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

1999


 C. Guerra, V. Pascucci. “On Matching Sets of 3D Segments,” In Proceedings of SPIE Vision Geometry VIII, Denver, USA pp. 157-167. 1999.


C. Guerra, V. Pascucci. “3D Segment Matching Using the Hausdorff Distance,” In Proceedings of the IEEE Conference on Image Processing and its Applications, IPA99, pp. 18--22. 1999.


C. Guerra, V. Pascucci. “Segment Matching for Protein Secondary Structure Comparison,” In Proceedings of the Third International Conference on Computational Molecular Biology, RECOMB'99, ACM, Lyon, France pp. 30. 1999.


C.D. Hansen, T. Udeshi, S.G. Parker, P. Shirley. “Parallel Methods for Isosurface Visualization,” In Ninth SIAM Conference on Parallel Processing for Scientific Computing, Note: extended abstract, 1999.


R.E. Hogan, K.E. Mark, L. Wang, S.C. Joshi, M.I. Miller, R.D. Bucholz. “MR Imaging Deformation-Based Segmentation of the Hippocampus in Patients with Mesial Temporal Sclerosis and Temporal Lobe Epilepsy,” In Epilepsia, Vol. 40, No. 7, 1999.


M.A. Johnson, T.N. Truong. “High Level Ab Initio and Density Functional Theory Evaluation of Combustion Reaction Energetics: NO2 and HONO Elimination from Dimethylnitramine,” In Journal of Physical Chemistry, A, Vol. 103, No. 44, pp. 8840--8846. October, 1999.
DOI: 10.1021/jp9925029

ABSTRACT

Dimethylnitramine (DMNA) is used as a model system for investigating accurate and efficient electronic structure methods for nitramines. Critical points on the potential energy surfaces of DMNA, CH3NCH3, CH3NCH2, NO2, HONO, and the transition state to HONO elimination were located through geometry optimizations using the B1LYP, B3LYP, MPW1PW91, and BH&HLYP density functional methods, in addition to MP2, G2(MP2), and QCISD ab initio theories using the cc-pVDZ basis set. For cost-effective determination of nitramine reaction energetics, highly correlated single-point calculations at DFT geometries are recommended. Our best estimated reaction enthalpies for N-N bond scission and HONO elimination are 41.6 and −0.9 kcal/mol, respectively, determined at the QCISD(T)//QCISD level of theory. These numbers can be reproduced to within 1.3 kcal/mol for the N-N bond and to within 0.5 kcal/mol for the HONO reaction by calculating QCISD(T) energies at B1LYP geometries, thus saving considerable computational cost without sacrificing accuracy. Using the same strategy, the transition state energy for HONO elimination can be modeled to within 0.1 kcal/mol of the QCISD(T)//QCISD result.


 M.A. Johnson, T.N. Truong. “Importance of Polarization in Simulations of Condensed Phased Energetic Materials,” In Journal of Physical Chemistry, B, Vol. 103, No. 44, pp. 9392--9393. October, 1999.
DOI: 10.1021/jp992514u

ABSTRACT

An embedded cluster model is used to estimate the molecular dipole moment of crystalline dimethylnitramine (DMNA). The electrostatic potential due to the crystal is included in the calculation via the SCREEP (surface charge representation of the electrostatic embedding potential) approach. The resulting dipole moment for DMNA in the crystalline environment is 6.69 D. This number is more than 40% greater than the gas-phase value and 15% greater than the estimated dipole moment in the liquid phase, thus providing evidence of a strong polarization effect in condensed phases of DMNA.


 C.R. Johnson, S.G. Parker. “The SCIRun Parallel Scientific Computing Problem Solving Environment,” In Ninth SIAM Conference on Parallel Processing for Scientific Computing, 1999.


C.R. Johnson, S.G. Parker, C.D. Hansen, G.L. Kindlmann, Y. Livnat. “Interactive Simulation and Visualization,” In IEEE Computer, Vol. 32, No. 12, pp. 59--65. Dec, 1999.


M. Joshi, J. Cui, K. Doolittle, S. Joshi, D.C. Van Essen, L. Wang, M. Miller. “Brain Segmentation and the Generation of Cortical Surfaces,” In Neuroimage, Vol. 9, No. 5, pp. 461--476. May, 1999.


G.-S. Karamanos, C. Evangelinos, R.C. Boes, R.M. Kirby, G.E. Karniadakis. “Direct Numerical Simulation of Turbulence with a PC/Linux Cluster: Fact or Fiction?,” In Proceedings of SuperComputing 1999, Portland, OR, November, 1999.


G.L. Kindlmann, D.M. Weinstein. “Hue-Balls and Lit-Tensors for Direct Volume Rendering of Diffusion Tensor Fields,” In Proceedings of the IEEE Visualization 99, pp. 183--189. 1999.


R.M. Kirby, T.C. Warburton, I. Lomtev, G.E. Karniadakis. “A Discontinuous Galerkin Spectral/hp Method on Hybrid Grids,” In Journal of Applied Numerical Mathematics, Vol. 33, pp. 393--405. 1999.


R.M. Kirby, H. Marmanis, D.H. Laidlaw. “Visualizing Multivalued Data from 2D Incompressible Flows Using Concepts from Painting,” In Proceedings of IEEE Visualization 1999, San Francisco, CA, pp. 333--340. October, 1999.


Y. Livnat. “NOISE, WISE and SAGE: Algorithms for Rapid Isosurface Extraction,” SCI Institute Technical Report, No. UUSCI-1999-001, University of Utah, December, 1999.


I. Lomtev, R.M. Kirby, G.E. Karniadakis. “A Discontinuous Galerkin ALE Method for Compressible Viscous Flows in Moving Domains,” In Journal of Computational Physics, Vol. 155, pp. 128--159. 1999.


D. Maity, W.T. Duncan, T.N. Truong. “Direct Ab Initio Dynamics Studies of the Hydrogen Abstraction Reactions of Hydrogen Atom with Fluoromethanes,” In Journal of Physical Chemistry, A, Vol. 103, No. 13, pp. 2152--2159. March, 1999.
DOI: 10.1021/jp984281x

ABSTRACT

A direct ab initio dynamics study on the gas-phase reactions of atomic hydrogen with different fluoromethanes has been carried out. The thermal rate constants were calculated using canonical variational transition state (CVT) theory augmented by multidimensional semiclassical zero and small curvature tunneling approximations. The potential energy surfaces for the reactions were calculated using hybrid density functional theory, namely, Becke's half-and-half (BH) nonlocal exchange and the Lee−Yang−Parr (LYP) nonlocal correlation functionals using the cc-pVDZ basis set. The reaction energies and barrier heights were improved by single-point energy calculations along the minimum energy path (MEP) at the spin-projected fourth order Moller−Plesset perturbation theory (PMP4) using the cc-pVTZ basis set. The calculated forward and reverse thermal rate constants are in the good agreement with the experimental data. The electronic effects of fluorine substitution on the rate of this class of reactions are examined.


 P. McCormick, C.D. Hansen, E. Angel. “The Deferred Accumulation Buffer,” In Journal for Graphics Tools, Vol. 4, No. 3, pp. 35--46. 1999.


M. Miller, C.D. Hansen, C.R. Johnson. “The SCIRun Problem Solving Environment: Implementation within a Distributed Environment,” In Ninth SIAM Conference on Parallel Processing for Scientific Computing, Note: extended abstract, 1999.


M.I. Miller, S.C. Joshi, G.E. Christensen. “Large Deformation Fluid Diffeomorphisms For Landmark and Image Matching,” In Brain Warping, Edited by A. W. Toga and John Mazziotta, pp. 115--131. 1999.