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

1996


P. Pratt, M. Berzins. “Shock preserving quadratic interpolation for visualization on triangular meshes,” In Computers & Graphics, Vol. 20, No. 5, pp. 723--730. 1996.
DOI: 10.1016/S0097-8493(96)00046-5

ABSTRACT

A new interpolation method for visualizing shock-type solutions on triangular meshes is presented. The method combines standard linear and quadratic interpolants in such a way as to avoid supurious numerical values. The effectiveness of the method is demonstrated on test problems.



G.J. Ryder, M. Berzins, T.H.C. Childs. “Modelling Simple Feature Creation in Selective Laser Sintering,” In Proc 7th Symposium on Solid Free Form Fabrication, University of Texas at Austin, Edited by J.W. Barlow et al., pp. 567--574. 1996.



P.A. Sleigh, M. Berzins, P.H. Gaskell. “A Reliable and Accurate Technique for the Modelling of Complex Hydraulic Flows,” In Proceedings of the First International Symposium on Finite Volumes for Complex Applications, Hermes, Paris, pp. 635--642. 1996.
ISBN: 2-86601-556-8



J.D.B. Smith, A.S. Tomlin, M. Berzins, V. Pennington, M.J. Pilling. “Modelling the effects of Concentrated Emissions Sources on Tropospheric Ozone,” In Proceedings of the 3rd Workshop on Modelling of Chemical Reaction Systems, Heidelberg, Germany, Published on CD-ROM, July, 1996.
ISBN: 3-932217-00-4

ABSTRACT

Numerical models that describe the chemical processes occurring in the troposphere, in the main, are still using fixed or telescopic grids to provide greater detail where it is required, such as near large emissions sources. While the use of adaptive grids has become well accepted in the fields of aeronautical and mechanical engineering, the adoption of adaptive gridding techniques in atmospheric modelling has been somewhat slower. Tomlin et al [1] recently demonstrated the use of time-dependent adaptive mesh gridding techniques applied to the investigation of a single power station plume, with regards to regional ozone levels. The results of that paper highlighted the differences in the total and peak concentrations of ozone arising from using fixed grids, as opposed to using adaptive grids.

Ozone concentrations in the atmospheric boundary layer, the bottom kilometre of the troposphere, are dependent on the interactions of nitrogen oxides and the volatile organic compounds (VOCs) that are emitted from both anthropogenic and biogenic sources. There are many more chemical species involved in the processes of the atmospheric boundary layer than in the stratosphere. This makes the use of detailed chemical mechanisms with fine mesh resolution difficult in two space dimensions, and prohibitively expensive for three space dimensions.

This paper investigates the effects of multiple point sources interacting with the more diffuse area sources arising from urban emissions, and will show the differences arising from the use of adaptive gridding techniques rather than fixed grids. The numerical code, SPRINT2D, provides spatial and temporal error controls for limiting the adaptation of the grid for a length scale ranging from a few hundred metres to a few hundred kilometres.

Comparisons will also be made between a systematically reduced mechanism, CBMLeeds[2], and the Generic Reaction Set (GRS) of Azzi et al [3] to see the advantages of the two approaches. CBMLeeds originates from the CBM-Ex scheme of Gery et al [4], which uses lumped organic species, as opposed to the heavily parameterised organic chemistry of the GRS.


1995


M. Berzins, J.M. Ware. “Positive Cell Centered Finite Volume Discretisation Methods for Hyperbolic Equations on Irregular Meshes,” In Applied Numerical Mathematics, Vol. 16, pp. 417--438. 1995.

ABSTRACT

The conditions sufficient to ensure positivity and linearity preservation for a cell-centered finite volume schemefor time-dependent hyperbolic equations using irregular one-dimensional and triangular two-dimensional meshes arederived. The conditions require standard flux limiters to be modified and also involve possible constraints on themeshes. The accuracy of this finite volume scheme is considered and is illustrated by two simple numerical examples.



M. Berzins, P. Gaskell, A. Sleigh, A.S. Tomlin, J. Ware. “An adaptive CFD solver for time-dependent environmental flow problems,” In Proceedings of the Institute of Computational Fluid Dynamics Conference, Edited by K.W. Morton, M.J. Baines, Oxford University Press, pp. 311-317. 1995.



M. Berzins, T.H.C. Childs, K.W. Dalgarno, G.R. Ryder, G. Stein. “Densification and Distortion in Selective Laser Sintering of Polycarbonate,” In Proc 6th Symposium on Solid Free Form Fabrication, University of Texas at Austin, Edited by J.W. Barlow et al., pp. 196--203. 1995.



M. Berzins. “Temporal Error Control in the Method of Lines for Convection Dominated Equations,” In SIAM Journal on Scientific Computing, Vol. 16, pp. 558--580. 1995.



D.C. Hodgson, P.K. Jimack, P. Selwood, M. Berzins. “Scalable, Parallel Generation of Partitioned Unstructured Meshes,” In Parallel C.F.D. -- Implementations and Results using Parallel Computers, Parallel CFD Conference 1995, pasadena, California, Edited by A. Ecer and J. Periaux and N. Satufoka and S. Taylor, pp. 665-672. June, 1995.
ISBN: 0-444 823220



P.A. Sleigh, P.H. Gaskell, M. Berzins, J.M. Ware, N.G. Wright. “A Reliable and Accurate Technique for the Modelling of Practically Occurring Open Channel Flow,” In Proceedings of the Ninth International Conference on Numerical Methods in Laminar and Turbulent Flow, Pineridge Press, pp. 881--892. 1995.



W. Speares, M. Berzins. “A Fast 3-D Unstructured Mesh Adaptation Algorithm with Time-Dependent Upwind Euler Shock Diffraction Calculations,” In Proc. of 6th International Symposium on Computational Fluid Dynamics, Vol. 3, Edited by M. Hafez and K. Oshima, pp. 1181--1188. 1995.



W. Speares, M. Berzins. “A 3D Unstructured Mesh Adaption Algorithm for Time Dependent Shock Dominated Problems,” School of Computer Studies Research Report, No. 95.33, University of Leeds, 1995.



A. Tomlin, J.M. Ware, J. Smith, M. Berzins, M.J. Pilling. “Efficient High Resolution Methods for Air Pollution Models,” In International Conference on Air Pollution - Proceedings, Vol. 1, Computational Mechanics Inc, pp. 201--208. 1995.



C. Walshaw, M. Berzins. “Dynamic Load-Balancing For PDE Solvers On Adaptive Unstructured Meshes,” In Concurrency, Vol. 7, No. 1, pp. 17--28. 1995.



C. Walshaw, M. Berzins. “Adaptive Time-dependent CFD on Distributed Unstructured Meshes,” In Parallel Computational Fluid Dynamics: New Trends and Advances, Elsevier Science, pp. 191--198. 1995.



J.M. Ware, M. Berzins. “Adaptive Finite Volume Methods for Time-dependent P.D.E.s.,” In Modeling, Mesh Generation and Adaptive Numerical Methods for PDEs., IMA Volumes in Mathematics and Its Applications Series, Vol. 75, Springer Verlag, pp. 417--430. 1995.


1994


M. Berzins, J.M. Ware. “Reliable Finite Volume Methods for the Navier Stokes Equations.,” In Numerical methods for the Navier-Stokes equations, Notes on Numerical Fluid Mechanics, No. 47, Edited by F.K. Hebeker and R. Rannacher and G. Wittum, Springer, pp. 1-8. 1994.
DOI: 10.1007/978-3-663-14007-8_1



S.V. Pennington, M. Berzins. “New NAG Library Software for First-Order Partial Differential Equations,” In ACM Transactions on Mathematical Software, Vol. 20, No. 1, pp. 63--99. March, 1994.


1993


M. Berzins, J.M. Ware. “Reliable Finite Volume Methods for Time-Dependent Partial Differential Equations,” In MAFELAP 1993 Highlights, Edited by J.R. Whiteman and John Wiley, pp. 299--306. 1993.



J. Parker, M. Berzins, J.M. Cameron, K.A. Collins, C.M. Sawyer. “Final Report on SERC/DTI Parallel Applications Programme Collaboration Between EPCC, Rolls Royce ands Leeds University,” Edinburgh Parallel Computing Centre, September, 1993.