Bibliography

Technical Documentation

[Hucka et al 2008] Michael Hucka, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Sven Sahle, and Darren Wilkinson. . December, 2008. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions .

[Finney and Hucka 2003] Andrew Finney and Michael Hucka. Systems Biology Workbench Development Group. June, 2003. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions .

[GNU Coding Standards] Richard Stallman. Copyright © 1992-2004 Free Software Foundation, Inc.. GNU Coding Standards .

Books

[Angel 1997] Edward Angel. First edition. 0-201-85571-2. 1997. Addison--Wesley. Interactive Computer Graphics . A Top-Down Approach with OpenGL™ .

[Burger and Gillies 1989] Peter Burger and Duncan Gillies. First edition. 0-201-17439-1. 1989. Addison--Wesley Publishing Company. Interactive Computer Graphics . Functional, Procedural and Device-Level Methods .

[Foley et al. 1996] James D. Foley, Andries van Dam, Steven K. Feiner, and John F. Hughes. Second edition. 81-7808-038-9. 1996. Addison--Wesley Longman. Computer Graphics . Principles and Practice .

[Gardiner 1989] Crispin W. Gardiner. Copyright © 1989 Springer-Verlag. Second edition. 0-540-61634-9. Springer. Handbook of Stochastic Methods . For Physics, Chemistry and the Natural Sciences .

[Hartman and Wernecke 1996] Jed Hartman and Josie Wernecke. First edition. 0-201-47944-3. 1996. Addison--Wesley Publishing Company. The VRML 2.0 Handbook . Building Moving Worlds on the Web .

[Physics Handbook] Carl Nordling and Jonny Österman. Copyright © 1996 Carl Nordling and Jonny Österman. 91-44-16575-7. Studentlitteratur. Physics Handbook for Science and Engineering .

[Stroustrup 1997] Bjarne Stroustrup. Copyright © 1997 AT&T. Second edition. 0-201-88954-4. Addison Wesley. The C++ Programming Language . A Top-Down Approach with OpenGL™ .

Papers

[Baras and Malek Mansour 1997] F. Baras and M. Malek Mansour. Microscopic simulations of chemical instabilities . Advances in Chemical Physics ”. 393-474. Copyright © 1997 John Wiley & Sons, Inc.. I. Prigogine. Stuart A. Rice. 0-471-17458-0. 1997. 100.

[Elf et al. 2003] Johan Elf, Andreas Dončić, and Måns Ehrenberg. Mesoscopic reaction-diffusion in intracellular signaling . Proceedings of SPIE ”. 114-124. 2003. 5110.

[Elf and Ehrenberg 2004] Johan Elf and Måns Ehrenberg. Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases . IEE Systems Biology ”. 230-236. 2004. 2.

[Hattne et al. 2005] Johan Hattne, David Fange, and Johan Elf. Stochastic reaction-diffusion simulation with MesoRD . Bioinfomatics ”. 2923-2924. 2005. 21.

[Baras and Mansour 1997] F Baras and M.M. Mansour. Microscopic simulation of chemical instabilities . Advances in Chemical Physics ”. 393-475. 1997. 100.

[Gardiner et al. 1976] CWF Gardiner, KJ Mc Neil, DF Walls, and IS Matheson. Correlations in stochastic theories of Chemical Reactions . J Stat Phys ”. 307-331. 1976. 14.

[Kuramoto 1974] Y Kuramoto. Effects of Diffusion on the Fluctuations in Open Systems . Prog. Theor. Phys. ”. 711-713. 1974. 52.

[Smoluchowski, 1917] Marian Smoluchowski. . April, 1917. Versuch eine mathematischen theorie der koagulationskinetik kolloidaler losungen . Zeitschrift für physikalische Chemie ”. 129–168. 1917. 92.

[Fange et al. 2010] David Fange, Otto Berg, Sjoberg Paul, and Johan Elf. . Stochastic reaction-diffusion kinetics in the microscopic limit . Proc Natl Acad Sci USA ”. 19820–19825. September 2010. 107.

[Collins & Kimball 1949] Frank C. Collins and George E. Kimball. . 1949. Diffusion-controlled reaction rates . Journal of Colloid Science ”. 425-437. 1949. 4.

[Berg 1978] Otto G. Berg. . March 1949. On diffusion-controlled dissociation . Chemical Physics ”. 47-57. 1978. 31.