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 of 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. 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, Accepted for Publication, 2007.  [PDF]

  28. 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, Accepted for Publication, 2007.  [PDF]

  29. 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.  [PDF]

  30. 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]

  31. Michael Steffen, Robert M. Kirby and Martin Berzins, "Analysis and Reduction of Quadrature Errors in the Material Point Method (MPM)", International Journal of Numerical Methods in Engineering, Accepted for Publication, 2008.  [PDF]

  32. C.W. Hamman, J.C. Klewicki and R.M. Kirby, "On the Lamb vector divergence in Navier-Stokes flows", Journal of Fluid Mechanics, Accepted for Publication, 2008.  [PDF]

  33. 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, Accepted for Publication, 2008.  [PDF]

  34. Robert M. Kirby and Claudio Silva, "The Need For Verifiable Visualization", IEEE Computer Graphics and Applications , Accepted for Publication, 2008.  [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.
  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.
  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.
  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.
  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.
  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.

 

Last Updated: 06/20/08