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

2000


A. Deshmukh, C.C. Douglas, M. Ball, R.E. Ewing, C.R. Johnson, C. Kesselman, C. Lee. “Dynamic Data Driven Application Systems: Creating a dynamic and symbiotic coupling of application/simulations with measurements/experiments,” Note: 28 pages, Edited by W. Powell, R. Sharpley, National Science Foundation, 2000.



B.S. Duerstock, C.L. Bajaj, V. Pascucci, D.R. Schikore, K. Lin, R.B. Borgens. “Advances in Three-Dimensional Reconstruction of the Experimental Spinal Cord Injury,” In Computerized Medical Imaging and Graphics, Vol. 24, No. 6, pp. 389--406. 2000.



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



J.D. de St. Germain, J. McCorquodale, S.G. Parker, C.R. Johnson. “Uintah: A Massively Parallel Problem Solving Environment,” In Ninth IEEE International Symposium on High Performance and Distributed Computing, IEEE, Piscataway, NJ, pp. 33--41. Nov, 2000.



S. Ghorai, A.S. Tomlin, M. Berzins. “Resolution of pollutant concentrations in the boundary layer using a fully 3-D adaptive gridding technique,” In Atmospheric Environment, Vol. 34, No. 18, pp. 2851-2863. 2000.



C.E. Goodyer, R. Fairlie, M. Berzins, L.E. Scales. “An In-depth Investigation of the Multigrid Approach to Steady and Transient EHL Problems,” In Thinning Films and Tribological InterfacesProceedings of the 26th Leeds-Lyon Symposium on Tribology, Tribology Series, Vol. 38, Edited by D. Dowson, M. Priest, C.M. Taylor, P. Ehret, T.H.C. Childs, G. Dalmaz, A.A. Lubrecht, Y. Berthier, L. Flamand and J.-M. Georges, Elsevier, pp. 95--102. 2000.
ISSN: 0167-8922

ABSTRACT

Multigrid methods have proved robust and highly desirable in terms of the iteration speed in solving elastohydrodynamic lubrication (EHL) problems. Lubrecht, Venner and Ehret, amongst others, have shown that multigrid can be successfully used to obtain converged solutions for steady problems. steady problems.

A detailed study reinforces these results but also shows, in some cases, that while multigrid techniques give initial rapid convergence, the residuals - having dropped to a low level - may reach a stalling point, mainly due to the cavitation region. The study will explain this behaviour in terms of the iterative scheme and show how, if this happens, the errors in the fine grid solution can be reduced further. Example results of both steady and transient EHL problems (including a thermal viscoelastic case) are shown with further developments into adaptive meshes considered.



C.E. Goodyera, R. Fairliea, M. Berzinsa, L.E. Scales. “An in-depth investigation of the multigrid approach to steady and transient EHL problems,” In 26th Leeds-Lyon Symposium on Tribology, Vol. 38, Elsevier, pp. 95-102. 2000.

ABSTRACT

Multigrid methods have proved robust and highly desirable in terms of the iteration speed in solving elastohydrodynamic lubrication (EHL) problems. Lubrecht, Venner and Ehret, amongst others, have shown that multigrid can be successfully used to obtain converged solutions for steady problems, steady problems. A detailed study reinforces these results but also shows, in some cases, that while multigrid techniques give initial rapid convergence, the residuals - having dropped to a low level - may reach a stalling point, mainly due to the cavitation region. The study will explain this behaviour in terms of the iterative scheme and show how, if this happens, the errors in the fine grid solution can be reduced further. Example results of both steady and transient EHL problems (including a thermal viscoelastic case) are shown with further developments into adaptive meshes considered. © 2000 Elsevier Science B.V. All rights reserved.



T.C. Henderson, P.A. McMurtry, P.J. Smith, G.A. Voth, C.A. Wight, D.W. Pershing. “Simulating Accidental Fires and Explosions,” In Computing in Science and Engineering, Vol. 2, No. 2, pp. 64--76. 2000.
DOI: 10.1109/5992.825750

ABSTRACT

The Center for the Simulation of Accidental Fires and Explosions (C‐SAFE) at the University of Utah is focused on providing state‐of‐the‐art, science‐based tools for the numerical simulation of accidental fires and explosions, especially within the context of handling and storage of highly flammable materials. The objective of the C‐SAFE effort is to provide a scalable, high‐performance system composed of a problem‐solving environment in which fundamental chemistry and engineering physics are fully coupled with non‐linear solvers, optimization, computational steering, visualization and experimental data verification. The availability of simulations using this system will help to better evaluate the risks and safety issues associated with fires and explosions. Our five‐year product, termed Uintah 5.0, will be validated and documented for practical application to accidents involving both hydrocarbon and energetic materials.



R.E. Hogan, K.E. Mark, L. Wang, S. Joshi, M.I. Miller, R. Bucholz. “Mesial Temporal Sclerosis and Temporal Lobe Epilepsy: MR Imaging Deformation-Based Segmentation of the Hippocampus in Five Patients,” In Radiology, Vol. 216, No. 1, pp. 291--297. July, 2000.



R.E. Hogan, K.E. Mark, I. Choudhuri, L. Wang, S. Joshi, M.I. Miller, R. Bucholz. “Magnetic Resonance Imaging Deformation-Based Segmentation of the Hippocampus in Patients with Mesial Temporal Sclerosis and Temporal Lobe Epilepsy,” In J Digit Imaging, Vol. 13, No. 2 (Suppl. 1), pp. 217--218. May, 2000.



R.E. Hogan, R.D. Bucholz, I. Choudhuri, K.E. Mark, C.S. Butler, S. Joshi. “Shape-analysis of hippocampal surface structure in patients with unilateral mesial temporal sclerosis,” In Journal of Digital Imaging, Vol. 13, No. 2, pp. 39--42. 2000.



M. Ikits. “Coregistration of Pose Measurement Devices Using Nonlinear Least Squares Parameter Estimation,” School of Computing Technical Report, No. UUCS-00-018, University of Utah, 2000.



C.R. Johnson, S.G. Parker, D. Weinstein. “Large-Scale Computational Science Applications Using the SCIRun Problem Solving Environment,” In Proceedings of The International Supercomputer Conference 2000, 2000.



S. Joshi, M.I. Miller. “Landmark Matching Via Large Deformation Diffeomorphisms,” In IEEE Transactions on Image Processing, Vol. 9, No. 8, pp. 1357--1370. August, 2000.



G.L. Kindlmann, D.M. Weinstein, D. Hart. “Strategies for Direct Volume Rendering of Diffusion Tensor Fields,” In IEEE Trans. Vis & Comp. Graph., Vol. 6, No. 2, pp. 124--138. April-June, 2000.



J. Lewis, T.D. Sewell, R. Evans, G.A. Voth. “Electronic Structure Calculation of the Structures and Energies of the Three Pure Polymorphic Forms of Crystalline HMX,” In Journal of Physical Chemistry, B, Vol. 104, No. 5, pp. 1009--1013. January, 2000.
DOI: 10.1021/jp9926037

ABSTRACT

The molecular structures and energetic stabilities of the three pure polymorphic forms of crystalline HMX were calculated using a first-principles electronic-structure method. The computations were performed using the local density approximation in conjunction with localized “fireball” orbitals and a minimal basis set. Optimized cell parameters and molecular geometries were obtained, subject only to preservation of the experimental lattice angles and relative lattice lengths. The latter constraint was removed in some calculations for β-HMX. Within these constraints, the comparison between theory and experiment is found to be good. The structures, relative energies of the polymorphs, and bulk moduli are in general agreement with the available experimental data.



J.P. Lewis, K.R. Glaesemann, K. Van Opdorp, G.A. Voth. “Ab Initio Calculations of Reactive Pathways for Gas-Phase Alpha-Octahydro-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine (Alpha-HMX),” In Physical Chemistry, A, Vol. 104, pp. 11384--11389. 2000.

ABSTRACT

Using the BLYP and B3LYP level of density functional theory, four possible decomposition reaction pathways of HMX in the gas phase were investigated: N-NO2 bond dissociation, HONO elimination, C-N bond scission of the ring, and the concerted ring fission. The energetics of each of these four mechanisms are reported. Dissociation of the N-NO2 bond is putatively the initial mechanism of nitramine decomposition in the gas phase. Our results find the dissociation energy of this mechanism to be 41.8 kcal/mol at the BLYP level and 40.5 kcal/mol at the B3LYP level, which is comparable to experimental results. Three other mechanisms are calculated and found at the BLYP level to be energetically competitive to the nitrogennitrogen bond dissociation; however, at the B3LYP level these three other mechanisms are energetically less favorable. It is proposed that the HONO elimination and C-N bond scission reaction of the ring would be favorable in the condensed phase.



Y. Livnat, S.G. Parker, C.R. Johnson. “Fast Isosurface Extraction Methods for Large Image Data Sets,” In Handbook of Medical Imaging, Edited by A.N. Bankman, Academic Press, San Diego, CA pp. 731--745. Nov, 2000.



G.T. Long, S. Vyazovkin, B.A. Brems, C.A. Wight. “Competitive Vaporization and Decomposition of Liquid RDX,” In Journal of Physical Chemistry, B, Vol. 104, No. 11, pp. 2570--2574. February, 2000.
DOI: 10.1021/jp993334n

ABSTRACT

The thermal decomposition of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has been studied by thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). Activation energies as a function of the extent of conversion, α, have been determined by model-free isoconversional analysis of these data. In open pans, evaporation is a prevalent process with an activation energy of ∼100 kJ mol-1. Confining the system in either a pierced pan or a closed pan promotes liquid state decomposition of RDX that occurs with an activation energy of ∼200 kJ mol-1, which suggests scission of an N-N bond as the primary decomposition step. In such a confined environment, gas phase decomposition is a competing channel with an activation energy estimated to be ∼140 kJ mol-1. In a closed pan, RDX generates a heat release of ∼500 kJ mol-1 that is independent of both the heating rate, β, and the mass.



J.A. Nairn. “Fracture Mechanics of Composites with Residual Stresses, Traction-Loaded Cracks, and Imperfect Interfaces,” In European Structural Integrity Society: Fracture of Polymers, Composites and Adhesives, Vol. 27, pp. 111--121. 2000.
DOI: 10.1016/S1566-1369(00)80012-6

ABSTRACT

By partitioning the total stresses in a damaged composite into either mechanical and residual stresses or into initial and pertubation stresses, it was possible to derive several exact results for the energy release rate due to crack growth. These general results automatically include the effects of residual stresses, traction-loaded cracks, and imperfect interfaces. By considering approximate solutions based on admissible stress states and admissible strain states, it was possible to derive rigorous upper and lower bounds to the energy release rate for crack growth. Two examples of using these equations are mode I fracture in adhesive double cantilever beam specimens and analysis of microcracking in composite laminates.