Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

2006


G. Kumfert, D.E. Bernholdt, T.G.W. Epperly, J.A. Kohl, L.C. McInnes, S.G. Parker, J. Ray. “How the Common Component Architecture Advances Computational Science,” In J. Phys.: Conf. Ser., Vol. 46, pp. 479--493. 2006.



A. Lefohn, J.M. Kniss, R. Strzodka, S. Sengupta, J. Owens. “Glift: Generic, Efficient Random-Access GPU Data Structures,” In ACM Trans. Comp. Graph., Vol. 25, No. 1, pp. 1--37. January, 2006.



G. Li, X. Tricoche, C.D. Hansen. “GPUFLIC: Interactive and Accurate Dense Visualization of Unsteady Flows,” In Proceedings of Euro Vis 2006, pp. 29--34. 2006.



G. Li, X. Tricoche, C.D. Hansen. “Survey of Texture-based Techniques in Flow Visualization,” In VIsualization of Large and Unstructured Data Sets - Applications in Geospatial Planning, Modeling, and Engineering, Dagstuhl, Germany, GI-Edition, Lecture Notes in Informatics - Visualization of Large and Unstructured Data Sets. First workshop of the DFG's International Research Training Group, pp. 11--21. June, 2006.



O.E. Livne. “Clustering on Single Refinement Level: Berger-Rigoustos Algorithm,” SCI Institute Technical Report, No. UUSCI-2006-001, University of Utah, 2006.



O.E. Livne. “Minimum and Maximum Patch Size Clustering on a Single Refinement Level,” SCI Institute Technical Report, No. UUSCI-2006-002, University of Utah, 2006.



O.E. Livne. “Efficient Update of Persistent Patches in the Berger Rigoutsous Algorithm,” SCI Institute Technical Report, No. UUSCI-2006-003, University of Utah, 2006.



O.E. Livne. “Clustering Patches for Multi-Level Refined Grids: a Hierarchical Approach,” SCI Institute Technical Report, No. UUSCI-2006-004, University of Utah, 2006.



O.E. Livne. “ShockTube Problem - Status Report 1 Uni-Level Experiments,” SCI Institute Technical Report, No. UUSCI-2006-005, University of Utah, 2006.



O.E. Livne. “ICE Algorithm and the Davis Advection Scheme,” SCI Institute Technical Report, No. UUSCI-2006-006, University of Utah, 2006.



O.E. Livne. “ICE Algorithm for the Shocktube Problem,” SCI Institute Technical Report, No. UUSCI-2006-007, University of Utah, 2006.



L. Lorenzo, R.S. MacLeod, R.T. Whitaker, G. Adluru, E.V.R. DiBella. “Level Sets and Shape Models for Segmentation of Cardiac Perfusion MRI,” In Proceedings of International Society for Optical Engineering (SPIE) Conference on Medical Imaging 2006, Vol. 6144, pp. 1320--1331. 2006.



P. Lorenzen, M.W. Prastawa, B. Davis, G. Gerig, E. Bullitt, S. Joshi. “Multi-Modal Image Set Registration and Atlas Formation,” In Med Image Anal, Vol. 10, No. 3, pp. 440--451. June, 2006.



H. Lu, M. Berzins, C.E. Goodyer, P.K. Jimack, M. Walkley. “Adaptive High-order Finite Element Solution of Transient Elastohydrodynamic Lubrication Problems,” In Proc. IMechE Part J: J. Engrg. Tribology, Vol. 220, pp. 215--225. 2006.



H. Lu, M. Berzins, P.K. Jimack. “Application of the Adaptive Discontinuous Galerkin Method to Problems in Elastohydrodynamic Lubrication,” In Innovation in Engineering Computational Technology, Edited by B.H.V. Topping and G. Montero and R. Montenegro, Saxe-Coburg Publications, Stirling, pp. 169--191. 2006.



H. Lu. “High Order Finite Element Solution of Elastohydrodynamic Lubrication Problems,” Note: Advisor: Martin Berzins, School of Computing, University of Leeds, 2006.

ABSTRACT

In this thesis, a high-order finite element scheme, based upon the Discontinuous Galerkin (DG) method, is introduced to solve one- and two-dimensional Elastohydrodynamic Lubrication (EHL) problems (line contact and point contact). This thesis provides an introduction to elastohydrodynamic lubrication, including some history, and a description of the underlying mathematical model which is based upon a thin film approximation and a linear elastic model. Following this, typical nondimensionalizations of the equations are discussed, along with boundary conditions. Two families of problems are considered: line and point contacts. Following a review of existing numerical methods for EHL problems, a different numerical technique, known as the Discontinuous Galerkin method is described. This is motivated by the high accuracy requirement for the numerical simulation of EHL problems. This method is successfully applied to steady-state line contact problems. The free boundary is captured accurately using the moving-grid method and the penalty method respectively. Highly accurate numerical results are obtained at a low expense through the use of h-adaptivity methods based on discontinuity and high-order components respectively. Combined with the Crank-Nicolson method and other implicit schemes for the temporal discretization, highly accurate solutions are also obtained for transient line contact problems using the high order DG method for the spatial discretization. In particular, an extra pressure spike is captured, which is difficult to resolve when using low order schemes for spatial discretization. The extension of this high order DG method to the two-dimensional case (point contact) is straightforward. However, the computation in the two-dimensional case is more expensive due to the extra dimension. Hence p-multigrid is employed to improve the efficiency. Since the free boundary in the two-dimensional case is more complicated, only the penalty method is used to handle the cavitation condition. This thesis is ended with the conclusions and a discussion of future work.



T.J. Lujan, M.S. Dalton, B.M. Thompson B.J. Ellis, J.A. Weiss. “Effect of ACL Deficiency on MCL Strains and Joint Kinematics,” In Journal of Biomechanical Engineering, pp. (in press). November, 2006.



T.J. Lujan, C.J. Underwood, H.B. Henninger, B.M. Thompson, J.A. Weiss. “Effect of Dermatan Sulfate Glycosaminoglycans on the Quasi-Static Material Properties of the Human Medial Collateral Ligament,” In Journal of Orthopaedic Research, pp. (in press). October, 2006.



H. Marmanis, C.W. Hamman, R.M. Kirby. “A One-Dimensional Model of the Navier-Stokes,” SCI Institute Technical Report, No. UUSCI-2006-012, University of Utah, 2006.



L.C. McInnes, B.A. Allan, R. Armstrong, S.J. Benson, D.E. Bernholdt, T.L. Dahlgren, L.F. Diachin, M. Krishnan, J.A. Kohl, J.W. Larson, S. Lefantzi, J. Nieplocha, B. Norris, S.G. Parker, J. Ray, S. Zhou. “Parallel PDE-Based Simulations Using the Common Component Architecture,” In Numerical Solution of Partial Differential Equations on Parallel Computers, Lecture Notes in Computational Science and Engineering, Edited by A.M. Bruaset and P. Bjorstad and A. Tveito, Springer, pp. 327--284. 2006.
ISBN: 3-540-29076-1