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

2002


M. Walkley, P.K. Jimack, M. Berzins. “Anisotropic Adaptivity for Finite Element Solutions of 3-D Convection-Dominated Problems,” In Int. J. Numer. Meth. Fluids, Vol. 40, No. 3-4, pp. 551--559. 2002.



M. Walkley, M. Berzins. “A finite element model for the two-dimensional extended Boussinesq equations,” In International Journal for Numerical Methods in Fluids, Vol. 39, No. 10, pp. 865--885. 2002.


2001


I. Ahmad, M. Berzins. “MOL Solvers for Hyperbolic PDEs with Source Terms,” In Mathematics and Computers in Simulation, Vol. 56, pp. 1115--1125. 2001.



M. Berzins, A.S. Tomlin, S. Ghorai, I. Ahmad J.Ware. “Unstructured Mesh Adaptive Mesh MOL Solvers for Atmospheric Reacting Flow Problems,” In The Adaptive Method of Lines, Note: invited chapter, Edited by A. Vande Wouwer and Ph. Saucez and W. Schiesser, CRC Press, Boca Raton, Florida, USA., pp. 317--351. 2001.
ISBN: 1-58488-231-X



M. Berzins, L. Durbeck. “Unstructured Mesh Solvers for Hyperbolic PDEs with Source Terms: Error Estimates and Mesh Quality,” In Godunonv Methods: Theory and Applications, Note: Proc. of Godunov Conf. October 18-22, Oxford UK, Edited by E. Toro et al., Kluwer Academic/Plenum, pp. 117--124. 2001.



M. Berzins. “Modified Mass Matrices and Positivity Preservation for Hyperbolic and Parabolic PDEs,” In Communications in Numerical Methods in Engineering, Vol. 17, pp. 659--666. 2001.



C.E. Goodyer, R. Fairlie, M. Berzins, L.E. Scales. “Adaptive Techniques for Elastohydrodynamic Lubrication Solvers,” In Tribology Research: From Model Experiment to Industrial Problem, Proceedings of the 27th Leeds-Lyon Symposium on Tribology, Edited by G. Dalmaz et al., Elsevier, 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



I. Lagzi, A.S. Tomlin, T.Turanyi, L.Haszpra, M.Berzins. “The Simulation of Photochemical Smog Episodes in Hungary and Central Europe Using Adaptive Gridding Models,” In Lecture Notes in Computer Science (LCNS), Computational Science - ICCS 2001, Vol. 2074/2001, Springer Berlin / Heidelberg, pp. 67--76. 2001.
ISBN: 978-3-540-42233-4



M. Walkley, P.K. Jimack, M. Berzins. “Mesh Quality for Three-dimensional Finite Element Solutions on Anisotropic Meshes,” In Proceedings of FEM3D, GUKUTO International Series, Mathematical Sciences and Applications, Vol. 15, pp. 310--321. 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


2000


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.



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



M. Berzins. “Solution-Based Mesh Quality Indicators for Triangular and Tetrahedral Meshes,” In International Journal of Computational Geometry and Applications, Vol. 10, No. 3, pp. 333-346. June, 2000.



M. Berzins. “A New Metric for Dynamic Load Balancing,” In Applied Mathematical Modelling, Vol. 25, Note: Special issue on dynamic load balancing, pp. 141--151. 2000.



M. Berzins. “A Data-Bounded Quadratic Interpolant on Triangles and Tetrahedra,” In SIAM Journal on Scientific Computing, Vol. 22, No. 1, pp. 177--197. 2000.



S. Ghorai, A.S. Tomlin, M. Berzins. “Resolution of pollutant concentrations in the boundary layer using a fully 3-D adaptive gridding technique,” In Atmospheric Environment, Vol. 34, No. 18, pp. 2851-2863. 2000.



C.E. Goodyer, R. Fairlie, M. Berzins, L.E. Scales. “An In-depth Investigation of the Multigrid Approach to Steady and Transient EHL Problems,” In Thinning Films and Tribological InterfacesProceedings of the 26th Leeds-Lyon Symposium on Tribology, Tribology Series, Vol. 38, Edited by D. Dowson, M. Priest, C.M. Taylor, P. Ehret, T.H.C. Childs, G. Dalmaz, A.A. Lubrecht, Y. Berthier, L. Flamand and J.-M. Georges, Elsevier, pp. 95--102. 2000.
ISSN: 0167-8922

ABSTRACT

Multigrid methods have proved robust and highly desirable in terms of the iteration speed in solving elastohydrodynamic lubrication (EHL) problems. Lubrecht, Venner and Ehret, amongst others, have shown that multigrid can be successfully used to obtain converged solutions for steady problems. steady problems.

A detailed study reinforces these results but also shows, in some cases, that while multigrid techniques give initial rapid convergence, the residuals - having dropped to a low level - may reach a stalling point, mainly due to the cavitation region. The study will explain this behaviour in terms of the iterative scheme and show how, if this happens, the errors in the fine grid solution can be reduced further. Example results of both steady and transient EHL problems (including a thermal viscoelastic case) are shown with further developments into adaptive meshes considered.