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

2001


M. Walkley, P.K. Jimack, M. Berzins. “Anisotropic Adaptivity for Finite Element Solutions of 3-D Convection-Dominated Problems,” In Numerical Methods for Fluid Dynamics VII, Edited by M.J. Baines, ICFD, Oxford, pp. 525--531. 2001.
ISBN: 0 9524929 2 X



M. Walkley, P.K. Jimack, M. Berzins. “Mesh Quality and Anisotropic Adaptivity for Finite Element Solutions of 3-D Convection-Dominated Problems,” In Proceedings of ECCOMAS Computational Fluid Dynamics Conference 2001, Swansea, UK, 2001.
ISBN: 0 905 091 12 4



L. Wang, S.C. Joshi, M.I. Miller, J. Csernansky. “Statistical Analysis of Hippocampal Asymmetry in Schizophrenia,” In Neuroimage, Vol. 14, No. 3, pp. 531--545. September, 2001.



D. Weinstein, O. Portniaguine, L. Zhukov. “A Comparison of Dipolar and Focused Inversion for EEG Source Localization,” In Biomed. Technik, Vol. 46 (special issue), pp. 121--123. Sep, 2001.



J.A. Weiss, J.C. Gardiner. “Computational Modeling of Ligament Mechanics,” In Critical Reviews in Biomedical Engineering, Vol. 29, No. 3, pp. 1--70. 2001.



R. Westermann, C.R. Johnson, T. Ertl. “Topology Preserving Smoothing of Vector Fields,” In IEEE Trans. Vis & Comp. Graph., Vol. 7, No. 3, pp. 222--229. 2001.
DOI: 10.1109/2945.942690

ABSTRACT

Proposes a technique for topology-preserving smoothing of sampled vector fields. The vector field data is first converted into a scalar representation in which time surfaces implicitly exist as level sets. We then locally analyze the dynamic behavior of the level sets by placing geometric primitives in the scalar field and by subsequently distorting these primitives with respect to local variations in this field. From the distorted primitives, we calculate the curvature normal and we use the normal magnitude and its direction to separate distinct flow features. Geometrical and topological considerations are then combined to successively smooth dense flow fields, at the same time retaining their topological structure.

Keywords: vector field methods, ip image processing signal processing, surface processing, ncrr



R.T. Whitaker. “Reconstructing Terrain Maps from Dense Range Data,” In IEEE International Conference on Image Processing, pp. 165--168. October, 2001.



R.T. Whitaker, X. Xue. “Variable-Conductance, Level-Set Curvature for Image Denoising,” In IEEE International Conference on Image Processing, pp. 142--145. October, 2001.



D. Xiu, G.E. Karniadakis. “A Semi-Lagrangian High-Order Method for Navier-Stokes Equations,” In Journal of Computational Physics, Vol. 172, No. 2, pp. 658--684. 2001.
DOI: 10.1006/jcph.2001.6847

ABSTRACT

We present a semi-Lagrangian method for advection–diffusion and incompressible Navier–Stokes equations. The focus is on constructing stable schemes of secondorder temporal accuracy, as this is a crucial element for the successful application of semi-Lagrangian methods to turbulence simulations. We implement the method in the context of unstructured spectral/hp element discretization, which allows for efficient search-interpolation procedures as well as for illumination of the nonmonotonic behavior of the temporal (advection) error of the form: (see pdf for formula) We present numerical results that validate this error estimate for the advection–diffusion equation, and we document that such estimate is also valid for the Navier–Stokes equations at moderate or high Reynolds number. Two- and three-dimensional laminar and transitional flow simulations suggest that semi-Lagrangian schemes are more efficient than their Eulerian counterparts for high-order discretizations on nonuniform grids.



P. Yushkevich, S.M. Pizer, S. Joshi, J.S. Marron. “Intuitive, Localized Analysis of Shape Variability,” In Information Processing in Medical Imaging (IPMI), pp. 402--408. June, 2001.



S. Zhang, T.N. Truong. “Branching Ratio and Pressure Dependent Rate Constants of Multi-Channel Unimolecular Decomposition of Gas-Phase a-HMX: An Ab Initio Dynamics Study,” In Journal of Physical Chemistry, A, Vol. 105, pp. 2427--2434. 2001.
DOI: 10.1021/jp0043064

ABSTRACT

The dynamics of the initial thermal decomposition step of gas-phase α-HMX is investigated using the master equation method. Both the NO2 fission and HONO elimination channels were considered. The structures, energies, and Hessian information along the minimum energy paths (MEP) of these two channels were calculated at the B3LYP/cc-pVDZ level of theory. Thermal rate constants at the high-pressure limit were calculated using the canonical variational transition state theory (CVT), microcanonical variational transition state theory (μVT). The pressure-dependent multichannel rate constants and the branching ratio were calculated using the master equation method. Quantum tunneling effects in the HONO elimination are included in the dynamical calculations and found to be important at low temperatures. At the high-pressure limit, the NO2 fission channel is found to be dominant in the temperature range (500-1500 K). Both channels exhibit strong pressure dependence at high temperatures. Both reach the high-pressure limits at low temperatures. We found that the HONO elimination channel can compete with the NO2 fission, one in the low-pressure and/or hightemperature regime.



L. Zhukov, D.M. Weinstein, C.R. Johnson, R.S. Macleod. “Spatio-temporal Multi-dipole Source Localization Using ICA and Lead-Fields in FEM Head Models,” In Proceedings of the IEEE Engineering in Medicine and Biology Society 23rd Annual International Conference, Istanbul, Turkey Oct, 2001.


2000


O. Alter, P.O. Brown, D. Botstein. “Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling,” In Proceedings of the National Academy of Sciences, Vol. 97, No. 18, Proceedings of the National Academy of Sciences, pp. 10101--10106. August, 2000.
DOI: 10.1073/pnas.97.18.10101



Th. Apel, M. Berzins, P.K. Jimack, G. Kunert, A. Plaks, I. Tsukerman, M. Walkley. “Mesh Shape and Anistropic Elements: Theory and Practice,” In The Mathematics of Finite Elements and Applications X, Edited by J.R. Whiteman, Elsevier, pp. 367--376. 2000.



D.H. Barich, A.M. Orendt, R.J. Pugmire, D.M. Grant. “Carbon-13 Chemical Shift Tensors in Polycyclic Aromatic Compounds. 9. Biphenylene,” In Journal of Physical Chemistry, A, Vol. 104, No. 35, pp. 8290--8295. August, 2000.
DOI: 10.1021/jp001911y

ABSTRACT

The principal values of the 13C chemical-shift tensors of natural abundance biphenylene were measured at room temperature with the FIREMAT experiment. Of 18 crystallographically distinct positions (three sets of six congruent carbons each), the three primary bands have been resolved into seven single peaks and four degenerate peaks (two double, one triple, and one quadruple). Hence, eleven different chemical-shift tensors are reported. An interpretation of the data is made by comparison to carbon chemical-shift tensors in other molecules with similar chemical environments. Experimental and theoretical values based on a model of the asymmetric unit of the crystal unit cell are in good agreement.



D. Bedrov, G. Smith, T.D. Sewell. “Thermal Conductivity of Liquid Octahydro-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine (HMX) From Molecular Dynamics Simulations,” In Chemical Physics Letters, Vol. 324, No. 1-3, pp. 64--68. June, 2000.
DOI: 10.1016/S0009-2614(00)00559-5

ABSTRACT

The thermal conductivity of liquid octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) has been determined from imposed heat flux non-equilibrium molecular dynamics (NEMD) simulations using a previously published quantum chemistry-based atomistic potential. The thermal conductivity was determined in the temperature domain 550⩽T⩽800 K, which corresponds approximately to the existence limits of the liquid phase of HMX at atmospheric pressure. The NEMD predictions, which comprise the first reported values for thermal conductivity of HMX liquid, were found to be consistent with measured values for crystalline HMX. The thermal conductivity of liquid HMX was found to exhibit a much weaker temperature dependence than the shear viscosity and self-diffusion coefficients.



D. Bedrov, G.D. Smith. “Thermal Conductivity of Molecular Fluids from Molecular Dynamics Simulations: Application of a New Imposed-Flux Method,” In Journal of Chemical Physics, Vol. 113, No. 18, pp. 8080--8084. 2000.
DOI: 10.1063/1.1312309

ABSTRACT

We have applied a new nonequilibrium molecular dynamics (NEMD) method [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] previously applied to monatomic Lennard-Jones fluids in the determination of the thermal conductivity of molecular fluids. The method was modified in order to be applicable to systems with holonomic constraints. Because the method involves imposing a known heat flux it is particularly attractive for systems involving long-range and many-body interactions where calculation of the microscopic heat flux is difficult. The predicted thermal conductivities of liquid n-butane and water using the imposed-flux NEMD method were found to be in a good agreement with previous simulations and experiment.



D. Bedrov, G.D. Smith, T. Sewell. “Temperature-dependent shear viscosity coefficient of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX): A molecular dynamics simulation study,” In Journal of Chemical Physics, Vol. 112, No. 16, pp. 7203--7208. 2000.
DOI: 10.1063/1.481285

ABSTRACT

Equilibrium molecular dynamics methods were used in conjunction with linear response theory and a recently published potential-energysurface [J. Phys. Chem. B 103, 3570 (1999)] to compute the liquid shear viscosity and self-diffusion coefficient of the high explosive HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) over the temperature domain 550–800 K. Predicted values of the shear viscosity range from 0.0055 Pa *s at the highest temperature studied up to 0.45 Pa *s for temperatures near the melting point. The results, which represent the first publication of the shear viscosity of HMX, are found to be described by an Arrhenius rate law over the entire temperature domain studied. The apparent activation energy for the shear viscosity is found to scale with the heat of vaporization in a fashion consistent with those for a wide variety of simple nonmetallic liquids. The self-diffusion coefficient, which requires significantly shorter trajectories than the shear viscosity for accurate calculation, also exhibits an Arrhenius temperature dependence over the simulated temperature domain. This has potentially important implications for predictions of the shear viscosity at temperatures near the melting point.



M. Berzins, L. Durbeck, P.K. Jimack, M. Walkley. “Mesh Quality and Moving and Meshes for 2D and 3D Unstructured Mesh Solvers,” In Von Karman Institute for Fluid Mechanics 31st Lecture Series on Computational Fluid Mechanics, Edited by N.P. Weatherill and H. Deconinck, Von Karman Institute, March, 2000.
ISSN: 0377-8312



M. Berzins. “An Introduction to Mesh Quality,” In Lectures notes for 31st Lecture Series on Computational Fluid Mechanics, Rhode st Genessee, Brussels, Belgium, Edited by N.P. Weatherill and H. Deconink, Von Karman Institute for Fluid Mechanics, pp. 21 pages. March, 2000.
ISSN: 0377-8312