Skip to main content

Abstract

Computer simulation is a quickly expanding discipline that is entering fields as diverse as astrophysics, polymer physics, chemical physics, and even molecular biology and biochemistry. Our own field is theoretical biophysics where we collaborate with a number of experimental biological groups. Although standard algorithms have emerged since the 1960s, and have been implemented in a number of freely available or commercial simulation packages, there is a constant need for new developments that open up new areas of research. Here, two approaches are described where standard simulation methodology is being expanded to treat diffusional dynamics of multi-protein systems and to treat proton transport in macromolecules.

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 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. D.J. Bicout and M.J. Field, J. Phys. Chem. 100 (1996) 2489.

    Article  Google Scholar 

  2. D.L. Ermak and J.A. McGammon, J. Chem. Phys. 69 (1978) 1352.

    Article  ADS  Google Scholar 

  3. E. Dickinson, S.A. Allison and J.A. McCarnmon, J. Chem. Soc. Farad. Trans. 2 81 (1985) 591.

    Article  Google Scholar 

  4. P. Mazur and W. van Saarloos, Physica 115A (1982) 21.

    MathSciNet  ADS  Google Scholar 

  5. S.H. Northrup, in Cytochrome C: A Multi disciplinary Approach; (University Science Books, 1996) pp. 543.

    Google Scholar 

  6. R. G. Schmidt and J. Brickmann, Ber. Bunsenges. Phys. Chem. 101 (1997) 1816.

    Article  Google Scholar 

  7. R. Vuilleumier and D. Borgis, Chem. Phys. Lett. 284 (1998) 71.

    Article  ADS  Google Scholar 

  8. U. W. Schmitt and G. A. Voth, J. Phys. Chem. B102 (1998) 5547.

    Google Scholar 

  9. U. W. Schmitt and G. A. Voth, J. Chem. Phys. 111 (1999) 9361.

    Article  ADS  Google Scholar 

  10. D. Marx, M. E. Tuckerman, J. Hutter, and M. Parrinello, Nature 397 (1999) 601.

    Article  ADS  Google Scholar 

  11. M. E. Tuckerman, D. Marx, M. L. Klein, and M. Parrinello, Science 275 (1997) 817.

    Article  Google Scholar 

  12. M.A. Lill and V. Helms, J. Chem. Phys. 114 (2001) 1125.

    Article  ADS  Google Scholar 

  13. M.A. Lill, M.C. Hutter and V. Helms, J. Phys. Chem. A104 (2000) 8283.

    Article  Google Scholar 

  14. M.A. Lill and V. Helms, J. Chem. Phys. 114 (2001) 7985.

    Article  ADS  Google Scholar 

  15. M.A. Lill and V. Helms, J. Chem. Phys. 114 (2001) 7993.

    Article  ADS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer Science+Business Media New York

About this chapter

Cite this chapter

Helms, V., Gorba, C., Lill, M. (2003). Computer Simulation Meets Molecular Biology. In: Macias, A., Uribe, F., Diaz, E. (eds) Developments in Mathematical and Experimental Physics. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-0207-4_9

Download citation

  • DOI: https://doi.org/10.1007/978-1-4615-0207-4_9

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-4965-5

  • Online ISBN: 978-1-4615-0207-4

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics