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


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.



S.G. Parker, M. Miller, C.D. Hansen, C.R. Johnson. “Computational Steering and the SCIRun Integrated Problem Solving Environment,” In Proceedings of Dagstuhl 1997 Workshop on Scientific Visualization, Note: Invited and peer reviewed, Edited by Hans Hagen and Greg Nielson and Frits Post, pp. 257--266. 2000.



V. Pascucci, C.L. Bajaj. “Time Critical Isosurface Refinement and Smoothing,” In Proceedings of the ACM/IEEE Volume Visualization and Graphics Symposium 2000, Salt lake City, Utah, Note: UCRL-JC-139628, pp. 33--42. October, 2000.



M. Pernice. “A Hybrid Multigrid Method for the Steady-State Incompressible Navier-Stokes Equations,” In Applied Mathematics and Computation, Vol. 138, No. 2-3, pp. 341--353. 2000.

ABSTRACT

Multigrid methods for solving the steady-state incompressible Navier-Stokes equations require an appropriate smoother and coarse grid solution strategy to be effective. Classical pressure-correction methods, such as SIMPLE and SIMPLER, are widely used as solvers in engineering analysis codes, but can also be used as effective multigrid smoothers. An inexact Newton method preconditioned by a linear multigrid method with a pressurecorrection smoother can serve as a coarse grid solver. A hybrid nonlinear multigrid scheme based on combinations of these components is described. A standard benchmark problem is used to demonstrate the effectiveness of SIMPLER smoothing and the impact an inexact Newton coarse grid solver has on the resulting nonlinear multigrid scheme.



E. Reinhard, B. Smits, C.D. Hansen. “Dynamic Acceleration Structures for Interactive Ray Tracing,” In Proceedings Eurographics Workshop on Rendering, Brno, Czech Republic, pp. 299--306. June, 2000.



E. Reinhard, C.D. Hansen. “A Comparison of Parallel Compositing Techniques on Shared Memory Architectures,” In Proceedings of The 2nd Eurographics Workshop on Parallel Graphics and Visualization, Spain, pp. 115--124. September, 2000.



G. Scheuermann, W. Kollmann, X. Tricoche, T. Wischgoll. “Evolution of Topology in Axi-Symmetric and 3D Viscous Flows,” In Numerical Simulations of Incompressible Flows, World Scientific Publishing, New Jersey, pp. 622--643. 2000.



A. Shamir, V. Pascucci, C.L. Bajaj. “Multi-Resolution Dynamic Meshes with Arbitrary Deformations,” In Proceedings of IEEE Conference on Visualization (VIS-00), Salt lake City, Utah, Note: UCRL-JC-139680, pp. 423--430. 2000.



G.D. Smith, W. Paul, M. Monkenbusch, D. Richter. “A Comparison of Neutron Scattering Studies and Computer Simulations of Polymer Melts,” In Chemical Physics, Vol. 261, No. 1-2, pp. 61--74. 2000.
DOI: 10.1016/S0301-0104(00)00228-7

ABSTRACT

Neutron scattering and computer simulations are powerful tools for studying structural and dynamical properties of condensed matter systems in general and of polymer melts in particular. When neutron scattering studies and quantitative atomistic molecular dynamics simulations of the same material are combined, synergy between the methods can result in exciting new insights into polymer melts not obtainable from either method separately. We present here an overview of our recent efforts to combine neutron scattering and atomistic simulations in the study of melt dynamics of polyethylene and polybutadiene. Looking at polymer segmental motion on a picosecond time scale, we show how atomistic simulations can be used to identify molecular motions giving rise to relaxation processes observed in experimental dynamic susceptibility spectra. Examining larger length and longer time scale polymer dynamics involving chain self-diffusion and overall conformational relaxation, we show how simulation results can motivate experiment and how combined results of scattering and simulation can be used to critically test theories that attempt to describe melt dynamics of short polymer chains.



P. Sutton, C.D. Hansen. “Accelerated Isosurface Extraction in Time-varying Fields,” In IEEE Trans. Vis & Comp. Graph., Vol. 6, No. 2, pp. 98--107. 2000.



P.M. Sutton, C.D. Hansen, H.W. Shen, D. Schikore. “A Case Study of Isosurface Extraction Algorithm Performance,” In Proceeding of The Joint Eurographics - IEEE TCVG Symposium on Visualization 2000, Amsterdam, pp. 259--268. May, 2000.



T. Tasdizen, J.-P. Tarel, D.B. Cooper. “Improving the Stability of Algebraic Curves for Applications,” In IEEE Transactions on Image Processing, Vol. 9, No. 3, pp. 405--416. March, 2000.



T. Tasdizen, D.B. Cooper. “Boundary Estimation from Intensity/Color Images with Algebraic Curve Models,” In Proceedings 15th International Conference on Pattern Recognition. ICPR-2000, IEEE, 2000.
DOI: 10.1109/icpr.2000.905308

ABSTRACT

A concept and algorithm are presented for non-iterative robust estimation of piecewise smooth curves of maximal edge strength in small image windows-typically 8/spl times/8 to 32/spl times/32. This boundary-estimation algorithm has the nice properties that it uses all the data in the window and thus can find locally weak boundaries embedded in noise or texture and boundaries when there are more than two regions to be segmented in a window; it does not require step edges-but handles ramp edges well. The curve-estimates found are among the level sets of a dth degree polynomial fit to "suitable" weightings of the image gradient vector at each pixel in the image window. Since the polynomial fitting is linear least squares, the computation to this point is very fast. Level sets then chosen to be appropriate boundary curves are those having the highest differences in average gray level in regions to either side. This computation is also fast. The boundary curves and segmented regions found are suitable for all purposes but especially for indexing using algebraic curve invariants in this form.



A.S. Tomlin, S. Ghorai, G. Hart, M. Berzins. “3-D Adaptive Unstructured Meshes in Air Pollution Modelling,” In Environmental Modeling and Software, Vol. 15, No. 4, pp. 681--692. 2000.