Professor Kevin Burrage

Email: kb@maths.uq.edu.au
Phone: +61 07 3365 3487
Fax: + 61 7 3365 6136

Professional and Social Background

Kevin Burrage is a Federation Fellow (2003-2008). He is married to Pamela and they have two children: Matthew and Lauren.
The photos are out of date now but I like them and I do not look so old as I do in real life!

Kevin has joint positions in Mathematics, ITEE and the Institute for Molecular Biosicence.
He is Professor of Computational Mathematics at the University of Queensland and Co-Director of the Advanced Computational Modelling Centre

Areas of Interest

Multi-scale modelling, scientific parallel and grid computing, mathematical software, modelling in the biological sciences, numerical solution of differential equations (deterministic and stochastic), linear systems of equations, computational biology, engineering applications.

Links to collaborative research partners

Advanced Computational Modelling Centre
Centre of Magnetic Resonance
Institute for Molecular Bioscience
Queensland Department of Primary Industries
ARC Centre for Complex Systems
ARC Centre in Bioinformatics
Queensland Brain Institute

Stochastic Simulation Software

1. Discrete Modelling for Chemical Kinetics:
The Stochastic Simulation Algorithm (Gillespie) is a very powerful algorithm for the evolution of stochastic chemical kinetics. We have applied it to an interesting Genetic Regulatory Network using Matlab. We use an efficient sorting algorithm to speed up the perfomance of the SSA when choosing what reaction number should take place. This software is due to Margherita Carletti (Urbino) and Kevin Burrage. The software consists of two files main.m and ssa.m. The user just has to type main in the MATLAB command line.

main.m
ssa.m

Federation research

My work under the Federation Fellowship (2003-2007) involves four aspects:

development of mathematical models for understanding genetic regulation;
development of multi-scaled stochastic algorithms - extending the fundamental work of Gillespie and the stochastic simulation algorithm;
implementation in a parallel and grid environment of these algorithms;
three dimensional visualisation of cellular processes.

Here is some recent work that we have done on multi-scaled stochastic simulation for biological systems :

T.Tian and K. Burrage (2004), Bistability and switching in the Lysis/Lysogeny Genetic Regulatory Network of Bacteriophage lambda, Journal of Theoretical Biology, 227, 229-237.
K. Burrage and T.Tian (2003), Poisson Runge-Kutta methods for Chemical Reaction Systems, to appear in the Proceedings of the Hong Kong Conference on Scientific Computing, (2003).
K. Burrage, P. Burrage, S.Jeffrey, T. Pickett, R. Sidje and T. Tian (2003), A grid implementation of chemical kinetic simulation methods in genetic regulation, the Proceedings of the APAC03 Conference on Advanced Computing, Grid Applications and eResearch, ISBN 0-9579303-1-3.
K. Burrage, T.Tian and P. Burrage (2004), A multi-scaled approach for simulating Chemical Reaction Systems, Progress in Biophysics and Molecular Biology, 85, 217-234.
T.Tian and K. Burrage (2003), Stochastic Neural Network Models for Gene Regulatory Networks, Proceedings of the 2003 IEEE Congress on Evolutionary Computation.
K. Burrage, P.M. Burrage and T.Tian (2004), Numerical methods for strong solutions of SDES, Proceeding of the Royal Society London , vol. 460, no. 2041, 373-402.
T. E. Turner, S. Schnell and K. Burrage (2004), Stochastic approaches for modelling in vivo reactions, Computational Biology and Chemistry
K. Burrage and T. Tian (2004), Effective simulation techniques for Biological Systems, Proceedings of SPIE, Fluctuation and Noise in Biological, Biophysical and Biomdeical systems, Vol. 5467, 311-325.
M. Carletti, K. Burage and P. M. Burrage (2004), Numerical simulation of SDEs in biomathematical modelling, Mathematics and Computers in Simulation, vol. 64, 271-277
D. V. Nicolau Jr, F. Clark, J. Hancock and K. Burrage (2004), Lipid raft modulation of mebrane spatial phenomena, Poster at the ISMB2004 Conference, Glasgow.
P. M. Burrage, R. Herdiana, K. Burrage (2004), Adaptive stepsize based on control theory for SDEs, J. Comp. and App. Math., 170, 317-336.
T. Tian and K. Burrage (2004), Binomial leap methods for simulating stochastic chemical kinetics, submitted to J. Chem. Phys.
K. Burrage, P. M. Burrage, N. Hamilton and T. Tian (2004), Compute-intensive simulations for cellular models, to appear in Bioinformatics (book chapter).
K. Burrage, I. Lenane and G. Lythe (2005), Numerical methods for second order stochastic equations, preprint.
D. Nicolau jr, K. Burrage, R. G. Parton and J. Hancock (2005), Optimal microdomain characteristics for nano-scal protein-protein interactions, preprint.

Positions and scholarships

I have funds for PhD scholarships, Hons scholarships and postdoctoral positions in the broad areas of computational biology, modelling, simulation and visualisation - please contact me.

Stochastic Notes

Talks (pdf)

Research

Undergraduate study

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