On the Computational Power of Biochemistry

We explore the computational power of biochemistry with respect to basic chemistry, identifying complexation as the basic mechanism that distinguishes the former from the latter. We use two process algebras, the Chemical Ground Form (CGF) which is equivalent to basic chemistry, and the Biochemical Ground Form (BGF) which is a minimalistic extension of CGF with primitives for complexation. We characterize an expressiveness gap: CGF is not Turing complete while BGF supports a finite precise encoding of Random Access Machines, a well-known Turing powerful formalism.

[1]  Yukiko Matsuoka,et al.  Using process diagrams for the graphical representation of biological networks , 2005, Nature Biotechnology.

[2]  Chrisantha Fernando,et al.  Turing Complete Catalytic Particle Computers , 2007, ECAL.

[3]  Corrado Priami,et al.  Transactions on Computational Systems Biology VI , 2006, Trans. Computational Systems Biology.

[4]  Luca Cardelli,et al.  On process rate semantics , 2008, Theor. Comput. Sci..

[5]  Ian Stark,et al.  The Continuous pi-Calculus: A Process Algebra for Biochemical Modelling , 2008, CMSB.

[6]  Cosimo Laneve,et al.  Formal molecular biology , 2004, Theor. Comput. Sci..

[7]  Luca Cardelli,et al.  A Process Model of Rho GTP-binding Proteins in the Context of Phagocytosis , 2008, Electron. Notes Theor. Comput. Sci..

[8]  Luca Cardelli,et al.  Termination Problems in Chemical Kinetics , 2008, CONCUR.

[9]  Luca Cardelli,et al.  Artificial Biochemistry , 2009, Algorithmic Bioprocesses.

[10]  Luca Cardelli,et al.  Where membranes meet complexes , 2005 .

[11]  M. Magnasco CHEMICAL KINETICS IS TURING UNIVERSAL , 1997 .

[12]  Wolfgang Banzhaf,et al.  Advances in Artificial Life , 2003, Lecture Notes in Computer Science.

[13]  J. Weinstein,et al.  Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. , 2005, Molecular biology of the cell.

[14]  Roberto Gorrieri,et al.  On the Computational Power of Brane Calculi , 2006, Trans. Comp. Sys. Biology.

[15]  Matthew Cook,et al.  Computation with finite stochastic chemical reaction networks , 2008, Natural Computing.

[16]  D. A. Mcquarrie Stochastic approach to chemical kinetics , 1967, Journal of Applied Probability.

[17]  Cosimo Laneve,et al.  Modelization and Simulation of Nano Devices in $\mathtt{nano}\kappa$ Calculus , 2007, CMSB.

[18]  Corrado Priami,et al.  Application of a stochastic name-passing calculus to representation and simulation of molecular processes , 2001, Inf. Process. Lett..

[19]  Marvin Minsky,et al.  Computation : finite and infinite machines , 2016 .

[20]  Robin Milner,et al.  Communication and concurrency , 1989, PHI Series in computer science.

[21]  Corrado Priami,et al.  Beta Binders for Biological Interactions , 2004, CMSB.