Transactions on Computational Systems Biology XI pp 164-186

Part of the Lecture Notes in Computer Science book series (LNCS, volume 5750) | Cite as

A Projective Brane Calculus with Activate, Bud and Mate as Primitive Actions

  • Maria Pamela C. David
  • Johnrob Y. Bantang
  • Eduardo R. Mendoza

Abstract

We modify and extend Cardelli’s Brane Calculus and Danos and Pradalier’s Projective Brane Calculus (PBC) to improve consistency with biological characteristics of membrane reactions. We propose a Projective Activate-Bud-Mate (PABM) calculus as an alternative to the Phago-Exo-Pino (PEP) basic calculus of L. Cardelli. PABM uses a generalized formalism for Action activation with receptor-ligand type channel construction that incorporates multiple association and affinity similar to Priami’s beta binders. Calculus elements are finite. Volumes are associated with systems for more realistic compartment-based reaction probabilities. PABM also uses Brane domains that partition membranes into controllable, independent groupings of projective actions. Domains eliminate the need for parameters in Phago and Bud and allow lateral and cross-membrane interactions. We show that PABM can emulate bitonal membrane reactions. PABM also realizes the idea of L. Cardelli (Cardeli, 2004) on modeling molecules as systems.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Maria Pamela C. David
    • 1
  • Johnrob Y. Bantang
    • 1
    • 2
    • 3
  • Eduardo R. Mendoza
    • 1
    • 4
  1. 1.Faculty of Physics and Center for NanoscienceLudwig-Maximilians-Universität MünchenMünchenGermany
  2. 2.Max-Planck-Institut für Dynamik komplexer technischer SystemeMagdeburgGermany
  3. 3.National Institute of Physics, College of ScienceUniversity of the Philippines, DilimanQuezon CityPhilippines
  4. 4.Department of Computer ScienceUniversity of the Philippines, DilimanQuezon CityPhilippines

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