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Bibliography

References

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\begin{thebibliography}{WIDELABEL}

[Baeck93]
T. Bäck and H.-P. Schwefel. An overview of evolutionary algorithms for parameter optimization. Evolutionary Computation. 1. 1 - 23. 1997.

[Baeck97]
T. Bäck, D.B. Fogel, and Z. Michalewicz. Handbook of evolutionary computation. Oxford: IOP Publishing/Oxford University Press. 1997.

[Bell66]
M. Bell and M.C. Pike. Remark on algorithm 178 direct search. Communications of the Association for Computing Machinery. 9. 684 - 685. 1966.

[Brent72]
P.R. Brent. A new algorithm for minimizing a function of several variables without calculating derivatives. In Algorithms for minimization without derivatives, (Englewood Cliffs, NJ: Prentice-Hall, Inc.). 117 - 167. 1973.

[Burns85]
J.A. Burns, A. Cornish-Bowden, A.K. Groen, R. Heinrich, H. Kacser, J.W. Porteous, S.M. Rapoport, T.A. Rapoport, J.W. Stucki, J.M. Tager, R.J.A Wanders, and H.V. Westerhoff. Control of metabolic systems. Trends Biochem. Sci.. 10. 16. 1985.

[Cao07]
Y. Cao, D. T. Gillespie and L. R. Petzold Adaptive explicit-implicit tau-leaping method with automatic tau selection J. of Chem. Phys. 126, 224101 (2007).

[Corana87]
A. Corana, M. Marchesi, C. Martini, and S. Ridella. Minimizing multimodal functions of continuous variables with the "simulated annealing" algorithm. ACM Trans. Math. Softw.. 13. 262 - 280. 1987.

[Deuflhard96]
P. Deuflhard an J. Heroth. Dynamic dimension reduction in ODE models. In Scientific Computing in Chemical Engineering, (F. Keil et al. Springer). 29-43. 1996.

[Fletcher87]
R. Fletcher. Practical methods of optimization. 2nd Edition. Chichester: John Wiley & Sons. 1987.

[Fogel92]
D.B. Fogel, L.J. Fogel, and J.W. Atmar. Meta-evolutionary programming. 25th Asiloma Conference on Signals, Systems and Computers. IEEE Computer Society, Asilomar . 540 - 545. 1992.

[Gibson00]
M.A. Gibson and J. Bruck. Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels. J. Phys. Chem.. A104(9). 1876-1889. 2000.

[Giersch88]
C. Giersch. Control analysis of metabolic networks. 1. Homogeneous functions and the summation theorems for control coefficients. Eur. J. Biochem. 174. 509 - 513. 1988.

[Gill81]
P.E. Gill, W. Murray, and M.H. Wright. Practical Optimization. London, Academic Press. 1981.

[Gillespie76]
D.T. Gillespie. A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. J. Comp. Phys. 22. 403 - 434. 1976.

[Gillespie01]
D.T. Gillespie. Approximate accelerated stochastic simulation of chemically reacting systems. J. Comp. Phys. 115, 1716 (2001).

[Goldberg89]
D.E. Goldberg. Genetic algorithms in search, optimization and machine learning. Addison-Wesley, Reading, Mass.. 1989.

[Golub96]
G.H. Golub and C.F. van Loan. Matrix computations. Baltimore, 3rd Ed. Johns Hopkins Press. 1996.

[Heinrich74]
R. Heinrich and T.A. Rapoport. A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem.. 42. 89 - 95. 1974.

[Heinrich75]
R. Heinrich and T.A. Rapoport. Mathematical analysis of multienzyme systems. II. Steady-state and transient control. BioSystems. 7. 130 - 136. 1975.

[Hindmarsh83]
A.C. Hindmarsh. ODEPACK, A Systematized Collection of ODE Solvers. Scientific Computing, R. S. Stepleman et al. (eds.), North-Holland, Amsterdam, IMACS Transactions on Scientific Computation. 1. 55 - 64. 1983.

[Hooke61]
R. Hooke and T. A. Jeeves. "Direct search" solution of numerical and statistical problems. Journal of the Association for Computing Machinery. 8. 212 - 229. 1961.

[Kacser73]
H. Kacser and J.A. Burns. The control of flux. Symp. Soc. Exp. Biol.. 27. 65 - 104. 1973.

[Kaupe63]
Kaupe. Algorithm 178 direct search. Communications of the Association of Computing Machinery. 6. 313 - 314. 1963.

[Kennedy95]
J. Kennedy and R. Eberhart. Particle Swarm Optimization. Proceedings of the Fourth IEEE International Conference on Neural Networks, Perth, Australia. 1942 - 1948. 1995.

[Kirkpatrick83]
S. Kirkpatrick, J., C.D. Gelatt, and M. P. Vecchi. Optimization by simulated annealing. Science. 220. 671 - 680. 1983.

[Lam93]
H. Lam. Using CSP to Understand Complex Chemical Kinetics. Combustion Science and Technology. 89. 375 - 404. 1993.

[Levenberg44]
K. Levenberg. A method for the solution of certain nonlinear problems in least squares. Quart. Appl. Math.. 2. 164 - 168. 1944.

[Maier91]
W.L. Maier. A Fast Pseudo Random Number Generator. Dr. Dobb's Journal. May. 152 - 157. 1991.

[Marquardt63]
D.W. Marquardt. An algorithm for least squares estimation of nonlinear parameters. SIAM Journal. 11. 431 - 441. 1963.

[Matsumoto98]
M. Matsumoto and T. Nishimura. Mersenne twister: A 623-dimensionally equidistributed uniform pseudorandom number generator. ACM Trans. on Modeling and Computer Simulations . 8. 3 - 30. 1998.

[Michalewicz94]
Z. Michalewicz. Genetic algorithms + data structures = evolution programs. 3rd Edition. Springer-Verlag, Berlin.. 1994.

[Mitchell95]
M. Mitchell. An Introduction to Genetic Algorithms. MIT Press, Boston. . 1995.

[Nash84]
S. G. Nash. Newton-type minimization via the Lanczos method. SIAM Journal of Numerical Analysis. 21. 770 - 788. 1984.

[Nelder65]
J. A. Nelder and R. Mead. A simplex method for function minimization. Computer Journal. 7. 308 - 313. 1965.

[Petzold83]
L. Petzold. Automatic selection of methods for solving stiff and nonstiff systems of ordinary differential equations. SIAM J. Sci. Stat. Comput.. 4. 136 - 148. 1983.

[Powel64]
M.J.D. Powell. An efficient method for finding the minimum of a function of several variables without calculating derivatives. Comput. J.. 7. 155 - 162. 1964.

[Reder88]
C. Reder. Metabolic control theory: a structural approach. J. Theor. Biol.. 135. 175 - 201. 1988.

[Runarsson00]
T. Runarsson and X. Yao. Stochastic ranking for constrained evolutionary optimization. EEE Transactions on Evolutionary Computation. 4. 284 - 294. 2000.

[Surovtsova09]
I. Surovtsova, N. Simus, Th. Lorenz, A. König, S. Sahle and U. Kummer. Accessible Methods for the Dynamic Time-scale Decomposition of Biochemical Systems. Accepted for Bioinformatics. 2009.

[Swann72]
W.H. Swann. Direct search methods. Numerical methods for unconstrained optimization., W. Murray, ed. (London & New York: Academic Press). 13 - 28. 1972.

[Vallabhajosyula06]
R. R. Vallabhajosyula, V. Chickarmane, and H. M. Sauro. Conservation analysis of large biochemical networks. Bioinformatics. 22(3). 346 - 353. 2006.

[Westerhoff84]
H.V. Westerhoff and Y.-D. Chen. How do enzyme activities control species concentrations? An additional theorem in the theory of metabolic control. Eur. J. Biochem.. 142. 425 - 430. 1984.

[Wolf85]
A. Wolf, J. B. Swift, H. Swinney, and J. A. Vastano. Determining Lyapunov exponents from a time series. Physica. 16D. 285 - 317. 1985.

[Zobeley05]
J. Zobeley et al. A new time-dependent complexity reduction method for biochemical systems. In Transactions on Computational Systems (C. Prami et al., Springer). 90-110. 2005.

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