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


S.D. Ramsey, M. Bertram, C.D. Hansen. “Simplification of Arbitrary Polyhedral Meshes,” In IASTED Computer Graphics and Imaging (CGIM 2003), Honolulu, pp. 117--222. 2003.



M. Ramanath, J. Freire, J. Haritsa, P. Roy. “Searching for Efficient XML-to-Relational Mappings,” In Lecture Notes in Computer Science, Lecture Notes in Computer Science (LNCS), Vol. 2824, pp. 19--36. 2003.
ISBN: 978-3-540-20055-0
DOI: 10.1007/978-3-540-39429-7_2

ABSTRACT

We consider the problem of cost-based strategies to derive efficient relational configurations for XML applications that subscribe to an XML Schema. In particular, we propose a flexible framework for XML schema transformations and show how it can be used to design algorithms to search the space of equivalent relational configurations. We study the impact of the schema transformations and query workload on the search strategies for finding efficient XML-to-relational mappings. In addition, we propose several optimizations to speed up the search process. Our experiments indicate that a judicious choice of transformations and search strategies can lead to relational configurations of substantially higher quality than those recommended by previous approaches.



K. Riley, D. Ebert, C.D. Hansen, J. Levit. “Visually Accurate Multi-Field Weather Visualization,” In IEEE Visualization 2003, Seattle, pp. 279--286. 2003.



A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. “Image Reconstruction from Sensitivity Encoded MRI Data Using Extrapolated Iterations of Parallel Projections Onto Convex Sets,” In SPIE Medical Imaging, Vol. 5032, pp. 1829--1838. 2003.



A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. “Determination of the Sampling Density Compensation Function Using a Point Spread Function Modeling Approach and Gridding Approximation,” In Proceedings of 11th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), Toronto, pp. 477. 2003.



A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. “A Modified POCSENSE Technique for Accelerated Iterative Reconstruction from Sensitivity Encoded MRI Data,” In Proceedings of 11th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), Toronto, pp. 477. 2003.



A.R. Sanderson, C.R. Johnson. “Display of Vector Fields Using a Reaction-Diffusion Model,” SCI Institute Technical Report, No. UUSCI-2003-002, University of Utah, June, 2003.



J. Schpok, J. Simons, D.S. Ebert, C.D. Hansen. “A Real-Time Cloud Modeling, Rendering, and Animation System,” In ACM Symposium on Computer Animation, San Diego, pp. 160--166. 2003.



Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod. “Prior Model Selection for Bayesian Inverse Electrocardiography,” In Proceedings of the NFSI Conference 2003, Chieti, Italy, 2003.



Y. Serinagaoglu, R.S. MacLeod, D.H. Brooks. “A Bayesian Approach to Inclusion and Performance Analysis of Using Extra Information in Bioelectric Inverse Problems,” In Proceedings of the IEEE International Conference on Image Processing, 2003.



Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod. “Combining Numerical and Physiological Constraints in Inverse Electrocardiography,” In Int. J. Bioelectromag., Vol. 5, No. 1, pp. 215--217. 2003.



T.D. Sewell, R. Menikoff, D. Bedrov, G.D. Smith. “A Molecular Dynamics Simulation Study of Elastic Properties of HMX,” In Journal of Chemical Physics, Vol. 119, No. 14, pp. 7471--7426. 2003.
DOI: 10.1063/1.1599273



S. Shellman, K. Sikorski. “A Recursive Algorithm for the Infinity-Norm Fixed Point Problem,” In Journal of Complexity, Vol. 19, No. 6, pp. 799--834. 2003.
DOI: 10.1016/j.jco.2003.06.001



S.D. Shellman, K. Sikorski. “Algorithm 825: A deep-cut bisection envelope algorithm for fixed points,” In ACM Transactions on Mathematical Software (TOMS), Vol. 29, No. 3, pp. 309--325. September, 2003.
DOI: 10.1145/838250.838255

ABSTRACT

We present the BEDFix (Bisection Envelope Deep-cut Fixed point) algorithm for the problem of approximating a fixed point of a function of two variables. The function must be Lipschitz continuous with constant 1 with respect to the infinity norm; such functions are commonly found in economics and game theory. The computed approximation satisfies a residual criterion given a specified error tolerance. The BEDFix algorithm improves the BEFix algorithm presented in Shellman and Sikorski [2002] by utilizing "deep cuts," that is, eliminating additional segments of the feasible domain which cannot contain a fixed point. The upper bound on the number of required function evaluations is the same for BEDFix and BEFix, but our numerical tests indicate that BEDFix significantly improves the average-case performance. In addition, we show how BEDFix may be used to solve the absolute criterion fixed point problem with significantly better performance than the simple iteration method, when the Lipschitz constant is less than but close to 1. BEDFix is highly efficient when used to compute residual solutions for bivariate functions, having a bound on function evaluations that is twice the logarithm of the reciprocal of the tolerance. In the tests described in this article, the number of evaluations performed by the method averaged 31 percent of this worst-case bound. BEDFix works for nonsmooth continuous functions, unlike methods that require gradient information; also, it handles functions with minimum Lipschitz constants equal to 1, whereas the complexity of simple iteration approaches infinity as the minimum Lipschitz constant approaches 1. When BEDFix is used to compute absolute criterion solutions, the worst-case complexity depends on the logarithm of the reciprocal of 1-q, where q is the Lipschitz constant, as well as on the logarithm of the reciprocal of the tolerance.



G.D. Smith, D. Bedrov, O. Borodin. “Structural Relaxation and Dynamic Heterogeneity in a Polymer Melt at Attractive Surfaces,” In Physical Review Lett., Vol. 90, No. 22, pp. 226103.1--226103.4. 2003.
DOI: 10.1103/PhysRevLett.90.226103

ABSTRACT

Molecular dynamics simulations of polymer melts at flat and structured surfaces reveal that, for the former, slow dynamics and increased dynamic heterogeneity for an adsorbed polymer is due to densification of the polymer in a surface layer, while, for the latter, the energy topography of the surface plays the dominant role in determining dynamics of interfacial polymer. The dramatic increase in structural relaxation time for polymer melts at the attractive structured surface is largely the result of dynamic heterogeneity induced by the surface and does not resemble dynamics of a bulk melt approaching Tg.



G.D. Smith, D. Bedrov, O. Byutner, O. Borodin, C. Ayyagari, T.D. Sewell. “A Quantum-Chemistry-Based Potential for a Poly(ester urethane),” In Journal of Physical Chemistry, A, Vol. 107, No. 38, pp. 7552--7560. August, 2003.
DOI: 10.1021/jp0225018

ABSTRACT

We have carried out extensive high-level quantum chemistry studies of the geometry, charge distribution, conformational energies, and hydrogen-bonding energies of model compounds for a family of Estane thermoplastic urethanes (TPUs). Upon the basis of these studies, we have parametrized a classical potential for use in atomistic simulations of Estane TPUs that can also be applied directly or with minor extensions to a wide variety of polyesters and polyurethanes.



J.S. Smith, D. Bedrov, G.D. Smith. “A molecular dynamics simulation study of nanoparticle interactions in a model polymer-nanoparticle composite,” In Composites Science and Technology, Vol. 63, No. 11, pp. 1599--1605. August, 2003.
DOI: 10.1016/S0266-3538(03)00061-7

ABSTRACT

Molecular dynamics (MD) simulations were performed on a model polymer–nanoparticle composite (PNPC) consisting of spherical nanoparticles in a bead-spring polymer melt. The polymer-mediated effective interaction (potential of mean force) between nanoparticles was determined as a function of polymer molecular weight and strength of the polymer–nanoparticle interaction. For all polymer–nanoparticle interactions and polymer molecular weights investigated the range of the matrix-induced interaction was greater than the direct nanoparticle–nanoparticle interaction employed in the simulations. When the polymer–nanoparticle interactions were relatively weak the polymer matrix promoted nanoparticle aggregation, an effect that increased with polymer molecular weight. Increasingly attractive nanoparticle–polymer interactions led to strong adsorption of the polymer chains on the surface of the nanoparticles and promoted dispersion of the nanoparticles. For PNPCs with strongly adsorbed chains the matrix-induced interaction between nanoparticles reflected the structure (layering) imposed on the melt by the nanoparticle surface and was independent of polymer molecular weight. The nanoparticle second virial coefficient obtained from the potential of mean force was utilized as an indicator of dispersion or aggregation of the particles in the PNPC, and was found to be in qualitative agreement with the aggregation properties obtained from simulations of selected PNPCs with multiple nanoparticles.



J.P. Spinti, D.W. Pershing. “The Fate of Char-N at Pulverized Coal Conditions,” In Combustion and Flame, Vol. 135, No. 3, pp. 299--313. November, 2003.
DOI: 10.1016/S0010-2180(03)00168-8

ABSTRACT

The fate of char-N (nitrogen removed from the coal matrix during char oxidation) has been widely studied at fluidized bed conditions. This work extends the study of char-N to pulverized coal conditions. Coal chars from five parent coals were prepared and burned in a laboratory-scale pulverized coal combustor in experiments designed to identify the parameters controlling the fate of char-N. The chars were burned with natural gas (to simulate volatiles combustion) in both air and in a nitrogen-free oxidant composed of Ar, CO2, and O2. In some experiments, the char flames were doped with various levels of NO or NH3 to simulate formation of NOx from volatile-N (nitrogen removed during coal devolatilization). The conversion of char-N to NOx in chars burned in the nitrogen-free oxidant was 50–60% for lignites and 40–50% for bituminous coals. In char flames doped with NOx, the apparent conversion of char-N to NOx (computed using the NOx measurements made before and after the addition of char to the system) decreased significantly as the level of NOx doping increased. With 900 ppm NOx present before the addition of char, apparent conversion of char-N to NOx was close to 0% for most chars. While there is no clear correlation between nitrogen content of the char and char-N to NOx conversion at any level of NOx in the flame, the degree of char burnout within a given family of chars does play a role. Increasing the concentration of O2 in the system in both air and nitrogen-free oxidant experiments increased the conversion of char-N to NOx. The effects of temperature on NOx emissions were different at low (0 ppm) and high (900 ppm) levels of NOx present in the flame before char addition.



J.G. Stinstra, B. Hopenfeld, R.S. MacLeod. “A Model for the Passive Cardiac Conductivity,” In Int. J. Bioelectromag., Vol. 5, No. 1, pp. 185--186. 2003.



M. Styner, G. Gerig, S. Pizer, S. Joshi. “Automatic and Robust Computation of 3D Medial Models Incorporating Object Variability,” In International Journal of Computer Vision - Special UNC-MIDAG issue, Vol. 55, No. 2, Edited by O Faugeras and K Ikeuchi and J Ponce, Kluwer Academic, pp. 107--122. November-December, 2003.