Skip to main content

Abstract

When we talk about biological organisms as systems we refer to the enormous number of mutually reinforcing, competing and counter acting feedback mechanisms that regulate the biological processes in space and time. We cannot hope to capture all aspects of such a highly integrated system in any model. The first and most important step in the biological modeling process must, therefore, be to establish a clear picture of the purpose of the project.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Althaus CL, De Boer RJ (2008) Dynamics of immune escape during hiv/siv infection. PLoS Comput Biol 4:e1000103

    Article  PubMed  Google Scholar 

  2. Anderson RM, May RM (1988) Epidemiological parameters of HIV transmission. Nature 333:514–519

    Article  PubMed  CAS  Google Scholar 

  3. Anderson RM, May RM (1989) Complex dynamical behaviour in the interaction between HIV and the immune system. In: Goldbeter A (ed) Cell to Cell Signalling, From Experiements to Theoretical Models. Academic Press, New York

    Google Scholar 

  4. Arber W (1965) Host-controlled modification of bacteriophage. Annual Review of Microbiology 19:365–377

    Article  PubMed  CAS  Google Scholar 

  5. Berg HC, Purcell EM (1977) Physics of chemoreception, Biophysics Journal 20:193–219

    Article  CAS  Google Scholar 

  6. Berger EA, Murphy PM, Farber JM (1999) Chemokine receptors as HIV1coreceptors: roles in viral entry, tropism, and disease. Annual Review of Immunology 17:657–700

    Article  PubMed  CAS  Google Scholar 

  7. Bull AT, Slater JH (1982) Microbial Interactions and Communities. Academic Press, New York

    Google Scholar 

  8. Burke DS (1992) Human HIV vaccine trials: Does antibody dependent enhancement pose a genuine risk? Perspectives of Biological Medicine 35:511–530

    CAS  Google Scholar 

  9. Chrandrasekhar S (1943) Stochastic problems in physics and astronomy, Review of Modern Physics 15:1–89

    Article  Google Scholar 

  10. De Boer RJ (2007) Understanding the failure of cd8+ t-cell vaccination against simian/human immunodeficiency virus. J Virol 81:2838–2848

    Article  PubMed  Google Scholar 

  11. Fabiato A, Fabiato F (1977) Calcium release from the sarcoplasmic reticulum. Circulation Research 40:119–129

    Article  PubMed  CAS  Google Scholar 

  12. Forrester JW (1961) Industrial Dynamics. MIT Press, Massachusetts Institute of Technology

    Google Scholar 

  13. Franklin G, Powell JD, Emami-Naeini A (1996) Feedback Control of Dynamic Systems (4th edition). Prentice Hall, New Jersey

    Google Scholar 

  14. Hansen JE (1992) Carbohydrates of human immunodeficiency virus. APMIS (suppl. 27) 100:96–109

    Google Scholar 

  15. Hansen JE, Lund O, Tolstrup N, Gooley AA, Williams KL, Brunak S (1998) NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconj J 15:115–130

    Article  PubMed  CAS  Google Scholar 

  16. Huetter G, Nowak D, Mossner M, Ganepola S, Mussig A, Allers K, Schneider T, Hofmann J, Kuecherer C, Blau O, Blau IW, Hofmann WK, Thiel E (2009) Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation, New England Journal of Medicine 360:692–698

    Article  CAS  Google Scholar 

  17. Iglesias PA, Ingalls BP (1996) Control Theory and Systems Biology. CRC Press, New York

    Google Scholar 

  18. Iwami S, Nakaoka S, Takeuchi Y (2008) Viral diversity limits immune diversity in asymptomatic phase of hiv infection. Theor Popul Biol 73:332–341

    Article  PubMed  Google Scholar 

  19. Janeway Jr CA, Travers P, Walport M, Shlomchik MJ (2001) Immunobiology - The Immune System in Health and Disease. Garland Science, New York

    Google Scholar 

  20. Levine WS (1996) The Control Handbook. CRC Press, New York

    Google Scholar 

  21. Lund O, Hansen J, Mosekilde E, Nielsen JO, Hansen J-E S (1993) A model of enhancement and inhibition of HIV infection of monocytes by antibodies against HIV, Journal of Biological Physics 19:133–145

    Article  CAS  Google Scholar 

  22. Lund O, Hansen J, Sørensen AM, Mosekilde E, Nielsen JO, Hansen J-E S (1995) Increased adhesion as a mechanism of antibody-dependent and anti-body independent complement mediated enhancement of human immunodeficiency virus infection, Journal of Virology 69:2393–2400

    PubMed  CAS  Google Scholar 

  23. Lund O, Lund OS, Gram G, Nielsen SD, Schønning K, Nielsen JO, Hansen J-E S, Mosekilde E (1997) Gene therapy of T-helper cells in HIV infection: Mathematical model of the criteria for clinical effect, Bulletin of Mathematical Biology 59:725–745

    Article  PubMed  CAS  Google Scholar 

  24. Mayer G (2010) Microbiology and Immunology Online. School of Medicine, University of SouthCarolina, http://pathmicro.med.sc.edu/mayer/phage.htm

  25. Nielsen MH, Pedersen FS, Kjems J (2005) Molecular Strategies to inhibit HIV-1 replication, Retrovirus 2:10

    Article  Google Scholar 

  26. Nowak MA, Anderson RM, McLean AR, Wolfs TFW, Goudsmit J, May RM (1991) Antigenic diversity threshold and the development of AIDS. Science 254:963–969

    Article  PubMed  CAS  Google Scholar 

  27. Perelson AS, Essunger P, Cao Y, Vesanen M, Hurley A, Saksela K, Markowitz M, Ho DD (1997) Decay characteristics of HIV-1-infected compartments during combination therapy. Nature 6629:188–191

    Article  Google Scholar 

  28. Queinnec I, Tarbouriech S, Garcia G, Niculescu S-I (2007) Biology and Control Theory: Current Challenges. Lecture Notes in Control and Information Sciences 357

    Google Scholar 

  29. Sompayrac LM (2003) How the Immune System Works. Blackwell Publishers, Massachusetts

    Google Scholar 

  30. Storad CJ (1998) Inside AIDS: HIV Attacks the Immune System. Lerner Publications Co. Minneapolis

    Google Scholar 

  31. Takeda A, Robinson JE, Ho DD, Debouck C, Haighwood NL, Ennis FA (1992) Distinction of human immunodefieiency virus type 1 neutralization and infection enhancement by human monoclonal antibodies to glycoprotein 120, J Clin Invest 89:1952–1957

    Article  PubMed  CAS  Google Scholar 

  32. Zucchi R, Ronca-Testoni S (1997) The sarcoplasmic reticulum Ca2 + channel/ryanodine receptor: Modulation by endogenous effects, drugs and disease states, Pharmacological Reviews 49:1–51

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ole Lund .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag/Wien

About this chapter

Cite this chapter

Lund, O., Laugesen, J.L., Mosekilde, E. (2011). Concepts in Mechanism Based Modeling. In: Mosekilde, E., Sosnovtseva, O., Rostami-Hodjegan, A. (eds) Biosimulation in Biomedical Research, Health Care and Drug Development. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0418-7_2

Download citation

Publish with us

Policies and ethics