Log-gain Principles for Metabolic P Systems

Metabolic P systems, shortly MP systems, are a special class of P systems, introduced for expressing biological metabolism. Their dynamics are computed by metabolic algorithms which transform populations of objects according to a mass partition principle, based on suitable generalizations of chemical laws. In this paper, the basic principles of MP systems are formulated for introducing the Log-gain principles, and it is shown how to use them for constructing MP models from experimental data of given metabolic processes.

[1]  Florent Jacquemard,et al.  An Analysis of a Public Key Protocol with Membranes , 2005 .

[2]  Andrzej Ehrenfeucht,et al.  Events and modules in reaction systems , 2007, Theor. Comput. Sci..

[3]  Vincenzo Manca,et al.  Predator-prey dynamics in P systems ruled by metabolic algorithm , 2008, Biosyst..

[4]  Vincenzo Manca,et al.  Discrete solutions to differential equations by metabolic P systems , 2007, Theor. Comput. Sci..

[5]  Vincenzo Manca,et al.  String Rewriting and Metabolism: A logical perspective , 1998 .

[6]  Vincenzo Manca,et al.  Dynamical aspects of P systems. , 2003, Bio Systems.

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

[8]  Vincenzo Manca,et al.  Relational state transition dynamics , 2008, J. Log. Algebraic Methods Program..

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

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

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

[12]  Gabriel Ciobanu,et al.  A P System Description of the Sodium-Potassium Pump , 2004, Workshop on Membrane Computing.

[13]  Cristian S. Calude,et al.  Proceedings of the Workshop on Multiset Processing: Multiset Processing, Mathematical, Computer Science, and Molecular Computing Points of View , 2000 .

[14]  Petr Kůrka,et al.  Topological and symbolic dynamics , 2003 .

[15]  Andrzej Ehrenfeucht,et al.  Reaction Systems , 2007, Fundam. Informaticae.

[16]  Bianco Luca,et al.  Membrane models of biological systems , 2007 .

[17]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[18]  Yasuhiro Suzuki,et al.  Symbolic chemical system based on abstract rewriting system and its behavior pattern , 2006, Artificial Life and Robotics.

[19]  Gheorghe Paun,et al.  Membrane Computing , 2002, Natural Computing Series.

[20]  Hiroshi Tanaka,et al.  Modeling p53 Signaling Pathways by Using Multiset Processing , 2006, Applications of Membrane Computing.

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

[22]  Yew-Soon Ong,et al.  Advances in Natural Computation, First International Conference, ICNC 2005, Changsha, China, August 27-29, 2005, Proceedings, Part I , 2005, ICNC.

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

[24]  Vincenzo Manca,et al.  Psim: a simulator for biomolecular dynamics based on P systems , 2007, 2007 IEEE Congress on Evolutionary Computation.

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

[26]  Vincenzo Manca,et al.  From String Rewriting to Logical Metabolic Systems , 1999, Grammatical Models of Multi-Agent Systems.

[27]  Vincenzo Manca,et al.  Reaction-Driven Membrane Systems , 2005, ICNC.

[28]  J. Busch,et al.  On the Optimality of the Binary Algorithm for the Jacobi Symbol , 2007, Fundam. Informaticae.

[29]  Vincenzo Manca,et al.  MP Systems Approaches to Biochemical Dynamics: Biological Rhythms and Oscillations , 2006, Workshop on Membrane Computing.

[30]  Natasa Jonoska,et al.  Knee joint injury and repair modeled by membrane systems , 2008, Biosyst..

[31]  Vincenzo Manca Discrete Simulations of Biochemical Dynamics , 2007, DNA.

[32]  Hiroshi Tanaka,et al.  Artificial Life Applications of a Class of P Systems: Abstract Rewriting Systems on Multisets , 2000, WMP.

[33]  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.

[34]  Marian Gheorghe,et al.  Towards a P Systems Pseudomonas Quorum Sensing Model , 2006, Workshop on Membrane Computing.

[35]  Andrzej Ehrenfeucht,et al.  Basic Notions of Reaction Systems , 2004, Developments in Language Theory.

[36]  Mario J. Pérez-Jiménez,et al.  A Study of the Robustness of the EGFR Signalling Cascade Using Continuous Membrane Systems , 2005, IWINAC.

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

[38]  Vincenzo Manca,et al.  Evolution and Oscillation in P Systems: Applications to Biological Phenomena , 2004, Workshop on Membrane Computing.

[39]  Vincenzo Manca Metabolic P systems for biochemical dynamics , 2007 .

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

[41]  Yasuhiro Suzuki,et al.  Investigation of tritrophic interactions in an ecosystem using abstract chemistry , 2006, Artificial Life and Robotics.

[42]  Vincenzo Manca,et al.  Toward a Representation of Hybrid Functional Petri Nets by MP Systems , 2007, IWNC.

[43]  Arto Salomaa,et al.  Grammatical Models of Multi-Agent Systems , 1999, Grammatical Models of Multi-Agent Systems.

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

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

[46]  Vincenzo Manca,et al.  The metabolic algorithm for P systems: Principles and applications , 2008, Theor. Comput. Sci..

[47]  John W. Sutherland,et al.  General Systems Theory: Foundations, Developments, Applications , 1974 .

[48]  Vincenzo Manca,et al.  A Membrane System for the Leukocyte Selective Recruitment , 2003, Workshop on Membrane Computing.