Publications


    Books:
  1. George Em Karniadakis and Robert M. Kirby, Parallel Scientific Computing in C++ and MPI, Cambridge University  Press, UK, 628 pages, 2003.


    Book Chapters:
  1. R.M. Kirby, G.E. Karniadakis, O. Mikulchenko and K. Mayaram, "Integrated Simulation for MEMS: Coupling Flow-Structure-Thermal-Electrical Domains", The CRC Handbook of MEMS, CRC Press, Boca Raton, FL,  pages 5-1 - 5-25, 2001. Editor: M. Gad-el-Hak. 

  2. Robert M. Kirby and George Em Karniadakis, "Under-Resolution and Diagnostics in Spectral Simulations of Complex-Geometry Flows", Turbulent Flow Computation, Kluwer Academic Publishers, The Netherlands, pages 1 - 42, 2001. Editors: D. Drikakis and B. Geurts.

  3. Robert M. Kirby and George Em Karniadakis, "Spectral Element and hp Methods", Encyclopedia of Computational Mechanics, John Wiley and Sons, NY, Volume 3, Chapter 3, pages 61 - 88, 2004. Editors: E. Stein, R. de Borst and T.J.R. Hughes. 

  4. Robert M. Kirby, Daniel F. Keefe and David H. Laidlaw, "Painting and Visualization", Visualization Handbook, Academic Press, pages 873 - 891, 2004.Editors:  C. Hansen and C. Johnson.


  Journal Publications:
  1. I. Lomtev, R.M. Kirby, and G.E. Karniadakis, "A Discontinuous Galerkin ALE Method for Compressible Viscous Flows in Moving Domains",  Journal of Computational Physics, Vol. 155, 128-159, 1999.

  2. R.M. Kirby, T.C. Warburton, I. Lomtev, and G.E. Karniadakis,  "A Discontinuous Galerkin Spectral/hp Method on Hybrid Grids",  Journal of Applied Numerical Mathematics, Vol. 33, 393-405, 1999.

  3. R.M. Kirby, G.E. Karniadakis, O. Mikulchenko, and K. Mayaram, "An Integrated Simulator for Coupled Domain Problems in MEMS",  Journal of Microelectromechanical Systems, Vol. 10, 3:379-399, 2001.

  4. Robert M. Kirby and George Em Karniadakis, "Coarse Resolution Turbulence Simulations With Spectral Vanishing Viscosity - Large-Eddy Simulations (SVV-LES)", Journal of Fluids Engineering, Vol. 124, 4:886-891, 2002.

  5. Robert M. Kirby and George Em Karniadakis, "De-Aliasing on Non-Uniform Grids: Algorithms and Applications", Journal of Computational Physics, Vol. 191, pages 249-264, 2003. [PDF]

  6. Robert M. Kirby and Zohar Yosibash, "Solution of von-Karman dynamic non-linear plate equations using a pseudo-spectral method", Computer Methods in Applied Mechanics and Engineering, Vol. 193/6-8, pages 575-599, 2004. [PDF]

  7. Z. Yosibash, R.M. Kirby and D. Gottlieb, "Collocation methods for the solution of von-Karman dynamic non-linear plate systems", Journal of Computational Physics, Vol. 200, Issue 2, pages 432-461, 2004. [PDF]

  8. Frank Stenger, Thomas Cook and Robert M. Kirby, "Sinc Solution of Biharmonic Problems", Canadian Applied Mathematics Quarterly, Vol. 12, Number 3, pages 391-413, 2004. [PDF]

  9. Zohar Yosibash and Robert M. Kirby, "Dynamic response of various  von-Karman non-linear plate models and their 3-D counterparts", International Journal of Solids and Structures, Vol. 42, pages 2517-2531, 2005. [PDF]

  10. David H. Laidlaw, Robert M. Kirby, Cullen D. Jackson, J. Scott Davidson, Timothy S. Miller, Marco da Silva, William H. Warren and Michael Tarr, "Comparing 2D Vector Field Visualization Methods: A User Study", IEEE Transactions on Visualization and Computer Graphics, Vol. 11, Number 1, pages 59-70, 2005. [PDF]

  11. Robert M. Kirby and George Em Karniadakis, "Selecting the Numerical Flux in Discontinuous Galerkin Methods for Diffusion Problems", Journal of Scientific Computing, Vol. 22/23, pages 385-411, 2005. [PDF]

  12. Robert M. Kirby and Spencer J. Sherwin, "Stabilisation of spectral/hp element methods through spectral vanishing viscosity: Application to fluid mechanics modelling", Computer Methods in Applied Mechanics and Engineering, Vol. 195, pages 3128-2144, 2006. [PDF]

  13. Blake Nelson and Robert M. Kirby, "Ray-Tracing Polymorphic Multi-Domain Spectral/hp Elements for Isosurface Rendering",  IEEE Transactions on Visualization and Computer Graphics, Vol. 12, Number 1, pages 114-125, 2006.  [PDF]

  14. S.J. Sherwin, R.M. Kirby, J. Peiro, R.L. Taylor and O.C. Zienkiewicz, "On 2D Elliptic Discontinuous Galerkin Methods", International Journal for Numerical Methods in Engineering, Vol. 65, Issue 5, pages 752-784, 2006.  [PDF]

  15. A.R. Sanderson, R.M. Kirby, C.R. Johnson and L. Yang, "Revisiting Reaction-Diffusion Models for Texture Synthesis", Journal of Graphics Tools, Vol. 11, Number 3, pages 47-71, 2006.

  16. Robert M. Kirby and Spencer J. Sherwin, "Aliasing Errors Due to Quadratic Non-Linearities On Triangular Spectral/hp Element Discretisations", Journal of Engineering Mathematics, Vol. 56, pages 273-288, 2006.  [PDF]

  17. Irina Ionescu, James E. Guilkey, Martin Berzins, Robert M. Kirby and Jeffrey A. Weiss, "Simulation of Soft Tissue Failure Using the Material Point Method", Journal of Biomechanical Engineering, Vol. 128, Issue 6, pages 917-924, 2006.  [PDF]

  18. Elijah P. Newren, Aaron L. Fogelson, Robert D. Guy and Robert M. Kirby, "Unconditionally Stable Discretizations of the Immersed Boundary Equations", Journal of Computational Physics, Vol. 222, Issue 2, pages 702-719, 2007.  [PDF]

  19. Robert M. Kirby, Zohar Yosibash and George Em Karniadakis, "Towards Stable Coupling Methods for High-Order Discretizations of Fluid-Structure Interaction: Algorithms and Observations", Journal of Computational Physics, Vol. 223, Issue 2, pages 489-518, 2007.  [PDF]

  20. Sarah E. Geneser, Robert M. Kirby, Dongbin Xiu and Frank B. Sachse, "Stochastic Markovian Modeling of Electrophysiology of Ion Channels: Reconstruction of Standard Deviations in Macroscopic Currents", Journal of Theoretical Biology, Vol. 245, Issue 4, pages 627-637, 2007.  [PDF]

  21. C.W. Hamman, R.M. Kirby and M. Berzins,  "Parallelization and Scalability of a Spectral Element Channel Flow Solver for Incompressible Navier-Stokes Equations",  Concurrency and Computation: Practice and Experience, Volume 19, Issue 11, pages 1403-1422, 2007.  [PDF]

  22. Miriah Meyer, Blake Nelson, Robert M. Kirby and Ross Whitaker, "Particle Systems for Efficient and Accurate Finite Element Visualization", IEEE Transactions on Visualization and Computer Graphics, Vol. 13, Number 5, pages 1015-1026, 2007.  [PDF]

  23. Sean Curtis, Robert M. Kirby, Jennifer K. Ryan and Chi-Wang Shu, "Post-processing for the Discontinuous Galerkin Method Over Non-Uniform Meshes", SIAM Journal of Scientific Computing, Vol. 30, Number 1, pages 272-289, 2007. [PDF]

  24. Miriah Meyer, Robert M. Kirby and Ross Whitaker, "Topology, Accuracy, and Quality of Isosurface Meshes Using Dynamic Particles", IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization Issue), Vol. 13, Number 6, pages 1704-1711, 2007. [PDF]

  25. Sarah E. Geneser, Robert M. Kirby and Robert S. MacLeod, "Application of Stochastic Finite Element Methods to Study the Sensitivity of ECG Forward Modeling to Organ Conductivity", IEEE Transactions on Biomedical Engineering, Vol. 55, Number 1, pages 31-40, 2007.  [PDF]

  26. J.S. Hesthaven and R.M. Kirby, "Filtering in Legendre Spectral Methods", Mathematics of Computation, Vol. 77, Number 263, pages 1425-1452, 2008[PDF]

  27. Elijah P. Newren, Aaron L. Fogelson, Robert D. Guy and Robert M. Kirby, "A Comparison of Implicit Solvers for the Immersed Boundary Equations", Computer Methods in Applied Mechanics and Engineering, Vol. 197, Issues 25-28, pages 2290-2304, 2008.  [PDF]

  28. Michael Steffen, Sean Curtis, Robert M. Kirby and Jennifer K. Ryan, "Investigation of Smoothness-Increasing Accuracy-Conserving Filters for Improving Streamline Integration Through Discontinuous Fields", IEEE Transactions on Visualization and Computer Graphics, Vol. 14, Number 3, pages 680-692, 2008.  [PDF]

  29. Michael Steffen, Robert M. Kirby and Martin Berzins, "Analysis and Reduction of Quadrature Errors in the Material Point Method (MPM)", International Journal for Numerical Methods in Engineering, Vol. 76, Issue 6, pages 922-948, 2008.  [PDF]

  30. C.W. Hamman, J.C. Klewicki and R.M. Kirby, "On the Lamb vector divergence in Navier-Stokes flows", Journal of Fluid Mechanics, Vol. 610, pages 261-284, 2008. [PDF]

  31. Tobias Preusser, Hanno Scharr, Kai Krajsek and Robert M. Kirby, "Building Blocks for Computer Vision with Stochastic Partial Differential Equations", International Journal of Computer Vision, Vol. 80, Number 3, pages 375-405, 2008.  [PDF]

  32. Robert M. Kirby and Claudio Silva, "The Need For Verifiable Visualization", IEEE Computer Graphics and Applications , Vol. 28, Number 5, pages 78-83, 2008. [PDF]

  33. I. Melatti, R. Palmer, G. Sawaya, Y. Yang, R.M. Kirby and G. Gopalakrishnan, "Parallel and distributed model checking in Eddy", International Journal for Software Tools for Technology Transfer, Vol. 11, Number 1, pages 13-25, 2009.  [PDF]

  34. Allen R. Sanderson, Miriah D. Meyer, Robert M. Kirby and Chris R. Johnson, "A Framework for Exploring Numerical Solutions of Advection-Reaction-Diffusion Equations Using a GPU-Based Approach",  Computing and Visualization in Science, Vol. 12, pages 155-170, 2009.  [PDF]

  35. David Walfisch, Jennifer K. Ryan, Robert M. Kirby and Robert Haimes, "One-Sided Smoothness-Increasing Accuracy-Conserving Filtering for Enhanced Streamline Integration through Discontinuous Fields", Journal of Scientific Computing , Vol. 38, Number 2, pages 164-184, 2009. [PDF]

  36. Miriah Meyer, Ross Whitaker, Robert M. Kirby, Christian Ledergerber and Hanspeter Pfister, "Particle-based Sampling and Meshing of Surfaces in Multimaterial Volumes", IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization Issue), Vol. 14, Number 6, pages 1539-1546, 2008.  [PDF]

  37. M. Steffen, P.C. Wallstedt, J.E. Guilkey, R.M. Kirby and M. Berzins, "Examination and Analysis of Implementation Choices within the Material Point Method", Computer Modeling in Engineering and Science, Vol. 31, Number 2, pages 107-128, 2008.  [PDF]

  38. Tobias Martin, Elaine Cohen and Robert M. Kirby, "Volumetric Parameterization and Trivariate B-spline Fitting using Harmonic Functions", Computer Aided Geometric Design, Vol. 26, Issue 6, pages 648-664, 2009.  [PDF]

  39. J. Samuel Preston, Tolga Tasdizen, Christi M. Terry, Alfred K. Cheung and Robert M. Kirby, "Using the Stochastic Collocation Method for the Uncertainty Quantification of Drug Concentration Due to Depot Shape Variability", IEEE Transactions on Biomedical Engineering, Vol. 56, Number 3, pages 609-619, 2009. [PDF]

  40. T. Etiene, C. Scheidegger, L.G. Nonato, R.M. Kirby and C.T. Silva, "Verifiable Visualization for Isosurface Extraction", IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization Issue), Vol 15., Number 6, pages 1227-1234, 2009.  [PDF]

  41. Joseph D. Frazier, Peter K. Jimack and Robert M. Kirby, "On the Use of Adjoint-Based Sensitivity Estimates to Control Local Mesh Refinement", Communications on Computational Physics, Vol. 7, Number 3, pages 631-638, 2010.  [PDF]

  42. E. Cohen, T. Martin, R.M. Kirby, T. Lyche and R.F. Riesenfeld, "Analysis-aware Modeling: Understanding Quality Considerations in Modeling for Isogeometric Analysis", Computer Methods in Applied Mechanics and Engineering, Vol. 199, Issues 5-8, pages 334-356, 2010.  [PDF]

  43. Michael Steffen, Robert M. Kirby and Martin Berzins, "Decoupling and Balancing of Space and Time Errors in the Material Point Method (MPM)", International Journal for Numerical Methods in Engineering , Vol. 82, pages 1207-1243, 2010.  [PDF]

  44. Salman Pervez, Ganesh Gopalakrishnan, Robert M. Kirby, Rajeev Thakur and William Gropp, "Formal methods applied to high performance computing software design: a case study of MPI one-sided communication based locking", Software: Practice and Experience, Vol. 40, Issue 1, pages 23-43, 2010.  [PDF]

  45. Dafang Wang, Robert M. Kirby and Chris R. Johnson, "Resolution Strategies for the Finite Element Based Solution of the Electrocardiographic Inverse Problem", IEEE Transactions on Biomedical Engineering, Vol. 57, Issue 2, pages 220-237, 2010. [PDF]

  46. Hanieh Mirzaee, Jennifer K. Ryan and Robert M. Kirby, "Quantificiation of Errors Introduced in the Numerical Approximation and Implementation of Smoothness-Increasing Accuracy Conserving (SIAC) Filtering of Discontinuous Galerkin (DG) Fields", Journal of Scientific Computing, Vol. 45, pages 447-470, 2010. [PDF]

  47. Guodong Li, Robert Palmer, Michael DeLisi, Ganesh Gopalakrishnan and Robert M. Kirby, "Formal Specification of MPI 2.0: Case Study in Specifying a Practical Concurrent Programming API", Science of Computer Programming, Vol. 76, pages 65-81, 2011. [PDF]

  48. Yu Yang, Xiaofang Chen, Ganesh Gopalakrishnan and Robert M. Kirby, "Distributed Dynamic Partial Order Reduction", International Journal on Software Tools for Technology Transfer, Vol. 12, Number 2, pages 113-122, 2010. [PDF]

  49. Peter E. J. Vos, Spencer J. Sherwin and Robert M. Kirby, "h-p Efficiently: Implementing Finite and Spectral/hp Element Methods to Achieve Optimal Performance for Low- and High-Order Discretisations", Journal of Computational Physics, Vol. 229, Issue 13, pages 5161-5181, 2010. [PDF]

  50. S.E. Geneser, J.D. Hinkle, R.M. Kirby, B. Wang, B. Salter and S. Joshi, "Quantifying Variability in Radiation Dose Due to Respiratory-Induced Tumor Motion", Medical Image Analysis, Vol. 15, Issue 4, pages 640-649, 2011. [PDF]

  51. Peter K. Jimack and Robert M. Kirby, "Towards the Development on an h-p-Refinement Strategy Based Upon Error Estimate Sensitivity", Computers and Fluids, Vol. 46, Issue 1, pages 277-281, 2011. [PDF]

  52. C.D. Cantwell, S.J. Sherwin, R.M. Kirby and P.H.J. Kelly, "From h to p Efficiently: Strategy Selection for Operator Evaluation on Hexahedral and Tetrahedral Elements", Computers and Fluids, Vol. 43, Issue 1, pages 23-28, 2011. [PDF]

  53. Peter E.J. Vos, Sehun Chun, Alessandro Bolis, Claes Eskilsson, Robert M. Kirby and Spencer J. Sherwin, "A Generic Framework for Time-Stepping PDEs: General Linear Methods, Object-Oriented Implementations and Applications to Fluid Problems", International Journal of Computational Fluid Dynamics, Vol. 25, Issue 3, pages 107-125, 2011. [PDF]

  54. Dafang Wang, Robert M. Kirby and Chris R. Johnson, "Finite-Element-Based Discretization and Regularization Strategies for 3D Inverse Electrocardiography", IEEE Transactions on Biomedical Engineering, Vol. 58, Issue 6, pages 1827-1838, 2011. [PDF]

  55. Samuel A. Isaacson and Robert M. Kirby, "Numerical Solution of Linear Volterra Integral Equations of the Second Kind with Sharp Gradients", Journal of Computational and Applied Mathematics, Vol. 235, Issue 14, pages 4383-4401, 2011. [PDF]

  56. C.D. Cantwell, S.J. Sherwin, R.M. Kirby and P.H. Kelly, "From h to p Efficiently: Selecting the Optimal Spectral/hp Discretisation in Three Dimensions", Math. Model. Nat. Phenom., Vol. 6, No. 3, pages 84-96, 2011. [PDF]

  57. Tobias Martin, Elaine Cohen and Robert M. Kirby, "Direct Isosurface Visualization of Hex-Based High-Order Geometry and Attribute Representations", IEEE Transactions on Visualization and Computer Graphics, Vol. 18, No. 5, pages 753-766, 2012. [PDF]

  58. Tiago Etiene, L. Gustavo Nonato, Carlos Scheidegger, Julien Tierny, Thomas J. Peters, Valerio Pascucci, Robert M. Kirby and Claudio T. Silva, "Topology Verification for Isosurface Extraction", IEEE Transactions on Visualization and Computer Graphics, Vol. 18, No. 6, pages 952-965, 2012. [PDF]

  59. Robert M. Kirby, Bernardo Cockburn and Spencer J. Sherwin, "To CG or to HDG: A Comparative Study", Journal of Scientific Computing, Vol. 51, No. 1, pages 183-212, 2012. [PDF]

  60. Ganesh Gopalakrishnan, Robert M. Kirby, Stephen Siegel, Rajeev Thakur, William Gropp, Ewing Lusk, Bronis R. de Supinski, Martin Schultz and Greg Bronevetsky, "Formal Analysis of MPI-Based Parallel Programs: Present and Future", Communications of the ACM, Vol. 54, No. 12, pages 82-91, 2011. [PDF]

  61. Z. Fu, W.-K. Jeong, Y. Pan, R. M. Kirby, and R. T. Whitaker, "A fast iterative method for solving the Eikonal equation on triangulated surfaces", SIAM Journal of Scientific Computing, Vol. 33, No. 5, pages 2468-2488, 2011. [PDF]

  62. Hanieh Mirzaee, Liangyue, Jennifer K. Ryan and Robert M. Kirby, "Smoothness-Increasing Accuracy-Conserving (SIAC) Postprocessing for Discontinuous Galerkin Solutions Over Structured Triangular Meshes", SIAM Journal of Numerical Analysis, Vol. 49, No. 5, pages 1899-1920, 2011. [PDF]

  63. Hanieh Mirzaee, Jennifer K. Ryan and Robert M. Kirby, "Efficient Implementation of Smoothness-Increasing Accuracy-Conserving (SIAC) Filters for Discontinuous Galerkin Solutions", Journal of Scientific Computing, Vol. 52, No. 1, pages 85-112, 2012. [PDF]

  64. Darrell Swenson, Sarah E. Geneser, Jeroen G. Stinstra, Robert M. Kirby and Robert S. MacLeod, "Cardiac Position Sensitivity Study in the Electrocardiographic Forward Problem Using Stochastic Collocation and Boundary Element Methods",Annals of Biomedical Engineering, Vol. 39, No. 12, pages 2900-2910, 2011. [PDF]

  65. Blake Nelson, Robert Haimes and Robert M. Kirby, "GPU-Based Interactive Cut-Surface Extraction From High-Order Finite Element Fields", IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization Issue), Vol. 17, No. 12, pages 1803-1811, 2011. [PDF]

  66. Inga Altrogge, Tobias Preusser, Tim Kroger, Sabrina Haase, Tobren Patz and Robert M. Kirby, "Sensitivity Analysis for the Optimization of Radiofrequency Ablation in the Presence of Material Parameter Uncertainty",International Journal for Uncertainty Quantification, Vol. 2, Issue 3, pages 295-321, 2012. [PDF]

  67. Tobias Martin, Elaine Cohen and Robert M. Kirby, "Mixed-Element Volume Completion for NURBS Surfaces", Computers & Graphics, Vol. 36, Issue 5, pages 548-554, 2012. [PDF]

  68. Kristin Potter, Robert M. Kirby, Dongbin Xiu and Chris R. Johnson, "Interactive Visualization of Probability And Cumulative Density Functions", International Journal for Uncertainty Quantification, Vol. 2, Issue 4, pages 397-412, 2012. [PDF]

  69. James King, Hanieh Mirzaee, Jennifer K. Ryan and Robert M. Kirby, "Smoothness-Increasing Accuracy-Conserving (SIAC) Filtering for discontinuous Galerkin Solutions: Improved Errors Versus Higher-Order Accuracy", Journal of Scientific Computing, Vol. 53, Issue 1, pages 129-149, 2012. [PDF]

  70. Hanne Tiesler, Robert M. Kirby, Dongbin Xiu and Tobias Preusser, "Stochastic Collocation for Optimal Problems with Stochastic PDE Constraints", SIAM Journal of Control and Optimization, Vol. 50, Issue 5, pages 2659-2682, 2012. [PDF]

  71. Blake Nelson, Eric Liu, Robert Haimes and Robert M. Kirby, "ElVis: A System for the Accurate and Interactive Visualization of High-Order Finite Element Solutions", IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization Issue), Vol. 18, No. 12, pages 2325-2334, 2012. [PDF]

  72. Torben Patz, Tobias Preusser and Robert M. Kirby, "Ambrosio-Tortorelli Segmentation of Stochastic Images: Model Extensions, Theoretical Investigations and Numerical Methods", International Journal of Computer Vision, Vol. 103, Issue 2, pages 190-212, 2013. [PDF]

  73. Chao Yang, Dongbin Xiu and Robert M. Kirby, "Visualization of Covariance and Cross-Covariance Fields", International Journal for Uncertainty Quantification, Vol. 3, No. 1, pages 25-38, 2013. [PDF]

  74. Hanieh Mirzaee, James King, Jennifer K. Ryan and Robert M. Kirby, "Smoothness-Increasing Accuracy-Conserving (SIAC) Filters for Discontinuous Galerkin Solutions Over Unstructured Triangular Meshes", SIAM Journal of Scientific Computing, Vol. 35, No. 1, pages 212-230, 2013. [PDF]

  75. Varun Shankar, Grady B. Wright, Aaron L. Fogelson and Robert M. Kirby, "A Study Of Different Modeling Choices For Simulating Platelets With The Immersed Boundary Method", Applied Numerical Mathematics, Vol. 63, pages 58-77, 2013. [PDF]

  76. Robert M. Kirby and Miriah Meyer, "Visualization Collaborations: Reflections on What Works and Why", IEEE Computer Graphics and Applications, Volume 33, Issue 6, pages 82-88, 2013. [PDF]

  77. Dafang Wang, Robert M. Kirby, Rob S. MacLeod and Chris R. Johnson, "Inverse electrocardiographic source localization of ischemia: an optimization framework and finite element solution", Journal of Computational Physics, Vol. 250, Issue 1, pages 403-424, 2013. [PDF]

  78. Blake Nelson, Robert M. Kirby, Robert Haimes, "GPU-Based Volume Visualization From High-Order Finite Element Fields", IEEE Transactions on Visualization and Computer Graphics, Vol. 20, No. 1, pages 70-83, 2014. [PDF]

  79. Tiago Etiene, Daniel Jonsson, Timo Ropinski, Carlos Scheidegger, Joao Comba, L. Gustavo Nonato, Robert M. Kirby, Anders Ynnerman and Claudio T. Silva, "Verifying Volume Rendering Using Discretization Error Analysis", IEEE Transactions on Visualization and Computer Graphics, Vol. 20, No. 1, pages 140-154, 2014. [PDF]

  80. Hanieh Mirzaee, Jennifer K. Ryan and Robert M. Kirby, "Smoothness-Increasing Accuracy-Conserving (SIAC) Filtering for Discontinuous Galerkin Solutions: Applications to Structured Tetrahedral Meshes", Journal of Scientific Computing, Vol. 58, No. 3, pages 690-704, 2014. [PDF]

  81. Zhisong Fu, Robert M. Kirby and Ross T. Whitaker, "A Fast Iterative Method for Solving the Eikonal Equation on Tetrahedral Domains", SIAM Journal of Scientific Computing, Vol. 35, No. 5, pages C473-C494, 2013. [PDF]

  82. Ross T. Whitaker, Mahsa Mirzargar and Robert M. Kirby, "Contour Boxplots: A Method for Characterizing Uncertainty in Feature Sets from Simulation Ensembles", IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization Issue), Vol. 19, Issue 12, pages 2713-2722, 2013. [PDF]

  83. Blake Nelson, Robert M. Kirby and Steven Parker, "Optimal Expression Evaluation Through the Use of Expression Templates When Evaluating Dense Linear Algebra Operations", ACM Transactions on Mathematical Software, Vol. 40, Issue 3, pages 21:1-21:21, 2014. [PDF]

  84. Zhisong Fu, T. James Lewis, Robert M. Kirby and Ross T. Whitaker, "Architecting the Finite Element Method Pipeline for the GPU", Journal of Computational and Applied Mathematics, Volume 257, pages 195-211, 2014. [PDF]

  85. C.D. Cantwell, S. Yakovlev, R.M. Kirby, N.S. Peters and S.J. Sherwin, "High-order continuous spectral/hp element discretisation for reaction-diffusion problems on a surface", Journal of Computational Physics, Vol. 257, Part A, pages 813-829, 2014. [PDF]

  86. James King, Sergey Yakovlev, Zhisong Fu, Robert M. Kirby and Spencer J. Sherwin, "Exploiting Batch Processing on Streaming Architectures to Solve 2D Elliptic Finite Element Problems: A Hybridized Discontinuous Galerkin (HDG) Case Study", Journal of Scientific Computing, Volume 60, pages 457-482, 2014. [PDF]

  87. Varun Shankar, Grady B. Wright, Aaron L. Fogelson and Robert M. Kirby, "A Radial Basis Function (RBF)-Finite Difference Method for the Simulation of Reaction-Diffusion Equations on Stationary Platelets within the Augmented Forcing Method", International Journal for Numerical Methods in Fluids, Volume 75, Issue 1, pages 1-22, 2014. [PDF]

  88. A. Bolis, C.D. Cantwell, R.M. Kirby and S.J. Sherwin, "h to p efficiently: Optimal implementation strategies for explicit time-dependent problems using the spectral/hp element method", International Journal for Numerical Methods in Fluids, Volume 75, Issue 8, pages 591-607, 2014. [PDF]

  89. Liam C. Jacobson, Robert M. Kirby and Valeria Molinero, "How Short Is Too Short for the Interactions of a Water Potential? Exploring the Parameter Space of a Coarse-Grained Water Model Using Uncertainty Quantification", Journal of Physical Chemistry, In Press, 2014. [PDF]

  90. Zhisong Fu, Sergey Yakovlev, Robert M. Kirby and Ross T. Whitaker, "Fast Parallel Solver for Levelset Equations on Unstructured Meshes", Concurrency and Computation: Practice and Experience, Accepted, 2014. [PDF]

  91. Mahsa Mirzargar, Ross T. Whitaker and Robert M. Kirby, "Curve Boxplot: Generalization of Boxplot for Ensembles of Curves", IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization Issue), Accepted, 2014. [PDF]

  92. Varun Shankar, Grady B. Wright, Robert M. Kirby and Aaron L. Fogelson, "A Radial Basis Function (RBF)-Finite Difference (FD) Method for Diffusion and Reaction-Diffusion Equations on Surfaces", Journal of Scientific Computing, Accepted, 2014. [PDF]
 
  Refereed Conference and Workshop Publications:
  1. R.M. Kirby, H. Marmanis and D.H. Laidlaw, "Visualizing Multivalued Data from 2D Incompressible Flows Using Concepts from Painting",  Proceedings of IEEE Visualization 1999, San Francisco, CA, pages 333-340 October 1999. 

  2. G-S Karamanos, C. Evangelinos, R.C. Boes, R.M. Kirby and G.E. Karniadakis, "Direct Numerical Simulation of Turbulence with a PC/Linux Cluster: Fact or Fiction?", Proceedings of SuperComputing 1999, Portland, OR, November 1999. 

  3. A. Forsberg, R.M. Kirby, D.H. Laidlaw, G.E. Karniadakis, A. van Dam, and J. Elion, "Immersive Virtual Reality for Visualizing Flow Through an Artery", Proceedings of IEEE Visualization 2000, Salt Lake City, UT, pages 457-460, October 2000.

  4. D.H. Laidlaw, R.M. Kirby, J.S. Davidson, T.S. Miller, M. da Silva, W.H. Warren, and M. Tarr, "Quantitative Comparative Evaluation of 2D Vector Field Visualization Methods", Proceedings of IEEE Visualization 2001, San Diego, CA, pages 143-150, October 2001.

  5. Allen Sanderson, Chris R. Johnson, and Robert M. Kirby, "Display of Vector Fields Using a Reaction-Diffusion Model", Proceedings of IEEE Visualization 2004, Austin, TX, pages 115-122, October 2004.

  6. I. Ionescu, J. Guilkey, M. Berzins, R.M. Kirby and J. Weiss. "Computational Simulation of Penetrating Trauma in Biological Soft Tissues Using the Material Point Method". Proceedings of Medicine Meets Virtual Reality 13 (MMVR 2005), Long Beach, California, USA, pages 213-218, January 26-29, 2005. 

  7. M. Berzins, R.M. Kirby, and C.R. Johnson, "Integrating Teaching and Research in HPC: Experiences and Opportunities" Lecture Notes in Computer Science, Volume 3515.  Proceedings of Computational Science - ICCS 2005, 5th International Conference, Atlanta, GA, USA, May 22-25,  2005.

  8. Robert Palmer, Steve Barrus, Yu Yang, Ganesh Gopalakrishnan, and Robert M. Kirby, "Gauss: A Framework for Verifying Scientific Computing Software", Electronic Notes on Theoretical Computer Science (ENTCS), Vol. 144, No. 3, pages 95-106, February 2006.

  9. I. Melatti, R. Palmer, G. Sawaya, Y. Yang, R.M. Kirby and G. Gopalakrishnan, "Parallel and distributed model checking in Eddy".  Lecture Notes in Computer Science. Volume 3925.  Proceedings of Model Checking Software: 13th International SPIN Workshop, Vienna, Austria, March 30 - April 1, 2006. 

  10. R.M. Kirby, C.R. Johnson and M. Berzins, "Involving Undergraduates in Computational Science and Engineering Research: Successes and Challenges".  Lecture Notes in Computer Science, Volume 3992.  Proceedings of Computational Science - ICCS 2006: 6th International Conference, Reading, UK, May 28-31, 2006.

  11. Salman Pervez, Ganesh Gopalakrishnan, Robert M. Kirby, Rajeev Thakur and William Gropp, "Formal Verification of Programs That Use MPI One-Sided Communications".  Proceedings of EuroPVM-MPI 2006, Bonn, Germany, September 17-20, 2006.

  12. Yu Yang, Xiaofang Chen, Ganesh Gopalakrishnan and Robert M. Kirby, "Distributed Dynamic Partial Order Reduction Based Verification of
    Threaded Software", Proceedings of Model Checking Software: 14th International SPIN Workshop, Berlin, Germany, July 1-3, 2007.

  13. Robert Palmer, Michael Delisi, Ganesh Gopalakrishnan and Robert M. Kirby, "An Approach to Formalization and Analysis of Message Passing Libraries''.  Proceedings of the 12th International Workshop on Formal Methods for Industrial Critical Systems (FMICS), Berlin, Germany, July 1-2, 2007.

  14. Robert Palmer, Ganesh Gopalakrishnan and Robert M. Kirby, "Semantics Driven Dynamic Partial-Order Reduction of MPI-based Parallel Programs".  Proceedings of Parallel and Distributed Systems: Testing and Debugging (PADTAD), London, England, July 9, 2007.

  15. Salman Pervez, Ganesh Gopalakrishnan, Robert M. Kirby, Robert Palmer, Rajeev Thakur and William Gropp, "Practical Model Checking Method for Verifying Correctness of MPI Programs", Proceedings of EuroPVM-MPI 2007, Paris, France, September 30 - October 3, 2007.

  16. Tim Kroger, Inga Altrogge, Olaf Konrad, Robert M. Kirby and Tobias Preusser, "Estimation of Probability Density Functions for Parameter Sensitivity Analyses", Proceedings of Simulation and Visualization (SimVis) 2008, Magdeburg, Germany, February 28-29, 2008.

  17. Tobias Martin, Elaine Cohen and Robert M. Kirby, "Volumetric Parameterization and Trivariate B-spline Fitting using Harmonic Functions",  Proceedings of ACM Solid and Physical Modeling, Stony Brook, NY, June 2-4, 2008.

  18. Sarvani Vakkalanka, Ganesh Gopalakrishnan and Robert Kirby, "Dynamic Verification of MPI programs with Reductions in Presence of Split Operations and Relaxed Orderings", 20th International Conference on Computer Aided Verification (CAV 2008), Princeton, NJ, July 7-14, 2008.

  19. Sarvani Vakkalanka, Michael DeLisi, Ganesh Gopalakrishnan and Robert M. Kirby, "Scheduling Considerations for building Dynamic Verification Tools for MPI", Proceedings of Parallel and Distributed Systems: Testing and Debugging (PADTAD), Seattle, WA, July 20-21, 2008.

  20. Yu Yang, Xiaofang Chen, Ganesh Gopalakrishnan and Robert M. Kirby, "Efficient Stateful Dynamic Partial Order Reduction", Proceedings of Model Checking Software: 15th International SPIN Workshop, Los Angeles, CA, August 10-12, 2008.

  21. Sarvani Vakkalanka, Michael DeLisi, Ganesh Gopalakrishnan, Robert M. Kirby, Rajeev Thakur and William Gropp, "Implementing Efficient Dynamic Formal Verification Methods for MPI Programs", Proceedings of EuroPVM-MPI 2008, Dublin, Ireland, September 7-10, 2008.

  22. Subodh Sharma, Sarvani Vakkalanka, Ganesh Gopalakrishnan, Robert M. Kirby, Rajeev Thakur and William Gropp, "A Formal Approach to Detect Functionally Irrelevant Barriers in MPI Programs", Proceedings of EuroPVM-MPI 2008, Dublin, Ireland, September 7-10, 2008.

  23. R. Whitaker, R.M. Kirby, J. Sinstra and M. Meyer, "Multimaterial Meshing of MRI Head Data for Bioelectric Field Simulation", Proceedings of the 17th International Meshing Roundtable, 2008.

  24. Anh Vo, Sarvani Vakkalanka, Michael Delisi, Ganesh Gopalakrishnan, Robert M. Kirby and Rajeev Thakur, "Formal Verification of Practical MPI Programs", Proceedings of 14th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), Raleigh, NC, February 14-18, 2009.

  25. S.E. Geneser, R.M. Kirby, B. Wang, B. Salter and S. Joshi, "Incorporating Patient Breathing Variability into a Stochastic Model of Dose Deposition for Stereotactic Body Radiation Therapy", Proceedings of Information Processing in Medical Imaging 2009, Williamsburg, VA, Lecture Notes in Computer Science (LNCS) 5636, Pages 688-700, July 5-10, 2009.

  26. Anh Vo, Sarvani Vakkalanka, Jason Williams, Ganesh Gopalakrishnan, Robert M. Kirby and Rajeev Thakur, "Sound and Efficient Dynamic Verification of MPI Programs with Probe Non-Determinism", Proceedings of EuroPVM-MPI 2009, Espoo, Finland, September 7-10, 2009.

  27. Sriram Aananthakrishnan, Michael DeLisi, Sarvani Vakkalanka, Anh Vo, Ganesh Gopalakrishnan, Robert M. Kirby and Rajeev Thakur, "How Formal Dynamic Verification Tools Facilitate Novel Currency Visualizations", Proceedings of EuroPVM-MPI 2009, Espoo, Finland, September 7-10, 2009.

  28. Sarvani Vakkalanka, Anh Vo, Ganesh Gopalakrishnan and Robert M. Kirby, "Reduced Execution Semantics of MPI: From Theory to Practice", Proceedings of the 16th International Symosium on Formal Methods 2009 (FM2009), Eindhoven, the Netherlands, November 2-6, 2009.

  29. Sarvani Vakkalanka, Anh Vo, Ganesh Gopalakrishnan and Robert M. Kirby, "Precise Dynamic Analysis for Slack Elasticity: Adding Buffering Without Adding Bugs", Proceedings of EuroMPI 2010, Stuttgart, Germany, September 12-15, 2010.

  30. Anh Vo, Ganesh Gopalakrishnan, Robert M. Kirby, Bronis R. de Supinski, Martin Schulz and Greg Bronevetsky, "Large Scale Verification of MPI Programs Using Lamport Clocks with Lazy Update", Proceedings of The Twentieth International Conference on Parallel Architectures and Compilation Techniques (PACT). Galveston, TX, October 10-14, 2011.

  31. Tiago Etiene, Robert M. Kirby and Claudio Silva, "A Study of Discretization Errors in Volume Rendering Integral Approximations", EuroRVVV Workshop (held in conjunction with EuroVis), June 17-18, 2013.

  32. James King and Robert M. Kirby, "A Scalable, Efficient Scheme for the Evaluation of Stencil Computations over Unstructured Meshes", IEEE SuperComputing 2013, Denver, CO, November 17-22, 2013. [PDF]

  33. Shankar Shastry and Robert M. Kirby, "On Interpolation Errors over Quadratic Nodal Triangular Finite Elements", 22nd International Meshing Roundtable, Orlando, FL, October 13-16, 2013. [PDF]

  34. H. Bhatia, V. Pascucci, R.M. Kirby and P.-T. Bremer, "Extracting Features from Time-Dependent Vector Fields Using Internal Reference Frames", Eurographics Conference on Visualization (EuroVis), Swansea, Wales, UK, June 9-13, 2014. [PDF]
 

  Other Publication Venues:
  1. Kirk E. Jordan, Robert M. Kirby, Claudio Silva and Thomas J. Peters, "Through a New Looking Glass: Mathematically Precise Visualization", SIAM News, Vol. 43, Number 5, June 2010. [PDF]  

  2. (Invited) Tiago Etiene, Hoa Nguyen, Robert M. Kirby and Claudio T. Silva, "'Flow Visualization' Juxtaposed With 'Visualization of Flow': Synergistic Opportunities Between Two Communities", 51st AIAA Aerospace Meeting, January 7-10, 2013. [PDF]  

  3. Mary Hall, Robert M. Kirby, Feifei Li, Miriah Meyer, Valerio Pascucci, Jeff M. Phillips, Rob Ricci, Jacobus Van der Merwe and Suresh Venkatasubramanian, "Rethinking Abstractions for Big Data: Why, Where, How, and What", arXiv:1306.3295v1, 2013. [PDF]  

 

Last Updated: 08/07/14