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Scientific Computing

Numerical simulation of real-world phenomena provides fertile ground for building interdisciplinary relationships. The SCI Institute has a long tradition of building these relationships in a win-win fashion – a win for the theoretical and algorithmic development of numerical modeling and simulation techniques and a win for the discipline-specific science of interest. High-order and adaptive methods, uncertainty quantification, complexity analysis, and parallelization are just some of the topics being investigated by SCI faculty. These areas of computing are being applied to a wide variety of engineering applications ranging from fluid mechanics and solid mechanics to bioelectricity.


Martin Berzins

Parallel Computing

Mike Kirby

Finite Element Methods
Uncertainty Quantification

Valerio Pascucci

Scientific Data Management

Chris Johnson

Problem Solving Environments

Ross Whitaker


Chuck Hansen


Scientific Computing Project Sites:

Publications in Scientific Computing:

Scalable Parallel Building Blocks for Custom Data Analysis
T. Peterka, R. Ross, A. Gyulassy, V. Pascucci, W. Kendall, H.-W. Shen, T.-Y. Lee, A. Chaudhuri. In Proceedings of the 2011 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), pp. 105--112. October, 2011.
DOI: 10.1109/LDAV.2011.6092324

We present a set of building blocks that provide scalable data movement capability to computational scientists and visualization researchers for writing their own parallel analysis. The set includes scalable tools for domain decomposition, process assignment, parallel I/O, global reduction, and local neighborhood communicationtasks that are common across many analysis applications. The global reduction is performed with a new algorithm, described in this paper, that efficiently merges blocks of analysis results into a smaller number of larger blocks. The merging is configurable in the number of blocks that are reduced in each round, the number of rounds, and the total number of resulting blocks. We highlight the use of our library in two analysis applications: parallel streamline generation and parallel Morse-Smale topological analysis. The first case uses an existing local neighborhood communication algorithm, whereas the latter uses the new merge algorithm.

Adaptive Extraction and Quantification of Geophysical Vortices
S. Williams, M. Petersen, P.-T. Bremer, M. Hecht, V. Pascucci, J. Ahrens, M. Hlawitschka, B. Hamann. In IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2011 IEEE Visualization Conference, Vol. 17, No. 12, pp. 2088--2095. 2011.

PIDX: Efficient Parallel I/O for Multi-resolution Multi-dimensional Scientific Datasets
S. Kumar, V. Vishwanath, P. Carns, B. Summa, G. Scorzelli, V. Pascucci, R. Ross, J. Chen, H. Kolla, R. Grout. In Proceedings of The IEEE International Conference on Cluster Computing, pp. 103--111. September, 2011.

Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing
T.A. Quinn, S. Granite, M.A. Allessie, C. Antzelevitch, C. Bollensdorff, G. Bub, R.A.B. Burton, E. Cerbai, P.S. Chen, M. Delmar, D. DiFrancesco, Y.E. Earm, I.R. Efimov, M. Egger, E. Entcheva, M. Fink, R. Fischmeister, M.R. Franz, A. Garny, W.R. Giles, T. Hannes, S.E. Harding, P.J. Hunter, s, G. Iribe, J. Jalife, C.R. Johnson, R.S. Kass, I. Kodama, G. Koren, P. Lord, V.S. Markhasin, S. Matsuoka, A.D. McCulloch, G.R. Mirams, G.E. Morley, S. Nattel, D. Noble, S.P. Olesen, A.V. Panfilov, N.A. Trayanova, U. Ravens, S. Richard, D.S. Rosenbaum, Y. Rudy, F. Sachs, F.B. Sachse, D.A. Saint, U. Schotten, O. Solovyova, P. Taggart, L. Tung, A. Varrò, P.G. Volders, K. Wang, J.N. Weiss, E. Wettwer, E. White, R. Wilders, R.L. Winslow, P. Kohl. In Progress in Biophysics and Molecular Biology, Vol. 107, No. 1, Elsevier, pp. 4--10. October, 2011.
DOI: 10.1016/j.pbiomolbio.2011.07.001
PubMed Central ID: PMC3190048

Cardiac experimental electrophysiology is in need of a well-defined Minimum Information Standard for recording, annotating, and reporting experimental data. As a step toward establishing this, we present a draft standard, called Minimum Information about a Cardiac Electrophysiology Experiment (MICEE). The ultimate goal is to develop a useful tool for cardiac electrophysiologists which facilitates and improves dissemination of the minimum information necessary for reproduction of cardiac electrophysiology research, allowing for easier comparison and utilisation of findings by others. It is hoped that this will enhance the integration of individual results into experimental, computational, and conceptual models. In its present form, this draft is intended for assessment and development by the research community. We invite the reader to join this effort, and, if deemed productive, implement the Minimum Information about a Cardiac Electrophysiology Experiment standard in their own work.

Keywords: Minimum Information Standard; Cardiac electrophysiology; Data sharing; Reproducibility; Integration; Computational modelling

Quantifying variability in radiation dose due to respiratory-induced tumor motion
S.E. Geneser, J.D. Hinkle, R.M. Kirby, Bo Wang, B. Salter, S. Joshi. In Medical Image Analysis, Vol. 15, No. 4, pp. 640--649. 2011.
DOI: 10.1016/

Using Hybrid Parallelism to improve memory use in Uintah
Q. Meng, M. Berzins, J. Schmidt. In Proceedings of the TeraGrid 2011 Conference, Salt Lake City, Utah, ACM, July, 2011.
DOI: 10.1145/2016741.2016767

The Uintah Software framework was developed to provide an environment for solving fluid-structure interaction problems on structured adaptive grids on large-scale, long-running, data-intensive problems. Uintah uses a combination of fluid-flow solvers and particle-based methods for solids together with a novel asynchronous task-based approach with fully automated load balancing. Uintah's memory use associated with ghost cells and global meta-data has become a barrier to scalability beyond O(100K) cores. A hybrid memory approach that addresses this issue is described and evaluated. The new approach based on a combination of Pthreads and MPI is shown to greatly reduce memory usage as predicted by a simple theoretical model, with comparable CPU performance.

Keywords: Uintah, C-SAFE, parallel computing

Establishing Multiscale Models for Simulating Whole Limb Estimates of Electric Fields for Osseointegrated Implants
B.M. Isaacson, J.G. Stinstra, R.D. Bloebaum, COL P.F. Pasquina, R.S. MacLeod. In IEEE Transactions on Biomedical Engineering, Vol. 58, No. 10, pp. 2991--2994. 2011.
DOI: 10.1109/TBME.2011.2160722
PubMed ID: 21712151
PubMed Central ID: PMC3179554

Although the survival rates of warfighters in recent conflicts are among the highest in military history, those who have sustained proximal limb amputations may present additional rehabilitation challenges. In some of these cases, traditional prosthetic limbs may not provide adequate function for service members returning to an active lifestyle. Osseointegration has emerged as an acknowledged treatment for those with limited residual limb length and those with skin issues associated with a socket together. Using this technology, direct skeletal attachment occurs between a transcutaneous osseointegrated implant (TOI) and the host bone, thereby eliminating the need for a socket. While reports from the first 100 patients with a TOI have been promising, some rehabilitation regimens require 12-18 months of restricted weight bearing to prevent overloading at the bone-implant interface. Electrically induced osseointegration has been proposed as an option for expediting periprosthetic fixation and preliminary studies have demonstrated the feasibility of adapting the TOI into a functional cathode. To assure safe and effective electric fields that are conducive for osseoinduction and osseointegration, we have developed multiscale modeling approaches to simulate the expected electric metrics at the bone--implant interface. We have used computed tomography scans and volume segmentation tools to create anatomically accurate models that clearly distinguish tissue parameters and serve as the basis for finite element analysis. This translational computational biological process has supported biomedical electrode design, implant placement, and experiments to date have demonstrated the clinical feasibility of electrically induced osseointegration.

IMPICE Method for Compressible Flow Problems in Uintah
L.T. Tran, M. Berzins. In International Journal For Numerical Methods In Fluids, Note: Published online 20 July, 2011.

Scalable parallel regridding algorithms for block-structured adaptive mesh renement
J. Luitjens, M. Berzins. In Concurrency And Computation: Practice And Experience, Vol. 23, No. 13, John Wiley & Sons, Ltd., pp. 1522--1537. 2011.
ISSN: 1532--0634
DOI: 10.1002/cpe.1719

ZAPP – A management framework for distributed visualization systems
G. Tamm, A. Schiewe, J. Krüger. In Proceedings of CGVCVIP 2011 : IADIS International Conference on Computer Graphics, Visualization, Computer Vision And Image Processing, pp. (accepted). 2011.

Real-time magnetic resonance imaging-guided radiofrequency atrial ablation and visualization of lesion formation at 3 Tesla
G.R. Vergara, S. Vijayakumar, E.G. Kholmovski, J.J. Blauer, M.A. Guttman, C. Gloschat, G. Payne, K. Vij, N.W. Akoum, M. Daccarett, C.J. McGann, R.S. Macleod, N.F. Marrouche. In Heart Rhythm, Vol. 8, No. 2, pp. 295--303. 2011.
PubMed ID: 21034854

Association of left atrial fibrosis detected by delayed-enhancement magnetic resonance imaging and the risk of stroke in patients with atrial fibrillation
M. Daccarett, T.J. Badger, N. Akoum, N.S. Burgon, C. Mahnkopf, G.R. Vergara, E.G. Kholmovski, C.J. McGann, D.L. Parker, J. Brachmann, R.S. Macleod, N.F. Marrouche. In Journal of the American College of Cardiology, Vol. 57, No. 7, pp. 831--838. 2011.
PubMed ID: 21310320

MRI of the left atrium: predicting clinical outcomes in patients with atrial fibrillation
M. Daccarett, C.J. McGann, N.W. Akoum, R.S. MacLeod, N.F. Marrouche. In Expert Review of Cardiovascular Therapy, Vol. 9, No. 1, pp. 105--111. 2011.
PubMed ID: 21166532

Finite Element Based Discretization and Regularization Strategies for 3D Inverse Electrocardiography
D. Wang, R.M. Kirby, C.R. Johnson. In IEEE Transactions for Biomedical Engineering, Vol. 58, No. 6, pp. 1827--1838. 2011.
PubMed ID: 21382763
PubMed Central ID: PMC3109267

We consider the inverse electrocardiographic problem of computing epicardial potentials from a body-surface potential map. We study how to improve numerical approximation of the inverse problem when the finite-element method is used. Being ill-posed, the inverse problem requires different discretization strategies from its corresponding forward problem. We propose refinement guidelines that specifically address the ill-posedness of the problem. The resulting guidelines necessitate the use of hybrid finite elements composed of tetrahedra and prism elements. Also, in order to maintain consistent numerical quality when the inverse problem is discretized into different scales, we propose a new family of regularizers using the variational principle underlying finite-element methods. These variational-formed regularizers serve as an alternative to the traditional Tikhonov regularizers, but preserves the L2 norm and thereby achieves consistent regularization in multiscale simulations. The variational formulation also enables a simple construction of the discrete gradient operator over irregular meshes, which is difficult to define in traditional discretization schemes. We validated our hybrid element technique and the variational regularizers by simulations on a realistic 3-D torso/heart model with empirical heart data. Results show that discretization based on our proposed strategies mitigates the ill-conditioning and improves the inverse solution, and that the variational formulation may benefit a broader range of potential-based bioelectric problems.

A Diffusion Approach to Network Localization
Y. Keller, Y. Gur. In IEEE Transactions on Signal Processing, Vol. 59, No. 6, pp. 2642--2654. 2011.
DOI: 10.1109/TSP.2011.2122261

Full-Resolution Interactive CPU Volume Rendering with Coherent BVH Traversal
A. Knoll, S. Thelen, I. Wald, C.D. Hansen, H. Hagen, M.E. Papka. In Proceedings of IEEE Pacific Visualization 2011, pp. 3--10. 2011.

From h to p Efficiently: Strategy Selection for Operator Evaluation on Hexahedral and Tetrahedral Elements
C.D. Cantwell, S.J. Sherwin, R.M. Kirby, P.H.J. Kelly. In Computers and Fluids, Vol. 43, No. 1, pp. 23--28. 2011.
DOI: 10.1016/j.compfluid.2010.08.012

Using Adjoint Error Estimation Techniques for Elastohydrodynamic Lubrication Line Contact Problems
D.E. Hart, M. Berzins, C.E. Goodyer, P.K. Jimack. In International Journal for Numerical Methods in Fluids, Vol. 67, Note: Published online 29 October, pp. 1559--1570. 2011.

Finite element modeling of subcutaneous implantable defibrillator electrodes in an adult torso
M. Jolley, J. Stinstra, J. Tate, S. Pieper, R.S. Macleod, L. Chu, P. Wang, J.K. Triedman. In Heart Rhythm, Vol. 7, No. 5, pp. 692--698. May, 2010.
DOI: 10.1016/j.hrthm.2010.01.030
PubMed ID: 20230927
PubMed Central ID: PMC3103844

Total subcutaneous implantable subcutaneous defibrillators are in development, but optimal electrode configurations are not known.

We used image-based finite element models (FEM) to predict the myocardial electric field generated during defibrillation shocks (pseudo-DFT) in a wide variety of reported and innovative subcutaneous electrode positions to determine factors affecting optimal lead positions for subcutaneous implantable cardioverter-defibrillators (S-ICD).

An image-based FEM of an adult man was used to predict pseudo-DFTs across a wide range of technically feasible S-ICD electrode placements. Generator location, lead location, length, geometry and orientation, and spatial relation of electrodes to ventricular mass were systematically varied. Best electrode configurations were determined, and spatial factors contributing to low pseudo-DFTs were identified using regression and general linear models.

A total of 122 single-electrode/array configurations and 28 dual-electrode configurations were simulated. Pseudo-DFTs for single-electrode orientations ranged from 0.60 to 16.0 (mean 2.65 +/- 2.48) times that predicted for the base case, an anterior-posterior configuration recently tested clinically. A total of 32 of 150 tested configurations (21%) had pseudo-DFT ratios /=1, indicating the possibility of multiple novel, efficient, and clinically relevant orientations. Favorable alignment of lead-generator vector with ventricular myocardium and increased lead length were the most important factors correlated with pseudo-DFT, accounting for 70% of the predicted variation (R(2) = 0.70, each factor P < .05) in a combined general linear modl in which parameter estimates were calculated for each factor.

Further exploration of novel and efficient electrode configurations may be of value in the development of the S-ICD technologies and implant procedure. FEM modeling suggests that the choice of configurations that maximize shock vector alignment with the center of myocardial mass and use of longer leads is more likely to result in lower DFT.

A New Family of Variational-Form-Based Regularizers for Reconstructing Epicardial Potentials from Body-Surface Mapping
D.F. Wang, R.M. Kirby, R.S. MacLeod, C.R. Johnson. In Computing in Cardiology, 2010, pp. 93--96. 2010.