occur at high elevations and pure autotetraploid populations occur at low elevations with mixed ploidy populations between. We planted 3134 seedlings in 2004 and 3890 juveniles (bolting) in 2005 among nine plots, three in each of the diploid, mixed ploidy, and tetraploid zones, and monitored survival until 2008. For both seedlings and juvenile plants, elevation significantly influenced survival. The juvenile plants also showed a significant ploidy by elevation interaction, indicating that diploids and tetraploids survived best at their native elevations. In contrast, we found no evidence of local adaptation to plot within elevation. This suggests that the current distribution of diploids and tetraploids across elevations is the result of adaptation and that genome duplication may have facilitated the invasion of lower elevation habitats by limiting the movement of maladapted alleles from diploid populations at higher elevations. PMID:23730769

  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. 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

  1. 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

  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.

  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. Influence of local adaptation and interstock hybridization on the cardiovascular performance of largemouth bass Micropterus salmoides.

    PubMed

    Cooke, Steven J; Philipp, David P

    2005-06-01

    In this study, the cardiovascular response to exhaustive exercise among differentiated stocks of largemouth bass Micropterus salmoides was compared at 10 degrees C and 20 degrees C to assess the level of their local adaptation. In addition, the impact that interstock hybridization had on adaptive differences was assessed using F1 hybrids. To accomplish these assessments, four genetically distinct stocks of fish were produced using adults from two regions in the midwestern United States identified as distinct conservation management units (central Illinois, IL and southeastern Wisconsin, WI): both P1 stocks and both reciprocal F1 interstock hybrids. Cardiac variables (both resting and maximal) were consistently lowest for the IL x IL stock relative to the WI x WI stock and both F1 interstock hybrids. Interestingly, however, all groups of fish were able to maintain similar levels of cardiac scope. All fish responded to exercise by increasing heart rate and decreasing stroke volume, consistent with the notion that largemouth bass modulate cardiac output via frequency. After exercise, cardiac variables returned to resting levels 25-35% more rapidly for IL x IL fish relative to all other groups at 20 degrees C. At 10 degrees C, recovery rates for both P1 stocks were similar but more rapid than the interstock hybrids. Collectively, these results indicate that the locally adapted stock (IL x IL) exhibited cardiovascular adaptations that enabled rapid cardiovascular recovery and maintenance of low resting cardiac output and heart rate. Conversely, the translocated stock (WI x WI) and the interstock hybrids required longer for cardiovascular variables to recover after exercise and exhibited higher resting levels of cardiac output and heart rate. This study provides some of the first direct evidence of a physiological mechanism by which mixing stocks could potentially decrease fitness and illustrates the magnitude of the intraspecific diversity of cardiovascular performance.

  5. Genetic variation and local adaptation at a cheatgrass (Bromus tectorum) invasion edge in western Nevada.

    PubMed

    Leger, Elizabeth A; Espeland, Erin K; Merrill, Keith R; Meyer, Susan E

    2009-11-01

    Cheatgrass (Bromus tectorum) is an invasive weed in western North America found primarily growing at elevations less than 2200 m. We asked whether cheatgrass is capable of becoming adapted to a marginal habitat, by investigating a population at a high elevation invasion edge. We used a combination of methods, including reciprocal field transplants, controlled environment studies and molecular analysis. High levels of SSR gene diversity (0.50 vs. 0.43) and comparable variation in phenotypic traits were observed at both the invasion edge and a low elevation, high-density population. Three heterozygotes were observed in the edge population, which is unusual in this predominantly self-pollinating plant. Plants from high elevations germinated more slowly in a growth chamber and had slower seedling growth rates. Survivorship was low at the edge (13%), compared with the low elevation site (55%), but surviving plants were of similar size and had equivalent reproductive output. Seed size positively affected survival and plant performance in the field and this trait was inherited. Emergence timing affected survival at the low elevation site and germination timing was also inherited. Local adaptation was seen in the low, rather than in the high elevation site, because of differential survival. While there was no evidence for local adaptation to the high elevation site observed in the field, family level and genotype-level differences in traits that affected field performance, high genetic diversity at the invasion edge, and evidence of outcrossing in this highly selfing species indicates that the potential for adaptation to a marginal habitat exists within this population. PMID:19769691

  6. Adapted waveform analysis, wavelet packets, and local cosine libraries as a tool for image processing

    NASA Astrophysics Data System (ADS)

    Coifman, Ronald R.; Woog, Lionel J.

    1995-09-01

    Adapted wave form analysis, refers to a collection of FFT like adapted transform algorithms. Given an image these methods provide special matched collections of templates (orthonormal bases) enabling an efficient coding of the image. Perhaps the closest well known example of such coding method is provided by musical notation, where each segment of music is represented by a musical score made up of notes (templates) characterised by their duration, pitch, location and amplitude, our method corresponds to transcribing the music in as few notes as possible. The extension to images and video is straightforward we describe the image by collections of oscillatory patterns (paint brush strokes)of various sizes locations and amplitudes using a variety of orthogonal bases. These selected basis functions are chosen inside predefined libraries of oscillatory localized functions (trigonometric and wavelet-packets waveforms) so as to optimize the number of parameters needed to describe our object. These algorithms are of complexity N log N opening the door for a large range of applications in signal and image processing, such as compression, feature extraction denoising and enhancement. In particular we describe a class of special purpose compressions for fingerprint irnages, as well as denoising tools for texture and noise extraction. We start by relating traditional Fourier methods to wavelet, wavelet-packet based algorithms using a recent refinement of the windowed sine and cosine transforms. We will then derive an adapted local sine transform show it's relation to wavelet and wavelet-packet analysis and describe an analysis toolkit illustrating the merits of different adaptive and nonadaptive schemes.

  7. Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?

    PubMed Central

    Fraïsse, Christelle; Roux, Camille; Welch, John J.; Bierne, Nicolas

    2014-01-01

    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

  8. 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.

  9. 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

  10. 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.

  11. A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation.

    PubMed

    Lowry, David B; Willis, John H

    2010-09-28

    The role of chromosomal inversions in adaptation and speciation is controversial. Historically, inversions were thought to contribute to these processes either by directly causing hybrid sterility or by facilitating the maintenance of co-adapted gene complexes. Because inversions suppress recombination when heterozygous, a recently proposed local adaptation mechanism predicts that they will spread if they capture alleles at multiple loci involved in divergent adaptation to contrasting environments. Many empirical studies have found inversion polymorphisms linked to putatively adaptive phenotypes or distributed along environmental clines. However, direct involvement of an inversion in local adaptation and consequent ecological reproductive isolation has not to our knowledge been demonstrated in nature. In this study, we discovered that a chromosomal inversion polymorphism is geographically widespread, and we test the extent to which it contributes to adaptation and reproductive isolation under natural field conditions. Replicated crosses between the prezygotically reproductively isolated annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus, revealed that alternative chromosomal inversion arrangements are associated with life-history divergence over thousands of kilometers across North America. The inversion polymorphism affected adaptive flowering time divergence and other morphological traits in all replicated crosses between four pairs of annual and perennial populations. To determine if the inversion contributes to adaptation and reproductive isolation in natural populations, we conducted a novel reciprocal transplant experiment involving outbred lines, where alternative arrangements of the inversion were reciprocally introgressed into the genetic backgrounds of each ecotype. Our results demonstrate for the first time in nature the contribution of an inversion to adaptation, an annual/perennial life-history shift, and multiple reproductive

  12. 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.

  13. Solution-based adaptive parallel patterning by laser-induced local plasmonic surface defunctionalization.

    PubMed

    Kang, Bongchul; Kim, Jongsu; Yang, Minyang

    2012-12-17

    Adaptive mass fabrication method based on laser-induced plasmonic local surface defunctionalization was suggested to realize solution-based high resolution self-patterning on transparent substrate in parallel. After non-patterned functional monolayer was locally deactivated by laser-induced metallic plasma species, various micro/nano metal structures could be simultaneously fabricated by the parallel self-selective deposition of metal nanoparticles on a specific region. This method makes the eco-friendly and cost-effective production of high resolution pattern possible. Moreover, it can respond to design change actively due to the broad controllable range and easy change of key patterning specifications such as a resolution (subwavelength~100 μm), thickness (100 nm~6 μm), type (dot and line), and shape.

  14. 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.

  15. 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

  16. 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

  17. Using a "time machine" to test for local adaptation of aquatic microbes to temporal and spatial environmental variation.

    PubMed

    Fox, Jeremy W; Harder, Lawrence D

    2015-01-01

    Local adaptation occurs when different environments are dominated by different specialist genotypes, each of which is relatively fit in its local conditions and relatively unfit under other conditions. Analogously, ecological species sorting occurs when different environments are dominated by different competing species, each of which is relatively fit in its local conditions. The simplest theory predicts that spatial, but not temporal, environmental variation selects for local adaptation (or generates species sorting), but this prediction is difficult to test. Although organisms can be reciprocally transplanted among sites, doing so among times seems implausible. Here, we describe a reciprocal transplant experiment testing for local adaptation or species sorting of lake bacteria in response to both temporal and spatial variation in water chemistry. The experiment used a -80°C freezer as a "time machine." Bacterial isolates and water samples were frozen for later use, allowing transplantation of older isolates "forward in time" and newer isolates "backward in time." Surprisingly, local maladaptation predominated over local adaptation in both space and time. Such local maladaptation may indicate that adaptation, or the analogous species sorting process, fails to keep pace with temporal fluctuations in water chemistry. This hypothesis could be tested with more finely resolved temporal data.

  18. 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

    2016-03-10

    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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. Sex, horizontal transmission, and multiple hosts prevent local adaptation of Crithidia bombi, a parasite of bumblebees (Bombus spp.).

    PubMed

    Erler, Silvio; Popp, Mario; Wolf, Stephan; Lattorff, H Michael G

    2012-05-01

    Local adaptation within host-parasite systems can evolve by several non-exclusive drivers (e.g., host species-genetic adaptation; ecological conditions-ecological adaptation, and time-temporal adaptation). Social insects, especially bumblebees, with an annual colony life history not only provide an ideal system to test parasite transmission within and between different host colonies, but also parasite adaptation to specific host species and environments. Here, we study local adaptation in a multiple-host parasite characterized by high levels of horizontal transmission. Crithidia bombi occurs as a gut parasite in several bumblebee species. Parasites were sampled from five different host species in two subsequent years. Population genetic tools were used to test for the several types of adaptation. Although we found no evidence for local adaptation of the parasite toward host species, there was a slight temporal differentiation of the parasite populations, which might have resulted from severe bottlenecks during queen hibernation. Parasite populations were in Hardy-Weinberg equilibrium and showed no signs of linkage disequilibrium suggesting that sexual reproduction is an alternative strategy in this otherwise clonal parasite. Moreover, high levels of multiple infections were found, which might facilitate sexual genetic exchange. The detection of identical clones in different host species suggested that horizontal transmission occurs between host species and underpins the lack of host-specific adaptation.

  4. 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

  5. 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

  6. 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.

  7. Translation and adaption of the interRAI suite to local requirements in Belgian hospitals

    PubMed Central

    2012-01-01

    Background The interRAI Suite contains comprehensive geriatric assessment tools designed for various healthcare settings. Although each instrument is developed for a particular population, together they form an integrated health evaluation system. The interRAI Acute Care Minimum Data Set (interRAI AC) is tailored for hospitalized older persons. Our aim in this study was to translate and adapt the interRAI AC to the Belgian hospital context, where it can be used together with the interRAI Home Care (HC) and the interRAI Long Term Care Facility (LTCF). Methods A systematic, comprehensive, and rigorous 10-step approach was used to adapt the interRAI AC to local requirements. After linguistic translation by an official translator, five researchers assessed the translation for appropriate hospital jargon. Three researchers double-checked for translation accuracy and proposed additional items. A provisional version was converted into the three official languages of Belgium—Flemish, French, and German. Next, a multidisciplinary panel of nine experts judged item relevance to the Belgian care context and advised which country-specific items should be added. After these suggestions were incorporated into the interRAI AC, hospital staff from nine Flemish hospitals field-tested the tool in their practice. After evaluating field-test results, we compared the interRAI AC with Belgian versions of the interRAI HC and interRAI LTCF. Next, the Flemish, French, and German versions of the Belgian interRAI portfolio were harmonized. Finally, we submitted the Belgian interRAI AC to the interRAI organization for ratification. Results Eighteen administrative items of the interRAI AC were adapted to the Belgian healthcare context (e.g., usual residence, formal community services prior to admission). Fourteen items assessing the ‘informal caregiver’, and 17 items, including country-specific items, were added (e.g., advanced directive for euthanasia). Conclusions The interRAI AC was

  8. 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.

  9. Locally adaptive regression filter-based infrared focal plane array non-uniformity correction

    NASA Astrophysics Data System (ADS)

    Li, Jia; Qin, Hanlin; Yan, Xiang; Huang, He; Zhao, Yingjuan; Zhou, Huixin

    2015-10-01

    Due to the limitations of the manufacturing technology, the response rates to the same infrared radiation intensity in each infrared detector unit are not identical. As a result, the non-uniformity of infrared focal plane array, also known as fixed pattern noise (FPN), is generated. To solve this problem, correcting the non-uniformity in infrared image is a promising approach, and many non-uniformity correction (NUC) methods have been proposed. However, they have some defects such as slow convergence, ghosting and scene degradation. To overcome these defects, a novel non-uniformity correction method based on locally adaptive regression filter is proposed. First, locally adaptive regression method is used to separate the infrared image into base layer containing main scene information and the detail layer containing detailed scene with FPN. Then, the detail layer sequence is filtered by non-linear temporal filter to obtain the non-uniformity. Finally, the high quality infrared image is obtained by subtracting non-uniformity component from original image. The experimental results show that the proposed method can significantly eliminate the ghosting and the scene degradation. The results of correction are superior to the THPF-NUC and NN-NUC in the aspects of subjective visual and objective evaluation index.

  10. Protein Secondary Structure Prediction Using Local Adaptive Techniques in Training Neural Networks

    NASA Astrophysics Data System (ADS)

    Aik, Lim Eng; Zainuddin, Zarita; Joseph, Annie

    2008-01-01

    One of the most significant problems in computer molecular biology today is how to predict a protein's three-dimensional structure from its one-dimensional amino acid sequence or generally call the protein folding problem and difficult to determine the corresponding protein functions. Thus, this paper involves protein secondary structure prediction using neural network in order to solve the protein folding problem. The neural network used for protein secondary structure prediction is multilayer perceptron (MLP) of the feed-forward variety. The training set are taken from the protein data bank which are 120 proteins while 60 testing set is the proteins which were chosen randomly from the protein data bank. Multiple sequence alignment (MSA) is used to get the protein similar sequence and Position Specific Scoring matrix (PSSM) is used for network input. The training process of the neural network involves local adaptive techniques. Local adaptive techniques used in this paper comprises Learning rate by sign changes, SuperSAB, Quickprop and RPROP. From the simulation, the performance for learning rate by Rprop and Quickprop are superior to all other algorithms with respect to the convergence time. However, the best result was obtained using Rprop algorithm.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Tailoring the visual communication of climate projections for local adaptation practitioners in Germany and the UK.

    PubMed

    Lorenz, Susanne; Dessai, Suraje; Forster, Piers M; Paavola, Jouni

    2015-11-28

    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

  16. 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

  17. Tailoring the visual communication of climate projections for local adaptation practitioners in Germany and the UK.

    PubMed

    Lorenz, Susanne; Dessai, Suraje; Forster, Piers M; Paavola, Jouni

    2015-11-28

    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.

  18. Reproductive isolation and local adaptation quantified for a chromosome inversion in a malaria mosquito.

    PubMed

    Ayala, Diego; Guerrero, Rafael F; Kirkpatrick, Mark

    2013-04-01

    Chromosome inversions have long been thought to be involved in speciation and local adaptation. We have little quantitative information, however, about the effects that inversion polymorphisms have on reproductive isolation and viability. Here we provide the first estimates from any organism for the total amount of reproductive isolation associated with an inversion segregating in natural populations. We sampled chromosomes from 751 mosquitoes of the malaria vector Anopheles funestus along a 1421 km transect in Cameroon that traverses savannah, highland, and rainforest ecological zones. We then developed a series of population genetic models that account for selection, migration, and assortative mating, and fit the models to the data using likelihood. Results from the best-fit models suggest there is strong local adaptation, with relative viabilities of homozygotes ranging from 25% to 130% compared to heterozygotes. Viabilities vary qualitatively between regions: the inversion is underdominant in the savannah, whereas in the highlands it is overdominant. The inversion is also implicated in strong assortative mating. In the savannah, the two homozygote forms show 92% reproductive isolation, suggesting that this one inversion can generate most of the genetic barriers needed for speciation.

  19. 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

  20. L1-norm locally linear representation regularization multi-source adaptation learning.

    PubMed

    Tao, Jianwen; Wen, Shiting; Hu, Wenjun

    2015-09-01

    In most supervised domain adaptation learning (DAL) tasks, one has access only to a small number of labeled examples from target domain. Therefore the success of supervised DAL in this "small sample" regime needs the effective utilization of the large amounts of unlabeled data to extract information that is useful for generalization. Toward this end, we here use the geometric intuition of manifold assumption to extend the established frameworks in existing model-based DAL methods for function learning by incorporating additional information about the target geometric structure of the marginal distribution. We would like to ensure that the solution is smooth with respect to both the ambient space and the target marginal distribution. In doing this, we propose a novel L1-norm locally linear representation regularization multi-source adaptation learning framework which exploits the geometry of the probability distribution, which has two techniques. Firstly, an L1-norm locally linear representation method is presented for robust graph construction by replacing the L2-norm reconstruction measure in LLE with L1-norm one, which is termed as L1-LLR for short. Secondly, considering the robust graph regularization, we replace traditional graph Laplacian regularization with our new L1-LLR graph Laplacian regularization and therefore construct new graph-based semi-supervised learning framework with multi-source adaptation constraint, which is coined as L1-MSAL method. Moreover, to deal with the nonlinear learning problem, we also generalize the L1-MSAL method by mapping the input data points from the input space to a high-dimensional reproducing kernel Hilbert space (RKHS) via a nonlinear mapping. Promising experimental results have been obtained on several real-world datasets such as face, visual video and object.

  1. 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.

  2. 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

  3. Adaptive local multi-atlas segmentation: application to the heart and the caudate nucleus.

    PubMed

    van Rikxoort, Eva M; Isgum, Ivana; Arzhaeva, Yulia; Staring, Marius; Klein, Stefan; Viergever, Max A; Pluim, Josien P W; van Ginneken, Bram

    2010-02-01

    Atlas-based segmentation is a powerful generic technique for automatic delineation of structures in volumetric images. Several studies have shown that multi-atlas segmentation methods outperform schemes that use only a single atlas, but running multiple registrations on volumetric data is time-consuming. Moreover, for many scans or regions within scans, a large number of atlases may not be required to achieve good segmentation performance and may even deteriorate the results. It would therefore be worthwhile to include the decision which and how many atlases to use for a particular target scan in the segmentation process. To this end, we propose two generally applicable multi-atlas segmentation methods, adaptive multi-atlas segmentation (AMAS) and adaptive local multi-atlas segmentation (ALMAS). AMAS automatically selects the most appropriate atlases for a target image and automatically stops registering atlases when no further improvement is expected. ALMAS takes this concept one step further by locally deciding how many and which atlases are needed to segment a target image. The methods employ a computationally cheap atlas selection strategy, an automatic stopping criterion, and a technique to locally inspect registration results and determine how much improvement can be expected from further registrations. AMAS and ALMAS were applied to segmentation of the heart in computed tomography scans of the chest and compared to a conventional multi-atlas method (MAS). The results show that ALMAS achieves the same performance as MAS at a much lower computational cost. When the available segmentation time is fixed, both AMAS and ALMAS perform significantly better than MAS. In addition, AMAS was applied to an online segmentation challenge for delineation of the caudate nucleus in brain MRI scans where it achieved the best score of all results submitted to date.

  4. Increased sedentariness in European Blackbirds following urbanization: a consequence of local adaptation?

    PubMed

    Partecke, Jesko; Gwinner, Eberhard

    2007-04-01

    Urbanization changes local environmental conditions and may lead to altered selection regimes for life history traits of organisms thriving in cities. Previous studies have reported changes in breeding phenology and even trends toward increased sedentariness in migratory bird species colonizing urban areas. However, does the change in migratory propensity simply represent a phenotypic adjustment to local urban environment, or is it genetically based and hence the result of local adaptation? To test this, we hand-raised European Blackbirds (Turdus merula) from urban and forest populations, quantified their nocturnal activity and fat deposition covering two complete migratory cycles and examined the consequences of a reduced migratory propensity for the timing of gonadal development (a physiological measure of the seasonal timing of reproduction). Although nocturnal activities differed strikingly between fall and spring seasons, with low activities during the fall and high activities during the spring seasons, our data confirm, even in birds kept from early life under common-garden conditions, a change toward reduced migratoriness in urban blackbirds. The first score of a principal component analysis including amount of nocturnal activity and fat deposition, defined as migratory disposition, was lower in urban than in forest males particularly during their first year, whereas females did not differ. The results suggest that the intrinsic but male-biased difference is genetically determined, although early developmental effects cannot be excluded. Moreover, individuals with low migratory disposition developed their gonads earlier, resulting in longer reproductive seasons. Since urban conditions facilitate earlier breeding, intrinsic shifts to sedentariness thus seem to be adaptive in urban habitats. These results corroborate the idea that urbanization has evolutionary consequences for life history traits such as migratory behavior.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. A High Order, Locally-Adaptive Method for the Navier-Stokes Equations

    NASA Astrophysics Data System (ADS)

    Chan, Daniel

    1998-11-01

    I have extended the FOSLS method of Cai, Manteuffel and McCormick (1997) and implemented it within the framework of a spectral element formulation using the Legendre polynomial basis function. The FOSLS method solves the Navier-Stokes equations as a system of coupled first-order equations and provides the ellipticity that is needed for fast iterative matrix solvers like multigrid to operate efficiently. Each element is treated as an object and its properties are self-contained. Only C^0 continuity is imposed across element interfaces; this design allows local grid refinement and coarsening without the burden of having an elaborate data structure, since only information along element boundaries is needed. With the FORTRAN 90 programming environment, I can maintain a high computational efficiency by employing a hybrid parallel processing model. The OpenMP directives provides parallelism in the loop level which is executed in a shared-memory SMP and the MPI protocol allows the distribution of elements to a cluster of SMP's connected via a commodity network. This talk will provide timing results and a comparison with a second order finite difference method.

  10. 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…

  11. 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.

  12. 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

  13. 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

  14. Local dynamic stability of amputees wearing a torsion adapter compared to a rigid adapter during straight-line and turning gait.

    PubMed

    Segal, Ava D; Orendurff, Michael S; Czerniecki, Joseph M; Shofer, Jane B; Klute, Glenn K

    2010-10-19

    Lower limb amputees have decreased balance during daily ambulation compared to nonamputees. An optimally compliant torsion adapter, which enables transverse plane rotation at the socket-pylon junction may reduce limb asymmetries and improve comfort leading to increased confidence and stability during gait. The purpose of this study was to determine if the presence of a torsion adapter affects amputee sensitivity to local perturbations (local dynamic stability) during straight-line walking and during a turning task. Ten unilateral transtibial amputees were fit with a torsion and rigid adapter in random order and blinded to the condition. After a 3-week acclimation period, kinematic data were collected while subjects walked in a straight-line on a treadmill and around a 1-m radius circular path at constant speed. Maximum finite-time Lyapunov exponents (λ), an estimator of local dynamic stability, were calculated for the amputee's sagittal plane hip, knee and ankle angles for each condition. The prosthetic limb λ was greater during a turn compared to straight-line walking, suggesting amputees are less stable while turning. There were no statistically significant differences found in λ between adapters during both walking conditions, suggesting the torsion adapter had no effect on amputee stability; however, high inter-subject variability due to the examined population and turning task may have masked a small decrease in prosthetic limb hip and knee stability for the torsion adapter during straight-line gait. Therefore, the torsion adapter's added degree of freedom may have a small adverse effect on prosthetic limb stability during straight-line walking and no effect on turning.

  15. 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.

  16. 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 loc