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


C.E. Goodyer, R. Fairlie, M. Berzins, L.E. Scales. “Adaptive Mesh Methods for Elastohydrodynamic Lubrication,” In ECCOMAS CFD 2001: Computational Fluid Dynamics Conference Proceedings, Institute of Mathematics and its Applications, 2001.
ISBN: 0-905-091-12-4



C.E. Goodyer. “Adaptive Numerical Methods for Elastohydrodynamic Lubrication,” Note: Advisor: Martin Berzins, School of Computing, University of Leeds, May, 2001.

ABSTRACT

Numerical solutions to elastohydrodynamic lubrication problems have been computed
for the last half century. Over the past decade multilevel techniques have been successfully
applied in several solvers and significant speed-ups achieved. The aim of numerical
research in this field is to develop techniques in order to calculate accurate solutions to
demanding industrial problems as efficiently as possible.

In this work the numerical solver, previously developed by Nurgat, is examined. Despite
being successful in achieving converged results on a single grid, there were some
unresolved issues relating to the multigrid performance. These problems are explained
and the necessary modifications to the method used are detailed.

There is much current interest in obtaining results to transient elastohydrodynamic
lubrication problems. These are examined in detail and the justification for the methods
used are discussed. Example results for industrially relevant cases, such as variation of
lubricant entrainment, oscillation of the applied load and the presence of surface defects
are considered.

In many other fields, adaptation in both space and time is used to increase performance
and accuracy. However, these techniques are not currently used for elastohydrodynamic
lubrication problems. It is shown that they can be successfully applied and substantial
benefits accrued.

A method of variable timestepping has been introduced and results are presented
showing that not only is it as accurate as fixed time stepping methods, but that the computational
work required to obtain these solutions is significantly reduced. Local error
control on each individual timestep is also implemented.

Adaptation of the spatial mesh is also developed. By developing a hierarchy of refined
meshes within the multigrid structure it is seen how significantly fewer computational
points are used in the most expensive numerical calculations. This, in turn, means that
the computational time required is reduced. Different criteria for adaptation are explained
and results presented showing the relative levels of accuracy and speed-up achieved.



A. Gothandaraman, R.T. Whitaker, J. Gregor. “Total Variation For The Removal of Blocking Effects in DCT based Encoding,” In IEEE International Conference on Image Processing, pp. 455--458. October, 2001.



C. Guerra, V. Pascucci. “Finding Line Segments with Tabu Search,” In IEICE Transactions on Information & Systems, Vol. E84-D, No. 12, pp. 1739-1744. December, 2001.



S. Gumhold, X. Wang, R.S. MacLeod. “Feature Extraction from Point Clouds,” In Proceedings, 10th International Meshing Round Table, Sandia National Laboratories, pp. 293--305. 2001.



G. Higgins, B. Athey, J. Bassingthwaighte, J. Burgess, H. Champion, K. Cleary, P. Dev, J. Duncan, M. Hopmeier, D. Jenkins, C.R. Johnson, H. Kelly, R. Leitch, W. Lorensen, D. Metaxas, V. Spitzer, N. Vaidehi, K. Vosburgh, R. Winslow. “Modeling and Simulation in Medicine: Towards an Integrated Framework,” In Computer Aided Surgery, Vol. 6, No. 1, Note: Final report of the meeting of the same title held July 20-21, 2000, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA., 2001.
DOI: 10.1002/igs.1008



M. Ikits, J.D. Brederson, C.D. Hansen, J.M. Hollerbach. “An Improved Calibration Framework for Electromagnetic Tracking Devices,” In Proceedings of IEEE Virtual Reality Conference 2001, Yokohama, Japan, pp. 63--70. Mar, 2001.



M. Ikits, J.D. Brederson, C.D. Hansen, J.M. Hollerbach. “Calibration of 6DOF Electromagnetic Tracking Devices,” In IEEE VR2001, Japan, pp. 63--70. 2001.



C.R. Johnson, D. Brederson, C.D. Hansen, M. Ikits, G. Kindlmann, Y. Livnat, S.G. Parker, D.M. Weinstein, R.T. Whitaker. “Computational Field Visualization,” In Computer Graphics, Vol. 35, No. 4, pp. 5--9. 2001.



C.R. Johnson, Y. Livnat, L. Zhukov, D. Hart, G. Kindlmann. “Computational Field Visualization,” In Mathematics Unlimited -- 2001 and Beyond, Vol. 2, Edited by B. Engquist and W. Schmid, Springer-Verlag, pp. 605--630. 2001.



C.R. Johnson, M. Mohr, U. Ruede, A. Samsonov, K. Zyp. “Multilevel Methods for Inverse Bioelelectric Field Problems,” In Lecture Notes in Computational Science and Engineering - Multiscale and Multiresolution Methods: Theory and Applications, Vol. 20, Edited by T.J. Barth and T.F. Chan and R. Haimes, Springer-Verlag Publishing, Heidelberg pp. 331--346. October, 2001.



C.R. Johnson. “Adaptive Finite Element and Local Regularization Methods for the Inverse ECG Problem,” In Inverse Problems in Electrocardiology, Advances in Computational Biomedicine, Vol. 5, Edited by Peter Johnston, WIT Press, pp. 51--88. 2001.



C.R. Johnson. “Computational Bioimaging for Medical Diagnosis and Treatment,” In Communications of the ACM, Vol. 44, No. 3, pp. 74--76. March, 2001.



S. Joshi, S. Pizer, P.T. Fletcher, A. Thall, G. Tracton. “Multi-scale 3-D Deformable Model Segmentation Based on Medial Description,” In Information Processing in Medical Imaging (IPMI), Edited by MF Insana and RM Leahy, pp. 64--77. June, 2001.



R.M. Kirby, G.E. Karniadakis, O. Mikulchenko, K. Mayaram. “Integrated Simulation for MEMS: Coupling Flow-Structure-Thermal-Electrical Domains,” In The MEMS Handbook, Edited by M. Gad-el-Hak, Informa UK Limited, 2001.



R.M. Kirby, G.E. Karniadakis. “Under-Resolution and Diagnostics in Spectral Simulations of Complex-Geometry Flows,” In Turbulent Flow Computation, Edited by D. Drikakis and B. Geurts, Springer, pp. 1--42. 2001.



R.M. Kirby, G.E. Karniadakis, O. Mikulchenko, K. Mayaram. “An Integrated Simulator for Coupled Domain Problems in MEMS,” In Journal of Microelectromechanical Systems, Vol. 10, No. 3, pp. 379--399. 2001.



J.M. Kniss, G. Kindlmann, C.D. Hansen. “Interactive Volume Rendering Using Multi-Dimensional Transfer Functions and Direct Manipulation Widgets,” In Proceeding of IEEE Visualization 2001, pp. 255--262. October, 2001.



J.M. Kniss, P. McCormick, A. McPherson, J. Ahrens, J. Painter, A. Keahey, C.D. Hansen. “Interactive Texture-based Volume Rendering for Large Datasets,” In IEEE Comp. Graph. & Applic., Vol. 21, No. 4, pp. 52--61. July/August, 2001.



J.M. Kniss, P. McCormick, A. McPherson, J. Ahrens, J. Painter, A. Keahey, C.D. Hansen. “T-Rex, Texture-based Volume Rendering for Extremely Large Datasets,” In IEEE Comp. Graph. & Applic., Vol. 21, No. 4, pp. 52--61. 2001.