Scientific Grand Challenges: Opportunities in biology at the Extreme Scale of Computing|
M. Ellisman, R. Stevens, M. Colvin, T. Schlick, E. Delong, G. Olsen, J. George, G. Karniakadis, C.R. Johnson, N. Sematova. Note: DOE Office of Advanced Scientific Computing Research, August, 2009.
Incorporating patient breathing variability into a stochastic model of dose deposition for stereotactic body radiation therapy|
S.E. Geneser, R.M. Kirby, Brian Wang, B. Salter, S. Joshi. In Information Processing in Medical Imaging, Lecture Notes in Computer Science LNCS, Vol. 5636, pp. 688--700. 2009.
PubMed ID: 19694304
Finite Element Discretization Strategies for the Inverse Electrocardiographic (ECG) Problem|
D.F. Wang, R.M. Kirby, C.R. Johnson. In Proceedings of the 11th World Congress on Medical Physics and Biomedical Engineering, Munich, Germany, Vol. 25/2, pp. 729-732. September, 2009.
Finite Element Refinements for Inverse Electrocardiography: Hybrid-Shaped Elements, High-Order Element Truncation and Variational Gradient Operator|
D.F. Wang, R.M. Kirby, C.R. Johnson. In Proceeding of Computers in Cardiology 2009, Park City, September, 2009.
A Framework for Exploring Numerical Solutions of Advection Reaction Diffusion Equations using a GPU Based Approach|
A.R. Sanderson, M.D. Meyer, R.M. Kirby, C.R. Johnson. In Journal of Computing and Visualization in Science, Vol. 12, pp. 155--170. 2009.
Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples|
R.S. MacLeod, J.G. Stinstra, S. Lew, R.T. Whitaker, D.J. Swenson, M.J. Cole, J. Krüger, D.H. Brooks, C.R. Johnson. In Philosophical Transactions of The Royal Society A, Mathematical, Physical & Engineering Sciences, Vol. 367, No. 1896, pp. 2293--2310. 2009.
Hexahedral Mesh Generation for Biomedical Models in SCIRun|
J.F. Shepherd, C.R. Johnson. In Engineering with Computers, Vol. 25, No. 1, pp. 97--114. 2009.
Comparison of Consistent Integration Versus Adaptive Quadrature for Taming Aliasing Errors|
SCI Technical Report, H. Mirzaee, C. Eskilsson, S.J. Sherwin, R.M. Kirby. No. UUSCI-2009-008, SCI Institute, University of Utah, 2009.
The SCIJump Framework for Parallel and Distributed Scientific Computing|
S.G. Parker, K. Damevski, A. Khan, A. Swaminathan, C.R. Johnson. In Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications, Edited by Manish Parashar and Xiaolin Li and Sumir Chandra, Wiley-Blackwell, pp. 149--170. 2009.
A Meshing Pipeline for Biomedical Models|
M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson. In Engineering with Computers, Vol. 25, No. 1, SpringerLink, pp. 115-130. 2009.
Formal Verification of Practical MPI Programs|
A. Vo, S. Vakkalanka, M. Delisi, G. Gopalakrishnan, R.M. Kirby, R. Thakur. In Proceedings of 14th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), Raleigh, NC, pp. 261--270. February 14-18, 2009.
Particle-based Sampling and Meshing of Surfaces in Multimaterial Volumes|
M.D. Meyer, R.T. Whitaker, R.M. Kirby, C. Ledergerber, H. Pﬁster. In IEEE Transactions on Visualization and Computer Graphics, Vol. 14, No. 6, pp. 1539--1546. 2008.
Hexahedral Mesh Generation Constraints|
J.F. Shepherd, C.R. Johnson. In Journal of Engineering with Computers, Vol. 24, No. 3, pp. 195--213. 2008.
Filtering in Legendre Spectral Methods|
J.S. Hesthaven, R.M. Kirby. In Mathematics of Computation, Vol. 77, No. 263, pp. 1425--1452. 2008.
An Approach to Formalization and Analysis of Message Passing Libraries|
R. Palmer, M. DeLisi, G. Gopalakrishnan, R.M. Kirby. In Proceedings of the 12th International Workshop on Formal Methods for Industrial Critical Systems (FMICS 2007), Berlin, Germany, Vol. 4916/2008, Note: Awarded Best Paper., pp. 164--181. 2008.
Application of Stochastic Finite Element Methods to Study the Sensitivity of ECG Forward Modeling to Organ Conductivity|
S.E. Geneser, R.M. Kirby, R.S. MacLeod. In IEEE Transations on Biomedical Engineering, Vol. 55, No. 1, pp. 31--40. January, 2008.
A Comparison of Implicit Solvers for the Immersed Boundary Equations|
E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby. In Computer Methods in Applied Mechanics and Engineering, Vol. 197, No. 25--28, pp. 2290--2304. 2008.
Investigation of Smoothness-Increasing Accuracy-Conserving Filters for Improving Streamline Integration Through Discontinuous Fields|
M. Steffen, S. Curtis, R.M. Kirby, J.K. Ryan. In IEEE Transactions on Visualization and Computer Graphics, Vol. 14, No. 3, pp. 680--692. 2008.
Analysis and Reduction of Quadrature Errors in the Material Point Method (MPM)|
M. Steffen, R.M. Kirby, M. Berzins. In International Journal for Numerical Methods in Engineering, Vol. 76, No. 6, pp. 922--948. 2008.
Volumetric Parameterization and Trivariate B-spline Fitting using Harmonic Functions|
T. Martin, E. Cohen, R.M. Kirby. In Proceedings of ACM Solid and Physical Modeling, Stony Brook, NY, Note: Awarded Best Paper, pp. 269-280. 2008.