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.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.



N. Touheed, P. Selwood, P.K. Jimack, M. Berzins. “A Comparison of Some Dynamic Load Balancing Algorithms for a Parallel Adaptive Flow Solver,” In Parallel Computing, Vol. 26, No. 12, pp. 1535--1554. 2000.



X. Tricoche, G. Scheuermann, H. Hagen. “Higher Order Singularities in Piecewise Linear Vector Fields,” In The Mathematics of Surfaces IX, Springer, London, pp. 99--113. 2000.



X. Tricoche, G. Scheuermann, H. Hagen. “A Topology Simplification Method for 2D Vector Fields,” In Proceedings of IEEE Visualization 2000, pp. 359--366. 2000.



T.N. Truong. “Reaction Class Transition State Theory: Hydrogen Abstraction Reactions by Hydrogen Atoms as Test Cases,” In Journal of Chemical Physics, Vol. 113, No. 12, pp. 4957-4964. 2000.
DOI: 10.1063/1.1287839

ABSTRACT

We present a new method called Reaction Class Transition State Theory (RC-TST) for estimating thermal rate constants of a large number of reactions in a class. This method is based on the transition state theory framework within the reaction class approach. Thermal rate constants of a given reaction in a class relative to those of its principal reaction can be efficiently predicted from only its differential barrier height and reaction energy. Such requirements are much less than what is needed by the conventional TST method. Furthermore, we have shown that the differential energetic information can be calculated at a relatively low level of theory. No frequency calculation beyond those of the principal reaction is required for this theory. The new theory was applied to a number of hydrogen abstraction reactions. Excellent agreement with experimental data shows that the RC-TST method can be very useful in design of fundamental kinetic models of complex reactions.



T.N. Truong, D.K. Maity, T.-T.T. Truong. “A combined reaction class approach with integrated molecular orbital+molecular orbital (IMOMO) methodology: A practical tool for kinetic modeling,” In Journal of Chemical Physics, Vol. 112, No. 1, pp. 24--30. 2000.
DOI: 10.1063/1.480558

ABSTRACT

We present a new practical computational methodology for predicting thermal rate constants of reactions involving large molecules or a large number of elementary reactions in the same class. This methodology combines the integrated molecular orbital+molecular orbital (IMOMO) approach with our recently proposed reaction class models for tunneling. With the new methodology, we show that it is possible to significantly reduce the computational cost by several orders of magnitude while compromising the accuracy in the predicted rate constants by less than 40% over a wide range of temperatures. Another important result is that the computational cost increases only slightly as the system size increases.



D.C. Van Essen, H.A. Drury, S. Joshi, M. Miller. “Functional and Structural Mapping of Human Cerebral Cortex: Solutions are in the Surfaces,” In Adv Neurol, Vol. 84, pp. 23--34. 2000.



S. Vyazovkin, C.A. Wight. “Estimating Realistic Confidence Intervals for the Activation Energy Determined from Thermoanalytical Measurements,” In Analytical Chemistry, Vol. 72, No. 14, pp. 3171--3175. June, 2000.
DOI: 10.1021/ac000210u

ABSTRACT

A statistical procedure is proposed for estimating realistic confidence intervals for the activation energy determined by using an advanced isoconversional method. Nine sets of five thermogravimetric measurements have been produced for the process of gassification of ammonium nitrate at five different heating rates. Independent estimates of the confidence intervals for the activation energy have been obtained from these data sets. Agreement with these independent estimates demonstrates that the proposed statistical procedure is capable of adequately estimating the actual uncertainty in the activation energy determined from a small number of measurements. The resulting averaged relative errors in the activation energy were found to be 26, 21, and 17% for three, four, and five heating rate estimates, respectively.