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

2005


S. Zhang, D.H. Laidlaw, G. Kindlmann. “Diffusion Tensor MRI Visualization,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 327--340. 2005.
ISBN: 0-12-387582-X


2004


O. Alter, G.H. Golub. “Integrative Analysis of Genome-Scale Data by Using Pseudoinverse Projection Predicts Novel Correlation Between DNA Replication and RNA Transcription,” In Proceedings of the National Academy of Sciences, Vol. 101, No. 47, Proceedings of the National Academy of Sciences, pp. 16577--16582. November, 2004.
DOI: 10.1073/pnas.0406767101



O. Alter, G.H. Golub, P.O. Brown, D. Botstein. “Novel Genome-Scale Correlation Between DNA Replication and RNA Transcription During the Cell Cycle in Yeast is Predicted by Data-Driven Models,” In Proceedings of the Miami Nature Biotechnology Winter Symposium on the Cell Cycle, Chromosomes and Cancer, Vol. 15, Edited by M.P. Deutscher and S. Black and P.E. Boehmer and G. D'Urso and T. Fletcher and F. Huijing and A. Marshall and B. Pulverer and B. Renault and J.D. Rosenblatt and J.M. Slingerland and W.J. Whelan, 2004.



S. Amer-Yahia, F. Du, J. Freire. “A Comprehensive Solution to the XML-to-Relational Mapping Problem,” In Proceedings of the 6th Annual ACM International Workshop on Web Information and Data Management, Washington DC, USA, pp. 31--38. 2004.
ISBN: 1-58113-978-0



A.E. Anderson, C.L. Peters, B.D. Tuttle, J.A. Weiss. “Development and Validation of a Subject-Specific Finite Element Model of the Pelvis: Assessment of Model Sensitivity,” In Proceedings of The 6th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, pp. (6 pages). 2004.



A.E. Anderson, C.L. Peters, B.D. Tuttle, J.A. Weiss. “A Subject-Specific Finite Element Model of the Pelvis Accurately Predicts Cortical Strains Under Acetabular Loading,” In Proceedings of 50th Annual Meeting of the Orthopaedic Research Society, San Francisco, CA, Vol. 29, pp. 1334. March, 2004.



C. Ayyagari, D. Bedrov, G.D. Smith. “A Molecular Dynamics Simulation Study of The Influence of Free Surfaces on the Morphology of Self-Associating Polymers,” In Polymer, Vol. 45, No. 13, pp. 4549--4558. June, 2004.
DOI: 10.1016/j.polymer.2004.04.044

ABSTRACT

Molecular dynamics simulations of thin films and bulk melts of model self-associating polymers have been performed in order to gain understanding of the influence of free surfaces on the morphology of these polymers. The self-associating polymers were represented by a simple bead-necklace model with attractive groups (stickers) at the chain ends (end-functionalized polymer) and in the chain interior (interior-functionalized polymer). The functionalized groups were found to form clusters in the melt whose size is representative of that found experimentally in many ionomer melts. While the size distribution and shape of the clusters in the thin films were found to be relatively unperturbed compared to their corresponding bulk melts, the morphology of the self-associating melts was found to be significantly perturbed by the free surfaces. Specifically, a strong depletion of stickers near the interface and the emergence of clearly defined layers of stickers parallel to the surface was observed. Increased bridging of clusters by the functionalized polymers was also observed near the free surface. We conclude that these effects can be associated with a high free energy for stickers in the low-density interfacial regime: stickers prefer to be in the higher-density interior of the film where relatively unperturbed sticker clusters can form.

Keywords: Molecular dynamics, Ionomers, Telechelic polymers



B. Banerjee. “MPM Validation: Sphere-Cylinder Impact: Low Resolution Simulations,” C-SAFE Internal Report, No. C-SAFE-CD-IR-04-002, Department of Mechanical Engineering, University of Utah, August, 2004.

ABSTRACT

This report compares the simulated and experimental axial velocity and axial strain histories observed during a low resolution study of the impact of an aluminum sphere on an aluminum plate supported by a hollow aluminum cylinder. In a previous report, an optimal set of input parameters was identified that minimizes ringing and reduces energy increase over the time of the simulations. These input parameters were used in the simulations discussed in this report. We observe that though the initial time of arrival of the stress wave at various locations matches the experimentally observed data, the time evolution of velocities and strains can be considerably different from the experimental data.



B. Banerjee. “MPM Validation: Sphere-Cylinder Impact: Medium Resolution Simulations,” C-SAFE Internal Report, No. C-SAFE-CD-IR-04-003, Department of Mechanical Engineering, University of Utah, August, 2004.

ABSTRACT

In a previous report we compared the experimental and the computed axial velocity and axial strain from a low spatial resolution study of the impact of an aluminum sphere on an aluminum plate supported by a hollow aluminum cylinder. We report results from a higher resolution study of the same problem using input parameters that conserve both momentum and energy quite accurately. The simulations show a slower wave speed than the experiments which suggests that the elastic moduli and density of the material used in the experiments may be different from those used in the simulations. The simulated free surface velocity also differs from the experimental data. Further study is required to determine the cause of these differences.



B. Banerjee. “MPM Validation: Sphere-Cylinder Impact Tests : Energy Balance,” C-SAFE Internal Report, No. C-SAFE-CD-IR-04-001, Department of Mechanical Engineering, University of Utah, 2004.

ABSTRACT

This report discusses the energy balance results observed during the simulation of the impact of an aluminum sphere on an aluminum plate supported by a hollow aluminum cylinder. Due to the high impact velocity, there is considerable ringing of the cylinder which causes the sum of the mechanical energies to increase. An optimal set of input parameters is identified that minimizes ringing and reduces energy increase over the time of the simulation.



B. Banerjee, D.O. Adams. “On Predicting the Effective Elastic Properties of Polymer Bonded Explosives Using the Recursive Cell Method,” In International Journal of Solids and Structures, Vol. 41, No. 2, pp. 481--509. January, 2004.
DOI: 10.1016/j.ijsolstr.2003.09.016

ABSTRACT

Polymer bonded explosives are particulate composites containing elastic particles in a viscoelastic binder. The particles occupy an extremely high fraction of the volume, often greater than 90%. Under low strain rate loading (∼0.001–1 s−1) and at room temperature and higher, the elastic modulus of the particles can be four orders of magnitude higher than that of the binder. Rigorous bounds and analytical estimates for the effective elastic properties of these materials have been found to be inaccurate. The computational expense of detailed numerical simulations for the determination of effective properties of these composites has led to the search for a faster technique. In this work, one such technique based on a real-space renormalization group approach is explored as an alternative to direct numerical simulations in determining the effective elastic properties of PBX 9501. The method is named the recursive cell method (RCM). The differential effective medium approximation, the finite element method, and the generalized method of cells (GMC) are investigated with regard to their suitability as homogenizers in the RCM. Results show that the RCM overestimates the effective properties of particulate composites and PBX 9501 unless large blocks of subcells are renormalized and the particles in a representative volume element are randomly distributed. The GMC homogenizer is found to provide better estimates of effective elastic properties than the finite element based homogenizer for composites with particle volume fractions less than 0.80.



D. Barbosa, J. Freire, A. Mendelzon. “Information Preservation in XML-to-Relational Mappings,” In Database and XML Technologies, Lecture Notes in Computer Science (LNCS), Vol. 3186/2004, pp. 66--81. 2004.
ISBN: 978-3-540-22969-8



S.G. Bardenhagen, E.M. Kober. “The Generalized Interpolation Material Point Method,” In Computer Modeling in Engineering and Sciences, Vol. 5, No. 6, pp. 477--495. 2004.

ABSTRACT

The Material Point Method (MPM) discrete solution procedure for computational solid mechanics is generalized using a variational form and a Petrov-Galerkin discretization scheme, resulting in a family of methods named the Generalized Interpolation Material Point (GIMP) methods. The generalization permits iden- tification with aspects of other point or node based discrete solution techniques which do not use a body–fixed grid, i.e. the "meshless methods". Similarities are noted and some practical advantages relative to some of these methods are identified. Examples are used to demon- strate and explain numerical artifact noise which can be expected in MPM calculations. This noise results in non-physical local variations at the material points, where constitutive response is evaluated. It is shown to destroy the explicit solution in one case, and seriously degrade it in another. History dependent, inelastic constitutive laws can be expected to evolve erroneously and report inac- curate stress states because of noisy input. The noise is due to the lack of smoothness of the interpolation func- tions, and occurs due to material points crossing compu- tational grid boundaries. The next degree of smoothness available in the GIMP methods is shown to be capable of eliminating cell crossing noise.



D. Bedrov, G.D. Smith, J.F. Douglas. “Structural and Dynamic Heterogeneity in a Telechelic Polymer Solution,” In Polymer, Vol. 45, No. 11, pp. 3961--3966. May, 2004.
DOI: 10.1016/j.polymer.2004.01.082

ABSTRACT

We utilize molecular dynamics simulations to investigate the implications of micelle formation on structural relaxation and polymer bead displacement dynamics in a model telechelic polymer solution. The transient structural heterogeneity associated with incipient micelle formation is found to lead to a ‘caging’ of the telechelic chain end-groups within dynamic clusters on times shorter than the structural relaxation time governing the cluster (micelle) lifetime. This dynamical regime is followed by ordinary diffusion on spatial scales larger than the inter-micelle separation at long times. As with associating polymers, glass-forming liquids and other complex heterogeneous fluids, the structural τs relaxation time increases sharply upon a lowering temperature T, but the usual measures of dynamic heterogeneity in glass-forming liquids (non-Gaussian parameter α2(t), product of diffusion coefficient D and shear viscosity η, non-Arrhenius T-dependence of τs) all indicate a return to homogeneity at low T that is not normally observed in simulations of these other complex fluids. The greatest increase in dynamic heterogeneity is found on a length scale that lies intermediate to the micellar radius of gyration and intermicellar spacing. We suggest that the limited size of the clusters that form in our (low concentration) system limit the relaxation time growth and thus allows the fluid to remain in equilibrium at low T.



D. Bedrov, G.D. Smith, W. Paul. “Anomalous Pressure Dependence of the Structure Factor in 1,4-Polybutadiene Melts. A Molecular Dynamics Simulation Study,” In Physical Review, E, Vol. 70, No. 1, pp. 011804. July, 2004.
DOI: 10.1103/PhysRevE.70.011804

ABSTRACT

Neutron scattering has shown the first diffraction peak in the structure factor of a 1,4-polybutadiene melt under compression to move to larger q values as expected but to decrease significantly in intensity. Simulations reveal that this behavior does not result from loss of structure in the polymer melt upon compression but rather from the generic effects of differences in the pressure dependence of the intermolecular and intramolecular contributions to the melt structure factor and differences in the pressure dependence of the partial structure factors for carbon–carbon and carbon–deuterium intermolecular correlations. This anomalous pressure dependence is not seen for protonated melts.



F.F. Bernardon, C.A. Pagot, J.L.D. Comba, C.T. Silva. “GPU-based Tiled Ray Casting using Depth Peeling,” SCI Institute Technical Report, No. UUSCI-2004-006, University of Utah, 2004.



M. Berzins. “Variable Order Finite Elements and Positivity Preservation for Hyperbolic PDEs,” In Applied Numerical Mathematics, Vol. 48, No. 3-4, pp. 253--439. March, 2004.



R. Borgo, V. Pascucci, R. Scopigno. “Massive Data Pre-Processing with a Cluster Based Approach,” In Proceedings of the 2004 Eurographics Symposium on Parallel Graphics and Visualization (EG-PGV-04), Note: UCRL-PROC-208678, Eurographics Association, Aire-la-Ville, Switzerland pp. 67--74. June, 2004.



P.-T. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci. “A Topological Hierarchy for Functions on Triangulated Surfaces,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 10, No. 4, Note: UCRL-JRNL-208700, pp. 385-396. July/August, 2004.



P.-T. Bremer, V. Pascucci, B. Hamann. “Maximizing adaptivity in hierarchical topological models,” In Trends in Software, Note: UCRL-BOOK-200013, Edited by T. Moeller and B. Hamann and B. Russell, Springer, pp. 121--130. January, 2004.