Research questions in state transition models of biomolecular dynamics

Recent developments of discrete models to analyse biological processes motivate the revisitation of typical concepts of classical dynamics in a completely discrete context, such as that provided by state transition systems. Dynamics of discrete systems, besides being instrumental to the analysis of metabolic processes in the context of P systems, in general prove most natural in the representation of biomolecular dynamics, where the symbolic entities which come into play are easily amenable to strings or related structures, ranging from multisets to dynamical networks. This work aims at identifying relevant problems outstanding in this area and at outlining research strategies. [ DOI : 10.1685/CSC06089] About DOI

[1]  Giancarlo Mauri,et al.  Dynamical probabilistic P systems , 2006, Int. J. Found. Comput. Sci..

[2]  Vincenzo Manca,et al.  P systems with reaction maps , 2006, Int. J. Found. Comput. Sci..

[3]  Andrew Wuensche,et al.  Basins of attraction in network dynamics: A conceptual framework for biomolecular networks , 2003 .

[4]  Lars Folke Olsen,et al.  Biochemical oscillations and cellular rhythms: The molecular bases of periodic and chaotic behaviour: Albert Goldbeter. Cambridge University Press, Cambridge, 1996. $99.95 (cloth), 605 + xxiv pp , 1997 .

[5]  Pérez Jiménez,et al.  P systems-based Modelling of Cellular Signalling Pathways , 2006 .

[6]  Vincenzo Manca,et al.  State Transition Dynamics: Basic Concepts and Molecular Computing Perspectives , 2005 .

[7]  Pietro Hiram Guzzi,et al.  Mitotic Oscillators as MP Graphs , 2006, Workshop on Membrane Computing.

[8]  A Goldbeter,et al.  A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Vincenzo Manca,et al.  Evolutions and Oscillations of P Systems: Theorethical Considerations and Applications to Biochemical Phenomena , 2006 .

[10]  A. Goldbeter,et al.  Biochemical Oscillations And Cellular Rhythms: Contents , 1996 .

[11]  Douglas Lind,et al.  An Introduction to Symbolic Dynamics and Coding , 1995 .

[12]  Gheorghe Paun,et al.  Computing with Membranes , 2000, J. Comput. Syst. Sci..

[13]  Vincenzo Manca.  Topics and Problems in Metabolic P Systems , 2006 .

[14]  Vincenzo Manca,et al.  Biological networks in metabolic P systems , 2008, Biosyst..

[15]  Vincenzo Manca,et al.  Discrete dynamics in biological models , 2002 .

[16]  Vincenzo Manca,et al.  A Relational View of Recurrence and Attractors in State Transition Dynamics , 2006, RelMiCS.

[17]  Vincenzo Manca,et al.  P Systems for Biological Dynamics , 2006, Applications of Membrane Computing.

[18]  Giuditta Franco.  Biomolecular Computing – Combinatorial Algorithms and Laboratory Experiments (Doctoral Thesis) , 2006 .

[19]  Vincenzo Manca,et al.  P Systems and the Modeling of Biochemical Oscillations , 2005, Workshop on Membrane Computing.