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

2003


 T. Tasdizen, R.T. Whitaker, P. Burchard, S. Osher. “Geometric Surface Processing via Normal Maps,” In ACM Transactions on Graphics, 2003.


T. Tasdizen, R.T. Whitaker. “Cramer-Rao Bounds for Nonparametric Surface Reconstruction from Range Data,” In Proceedings of Fourth International Conference on 3-D Imaging and Modeling, pp. 70--77. October, 2003.


T. Tasdizen, R.T. Whitaker. “Anisotropic diffusion of surface normals for feature preserving surface reconstruction,” In Proceedings of Fourth International Conferenceon 3-D Imaging and Modeling, pp. 353--360. October, 2003.


T. Tasdizen, R.T. Whitaker. “Feature preserving variational smoothing of terrain data,” In IEEE Workshop on Variational, Geometric and Level Set Methods in Computer Vision, October, 2003.


X. Tricoche, G. Scheuermann. “Topology Simplification of Symmetric, Second Order 2D Tensor Fields,” In Geometric Modeling Methods in Scientific Visualization, Springer, Berlin, pp. 171--184. 2003.


R. Van Uitert, D. Weinstein, C.R. Johnson. “Volume Currents in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models,” In Annals of Biomedical Engineering, Vol. 31, pp. 21--31. 2003.


R. Van Uitert, C.R. Johnson. “Influence of Brain Conductivity on Magnetoencephalographic Simulations in Realistic Head Models,” In The 25th Annual International Conference of the IEEE Engineering In Medicine And Biology Society, Vol. 3, pp. 2136--2139. September, 2003.


A. Violi, G.A. Voth, A.F. Sarofim. “A Time-scale Problem for the Formation of Soot Precursors in Premixed Flames,” In American Chemical Society, Division of Fuel Chemistry, Vol. 48, No. 2, pp. 545--547. 2003.


D.M. Weinstein, J.V. Tranquillo, C.S. Henriquez, C.R. Johnson. “BioPSE Case Study: Modeling, Simulation, and Visualization of Three Dimensional Mouse Heart Propagation,” In International Journal of Bioelectromagnetism, Vol. 5, No. 1, pp. 314--315. 2003.


C. Wyman, C.D. Hansen. “Penumbra Maps: Approximate Soft Shadows in Real-Time,” In Eurographics Rendering Symposium, Belguim, pp. 202--207. 2003.


D. Xiu, G.E. Karniadakis. “Modeling Uncertainty in Flow Simulations via Generalized Polynomial Chaos,” In Journal of Computational Physics, Vol. 187, No. 1, pp. 137--167. 2003.
DOI: 10.1016/S0021-9991(03)00092-5

ABSTRACT

We present a new algorithm to model the input uncertainty and its propagation in incompressible flow simulations. The stochastic input is represented spectrally by employing orthogonal polynomial functionals from the Askey scheme as trial basis to represent the random space. A standard Galerkin projection is applied in the random dimension to obtain the equations in the weak form. The resulting system of deterministic equations is then solved with standard methods to obtain the solution for each random mode. This approach can be considered as a generalization of the original polynomial chaos expansion, first introduced by Wiener [Am. J. Math. 60 (1938) 897]. The original method employs the Hermite polynomials (one of the 13 members of the Askey scheme) as the basis in random space. The algorithm is applied to micro-channel flows with random wall boundary conditions, and to external flows with random freestream. Efficiency and convergence are studied by comparing with exact solutions as well as numerical solutions obtained by Monte Carlo simulations. It is shown that the generalized polynomial chaos method promises a substantial speed-up compared with the Monte Carlo method. The utilization of different type orthogonal polynomials from the Askey scheme also provides a more efficient way to represent general non-Gaussian processes compared with the original Wiener–Hermite expansions.

Keywords: Polynomial chaos, Uncertainty, Fluids, Stochastic modeling


 D. Xiu, G.E. Karniadakis. “A New Stochastic Approach to Transient Heat Conduction Modeling with Uncertainty,” In International Journal of Heat and Mass Transfer, Vol. 46, No. 24, pp. 4681--4693. 2003.
DOI: 10.1016/S0017-9310(03)00299-0

ABSTRACT

We present a generalized polynomial chaos algorithm for the solution of transient heat conduction subject to uncertain inputs, i.e. random heat conductivity and capacity. The stochastic input and solution are represented spectrally by the orthogonal polynomial functionals from the Askey scheme, as a generalization of the original polynomial chaos idea of Wiener [Am. J. Math. 60 (1938) 897]. A Galerkin projection in random space is applied to derive the equations in the weak form. The resulting set of deterministic equations is subsequently discretized by the spectral/hp element method in physical space and integrated in time. Numerical examples are given and the convergence of the chaos expansion is demonstrated for a model problem.

Keywords: Uncertainty, Stochastic modeling, Polynomial chaos, Transient heat conduction, Random medium


 P. Yushkevich, S. Joshi, S.M. Pizer, J.G. Csernansky, L. Wang. “Feature Selection for Shape-Based Classification of Biological Objects,” In Inf Process Med Imaging, Vol. 18, pp. 114--125. July, 2003.


P. Yushkevich, P.T. Fletcher, S. Joshi, A. Thall, S.M. Pizer. “Continuous Medial Representations for Geometric Object Modeling in 2D and 3D,” In Image and Vision Computing, Special Issue on Generative Model-based Vision, Vol. 21, No. 1, pp. 17--27. 2003.


K. Zyp. “The Transfer Operator for Multigrid on Inverse Bioelectric Field Problems,” SCI Institute Technical Report, No. UUSCI-2003-001, Note: Masters thesis, University of Utah, May, 2003.

2002


 B. Banerjee, D.O. Adams. “Micromechanics-Based Prediction of Thermoelastic Properties of High Energy Materials,” In Constitutive Modeling of Geomaterials, In Constitutive Modeling of Geomaterials, Edited by H.I. Ling et al., CRC Press, New York, pp. 158--164. 2002.

ABSTRACT

High energy materials such as polymer bonded explosives are commonly used as propellants. These particulate composites contain explosive crystals suspended in a rubbery binder. However, the explosive nature of these materials limits the determination of their mechanical properties by experimental means. Therefore micromechanics-based methods for the determination of the effective thermoelastic properties of polymer bonded explosives are investigated in this research. Polymer bonded explosives are twocomponent particulate composites with high volume fractions of particles (volume fraction > 90%) and high modulus contrast (ratio of Young’s modulus of particles to binder of 5,000-10,000). Experimentally determined elastic moduli of one such material, PBX 9501, are used to validate the micromechanics methods examined in this research. The literature on micromechanics is reviewed; rigorous bounds on effective elastic properties and analytical methods for determining effective properties are investigated in the context of PBX 9501. Since detailed numerical simulations of PBXs are computationally expensive, simple numerical homogenization techniques have been sought. Two such techniques explored in this research are the Generalized Method of Cells and the Recursive Cell Method. Effective properties calculated using these methods have been compared with finite element analyses and experimental data.


 D. Bedrov, G.D. Smith, K.F. Freed, J. Dudowicz. “A Comparison of Self-Assembly in Lattice and Off-Lattice Model Amphiphile Solutions,” In Journal of Chemical Physics, Vol. 116, No. 12, pp. 4765--4768. 2002.
DOI: 10.1063/1.1461355

ABSTRACT

Lattice Monte Carlo and off-lattice molecular dynamics simulations of h1t4 and h4t1 (head/tail) amphiphile solutions have been performed as a function of surfactant concentration and temperature. The lattice and off-lattice systems exhibit quite different self-assembly behavior at equivalent thermodynamic conditions. We found that in the weakly aggregating regime (no preferred-size micelles), all models yield similar micelle size distributions at the same average aggregation number, albeit at different thermodynamic conditions (temperatures). In the strongly aggregating regime, this mapping between models (through temperature adjustment) fails, and the models exhibit qualitatively different micellization behavior.


 D. Bedrov, G.D. Smith, T.D. Sewell. “Molecular Dynamics Simulations of HMX Crystal Polymorphs Using A Flexible Molecule Force Field,” In Journal of Computer-Aided Materials Design, Vol. 8, No. 2-3, pp. 77--85. 2002.
DOI: 10.1023/A:1020046817543

ABSTRACT

Molecular dynamics simulations using a recently developed quantum chemistry-based atomistic force field [J. Phys. Chem. B, 103 (1999) 3570 ] were performed in order to obtain unit cell parameters, coefficients of thermal expansion, and heats of sublimation for the three pure crystal polymorphs of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX). The predictions for β-, α-, and δ-HMX showed good agreement with the available experimental data. For the case of β-HMX, anisotropic sound speeds were calculated from the molecular dynamics simulation-predicted elastic coefficients and compared with recent Impulsive Stimulated Light Scattering (ISLS) sound speed measurements. The level of agreement is encouraging.


 M. Benedikt, J. Freire, P. Godefroid. “VeriWeb: Automatically Testing Dynamic Web Sites,” In In Proceedings of 11th International World Wide Web Conference 2002, 2002.


P. Bohannon, J. Freire, J. Haritsa, M. Ramanath, P. Roy, J. Simeon. “LegoDB: Customizing Relational Storage for XML Documents,” In Proceedings of the 28th international conference on Very Large Data Bases, Hong Kong, China, pp. 1091--1094. 2002.